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The University of California, Berkeley , is a public research university located in Berkeley, California. According to the 2014 Academic Ranking of World Universities, the University of California, Berkeley is the fourth best university in the world. It is the most selective – and highest ranked in U.S. News and ARWU – public university in the world for undergraduate education. Aside from its academic prestige, UC Berkeley is also well known for producing a high number of entrepreneurs.The university occupies 1,232 acres on the eastern side of the San Francisco Bay with the central campus resting on 178 acres . Berkeley is the flagship institution of the 10 campus University of California system and one of only two UC campuses operating on a semester calendar, the other being UC Merced.Established in 1868 as the result of the merger of the private College of California and the public Agricultural, Mining, and Mechanical Arts College in Oakland, Berkeley is the oldest institution in the UC system and offers approximately 350 undergraduate and graduate degree programs in a wide range of disciplines. The University of California has been charged with providing both "classical" and "practical" education for the state's people. Cal co-manages three United States Department of Energy National Laboratories, including the Los Alamos National Laboratory, Lawrence Livermore National Laboratory and Lawrence Berkeley National Laboratory for the U.S. Department of Energy.Berkeley faculty, alumni, and researchers have won 72 Nobel Prizes , 9 Wolf Prizes, 7 Fields Medals, 18 Turing Awards, 45 MacArthur Fellowships, 20 Academy Awards, and 11 Pulitzer Prizes. To date, UC Berkeley scientists have discovered 6 chemical elements of the periodic table . Along with Berkeley Lab, UC Berkeley researchers have discovered 16 chemical elements in total – more than any other university in the world. Berkeley is a founding member of the Association of American Universities and continues to have very high research activity with $730.7 million in research and development expenditures in the fiscal year ending June 30, 2014. Berkeley physicist J. Robert Oppenheimer was the scientific director of the Manhattan Project that developed the first atomic bomb in the world, which he personally headquartered at Los Alamos, New Mexico, during World War II. Faculty member Edward Teller was the "father of the hydrogen bomb". Former United States Secretary of Energy and Nobel laureate Steven Chu , was Director of Berkeley Lab, 2004–2009.The athletic teams at UC Berkeley are known as the California Golden Bears and are members of both the Pacific-12 Conference and the Mountain Pacific Sports Federation in the NCAA. Wikipedia.


Westheimer G.,University of California at Berkeley
Journal of the Optical Society of America A: Optics and Image Science, and Vision | Year: 2013

Analysis of retinal image formation for beams of coherent and incoherent radiation emphasizes the role of the Poynting vector's inclination with respect to the retinal image plane. Coherent beams interfere and give rise to a single Poynting vector that highlights the unique direction of incidence of energy flow, whereas multiple incoherent beams, especially incoherent extended sources in the pupil, generate electro-magnetic disturbances in the image plane each characterized by Poynting vectors of their own. As a result, the Stiles-Crawford diminution of luminant efficiency adds differently depending on the coherence of the entering light. Two practical considerations follow: first, in performing diffraction calculations for the retinal image from known wavefronts in the pupil plane, apodization terms should not be factored in, and, second, in principle, for perfect imaging in standard target viewing, Stiles-Crawford integration with increasing pupil diameter is not expected. © 2013 Optical Society of America.


Degruyter W.,University of California at Berkeley | Bonadonna C.,University of Geneva
Geophysical Research Letters | Year: 2012

We introduce a novel analytical expression that allows for fast assessment of mass flow rate of both vertically-rising and bent-over volcanic plumes as a function of their height, while first order physical insight is maintained. This relationship is compared with a one-dimensional plume model to demonstrate its flexibility and then validated with observations of the 1980 Mount St. Helens and of the 2010 Eyjafjallajkull eruptions. The influence of wind on the dynamics of volcanic plumes is quantified by a new dimensionless parameter () and it is shown how even vertically-rising plumes, such as the one associated with the Mount St. Helens 1980 eruption, can be significantly affected by strong wind. Comparison between a one-dimensional model and the analytical equation gives an R 2-value of 0.88, while existing expressions give negative R 2-values due to their inability to adapt to different source and atmospheric conditions. Therefore, this new expression has important implications both for current strategies of real-time forecasting of ash transport in the atmosphere and for the characterization of explosive eruptions based on the study of tephra deposits. In addition, this work provides a framework for the application of more complete three-dimensional numerical models as it greatly reduces the parameter space that needs to be explored. © 2012. American Geophysical Union. All Rights Reserved.


Rothman J.E.,Yale University | Schekman R.,University of California at Berkeley
Cell | Year: 2011

F.-Ulrich Hartl and Arthur Horwich will share this year's Lasker Basic Medical Science Award for the discovery of the cell's protein-folding machinery, exemplified by cage-like structures that convert newly synthesized proteins into their biologically active forms. Their fundamental findings reveal mechanisms that operate in normal physiologic processes and help to explain the problems that arise in diseases of protein folding. © 2011 Elsevier Inc.


Sato Y.,Harvard University | Packard R.E.,University of California at Berkeley
Reports on Progress in Physics | Year: 2012

We present an overview of recent developments related to superfluid helium quantum interference devices (SHeQUIDs). We discuss the physics of two reservoirs of superfluid helium coupled together and describe the quantum oscillations that result from varying the coupling strength. We explain the principles behind SHeQUIDs that can be built based on these oscillations and review some techniques and applications. © 2012 IOP Publishing Ltd.


Shane B.,University of California at Berkeley
American Journal of Clinical Nutrition | Year: 2011

This article presents a historical perspective on the different methods used to measure folate status in populations and clinical settings. I discuss some of the advantages and limitations of these procedures. For >50 y researchers have used microbiological assay methods to assess folate status in clinical settings and in population-based studies, such as NHANES. Serum and red blood cell folate values obtained with the Lactobacillus casei assay have formed the basis for current ranges and cutoffs for the establishment of folate sufficiency and for the current dietary reference intakes for folate. Over the past 30 y competitive folate protein binding assays, which are available in kit form, have supplanted microbiological assays in many clinical laboratories because of their ease of use. Several NHANES cycles have used these assays. Folate concentrations obtained with these kits are lower than those from microbiological assays and show a wide variation between different protein binding assay kits. This variation has complicated the setting of values for normal ranges of folate status and the comparison of status changes between different NHANES cycles. The recent development of mass spectrometry methods for folate opens up the possibility of measurement of individual folate vitamers such as folic acid. Past experience with microbiological and competitive protein binding assays indicates some of the technical problems that research will need to address before this promise becomes reality. © 2011 American Society for Nutrition.


Commins E.D.,University of California at Berkeley
Annual Review of Nuclear and Particle Science | Year: 2012

The history of electron spin is summarized. Topics include the discovery of electron spin, the birth of quantum electrodynamics, the invention of magnetic resonance, the invention of renormalization, the anomalous magnetic moment of the electron in experiment and theory, and searches for the electron electric dipole moment. © 2012 by Annual Reviews.


Javey A.,University of California at Berkeley
Nano Letters | Year: 2010

Gas phase p-doping of InAs nanowires with Zn atoms is demonstrated as an effective route for enabling postgrowth dopant profiling of nanostructures. The versatility of the approach is demonstrated by the fabrication of high-performance gated diodes and p-MOSFETs. High Zn concentrations with electrically active content of ̃1× 1019 cm-3 are achieved which is essential for compensating the electron-rich surface layers of InAs to enable heavily p-doped structures. This work could have important practical implications for the fabrication of planar and nonplanar devices based on InAs and other III-V nanostructures which are not compatible with conventional ion implantation processes that often cause severe lattice damage with local stoichiometry imbalance. © 2010 American Chemical Society.


Guzman M.G.,University of California at Berkeley
Lancet | Year: 2015

Dengue viruses have spread rapidly within countries and across regions in the past few decades, resulting in an increased frequency of epidemics and severe dengue disease, hyperendemicity of multiple dengue virus serotypes in many tropical countries, and autochthonous transmission in Europe and the USA. Today, dengue is regarded as the most prevalent and rapidly spreading mosquito-borne viral disease of human beings. Importantly, the past decade has also seen an upsurge in research on dengue virology, pathogenesis, and immunology and in development of antivirals, vaccines, and new vector-control strategies that can positively impact dengue control and prevention. Copyright © 2015 Elsevier Ltd. All rights reserved.


Graves D.B.,University of California at Berkeley
Plasma Processes and Polymers | Year: 2014

Cold atmospheric plasmas (CAP) formed in air generate reactive oxygen and nitrogen species (RONS). RONS are biologically and therapeutically active agents and experimental evidence suggests that air plasmas shrink tumors by increasing oxidative and nitrosative stress on neoplastic tissue. Most mainline anti-cancer therapies - including ionizing radiation and chemotherapies - also operate primarily via this pro-oxidant, oxidative, and nitrosative stress mechanism. The main disadvantage of these conventional therapies is the development of treatment-resistant cells. A key question for plasma cancer therapies is therefore whether or not cold plasma will lead to similar oxidative stress resistance. However, there are hints that combining nitrosative stress with oxidative stress via air plasma might avoid this problem. Plasma-based cancer treatment may be a powerful and practical anti-cancer agent, acting either alone or in combination with other therapies. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Burgmann R.,University of California at Berkeley | Chadwell D.,University of California at San Diego
Annual Review of Earth and Planetary Sciences | Year: 2014

Seafloor geodetic techniques allow for measurements of crustal deformation over the ∼70% of Earth's surface that is inaccessible to the standard tools of tectonic geodesy. Precise underwater measurement of position, displacement, strain, and gravity poses technical, logistical, and cost challenges. Nonetheless, acoustic ranging; pressure sensors; underwater strain-, tilt- and gravimeters; and repeat multibeam sonar and seismic measurements are able to capture small-scale or regional deformation with approximately centimeter-level precision. Pioneering seafloor geodetic measurements offshore Japan, Cascadia, and Hawaii have substantially contributed to advances in our understanding of the motion and deformation of oceanic tectonic plates, earthquake cycle deformation in subduction zones, and the deformation of submarine volcanoes. Nontectonic deformation related to down-slope mass movement and underwater extraction of hydrocarbons or other resources represent other important targets. Recent technological advances promise further improvements in precision as well as the development of smaller, more autonomous, and less costly seafloor geodetic systems. © 2014 by Annual Reviews. All rights reserved.


Watanabe H.,University of California at Berkeley | Oshikawa M.,University of Tokyo
Physical Review Letters | Year: 2015

In analogy with crystalline solids around us, Wilczek recently proposed the idea of "time crystals" as phases that spontaneously break the continuous time translation into a discrete subgroup. The proposal stimulated further studies and vigorous debates whether it can be realized in a physical system. However, a precise definition of the time crystal is needed to resolve the issue. Here we first present a definition of time crystals based on the time-dependent correlation functions of the order parameter. We then prove a no-go theorem that rules out the possibility of time crystals defined as such, in the ground state or in the canonical ensemble of a general Hamiltonian, which consists of not-too-long-range interactions. © 2015 American Physical Society.


Gee C.L.,University of California at Berkeley
Science signaling | Year: 2012

Prokaryotic cell wall biosynthesis is coordinated with cell growth and division, but the mechanisms regulating this dynamic process remain obscure. Here, we describe a phosphorylation-dependent regulatory complex that controls peptidoglycan (PG) biosynthesis in Mycobacterium tuberculosis. We found that PknB, a PG-responsive Ser-Thr protein kinase (STPK), initiates complex assembly by phosphorylating a kinase-like domain in the essential PG biosynthetic protein, MviN. This domain was structurally diverged from active kinases and did not mediate phosphotransfer. Threonine phosphorylation of the pseudokinase domain recruited the FhaA protein through its forkhead-associated (FHA) domain. The crystal structure of this phosphorylated pseudokinase-FHA domain complex revealed the basis of FHA domain recognition, which included unexpected contacts distal to the phosphorylated threonine. Conditional degradation of these proteins in mycobacteria demonstrated that MviN was essential for growth and PG biosynthesis and that FhaA regulated these processes at the cell poles and septum. Controlling this spatially localized PG regulatory complex is only one of several cellular roles ascribed to PknB, suggesting that the capacity to coordinate signaling across multiple processes is an important feature conserved between eukaryotic and prokaryotic STPK networks.


Gronert K.,University of California at Berkeley
Experimental Eye Research | Year: 2010

Acute inflammation is a frequent, essential and beneficial response to maintain normal tissue function. PMN are the primary effector cells of acute inflammatory responses and their timely resolution by macrophages from an injured, stressed or infected tissues are required for the successful execution of this routine tissue response. Dysregulation of this fundamental program is a major factor in the global disease burden and contributes to many ocular diseases. Counter-regulatory signals are critical to the controlled activation of innate and adaptive immune responses in the eye and recent studies have identified two circuits in the cornea, uvea and/or retina, namely 15-lipoxygenase and heme-oxygenase, which control inflammation, promote resolution of PMN and afford neuroprotection. The role of these counter-regulator and pro-resolution circuits may provide insight into ocular inflammatory diseases and opportunities to restore stressed ocular tissue to a pre-inflammatory state, namely homeostasis, rather than limiting therapeutic options to palliative inhibition of pro-inflammatory circuits. © 2010 Elsevier Ltd.


Kihlstrom J.F.,University of California at Berkeley
Cortex | Year: 2013

The neurophysiological substrates of hypnosis have been subject to speculation since the phenomenon got its name. Until recently, much of this research has been geared toward understanding hypnosis itself, including the biological bases of individual differences in hypnotizability, state-dependent changes in cortical activity occurring with the induction of hypnosis, and the neural correlates of response to particular hypnotic suggestions (especially the clinically useful hypnotic analgesia). More recently, hypnosis has begun to be employed as a method for manipulating subjects' mental states, both cognitive and affective, to provide information about the neural substrates of experience, thought, and action. This instrumental use of hypnosis is particularly well-suited for identifying the neural correlates of conscious and unconscious perception and memory, and of voluntary and involuntary action. © 2012 Elsevier Ltd.


Chua L.O.,University of California at Berkeley
Proceedings of the IEEE | Year: 2012

This tutorial clarifies the axiomatic definition of (v α i β) circuit elements via a lookup table dubbed an A-pad, of admissible (v i) signals measured via Gedanken probing circuits. The elements are ordered via a complexity metric. Under this metric, the memristor emerges naturally as the fourth element, characterized by a state-dependent Ohm's law. A logical generalization to memristive devices reveals a common fingerprint consisting of a dense continuum of pinched hysteresis loops whose area decreases with the frequency ω and tends to a straight line as ω → for all bipolar periodic signals and for all initial conditions. This common fingerprint suggests that the term memristor be used henceforth as a moniker for memristive devices. © 1963-2012 IEEE.


The reaction mechanisms for hydrogenation of carbon dioxide catalyzed by PNP-ligated (PNP = 2,6-bis(di-iso-propylphosphinomethyl)pyridine) metal pincer complexes, (PNP)IrH3 (1-Ir), trans-(PNP)Fe(H)2CO (1-Fe) and (PNP)CoH3 (1-Co), were studied computationally by using the density functional theory (DFT). 1-Ir is a recently reported high efficiency catalyst for the formation of formic acid from H2 and CO2. 1-Fe and 1-Co are computationally designed low-cost base metal complexes for catalytic CO2 reduction. For the formation of formic acid from H 2 and CO2 catalyzed by 1-Ir, 1-Fe, and 1-Co, the reaction pathways with direct H2 cleavage by OH- without the participation of the PNP ligand are about 20 kcal mol-1 more favorable than a previously postulated H2 cleavage mechanism that involves the aromatization and dearomatization of the pyridine ring in the PNP ligand. This finding reveals the essential role of the base, OH-, in the catalytic CO2 reduction cycle and suggests that the incorporation of strong bases and unsaturated ligands may be critical for new catalyst design in the area of hydrogen activation and low energy proton transfers. The calculated overall enthalpy barriers for the formation of formic acid from H2 and CO2 catalyzed by 1-Ir, 1-Fe, and 1-Co are 18.6, 21.9, and 22.6 kcal mol-1, respectively. Such low barriers explain the observed unprecedented high catalytic acitivity of 1-Ir and indicate that 1-Fe and 1-Co can be considered as promising low-cost catalyst candidates for fast hydrogenation of CO2. © 2011 American Chemical Society.


Carter B.E.,University of California at Berkeley
Molecular Phylogenetics and Evolution | Year: 2012

Cryptic lineage diversification is an important component of global biodiversity, but it presents challenges to our ability to catalog and understand that diversity. Because of their relative morphological simplicity and broad geographic distributions, bryophytes are an ideal study group for investigating this phenomenon. This study generated molecular data from 109 ingroup individuals to test morphological species circumscriptions and examine patterns of cryptic lineage diversification within the small north temperate moss genus Scleropodium (Brachytheciaceae). Maximum Parsimony and Bayesian phylogenetic analyses and statistical parsimony network analyses of ITS and chloroplast rps4, psbA2 and trnG regions indicate that the genus comprises six distinct molecular groups. Five of these molecular groups correspond to previously recognized species: S. californicum (Lesq.) Kindb., S. cespitans (Müll.) Koch, S. julaceum Lawton, S. obtusifolium (Mitt.) Kindb. in Macoun and S. touretii Brid. (Koch). However, the sixth group does not correspond to any existing species. Maximum parsimony and Bayesian posterior probability support for the monophyly of species varied widely and depended on both the dataset (ITS, chloroplast, combined) and the analysis method (Parsimony/Bayesian). Low phylogenetic resolution of species is attributable to the lack of informative DNA sequence vaiation and incongruent placements of three accessions in the chloroplast and ITS gene trees, both suggesting recent divergence within the genus. Re-examination of the herbarium vouchers for the sixth molecular group reveals that they form a group nested within the morphological circumscription of S. obtusifolium. One subtle morphological character (relative frequency of a costa spine) was identified that has utility in discriminating these two genetically distinct but morphologically very similar species. © 2012 Elsevier Inc.


Harvey A.G.,University of California at Berkeley | Harvey A.G.,University of Bergen
Annual Review of Clinical Psychology | Year: 2011

Evidence for the importance of sleep in the mood disorders has mushroomed over the past decade. Among adolescents and adults with a mood disorder, sleep disturbance is a risk factor for episodes, can contribute to relapse, has an adverse impact on emotion regulation, is critical for cognitive functioning, compromises health, and may contribute to substance use comorbidity and suicidality. This evidence has triggered a shift away from viewing sleep disturbance as an epiphenomenon, toward viewing sleep disturbance as an important but under-recognized mechanism in the multifactorial cause and maintenance of the mood disorders. Because the biology underpinning the sleep and circadian system is an open system, readily influenced by inputs from the environment, sleep in the mood disorders represents a unique and exciting domain for interdisciplinary research across behavioral, social, cognitive, and neurobiological levels of explanation. Together, the accumulated evidence has informed a range of novel, powerful, simple, and inexpensive treatments with potential for massive improvements to public health, including improving quality of life, reducing length and severity of episodes, and reducing the risk of subsequent episodes in the large number of individuals who suffer from mood disorders. Copyright © 2011 by Annual Reviews. All rights reserved.


Tsutsui N.D.,University of California at Berkeley
Biology Letters | Year: 2013

Hamilton is probably best known for his seminal work demonstrating the role of kin selection in social evolution. His work made it clear that, for individuals to direct their altruistic behaviours towards appropriate recipients (kin), mechanisms must exist for kin recognition. In the social insects, colonies are typically comprised of kin, and colony recognition cues are used as proxies for kinship cues. Recent years have brought rapid advances in our understanding of the genetic and molecular mechanisms that are used for this process. Here, I review some of the most notable advances, particularly the contributions from recent ant genome sequences and molecular biology. © 2013 The Author(s) Published by the Royal Society. All rights reserved.


Zaletel M.P.,University of California at Berkeley | Mong R.S.K.,California Institute of Technology
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We show that the model wave functions used to describe the fractional quantum Hall effect have exact representations as matrix product states (MPS). These MPS can be implemented numerically in the orbital basis of both finite and infinite cylinders, which provides an efficient way of calculating arbitrary observables. We extend this approach to the charged excitations and numerically compute their Berry phases. Finally, we present an algorithm for numerically computing the real-space entanglement spectrum starting from an arbitrary orbital basis MPS, which allows us to study the scaling properties of the real-space entanglement spectra on infinite cylinders. The real-space entanglement spectrum obeys a scaling form dictated by the edge conformal field theory, allowing us to accurately extract the two entanglement velocities of the Moore-Read state. In contrast, the orbital space spectrum is observed to scale according to a complex set of power laws that rule out a similar collapse. © 2012 American Physical Society.


Purcell A.,University of California at Berkeley
Annual Review of Phytopathology | Year: 2013

The history of advances in research on Xylella fastidiosa provides excellent examples of how paradigms both advance and limit our scientific understanding of plant pathogens and the plant diseases they cause. I describe this from a personal perspective, having been directly involved with many persons who made paradigm-changing discoveries, beginning with the discovery that a bacterium, not a virus, causes Pierce's disease of grape and other plant diseases in numerous plant species, including important crop and forest species. © Copyright ©2013 by Annual Reviews. All rights reserved.


Horava P.,University of California at Berkeley | Horava P.,Lawrence Berkeley National Laboratory
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2010

We present a family of nonrelativistic Yang-Mills gauge theories in D+1 dimensions whose free-field limit exhibits quantum critical behavior with gapless excitations and dynamical critical exponent z=2. The ground state wavefunction is intimately related to the partition function of relativistic Yang-Mills in D dimensions. The gauge couplings exhibit logarithmic scaling and asymptotic freedom in the upper critical spacetime dimension, equal to 4+1. The theories can be deformed in the infrared by a relevant operator that restores Poincaré invariance as an accidental symmetry. In the large-N limit, our nonrelativistic gauge theories can be expected to have weakly curved gravity duals. © 2010 Elsevier B.V.


Morris Jr. J.W.,University of California at Berkeley
ISIJ International | Year: 2011

The inherent brittle mode in dislocated lath martensitic steel is cleavage on {100} planes in the microstructure. The transition to {100} cleavage fracture on cooling determines the minimum value of the ductiule- brittle transition temperature. A half-century of research on the microstructure and toughness of lath martensitic steels has produced a semi-quantitative understanding of the brittle transition to cleavage. The results identify the crystallographic "block" of lath martensite as the effective grain size that controls cleavage, and clarify why the internal structure of a block has the microstructure it adopts. The ductilebrittle transition temperature is strongly affected by the block size. Several effective metallurgical processes are now available to refine the block size without excessive strengthening, leading to martensitic structural steels that combine high strength with good low-temperature toughness. © 2011 ISIJ.


Riley L.W.,University of California at Berkeley
Clinical Microbiology and Infection | Year: 2014

Pathogenic Escherichia coli strains cause a wide variety of intestinal and extraintestinal infections. The widespread geographical clonal dissemination of intestinal pathogenic E. coli strains, such as E. coli O157:H7, is well recognized, and its spread is most often attributed to contaminated food products. On the other hand, the clonal dissemination of extraintestinal pathogenic E. coli (ExPEC) strains is also recognized, but the mechanism of their spread is not well explained. Here, I describe major pandemic clonal lineages of ExPEC based on multilocus sequence typing (MLST), and discuss possible reasons for their global dissemination. These lineages include sequence type (ST)131, ST393, ST69, ST95, and ST73, which are all associated with both community-onset and healthcare-associated infections, in particular urinary tract infections and bloodstream infections. As with many other types of drug-resistant Gram-negative and Gram-positive bacterial infections, drug-resistant ExPEC infections are recognized to be caused by a limited set of clonal lineages. However, reported observations on these major pandemic lineages suggest that the resistance phenotype is not necessarily the determinant of their clonal dissemination. Both epidemiological factors and their intrinsic biological 'fitness' are likely to contribute. An important public health and clinical concern is that pandemicity itself may be a determinant of progressive drug resistance acquisition by clonal lineages. New research is urgently needed to better understand the epidemiological and biological causes of ExPEC pandemicity. © 2014 European Society of Clinical Microbiology and Infectious Diseases.


Given the lack of complete vital registration data in most developing countries, for many countries it is not possible to accurately estimate under-five mortality rates from vital registration systems. Heavy reliance is often placed on direct and indirect methods for analyzing data collected from birth histories to estimate under-five mortality rates. Yet few systematic comparisons of these methods have been undertaken. This paper investigates whether analysts should use both direct and indirect estimates from full birth histories, and under what circumstances indirect estimates derived from summary birth histories should be used. Usings Demographic and Health Surveys data from West Africa, East Africa, Latin America, and South/Southeast Asia, I quantify the differences between direct and indirect estimates of under-five mortality rates, analyze data quality issues, note the relative effects of these issues, and test whether these issues explain the observed differences. I find that indirect estimates are generally consistent with direct estimates, after adjustment for fertility change and birth transference, but don't add substantial additional insight beyond direct estimates. However, choice of direct or indirect method was found to be important in terms of both the adjustment for data errors and the assumptions made about fertility. Although adjusted indirect estimates are generally consistent with adjusted direct estimates, some notable inconsistencies were observed for countries that had experienced either a political or economic crisis or stalled health transition in their recent past. This result suggests that when a population has experienced a smooth mortality decline or only short periods of excess mortality, both adjusted methods perform equally well. However, the observed inconsistencies identified suggest that the indirect method is particularly prone to bias resulting from violations of its strong assumptions about recent mortality and fertility. Hence, indirect estimates of under-five mortality rates from summary birth histories should be used only for populations that have experienced either smooth mortality declines or only short periods of excess mortality in their recent past. Please see later in the article for the Editors' Summary.


Ritchie L.D.,University of California at Berkeley
American Journal of Clinical Nutrition | Year: 2012

Background: Little is known about the effect of eating frequency on adiposity. Objective: The study aim was to assess the prospective relation of an objective measure of eating frequency with adiposity in girls from ages 9-10 to 19-20 y. Design: By using data from 3-d diet records collected from 2372 girls in the National Heart, Lung, and Blood Institute Growth and Health Study, meal, snack, and total eating frequencies aggregated over the first 2 study years were examined in relation to 10-y change in BMI and waist circumference (WC). Results: Eating frequency was lower in black and older girls than in white and younger girls (P < 0.0001). In whites, lower initial snack and total eating frequencies were related to greater 10-y increases in BMI (P = 0.023 and 0.012, respectively) and WC (P = 0.030 and 0.015, respectively). In blacks, lower initial meal and snack frequencies were related to greater increases in BMI (P = 0.004 and 0.022, respectively) and WC (P = 0.052 and 0.005, respectively). Also, in blacks, lower initial total eating frequency was related to greater increases in WC (P = 0.010). After adjustment for baseline adiposity measure, race, parental education, physical activity, television and video viewing, total energy intake, and dieting for weight loss, lower initial total eating frequency remained related to greater 10-y increases in BMI (P = 0.013) and WC (P = 0.036). Conclusions: A lower eating frequency predicts a greater gain in adiposity in adolescent females. Intervention trials are needed to test if changing the frequency of eating can affect obesity risk. © 2012 American Society for Nutrition.


Valiant G.,University of California at Berkeley
Proceedings - Annual IEEE Symposium on Foundations of Computer Science, FOCS | Year: 2012

Given a set of n d-dimensional Boolean vectors with the promise that the vectors are chosen uniformly at random with the exception of two vectors that have Pearson - correlation ρ (Hamming distance d·1-ρ/2), how quickly can one find the two correlated vectors? We present an algorithm which, for any constants ε, ρ > 0 d ≫ log n/ρ2, finds the correlated pair with high probability, and runs in time O(n 3ω/4+ε) < O(n1.8) where ω < 2.38 is the exponent of matrix multiplication. Provided that d is suf.ciently large, this runtime can be further reduced. These are the first subquadratic-time algorithms for this problem for which ρ does not appear in the exponent of n, and improves uopn O(n2-O(ρ)), given by Paturi et al. [15], Locality Sensitive Hashing (LSH) [11] and the Bucketing Codes approach [6]. Applications and extensions of this basic algorithm yield improved algorithms for several other problems: Approximate Closest Pair: For any suf.ciently small constant ε > 0, given n vectors Rd, our algorithm returns a pair of vectors whose Euclidean distance differs from that of the closest pair by a factor of at most 1+ε, and runs in time O(n2-Θ(√ε)). The best previous algorithms (including LSH) have runtime O(n2-O(ε)) . Learning Sparse Parity with Noise: Given samples from an instance of the learning parity with noise problem where each example has length n, the true parity set has size at most k ≪ n, and the noise rate is η, our algorithm identi.es the set of k indices in time nω+ε/3 k poly(1/1-2η) < n0.8k poly(1/1-2η). This is the first algorithm with no dependence on η in the exponent of n, aside from the trivial brute-force algorithm. Learning k-Juntas with Noise: Given uniformly random length n Boolean vectors, together with a label, which is some function of just k ≪ n of the bits, perturbed by noise rate η, return the set of relevant indices. Leveraging the reduction of Feldman et al. [7] our result for learning k-parities implies an algorithm for this problem with runtime n ω+ε/3 k poly(1/1-2η) < n0.8k poly(1/1-2η), which improves on the previous best of > n k(1-2/2k) poly(1/1-2η), from [8]. Learning k-Juntas without Noise: Our results for learning sparse parities with noise imply an algorithm for learning juntas without noise with runtime nω+ε/4 k poly(n) < n0.6k poly(n) which improves on the runtime n ω+1/ω poly(n) ≈ n0.7k poly(n) of Mossel et al. [13]. © 2012 IEEE.


Sly A.,University of California at Berkeley | Sun N.,Stanford University
Proceedings - Annual IEEE Symposium on Foundations of Computer Science, FOCS | Year: 2012

The class of two-spin systems contains several important models, including random independent sets and the Ising model of statistical physics. We show that for both the hard-core (independent set) model and the anti-ferromagnetic Ising model with arbitrary external field, it is NP-hard to approximate the partition function or approximately sample from the model on regular graphs when the model has non-uniqueness on the corresponding regular tree. Together with results of Jerrum - Sinclair, Weitz, and Sinclair - Srivastava - Thurley giving FPRAS's for all other two-spin systems except at the uniqueness threshold, this gives an almost complete classification of the computational complexity of two-spin systems on bounded-degree graphs. Our proof establishes that the normalized log-partition function of any two-spin system on bipartite locally tree-like graphs converges to a limiting "free energy density" which coincides with the (non-rigorous) Be the prediction of statistical physics. We use this result to characterize the local structure of two-spin systems on locally tree-like bipartite expander graphs, which then become the basic gadgets in a randomized reduction to approximate MAX-CUT. Our approach is novel in that it makes no use of the second moment method employed in previous works on these questions. © 2012 IEEE.


Sekhon J.S.,University of California at Berkeley
Journal of Statistical Software | Year: 2011

Matching is an R package which provides functions for multivariate and propensity score matching and for finding optimal covariate balance based on a genetic search algorithm. A variety of univariate and multivariate metrics to determine if balance actually has been obtained are provided. The underlying matching algorithm is written in C++, makes extensive use of system BLAS and scales efficiently with dataset size. The genetic algorithm which finds optimal balance is parallelized and can make use of multiple CPUs for a cluster of computers. A large number of options are provided which control exactly how the matching is conducted and how balance is evaluated.


Mebane Jr. W.R.,University of Michigan | Sekhon J.S.,University of California at Berkeley
Journal of Statistical Software | Year: 2011

genoud is an R function that combines evolutionary algorithm methods with a derivative based (quasi-Newton) method to solve difficult optimization problems. genoud may also be used for optimization problems for which derivatives do not exist. genoud solves problems that are nonlinear or perhaps even discontinuous in the parameters of the function to be optimized. When the function to be optimized (for example, a log-likelihood) is nonlinear in the model's parameters, the function will generally not be globally concave and may have irregularities such as saddlepoints or discontinuities. Optimization methods that rely on derivatives of the objective function may be unable to find any optimum at all. Multiple local optima may exist, so that there is no guarantee that a derivative-based method will converge to the global optimum. On the other hand, algorithms that do not use derivative information (such as pure genetic algorithms) are for many problems needlessly poor at local hill climbing. Most statistical problems are regular in a neighborhood of the solution. Therefore, for some portion of the search space, derivative information is useful. The function supports parallel processing on multiple CPUs on a single machine or a cluster of computers.


Williams V.V.,University of California at Berkeley | Williams V.V.,Stanford University
Proceedings of the Annual ACM Symposium on Theory of Computing | Year: 2012

We develop an automated approach for designing matrix multiplication algorithms based on constructions similar to the Coppersmith-Winograd construction. Using this approach we obtain a new improved bound on the matrix multiplication exponent ω < 2.3727. © 2012 ACM.


Graves D.B.,University of California at Berkeley
Clinical Plasma Medicine | Year: 2014

It is postulated that cold atmospheric plasma (CAP) can trigger a therapeutic shielding response in tissue by creating a time- and space-localized, burst-like form of oxy-nitrosative stress on near-surface exposed cells through the flux of plasma-generated reactive oxygen and nitrogen species (RONS). RONS-exposed surface layers of cells communicate to the deeper levels of tissue via a form of the 'bystander effect,' similar to responses to other forms of cell stress. In this proposed model of CAP therapeutics, the plasma stimulates a cellular survival mechanism through which aerobic organisms shield themselves from infection and other challenges. © 2014 Elsevier GmbH.


Shen K.J.,University of California at Berkeley | Bildsten L.,University of California at Santa Barbara
Astrophysical Journal | Year: 2014

The progenitor channel responsible for the majority of Type Ia supernovae is still uncertain. One emergent scenario involves the detonation of a He-rich layer surrounding a C/O white dwarf, which sends a shock wave into the core. The quasi-spherical shock wave converges and strengthens at an off-center location, forming a second, C-burning, detonation that disrupts the whole star. In this paper, we examine this second detonation of the double detonation scenario using a combination of analytic and numeric techniques. We perform a spatially resolved study of the imploding shock wave and outgoing detonation and calculate the critical imploding shock strengths needed to achieve a core C detonation. We find that He detonations in recent two-dimensional simulations yield converging shock waves that are strong enough to ignite C detonations in high-mass C/O cores, with the caveat that a truly robust answer requires multi-dimensional detonation initiation calculations. We also find that convergence-driven detonations in low-mass C/O cores and in O/Ne cores are harder to achieve and are perhaps unrealized in standard binary evolution. © 2014. The American Astronomical Society. All rights reserved.


MacCoun R.J.,University of California at Berkeley
Frontiers in Psychiatry | Year: 2013

There is a perennial expert debate about the criteria to be included or excluded for the DSM diagnoses of substance use dependence. Yet analysts routinely report evidence for the unidimensionality of the resulting checklist. If in fact the checklist is unidimensional, the experts are wrong that the criteria are distinct, so either the experts are mistaken or the reported unidimensionality is spurious. I argue for the latter position, and suggest that the traditional reflexive measurement model is inappropriate for the DSM; a formative measurement model would be a more accurate characterization of the institutional process by which the checklist is created, and a network or causal model would be a more appropriate foundation for a scientifically grounded diagnostic system. © 2013 MacCoun.


Bower G.C.,University of California at Berkeley
Astrophysical Journal Letters | Year: 2011

Tidal disruptions of stars by massive black holes produce transient accretion flows that flare at optical, UV, and X-ray wavelengths. At late times, these accretion flows may launch relativistic jets that can be detected through the interaction of the jet with the dense interstellar medium of the galaxy. We present an upper limit for the flux density of a radio counterpart to a tidal disruption event detected by GALEX that is a factor of six below theoretical predictions. We also examine existing radio surveys for transients with a timescale of 1 yr and use these to set a 2σ upper limit on the rate of tidal disruption events producing relativistic jets of ∼14 × 10 -7 Mpc-3 yr-1. This rate is an order of magnitude lower than the highest values from theoretical models and is consistent with detection rates from optical and X-ray surveys. © 2011. The American Astronomical Society. All rights reserved.


Species distribution models (SDMs) are increasingly used for extrapolation, or predicting suitable regions for species under new geographic or temporal scenarios. However, SDM predictions may be prone to errors if species are not at equilibrium with climatic conditions in the current range and if training samples are not representative. Here the controversial "Pleistocene rewilding" proposal was used as a novel example to address some of the challenges of extrapolating modeled species-climate relationships outside of current ranges. Climatic suitability for three proposed proxy species (Asian elephant, African cheetah and African lion) was extrapolated to the American southwest and Great Plains using Maxent, a machine-learning species distribution model. Similar models were fit for Oryx gazella, a species native to Africa that has naturalized in North America, to test model predictions. To overcome biases introduced by contracted modern ranges and limited occurrence data, random pseudo-presence points generated from modern and historical ranges were used for model training. For all species except the oryx, models of climatic suitability fit to training data from historical ranges produced larger areas of predicted suitability in North America than models fit to training data from modern ranges. Four naturalized oryx populations in the American southwest were correctly predicted with a generous model threshold, but none of these locations were predicted with a more stringent threshold. In general, the northern Great Plains had low climatic suitability for all focal species and scenarios considered, while portions of the southern Great Plains and American southwest had low to intermediate suitability for some species in some scenarios. The results suggest that the use of historical, in addition to modern, range information and randomly sampled pseudo-presence points may improve model accuracy. This has implications for modeling range shifts of organisms in response to climate change.


Chu V.W.,University of California at Berkeley
Progress in Physical Geography | Year: 2014

Understanding Greenland ice sheet (GrIS) hydrology is essential for evaluating response of ice dynamics to a warming climate and future contributions to global sea level rise. Recently observed increases in temperature and melt extent over the GrIS have prompted numerous remote sensing, modeling, and field studies gauging the response of the ice sheet and outlet glaciers to increasing meltwater input, providing a quickly growing body of literature describing seasonal and annual development of the GrIS hydrologic system. This system is characterized by supraglacial streams and lakes that drain through moulins, providing an influx of meltwater into englacial and subglacial environments that increases basal sliding speeds of outlet glaciers in the short term. However, englacial and subglacial drainage systems may adjust to efficiently drain increased meltwater without significant changes to ice dynamics over seasonal and annual scales. Both proglacial rivers originating from land-terminating glaciers and subglacial conduits under marine-terminating glaciers represent direct meltwater outputs in the form of fjord sediment plumes, visible in remotely sensed imagery. This review provides the current state of knowledge on GrIS surface water hydrology, following ice sheet surface meltwater production and transport via supra-, en-, sub-, and proglacial processes to final meltwater export to the ocean. With continued efforts targeting both process-level and systems analysis of the hydrologic system, the larger picture of how future changes in Greenland hydrology will affect ice sheet glacier dynamics and ultimately global sea level rise can be advanced. © The Author(s) 2013.


Nomura Y.,University of California at Berkeley
Foundations of Physics | Year: 2013

Quantum mechanics introduces the concept of probability at the fundamental level, yielding the measurement problem. On the other hand, recent progress in cosmology has led to the "multiverse" picture, in which our observed universe is only one of the many, bringing an apparent arbitrariness in defining probabilities, called the measure problem. In this paper, we discuss how these two problems are related with each other, developing a picture for quantum measurement and cosmological histories in the quantum mechanical universe. In order to describe the cosmological dynamics correctly within the full quantum mechanical context, we need to identify the structure of the Hilbert space for a system with gravity. We argue that in order to keep spacetime locality, the Hilbert space for dynamical spacetime must be defined only in restricted spacetime regions: in and on the (stretched) apparent horizon as viewed from a fixed reference frame. This requirement arises from eliminating all the redundancies and overcountings in a general relativistic, global spacetime description of nature. It is responsible for horizon complementarity as well as the "observer dependence" of horizons/spacetime-these phenomena arise to represent changes of the reference frame in the relevant Hilbert space. This can be viewed as an extension of the Poincaré transformation in the quantum gravitational context. Given an initial condition, the evolution of the multiverse state obeys the laws of quantum mechanics-it evolves deterministically and unitarily. The beginning of the multiverse, however, is still an open issue. © 2013 The Author(s).


Shen Y.R.,University of California at Berkeley
Journal of Physical Chemistry C | Year: 2012

A detailed description on the basic theory of optical sum-frequency generation from an interfacial system is presented. Both the interface and the bulk generally contribute to the sum-frequency output. Two seemingly different approaches to specify bulk nonlinearity that includes electric-quadrupole and magnetic-dipole contributions are shown to yield the same sum-frequency output if surface nonlinearity is properly taken into account. The question of whether surface and bulk nonlinearities can be uniquely defined and separately measured is discussed. It is shown that the answer is affirmative. Truly bulk and truly surface nonlinear susceptibilities can be uniquely defined and separately deduced from measurements of transmitted and reflected sum-frequency generation. © 2012 American Chemical Society.


Rabosky D.L.,University of California at Berkeley
Nature communications | Year: 2013

Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fishes that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability'-the capacity of organisms to evolve-shapes the dynamics of speciation through time at the largest phylogenetic scales.


McQuinn M.,University of California at Berkeley
Astrophysical Journal Letters | Year: 2014

Recently, Thornton and coworkers confirmed a class of millisecond radio bursts likely of extragalactic origin that is well-suited for estimating dispersion measures (DMs). We calculate the probability distribution of DM(z) in different models for how the cosmic baryons are distributed (both analytically and with cosmological simulations). We show that the distribution of DM is quite sensitive to whether the "missing" baryons lie around the virial radius of 1011-1013 M halos or further out, which is not easily constrained with other observational techniques. The intrinsic contribution to DM from each source could complicate studies of the extragalactic contribution. This difficulty is avoided by stacking based on the impact parameter to foreground galaxies. We show that a stacking analysis using a sample of 100 DM measurements from arcminute-localized, z ≳ 0.5 sources would place interesting constraints at 0.2-2 halo virial radii on the baryonic mass profile surrounding different galaxy types. Conveniently for intergalactic studies, sightlines that intersect intervening galactic disks should be easily identified owing to scattering. A detectable level of scattering may also result from turbulence in the circumgalactic medium. © 2014. The American Astronomical Society. All rights reserved.


Audet P.,University of California at Berkeley
Journal of Geophysical Research E: Planets | Year: 2011

The spectral relations (admittance and correlation) between gravity and topography are often used to obtain information on the density structure, flexural support, and heat flow of planetary lithospheres. Mapping spatial variations in these quantities requires spatiospectral analysis techniques. Here we describe the application of a directional, continuous spherical wavelet transform using a wavelet basis constructed from the superposition of azimuthally adjacent complex Morlet wavelets, in a manner similar to the "fan" wavelet developed in the plane. The method is applied to gravity and topography of the Earth, Venus, Mars, and the Moon. The wavelet coefficients are used to compute isotropic and directional wavelet autospectra and cross spectra, which are then combined to form the admittance and correlation functions. The resulting maps offer insights into lithospheric structure of the terrestrial planets. In particular we show that the Earth and Venus have uniformly low positive admittance and high correlation, whereas Mars and the Moon display hemispherical contrasts with large negative and anisotropic coefficients coinciding with lowlands. As has long been known, the two largest impact basins in the inner solar system, the South Pole-Aitken basin on the Moon and the Hellas basin on Mars, display low positive admittance and high correlation, indicating isostatic compensation. In contrast, most other impact basins, particularly the Martian and lunar mascons, show negative coefficients at low wavelet degrees suggesting flexural support by a strong lithosphere. These results imply that, although simple isotropic flexural models can account for most observations, future models may need to incorporate anisotropy as an additional parameter. © 2011 by the American Geophysical Union.


Ott M.,University of California at San Francisco | Geyer M.,Max Planck Institute of Molecular Physiology | Zhou Q.,University of California at Berkeley
Cell Host and Microbe | Year: 2011

Thirteen years ago, human cyclin T1 was identified as part of the positive transcription elongation factor b (P-TEFb) and the long-sought host cofactor for the HIV-1 transactivator Tat. Recent years have brought new insights into the intricate regulation of P-TEFb function and its relationship with Tat, revealing novel mechanisms for controlling HIV transcription and fueling new efforts to overcome the barrier of transcriptional latency in eradicating HIV. Moreover, the improved understanding of HIV and Tat forms a basis for studying transcription elongation control in general. Here, we review advances in HIV transcription research with a focus on the growing family of cellular P-TEFb complexes, structural insights into the interactions between Tat, P-TEFb, and TAR RNA, and the multifaceted regulation of these interactions by posttranscriptional modifications of Tat. © 2011 Elsevier Inc.


Gopnik A.,University of California at Berkeley
Behavioral and Brain Sciences | Year: 2011

My research program proposes that children have representations and learning mechanisms that can be characterized as causal models of the world-coherent, structured hypotheses with consistent relationships to probabilistic patterns of evidence. We also propose that Bayesian inference is one mechanism by which children learn these models from data. These proposals are straightforward psychological hypotheses and far from Bayesian Fundamentalism. © 2011 Cambridge University Press.


Horvitz E.,Microsoft | Mulligan D.,University of California at Berkeley
Science | Year: 2015

Large-scale aggregate analyses of anonymized data can yield valuable results and insights that address public health challenges and provide new avenues for scientific discovery.These methods can extend our knowledge and provide new tools for enhancing health and wellbeing. However, they raise questions about how to best address potential threats to privacy while reaping benefits for individuals and to society as a whole.The use ofmachine learning tomake leaps across informational and social contexts to infer health conditions and risks from nonmedical data provides representative scenarios for reflections on directions with balancing innovation and regulation.


Smith N.,University of California at Berkeley
Monthly Notices of the Royal Astronomical Society | Year: 2010

Eta Carinae shows broad peaks in near-infrared (IR) JHKL photometry, roughly correlated with times of periastron passage in the eccentric binary system. After correcting for secular changes attributed to reduced extinction from the thinning Homunculus nebula, these peaks have IR spectral energy distributions (SEDs) consistent with emission from hot dust at 1400-1700 K. The excess SEDs are clearly inconsistent, however, with the excess being entirely due to free-free wind or photospheric emission. One must conclude, therefore, that the broad near-IR peaks associated with Eta Carinae's 5.5 yr variability are due to thermal emission from hot dust. I propose that this transient hot dust results from episodic formation of grains within compressed post-shock zones of the colliding winds, analogous to the episodic dust formation in Wolf-Rayet (WR) binary systems like WR 140 or the post-shock dust formation seen in some supernovae like SN 2006jc. This dust formation in Eta Carinae seems to occur preferentially near and after periastron passage; near-IR excess emission then fades as the new dust disperses and cools. With the high grain temperatures and Eta Car's C-poor abundances, the grains are probably composed of corundum or similar species that condense at high temperatures, rather than silicates or graphite. Episodic dust formation in Eta Car's colliding winds significantly impacts our understanding of the system, and several observable consequences are discussed. © 2009 The Author. Journal compilation © 2009 RAS.


Shearer P.,University of California at San Diego | Burgmann R.,University of California at Berkeley
Annual Review of Earth and Planetary Sciences | Year: 2010

The 2004 Sumatra-Andaman earthquake has been extensively studied because of its great size and devastating consequences. Large amounts of high-quality seismic, geodetic, and geologic data have led to a number of proposed models for its length, duration, fault geometry, rupture velocity, and slip history. The latest of these models vary in their details but now largely agree in their large-scale features, which include significant coseismic slip along the entire 1300-to 1500-km rupture, the bulk of which occurred fast enough to radiate seismic waves. The earthquake's enormous size has challenged conventional processing approaches and stimulated the development of new analysis and inversion methods, including multiple-source inversions, high-frequency body-wave imaging, and satellite observations of tsunami heights and gravity changes. The Sumatra megathrust earthquake was the largest in 40 years and is by far the best documented, but it does not seem fundamentally different in its properties from other large subduction-zone earthquakes. Copyright © 2010 by Annual Reviews. All rights reserved.


Vishwanath A.,University of California at Berkeley | Vishwanath A.,Lawrence Berkeley National Laboratory | Senthil T.,Massachusetts Institute of Technology
Physical Review X | Year: 2013

We discuss physical properties of "integer"topological phases of bosons in D = 3 + 1 dimensions, protected by internal symmetries like time reversal and/or charge conservation. These phases invoke interactions in a fundamental way but do not possess topological order; they are bosonic analogs of freefermion topological insulators and superconductors. While a formal cohomology-based classification of such states was recently discovered, their physical properties remain mysterious. Here, we develop a field-theoretic description of several of these states and show that they possess unusual surface states, which, if gapped, must either break the underlying symmetry or develop topological order. In the latter case, symmetries are implemented in a way that is forbidden in a strictly two-dimensional theory. While these phases are the usual fate of the surface states, exotic gapless states can also be realized. For example, tuning parameters can naturally lead to a deconfined quantum critical point or, in other situations, to a fully symmetric vortex metal phase. We discuss cases where the topological phases are characterized by a quantized magnetoelectric response Θ, which, somewhat surprisingly, is an odd multiple of 2π. Two different surface theories are shown to capture these phenomena: The first is a nonlinear sigma model with a topological term. The second invokes vortices on the surface that transform under a projective representation of the symmetry group. We identify a bulk-field theory consistent with these properties, which is a multicomponent background-field theory supplemented, crucially, with a topological term. We also provide bulk sigma-model field theories of these phases and discuss a possible topological phase characterized by the thermal analog of the magnetoelectric effect.


McDonald K.L.,University of California at Berkeley
Microscopy and Microanalysis | Year: 2014

A variety of specimens including bacteria, ciliates, choanoflagellates (Salpingoeca rosetta), zebrafish (Danio rerio) embryos, nematode worms (Caenorhabditis elegans), and leaves of white clover (Trifolium repens) plants were high pressure frozen, freeze-substituted, infiltrated with either Epon, Epon-Araldite, or LR White resins, and polymerized. Total processing time from freezing to blocks ready to section was about 6 h. For epoxy embedding the specimens were freeze-substituted in 1% osmium tetroxide plus 0.1% uranyl acetate in acetone. For embedding in LR White the freeze-substitution medium was 0.2% uranyl acetate in acetone. Rapid infiltration was achieved by centrifugation through increasing concentrations of resin followed by polymerization at 100°C for 1.5-2 h. The preservation of ultrastructure was comparable to standard freeze substitution and resin embedding methods that take days to complete. On-section immunolabeling results for actin and tubulin molecules were positive with very low background labeling. The LR White methods offer a safer, quicker, and less-expensive alternative to Lowicryl embedding of specimens processed for on-section immunolabeling without traditional aldehyde fixatives. © Microscopy Society of America 2014.


Dawson R.I.,University of California at Berkeley
Astrophysical Journal Letters | Year: 2014

It is debated whether the two hot Jupiter populations - those on orbits misaligned from their host star's spin axis and those well-aligned - result from two migration channels or from two tidal realignment regimes. Here I demonstrate that equilibrium tides raised by a planet on its star can account for three observed spin-orbit alignment trends: the aligned orbits of hot Jupiters orbiting cool stars, the planetary mass cut-off for retrograde planets, and the stratification by planet mass of cool host stars' rotation frequencies. The first trend can be caused by strong versus weak magnetic braking (the Kraft break), rather than realignment of the star's convective envelope versus the entire star. The second trend can result from a small effective stellar moment of inertia participating in the tidal realignment in hot stars, enabling massive retrograde planets to partially realign to become prograde. The third trend is attributable to higher-mass planets more effectively counteracting braking to spin up their stars. Both hot and cool stars require a small effective stellar moment of inertia participating in the tidal realignment, e.g., an outer layer weakly coupled to the interior. I demonstrate via Monte Carlo that this model can match the observed trends and distributions of sky-projected misalignments and stellar rotation frequencies. I discuss implications for inferring hot Jupiter migration mechanisms from obliquities, emphasizing that even hot stars do not constitute a pristine sample. © 2014. The American Astronomical Society. All rights reserved.


Komeili A.,University of California at Berkeley
FEMS Microbiology Reviews | Year: 2012

Magnetotactic bacteria (MB) are remarkable organisms with the ability to exploit the earth's magnetic field for navigational purposes. To do this, they build specialized compartments called magnetosomes that consist of a lipid membrane and a crystalline magnetic mineral. These organisms have the potential to serve as models for the study of compartmentalization as well as biomineralization in bacteria. Additionally, they offer the opportunity to design applications that take advantage of the particular properties of magnetosomes. In recent years, a sustained effort to identify the molecular basis of this process has resulted in a clearer understanding of the magnetosome formation and biomineralization. Here, I present an overview of MB and explore the possible molecular mechanisms of membrane remodeling, protein sorting, cytoskeletal organization, iron transport, and biomineralization that lead to the formation of a functional magnetosome organelle. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd.


Alam M.-R.,University of California at Berkeley
Physical Review Letters | Year: 2012

Here we show that floating objects in stratified fluids can be cloaked against broadband incident waves by properly architecting the bottom corrugations. The presented invisibility cloaking of gravity waves is achieved utilizing a nonlinear resonance concept that occurs between surface and internal waves mediated by the bottom topography. Our cloak bends wave rays from the surface into the body of the fluid. Wave rays then pass underneath the floating object and may be recovered back to the free surface at the downstream bearing no trace of diffraction or scattering. The cloak is the proper architecture of bottom corrugations only, and hence is surface noninvasive. The presented scheme is a nonlinear alternative to the transformation-based cloaking, but in the context of dispersive waves. © 2012 American Physical Society.


Neuscamman E.,University of California at Berkeley
Physical Review Letters | Year: 2012

The accurate but expensive product of geminals ansatz may be approximated by a geminal power, but this approach sacrifices size consistency. Here, we show both analytically and numerically that a size consistent form very similar to the product of geminals can be recovered using a network of location-specific Jastrow factors. Upon variational energy minimization, the network creates particle number projections that remove the charge fluctuations responsible for size inconsistency. This polynomial cost approach captures strong many-electron correlations, giving a maximum error of just 1.8kcal/mol during the double-bond dissociation of H 2O in an STO-3G atomic orbital basis. © 2012 American Physical Society.


Shapira M.,University of California at Berkeley
Trends in Ecology and Evolution | Year: 2016

Our understanding of species evolution is undergoing restructuring. It is well accepted that host-symbiont coevolution is responsible for fundamental aspects of biology. However, the emerging importance of plant- and animal-associated microbiotas to their hosts suggests a scale of coevolutionary interactions many-fold greater than previously considered. This review builds on current understanding of symbionts and their contributions to host evolution to evaluate recent data demonstrating similar contributions of gut microbiotas. It further considers a multilayered model for microbiota to account for emerging themes in host-microbiota interactions. Drawing on the structure of bacterial genomes, this model distinguishes between a host-adapted core microbiota, and a flexible, environmentally modulated microbial pool, differing in constraints on their maintenance and in their contributions to host adaptation. Gut microbiotas expand current notions on how symbionts shape host evolution.The hologenome model proposes that the host genome and its microbiome combined make a unit of evolution jointly undergoing selection.To account for emerging themes in host-microbiota interactions, a multilayered model distinguishes between a host-adapted core microbiota and an environmentally modulated flexible microbial pool, and a range of intermediates in between. Contributions of gut microbes to host adaptation reflect this multilayered model. © 2016 Elsevier Ltd.


Hopkins P.F.,University of California at Berkeley
Monthly Notices of the Royal Astronomical Society | Year: 2013

We propose a new, physically motivated fitting function for density probability distribution functions (PDFs) in turbulent, ideal gas. Although it is generally known that when gas is isothermal, the PDF is approximately lognormal in the core, high-resolution simulations show large deviations from exact lognormality. The proposed function provides an extraordinarily accurate description of the density PDFs in simulations with Mach numbers ~0.1-15 and dispersion in log (ρ) from ~0.01 to 4 dex. Compared to a lognormal or lognormal-skewkurtosis model, the fits are improved by orders of magnitude in the wings of the distribution (with fewer free parameters). This is true in simulations using a variety of distinct numerical methods, including or excluding magnetic fields. Deviations from lognormality are represented by a parameter T that appears to increase systematically with the compressive Mach number of the simulations. The proposed distribution can be derived from intermittent cascade models of the longitudinal (compressive) velocity differences, which should be directly related to density fluctuations, and we also provide a simple interpretation of the density PDF as the product of a continuous-time relaxation process. As such this parameter T is consistent with the same single parameter needed to explain the (intermittent) velocity structure functions; its behaviour is consistent with turbulence becoming more intermittent as it becomes more dominated by strong shocks. It provides a new and unique probe of the role of intermittency in the density (not just velocity) structure of turbulence. We showthat this naturally explains some apparent contradictory results in the literature (for example, in the dispersion-Mach number relation) based on use of different moments of the density PDF, as well as differences based on whether volume-weighted or mass-weighted quantities are measured. We show how these are fundamentally related to the fact that mass conservation requires violations of lognormal statistics. © 2013 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society.


Hopkins P.F.,University of California at Berkeley
Monthly Notices of the Royal Astronomical Society | Year: 2013

We develop an analytic framework to understand fragmentation in turbulent, self-gravitating media. In previous work, we showed how some properties of turbulence can be predicted by application of the excursion-set formalism. Here, we generalize this to understand fully time-dependent gravo-turbulent fragmentation and collapse. We show that turbulent systems are always gravitationally unstable in a probabilistic sense. The fragmentation mass spectrum, size-mass-density-linewidth relations of collapsing objects, their correlation functions and clustering, the range of spatial scales over which fragmentation occurs, and the time-dependent rate of collapse/fragmentation (as a function of size/mass) are analytically predictable. We show how these depend on bulk properties of turbulence; fragmentation is promoted at higher Mach numbers and shallower power spectra. We also generalize the model to properly include rotation, complicated gas equations of state, collapsing/expanding backgrounds, magnetic fields, intermittency and non-normal statistics (with inherently correlated fluctuations). This allows us to formally derive how fragmentation is suppressed with "stiffer" equations of state (e.g. higher polytropic index γ) or differently driven turbulence (solenoidal versus compressive). The suppression appears at an "effective sonic scale" where bM(Rs, γcrit[Rs]) ̃ 1, with γcrit being the (scale-dependent) critical density for fragmentation. Gas becomes stable against collapse below this scale forγ >4/3; however, fragmentation still occurs on larger scales. We show that the scale-free nature of turbulence and gravity generically drives mass spectra and correlation functions towards universal shapes (observed in a wide variety of astrophysical phenomena), with weak residual dependence on many properties of the media. We find that correlated fluctuations on different scales, non-Gaussian density distributions and intermittency have surprisingly small effects on the fragmentation process. We demonstrate that this is because fragmentation cascades on small scales are generically "frozen in" when large-scale fluctuations push the "parent" region above the collapse threshold; though they collapse, their statistics are only weakly modified by the collapse process. Finally, with thermal or turbulent support, structure develops "top-down" in time via a fragmentation cascade, but we show that significant rotational/angular momentum support reverses the sense of structure formation to "bottom-up" growth via mergers of bound clumps, and introduces a characteristic "maximal instability scale" distinct from the Toomre scale. © 2013 The Author. Published by Oxford University Press on behalf of the Royal Astronomical Society.


Levy D.L.,University of Wyoming | Heald R.,University of California at Berkeley
Annual Review of Cell and Developmental Biology | Year: 2012

Cell size varies widely among different organisms as well as within the same organism in different tissue types and during development, which places variable metabolic and functional demands on organelles and internal structures. A fundamental question is how essential subcellular components scale to accommodate cell size differences. Nuclear transport has emerged as a conserved means of scaling nuclear size. A meiotic spindle scaling factor has been identified as the microtubule-severing protein katanin, which is differentially regulated by phosphorylation in two different-sized frog species. Anaphase mechanisms and levels of chromatin compaction both act to coordinate cell size with spindle and chromosome dimensions to ensure accurate genome distribution during cell division. Scaling relationships and mechanisms for many membrane-bound compartments remain largely unknown and are complicated by their heterogeneity and dynamic nature. This review summarizes cell and organelle size relationships and the experimental approaches that have elucidated mechanisms of intracellular scaling. Copyright © 2012 by Annual Reviews. All rights reserved.


Neumark D.M.,University of California at Berkeley
Chemical Physics Letters | Year: 2010

We report a systematic study of the photoelectron spectroscopy of hydrated electrons in liquid water jets using multiple precursors and photodetachment wavelengths. Hydrated electrons were generated in and detached from liquid microjets using two photons from a single nanosecond laser pulse at 266 or 213 nm. Solutions of 50 to 250 mM potassium hexacyanoferrate(II) or potassium iodide were used to provide precursor anions. All of our experimental conditions yield similar results, giving a mean vertical binding energy of 3.6 ± 0.1 eV at a temperature of ∼280 K, a slightly higher value than in recent reports. © 2010 Elsevier B.V. All rights reserved.


Guzman M.G.,Institute of Tropical Medicine | Harris E.,University of California at Berkeley
The Lancet | Year: 2015

Summary Dengue viruses have spread rapidly within countries and across regions in the past few decades, resulting in an increased frequency of epidemics and severe dengue disease, hyperendemicity of multiple dengue virus serotypes in many tropical countries, and autochthonous transmission in Europe and the USA. Today, dengue is regarded as the most prevalent and rapidly spreading mosquito-borne viral disease of human beings. Importantly, the past decade has also seen an upsurge in research on dengue virology, pathogenesis, and immunology and in development of antivirals, vaccines, and new vector-control strategies that can positively impact dengue control and prevention. © 2015 Elsevier Ltd.


Gillespie R.G.,University of California at Berkeley
Evolutionary Applications | Year: 2016

Research on the dynamics of biodiversity has progressed tremendously over recent years, although in two separate directions - ecological, to determine change over space at a given time, and evolutionary, to understand change over time. Integration of these approaches has remained elusive. Archipelagoes with a known geological chronology provide an opportunity to study ecological interactions over evolutionary time. Here, I focus on the Hawaiian archipelago and summarize the development of ecological and evolutionary research; I emphasize spiders because they have attributes allowing analysis of ecological affinities in concert with diversification. Within this framework, I highlight recent insights from the island chronosequence, in particular the importance of (i) selection and genetic drift in generating diversity; (ii) fusion and fission in fostering diversification; and (iii) variability upon which selection can act. Insights into biodiversity dynamics at the nexus of ecology and evolution are now achievable by integrating new tools, in particular (i) ecological metrics (interaction networks, maximum entropy inference) across the chronosequence to uncover community dynamics and (ii) genomic tools to understand contemporaneous microevolutionary change. The work can inform applications of invasion and restoration ecology by elucidating the importance of changes in abundances, interaction strengths, and rates of evolutionary response in shaping biodiversity. © 2016 John Wiley & Sons Ltd.


Chiang E.,University of California at Berkeley | Laughlin G.,University of California at Santa Cruz
Monthly Notices of the Royal Astronomical Society | Year: 2013

Close-in super-Earths, with radii R ≈ 2-5R⊕ and orbital periods P < 100 d, orbit more than half, and perhaps nearly all, Sun-like stars in the Universe. We use this omnipresent population to construct the minimum-mass extrasolar nebula (MMEN), the circumstellar disc of solar-composition solids and gas from which such planets formed, if they formed near their current locations and did not migrate. In a series of back-of-the-envelope calculations, we demonstrate how in situ formation in the MMEN is fast, efficient, and can reproduce many of the observed properties of close-in super-Earths, including their gas-to-rock fractions. Testable predictions are discussed. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Jha S.,University of Texas at Austin | Kremen C.,University of California at Berkeley
Molecular Ecology | Year: 2013

Potential declines in native pollinator communities and increased reliance on pollinator-dependent crops have raised concerns about native pollinator conservation and dispersal across human-altered landscapes. Bumble bees are one of the most effective native pollinators and are often the first to be extirpated in human-altered habitats, yet little is known about how bumble bees move across fine spatial scales and what landscapes promote or limit their gene flow. In this study, we examine regional genetic differentiation and fine-scale relatedness patterns of the yellow-faced bumble bee, Bombus vosnesenskii, to investigate how current and historic habitat composition impact gene flow. We conducted our study across a landscape mosaic of natural, agricultural and urban/suburban habitats, and we show that B. vosnesenskii exhibits low but significant levels of differentiation across the study system (FST = 0.019, Dest = 0.049). Most importantly, we reveal significant relationships between pairwise FST and resistance models created from contemporary land use maps. Specifically, B. vosnesenskii gene flow is most limited by commercial, industrial and transportation-related impervious cover. Finally, our fine-scale analysis reveals significant but declining relatedness between individuals at the 1-9 km spatial scale, most likely due to local queen dispersal. Overall, our results indicate that B. vosnesenskii exhibits considerable local dispersal and that regional gene flow is significantly limited by impervious cover associated with urbanization. © 2013 Blackwell Publishing Ltd.


Feldmann R.,University of California at Berkeley
Monthly Notices of the Royal Astronomical Society | Year: 2013

Observations show that star formation in galaxies is closely correlated with the abundance of molecular hydrogen. Modelling this empirical relation from first principles proves challenging, however, and many questions regarding its properties remain open. For instance, the exact functional form of the relation is still debated and it is also unknown whether it applies at z > 4, where carbon monoxide observations are sparse. Here, we analyse how the shape of the star formation-gas relation affects the cosmic star formation history and global galaxy properties using an analytic model that follows the average evolution of galaxies in dark matter haloes across cosmic time. We show that a linear relation with an H2 depletion time of ∼2.5 Gyr, as found in studies of nearby galaxies, results in good agreement with current observations of galaxies at both low and high redshift. These observations include the evolution of the cosmic star formation rate density, the z ∼ 4-9 UV luminosity function, the evolution of the mass-metallicity relation, the relation between stellar and halo mass, and the gas-to-stellar mass ratios of galaxies. In contrast, the short depletion times that result from adopting a highly super-linear star formation-gas relation lead to large star formation rates, substantial metal enrichment (∼0.1 Zȯ) and low gas-to-stellar mass ratios already at z ≳ 10, in disagreement with observations. These results can be understood in terms of an equilibrium picture of galaxy evolution in which gas inflows, outflows and star formation drive the metallicities and gas fractions towards equilibrium values that are determined by the ratio of the accretion time to the gas-depletion time. In this picture, the cosmic modulation of the accretion rate is the primary process that drives the evolution of stellar masses, gas masses and metallicities of galaxies from high redshift until today. © 2013 The Author.


Hariharan I.K.,University of California at Berkeley
Science Signaling | Year: 2012

In various organisms, including flies, amphibians, and mammals, major developmental transitions such as metamorphosis and puberty are triggered by specific hormones. The requirement for a hormone to proceed to the next stage allows the organism to reestablish the temporal coordination of development between multiple organs that might develop at slightly different rates. Additionally, organisms appear to have evolved mechanisms for delaying these transitions in situations where growth in an organ is abnormal or delayed. New evidence in the fruit fly Drosophila melanogaster indicates that DILP8, a protein of the insulin and relaxin family, delays the onset of metamorphosis under several conditions that alter growth in imaginal discs. Similar mechanisms might operate in disease states in humans where alterations in growth or tissue inflammation can delay puberty.


Holt L.J.,University of California at Berkeley
FEBS Letters | Year: 2012

Multiple post-translational regulation systems regulate cell biology. Two key mechanisms that coordinate the myriad processes of cell replication are phosphorylation and ubiquitin-mediated degradation of proteins. Regulatory modules have evolved to integrate these two control systems at key decision points in the cell division cycle. These modules enable information to be processed with high fidelity by filtering noise, improving specificity, generating feedback loops, and optimizing spatiotemporal coordination of cellular processes. This review provides examples of these modules and considers the advantages of this signaling nexus. © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.


As urban agriculture grows in popularity throughout North America, vacant lots, underutilized parks, and other open spaces are becoming prime targets for food production. In many post-industrial landscapes and in neighborhoods with a high density of old housing stock, the risk of lead (Pb) contamination at such sites is raising concerns. This paper evaluates the extent to which soil Pb contamination may be an obstacle to the expansion of urban agriculture in Oakland, California. Using a combination of soil sampling at 112 sites, GIS, " hot spot" analysis, and reconstructed land use histories, the research reveals that soil Pb concentrations are generally lower than federal screening levels of 400 ppm, but significantly higher in West Oakland, the city's oldest area and home to a predominantly low-income and African American population. Lead levels are significantly lower in the affluent, predominantly white Oakland hills. Spatial analysis at city- and neighborhood-scales reveals clusters of Pb contamination related to land use history. Site-scale analyses at 12 sites reveals a high level of variability (in some cases related to land use history) that must be taken into consideration when planning for urban agriculture. © 2012 Elsevier Ltd.


Liskey C.W.,Urbana University | Hartwig J.F.,University of California at Berkeley
Journal of the American Chemical Society | Year: 2012

The borylation of secondary C-H bonds, specifically secondary C-H bonds of cyclic ethers, with a catalyst generated from tetramethylphenanthroline and an iridium precursor is reported. This borylation occurs with unique selectivity for the C-H bonds located β to the oxygen atoms over the weaker C-H bonds located α to oxygen atoms. Mechanistic studies imply that the C-H bond cleavage occurs directly at the β position rather than at the α position followed by isomerization of a reaction intermediate. © 2012 American Chemical Society.


Gillespie R.G.,University of California at Berkeley
Current Biology | Year: 2013

The spectacular adaptive radiation of cichlid fish in Lake Tanganyika encompasses extensive morphological convergence and co-occurrence of ecologically similar species, forcing a reevaluation of non-equilibrium dynamics in community assembly. © 2013 Elsevier Ltd All rights reserved.


Sigwart J.D.,Queens University of Belfast | Lindberg D.R.,University of California at Berkeley
Systematic Biology | Year: 2015

Mollusks are the most morphologically disparate living animal phylum, they have diversified into all habitats, and have a deep fossil record. Monophyly and identity of their eight living classes is undisputed, but relationships between these groups and patterns of their early radiation have remained elusive. Arguments about traditional morphological phylogeny focus on a small number of topological concepts but often without regard to proximity of the individual classes. In contrast, molecular studies have proposed a number of radically different, inherently contradictory, and controversial sister relationships. Here, we assembled a data set of 42 unique published trees describing molluscan interrelationships. We used these data to ask several questions about the state of resolution of molluscan phylogeny compared with a null model of the variation possible in random trees constructed from a monophyletic assemblage of eight terminals. Although 27 different unique trees have been proposed from morphological inference, the majority of these are not statistically different from each other. Within the available molecular topologies, only four studies to date have included the deep sea class Monoplacophora; but 36.4% of all trees are not significantly different. We also present supertrees derived from two data partitions and three methods, including all available molecular molluscan phylogenies, which will form the basis for future hypothesis testing. The supertrees presented here were not constructed to provide yet another hypothesis of molluscan relationships, but rather to algorithmically evaluate the relationships present in the disparate published topologies. Based on the totality of available evidence, certain patterns of relatedness among constituent taxa become clear. The internodal distance is consistently short between a few taxon pairs, particularly supporting the relatedness of Monoplacophora and the chitons, Polyplacophora. Other taxon pairs are rarely or never found in close proximity, such as the vermiform Caudofoveata and Bivalvia. Our results have specific utility for guiding constructive research planning to better test relationships in Mollusca as well as other problematic groups. Taxa with consistently proximate relationships should be the focus of a combined approach in a concerted assessment of potential genetic and anatomical homology, whereas unequivocally distant taxa will make the most constructive choices for exemplar selection in higher level phylogenomic analyses. © 2014 © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.


Walter N.G.,University of Michigan | Bustamante C.,University of California at Berkeley
Chemical Reviews | Year: 2014

The March 2014 Special issue of Chemical Reviews has assembled some of the leading experts in the field with the goal of having them present the single molecule methods and their applications. Greene and colleagues in their article, explain that DNA often plays an active, dynamic role in directing the biological functions of DNA/protein complexes. Wuite and colleagues introduce optical tweezers as a complementary tool to probe DNA/protein interactions. They highlight the plethora of assays that have been developed to perform single molecule force measurements that quantify the mechanical properties of DNA. Ando and colleagues then introduce us to recent advances in atomic force microscopy (AFM) that have allowed them to directly image any biopolymer at near video rates without the need for attaching fluorophore labels or handles for tweezing. Transitioning into applications of single molecule tools, Bustamante and colleagues describe how a process as complex as transcription.


Dornfeld D.A.,University of California at Berkeley
International Journal of Precision Engineering and Manufacturing - Green Technology | Year: 2014

The pressing needs of energy, water and other resource conservation worldwide is a major engineering challenge. In manufacturing, developing green technologies (from process and tooling to the entire enterprise) is one way to insure that future manufacturing systems are sustainable. To do this, innovation in advanced manufacturing is needed. The basic requirements of green technology are discussed along with methods and tools to insure they are effectively applied and their impacts measured. For situations in which the manufacturing environmental burden is less than the burden for the use of the product leveraging is proposed to insure a total life cycle impact reduction. Examples of several green technologies are presented. © KSPE and Springer 2014.


Collins K.,University of California at Berkeley
Current Opinion in Chemical Biology | Year: 2011

The eukaryotic ribonucleoprotein reverse transcriptase (RT) telomerase uses a template within its integral RNA subunit to extend chromosome ends by synthesis of single-stranded telomeric repeats. Telomerase is adapted to its unique cellular role by an ability to release product DNA in single-stranded form, regenerating free template from the product-template hybrid. Furthermore, by retaining a template-independent grip on the single-stranded product, telomerase can catalyze processive repeat synthesis. These specialized nucleic acid handling properties are dependent on the protein and RNA domain network within an active RNP. RNP domain architecture and mechanisms for single-stranded DNA handling have been a focus of recent studies highlighted here. © 2011 Elsevier Ltd.


Blanch H.W.,University of California at Berkeley
Current Opinion in Biotechnology | Year: 2012

While engineering of new biofuels pathways into microbial hosts has received considerable attention, innovations in bioprocessing are required for commercialization of both conventional and next-generation fuels. For ethanol and butanol, reducing energy costs for product recovery remains a challenge. Fuels produced from heterologous aerobic pathways in yeast and bacteria require control of aeration and cooling at large scales. Converting lignocellulosic biomass to sugars for fuels production requires effective biomass pretreatment to increase surface area, decrystallize cellulose and facilitate enzymatic hydrolysis. Effective means to recover microalgae and extract their intracellular lipids remains a practical and economic bottleneck in algal biodiesel production. © 2011 Elsevier Ltd.


Lombrozo T.,University of California at Berkeley
Cognitive Psychology | Year: 2010

Both philosophers and psychologists have argued for the existence of distinct kinds of explanations, including teleological explanations that cite functions or goals, and mechanistic explanations that cite causal mechanisms. Theories of causation, in contrast, have generally been unitary, with dominant theories focusing either on counterfactual dependence or on physical connections. This paper argues that both approaches to causation are psychologically real, with different modes of explanation promoting judgments more or less consistent with each approach. Two sets of experiments isolate the contributions of counterfactual dependence and physical connections in causal ascriptions involving events with people, artifacts, or biological traits, and manipulate whether the events are construed teleologically or mechanistically. The findings suggest that when events are construed teleologically, causal ascriptions are sensitive to counterfactual dependence and relatively insensitive to the presence of physical connections, but when events are construed mechanistically, causal ascriptions are sensitive to both counterfactual dependence and physical connections. The conclusion introduces an account of causation, an " exportable dependence theory," that provides a way to understand the contributions of physical connections and teleology in terms of the functions of causal ascriptions. © 2010 Elsevier Inc.


Fargione J.E.,Nature Conservancy | Plevin R.J.,University of California at Berkeley | Hill J.D.,University of Minnesota
Annual Review of Ecology, Evolution, and Systematics | Year: 2010

The ecological impact of biofuels is mediated through their effects on land, air, and water. In 2008, about 33.3 million ha were used to produce food-based biofuels and their coproducts. Biofuel production from food crops is expected to increase 170 by 2020. Economic model estimates for land-use change (LUC) associated with food-based biofuels are 67365 ha 10-6 l -1, leading to increased greenhouse gas emissions for decades compared to business as usual. Biodiversity is reduced by about 60 in U.S. corn and soybean fields and by about 85 in Southeast Asian oil palm plantations compared to unconverted habitat. Consequently, the largest ecological impact of biofuel production may well come from market-mediated LUC. Mitigating this impact requires targeting biofuel production to degraded and abandoned cropland and rangeland; increasing crop yields and livestock production efficiency; use of wastes, residues, and wildlife-friendly crops; and compensatory offsite mitigation for residual direct and indirect impacts. Copyright © 2010 by Annual Reviews. All rights reserved.


Hellerstein J.M.,University of California at Berkeley
SIGMOD Record | Year: 2010

The rise of multicore processors and cloud computing is putting enormous pressure on the software community to find solutions to the difficulty of parallel and distributed programming. At the same time, there is more-and more varied-interest in data-centric programming languages than at any time in computing history, in part because these languages parallelize naturally. This juxtaposition raises the possibility that the theory of declarative database query languages can provide a foundation for the next generation of parallel and distributed programming languages. In this paper I reflect on my group's experience over seven years using Data log extensions to build networking protocols and distributed systems. Based on that experience, I present a number of theoretical conjectures that may both interest the database community, and clarify important practical issues in distributed computing. Most importantly, I make a case for database researchers to take a leadership role in addressing the impending programming crisis. This is an extended version of an invited lecture at the ACM PODS 2010 conference [32].


Graves D.B.,University of California at Berkeley
Physics of Plasmas | Year: 2014

Gas discharge plasmas formed at atmospheric pressure and near room temperature have recently been shown to be potentially useful for surface and wound sterilization, antisepsis, bleeding cessation, wound healing, and cancer treatment, among other biomedical applications. This tutorial review summarizes the field, stressing the likely role of reactive oxygen and nitrogen species created in these plasmas as the biologically and therapeutically active agents. Reactive species, including radicals and non-radical compounds, are generated naturally within the body and are now understood to be essential for normal biological functions. These species are known to be active agents in existing therapies for wound healing, infection control, and cancer treatment. But they are also observed at elevated levels in persons with many diseases and are associated with aging. The physical and chemical complexity of plasma medical devices and their associated biochemical effects makes the development of safe, effective plasma medical devices and procedures a challenge, but encouragingly rapid progress has been reported around the world in the last several years. © 2014 AIP Publishing LLC.


Lee T.E.,California Institute of Technology | Haffner H.,University of California at Berkeley | Cross M.C.,California Institute of Technology
Physical Review Letters | Year: 2012

We study an open quantum system of atoms with a long-range Rydberg interaction, laser driving, and spontaneous emission. Over time, the system occasionally jumps between a state of low Rydberg population and a state of high Rydberg population. The jumps are inherently collective, and in fact, exist only for a large number of atoms. We explain how entanglement and quantum measurement enable the jumps, which are otherwise classically forbidden. © 2012 American Physical Society.


Trost B.M.,Stanford University | Bartlett M.J.,Stanford University | Bartlett M.J.,University of California at Berkeley
Accounts of Chemical Research | Year: 2015

(Chemical Equation Presented). The development of catalytic enantioselective transformations has been the focus of many research groups over the past half century and is of paramount importance to the pharmaceutical and agrochemical industries. Since the award of the Nobel Prize in 2001, the field of enantioselective transition metal catalysis has soared to new heights, with the development of more efficient catalysts and new catalytic transformations at increasing frequency. Furthermore, catalytic reactions that allow higher levels of redox- and step-economy are being developed. Thus, alternatives to asymmetric alkene dihydroxylation and the enantioselective reduction of α,β-unsaturated ketones can invoke more strategic C-C bond forming reactions, such as asymmetric aldol reactions of an aldehyde with α-hydroxyketone donors or enantioselective alkynylation of an aldehyde, respectively. To facilitate catalytic enantioselective addition reactions, including the aforementioned aldol and alkynylation reactions, our lab has developed the ProPhenol ligand.In this Account, we describe the development and application of the ProPhenol ligand for asymmetric additions of both carbon- and heteroatom-based nucleophiles to various electrophiles. The ProPhenol ligand spontaneously forms chiral dinuclear metal complexes when treated with an alkyl metal reagent, such as Et2Zn or Bu2Mg. The resulting complex contains both a Lewis acidic site to activate an electrophile and a Brønsted basic site to deprotonate a pronucleophile. Initially, our research focused on the use of Zn-ProPhenol complexes to facilitate the direct aldol reaction. Fine tuning of the reaction through ligand modification and the use of additives enabled the direct aldol reaction to proceed in high yields and stereoselectivities with a broad range of donor substrates, including acetophenones, methyl ynones, methyl vinyl ketone, acetone, α-hydroxy carbonyl compounds, and glycine Schiff bases. Additionally, an analogous magnesium ProPhenol complex was used to facilitate enantioselective diazoacetate aldol reactions with aryl, α,β-unsaturated, and aliphatic aldehydes.The utility of bimetallic ProPhenol catalysts was extended to asymmetric additions with a wide range of substrate combinations. Effective pronucleophiles include oxazolones, 2-furanone, nitroalkanes, pyrroles, 3-hydroxyoxindoles, alkynes, meso-1,3-diols, and dialkyl phosphine oxides. These substrates were found to be effective with a number of electrophiles, including aldehydes, imines, nitroalkenes, acyl silanes, vinyl benzoates, and α,β-unsaturated carbonyls. A truly diverse range of enantioenriched compounds have been prepared using the ProPhenol ligand, and the commercial availability of both ligand enantiomers makes it ideally suited for the synthesis of complex molecules. To date, enantioselective ProPhenol-catalyzed reactions have been used in the synthesis of more than 20 natural products. © 2015 American Chemical Society.


Klinman J.P.,University of California at Berkeley
Accounts of Chemical Research | Year: 2015

ConspectusThe grand challenge in enzymology is to define and understand all of the parameters that contribute to enzymes' enormous rate accelerations. The property of hydrogen tunneling in enzyme reactions has moved the focus of research away from an exclusive focus on transition state stabilization toward the importance of the motions of the heavy atoms of the protein, a role for reduced barrier width in catalysis, and the sampling of a protein conformational landscape to achieve a family of protein substates that optimize enzyme-substrate interactions and beyond.This Account focuses on a thermophilic alcohol dehydrogenase for which the chemical step of hydride transfer is rate determining across a wide range of experimental conditions. The properties of the chemical coordinate have been probed using kinetic isotope effects, indicating a transition in behavior below 30 °C that distinguishes nonoptimal from optimal C-H activation. Further, the introduction of single site mutants has the impact of either enhancing or eliminating the temperature dependent transition in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium exchange and fluorescent lifetimes and Stokes shifts, have also been pursued. These studies allow the correlation of spatially resolved transitions in protein motions with catalysis. It is now possible to define a long-range network of protein motions in ht-ADH that extends from a dimer interface to the substrate binding domain across to the cofactor binding domain, over a distance of ca. 30 Å. The ongoing challenge to obtaining spatial and temporal resolution of catalysis-linked protein motions is discussed. © 2014 American Chemical Society.


Zohdi T.I.,University of California at Berkeley
Journal of Computational Physics | Year: 2013

This work addresses the impact and deposition of charged "cluster-droplets", comprised of particulates, on electrified surfaces. A direct numerical method is developed, based on an implicit, staggered, time-stepping scheme which separates the impulsive and continuous forces between particles, in conjunction with an iterative solution method that automatically adapts the time-step sizes to control the rates of convergence within a time-step. This approach is used to investigate the post-impactstructure of charged particulate clusterdroplets. Particulate cluster-droplet impact has wide-ranging application to areas such as inkjet printing, sprays, coatings, etc. A series of numerical examples are provided, where we investigate the effect of progressively increasing the electric field strength on the impacted substrate, leading to a more coherent cluster deposition. An analysis is also provided for the interaction of charged cluster-droplets with electromagnetic fields. © 2012 Elsevier Inc.


Ziolkowska J.R.,University of California at Berkeley
Applied Energy | Year: 2014

The question of increasing biofuels production and the development of different biofuels production technologies has become controversial. On the one hand, production of corn-based biofuels creates a 'food/feed vs. fuel' tradeoff condition, along with subsequent uncertainties for both consumers and producers (farmers). On the other, advanced biofuels (from, e.g., switchgrass, miscanthus, algae), although acknowledged as environmentally friendly, are not available on a large commercial scale yet.In addition, the limited resource availability for the production of biofuels feedstocks and the question of a sustainable biofuels production are major issues impacting decision making. Most recently, climatic conditions and the 2011-2012 drought in the US have imposed new uncertainties that need to be considered in policy- making processes.By using a multi-objective optimization model, the paper presents an approach of modeling sustainable biofuels production from conventional and advanced biofuels feedstocks, under the condition of limited resources and uncertainty resulting from incomplete information or missing knowledge about the consequences of possible policy actions. © 2013 Elsevier Ltd.


Hopkins P.F.,University of California at Berkeley
Monthly Notices of the Royal Astronomical Society: Letters | Year: 2012

Observations of active galactic nuclei (AGN) have suggested a possible delay between the peak of star formation (on some scale) and AGN activity. Inefficient fuelling (and/or feedback) from fast stellarwinds has been invoked to explain this, butwe argue this is unlikely in bright systems accreting primarily cold dense gas. We show that such a delay can arise even in bright quasars for purely dynamical reasons. If some large-scale process produces rapid inflow, smaller scales will quickly become gas dominated. As the gas density peaks, so does the star formation rate (SFR). However, gravitational torques which govern further inflow are relatively inefficient in gas-dominated systems; as more gas is turned into stars, the stars provide an efficient angular momentum sink allowing more rapid inflow. Moreover, the gas provided to the central regions in mergers or strong disc instabilities will typically be ~100 times larger than that needed to fuel the black hole (BH); the system is effectively in the 'infinite gas supply' limit. BH growth can therefore continue for some time while the gas supply exhausts, until it has significantly depleted to the point where the BH is finally 'starved'. Both of these effects act together with comparable magnitude, and mean that the peak of BH growth can lag the peak in the SFR measured at a given scale by a time-scale corresponding to the gas exhaustion time on that scale (~10-100 local dynamical times). This predicts that the inferred delay will vary in a specific manner with the radius over which the SFR is measured. We discuss possible implications for the role of AGN feedback in suppressing star formation activity. © 2012 The Author. Monthly Notices of the Royal Astronomical Society © 2012 RAS.


Nguyen C.T.-C.,University of California at Berkeley
IEEE Communications Magazine | Year: 2013

An evaluation of the potential for MEMS technologies to realize the RF front-end frequency gating spectrum analyzer function needed by true software-defined cognitive radios and ultra-low-power autonomous sensor network radios is presented. Here, RF channel selection, as opposed to band selection that removes all interferers, even those in band, and passes only the desired channel, is key to substantial potential increases in call volume with simultaneous reductions in power consumption. The relevant MEMS technologies most conducive to RF channel-selecting front-ends include vibrating micromechanical resonators that exhibit record on-chip Qs at gigahertz frequencies; resonant switches that provide extremely efficient switched-mode power gain for both transmit and receive paths; medium-scale integrated micromechanical circuits that implement on/off switchable filter-amplifier banks; and fabrication technologies that integrate MEMS together with foundry CMOS transistors in a fully monolithic low-capacitance single-chip process. The many issues that make realization of RF channel selection a truly challenging proposition include resonator drift stability, mechanical circuit complexity, repeatability and fabrication tolerances, and the need for resonators at gigahertz frequencies with simultaneous high Ω (>30,000) and low impedance (e.g., 50 W for conventional systems). Some perspective on which resonator technologies might best achieve these simultaneous attributes is provided. © 1979-2012 IEEE.


Korpela E.J.,University of California at Berkeley
Annual Review of Earth and Planetary Sciences | Year: 2012

Volunteer computing, also known as public-resource computing, is a form of distributed computing that relies on members of the public donating the processing power, Internet connection, and storage capabilities of their home computers. Projects that utilize this mode of distributed computation can potentially access millions of Internet-attached central processing units (CPUs) that provide PFLOPS (thousands of trillions of floating-point operations per second) of processing power. In addition, these projects can access the talents of the volunteers themselves. Projects span a wide variety of domains including astronomy, biochemistry, climatology, physics, and mathematics. This review provides an introduction to volunteer computing and some of the difficulties involved in its implementation. I describe the dominant infrastructure for volunteer computing in some depth and provide descriptions of a small number of projects as an illustration of the variety of projects that can be undertaken. © 2012 by Annual Reviews. All rights reserved.


Ollivier H.,University of California at Berkeley
Journal of Environmental Economics and Management | Year: 2012

This paper assesses the long term impacts of an international transfer called the Reduced Emissions from Deforestation and Degradation (REDD) mechanism, which aims at preserving tropical forests of the recipient economy. This two-sector economy faces a dilemma between economic growth and deforestation. The rural sector can substitute reproducible capital for agricultural land whereas the manufacturing sector only requires capital. The model shows that the REDD mechanism has a non-monotonic effect on steady state welfares. For low transfer schemes, the agricultural output increases with the transfer even though less land is under cultivation. For high transfer schemes, the increase in the transfer may not offset the decrease in the agricultural output. The open-loop symmetric Nash equilibrium in a dynamic deforestation game predicts that redistributing the transfer among a finite number of producers is less efficient in reducing deforestation than in the social optimum. © 2012 Elsevier Inc.


England S.L.,University of California at Berkeley
Space Science Reviews | Year: 2012

Solar thermal tides are planetary-scale waves in the neutral atmosphere with periods that are harmonics of 24 hours. In the thermosphere, they can achieve significant amplitude and can be the dominant source of variation in the atmosphere. Through their modification of the neutral atmosphere, they can also significantly modify the ionosphere, especially at low-latitudes where the dynamics of the Earth's ionosphere is determined to a large extent by the neutral atmosphere. Much recent work has focused on characterizing and understanding the impact of one sub-group of tides, known as non-migrating tides, on the ionosphere. Whereas migrating tides are responsible for creating strong day-night variations in the ionosphere, non-migrating tides create longitudinal variations in the ionosphere, the signature of which can only be detected with distributed networks of ground-based observations or spacecraft. The present work reviews the recent observations and modeling efforts that have helped to characterize and explain this longitudinal variability. Emphasis is placed on the characteristics of tides throughout the thermosphere, their impacts on the chemical composition of the thermosphere, and impacts on the ionosphere. © 2011 Springer Science+Business Media B.V.


He L.,University of California at Berkeley
Science Signaling | Year: 2010

The classic "two-hit" model of tumor-suppressor inactivation, originally established by mathematical modeling of cancer incidence, implies that tumorigenesis requires complete loss of function of tumor-suppressor genes. Although this is true in some tumor types, the exact nature of tumor-suppressor deregulation varies depending on tissue type, stage of cancer development, nature of coexisting molecular lesions, and environmental factors. Emerging evidence has indicated the functional importance of PTEN (phosphatase and tensin homolog) dosage during tumor development. Among the key regulators of PTEN dosage are a number of noncoding RNAs, including microRNAs (miRNAs) and pseudogenes, which regulate PTEN abundance at the posttranscriptional level. Various studies have revealed the essential roles of these PTEN-targeting noncoding RNAs during tumor development, thus providing a paradigm to explore the molecular mechanisms underlying the dosage-dependent effects of key oncogenes and tumor suppressors.


Levi D.M.,University of California at Berkeley
Visual Neuroscience | Year: 2013

Over the last 35 years or so, there has been substantial progress in revealing and characterizing the many interesting and sometimes mysterious sensory abnormalities that accompany amblyopia. A goal of many of the studies has been to try to make the link between the sensory losses and the underlying neural losses, resulting in several hypotheses about the site, nature, and cause of amblyopia. This article reviews some of these hypotheses, and the assumptions that link the sensory losses to specific physiological alterations in the brain. Despite intensive study, it turns out to be quite difficult to make a simple linking hypothesis, at least at the level of single neurons, and the locus of the sensory loss remains elusive. It is now clear that the simplest notion-that reduced contrast sensitivity of neurons in cortical area V1 explains the reduction in contrast sensitivity-is too simplistic. Considerations of noise, noise correlations, pooling, and the weighting of information also play a critically important role in making perceptual decisions, and our current models of amblyopia do not adequately take these into account. Indeed, although the reduction of contrast sensitivity is generally considered to reflect early neural changes, it seems plausible that it reflects changes at many stages of visual processing. © 2013 Cambridge University Press.


Theil E.C.,Childrens Hospital Oakland Research Institute | Theil E.C.,University of California at Berkeley
Current Opinion in Chemical Biology | Year: 2011

The ferritin superfamily is composed of ancient, nanocage proteins with an internal cavity, 60% of total volume, that reversibly synthesize solid minerals of hydrated ferric oxide; the minerals are iron concentrates for cell nutrition as well as antioxidants due to ferrous and oxygen consumption during mineralization. The cages have multiple iron entry/exit channels, oxidoreductase enzyme sites, and, in eukaryotes, Fe(III)O nucleation channels with clustered exits that extend protein activity to include facilitated mineral growth. Ferritin protein cage differences include size, amino acid sequence, and location of the active sites, oxidant substrate and crystallinity of the iron mineral. Genetic regulation depends on iron and oxygen signals, which in animals includes direct ferrous signaling to RNA to release and to ubiquitin-ligases to degrade the protein repressors. Ferritin biosynthesis forms, with DNA, mRNA and the protein product, a feedback loop where the genetic signals are also protein substrates. The ferritin protein nanocages, which are required for normal iron homeostasis and are finding current use in the delivery of nanodrugs, novel nanomaterials, and nanocatalysts, are likely contributors to survival and success during the transition from anaerobic to aerobic life. © 2011.


Sposito G.,University of California at Berkeley
Vadose Zone Journal | Year: 2013

It is widely understood that crop production must increase at least twice as fast as human population growth during the coming 40 yr to meet global food demand. Tested strategies for achieving this goal have not yet emerged, but some stipulations to guide in the search for them can be made. Adverse ecological impacts of land conversion to agricultural use and freshwater withdrawals for irrigation will strongly limit the viability of these two traditional approaches to increasing crop production, whereas abundant opportunity exists for optimizing soil water availability to and consumption by rainfed crops to increase their yields by twofold or more. This optimization, however, will require major campaigns in multidisciplinary basic research on positive plant-soil feedbacks that increase crop biomass by influencing the rhizosphere, through which 40% of the global freshwater flow passes annually. © Soil Science Society of America, All rights reserved.


Werblin F.S.,University of California at Berkeley
Visual Neuroscience | Year: 2010

Early retinal studies categorized ganglion cell behavior as either linear or nonlinear and rectifying as represented by the familiar X- and Y-type ganglion cells in cat. Nonlinear behavior is in large part a consequence of the rectifying nonlinearities inherent in synaptic transmission. These nonlinear signals underlie many special functions in retinal processing, including motion detection, motion in motion, and local edge detection. But linear behavior is also required for some visual processing tasks. For these tasks, the inherently nonlinear signals are linearized by crossover inhibition. Linearization utilizes a circuitry whereby nonlinear ON inhibition adds with nonlinear OFF excitation or ON excitation adds with OFF inhibition to generate a more linear postsynaptic voltage response. Crossover inhibition has now been measured in most bipolar, amacrine, and ganglion cells. Functionally crossover inhibition enhances edge detection, allows ganglion cells to recognize luminance-neutral patterns with their receptive fields, permits ganglion cells to distinguish contrast from luminance, and maintains a more constant conductance during the light response. In some cases, crossover extends the operating range of cone-driven OFF ganglion cells into the scotopic levels. Crossover inhibition is also found in neurons of the lateral geniculate nucleus and V1. Copyright © 2010 Cambridge University Press.


Reyes J.C.,University of Los Andes, Colombia | Chopra A.K.,University of California at Berkeley
Earthquake Engineering and Structural Dynamics | Year: 2011

The modal pushover analysis (MPA) procedure, presently restricted to one horizontal component of ground motion, is extended to three-dimensional analysis of buildings-symmetric or unsymmetric in plan-subjected to two horizontal components of ground motion, simultaneously. Also presented is a variant of this method, called the practical modal pushover analysis (PMPA) procedure, which estimates seismic demands directly from the earthquake response (or design) spectrum. Its accuracy in estimating seismic demands for very tall buildings is evaluated, demonstrating that for nonlinear systems this procedure is almost as accurate as the response spectrum analysis procedure is for linear systems. Thus, for practical applications, the PMPA procedure offers an attractive alternative whereby seismic demands can be estimated directly from the (elastic) design spectrum, thus avoiding the complications of selecting and scaling ground motions for nonlinear response history analysis. © 2010 John Wiley & Sons, Ltd.


Su Y.,University of California at Berkeley
Nature Nanotechnology | Year: 2016

Photoelectrochemistry is one of several promising approaches for the realization of efficient solar-to-fuel conversion. Recent work has shown that photoelectrodes made of semiconductor nano-/microwire arrays can have better photoelectrochemical performance than their planar counterparts because of their unique properties, such as high surface area. Although considerable research effort has focused on studying wire arrays, the inhomogeneity in the geometry, doping, defects and catalyst loading present in such arrays can obscure the link between these properties and the photoelectrochemical performance of the wires, and correlating performance with the specific properties of individual wires is difficult because of ensemble averaging. Here, we show that a single-nanowire-based photoelectrode platform can be used to reliably probe the current–voltage (I–V) characteristics of individual nanowires. We find that the photovoltage output of ensemble array samples can be limited by poorly performing individual wires, which highlights the importance of improving nanowire homogeneity within an array. Furthermore, the platform allows the flux of photogenerated electrons to be quantified as a function of the lengths and diameters of individual nanowires, and we find that the flux over the entire nanowire surface (7–30 electrons nm-2 s-1) is significantly reduced as compared with that of a planar analogue (∼1,200 electrons nm-2 s-1). Such characterization of the photogenerated carrier flux at the semiconductor/electrolyte interface is essential for designing nanowire photoelectrodes that match the activity of their loaded electrocatalysts. © 2016 Nature Publishing Group


Rosner D.K.,University of California at Berkeley
Proceedings of the ACM Conference on Computer Supported Cooperative Work, CSCW | Year: 2012

Drawing on a three-month bookbinding apprenticeship, this paper examines how people's coordination work is tightly bound up in material practices, the union of material arrangements and social relations. Through the construction of a book, I reveal how sensitivities to delicacy, flexibility and delay emerge through detailed engagements with the book, the binders and the workshop environment. From small adjustments of the hand, to the coordination and exchange of materials and tools, the accomplishment of each task rests on how digital and age-old resources are woven into everyday collaborative practice. This approach extends how computer-supported cooperative work (CSCW) frames and mobilizes the material to recognize materials as compositional elements, surfaces and flows. It also contributes to conversations on digital materiality by emphasizing the temporality of material practice. Thus, I use the bookbinding workshop as a resource for understanding the ways materials, techniques, and relationships are continually rebound in a digital age. © 2012 ACM.


Hochbaum D.S.,University of California at Berkeley
IEEE Transactions on Pattern Analysis and Machine Intelligence | Year: 2010

In partitioning, clustering, and grouping problems, a typical goal is to group together similar objects, or pixels in the case of image processing. At the same time, another goal is to have each group distinctly dissimilar from the rest and possibly to have the group size fairly large. These goals are often combined as a ratio optimization problem. One example of such a problem is a variant of the normalized cut problem, another is the ratio regions problem. We devise here the first polynomial time algorithms solving optimally the ratio region problem and the variant of normalized cut, as well as a few other ratio problems. The algorithms are efficient and combinatorial, in contrast with nonlinear continuous approaches used in the image segmentation literature, which often employ spectral techniques. Such techniques deliver solutions in real numbers which are not feasible to the discrete partitioning problem. Furthermore, these continuous approaches are computationally expensive compared to the algorithms proposed here. The algorithms presented here use as a subroutine a minimum s,t-cut procedure on a related graph which is of polynomial size. The output consists of the optimal solution to the respective ratio problem, as well as a sequence of nested solutions with respect to any relative weighting of the objectives of the numerator and denominator. © 2006 IEEE.


Huang Y.,University of California at Berkeley
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

Commutator-based entropic uncertainty relations in multidimensional position and momentum spaces are derived, twofold generalizing previous entropic uncertainty relations for one-mode states. They provide optimal lower bounds and imply the multidimensional variance-based uncertainty principle. The article concludes with an open conjecture. © 2011 American Physical Society.


Costello M.J.,University of Auckland | Wieczorek J.,University of California at Berkeley
Biological Conservation | Year: 2014

There is increasing pressure from the scientific community, including funding agencies, journals and peers, for authors to publish the biodiversity data used in published articles and other scientific literature. This enables reproducibility of research and creates new opportunities for integrating data between research projects and analysing data in additional ways. The long-term availability of data is especially important in conservation science because field data can be costly to collect. In addition, historic data, especially on threatened species and their associated biota, become more valuable over time. This paper summarises current standards and best practices for the management and publication of biodiversity data. It includes recommendations for citing sources of species determination and standards for formatting species distribution data. Whenever possible, data should be published for inclusion in data access platforms that integrate datasets (e.g. GBIF, GenBank) and so enable new analyses and broader impact. Data centres (e.g. PANGAEA) provide added value in quality checks on data. A minimum standard recommended is that data should be permanently archived in an online, open-access repository with sufficient metadata for potential users to understand how and why they were collected. © 2013 Elsevier Ltd.


Luntz A.C.,SLAC | McCloskey B.D.,University of California at Berkeley | McCloskey B.D.,Lawrence Berkeley National Laboratory
Chemical Reviews | Year: 2014

The major issue confronting complete electrification of road transport is simply a battery problem. While both metrics are undoubtedly important, which of the two is the most important for EV applications is somewhat debated, even among the different EV manufacturers. Traditional car companies emphasize more the importance of energy density, while Tesla emphasizes more the specific energy since they tend to design a car around the battery pack. The history of rechargeable non-aqueous Li-air batteries at this stage is so short that the field must be considered a work in progress. In fact, even the basic mechanisms and rationale for many of the fundamental properties of Li-air are still in dispute among many of the researchers in the field.


Delarue M.,University of California at Berkeley
Nature Physics | Year: 2016

In natural settings, microbes tend to grow in dense populations where they need to push against their surroundings to accommodate space for new cells. The associated contact forces play a critical role in a variety of population-level processes, including biofilm formation, the colonization of porous media, and the invasion of biological tissues. Although mechanical forces have been characterized at the single-cell level, it remains elusive how collective pushing forces result from the combination of single-cell forces. Here, we reveal a collective mechanism of confinement, which we call self-driven jamming, that promotes the build-up of large mechanical pressures in microbial populations. Microfluidic experiments on budding yeast populations in space-limited environments show that self-driven jamming arises from the gradual formation and sudden collapse of force chains driven by microbial proliferation, extending the framework of driven granular matter. The resulting contact pressures can become large enough to slow down cell growth, to delay the cell cycle in the G1 phase, and to strain or even destroy the micro-environment through crack propagation. Our results suggest that self-driven jamming and build-up of large mechanical pressures is a natural tendency of microbes growing in confined spaces, contributing to microbial pathogenesis and biofouling. © 2016 Nature Publishing Group


Lee J.,University of California at Berkeley
Nature Physics | Year: 2016

Electrostatic confinement of charge carriers in graphene is governed by Klein tunnelling, a relativistic quantum process in which particle–hole transmutation leads to unusual anisotropic transmission at p–n junction boundaries. Reflection and transmission at these boundaries affect the quantum interference of electronic waves, enabling the formation of novel quasi-bound states. Here we report the use of scanning tunnelling microscopy to map the electronic structure of Dirac fermions confined in quantum dots defined by circular graphene p–n junctions. The quantum dots were fabricated using a technique involving local manipulation of defect charge within the insulating substrate beneath a graphene monolayer. Inside such graphene quantum dots we observe resonances due to quasi-bound states and directly visualize the quantum interference patterns arising from these states. Outside the quantum dots Dirac fermions exhibit Friedel oscillation-like behaviour. Bolstered by a theoretical model describing relativistic particles in a harmonic oscillator potential, our findings yield insights into the spatial behaviour of electrostatically confined Dirac fermions. © 2016 Nature Publishing Group


Buckland M.,University of California at Berkeley
Journal of the American Society for Information Science and Technology | Year: 2012

During the 20th century there was a strong desire to develop an information science from librarianship, bibliography, and documentation and in 1968 the American Documentation Institute changed its name to the American Society for Information Science. By the beginning of the 21st century, however, departments of (library and) information science had turned instead towards the social sciences. These programs address a variety of important topics, but they have been less successful in providing a coherent explanation of the nature and scope of the field. Progress can be made towards a coherent, unified view of the roles of archives, libraries, museums, online information services, and related organizations if they are treated as information-providing services. However, such an approach seems significantly incomplete on ordinary understandings of the providing of information. Instead of asking what information science is or what we might wish it to become, we ask instead what kind of field it can be given our assumptions about it. We approach the question by examining some keywords: science, information, knowledge, and interdisciplinary. We conclude that if information science is concerned with what people know, then it is a form of cultural engagement, and at most, a science of the artificial. © 2011 ASIS&T.


Su X.,University of California at Berkeley
Operations Research | Year: 2010

We study a dynamic pricing problem for a class of products with stable consumption patterns (e.g., household items, staple foods). Consumers may stock up the product at current prices for future consumption, but they incur inventory holding costs. We model this situation as a dynamic game over an infinite time horizon: in each period, the seller sets a price, and each consumer chooses how many units to buy. We develop a solution methodology based on rational expectations. By endowing each player with beliefs, we decouple the dynamic game into individual dynamic programs for each player. We solve for the rational expectations equilibrium, where all players make optimal dynamic decisions given correct beliefs about others' behavior. In equilibrium, the seller may either charge a constant fixed price or offer periodic price promotions at predictable time intervals. We show that promotions are useful when frequent shoppers are willing to pay more for the product than are occasional shoppers. We also develop several model extensions to study the impact of consumer stockpiling on the seller's inventory, production, and rationing strategies. ©2010 INFORMS.


Ormel C.W.,University of California at Berkeley
Monthly Notices of the Royal Astronomical Society | Year: 2013

Gravitating bodies significantly alter the flow pattern (density and velocity) of the gas that attempts to stream past. Still, small protoplanets in the Mars-super-Earth range can only bind limited amounts of nebular gas; until the so-called critical core mass has been reached (̃1-10 M⊕) this gas is in near hydrostatic equilibrium with the nebula. Here we aim for a general description of the flow pattern surrounding these low-mass, embedded planets. Using various simplifying assumptions (subsonic, 2D, inviscid flow, etc.), we reduce the problem to a partial differential equation that we solve numerically as well as approximate analytically. It is found that the boundary between the atmosphere and the nebula gas strongly depends on the value of the disc headwind (deviation from Keplerian rotation).With increasing headwind the atmosphere decreases in size and also becomes more asymmetrical. Using the derived flow pattern for the gas, trajectories of small solid particles, which experience both gas drag and gravitational forces, are integrated numerically. Accretion rates for small particles (dust) are found to be low, as they closely follow the streamlines, which curl away from the planet. However, pebble-size particles achieve large accretion rates, in agreement with previous numerical and analytical works. © 2012 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Hopkins P.F.,University of California at Berkeley
Monthly Notices of the Royal Astronomical Society | Year: 2013

Recently, we have shown that if the interstellar medium is governed by supersonic turbulent flows, the excursion-set formalism can be used to calculate the statistics of self-gravitating objects over a wide range of scales. On the largest self-gravitating scales ('first crossing'), these correspond to giant molecular clouds (GMCs), and on the smallest non-fragmenting self-gravitating scales ('last crossing'), to protostellar cores. Here, we extend this formalism to rigorously calculate the autocorrelation and cross-correlation functions of cores (and by extension, young stars) as a function of spatial separation and mass, in analogy to the cosmological calculation of halo clustering. We show that this generically predicts that star formation is very strongly clustered on small scales: stars form in clustered regions, themselves inside GMCs. Outside the binary-star regime, the projected correlation function declines as a weak power law, until a characteristic scale which corresponds to the characteristic mass scale of GMCs. On much larger scales the clustering declines such that star formation is not strongly biased on galactic scales, relative to the actual dense gas distribution. The precise correlation function shape depends on properties of the turbulent spectrum, but its qualitative behaviour is quite general. The predictions agree well with observations of young star and core autocorrelation functions over ~4 dex in radius. Clustered star formation is a generic consequence of supersonic turbulence if most of the power in the velocity field, hence the contribution to density fluctuations, comes from large scales ~h. The distribution of self-gravitating masses near the sonic length is then imprinted by fluctuations on larger scales. We similarly show that the fraction of stars formed in 'isolated' modes should be small, ≲10 per cent. © 2012 The Author.


Chung S.T.L.,University of California at Berkeley
Optometry and Vision Science | Year: 2013

Following the onset of central vision loss, most patients develop an eccentric retinal location outside the affected macular region, the preferred retinal locus (PRL), as their new reference for visual tasks. The first goal of this article is to present behavioral evidence showing the presence of experience-dependent plasticity in people with central vision loss. The evidence includes the presence of oculomotor re-referencing of fixational saccades to the PRL; the characteristics of the shape of the crowding zone (spatial region within which the presence of other objects affects the recognition of a target) at the PRL are more "foveal-like" instead of resembling those of the normal periphery; and the change in the shape of the crowding zone at a para-PRL location that includes a component referenced to the PRL. These findings suggest that there is a shift in the referencing locus of the oculomotor and the sensory visual system from the fovea to the PRL for people with central vision loss, implying that the visual system for these individuals is still plastic and can be modified through experiences. The second goal of the article is to demonstrate the feasibility of applying perceptual learning, which capitalizes on the presence of plasticity, as a tool to improve functional vision for people with central vision loss. Our finding that visual function could improve with perceptual learning presents an exciting possibility for the development of an alternative rehabilitative strategy for people with central vision loss. Copyright © 2013 American Academy of Optometry.


Hopkins P.F.,University of California at Berkeley
Monthly Notices of the Royal Astronomical Society | Year: 2013

Various formulations of smoothed particle hydrodynamics (SPH) have been proposed, intended to resolve certain difficulties in the treatment of fluid mixing instabilities. Most have involved changes to the algorithm which either introduces artificial correction terms or violates what is arguably the greatest advantage of SPH over other methods: manifest conservation of energy, entropy, momentum and angular momentum. Here, we show how a class of alternative SPH equations of motion (EOM) can be derived self-consistently from a discrete particle Lagrangian-guaranteeing manifest conservation-in a manner which tremendously improves treatment of these instabilities and contact discontinuities. Saitoh & Makino recently noted that the volume element used to discretize the EOM does not need to explicitly invoke the mass density (as in the 'standard' approach); we show how this insight, and the resulting degree of freedom, can be incorporated into the rigorous Lagrangian formulation that retains ideal conservation properties and includes the '∇h' terms that account for variable smoothing lengths. We derive a general EOM for any choice of volume element (particle 'weights') and method of determining smoothing lengths. We then specify this to a 'pressure-ntropy formulation' which resolves problems in the traditional treatment of fluid interfaces. Implementing this in a new version of the GADGET code, we show it leads to good performance in mixing experiments (e.g. Kelvin-Helmholtz and 'blob' tests). And conservation is maintained even in strong shock/blastwave tests, where formulations without manifest conservation produce large errors. This also improves the treatment of subsonic turbulence and lessens the need for large kernel particle numbers. The code changes are trivial and entail no additional numerical expense. This provides a general framework for self-consistent derivation of different 'flavours' of SPH. © 2012 The Author Published by Oxford University Press on behalf of the Royal Astronomical Society.


Spear R.C.,University of California at Berkeley
Journal of the Royal Society Interface | Year: 2012

Currently schistosomiasis transmission has been suppressed to low levels in many historically endemic areas of China by widespread use of praziquantel in human and bovine populations and application of niclosamide for snail control. However, re-emergent transmission has signalled the need for sustainable interventions beyond these repeated chemical interventions. To take advantage of ongoing investment in rural infrastructure, an index of schistosomiasis transmission potential is needed to identify villages where environmental modifications would be particularly effective. Based on a retrospective analysis of data from 10 villages in Sichuan Province, an index linked to the basic reproductive number is shown to have promise in meeting this need. However, a lack of methods for estimating the spatial components of the proposed metric and for estimating the import of cercariae and miracidia from neighbouring villages leads to significant uncertainty in its estimation. These findings suggest a priority effort to develop methods for measuring the free-swimming forms of the parasite in surface waters. This need is underscored by the high cost and limited sensitivity of current methods for diagnosing human infection and mounting evidence of the inadequacy of snail surveys to identify environments supporting low levels of transmission. © 2011 The Royal Society.


Nachman M.W.,University of California at Berkeley
Molecular Ecology | Year: 2013

Nearly 25 years ago, Allan Wilson and colleagues isolated DNA sequences from museum specimens of kangaroo rats (Dipodomys panamintinus) and compared these sequences with those from freshly collected animals (Thomas et al.). The museum specimens had been collected up to 78 years earlier, so the two samples provided a direct temporal comparison of patterns of genetic variation. This was not the first time DNA sequences had been isolated from preserved material, but it was the first time it had been carried out with a population sample. Population geneticists often try to make inferences about the influence of historical processes such as selection, drift, mutation and migration on patterns of genetic variation in the present. The work of Wilson and colleagues was important in part because it suggested a way in which population geneticists could actually study genetic change in natural populations through time, much the same way that experimentalists can do with artificial populations in the laboratory. Indeed, the work of Thomas et al. () spawned dozens of studies in which museum specimens were used to compare historical and present-day genetic diversity (reviewed in Wandeler et al.). All of these studies, however, were limited by the same fundamental problem: old DNA is degraded into short fragments. As a consequence, these studies mostly involved PCR amplification of short templates, usually short stretches of mitochondrial DNA or microsatellites. In this issue, Bi et al. () report a breakthrough that should open the door to studies of genomic variation in museum specimens. They used target enrichment (exon capture) and next-generation (Illumina) sequencing to compare patterns of genetic variation in historic and present-day population samples of alpine chipmunks (Tamias alpinus) (Fig. 1). The historic samples came from specimens collected in 1915, so the temporal span of this comparison is nearly 100 years. © 2013 John Wiley & Sons Ltd.


The hydrogenation of dimethyl carbonate to methanol catalyzed by a PNN-ligated ruthenium complex (PNN)Ru(CO)(H) was studied computationally using the density functional theory at the range-separated and dispersion-corrected ωB97X-D functional level in conjunction with an all-electron 6-31++G(d,p) basis set (Stuttgart ECP28MWB basis set for Ru). A direct metal hydride and ligand proton transfer mechanism with three cascade catalytic cycles for the hydrogenation of dimethyl carbonate, methyl formate, and formaldehyde to methanol is proposed. The resting state in the catalytic reaction is the trans dihydride complex trans-(PNN)Ru(H) 2(CO). Calculation results indicate that the rate-determining step in the whole reaction is the formation of the second methanol molecule through simultaneous breaking of a C-OCH 3 bond and transferring a ligand methylene proton to the dissociated CH 3O - in the catalytic cycle for hydrogenation of methyl formate. The essential role of the noninnocent PNN pincer ligand is to split H 2 and assist methanol formation through the aromatization and dearomatization of the pyridine ring in the ligand. A new iron pincer complex, trans-(PNN)Fe(H) 2(CO), is proposed and evaluated as a promising low-cost and high efficiency catalyst for this reaction. © 2012 American Chemical Society.


Wendelken C.,University of California at Berkeley
Frontiers in Human Neuroscience | Year: 2015

Reasoning depends on the contribution of posterior parietal cortex (PPC). But PPC is involved in many basic operations—including spatial attention, mathematical cognition, working memory, long-term memory, and language—and the nature of its contribution to reasoning is unclear. Psychological theories of the processes underlying reasoning make divergent claims about the neural systems that are likely to be involved, and better understanding the specific contribution of PPC can help to inform these theories. We set out to address several competing hypotheses, concerning the role of PPC in reasoning: (1) reasoning involves application of formal logic and is dependent on language, with PPC activation for reasoning mainly reflective of linguistic processing; (2) reasoning involves probabilistic computation and is thus dependent on numerical processing mechanisms in PPC; and (3) reasoning is built upon the representation and processing of spatial relations, and PPC activation associated with reasoning reflects spatial processing. We conducted two separate meta-analyses. First, we pooled data from our own studies of reasoning in adults, and examined activation in PPC regions of interest (ROI). Second, we conducted an automated meta-analysis using Neurosynth, in which we examined overlap between activation maps associated with reasoning and maps associated with other key functions of PPC. In both analyses, we observed reasoning-related activation concentrated in the left Inferior Parietal Lobe (IPL). Reasoning maps demonstrated the greatest overlap with mathematical cognition. Maintenance, visuospatial, and phonological processing also demonstrated some overlap with reasoning, but a large portion of the reasoning map did not overlap with the map for any other function. This evidence suggests that the PPC’s contribution to reasoning may be most closely related to its role in mathematical cognition, but that a core component of this contribution may be specific to reasoning. © 2015 Wendelken.


Callaway D.S.,University of California at Berkeley
IEEE Transactions on Energy Conversion | Year: 2010

Sequential wind simulation models have been developed to forecast effective load-carrying capability (ELCC), but they produce data that follow a Gaussian distribution, which can be considerably different from real wind-speed distributions, and they do not explicitly model the influence of temperature on the evolution of wind speed. The latter issue is of significant importance considering the strength of correlation between electricity load and temperature and the influence electricity load shapes have on system reliability. This paper presents a new approach to reliability estimation of wind facilities that models wind-speed distributions nonparametrically and includes the effect of temperature on the evolution of wind speed. A relatively long tall tower anemometer dataset is then used to test whether or not the model output produces ELCC distributions that are statistically similar to observed distributions. Results indicate that, relative to temperature independent models, temperature-dependent time-series models are better at both short-term wind-speed forecasting and long-term reliability forecasting. Results also show that reliability forecasts are relatively unaffected by the shape of the wind-speed distribution. Finally, it is apparent that model performance is robust to variation in the average wind power in the years used for model parameterization. © 2010 IEEE.


Ye Y.,University of California at Berkeley
Nature Nanotechnology | Year: 2016

Electrically controlling the flow of charge carriers is the foundation of modern electronics. By accessing the extra spin degree of freedom (DOF) in electronics, spintronics allows for information processes such as magnetoresistive random-access memory. Recently, atomic membranes of transition metal dichalcogenides (TMDCs) were found to support unequal and distinguishable carrier distribution in different crystal momentum valleys. This valley polarization of carriers enables a new DOF for information processing. A variety of valleytronic devices such as valley filters and valves have been proposed, and optical valley excitation has been observed. However, to realize its potential in electronics it is necessary to electrically control the valley DOF, which has so far remained a significant challenge. Here, we experimentally demonstrate the electrical generation and control of valley polarization. This is achieved through spin injection via a diluted ferromagnetic semiconductor and measured through the helicity of the electroluminescence due to the spin–valley locking in TMDC monolayers. We also report a new scheme of electronic devices that combine both the spin and valley DOFs. Such direct electrical generation and control of valley carriers opens up new dimensions in utilizing both the spin and valley DOFs for next-generation electronics and computing. © 2016 Nature Publishing Group


Zohdi T.I.,University of California at Berkeley
Archives of Computational Methods in Engineering | Year: 2010

This work addresses the modeling and simulation of charged particulate jets in the presence of electromagnetic fields. The presentation is broken into two main parts: (1) the dynamics of charged streams of particles and their interaction with electromagnetic fields and (2) the coupled thermal fields that arise within the jet. An overall model is built by assembling submodels of the various coupled physical events to form a system that is solved iteratively. Specifically, an approach is developed whereby the dynamics of charged particles, accounting for their collisions, inter-particle near-fields, interaction with external electromagnetic fields and coupled thermal effects are all computed implicitly in an iterative, modular, manner. A staggered, temporally-adaptive scheme is developed to resolve the multiple fields involved and the drastic changes in the physical configuration of the stream, for example when impacting a solid wall or strong localized electromagnetic field. Qualitative analytical results are provided to describe the effects of the electromagnetic fields and quantitative numerical results are provided for complex cases. © 2010 CIMNE, Barcelona, Spain.


De A.,University of California at Berkeley
Proceedings of the Annual IEEE Conference on Computational Complexity | Year: 2011

In this paper, we prove the following results about the INW pseudorandom generator: • It fools constant width permutation branching programs with error e using a seed of length O(logn · log(1/ε)). • It fools constant width regular branching programs with error ε using a seed of length O(logn · (log log n + log(1/ε))). These results match the recent results of Koucký et al. (STOC 2011) and Braverman et al. and Brody and Verbin (FOCS 2010). However, our analysis gives a better dependence of the seed length on the width for permutation branching programs than the results of Koucky et al. (STOC 2011). Perhaps, more significantly, our proof method is entirely different and linear algebraic in nature as opposed to the group theoretic methods of [1] and the information theoretic and probabilistic methods of [2], [3]. Along the way, we also obtain pseudorandom generators for the "small biased spaces" for group products [4] with a seed length O(logn · (log G| +log(1/ε))). Previously, it was possible to get O(logn ε (|G| O(1) +log(1/ε))) using the pseudorandom generator of [1]. © 2011 IEEE.


Robinson J.C.,University of California at Berkeley
Health Affairs | Year: 2013

Two overarching frameworks compete to address the organizational ills of the health care system. One framework diagnoses lack of coordination and prescribes integration and global payment. The other diagnoses loss of focus and prescribes specialization and episode payment. This article, based on research and interviews, assesses how the two frameworks manifest themselves at two high-volume orthopedic hospitals in Irvine, California. The Kaiser Permanente IrvineMedical Center is part of a large and diversified health system. The Hoag Orthopedic Instituteis a single-specialty facility jointly owned by the physicians and the hospital. Market outcomes, such as the merger of the Hoag specialty hospital into a larger diversified health system,suggest that Kaiser's focus on coordination of patient care from preadmission to postdischargeis a key factor in its success. But Hoag's specialization also leads to improved efficiencies.The integrated approach appears to be prevailing. At the same time, large diversified organizations might obtain further efficiencies by pursuing service-line strategies as described in this article-for instance, by providing incentives for efficiency and quality for each specialtyand type of care. © 2013 Project HOPE- The People-to-People Health Foundation, Inc.


Hayes T.B.,University of California at Berkeley
Molecular biology of the cell | Year: 2010

I am honored to receive the E. E. Just Award for 2010. In my invited essay, I have opted to discuss the state of diversity in the biological sciences with some recommendations for moving forward toward a more positive and inclusive academy. The need to develop cohorts of minority scientists as support groups and to serve as role models within our institutions is stressed, along with the need to ensure that minority scientists are truly included in all aspects of the academy. It is imperative that we increase our efforts to prepare for the unique challenges that we will face as the United States approaches a "majority minority" population in the next 50 years.


Alvarez W.,University of California at Berkeley
Earth and Planetary Science Letters | Year: 2010

In plate tectonic theory, collision between two continents should quickly terminate because of continental buoyancy. If convergence is to continue, it should do so at a new subduction zone where oceanic crust can be consumed. The protracted continental collisions in the Alps, Zagros, and Himalayas, which have continued to deform continental crust since the early or middle Cenozoic, are therefore anomalies in standard plate tectonic theory. It is commonly held that plates are driven by slab pull, but this does not account for the continuing Tethyan collisions where the descending slab has detached from the subducting continent. These protracted continental collisions are better explained by horizontal traction of the mantle on the base of deep continental roots, dragging the northern and southern continents together along a Tethyan axis of mantle convergence. "Continental undertow" thus resolves the collision anomaly in plate tectonics. © 2010 Elsevier B.V.


Turiel E.,University of California at Berkeley
Child Development | Year: 2010

J. E. Grusec and M. Davidov (this issue) have taken good steps in formulating a domain-specific view of parent-child interactions. This commentary supports the introduction of domain specificity to analyses of parenting. Their formulation is an advance over formulations that characterized parental practices globally. This commentary calls for inclusion of definitions of the classification system of domain-specific interactions and criteria for each domain. It is also maintained that Grusec and Davidov's domains of social interaction imply that processes of development are involved, along with socialization; that bidirectionality in parent-child relations needs to be extended to include mutual influences and the construction of domains of social thought; and that conflicts and opposition within families coexist with compliance and social harmony. © 2010, Copyright the Author(s). Journal Compilation © 2010, Society for Research in Child Development, Inc.


Anderson K.,Australian National University | Rausser G.,University of California at Berkeley | Swinnen J.,Stanford University
Journal of Economic Literature | Year: 2013

The agricultural and food sector is an ideal case for investigating the political economy of public policies. Many of the policy developments in this sector since the 1950s have been sudden and transformational, while others have been gradual but persistent. This article reviews and synthesizes the literature on trends and fuctuations in market distortions and the political-economy explanations that have been advanced. Based on a rich global data set covering a half-century of evidence on commodities, countries, and policy instruments, we identify hypotheses that have been explored in the literature on the extent of market distortions and the conditions under which reform may be feasible.


Buchanan B.B.,University of California at Berkeley
Annual Review of Plant Biology | Year: 2016

After a brief discussion of my graduate work at Duke University, I describe a series of investigations on redox proteins at the University of California, Berkeley. Starting with ferredoxin from fermentative bacteria, the Berkeley research fostered experiments that uncovered a pathway for fixing CO2 in bacterial photosynthesis. The carbon work, in turn, opened new vistas, including the discovery that thioredoxin functions universally in regulating the Calvin-Benson cycle in oxygenic photosynthesis. These experiments, which took place over a 50-year period, led to the formulation of a set of biological principles and set the stage for research demonstrating a role for redox in the regulation of previously unrecognized processes extending far beyond photosynthesis. Copyright © 2016 by Annual Reviews. All rights reserved.


Segalman R.A.,University of California at Berkeley
Macromolecules | Year: 2010

A study was conducted to demonstrate tuning of poly(3-alkylthiophenes) (P3AT) crystallization through systematic side chain functionalization. It provided detailed information about the thermal, structural, and electronic properties of a P3AT, poly(3-(20-ethyl)hexylthiophene) (P3EHT). Its properties were compared to two more common P3ATs, poly(3-hexylthiophene), and poly(3-dodecylthiophene) (P3DDT). Three different molecular weights of each type of polymer were synthesized and the molecular weights were controlled such that the average number of thiophene repeat units per chain was approximately the same between the P3HT, P3DDT, and P3EHT series. It was shown that P3DDT and P3EHT, with melting transitions sufficiently removed from the thermal degradation temperature, exhibited a nematic liquid crystalline phase observed by polarized optical microscopy (POM), with a molecular weight-dependent nematic-isotropic transition temperature.


Hurley J.H.,University of California at Berkeley | Hurley J.H.,Lawrence Berkeley National Laboratory
EMBO Journal | Year: 2015

The ESCRT proteins are an ancient system that buds membranes and severs membrane necks from their inner face. Three "classical" functions of the ESCRTs have dominated research into these proteins since their discovery in 2001: the biogenesis of multivesicular bodies in endolysosomal sorting; the budding of HIV-1 and other viruses from the plasma membrane of infected cells; and the membrane abscission step in cytokinesis. The past few years have seen an explosion of novel functions: the biogenesis of microvesicles and exosomes; plasma membrane wound repair; neuron pruning; extraction of defective nuclear pore complexes; nuclear envelope reformation; plus-stranded RNA virus replication compartment formation; and micro- and macroautophagy. Most, and perhaps all, of the functions involve the conserved membrane-neck-directed activities of the ESCRTs, revealing a remarkably widespread role for this machinery through a broad swath of cell biology. ESCRT complexes are required for membrane remodeling and scission; this review highlights their role in cellular processes ranging from exosome generation to the reformation of the nuclear envelope. © 2015 The Author.


Jutte D.P.,University of California at Berkeley
Health Affairs | Year: 2014

Measurement can help community development and health practitioners align and optimize their investments and leverage additional resources to achieve shared goals. However, there is no clear guidance for reconciling the established systems for measuring community development activities and outputs-such as housing units built, jobs created, and people served-with the outcomes and impacts of health. We therefore reviewed community development measurement systems-encompassing assessment, monitoring, evaluation, and standards-and identified strategies for using those systems to support health in community development decision making. We highlight promising innovations by organizations such as the Reinvestment Fund and NeighborWorks America and place these in an ecosystem framework to illustrate opportunities for shared measurement. We then discuss policies and processes to build the ecosystem's infrastructure, balance stakeholders' priorities within the ecosystem, and use it to drive investments in health. © 2014 Project HOPE-The People-to-People Health Foundation, Inc.


Buffett B.A.,University of California at Berkeley
Earth and Planetary Science Letters | Year: 2010

Dissipation due to tidally driven flow in the Earth's liquid core is detected in observations of nutations. One source of dissipation is due to electromagnetic core-mantle coupling, but this mechanism requires a high electrical conductivity on the mantle side of the boundary and a strong radial magnetic field. An alternative mechanism is viable in the presence of fluid stratification at the top of the core. Stratification causes the fluid close to the core-mantle boundary to be trapped by the effects of topography. Further from the boundary the stratified fluid is swept past the mantle with the underlying tidal flow. Shear in the flow induces electric currents where the fluid is permeated with a radial magnetic field. The resulting dissipation is only weakly dependent on the electrical conductivity of the mantle and the required strength of the radial magnetic field can be lowered. For a representative calculation we explain the observed dissipation with a radial field of 0.5mT and a mantle conductivity of 1000S/m, provided the buoyancy frequency in the stratified layer is 0.09s-1. Such a strong stratification has recently been proposed on the basis of chemical interactions between the core and the mantle. Nutation observations support the presence of stratification to the extent that the resulting dissipation mechanism is more compatible with conventional estimates for the radial magnetic field and the mantle conductivity. © 2010 Elsevier B.V.


Lemoine D.M.,University of California at Berkeley
Journal of Climate | Year: 2010

Uncertainty about biases common across models and about unknown and unmodeled feedbacks is important for the tails of temperature change distributions and thus for climate risk assessments. This paper develops a hierarchical Bayes framework that explicitly represents these and other sources of uncertainty. It then uses models' estimates of albedo, carbon cycle, cloud, and water vapor-lapse rate feedbacks to generate posterior probability distributions for feedback strength and equilibrium temperature change. The posterior distributions are especially sensitive to prior beliefs about models' shared structural biases: nonzero probability of shared bias moves some probability mass toward lower values for climate sensitivity even as it thickens the distribution's positive tail. Obtaining additional models of these feedbacks would not constrain the posterior distributions as much as narrowing prior beliefs about shared biases or, potentially, obtaining feedback estimates having biases uncorrelated with those impacting climate models. Carbon dioxide concentrations may need to fall below current levels to maintain only a 10% chance of exceeding official 28C limits on global average temperature change. © 2010 American Meteorological Society.


Harris C.,University of California at Berkeley
Scandinavian journal of work, environment & health | Year: 2011

Workplace studies have linked hand/wrist tendinosis to forceful and repetitive hand exertions, but the associations are not consistent. We report findings from a prospective study of right wrist tendinosis among blue-collar workers. Workers (N=413) at four industries were followed for 28 months with questionnaires and physical examinations every 4 months to identify incident cases of right wrist tendinosis. Exposure assessment of force and repetition were based on field measurements and video analysis to determine repetition rate and the percent time (% time) in heavy pinch (>1 kg-force) or power grip (>4 kg-force). All exposure variables were measured at the level of the individual and task. For workers responsible for >1 task, a time-weighted average exposure was calculated based on task hours per week. A proportional hazards model was used to assess the relationship between exposures and incidence of wrist tendinosis. During the 481 person-years of follow-up, there were 26 incident cases of right wrist tendinosis [incidence rate (IR) 5.40 cases per 100 person-years]. Adjusting for age, gender, and repetition, wrist tendinosis was associated with % time spent in heavy pinch [hazard ratio (HR) 5.01, 95% CI 1.27-19.79). Composite exposure measure American Conference of Industrial Hygienists Threshold Limit Value (ACGIH-TLV) for hand activity level (HR 3.95, 95% CI 1.52-10.26) was also associated with the outcome for the medium-exposure group using video-based total repetition rate. The workplace factors predicting wrist tendinosis were time-weighted average values of % time spent in heavy pinch and the ACGIH-TLV for Hand Activity Level. The % time spent in power grip was not a significant predictor, nor were any measures of repetition. An exposure-response relationship was observed for the % time spent in heavy pinch. These findings may improve programs for preventing occupational wrist tendinosis.


Hearst M.A.,University of California at Berkeley
Communications of the ACM | Year: 2011

Users will speak rather than type, watch video rather than read, and use technology socially rather than alone.


Kraichak E.,University of California at Berkeley
American Journal of Botany | Year: 2012

• Premise of the study: Many links between form and function are described in the context of adaptation. Several morphological and life-history traits in the leafy liverwort family Lejeuneaceae (Marchantiophyta) have been hypothesized to be adaptations for living on the surface of leaves of vascular plants (epiphylly). There have been, however, no rigorous tests of these hypotheses. • Methods: Using a recently published phylogeny of Lejeuneaceae and trait data from published monographs, I tested the correlations of putative adaptive traits with the incidence of epiphylly. Both cross-species and phylogenetic-based analyses of trait data were performed to distinguish the patterns of shared evolutionary history from independent origins of putatively adaptive traits. The rates of transitions between different combinations of character states were also calculated to determine whether traits were more likely to evolve in the presence of epiphylly. • Key results: Only one trait, production of asexual propagules, was correlated with epiphylly in the phylogenetic-based analysis. The rate of transition to asexual propagules was also signifi cantly higher in the presence of epiphylly. Other traits correlated with epiphylly appeared to be the results of shared evolutionary history among sister taxa and therefore not due to adaptive evolution. • Conclusion: The present study distinguished production of asexual propagules from other traits as a key adaptive response to living on the leaf surface. No other putative "adaptive" traits to epiphylly showed evidence of being specifi c adaptation to epiphylly. The results highlight the importance of phylogenetically controlled methods in determining an adaptive function of traits. © 2012 Botanical Society of America.


Klinman J.P.,University of California at Berkeley | Kohen A.,University of Iowa
Annual Review of Biochemistry | Year: 2013

The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C-H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial. © 2013 by Annual Reviews. All rights reserved.


Lisch D.,University of California at Berkeley
Nature Reviews Genetics | Year: 2013

For decades, transposable elements have been known to produce a wide variety of changes in plant gene expression and function. This has led to the idea that transposable element activity has played a key part in adaptive plant evolution. This Review describes the kinds of changes that transposable elements can cause, discusses evidence that those changes have contributed to plant evolution and suggests future strategies for determining the extent to which these changes have in fact contributed to plant adaptation and evolution. Recent advances in genomics and phenomics for a range of plant species, particularly crops, have begun to allow the systematic assessment of these questions. © 2013 Macmillan Publishers Limited.


Feng X.,University of California at Berkeley
Developmental cell | Year: 2013

Plants undergo alternation of generation in which reproductive cells develop in the plant body ("sporophytic generation") and then differentiate into a multicellular gamete-forming "gametophytic generation." Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes. Copyright © 2013 Elsevier Inc. All rights reserved.


Volkman L.E.,University of California at Berkeley
Virology | Year: 2015

Negatively-supercoiled-ds DNA molecules, including the genomes of baculoviruses, spontaneously wrap around cores of histones to form nucleosomes when present within eukaryotic nuclei. Hence, nucleosome management should be essential for baculovirus genome replication and temporal regulation of transcription, but this has not been documented. Nucleosome mobilization is the dominion of ATP-dependent chromatin-remodeling complexes. SWI/SNF and INO80, two of the best-studied complexes, as well as chromatin modifier TIP60, all contain actin as a subunit. Retrospective analysis of results of AcMNPV time course experiments wherein actin polymerization was blocked by cytochalasin D drug treatment implicate actin-containing chromatin modifying complexes in decatenating baculovirus genomes, shutting down host transcription, and regulating late and very late phases of viral transcription. Moreover, virus-mediated nuclear localization of actin early during infection may contribute to nucleosome management. © 2014 The Authors.


Chatman D.G.,University of California at Berkeley
Transportation | Year: 2014

Since immigrants will account for most urban growth in the United States for the foreseeable future, better understanding their travel patterns is a critical task for transportation and land use planners. Immigrants initially travel in personal vehicles far less than the US-born, even when controlling for demographics, but their reliance on autos increases the longer they live in the US. Cultural or habitual differences, followed by assimilation to auto use, could partly explain this pattern; and it may also be partly due to changes in locations and characteristics of home and work neighborhoods. Previous studies have rarely investigated non-work travel, and have not tested workplace land use measures, compared the relative influences of enclave and home neighborhood measures, or looked at the role of culturally-bound residential preferences or motivations for migration. This study relies on a unique and rich dataset consisting of a survey of US residents born in South Asia, Latin America, and the US, joined to spatial information in a GIS. I find that the home built environment is the most consistently influential factor in explaining the lower auto use of both recent and settled Latin American immigrants. Indian immigrants use autos less than would be expected given their home and work neighborhoods. There is little evidence that either ethnic enclaves, or cultural differences, play a role in lower auto use by immigrants. These results suggest there may be a role for neighborhood built environment policies in delaying immigrant assimilation to auto use in the US. © 2013 Springer Science+Business Media New York.


Forbes E.E.,University of Pittsburgh | Dahl R.E.,University of California at Berkeley
Journal of Child Psychology and Psychiatry and Allied Disciplines | Year: 2012

Background: Conceptual models and recent evidence indicate that neural response to reward is altered in depression. Taking a developmental approach to investigating reward function in adolescent depression can elucidate the etiology, pathophysiology and course of depression, a disorder that typically begins during adolescence and has high rates of recurrence. Methods: This conceptual review describes the what, when and how of altered reward function in adolescent depression. With the goal of generating new, testable hypotheses within a developmental affective neuroscience framework, we critically review findings and suggest future directions. Peer-reviewed empirical papers for inclusion in this critical review were obtained by searching PubMed, PsycInfo and ScienceDirect for the years 1990-2010. Results: A pattern of low striatal response and high medial prefrontal response to reward is evident in adolescents and adults with depression. Given the salience of social stimuli for positive affect and depression, reward function might be especially disrupted in response to social rewards. Because of changes in the dopamine system and reward function with aging, altered reward function in depression might be more evident during adolescence than later in life; however, low reward function may also be a stable characteristic of people who experience depression. Mechanisms of altered reward function in depression could include disrupted balance of corticostriatal circuit function, with disruption occurring as aberrant adolescent brain development. Conclusions: Future studies should examine responses to social rewards; employ longitudinal and prospective designs; and investigate patterns of functional connectivity in reward circuits. Understanding altered reward function in depression has potential implications for treatment development. A more rigorous approach to investigating anhedonia, threat-reward interactions and comorbid anxiety will be valuable to future progress in describing the role of reward function in the pathophysiology of depression. © 2011 Association for Child and Adolescent Mental Health.


Murat D.,University of California at Berkeley
Cold Spring Harbor perspectives in biology | Year: 2010

Mounting evidence in recent years has challenged the dogma that prokaryotes are simple and undefined cells devoid of an organized subcellular architecture. In fact, proteins once thought to be the purely eukaryotic inventions, including relatives of actin and tubulin control prokaryotic cell shape, DNA segregation, and cytokinesis. Similarly, compartmentalization, commonly noted as a distinguishing feature of eukaryotic cells, is also prevalent in the prokaryotic world in the form of protein-bounded and lipid-bounded organelles. In this article we highlight some of these prokaryotic organelles and discuss the current knowledge on their ultrastructure and the molecular mechanisms of their biogenesis and maintenance.


Bousso R.,University of California at Berkeley
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The near-horizon field B of an old black hole is maximally entangled with the early Hawking radiation R, by unitarity of the S-matrix. But B must be maximally entangled with the black hole interior A, by the equivalence principle. Causal patch complementarity fails to reconcile these conflicting requirements. The system B can be probed by a freely falling observer while there is still time to turn around and remain outside the black hole. Therefore, the entangled state of the BR system is dictated by unitarity even in the infalling patch. If, by monogamy of entanglement, B is not entangled with A, the horizon is replaced by a singularity or "firewall." To illustrate the radical nature of the ideas that are needed, I briefly discuss two approaches for avoiding a firewall: the identification of A with a subsystem of R; and a combination of patch complementarity with the Horowitz-Maldacena final-state proposal. © 2013 American Physical Society.


Chodera J.D.,University of California at Berkeley | Pande V.S.,Stanford University
Physical Review Letters | Year: 2011

To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along which kinetic behavior is presumed to be governed by diffusive dynamics. Here, we invoke the splitting probability as a test of the suitability of such a proposed reaction coordinate. Comparison of the observed splitting probability with that computed from the kinetic model provides a simple test to reject poor reaction coordinates. We demonstrate this test for a force spectroscopy measurement of a DNA hairpin. © 2011 American Physical Society.


Orenstein J.,University of California at Berkeley | Orenstein J.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2011

Rotation of the plane of polarization of reflected light (Kerr effect) is a direct manifestation of broken time-reversal symmetry and is generally associated with the appearance of a ferromagnetic moment. Here I identify magnetic structures that may arise within the unit cell of cuprate superconductors that generate polarization rotation despite the absence of a net moment. For these magnetic symmetries the Kerr effect is mediated by magnetoelectric coupling, which can arise when antiferromagnetic order breaks inversion symmetry. The structures identified are candidates for a time-reversal breaking phase in the pseudogap regime of the cuprates. © 2011 American Physical Society.


Bousso R.,University of California at Berkeley | Bousso R.,Lawrence Berkeley National Laboratory
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The firewall paradox is often presented as arising from double entanglement, but I argue that more generally the paradox is double purity. Near-horizon modes are purified by the interior, in the infalling vacuum. Hence, they cannot also be pure alone, or in combination with any third system, as demanded by unitarity. This conflict arises independently of the Page time, for entangled and for pure states. It implies that identifications of Hilbert spaces cannot resolve the paradox. Traditional complementarity requires the unitary identification of infalling matter with a scrambled subsystem of the Hawking radiation. Extending this map to the infalling vacuum overdetermines the out-state. More general complementarity maps ("A=RB," "ER=EPR") necessarily fail when the near-horizon zone is pure. I argue that pure-zone states span the microcanonical ensemble, and that this suffices to make the horizon a special place. I advocate that the ability to detect the horizon locally, rather than the degree or probability of violence, is what makes firewalls problematic. Conversely, if the production of matter at the horizon can be dynamically understood and shown to be consistent, then firewalls do not constitute a violation of the equivalence principle. © 2013 American Physical Society.


Levi D.M.,University of California at Berkeley
Optometry and Vision Science | Year: 2012

Experience-dependent plasticity is closely linked with the development of sensory function. Beyond this sensitive period, developmental plasticity is actively limited; however, new studies provide growing evidence for plasticity in the adult visual system. The amblyopic visual system is an excellent model for examining the "brakes" that limit recovery of function beyond the critical period. While amblyopia can often be reversed when treated early, conventional treatment is generally not undertaken in older children and adults. However, new clinical and experimental studies in both animals and humans provide evidence for neural plasticity beyond the critical period. The results suggest that perceptual learning and video game play may be effective in improving a range of visual performance measures and importantly the improvements may transfer to better visual acuity and stereopsis. These findings, along with the results of new clinical trials, suggest that it might be time to reconsider our notions about neural plasticity in amblyopia. © 2012 American Academy of Optometry.


Singh S.,University of California at Berkeley
Journal of Nanoscience and Nanotechnology | Year: 2010

Significant progress has been made in nanoscale drugs and delivery systems employing diverse chemical formulations to facilitate the rate of drug delivery and release from the human body. The biocompatible nanomaterials have been used in biological markers, contrast agents for biological imaging, healthcare products, pharmaceuticals, drug-delivery systems as well as in detection, diagnosis and treatment of various types of diseases. Nanomedicines offer delivery of potential drugs to human organs which were previously beyond reach of microscale drugs due to specific biological barriers. The nanoscale systems work as nanocarriers for the delivery of drugs. The nanocarriers are made of biocompatible and biodegradable materials such as synthetic proteins, peptides, lipids, polysaccharides, biodegradable polymers and fibers. This review article reports the recent developments in the field of nanomedicine covering biodegradable polymers, nanoparticles, cyclodextrin, dendrimeres, liposomes and lipid-based nanocarriers, nanofibers, nanowires and carbon nanotubes and their chemical functionalization for distribution to different organs, their solubility, surface, chemical and biological properties, stability and release systems. The toxicity and safety of nanomaterials on human health is also briefly discussed. Copyright © 2010 American Scientific Publishers.


Haggard H.M.,University of California at Berkeley
Physical Review Letters | Year: 2011

A major challenge for any theory of quantum gravity is to quantize general relativity while retaining some part of its geometrical character. We present new evidence for the idea that this can be achieved by directly quantizing space itself. We compute the Bohr-Sommerfeld volume spectrum of a tetrahedron and show that it reproduces the quantization of a grain of space found in loop gravity. © 2011 American Physical Society.


Flammia S.T.,California Institute of Technology | Liu Y.-K.,University of California at Berkeley
Physical Review Letters | Year: 2011

We describe a simple method for certifying that an experimental device prepares a desired quantum state ρ. Our method is applicable to any pure state ρ, and it provides an estimate of the fidelity between ρ and the actual (arbitrary) state in the lab, up to a constant additive error. The method requires measuring only a constant number of Pauli expectation values, selected at random according to an importance-weighting rule. Our method is faster than full tomography by a factor of d, the dimension of the state space, and extends easily and naturally to quantum channels. © 2011 American Physical Society.


Duster T.,University of California at Berkeley
Cold Spring Harbor Perspectives in Biology | Year: 2014

Humans are both similar and diverse in such a vast number of dimensions that for human geneticists and social scientists to decide which of these dimensions is a worthy focus of empirical investigation is a formidable challenge. For geneticists, one vital question, of course, revolves around hypothesizing which kind of social diversity might illuminate genetic variation-and vice versa (i.e., what genetic variation illuminates human social diversity). For example, are there health outcomes that can be best explained by genetic variation-or for social scientists, are health outcomes mainly a function of the social diversity of lifestyles and social circumstances of a given population? Indeed, what is a "population, " how is it bounded, and are those boundaries most appropriate or relevant for human genetic research, be they national borders, religious affiliation, ethnic or racial identification, or language group, to name but a few? For social scientists, the matter of what constitutes the relevant borders of a population is equally complex, and the answer is demarcated by the goal of the research project. Although race and caste are categories deployed in both human genetics and social science, the social meaning of race and caste as pathways to employment, health, or education demonstrably overwhelms the analytic and explanatory power of genetic markers of difference between human aggregates. © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.


Chevrier J.,University of California at Berkeley
American Journal of Epidemiology | Year: 2013

Thyroid hormones play a fundamental role in fetal and child development. While iodine deficiency-related maternal and child hypothyroidism may cause severe mental retardation, recent evidence suggests that milder forms of maternal hypothyroidism and hypothyroxinemia during pregnancy are also associated with altered neurodevelopment. On the other hand, hyperthyroidism during pregnancy has been associated with adverse fetal outcomes. Findings published by Abdelouahab et al. in the American Journal of Epidemiology (Am J Epidemiol. 2013;178(5):701-713) suggest that plasma concentrations of maternal polybrominated diphenyl ethers (PBDEs), which were used as flame retardants until recently and are detected in the tissues of virtually every North American, are associated with umbilical cord and maternal thyroid hormone levels during pregnancy. Although PBDEs have been consistently shown to reduce levels of free and total thyroxine in experimental animal studies, the direction of associations in human studies has been inconsistent. In this commentary, I discuss challenges beyond the factors often cited in the epidemiologic literature to explain inconsistent findings which more specifically apply to the study of PBDEs and thyroid hormones. These include the determination of iodine intake status, the method used to adjust for blood lipid concentrations, the measurement of free thyroid hormone levels, the possible effect of PBDE metabolites, and the potential for reverse causality. © 2013 © The Author 2013. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved.


Klinman J.P.,University of California at Berkeley
Biochemistry | Year: 2013

Quantum tunneling and protein dynamics have emerged as important components of enzyme function. This review focuses on soybean lipoxygenase-1, to illustrate how the properties of enzymatic C-H bond activation link protein motions to the fundamental bond making-breaking processes. © 2013 American Chemical Society.


Kapustin A.,California Institute of Technology | Thorngren R.,University of California at Berkeley
Physical Review Letters | Year: 2014

We study 't Hooft anomalies for a global discrete internal symmetry G. We construct examples of bosonic field theories in three dimensions with a nonvanishing 't Hooft anomaly for a discrete global symmetry. We also construct field theories in three dimensions with a global discrete internal symmetry G1×G2 such that gauging G1 necessarily breaks G2 and vice versa. This is analogous to the Adler-Bell-Jackiw axial anomaly in four dimensions and parity anomaly in three dimensions. © 2014 American Physical Society.


Dyatlov S.,University of California at Berkeley
Communications in Mathematical Physics | Year: 2011

We provide a rigorous definition of quasi-normal modes for a rotating black hole. They are given by the poles of a certain meromorphic family of operators and agree with the heuristic definition in the physics literature. If the black hole rotates slowly enough, we show that these poles form a discrete subset of ℂ. As an application we prove that the local energy of linear waves in that background decays exponentially once orthogonality to the zero resonance is imposed. © 2011 Springer-Verlag.


Vazirani U.,University of California at Berkeley | Vidick T.,California Institute of Technology
Physical Review Letters | Year: 2014

Quantum cryptography promises levels of security that are impossible to replicate in a classical world. Can this security be guaranteed even when the quantum devices on which the protocol relies are untrusted? This central question dates back to the early 1990s when the challenge of achieving device-independent quantum key distribution was first formulated. We answer this challenge by rigorously proving the device-independent security of a slight variant of Ekert's original entanglement-based protocol against the most general (coherent) attacks. The resulting protocol is robust: While assuming only that the devices can be modeled by the laws of quantum mechanics and are spatially isolated from each other and from any adversary's laboratory, it achieves a linear key rate and tolerates a constant noise rate in the devices. In particular, the devices may have quantum memory and share arbitrary quantum correlations with the eavesdropper. The proof of security is based on a new quantitative understanding of the monogamous nature of quantum correlations in the context of a multiparty protocol. © 2014 American Physical Society.


Putnam-Hornstein E.,University of California at Berkeley
Child Maltreatment | Year: 2011

This article presents a population-based study of early childhood injury mortality following a nonfatal allegation of maltreatment. Findings are based on a unique data set constructed by establishing child-level linkages between vital birth records, administrative child protective services records, and vital death records. These linked data reflect over 4.3 million children born in California between 1999 and 2006 and provide a longitudinal record of maltreatment allegations and death. Of interest was whether children reported for nonfatal maltreatment subsequently faced a heightened risk of unintentional and intentional injury mortality during the first 5 years of life. Findings indicate that after adjusting for risk factors at birth, children with a prior allegation of maltreatment died from intentional injuries at a rate that was 5.9 times greater than unreported children (95% CI [4.39, 7.81]) and died from unintentional injuries at twice the rate of unreported children (95% CI [1.71, 2.36]). A prior allegation to CPS proved to be the strongest independent risk factor for injury mortality before the age of five. © The Author(s) 2011.


Vijayaraghavan A.,System Insights | Dornfeld D.,University of California at Berkeley
CIRP Annals - Manufacturing Technology | Year: 2010

Reducing the energy consumption of machine tools can significantly improve the environmental performance of manufacturing systems. To achieve this, monitoring of energy consumption patterns in the systems is required. It is vital in these studies to correlate energy usage with the operations being performed in the manufacturing system. However, this can be challenging due to complexity of manufacturing systems and the vast number of data sources. Event stream processing techniques are applied to automate the monitoring and analysis of energy consumption in manufacturing systems. Methods to reduce usage based on the specific patterns discerned are discussed. © 2010 CIRP.


Roorda A.,University of California at Berkeley
Optometry and Vision Science | Year: 2010

Adaptive optics (AO) describes a set of tools to correct or control aberrations in any optical system. In the eye, AO allows for precise control of the ocular aberrations. If used to correct aberrations over a large pupil, for example, cellular level resolution in retinal images can be achieved. AO systems have been demonstrated for advanced ophthalmoscopy as well as for testing and/or improving vision. In fact, AO can be integrated to any ophthalmic instrument where the optics of the eye is involved, with a scope of applications ranging from phoropters to optical coherence tomography systems. In this article, I discuss the applications and advantages of using AO in a specific system, the AO scanning laser ophthalmoscope. Since the Borish award was, in part, awarded to me because of this effort, I felt it appropriate to select this as the topic for this article. Furthermore, users of AO scanning laser ophthalmoscope continue to appreciate the benefits of the technology, some of which were not anticipated at the time of development, and so it is time to revisit this topic and summarize them in a single article.© 2010 American Academy of Optometry.


Nazaroff W.W.,University of California at Berkeley
Environmental Research Letters | Year: 2013

Climate change will affect the concentrations of air pollutants in buildings. The resulting shifts in human exposure may influence public health. Changes can be anticipated because of altered outdoor pollution and also owing to changes in buildings effected in response to changing climate. Three classes of factors govern indoor pollutant levels in occupied spaces: (a) properties of pollutants; (b) building factors, such as the ventilation rate; and (c) occupant behavior. Diversity of indoor conditions influences the public health significance of climate change. Potentially vulnerable subpopulations include not only the young and the infirm but also those who lack resources to respond effectively to changing conditions. Indoor air pollutant levels reflect the sum of contributions from indoor sources and from outdoor pollutants that enter with ventilation air. Pollutant classes with important indoor sources include the byproducts of combustion, radon, and volatile and semivolatile organic compounds. Outdoor pollutants of special concern include particulate matter and ozone. To ensure good indoor air quality it is important first to avoid high indoor emission rates for all pollutants and second to ensure adequate ventilation. A third factor is the use of air filtration or air cleaning to achieve further improvements where warranted. © 2013 IOP Publishing Ltd.


Vosk R.,Weizmann Institute of Science | Altman E.,Weizmann Institute of Science | Altman E.,University of California at Berkeley
Physical Review Letters | Year: 2014

Using a renormalization group approach, we solve the time evolution of random Ising spin chains with generic interactions starting from initial states of arbitrary energy. As a function of the Hamiltonian parameters, the system is tuned through a dynamical transition, similar to the ground-state critical point, at which the local spin correlations establish true long-range temporal order. In the state with a dominant transverse field, a spin that starts in an up state loses its orientation with time, while in the "ordered" state it never does. As in ground-state quantum phase transitions, the dynamical transition has unique signatures in the entanglement properties of the system. When the system is initialized in a product state, the entanglement entropy grows as log(t) in the two "phases," while at the critical point it grows as logα(t), with α a universal number. This universal entanglement growth requires generic ("integrability breaking") interactions to be added to the pure transverse field Ising model. © 2014 American Physical Society.


Bousso R.,University of California at Berkeley | Bousso R.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2014

If information escapes from an evaporating black hole, then field modes just outside the horizon must be thermally entangled with distant Hawking radiation. But for an infalling observer to find empty space at the horizon, the same modes would have to be entangled with the black hole interior. Thus, unitarity appears to require a "firewall" at the horizon. Identifying the interior with the distant radiation promises to resolve the entanglement conflict and restore the vacuum. But the map must adjust for any interactions, or else the firewall will reappear if the Hawking radiation scatters off the cosmic microwave background. Such a map produces a "frozen vacuum," a phenomenon that is arguably worse than a firewall. An infalling observer is unable to excite the vacuum near the horizon. This allows the horizon to be locally detected and so violates the equivalence principle. © 2014 American Physical Society.


Welch M.D.,University of California at Berkeley | Way M.,Cancer Research UK Research Institute
Cell Host and Microbe | Year: 2013

Intracellular pathogens have developed elaborate mechanisms to exploit the different cellular systems of their unwilling hosts to facilitate their entry, replication, and survival. In particular, a diverse range of bacteria and viruses have evolved unique strategies to harness the power of Arp2/3-mediated actin polymerization to enhance their cell-to-cell spread. In this review, we discuss how studying these pathogens has revolutionized our molecular understanding of Arp2/3-dependent actin assembly and revealed key signaling pathways regulating actin assembly in cells. Future analyses of microbe-host interactions are likely to continue uncovering new mechanisms regulating actin assembly and dynamics, as well as unexpected cellular functions for actin. Further, studies with known and newly emerging pathogens will also undoubtedly continue to enhance our understanding of the role of the actin cytoskeleton during pathogenesis and potentially highlight future therapeutic approaches. © 2013 Elsevier Inc.


Pachucki M.A.,University of California at Berkeley
International Journal of Obesity | Year: 2012

Background: Analysis of dietary patterns is prominent in nutrition literatures, yet few studies have taken advantage of multiple repeated measurements to understand the nature of individual-level changes over time in food choice, or the relation between these changes and body mass index (BMI). Objective: To investigate changes in eating patterns at the individual level across three exam periods, and to prospectively examine the relation of eating trajectories to BMI at the cohort level. Design: The study included 3418 participants at baseline. Clinically measured BMI and dietary intake were assessed during three exam periods between 1991 and 2001 using a validated food frequency questionnaire. An individual's eating trajectory across exam periods was analyzed using sequence analysis, and then used to estimate outcomes of continuous BMI and categorical obesity status. Ordinary least squares regression models with robust standard errors were adjusted for socio-economic and demographic confounders, baseline BMI and baseline eating. Results: A total of 66.2% (n = 1614) of participants change their diet pattern during the study period, 33.8% (n = 823) remain stable. After accounting for potential confounders, an unhealthful trajectory is significantly associated with a 0.42 kg m -2 increase in BMI (confidence interval (CI): 0.1, 0.7). Those with an unhealthful trajectory are 1.79 times more likely to be overweight (relative risk ratio, 95% CI: 1.1, 2.8) and 2.4 times more likely to be obese (relative risk ratio, 95% CI: 1.3, 4.4). Moreover, a number of specific diet transitions between exams are predictive of weight gain or loss. Conclusion: Contextualizing an individual's current eating behaviors with an eye towards diet history may be an important boon in the reduction of obesity. Although it may not be realistic for many people to shift from the least to most healthful diet, results from this study suggest that consistent movement in an overall healthier direction is associated with less weight gain.© 2012 Macmillan Publishers Limited. All rights reserved.


Weston D.P.,University of California at Berkeley | Lydy M.J.,Southern Illinois University Carbondale
Environmental Science and Technology | Year: 2010

While studies have documented the presence of pyrethroid insecticides at acutely toxic concentrations in sediments, little quantitative data on sources exist Urban runoff, municipal wastewater treatment plants and agricultural drains in California's Sacramento-San Joaquin River Delta were sampled to understand their importance as contributors of these pesticides to surface waters. Nearly all residential runoff samples were toxic to the amphipod, Hyalella azteca, and contained pyrethroids at concentrations exceeding acutely toxic thresholds, in many cases by 10-fold. Toxicity identification evaluation data were consistent with pyrethroids, particularly bifenthrin and cyfluthrin, as the cause of toxicity. Pyrethroids passed through secondary treatment systems at municipal wastewater treatment facilities and were commonly found in the final effluent, usually near H. azfeca 96-h EC50 thresholds. Agricultural discharges in the study area only occasionally contained pyrethroids and were also occasional sources of toxicity related to the organophosphate insecticide chlorpyrifos. Discharge of the pyrethroid bifenthrin via urban stormwater runoff was sufficient to cause water column toxicity in two urban creeks, over at least a 30 km reach of the American River, and at one site in the San Joaquin River, though not in the Sacramento River. © 2010 American Chemical Society.


Bachtrog D.,University of California at Berkeley
Nature Reviews Genetics | Year: 2013

The human Y chromosome is intriguing not only because it harbours the master-switch gene that determines gender but also because of its unusual evolutionary history. The Y chromosome evolved from an autosome, and its evolution has been characterized by massive gene decay. Recent whole-genome and transcriptome analyses of Y chromosomes in humans and other primates, in Drosophila species and in plants have shed light on the current gene content of the Y chromosome, its origins and its long-term fate. Furthermore, comparative analysis of young and old Y chromosomes has given further insights into the evolutionary and molecular forces triggering Y-chromosome degeneration and into the evolutionary destiny of the Y chromosome. © 2013 Macmillan Publishers Limited. All rights reserved.


Duderstadt K.E.,Zernike Institute for Advanced Materials | Berger J.M.,University of California at Berkeley
Current Opinion in Structural Biology | Year: 2013

ATP-dependent initiation factors help process replication origins and coordinate replisome assembly to control the onset of DNA synthesis. Although the specific properties and regulatory mechanisms of initiator proteins can vary greatly between different organisms, certain nucleotide-binding elements and assembly patterns appear preserved not only within the three domains of cellular life (bacteria, archaea, and eukaryotes), but also with certain classes of double-stranded DNA viruses. Structural studies of replication initiation proteins, both as higher-order oligomers and in complex with cognate DNA substrates, are revealing how an evolutionarily related ATPase fold can support different modes of macromolecular assembly and function. Comparative studies between initiation systems in turn provide clues as to how duplex origin regions may be melted during initiation events. © 2012 Elsevier Ltd.


Miller E.A.,Columbia University | Schekman R.,University of California at Berkeley
Current Opinion in Cell Biology | Year: 2013

Long known as a coat system that generates small transport vesicles from the endoplasmic reticulum (ER), the COPII coat also drives ER export of cargo proteins that are too large to be contained within these canonical carriers. With crystal and cryo-EM structures giving an atomic level view of coat architecture, current advances in the field have focused on understanding how the coat adapts to the different geometries of the underlying cargo. Combined with a growing appreciation for the specific roles of individual COPII paralogs in diverse aspects of mammalian physiology, the field is poised to understand how coat assembly and post-translational modification permits structural rigidity but geometric flexibility to handle the diverse cargoes that exit the ER. © 2013 Elsevier Ltd.


Manzanillo P.S.,University of California at San Francisco | Shiloh M.U.,University of Texas Southwestern Medical Center | Portnoy D.A.,University of California at Berkeley | Cox J.S.,University of California at San Francisco
Cell Host and Microbe | Year: 2012

Cytosolic bacterial pathogens activate the cytosolic surveillance pathway (CSP) and induce innate immune responses, but how the host detects vacuolar pathogens like Mycobacterium tuberculosis is poorly understood. We show that M. tuberculosis also initiates the CSP upon macrophage infection via limited perforation of the phagosome membrane mediated by the ESX-1 secretion system. Although the bacterium remains within the phagosome, this permeabilization results in phagosomal and cytoplasmic mixing and allows extracellular mycobacterial DNA to access host cytosolic receptors, thus blurring the distinction between "vacuolar" and "cytosolic" pathogens. Activation of cytosolic receptors induces signaling through the Sting/Tbk1/Irf3 axis, resulting in IFN-β production. Surprisingly, Irf3-/- mice, which cannot respond to cytosolic DNA, are resistant to long-term M. tuberculosis infection, suggesting that the CSP promotes M. tuberculosis infection. Thus, cytosolic sensing of mycobacterial DNA plays a key role in M. tuberculosis pathogenesis and likely contributes to the high type I IFN signature in tuberculosis. © 2012 Elsevier Inc.


Williams V.V.,University of California at Berkeley
Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms | Year: 2011

The replacement paths problem for directed graphs is to find for given nodes s and t and every edge e on the shortest path between them, the shortest path between s and t which avoids e. For unweighted directed graphs on n vertices, the best known algorithm runtime was Õ(n2.5) by Roditty and Zwick. For graphs with integer weights in {-M,..., M}, Weimann and Yuster showed that one can use fast matrix multiplication and solve the problem in O(Mn2.584) time, a runtime which would be O(Mn2.33) if the exponent ω of matrix multiplication is 2. We improve on both of these algorithms. Our new algorithm also relies on fast matrix multiplication and runs in Mnω+o(1) time. Our result shows that, at least for small integer weights, the replacement paths problem in directed graphs may be easier than the related all pairs shortest paths problem in directed graphs, as the current best runtime for the latter is Ω (n2.5) time even if ω = 2.


Carlson S.M.,University of California at Berkeley | Cunningham C.J.,University of Washington | Westley P.A.H.,University of Alaska Fairbanks
Trends in Ecology and Evolution | Year: 2014

Evolutionary rescue occurs when adaptive evolutionary change restores positive growth to declining populations and prevents extinction. Here we outline the diagnostic features of evolutionary rescue and distinguish this phenomenon from demographic and genetic rescue. We then synthesize the rapidly accumulating theoretical and experimental studies of evolutionary rescue, highlighting the demographic, genetic, and extrinsic factors that affect the probability of rescue. By doing so, we clarify the factors to target through management and conservation. Additionally, we identify several putative cases of evolutionary rescue in nature, but conclude that compelling evidence remains elusive. We conclude with a horizon scan of where the field might develop, highlighting areas of potential application, and suggest areas where experimental evaluation will help to evaluate theoretical predictions. © 2014 The Authors.


Asmis K.R.,Fritz Haber Institute | Neumark D.M.,University of California at Berkeley | Neumark D.M.,Lawrence Berkeley National Laboratory
Accounts of Chemical Research | Year: 2012

Conjugate-base anions are ubiquitous in aqueous solution. Understanding the hydration of these anions at the molecular level represents a long-standing goal in chemistry. A molecular-level perspective on ion hydration is also important for understanding the surface speciation and reactivity of aerosols, which are a central component of atmospheric and oceanic chemical cycles. In this Account, as a means of studying conjugate-base anions in water, we describe infrared multiple-photon dissociation spectroscopy on clusters in which the sulfate, nitrate, bicarbonate, and suberate anions are hydrated by a known number of water molecules.This spectral technique, used over the range of 550-1800 cm -1, serves as a structural probe of these clusters. The experiments follow how the solvent network around the conjugate-base anion evolves, one water molecule at a time. We make structural assignments by comparing the experimental infrared spectra to those obtained from electronic structure calculations. Our results show how changes in anion structure, symmetry, and charge state have a profound effect on the structure of the solvent network. Conversely, they indicate how hydration can markedly affect the structure of the anion core in a microhydrated cluster.Some key results include the following. The first few water molecules bind to the anion terminal oxo groups in a bridging fashion, forming two anion-water hydrogen bonds. Each oxo group can form up to three hydrogen bonds; one structural result, for example, is the highly symmetric, fully coordinated SO 4 2-(H 2O) 6 cluster, which only contains bridging water molecules. Adding more water molecules results in the formation of a solvent network comprising water-water hydrogen bonding in addition to hydrogen bonding to the anion. For the nitrate, bicarbonate, and suberate anions, fewer bridging sites are available, namely, three, two, and one (per carboxylate group), respectively. As a result, an earlier onset of water-water hydrogen bonding is observed.When there are more than three hydrating water molecules (n > 3), the formation of a particularly stable four-membered water ring is observed for hydrated nitrate and bicarbonate clusters. This ring binds in either a side-on (bicarbonate) or top-on (nitrate) fashion. In the case of bicarbonate, additional water molecules then add to this water ring rather than directly to the anion, indicating a preference for surface hydration. In contrast, doubly charged sulfate dianions are internally hydrated and characterized by the closing of the first hydration shell at n = 12. The situation is different for the -O 2C(CH 2) 6CO 2- (suberate) dianion, which adapts to the hydration network by changing from a linear to a folded structure at n > 15. This change is driven by the formation of additional solute-solvent hydrogen bonds. © 2011 American Chemical Society.


O'Rourke D.,University of California at Berkeley
Science | Year: 2014

Recent advances in the science and technology of global supply chain management offer near-real-time demand-response systems for decision-makers across production networks. Technology is helping propel "fast fashion" and " lean manufacturing," so that companies are better able to deliver products consumers want most. Yet companies know much less about the environmental and social impacts of their production networks. The failure to measure and manage these impacts can be explained in part by limitations in the science of sustainability measurement, as well as by weaknesses in systems to translate data into information that can be used by decision-makers inside corporations and government agencies. There also remain continued disincentives for firms to measure and pay the full costs of their supply chain impacts. I discuss the current state of monitoring, measuring, and analyzing information related to supply chain sustainability, as well as progress that has been made in translating this information into systems to advance more sustainable practices by corporations and consumers. Better data, decision-support tools, and incentives will be needed to move from simply managing supply chains for costs, compliance, and risk reduction to predicting and preventing unsustainable practices.


Zhou Q.,University of California at Berkeley | Li T.,University of Iowa | Price D.H.,University of Iowa
Annual Review of Biochemistry | Year: 2012

Regulation of the elongation phase of transcription by RNA polymerase II (Pol II) is utilized extensively to generate the pattern of mRNAs needed to specify cell types and to respond to environmental changes. After Pol II initiates, negative elongation factors cause it to pause in a promoter proximal position. These polymerases are poised to respond to the positive transcription elongation factor P-TEFb, and then enter productive elongation only under the appropriate set of signals to generate full-length properly processed mRNAs. Recent global analyses of Pol II and elongation factors, mechanisms that regulate P-TEFb involving the 7SK small nuclear ribonucleoprotein (snRNP), factors that control both the negative and positive elongation properties of Pol II, and the mRNA processing events that are coupled with elongation are discussed. © 2012 by Annual Reviews. All rights reserved.


Robinson J.C.,University of California at Berkeley
Health Affairs | Year: 2010

Comparative effectiveness research has been promoted as a way to control health care costs, but there has been less discussion of the mechanisms through which new evidence actually will influence physician practice, patient preference, and manufacturer investment. Public and private insurers use conditional coverage, consumer cost sharing, provider contracting, and drug payment policies to manage and direct the flow of resources into the health care system. This paper examines how each of these approaches may be adapted to incorporate new evidence from comparative effectiveness research. © 2010 Project HOPE-The People-to-People Health Foundation, Inc.


Levine M.,University of California at Berkeley
Current Biology | Year: 2010

Regulatory DNAs serve as templates to bring weakly interacting transcription factors into close proximity so they can work synergistically to switch genes on and off in time and space. Most of these regulatory DNAs are enhancers that can work over long distances - a million base pairs or more in mammals - to control gene expression. Critical enhancers are sometimes even found within the introns of neighboring genes. This review summarizes well-defined examples of enhancers controlling key processes in animal development. Potential mechanisms of transcriptional synergy are discussed with regard to enhancer structure and contemporary ChIP-sequencing assays, whereby just a small fraction of the observed binding sites represent bona fide regulatory DNAs. Finally, there is a discussion of how enhancer evolution can produce novelty in animal morphology and of the prospects for reconstructing transitions in animal evolution by introducing derived enhancers in basal ancestors. © 2010 Elsevier Ltd. All rights reserved.


Zrazhevskiy P.,University of Washington | Sena M.,University of California at Berkeley | Gao X.,University of Washington
Chemical Society Reviews | Year: 2010

The emerging field of bionanotechnology aims at revolutionizing biomedical research and clinical practice via introduction of nanoparticle-based tools, expanding capabilities of existing investigative, diagnostic, and therapeutic techniques as well as creating novel instruments and approaches for addressing challenges faced by medicine. Quantum dots (QDs), semiconductor nanoparticles with unique photo-physical properties, have become one of the dominant classes of imaging probes as well as universal platforms for engineering of multifunctional nanodevices. Possessing versatile surface chemistry and superior optical features, QDs have found initial use in a variety of in vitro and in vivo applications. However, careful engineering of QD probes guided by application-specific design criteria is becoming increasingly important for successful transition of this technology from proof-of-concept studies towards real-life clinical applications. This review outlines the major design principles and criteria, from general ones to application-specific, governing the engineering of novel QD probes satisfying the increasing demands and requirements of nanomedicine and discusses the future directions of QD-focused bionanotechnology research (critical review, 201 references). © 2010 The Royal Society of Chemistry.


Lidicker Jr. W.Z.,University of California at Berkeley
Open Ecology Journal | Year: 2010

The role of mutually beneficial interactions (++, cooperation) is a rapidly growing research field in population dynamics, microevolution, and conservation biology. Such positive influences cause destabilizing pressures in population dynamics (anti-regulating factors), and can generate Allee effects. Not only can large demes benefit from such cooperation, but the loss of cooperation in small demes can produce a minimum threshold density. Interest in these phenomena grew rapidly to the middle of the 20th century, followed by about four decades in which interest waned. In the last 20 years attention to Allee effects has burgeoned once again. This renewal has produced new perspectives, including a more realistic framework for the way populations and communities are organized. A core concept for Allee effects emerges from the historical record and current views on population dynamics: Allee effects are demographic consequences of the collective actions of anti-regulating influences. Recent developments, including proposals for much new terminology, are reviewed and found to be helpful in building mechanistic understanding of the core concept. Support for the growing relevance of Allee effects to conservation biology as well as population and community dynamics is emphasized. Some new avenues for future research directions include improving our abilities to predict life history and environmental features that favor strong anti-regulation and hence Allee effects, the role of mutually positive interspecific relations in community function, and possible role of anti-regulation in restoration ecology. © William Z. Lidicker, Jr.


Joshi D.,Mahatma Gandhi Institute | Buehring G.C.,University of California at Berkeley
Breast Cancer Research and Treatment | Year: 2012

The three viruses most studied as possible causes of human breast cancer are mouse mammary tumor virus-like sequences (MMTV-LS), Epstein-Barr virus (EBV), and oncogenic (high risk) types of human papilloma virus (HPV). The first step in fulfilling traditional criteria for inferring that a cancer is caused by a virus is to demonstrate the virus in the affected tissue. Molecular techniques, compared to host antibody assessment and immunohistochemistry, are the most definitive in establishing viral presence. Results of 85 original molecular research investigations to detect one or more of the three viruses have been extremely divergent with no consensus reached. We evaluated the methodology of these studies for the following: type of molecular assay, DNA/RNA quality control, positive and negative assay controls, type of fixation, genome targets, methods for preventing and detecting molecular contamination, pathology of specimens processed, sample size, and proportion of specimens positive for the viral genome region targeted. Only seven of the studies convincingly demonstrated the presence of an oncogenic virus biomarker (EBV: 4/30 studies (13%); HPV 3/29 studies (10%), whereas 25 convincingly demonstrated absence of the virus studied (MMTV-LS: 4/25 (16%); EBV: 15/30 (50%); 6/29 (21%). The remainder of the studies suffered shortcomings, which, in our opinion, prevented a definitive conclusion. Only one of the studies compared frequency of the virus in breast tissue of breast cancer patients versus appropriate normal control subjects with no history of breast cancer. None of the studies were designed as epidemiologic studies to determine if the presence of the virus was significantly associated with breast cancer. Based on our evaluation, the data in the publications reviewed here remain preliminary, and do not justify a conclusion that MMTV-LS, HPV, or EBV are causally associated with breast cancer. However, they form a valuable basis for redirecting future studies. © 2012 Springer Science+Business Media, LLC.


Fox N.K.,Lawrence Berkeley National Laboratory | Brenner S.E.,Lawrence Berkeley National Laboratory | Brenner S.E.,University of California at Berkeley | Chandonia J.-M.,Lawrence Berkeley National Laboratory
Nucleic Acids Research | Year: 2014

Structural Classification of Proteins - extended (SCOPe, http://scop.berkeley.edu) is a database of protein structural relationships that extends the SCOP database. SCOP is a manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. Development of the SCOP 1.x series concluded with SCOP 1.75. The ASTRAL compendium provides several databases and tools to aid in the analysis of the protein structures classified in SCOP, particularly through the use of their sequences. SCOPe extends version 1.75 of the SCOP database, using automated curation methods to classify many structures released since SCOP 1.75. We have rigorously benchmarked our automated methods to ensure that they are as accurate as manual curation, though there are many proteins to which our methods cannot be applied. SCOPe is also partially manually curated to correct some errors in SCOP. SCOPe aims to be backward compatible with SCOP, providing the same parseable files and a history of changes between all stable SCOP and SCOPe releases. SCOPe also incorporates and updates the ASTRAL database. The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank (PDB) entries, increasing the number of structures classified in SCOP by 55% and including more than 65% of the protein structures in the PDB. © 2013 The Author(s). Published by Oxford University Press.


Kremen C.,University of California at Berkeley
Annals of the New York Academy of Sciences | Year: 2015

Conservation biologists are devoting an increasing amount of energy to debating whether land sparing (high-yielding agriculture on a small land footprint) or land sharing (low-yielding, wildlife-friendly agriculture on a larger land footprint) will promote better outcomes for local and global biodiversity. In turn, concerns are mounting about how to feed the world, given increasing demands for food. In this review, I evaluate the land-sparing/land-sharing framework-does the framework stimulate research and policy that can reconcile agricultural land use with biodiversity conservation, or is a revised framing needed? I review (1) the ecological evidence in favor of sparing versus sharing; (2) the evidence from land-use change studies that assesses whether a relationship exists between agricultural intensification and land sparing; and (3) how that relationship may be affected by socioeconomic and political factors. To address the trade-off between biodiversity conservation and food production, I then ask which forms of agricultural intensification can best feed the world now and in the future. On the basis of my review, I suggest that the dichotomy of the land-sparing/land-sharing framework limits the realm of future possibilities to two, largely undesirable, options for conservation. Both large, protected regions and favorable surrounding matrices are needed to promote biodiversity conservation; they work synergistically and are not mutually exclusive. A "both-and" framing of large protected areas surrounded by a wildlife-friendly matrix suggests different research priorities from the "either-or" framing of sparing versus sharing. Furthermore, wildlife-friendly farming methods such as agroecology may be best adapted to provide food for the world's hungry people. © 2015 New York Academy of Sciences.


Chua L.,University of California at Berkeley
Applied Physics A: Materials Science and Processing | Year: 2011

All 2-terminal non-volatile memory devices based on resistance switching are memristors, regardless of the device material and physical operating mechanisms. They all exhibit a distinctive "fingerprint" characterized by a pinched hysteresis loop confined to the first and the third quadrants of the v-i plane whose contour shape in general changes with both the amplitude and frequency of any periodic "sinewave- like" input voltage source, or current source. In particular, the pinched hysteresis loop shrinks and tends to a straight line as frequency increases. Though numerous examples of voltage vs. current pinched hysteresis loops have been published in many unrelated fields, such as biology, chemistry, physics, etc., and observed from many unrelated phenomena, such as gas discharge arcs, mercury lamps, power conversion devices, earthquake conductance variations, etc., we restrict our examples in this tutorial to solidstate and/or nano devices where copious examples of published pinched hysteresis loops abound. In particular, we sampled arbitrarily, one example from each year between the years 2000 and 2010, to demonstrate that the memristor is a device that does not depend on any particular material, or physical mechanism. For example, we have shown that spin-transfer magnetic tunnel junctions are examples of memristors. We have also demonstrated that both bipolar and unipolar resistance switching devices are memristors. The goal of this tutorial is to introduce some fundamental circuit-theoretic concepts and properties of the memristor that are relevant to the analysis and design of non-volatile nano memories where binary bits are stored as resistances manifested by the memristor's continuum of equilibrium states. Simple pedagogical examples will be used to illustrate, clarify, and demystify various misconceptions among the uninitiated. © The Author(s) 2011.


Behin-Aein B.,Purdue University | Datta D.,Purdue University | Salahuddin S.,University of California at Berkeley | Datta S.,Purdue University
Nature Nanotechnology | Year: 2010

The possible use of spin rather than charge as a state variable in devices for processing and storing information has been widely discussed, because it could allow low-power operation and might also have applications in quantum computing. However, spin-based experiments and proposals for logic applications typically use spin only as an internal variable, the terminal quantities for each individual logic gate still being charge-based. This requires repeated spin-to-charge conversion, using extra hardware that offsets any possible advantage. Here we propose a spintronic device that uses spin at every stage of its operation. Input and output information are represented by the magnetization of nanomagnets that communicate through spin-coherent channels. Based on simulations with an experimentally benchmarked model, we argue that the device is both feasible and shows the five essential characteristics for logic applications: concatenability, nonlinearity, feedback elimination, gain and a complete set of Boolean operations. © 2010 Macmillan Publishers Limited.


Hollick J.B.,University of California at Berkeley
Annual Review of Cell and Developmental Biology | Year: 2010

Paramutation describes a heritable change of gene expression that is brought about through interactions between homologous chromosomes. Genetic analyses in plants and, more recently, in mouse indicate that genomic sequences related to transcriptional control and molecules related to smallRNAbiology are necessary for specific examples of paramutation. Some of the molecules identified in maize are also required for normal plant development. These observations indicate a functional relationship between the nuclear mechanisms responsible for paramutation and modes of developmental gene control. Copyright © 2010 by Annual Reviews. All rights reserved.


Ritchie R.O.,University of California at Berkeley | Ritchie R.O.,Lawrence Berkeley National Laboratory
Nature Materials | Year: 2014

Li and Ortiz report on the penetration resistance and spatial localization of damage as a consequence of effective energy-dissipation mechanisms in the shell of the bivalve marine mollusc Placuna placenta, also called window pane oyster. In P. placenta, armor resistance is achieved in a similar fashion through the creation of a tiled assembly of 300-nm-thick elongated diamond-shaped crystals of calcite, aligned nominally parallel to the surface of the shell and again separated by organic nanolayers. Li and Ortiz, however, reveal a fascinating new twist in damage localization and energy absorption of natural armors, deformation by nanoscale twinning. They show that for P. placenta, 50-nm-thick nanotwins form around the penetration zone; these twin bands effectively accommodate the excess deformation and judiciously confine it to a small volume before the twins arrest at the organic interfaces between the calcite crystals. Through these intriguing nanoscale processes, the P. placenta shell can effectively resist predatory attack by obeying the two principles of armor material.


Levien M.,University of California at Berkeley
Journal of Agrarian Change | Year: 2011

This paper seeks to reconstruct David Harvey's theory of accumulation by dispossession (ABD) through an ethnography of a Special Economic Zone in Rajasthan, India. While Harvey sees ABD as an economic process of over-accumulated capital finding new outlets, I argue that it is an extra-economic process of coercive expropriation typically exercised by states to help capitalist overcome barriers to accumulation - in this case, the absence of fully capitalist rural land markets. In India's privately developed SEZs, the accumulation generated by this dispossession - which represents the disaccumulation of the peasantry - occurs through capitalist rentiers who develop rural land for mainly IT companies and luxury real estate, and profit from the appreciation of artificially cheap land acquired by the state. While such development has only minimally and precariously absorbed the labour of dispossessed farmers, it has generated a peculiar agrarian transformation through land speculation that has enlisted fractions of the rural elite into a chain of rentiership, drastically amplified existing class and caste inequalities, undermined food security and, surprisingly, fuelled non-productive economic activity and pre-capitalist forms of exploitation. © 2011 Blackwell Publishing Ltd.


Zadeh L.A.,University of California at Berkeley
Information Sciences | Year: 2014

Probability theory is a rigorous theory which rests on a firm foundation. The brilliant successes of probability theory are visible to all. What is problematical relates to the basic question: What is probability? There are many answers but no unanimity. What is suggested in this note are definitions of possibility and probability which are based on fuzzy logic. More concretely, the definitions are based on the concept of similarity. Similarity-based definition of probability reduces to the traditional frequency-based definition of probability when similarity is exact. © 2014 Elsevier Inc. All rights reserved.


Kamal A.,Yale University | Clarke J.,University of California at Berkeley | Devoret M.H.,Yale University
Nature Physics | Year: 2011

Non-reciprocal devices such as circulators and isolators belong to an important class of microwave components employed in applications including the measurement of mesoscopic circuits at cryogenic temperatures1-5. The measurement protocols usually involve an amplification chain that relies on circulators to separate input and output channels and to suppress backaction from different stages on the sample under test. In these devices the usual reciprocal symmetry of circuits is broken by the phenomenon of Faraday rotation based on magnetic materials and fields6. However, magnets are averse to on-chip integration, and magnetic fields are deleterious to delicate superconducting devices7,8. Here we present a new proposal that combines two stages of parametric modulation to emulate the action of a circulator. It is devoid of magnetic components and suitable for on-chip integration. As the design is free of any dissipative elements and based on reversible operation, the device operates noiselessly, giving it an important advantage over other non-reciprocal active devices for quantum information processing applications. © 2011 Macmillan Publishers Limited. All rights reserved.


Hansen K.D.,University of California at Berkeley
Nucleic acids research | Year: 2010

Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias is independent of organism and laboratory and impacts the uniformity of the reads along the transcriptome. We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias.


Maslowsky J.,University of Wisconsin - Madison | Ozer E.J.,University of California at Berkeley
Journal of Adolescent Health | Year: 2014

Purpose To present normative values of mean sleep duration from adolescence through young adulthood (ages 13-32 years), prevalence of short (<6 hours) and long (>10 hours) sleep durations, and differences in each by sex and race/ethnicity. Methods Mean sleep duration and prevalence of extremely short and long sleep were estimated using data from the United States National Longitudinal Study of Adolescent Health, Waves 1-4 (N = 15,701). Results Sleep duration showed age-related trends, with decreases across the adolescent period from 8.5 hours per night at age 13 years to 7.3 hours at age 18 years, an increase through the emerging adulthood period to 8.5 hours at age 22, and a gradual decline across early adulthood to 7.7 hours at age 32 years. Prevalence of extremely long and short sleep followed similar developmental trends. Adolescent girls reported lower mean sleep duration than did boys, but women reported longer average sleep duration than did men from age 19 years onward. Short sleep duration was most common among African-Americans at all ages. Long sleep was most common among African-Americans in adolescence and emerging adulthood and among Hispanics in early adulthood. Conclusions Sleep duration is developmentally patterned from adolescence through early adulthood. Mean and extreme sleep durations vary systematically by sex and race/ethnicity as well as age. These normative data on sleep duration will inform studies of the role of sleep in the etiology of a wide range of health conditions affecting adolescents and young adults. © 2014 Society for Adolescent Health and Medicine. All rights reserved.


O'Brien L.E.,Stanford University | Bilder D.,University of California at Berkeley
Annual Review of Cell and Developmental Biology | Year: 2013

Adult animals rely on populations of stem cells to ensure organ function throughout their lifetime. Stem cells are governed by signals from stem cell niches, and much is known about how single niches promote stemness and direct stem cell behavior. However, most organs contain a multitude of stem cell-niche units, which are often distributed across the entire expanse of the tissue. Beyond the biology of individual stem cell-niche interactions, the next challenge is to uncover the tissue-level processes that orchestrate spatial control of stem-based renewal, repair, and remodeling throughout a whole organ. Here we examine what is known about higher order mechanisms for interniche coordination in epithelial organs, whose simple geometry offers a promising entry point for understanding the regulation of niche number, distribution, and activity. We also consider the potential existence of stem cell territories and how tissue architecture may influence niche coordination. © 2013 by Annual Reviews. All rights reserved.


Miller W.H.,University of California at Berkeley
Journal of Chemical Physics | Year: 2012

Some coherence effects in chemical dynamics are described correctly by classical mechanics, while others only appear in a quantum treatment-and when these are observed experimentally it is not always immediately obvious whether their origin is classical or quantum. Semiclassical theory provides a systematic way of adding quantum coherence to classical molecular dynamics and thus provides a useful way to distinguish between classical and quantum coherence. Several examples are discussed which illustrate both cases. Particularly interesting is the situation with electronically non-adiabatic processes, where sometimes whether the coherence effects are classical or quantum depends on what specific aspects of the process are observed. © 2012 American Institute of Physics.


Taylor R.L.,University of California at Berkeley
International Journal for Numerical Methods in Engineering | Year: 2011

This paper describes the use of isogeometric methods to solve problems in finite deformation solid mechanics in which compressible and nearly incompressible behavior may be encountered. The work is based on a three-field variational structures in which displacements, mean stress and volume effects are independently approximated. Using this approach and tensor product NURBS approximations it is shown how the solution can be conducted in a standard approach, where main variables are organized at nodes (control points). This leads to an efficient procedure to solve large problems of a general form without the need to develop special solution strategies. The approach is demonstrated on some standard test problems. © 2010 John Wiley & Sons, Ltd.


Deacon T.W.,University of California at Berkeley
Proceedings of the National Academy of Sciences of the United States of America | Year: 2010

Explaining the extravagant complexity of the human language and our competence to acquire it has long posed challenges for natural selection theory. To answer his critics, Darwin turned to sexual selection to account for the extreme development of language. Many contemporary evolutionary theorists have invoked incredibly lucky mutation or some variant of the assimilation of acquired behaviors to innate predispositions in an effort to explain it. Recent evodevo approaches have identified developmental processes that help to explain how complex functional synergies can evolve by Darwinian means. Interestingly, many of these developmental mechanisms bear a resemblance to aspects of Darwin's mechanism of natural selection, often differing only in one respect (e.g., form of duplication, kind of variation, competition/cooperation). A common feature is an interplay between processes of stabilizing selection and processes of relaxed selection at different levels of organism function. These may play important roles in the many levels of evolutionary process contributing to language. Surprisingly, the relaxation of selection at the organism level may have been a source of many complex synergistic features of the human language capacity, and may help explain why so much language information is "inherited" socially.


Graves D.B.,University of California at Berkeley
Journal of Physics D: Applied Physics | Year: 2012

Reactive oxygen species (ROS) and the closely related reactive nitrogen species (RNS) are often generated in applications of atmospheric pressure plasmas intended for biomedical purposes. These species are also central players in what is sometimes referred to as redox or oxidationreduction biology. Oxidationreduction biochemistry is fundamental to all of aerobic biology. ROS and RNS are perhaps best known as disease-associated agents, implicated in diabetes, cancer, heart and lung disease, autoimmune disease and a host of other maladies including ageing and various infectious diseases. These species are also known to play active roles in the immune systems of both animals and plants and are key signalling molecules, among many other important roles. Indeed, the latest research has shown that ROS/RNS play a much more complex and nuanced role in health and ageing than previously thought. Some of the most potentially profound therapeutic roles played by ROS and RNS in various medical interventions have emerged only in the last several years. Recent research suggests that ROS/RNS are significant and perhaps even central actors in the actions of antimicrobial and anti-parasite drugs, cancer therapies, wound healing therapies and therapies involving the cardiovascular system. Understanding the ways ROS/RNS act in established therapies may help guide future efforts in exploiting novel plasma medical therapies. The importance of ROS and RNS to plant biology has been relatively little appreciated in the plasma biomedicine community, but these species are just as important in plants. It appears that there are opportunities for useful applications of plasmas in this area as well. © 2012 IOP Publishing Ltd.


Fisher A.J.,University of California at Berkeley
Journal of Consulting and Clinical Psychology | Year: 2015

Objective: The present article proposes a general framework and a set of specific methodological steps for conducting person-specific dynamic assessments, which yield information about syndrome structures and states that can be used to provide actionable information for the formulation of personalized interventions. It is proposed that researchers should (a) determine the relevant constituent inputs for a diagnostic system; (b) measure these inputs with as much detail as possible; (c) assess the correlational structure of system inputs via factor-analytic methods within individuals; and (d) subject the individual-level, latent dimension time series to dynamic analyses such as the dynamic factor model (Molenaar, 1985) to discern the time-dependent, dynamic relationships within and between system components. Method: An exemplar is provided wherein 10 individuals with clinically diagnosed generalized anxiety disorder completed surveys related to generalized anxiety disorder symptomatology for at least 60 consecutive days. These data were then subjected to person-specific exploratory and confirmatory factor analyses for the identification of latent symptom dimensions. Finally, dynamic factor models were used to model the dynamic interrelationships within and between symptom domains on a person-by-person basis. Results: Person-specific factor analyses returned models with 3 (n = 8) or 4 (n = 2) latent factors, all with excellent fit. Dynamic factor modeling successfully revealed the contemporaneous correlations and time-lagged predictive relationships between factors, providing prescriptive information for the formulation of targeted interventions. Conclusions: The proposed approach has the potential to inform the construction and implementation of personalized treatments by delineating the idiosyncratic structure of psychopathology on a person-by-person basis. © 2015 American Psychological Association.


Huang Y.,University of California at Berkeley
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2012

Uncertainty relations are fundamental in quantum mechanics. Here I propose state-independent variance-based uncertainty relations for two or more arbitrary observables in finite dimensional spaces. The uncertainty relations provide near-optimal lower bounds in some typical examples, and are useful for entanglement detection. © 2012 American Physical Society.


Martinson M.,San Francisco State University | Berridge C.,University of California at Berkeley
Gerontologist | Year: 2015

Purpose of the Study: The purpose of this study was to analyze the range of critiques of successful aging models and the suggestions for improvement as expressed in the social gerontology literature. Design and Methods: We conducted a systematic literature review using the following criteria: journal articles retrieved in the Abstracts in Social Gerontology, published 1987-2013, successful aging/ageing in the title or text (n = 453), a critique of successful aging models as a key component of the article. Sixty-seven articles met the criteria. Qualitative methods were used to identify key themes and inductively configure meanings across the range of critiques. Results: The critiques and remedies fell into 4 categories. The Add and Stir group suggested a multidimensional expansion of successful aging criteria and offered an array of additions. The Missing Voices group advocated for adding older adults' subjective meanings of successful aging to established objective measures. The Hard Hitting Critiques group called for more just and inclusive frameworks that embrace diversity, avoid stigma and discrimination, and intervene at structural contexts of aging. The New Frames and Names group presented alternative ideal models often grounded in Eastern philosophies. Implications: The vast array of criteria that gerontologists collectively offered to expand Rowe and Kahn's original successful model is symptomatic of the problem that a normative model is by definition exclusionary. Greater reflexivity about gerontology's use of "successful aging" and other normative models is needed. © 2014 The Author.


The implementation of membrane-based separations in the petrochemical industry has the potential to reduce energy consumption significantly relative to conventional separation processes. Achieving this goal, however, requires the development of new membrane materials with greater selectivity, permeability and stability than available at present. Here, we report composite materials consisting of nanocrystals of metal–organic frameworks dispersed within a high-performance polyimide, which can exhibit enhanced selectivity for ethylene over ethane, greater ethylene permeability and improved membrane stability. Our results suggest that framework–polymer interactions reduce chain mobility of the polymer while simultaneously boosting membrane separation performance. The increased stability, or plasticization resistance, is expected to improve membrane utility under real process conditions for petrochemical separations and natural gas purification. Furthermore, this approach can be broadly applied to numerous polymers that encounter aggressive environments, potentially making gas separations possible that were previously inaccessible to membranes. © 2016 Nature Publishing Group


Melis A.,University of California at Berkeley
Energy and Environmental Science | Year: 2012

The concept of "Photosynthetic Biofuels" entails the direct application of photosynthesis for the generation of fuels and chemicals, in a process where a single organism acts both as catalyst and processor, synthesizing and secreting ready to use product. Examples of photosynthetic fuel and chemicals generation are offered in this perspective.1 Physiological and genetic manipulation of green microalgae enabled diverting the natural flow of photosynthetic electron transport toward sustained generation of hydrogen gas, instead of the normally produced oxygen.2 Heterologous expression of a plant isoprene synthase gene in cyanobacteria and microalgae enabled the renewable generation of volatile isoprene (C 5H 8) hydrocarbons, derived from sunlight, carbon dioxide (CO 2) and water (H 2O). Photobioreactor design concepts and conditions for capturing the isoprene are presented. The process of generating isoprene (C 5H 8) hydrocarbons serves as a case study in the development of technologies for the renewable generation of a multitude of other fuels and useful chemicals.3 Green microalgae of the genus Botryococcus afford naturally occurring examples on how to divert the flow of photosynthetic metabolites toward high-value long-chain hydrocarbon products instead of the normally produced sugars. Members of the genus Botryococcus direct photosynthate toward tri-terpenoid botryococcene hydrocarbons or diene and triene alkanes, at the expense of investing photosynthate toward biomass accumulation.4 Lastly, methods are offered on how to improve the solar-to-biomass energy conversion efficiency of photosynthesis in high cell-density cultures, or canopies, under bright sunlight conditions. Goal of this effort is to improve efficiency, from the current-best of 2-3% up to a theoretical maximum of about 10%. Advances in each of the above-mentioned fields suggest blueprints of organism genetic and metabolic engineering, by which to improve the performance of photosynthesis and to divert cellular metabolic flux toward alternative high-value bio-products. Successful implementation of this R&D would lead to the generation of commercially viable fuels, chemicals, and other useful bio-products. © The Royal Society of Chemistry 2012.


Pearson P.D.,University of California at Berkeley | Moje E.,University of Michigan | Greenleaf C.,WestEd
Science | Year: 2010

We use conceptual and empirical lenses to examine synergies between inquiry science and literacy teaching and learning of K-12 (kindergarten through high school) curriculum. We address two questions: (i) how can reading and writing be used as tools to support inquiry-based science, and (ii) how do reading and writing benefit when embedded in an inquiry-based science setting? After elaborating the theoretical and empirical support for integrated approaches, we discuss how to support their implementation in today's complicated curricular landscape.


Kim S.Y.,University of California at Berkeley
Epilepsia | Year: 2012

The protection of the brain from blood-borne toxins, proteins, and cells is critical to the brain's normal function. Accordingly, a compromise in the blood-brain barrier (BBB) function accompanies many neurologic disorders, and is tightly associated with brain inflammatory processes initiated by both infiltrating leukocytes from the blood, and activation of glial cells. Those inflammatory processes contribute to determining the severity and prognosis of numerous neurologic disorders, and can both cause, and result from BBB dysfunction. In this review we examine the role of BBB and inflammatory responses, in particular activation of transforming grown factor β (TGFβ) signaling, in epilepsy, stroke, and Parkinson's disease. Wiley Periodicals, Inc. © 2012 International League Against Epilepsy.


Huang Z.,University of Illinois at Urbana - Champaign | Hartwig J.F.,University of Illinois at Urbana - Champaign | Hartwig J.F.,University of California at Berkeley
Angewandte Chemie - International Edition | Year: 2012

Copper is all bound up: The copper-catalyzed α-arylation of carbonyl compounds occurs through oxidative addition of iodoarenes to the C-bound Cu I enolate species 1 to form an aryl-CuIII intermediate (see scheme). Computational results provide insight into the origins of the relative reactivity of various CuI enolate complexes in the reactions with iodoarenes. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Shi Z.,University of California at Berkeley
Nature Materials | Year: 2016

Layer-stacking domain walls in bilayer graphene are emerging as a fascinating one-dimensional system that features stacking solitons structurally and quantum valley Hall boundary states electronically. The interactions between electrons in the 2D graphene domains and the one-dimensional domain-wall solitons can lead to further new quantum phenomena. Domain-wall solitons of varied local structures exist along different crystallographic orientations, which can exhibit distinct electrical, mechanical and optical properties. Here we report soliton-dependent 2D graphene plasmon reflection at different 1D domain-wall solitons in bilayer graphene using near-field infrared nanoscopy. We observe various domain-wall structures in mechanically exfoliated graphene bilayers, including network-forming triangular lattices, individual straight or bent lines, and even closed circles. The near-field infrared contrast of domain-wall solitons arises from plasmon reflection at domain walls, and exhibits markedly different behaviours at the tensile- and shear-type domain-wall solitons. In addition, the plasmon reflection at domain walls exhibits a peculiar dependence on electrostatic gating. Our study demonstrates the unusual and tunable coupling between 2D graphene plasmons and domain-wall solitons. © 2016 Nature Publishing Group


Damodaran A.R.,University of California at Berkeley
Nature Materials | Year: 2016

Domains and domain walls are critical in determining the response of ferroelectrics, and the ability to controllably create, annihilate, or move domains is essential to enable a range of next-generation devices. Whereas electric-field control has been demonstrated for ferroelectric 180° domain walls, similar control of ferroelastic domains has not been achieved. Here, using controlled composition and strain gradients, we demonstrate deterministic control of ferroelastic domains that are rendered highly mobile in a controlled and reversible manner. Through a combination of thin-film growth, transmission-electron-microscopy-based nanobeam diffraction and nanoscale band-excitation switching spectroscopy, we show that strain gradients in compositionally graded PbZr1−xTixO3 heterostructures stabilize needle-like ferroelastic domains that terminate inside the film. These needle-like domains are highly labile in the out-of-plane direction under applied electric fields, producing a locally enhanced piezoresponse. This work demonstrates the efficacy of novel modes of epitaxy in providing new modalities of domain engineering and potential for as-yet-unrealized nanoscale functional devices. © 2016 Nature Publishing Group


Duffell P.C.,University of California at Berkeley
Astrophysical Journal | Year: 2015

Planets in their formative years can migrate due to the influence of gravitational torques in the protoplanetary disk they inhabit. For low-mass planets in an isothermal disk, it is known that there is a strong negative torque on the planet due to its linear perturbation to the disk, causing fast inward migration. The current investigation demonstrates that in these same isothermal disks, for intermediate-mass planets, there is a strong positive nonlinear corotation torque due to the effects of gas being pulled through a gap on horseshoe orbits. For intermediate-mass planets, this positive torque can partially or completely cancel the linear (Type I) torque, leading to slower or outward migration, even in an isothermal disk. The effect is most significant for super-Earth and sub-Jovian planets, during the transition from a low-mass linear perturber to a nonlinear gap-opening planet, when the planet has opened a so-called "partial gap", though the precise values of these transition masses depend sensitively on the disk model (density profile, viscosity, and disk aspect ratio). In this study, numerical calculations of planet-disk interactions calculate these torques explicitly, and scalings are empirically constructed for migration rates in this weakly nonlinear regime. These results find outward migration is possible for planets with masses in the range 20-100 M, though this range depends on the disk model considered. In the disk models where torque reversal occurs, the critical planet-to-star mass ratio for torque reversal was found to have the robust scaling qcrit ∝ √α (h/r)3, where α is the dimensionless viscosity parameter and h/r is the disk aspect ratio. © 2015. The American Astronomical Society. All rights reserved.


Beatty K.E.,University of California at Berkeley
Molecular BioSystems | Year: 2011

Proteomic visualization serves as a complement to proteomic identification. In recent years, chemical biologists have made rapid progress developing new methods to tag and image defined sets of proteins. These researchers have requisitioned cellular machinery to place small, reactive analogues into biomolecules. The analogue has been labeled subsequently using a selective ligation reaction. Many groups have demonstrated the efficacy of the copper-catalyzed or strain-promoted azide-alkyne ligation; both enable rapid and precise labeling in complex biological mixtures. This review provides an overview of the methods which have been optimized to tag and fluorophore-label biomolecules for imaging subsets of the proteome in bacterial and mammalian cells. With the approaches described herein, it should be possible to image cells as they undergo changes over time. © The Royal Society of Chemistry 2011.


Murray G.,Swinburne University of Technology | Harvey A.,University of California at Berkeley
Bipolar Disorders | Year: 2010

Objective: Biological rhythm pathways are highlighted in a number of etiological models of bipolar disorder, and the management of circadian instability appears in consensus treatment guidelines. There are, however, significant conceptual and empirical limitations on our understanding of a hypothesised link between circadian, sleep, and emotion regulation processes in bipolar disorder. The aim of this article is to articulate the limits of scientific knowledge in relation to this hypothesis. Methods: A critical evaluation of various literatures was undertaken. The basic science of circadian and sleep processes, their involvement in normal emotion regulation, and the types of evidence suggesting circadian/sleep involvement in bipolar disorder are reviewed. Results: Multiple lines of evidence suggest that circadian and sleep-wake processes are causally involved in bipolar disorder. These processes demonstrably interact with other neurobiological pathways known to be important in bipolar disorder, but are unique in that they are open to behavioural manipulation. Conclusion: Further research into biological rhythm pathways to bipolar disorder is warranted. Person-environment feedback loops are fundamental to circadian adaptation, and models of circadian pathogenesis (and treatment) should recognize this complexity. © 2010 The Authors. Journal compilation © 2010 John Wiley & Sons A/S.


Smith M.T.,University of California at Berkeley
Annual Review of Public Health | Year: 2010

Benzene is a ubiquitous chemical in our environment that causes acute leukemia and probably other hematological cancers. Evidence for an association with childhood leukemia is growing. Exposure to benzene can lead to multiple alterations that contribute to the leukemogenic process, indicating a multimodal mechanism of action. Research is needed to elucidate the different roles of multiple metabolites in benzene toxicity and the pathways that lead to their formation. Studies to date have identified a number of polymorphisms in candidate genes that confer susceptibility to benzene hematotoxicity. However, a genome-wide study is needed to truly assess the role of genetic variation in susceptibility. Benzene affects the blood-forming system at low levels of occupational exposure, and there is no evidence of a threshold. There is probably no safe level of exposure to benzene, and all exposures constitute some risk in a linear, if not supralinear, and additive fashion. Copyright © 2010 by Annual Reviews. All rights reserved.


Maharbiz M.M.,University of California at Berkeley
Trends in Cell Biology | Year: 2012

The ability to synthesize biological constructs on the scale of the organisms we observe unaided is probably one of the more outlandish, yet recurring, dreams humans have had since they began to modify genes. This review brings together recent developments in synthetic biology, cell and developmental biology, computation, and technological development to provide context and direction for the engineering of rudimentary, autonomous multicellular ensembles. © 2012 Elsevier Ltd.


Zaletel M.P.,University of California at Berkeley
Physical Review B - Condensed Matter and Materials Physics | Year: 2014

Symmetry-protected topological states cannot be deformed to a trivial state so long as the symmetry is preserved, yet there is no local order parameter that can distinguish them from a trivial state. We demonstrate how to detect whether a two-dimensional ground state has symmetry-protected topological order; the measurements play a similar role as the topological entanglement entropy does for detecting anyons. For any finite Abelian onsite symmetry, the measurement completely determines the third cohomology class that characterizes the order. The proposed measurement is validated numerically using the infinite density matrix renormalization group for a model with Z2 symmetry-protected order. © 2014 American Physical Society.


Rappaport S.M.,University of California at Berkeley
Journal of Exposure Science and Environmental Epidemiology | Year: 2011

During the 1920s, the forerunners of exposure science collaborated with health professionals to investigate the causes of occupational diseases. With the birth of U.S. regulatory agencies in the 1970s, interest in the environmental origins of human diseases waned, and exposure scientists focused instead upon levels of selected contaminants in air and water. In fact, toxic chemicals enter the body not only from exogenous sources (air, water, diet, drugs, and radiation) but also from endogenous processes, including inflammation, lipid peroxidation, oxidative stress, existing diseases, infections, and gut flora. Thus, even though current evidence suggests that non-genetic factors contribute about 90% of the risks of chronic diseases, we have not explored the vast majority of human exposures that might initiate disease processes. The concept of the exposome, representing the totality of exposures received by a person during life, encompasses all sources of toxicants and, therefore, offers scientists an agnostic approach for investigating the environmental causes of chronic diseases. In this context, it is appropriate to regard the "environment" as the body's internal chemical environment and to define exposures as levels of biologically active chemicals in this internal environment. To explore the exposome, it makes sense to employ a top-down approach based upon biomonitoring (e.g. blood sampling) rather than a bottom-up approach that samples air, water, food, and so on. Because sources and levels of exposure change over time, exposomes can be constructed by analyzing toxicants in blood specimens obtained during critical stages of life. Initial investigations could use archived blood from prospective cohort studies to measure important classes of toxic chemicals, notably, reactive electrophiles, metals, metabolic products, hormone-like substances, and persistent organic compounds. The exposome offers health scientists an avenue for integrating research that is currently fractured along lines related to particular diseases and risk factors, and can thereby promote discovery of the key exposures responsible for chronic diseases. By embracing the exposome as its operational paradigm, exposure science can play a major role in discovering and mitigating these exposures. © 2011 Nature America, Inc. All rights reserved.


Kidd P.,University of California at Berkeley
Alternative Medicine Review | Year: 2011

Astaxanthin, a xanthophyll carotenoid, is a nutrient with unique cell membrane actions and diverse clinical benefits. This molecule neutralizes free radicals or other oxidants by either accepting or donating electrons, and without being destroyed or becoming a pro-oxidant in the process. Its linear, polar-nonpolar-polar molecular layout equips it to precisely insert into the membrane and span its entire width. In this position, astaxanthin can intercept reactive molecular species within the membrane's hydrophobic interior and along its hydrophilic boundaries. Clinically, astaxanthin has shown diverse benefits, with excellent safety and tolerability. In double-blind, randomized controlled trials (RCTs), astaxanthin lowered oxidative stress in overweight and obese subjects and in smokers. It blocked oxidative DNA damage, lowered C-reactive protein (CRP) and other inflammation biomarkers, and boosted immunity in the tuberculin skin test. Astaxanthin lowered triglycerides and raised HDL-cholesterol in another trial and improved blood flow in an experimental microcirculation model. It improved cognition in a small clinical trial and boosted proliferation and differentiation of cultured nerve stem cells. In several Japanese RCTs, astaxanthin improved visual acuity and eye accommodation. It improved reproductive performance in men and reflux symptoms in H. pylori patients. In preliminary trials it showed promise for sports performance (soccer). In cultured cells, astaxanthin protected the mitochondria against endogenous oxygen radicals, conserved their redox (antioxidant) capacity, and enhanced their energy production efficiency. The concentrations used in these cells would be attainable in humans by modest dietary intakes. Astaxanthin's clinical success extends beyond protection against oxidative stress and inflammation, to demonstrable promise for slowing age-related functional decline. Copyright © 2011 Alternative Medicine Review, LLC. All Rights Reserved.


Napoli J.L.,University of California at Berkeley
Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids | Year: 2012

All-trans-retinoic acid (atRA) provides essential support to diverse biological systems and physiological processes. Epithelial differentiation and its relationship to cancer, and embryogenesis have typified intense areas of interest into atRA function. Recently, however, interest in atRA action in the nervous system, the immune system, energy balance and obesity has increased considerably, especially concerning postnatal function. atRA action depends on atRA biosynthesis: defects in retinoid-dependent processes increasingly relate to defects in atRA biogenesis. Considerable evidence indicates that physiological atRA biosynthesis occurs via a regulated process, consisting of a complex interaction of retinoid binding-proteins and retinoid recognizing enzymes. An accrual of biochemical, physiological and genetic data have identified specific functional outcomes for the retinol dehydrogenases, RDH1, RDH10, and DHRS9, as physiological catalysts of the first step in atRA biosynthesis, and for the retinal dehydrogenases RALDH1, RALDH2, and RALDH3, as catalysts of the second and irreversible step. Each of these enzymes associates with explicit biological processes mediated by atRA. Redundancy occurs, but seems limited. Cumulative data support a model of interactions among these enzymes with retinoid binding-proteins, with feedback regulation and/or control by atRA via modulating gene expression of multiple participants. The ratio apo-CRBP1/holo-CRBP1 participates by influencing retinol flux into and out of storage as retinyl esters, thereby modulating substrate to support atRA biosynthesis. atRA biosynthesis requires the presence of both an RDH and an RALDH: conversely, absence of one isozyme of either step does not indicate lack of atRA biosynthesis at the site. This article is part of a Special Issue entitled: Retinoid and Lipid Metabolism. © 2011 Elsevier B.V.


Plucinski M.M.,University of California at Berkeley
Journal of the Royal Society, Interface / the Royal Society | Year: 2013

The distribution of health conditions is characterized by extreme inequality. These disparities have been alternately attributed to disease ecology and the economics of poverty. Here, we provide a novel framework that integrates epidemiological and economic growth theory on an individual-based hierarchically structured network. Our model indicates that, under certain parameter regimes, feedbacks between disease ecology and economics create clusters of low income and high disease that can stably persist in populations that become otherwise predominantly rich and free of disease. Surprisingly, unlike traditional poverty trap models, these localized disease-driven poverty traps can arise despite homogeneity of parameters and evenly distributed initial economic conditions.


Huang Y.,University of California at Berkeley
Physical Review B - Condensed Matter and Materials Physics | Year: 2014

We study the scaling of quantum discord (a measure of quantum correlation beyond entanglement) in spin models analytically and systematically. We find that at finite temperature the block scaling of quantum discord satisfies an area law for any two-local Hamiltonian. We show that generically and heuristically the two-site scaling of quantum discord is similar to that of correlation functions. In particular, at zero temperature it decays exponentially and polynomially in gapped and gapless (critical) systems, respectively; at finite temperature it decays exponentially in both gapped and gapless systems. We compute the two-site scaling of quantum discord in the XXZ chain, the XY chain (in a magnetic field), and the transverse field Ising chain at zero temperature. © 2014 American Physical Society.


Gutheim P.,University of California at Berkeley
IEEE Communications Magazine | Year: 2011

Context enabled mobile applications are considered to provide a richer experience and to enhance the user interaction by acquiring information that allows the identification of the user's current situation. Modern context inference infrastructures can source, process and deliver user information. However, a commercialization towards a context service has still been prohibited by the need for global service coverage and accurate context identification. With the advent of Next Generation Networks, telecom operators can leverage All-IP networks to design external service interfaces that integrate a diverse set of sources and context inference processes that are easily scalable, extendable, and robust at the same time. This article presents a telecom operator service that supplies mobile applications with context information to illustrate how context infrastructures can leverage NGN capabilities. The article introduces an innovative context inference approach involving third Party applications within the inference process itself. This is done by structuring the ontology context model in layers of complexity and inferring particular context information via modules, which are designed in collaboration with third party developers. Furthermore, the service is compliant with state-of-the-art IP Multimedia Subsystem infrastructures and provides an interface that uses HTTP/SOAP and HTTP/REST communication as well as the Session Initiation Protocol of the IMS. A first proof of concept indicates an increased service adoption, a higher accuracy of context, and an increased robustness towards errors. © 2006 IEEE.


Within conifers, active abscission of complete penultimate branch systems is not common and has been described mainly from juveniles. Here I present evidence for the abscission of penultimate branch systems within early so-called walchian conifers-trees with a plagiotropic branching pattern. The specimens studied originate from a middle Early Permian gymnosperm-dominated flora within the middle Clear Fork Group of north-central Texas. Complete branch systems of three walchian conifer morphotypes are preserved; all have pronounced swellings and smooth separation faces at their bases. The source plants grew in a streamside habitat under seasonally dry climatic conditions. The evolution of active branch abscission appears to correspond to an increase in the size of conifers, and this combination potentially contributed to the restructuring of conifer-rich late Paleozoic landscapes. Moreover, trees shedding branch systems and producing abundant litter have the potential to affect the fire regime, which is a factor of evolutionary importance because wildfires must have been a source of frequent biotic disturbance throughout the hyperoxic Early Permian. © 2013 The Paleontological Society. All rights reserved.


Carrasco M.A.,University of California at Berkeley
Palaeogeography, Palaeoclimatology, Palaeoecology | Year: 2013

It is becoming increasingly important to understand how present diversity patterns compare with past ones, in order to understand the extent of change that present faunas exhibit with respect to past baselines for such parameters as extinction rate and magnitude, ecological structure, and ecosystem function. However, these comparisons have been difficult to quantify because the modern and paleontological records are inherently different. This study examines how those differences affect comparisons of fossil and modern mammalian species diversity in the United States and suggests how the data can be treated to minimize their biases. I first compare extant mammalian species diversity to a paleo-baseline constructed from fossils covering the past 30 million years. Species-area relationships show that, contrary to expectations, today's mammalian diversity appears to have increased since the Holocene (11,500 to-500 years ago). This bump in diversity is the result of an increase in small mammal species in the modern dataset, in particular those that are the most difficult to identify and diagnose in the fossil record (e.g., Geomyidae and Heteromyidae). This increase results from neontological classifications of small mammal species that employ methodologies and characters (notably soft-tissue and molecular information) that cannot be used with fossils. One way to correct for these differences would be to reevaluate neontological species using the same morphological characters and species concept commonly used by paleontologists. © 2012 Elsevier B.V.


Vergara S.E.,University of California at Berkeley | Tchobanoglous G.,University of California at Davis
Annual Review of Environment and Resources | Year: 2012

Municipal solid waste (MSW) reflects the culture that produces it and affects the health of the people and the environment surrounding it. Globally, people are discarding growing quantities of waste, and its composition is more complex than ever before, as plastic and electronic consumer products diffuse. Concurrently, the world is urbanizing at an unprecedented rate. These trends pose a challenge to cities, which are charged with managing waste in a socially and environmentally acceptable manner. Effective waste management strategies depend on local waste characteristics, which vary with cultural, climatic, and socioeconomic variables, and institutional capacity. Globally, waste governance is becoming regionalized and formalized. In industrialized nations, where citizens produce far more waste than do other citizens, waste tends to be managed formally at a municipal or regional scale. In less-industrialized nations, where citizens produce less waste, which is mostly biogenic, a combination of formal and informal actors manages waste. Many waste management policies, technologies, and behaviors provide a variety of environmental benefits, including climate change mitigation. Key waste management challenges include integrating the informal waste sector in developing cities, reducing consumption in industrialized cities, increasing and standardizing the collection and analysis of solid waste data, and effectively managing increasingly complex waste while protecting people and the environment. © Copyright ©2012 by Annual Reviews. All rights reserved.


Grunwald M.,University of Vienna | Geissler P.L.,University of California at Berkeley
ACS Nano | Year: 2014

Nanoparticles with sticky patches have long been proposed as building blocks for the self-assembly of complex structures. The synthetic realizability of such patchy particles, however, greatly lags behind predictions of patterns they could form. Using computer simulations, we show that structures of the same genre can be obtained from a solution of simple isotropic spheres, with control only over their sizes and a small number of binding affinities. In a first step, finite clusters of well-defined structure and composition emerge from natural dynamics with high yield. In effect a kind of patchy particle, these clusters can further assemble into a variety of complex superstructures, including filamentous networks, ordered sheets, and highly porous crystals. © 2014 American Chemical Society.


D'Esposito M.,University of California at Berkeley | Postle B.R.,University of Wisconsin - Madison
Annual Review of Psychology | Year: 2015

For more than 50 years, psychologists and neuroscientists have recognized the importance of a working memory to coordinate processing when multiple goals are active and to guide behavior with information that is not present in the immediate environment. In recent years, psychological theory and cognitive neuroscience data have converged on the idea that information is encoded into working memory by allocating attention to internal representations, whether semantic long-term memory (e.g., letters, digits, words), sensory, or motoric. Thus, information-based multivariate analyses of human functional MRI data typically find evidence for the temporary representation of stimuli in regions that also process this information in nonworking memory contexts. The prefrontal cortex (PFC), on the other hand, exerts control over behavior by biasing the salience of mnemonic representations and adjudicating among competing, context-dependent rules. The "control of the controller" emerges from a complex interplay between PFC and striatal circuits and ascending dopaminergic neuromodulatory signals. © 2015 by Annual Reviews. All rights reserved.


MacCoun R.J.,University of California at Berkeley
Addiction | Year: 2011

Aims To examine the empirical consequences of officially tolerated retail sales of cannabis in the Netherlands, and possible implications for the legalization debate. Methods Available Dutch data on the prevalence and patterns of use, treatment, sanctioning, prices and purity for cannabis dating back to the 1970s are compared to similar indicators in Europe and the United States. Results The available evidence suggests that the prevalence of cannabis use among Dutch citizens rose and fell as the number of coffeeshops increased and later declined, but only modestly. The coffeeshops do not appear to encourage escalation into heavier use or lengthier using careers, although treatment rates for cannabis are higher than elsewhere in Europe. Scatterplot analyses suggest that Dutch patterns of use are very typical for Europe, and that the 'separation of markets' may indeed have somewhat weakened the link between cannabis use and the use of cocaine or amphetamines. Conclusions Cannabis consumption in the Netherlands is lower than would be expected in an unrestricted market, perhaps because cannabis prices have remained high due to production-level prohibitions. The Dutch system serves as a nuanced alternative to both full prohibition and full legalization. © 2011 The Author, Addiction © 2011 Society for the Study of Addiction.


Lightfoot K.G.,University of California at Berkeley
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

This Perspective presents an overview of the archaeology of pluralistic colonies (approximately late 1500s-1800s) in North America. It complements the other special feature papers in this issue on ancient societies in Mesoamerica, the Near East, the Armenian Highlands, Peru, and China by presenting another body of literature for examining the dynamics of change in multiethnic societies from a different time and place. In synthesizing archaeological investigations of mercantile, plantation, and missionary colonies, this Perspective shows how this research is relevant to the study of pluralism in both historic and ancient societies in three ways. (i) It enhances our understanding of interethnic relationships that took place in complex societies with imposing political hierarchies and labor structures. (ii) It helps us to refine the methods used by archaeologists to define and analyze multiethnic communities that were spatially delimited by ethnic neighborhoods. Finally, (iii) it presents more than a half century of experimentation with various models (e.g., acculturation, creolization, ethnogenesis, and hybridity) that have been used to study the dynamics of culture change in multiethnic societies.


Lisch D.,University of California at Berkeley
Current Opinion in Plant Biology | Year: 2012

Maize is a typical plant with respect to the proportion of its genome that is composed of transposable elements (TEs), but it is unusual in the number of well-characterized active TEs that it hosts. This has made it possible to examine in some detail the factors responsible for regulating the activity of these elements, particularly the means by which they are recognized and epigenetically silenced. That analysis has revealed that TE silencing is a complex process that involves careful distinctions of different developmental times and tissue types. The available evidence from maize and other species suggests that these distinctions are made in order to generate information in somatic tissues that can be used to induce or reinforce silencing in germinal tissues. © 2012 Elsevier Ltd.


Hariharan I.K.,University of California at Berkeley
Nature cell biology | Year: 2015

The kinase AMPK, a sensor of cellular energy stress, has been shown to oppose the growth-promoting activity of YAP, the transcriptional co-activator downstream of the Hippo signalling pathway. This finding may help to explain why the antidiabetic drug metformin, for which AMPK is a key effector, is linked to cancer-protective activity.


Shibata T.,University of California at Berkeley
Journal of vision | Year: 2011

Recent increased usage of stereo displays has been accompanied by public concern about potential adverse effects associated with prolonged viewing of stereo imagery. There are numerous potential sources of adverse effects, but we focused on how vergence-accommodation conflicts in stereo displays affect visual discomfort and fatigue. In one experiment, we examined the effect of viewing distance on discomfort and fatigue. We found that conflicts of a given dioptric value were slightly less comfortable at far than at near distance. In a second experiment, we examined the effect of the sign of the vergence-accommodation conflict on discomfort and fatigue. We found that negative conflicts (stereo content behind the screen) are less comfortable at far distances and that positive conflicts (content in front of screen) are less comfortable at near distances. In a third experiment, we measured phoria and the zone of clear single binocular vision, which are clinical measurements commonly associated with correcting refractive error. Those measurements predicted susceptibility to discomfort in the first two experiments. We discuss the relevance of these findings for a wide variety of situations including the viewing of mobile devices, desktop displays, television, and cinema.


Halpern J.,University of California at Berkeley
Bioethics | Year: 2012

There is an important gap in philosophical, clinical and bioethical conceptions of decision-making capacity. These fields recognize that when traumatic life circumstances occur, people not only feel afraid and demoralized, but may develop catastrophic thinking and other beliefs that can lead to poor judgment. Yet there has been no articulation of the ways in which such beliefs may actually derail decision-making capacity. In particular, certain emotionally grounded beliefs are systematically unresponsive to evidence, and this can block the ability to deliberate about alternatives. People who meet medico-legal criteria for decision-making capacity can react to health and personal crises with such capacity-derailing reactions. One aspect of this is that a person who is otherwise cognitively intact may be unable to appreciate her own future quality of life while in this complex state of mind. This raises troubling ethical challenges. We cannot rely on the current standard assessment of cognition to determine decisional rights in medical and other settings. We need to understand better how emotionally grounded beliefs interfere with decision-making capacity, in order to identify when caregivers have an obligation to intervene. © 2010 Blackwell Publishing Ltd.


Ornelas C.,University of California at Berkeley
New Journal of Chemistry | Year: 2011

The use of ferrocene-based compounds for medicinal applications is an active research area. Many reports have demonstrated that some ferrocenyl derivatives are highly active against several diseases, including cancer. This review focuses on the most relevant examples of ferrocene-based molecules that show anticancer activity. © 2011 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.


Most basic research on cancer concerns genetic changes in benign and malignant tumors. Yet evidence indicates that the majority of the mutations in tumors occur in the preneoplastic field stage of their development. That early stage is represented by grossly invisible, broad regions of "field cancerization" which have not, heretofore, been operationally analyzed in cell culture. Conditions are described for quantitating preneoplasia by increased saturation density followed by progression to transformation. These parameters are driven by Darwinian selection of spontaneously occurring, cumulative mutations, in accordance with recent genomic analyses of human cancer, just as it is in the evolution of species. The cell culture model will allow correlation of the preneoplastic increases in saturation density with genetic changes, and development of methods for demarcating fields during surgery so that they can be excised along with the tumor, thereby reducing the possibility of recurrence at the site. © 2011 WILEY Periodicals, Inc.


Arons J.,University of California at Berkeley
Space Science Reviews | Year: 2012

I outline, from a theoretical and somewhat personal perspective, significant features of Pulsar Wind Nebulae (PWNe) as Cosmic Accelerators. I pay special attention to the recently discovered gamma ray flares in the Crab Nebula's emission, focusing on the possibility, raised by the observations, that the accelerating electric field exceeds the magnetic field, suggesting that reconnection in the persistent current layer (a current sheet) plays a significant role in the behavior of this well studied Pevatron. I address the present status of the termination shock model for the particle accelerator that converts the wind flow energy to the observed non-thermal particle spectra, concluding that it has a number of major difficulties related to the transverse magnetic geometry of the shock wave. I discuss recent work on the inferred pair outflow rates, which are in excess of those predicted by existing theories of pair creation, and use those results to point out that the consequent mass loading of the wind reduces the wind's bulk flow 4-velocity to the point that dissipation of the magnetic field in a pulsar's wind upstream of the termination shock is restored to life as a viable model for the solution of the σ problem. I discuss some suggestions that current starvation in the current flow supporting the structured (striped) upstream magnetic field perhaps induces a transition to superluminal wave propagation. I show that current starvation probably does not occur, because those currents are carried in the current sheet separating the stripes rather than in the stripes themselves. © 2012 Springer Science+Business Media B.V.


Shirzaei M.,University of California at Berkeley
IEEE Geoscience and Remote Sensing Letters | Year: 2013

I present a multitemporal algorithm with an improved filtering scheme compared with earlier works that combines and inverts a large set of unwrapped interferograms to generate an accurate time series of the surface motion. This method statistically analyzes the interferometric phase noise to identify stable pixels. Then, it applies an iterative 2-D sparse phase unwrapping operator and low-pass filter to each interferogram to obtain reliable absolute phase changes. Moreover, it uses a re-weighted least squares approach to robustly estimate the time series of the surface motion, which is followed by a temporal low-pass filter that reduces the effects of atmospheric delay. During various stages of the analysis, this approach applies a variety of sophisticated wavelet-based filters to estimate the interferometric phase noise and to reduce the effects of systematic and random artefacts, such as spatially correlated and temporally uncorrelated components of the atmospheric delay, and the digital elevation model and orbital errors. To demonstrate the capability of this method for accurately measuring nonlinear surface motions, I analyze a large set of SAR data acquired by the ENVISAT satellite from 2003 through 2010 over the south flank of the Kilauea volcano, Hawaii. The validation test shows that my approach is able to retrieve the surface displacement with an average accuracy of 6.5 mm. © 2004-2012 IEEE.


Smith A.W.,University of California at Berkeley
Biochimica et Biophysica Acta - Biomembranes | Year: 2012

Though an increasing number of biological functions at the membrane are attributed to direct associations between lipid head groups and protein side chains or lipid protein hydrophobic attractive forces, surprisingly limited information is available about the dynamics of these interactions. The static in vitro representation provided by membrane protein structures, including very insightful lipid-protein binding geometries, still fails to recapitulate the dynamic behavior characteristic of lipid membranes. Experimental measures of the interaction time of lipid-protein association are very rare, and have only provided order-of-magnitude estimates in an extremely limited number of systems. In this review, a brief outline of the experimental approaches taken in this area to date is given. The bulk of the review will focus on two methods that are promising techniques for measuring lipid-protein interactions: time-resolved fluorescence microscopy, and two-dimensional infrared (2D IR) spectroscopy. Time-resolved fluorescence microscopy is the name given to a sophisticated toolbox of measurements taken using pulsed laser excitation and time-correlated single photon counting (TCSPC). With this technique the dynamics of interaction can be measured on the time scale of nanoseconds to milliseconds. 2D IR is a femtosecond nonlinear spectroscopy that can resolve vibrational coupling between lipids and proteins at molecular-scale distances and at time scales from femtoseconds to picoseconds. These two methods are poised to make significant advances in our understanding of the dynamic properties of biological membranes. This article is part of a Special Issue entitled: Membrane protein structure and function. © 2011 Elsevier B.V.


Levenson R.W.,University of California at Berkeley | Sturm V.E.,University of California at San Francisco | Haase C.M.,Northwestern University
Annual Review of Clinical Psychology | Year: 2014

Disruptions in emotional, cognitive, and social behavior are common in neurodegenerative disease and in many forms of psychopathology. Because neurodegenerative diseases have patterns of brain atrophy that are much clearer than those of psychiatric disorders, they may provide a window into the neural bases of common emotional and behavioral symptoms. We discuss five common symptoms that occur in both neurodegenerative disease and psychopathology (i.e., anxiety, dysphoric mood, apathy, disinhibition, and euphoric mood) and their associated neural circuitry. We focus on two neurodegenerative diseases (i.e., Alzheimer's disease and frontotemporal dementia) that are common and well characterized in terms of emotion, cognition, and social behavior and in patterns of associated atrophy. Neurodegenerative diseases provide a powerful model system for studying the neural correlates of psychopathological symptoms; this is ported by evidence indicating convergence with psychiatric syndromes (e.g., symptoms of disinhibition associated with dysfunction in orbitofrontal cortex in both frontotemporal dementia and bipolar disorder). We conclude that neurodegenerative diseases can play an important role in future approaches to the assessment, prevention, and treatment of mental illness. © 2014 by Annual Reviews.


Smith A.B.,University of California at Berkeley
Biological Conservation | Year: 2010

Conservation biologists use the species-area relationship for a variety of purposes, including upscaling diversity from small plots to regions, predicting species loss, and for identifying biodiversity hotspots and prioritizing actions to protect them. Despite its widespread use, several complications that affect the accuracy of its application are often overlooked. First, interpretation of the species-area relationship is a function of the census design used to construct it. Nested census designs guarantee only that one individual each of a given number of species is within the sampled area, but we are almost always concerned with the loss or protection of more than one individual of each species. Census designs using non-contiguous plots are useful for sampling large regions, but their interpretation is not straightforward because species number is a function of the spatial extent of the landscape and the size of the sample units. Second, power function behavior is often assumed, even though the species-area relationship often displays curvilinearity on log-log plots across scale ranges pertinent to conservation. Finally, applications of the species-area relationship often assume that the area of interest is contiguous while in practice it seldom is, and so calculations using the species-area relationship need to account for beta diversity between disjunctive areas. © 2009 Elsevier Ltd. All rights reserved.


Traeger C.P.,University of California at Berkeley
Journal of Environmental Economics and Management | Year: 2013

The uncertainty of future economic development affects the term structure of discount rates and, thus, the intertemporal weights that are to be used in cost benefit analysis. The U.K. and France have recently adopted a falling term structure to incorporate uncertainty and the U.S. is considering a similar step. A series of publications discusses the following concern: a seemingly analogous argument used to justify falling discount rates can also justify increasing discount rates. We show that increasing and decreasing discount rates mean different things, can coexist, are created by different channels through which risk affects evaluation, and have the same qualitative effect of making long-term payoffs more attractive. © 2013 Elsevier Inc.


Allen R.M.,University of California at Berkeley | Ziv A.,Ben - Gurion University of the Negev
Geophysical Research Letters | Year: 2011

We explore the use of real-time high-rate GPS displacement data for earthquake early warning using 1 Hz displacement waveforms from the April 4, 2010, M w 7.2 El Mayor-Cucapah earthquake. We compare these data to those provided by the broadband velocity and accelerometer instrumentation of the Southern California Seismic Network. The unique information provided by the GPS-based displacement timeseries is the permanent/static displacement. Using a simple algorithm that can be applied in real-time, we extract the static offset shortly after the S-wave arrival, around the time of the observed peak shaking at the same site, and before shaking at more distant locations. These data can be used, as they become available, to provide a robust estimate of the earthquake magnitude, which ranges from 6.8 to 7.0 in this case. We therefore conclude that real-time high-rate GPS can provide a useful and independent assessment of earthquake magnitude for the purpose of earthquake early warning and real-time earthquake information systems in general including tsunami warning systems. Copyright 2011 by the American Geophysical Union.


Tian Y.,University of California at Berkeley
Optics Express | Year: 2011

The key issue in passive autofocus is to choose robust focus measures to judge optical blur in defocused images. Existing focus measures are sensitive to image contrast (illumination) as they use image intensity. In this report we demonstrate a focus measure using phase congruency. The proposed focus measure is robust for noisy imaging sensors in varying illumination conditions, and has great balance of defocus sensitivity and effective range. Its advantages are shown with a number of synthetic image sequences. © 2010 Optical Society of America.


Chandler D.,University of California at Berkeley | Garrahan J.P.,University of Nottingham
Annual Review of Physical Chemistry | Year: 2010

We review a theoretical perspective of the dynamics of glass-forming liquids and the glass transition, a perspective developed during this past decade based on the structure of trajectory space. This structure emerges from spatial correlations of dynamics that appear in disordered systems as they approach nonergodic or jammed states. It is characterized in terms of dynamical heterogeneity, facilitation, and excitation lines. These features are associated with a newly discovered class of nonequilibrium phase transitions. Equilibrium properties have little, if anything, to do with it. The broken symmetries of these transitions are obscure or absent in spatial structures, but they are vivid in space-time (i.e., trajectory space). In our view, the glass transition is an example of this class of transitions. The basic ideas and principles we review were originally developed through the analysis of idealized and abstract models. Nevertheless, the central ideas are easily illustrated with reference to molecular dynamics of more realistic atomistic models, and we use that illustrative approach here. Copyright © 2010 by Annual Reviews. All rights reserved.


Chen Y.,University of California at Berkeley
IEEE Transactions on Information Theory | Year: 2015

This paper considers the matrix completion problem. We show that it is not necessary to assume joint incoherence, which is a standard but unintuitive and restrictive condition that is imposed by previous studies. This leads to a sample complexity bound that is orderwise optimal with respect to the incoherence parameter (as well as to the rank r and the matrix dimension n up to a log factor). As a consequence, we improve the sample complexity of recovering a semidefinite matrix from O(nr2log2n) to O(nr\log2n), and the highest allowable rank from Θ (√n log n) to Θ (n/log2n). The key step in proof is to obtain new bounds in terms of the ℓ∞2-norm, defined as the maximum of the row and column norms of a matrix. To illustrate the applicability of our techniques, we discuss extensions to singular value decomposition projection, structured matrix completion and semisupervised clustering, for which we provide orderwise improvements over existing results. Finally, we turn to the closely related problem of low-rank-plus-sparse matrix decomposition. We show that the joint incoherence condition is unavoidable here for polynomial-time algorithms conditioned on the planted clique conjecture. This means it is intractable in general to separate a rank- ω (√ n) positive semidefinite matrix and a sparse matrix. Interestingly, our results show that the standard and joint incoherence conditions are associated, respectively, with the information (statistical) and computational aspects of the matrix decomposition problem. © 1963-2012 IEEE.


Vance R.E.,Howard Hughes Medical Institute | Vance R.E.,University of California at Berkeley
Current Opinion in Immunology | Year: 2015

Inflammasomes comprise a family of cytosolic multi-protein complexes that sense infection, or other threats, and initiate inflammation via the recruitment and activation of the Caspase-1 protease. Although the precise molecular mechanism by which most inflammasomes are activated remains a subject of considerable debate, the NAIP/NLRC4 subfamily of inflammasomes is increasingly well understood. A crystal structure of NLRC4 was recently reported, and a domain in NAIPs that recognizes bacterial ligands was identified. In addition, gain-of-function mutations in NLRC4 have been shown to cause an auto-inflammatory syndrome in humans. Lastly, the NAIP/NLRC4 inflammasome has been shown to provide a novel form of cell intrinsic defense against Salmonella infection, involving expulsion of infected cells from the intestinal epithelium. © 2015 Elsevier Ltd.


Boettiger A.,Harvard University | Levine M.,University of California at Berkeley
Cell Reports | Year: 2013

Transcription is commonly held to be a highly stochastic process, resulting in considerable heterogeneity of gene expression among the different cells in a population. Here, we employ quantitative in situ hybridization methods coupled with high-resolution imaging assays to measure the expression of . snail, a developmental patterning gene necessary for coordinating the invagination of the mesoderm during gastrulation of the . Drosophila embryo. Our measurements of steady-state mRNAs suggest that there is very little variation in . snail expression across the different cells that make up the mesoderm and that synthesis approaches the kinetic limits of Pol II processivity. We propose that rapid transcription kinetics and negative autoregulation are responsible for the remarkable homogeneity of . snail expression and the coordination of mesoderm invagination. © 2013 The Authors.


Madrahimov S.T.,Urbana University | Hartwig J.F.,University of California at Berkeley
Journal of the American Chemical Society | Year: 2012

In depth mechanistic studies of iridium catalyzed regioselective and enantioselective allylic substitution reactions are presented. A series of cyclometalated allyliridium complexes that are kinetically and chemically competent to be intermediates in the allylic substitution reactions was prepared and characterized by 1D and 2D NMR spectroscopies and single-crystal X-ray difraction. The rates of epimerization of the less thermodynamically stable diastereomeric allyliridium complexes to the thermodynamically more stable allyliridium stereoisomers were measured. The rates of nucleophilic attack by aniline and by N-methylaniline on the isolated allyliridium complexes were also measured. Attack on the thermodynamically less stable allyliridium complex was found to be orders of magnitude faster than attack on the thermodynamically more stable complex, yet the major enantiomer of the catalytic reaction is formed from the more stable diastereomer. Comparison of the rates of nucleophilic attack to the rates of epimerization of the diastereomeric allyliridium complexes containing a weakly coordinating counterion showed that nucleophilic attack on the less stable allyliridium species is much faster than conversion of the less stable isomer to the more stable isomer. These observations imply that Curtin-Hammett conditions are not met during iridium catalyzed allylic substitution reactions by ≠ 3-≠ 1-≠ 3 interconversion. Rather, these data imply that when these conditions exist for this reaction, they are created by reversible oxidative addition, and the high selectivity of this oxidative addition step to form the more stable diastereomeric allyl complex leads to the high enantioselectivity. The stereochemical outcome of the individual steps of allylic substitution was assessed by reactions of deuterium-labeled substrates. The allylic substitution was shown to occur by oxidative addition with inversion of configuration, followed by an outer sphere nucleophilic attack that leads to a second inversion of configuration. This result contrasts the changes in configuration that occur during reactions of molybdenum complexes studied with these substrates previously. In short, these studies show that the factors that control the enantioselectivity of iridium-catalyzed allylic substitution are distinct from those that control enantioselectivity during allylic substitution catalyzed by palladium or molybdenum complexes and lead to the unique combination of high regioselectivity, enantioselectivity, and scope of reactive nucleophile. © 2012 American Chemical Society.


Gosling J.T.,University of Colorado at Boulder | Phan T.D.,University of California at Berkeley
Astrophysical Journal Letters | Year: 2013

Using Wind 3 s plasma and magnetic field data, we have identified nine reconnection exhausts within a solar wind disturbance on 1998 October 18-20 driven by a moderately fast interplanetary coronal mass ejection (ICME). Three of the exhausts within the ICME were associated with current sheets having local field shear angles, θ, ranging from 4° to 9°, the smallest reported values of θ yet associated with reconnection exhausts in a space plasma. They were observed in plasma characterized by extremely low (0.02-0.04) plasma β, and very high (281-383 km s-1) Alfvén speed, VA. Low β allows reconnection to occur at small θ and high VA leads to exhaust jets that are fast enough relative to the surrounding solar wind to be readily identified. Very small-θ current sheets are common in the solar wind at 1 AU, but typically are not associated with particularly low plasma β or high VA. On the other hand, small-θ current sheets should be common in the lower solar corona, a plasma regime of extremely low β and extremely high VA. Our observations lend credence to models that predict that reconnection at small-θ current sheets is primarily responsible for coronal heating. © 2013. The American Astronomical Society. All rights reserved.


Kriek M.,University of California at Berkeley | Conroy C.,University of California at Santa Cruz
Astrophysical Journal Letters | Year: 2013

This Letter utilizes composite spectral energy distributions (SEDs) constructed from NEWFIRM Medium-Band Survey photometry to constrain the dust attenuation curve in 0.5 < z < 2.0 galaxies. Based on similarities between the full SED shapes (0.3-8 μm), we have divided galaxies in 32 different spectral classes and stacked their photometry. As each class contains galaxies over a range in redshift, the resulting rest-frame SEDs are well sampled in wavelength and show various spectral features including Hα and the UV dust bump at 2175 Å. We fit all composite SEDs with flexible stellar population synthesis models, while exploring attenuation curves with varying slopes and UV bump strengths. The Milky Way and Calzetti law provide poor fits at UV wavelengths for nearly all SEDs. Consistent with previous studies, we find that the best-fit attenuation law varies with spectral type. There is a strong correlation between the best-fit dust slope and UV bump strength, with steeper laws having stronger bumps. Moreover, the attenuation curve correlates with specific star formation rate (SFR), with more active galaxies having shallower dust curves and weaker bumps. There is also a weak correlation with inclination. The observed trends can be explained by differences in the dust-to-star geometry, a varying grain size distribution, or a combination of both. Our results have several implications for galaxy evolution studies. First, the assumption of a universal dust model leads to biases in derived galaxy properties. Second, the presence of a dust bump may result in underestimated values for the UV slope, used to correct SFRs of distant galaxies. © 2013. The American Astronomical Society. All rights reserved..


Chan S.O.,University of California at Berkeley
Proceedings of the Annual ACM Symposium on Theory of Computing | Year: 2013

We show optimal (up to constant factor) NP-hardness for Max-k-CSP over any domain, whenever k is larger than the domain size. This follows from our main result concerning predicates over abelian groups. We show that a predicate is approximation resistant if it contains a subgroup that is balanced pairwise independent. This gives an unconditional analogue of Austrin-Mossel hardness result, bypassing the Unique-Games Conjecture for predicates with an abelian subgroup structure. Our main ingredient is a new gap-amplification technique inspired by XOR-lemmas. Using this technique, we also improve the NP-hardness of approximating Independent-Set on bounded-degree graphs, Almost-Coloring, Two-Prover-One- Round-Game, and various other problems. Copyright 2013 ACM.


Arcak M.,University of California at Berkeley
IEEE Transactions on Automatic Control | Year: 2011

A square matrix $E$ is said to be diagonally stable if there exists a diagonal matrix D > 0 satisfying DE+E T D < 0 . This notion has been instrumental in recent studies on stability of interconnected system models in communication and biological networks, in which the subsystems satisfy passivity properties and the matrix $E$ combines this passivity information with the interconnection structure. This paper presents a necessary and sufficient condition for diagonal stability when the digraph describing the network conforms to a cactus structure, which means that a pair of distinct simple circuits in the graph have at most one common vertex. In the special case of a single circuit, this diagonal stability test recovers the secant criterion that was recently derived for cyclic networks. The paper then incorporates the new diagonal stability test in network stability analysis where the diagonal entries of the matrix $D$ serve as weights in a Lyapunov function constructed from storage functions that verify passivity properties of the components. Finally, the paper illustrates this stability test on examples motivated by gene networks and population dynamics. © 2006 IEEE.


Harland R.M.,University of California at Berkeley | Grainger R.M.,University of Virginia
Trends in Genetics | Year: 2011

Research using Xenopus takes advantage of large, abundant eggs and readily manipulated embryos in addition to conserved cellular, developmental and genomic organization with mammals. Research on Xenopus has defined key principles of gene regulation and signal transduction, embryonic induction, morphogenesis and patterning as well as cell cycle regulation. Genomic and genetic advances in this system, including the development of Xenopus tropicalis as a genetically tractable complement to the widely used Xenopus laevis, capitalize on the classical strengths and wealth of achievements. These attributes provide the tools to tackle the complex biological problems of the new century, including cellular reprogramming, organogenesis, regeneration, gene regulatory networks and protein interactions controlling growth and development, all of which provide insights into a multitude of human diseases and their potential treatments. © 2011 Elsevier Ltd.


Napoli J.L.,University of California at Berkeley
IUBMB Life | Year: 2011

All-trans-retinoic acid (atRA) serves essential functions during embryogenesis and throughout postnatal vertebrate life. Insufficient or excess atRA causes teratogenic and/or toxic effects in the developing embryo: interference with atRA biosynthesis or signaling likely underlies some forms of cancer. Many symptoms of vitamin A (atRA precursor) deficiency and/or toxicity overlap with those of another pleiotropic agent-ethanol. These overlapping symptoms have prompted research to understand whether interference with atRA biosynthesis and/or action may explain (in part) pathology associated with excess ethanol consumption. Ethanol affects many aspects of retinoid metabolism and mechanisms of action site specifically, but no robust data support inhibition of vitamin A metabolism, resulting in decreased atRA in vivo during normal vitamin A nutriture. Actually, ethanol either has no effect on or increases atRA at select sites. Despite this realization, insight into whether interactions between ethanol and retinoids represent cause versus effect requires additional research. © 2011 International Union of Biochemistry and Molecular Biology, Inc.


Papavasiliou A.,Catholic University of Leuven | Oren S.S.,University of California at Berkeley
Operations Research | Year: 2013

In this paper we present a unit commitment model for studying the impact of large-scale wind integration in power systems with transmission constraints and system component failures. The model is formulated as a two-stage stochastic program with uncertain wind production in various locations of the network as well as generator and transmission line failures. We present a scenario selection algorithm for selecting and weighing wind power production scenarios and composite element failures, and we provide a parallel dual decomposition algorithm for solving the resulting mixed-integer program. We validate the proposed scenario selection algorithm by demonstrating that it outperforms alternative reserve commitment approaches in a 225 bus model of California with 130 generators and 375 transmission lines. We use our model to quantify day-ahead generator capacity commitment, operating cost impacts, and renewable energy utilization levels for various degrees of wind power integration. We then demonstrate that failing to account for transmission constraints and contingencies can result in significant errors in assessing the economic impacts of renewable energy integration. ©2013 INFORMS.


Lee E.A.,University of California at Berkeley
Proceedings - Design Automation Conference | Year: 2010

This paper argues that cyber-physical systems present a substantial intellectual challenge that requires changes in both theories of computation and dynamical systems theory. The CPS problem is not the union of cyber and physical problems, but rather their intersection, and as such it demands models that embrace both. Two complementary approaches are identified: cyberizing the physical (CtP) means to endow physical subsystems with cyber-like abstractions and interfaces; and physicalizing the cyber (PtC) means to endow software and network components with abstractions and interfaces that represent their dynamics in time. Copyright 2010 ACM.


Chuang J.,University of California at Berkeley
IEEE Communications Magazine | Year: 2011

Designing for competition is an important consideration for the design of future Internet architectures. Network architects should systematically consider the loci of competition in any proposed network architecture. To be economically sustainable, network architectures should encourage competition within each locus, anticipate and manage the interactions between the loci, and be adaptable to evolution in the loci. Given the longevity of network architectures relative to network technologies and applications, it is important to ensure that competition is not unnecessarily foreclosed at any particular locus of competition. © 2010 IEEE.


Schneider D.,University of California at Berkeley
Future of Children | Year: 2015

In the contemporary United States, marriage is closely related to money. Men and (perhaps to a lesser extent) women with more education, higher incomes, larger stocks of wealth, and more stable employment are more likely to marry than are people in more precarious economic positions. But is this relationship truly causal? That is, does economic insufficiency cause people to marry later and less often? Daniel Schneider reviews evidence from social experiments in areas such as early childhood education, human capital development, workforce training, and income support to assess whether programs that successfully increased the economic wellbeing of disadvantaged men and women also increased the likelihood that they would marry. These programs were not designed to affect marriage. But to the extent that they increased participants’ economic resources, they could have had such an effect. Examining these programs offers three key benefits. First, their experimental designs provide important insight into the causal role of economic resources for marriage. Second, they give us within-group comparisons of disadvantaged men and women, some of whom received economic “treatments” and some who did not. Third, they by and large assess interventions that are feasible and realistic within the constraints of U.S. policy making. Schneider describes each intervention in detail, discussing its target population, experimental treatment, evaluation design, economic effects, and, finally, any effects on marriage or cohabitation. Overall, he finds little evidence that manipulating men’s economic resources increased the likelihood that they would marry, though there are exceptions. For women, on the other hand, there is more evidence of positive effects. © 2015 by The Trustees of Princeton University, All rights reserved.


Gu C.,University of California at Berkeley
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems | Year: 2011

We present a projection-based nonlinear model order reduction method, named model order reduction via quadratic-linear systems (QLMOR). QLMOR employs two novel ideas: 1) we show that nonlinear ordinary differential equations, and more generally differential-algebraic equations (DAEs) with many commonly encountered nonlinear kernels can be re-written equivalently in a special representation, quadratic-linear differential algebraic equations (QLDAEs), and 2) we perform a Volterra analysis to derive the Volterra kernels, and we adapt the moment-matching reduction technique of nonlinear model order reduction method (NORM) to reduce these QLDAEs into QLDAEs of much smaller size. Because of the generality of the QLDAE representation, QLMOR has sign