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Cornell University is an American private Ivy League and federal land-grant research university located in Ithaca, New York. Founded in 1865 by Ezra Cornell and Andrew Dickson White, the university was intended to teach and make contributions in all fields of knowledge — from the classics to the science, and from the theoretical to the applied. These ideals, unconventional for the time, are captured in Cornell's motto, a popular 1865 Ezra Cornell quotation: "I would found an institution where any person can find instruction in any study."The university is broadly organized into seven undergraduate colleges and seven graduate divisions at its main Ithaca campus, with each college and division defining its own admission standards and academic programs in near autonomy. The university also administers two satellite medical campuses, one in New York City and one in Education City, Qatar. Cornell is one of three private land grant universities. Of its seven undergraduate colleges, three are state-supported statutory or contract colleges, including its agricultural and veterinary colleges. As a land grant college, it operates a cooperative extension outreach program in every county of New York and receives annual funding from the State of New York for certain educational missions. The Cornell University Ithaca Campus comprises 745 acres, but in actuality, is much larger due to the Cornell Plantations as well as the numerous university owned lands in New York.Since its founding, Cornell has been a co-educational, non-sectarian institution where admission is offered irrespective of religion or race. Cornell counts more than 245,000 living alumni, 34 Marshall Scholars, 29 Rhodes Scholars and 44 Nobel laureates as affiliated with the university. The student body consists of nearly 14,000 undergraduate and 7,000 graduate students from all 50 American states and 122 countries. Wikipedia.


Douglas A.E.,Cornell University
Journal of Chemical Ecology | Year: 2013

Recent advances in sequencing methods have transformed the field of microbial ecology, making it possible to determine the composition and functional capabilities of uncultured microorganisms. These technologies have been instrumental in the recognition that resident microorganisms can have profound effects on the phenotype and fitness of their animal hosts by modulating the animal signaling networks that regulate growth, development, behavior, etc. Against this backdrop, this review assesses the impact of microorganisms on insect-plant interactions, in the context of the hypothesis that microorganisms are biochemical brokers of plant utilization by insects. There is now overwhelming evidence for a microbial role in insect utilization of certain plant diets with an extremely low or unbalanced nutrient content. Specifically, microorganisms enable insect utilization of plant sap by synthesizing essential amino acids. They also can broker insect utilization of plant products of extremely high lignocellulose content, by enzymatic breakdown of complex plant polysaccharides, nitrogen fixation, and sterol synthesis. However, the experimental evidence for microbial-mediated detoxification of plant allelochemicals is limited. The significance of microorganisms as brokers of plant utilization by insects is predicted to vary, possibly widely, as a result of potentially complex interactions between the composition of the microbiota and the diet and insect developmental age or genotype. For every insect species feeding on plant material, the role of resident microbiota as biochemical brokers of plant utilization is a testable hypothesis. © 2013 Springer Science+Business Media New York.


Ablation of residual thyroid tissue after total or near-total thyroidectomy is widely accepted by many practitioners and endorsed by relevant professional societies in the United States and the international community for patients with defined risk factors, including age greater than 45 years, large tumors; tumors with undesirable histopathology; lymph node involvement; positive surgical margins; gross and possibly microscopic extrathyroidal extension; and, of course, evidence or suspicion of distal metastases, including mediastinal lymphadenopathy, pulmonary or osseous metastases or involvement of other organs. 131I therapy doses of 3.7-5.5 GBq (100-150 mCi) should be used, and additional activity should be used in the event there are additional findings on pretreatment whole-body scans. Depending upon the patient's age, general medical condition, and renal function, nuclear medicine practitioners should be prepared to perform whole body (blood or bone marrow) dosimetry in the event doses >5.5 GBq (150 mCi) are being considered to assure patient safety. Still unresolved is the role of 131I ablation in the so-called "low risk" patientparticularly in a patient who has undergone a near-total thyroidectomy in the hands of a skilled surgeon. If an ablative dose is to be administered, 0.9-1.8 MBq (25-50 mCi) appears to be sufficient to eliminate most if not all thyroid tissue. The problem is defining the "low-risk" patient. After review of the extensive literature on this subject, it appears that the thoughtful and informed practitioner must make a patient specific decision in this setting on the basis of his/her experience and review of the details in each case and continue to review the evidence on this subject as it becomes available. © 2011 Elsevier Inc. All rights reserved.


In the 1940 and 1950s, the Rockefeller and Ford Foundations initiated overseas rural and agricultural development activities in a number of countries in Asia and Latin America. They began with country programs. These programs often involved creating new institutions in the recipient countries, and while the perspective was long term - as long as it took to achieve program goals - the foundations also explicitly sought to work themselves out of a job and turn over responsibility to nationals. By 1960 the two foundations had moved beyond national assistance programs to invent a new model, the international agricultural research center, designed to improve the lives of poor rural people by increasing the productivity of developing world agriculture. Some of the national programs were morphed into international centers. The international agricultural research centers proved attractive to other donors and by the 1970s international agricultural research had become institutionalized in the form of the CGIAR and its associate centers. The 1960s India agricultural program of the Rockefeller Foundation comprised a team of about a dozen American scientists working in India assisting Indian scientists to invent new approaches to agricultural technology development. At the same time and also in India, the Ford Foundation pioneered the integrated rural development model. By the mid-1970s integrated rural development projects were the approach of choice for many donors. In the 1980s the Ford Foundation moved away from agriculture concentrating on broader social issues; the Government of India and Rockefeller Foundation decided Foundation scientists had, indeed, worked themselves out of their jobs and Rockefeller's India program was effectively closed down, although by then the international agricultural research centers, including ICRISAT in India, had attained a degree of maturity and stability. The Rockefeller Foundation invented another new model for agricultural research in the 1990s - the international rice biotechnology network, in which leading scientists from Asian countries, Western countries and the international centers worked together within a framework managed by Rockefeller scientists. In 2006, the Bill Melinda Gates Foundation entered the global agricultural scene in partnership with the Rockefeller Foundation to establish AGRA, yet another new model. By 2010 the Gates Foundation was annually spending about 10. times. what the 'old' foundations did and dominating international agricultural assistance, working across the spectrum of agricultural research, extension, and policy, largely focused in Africa.Five important lessons emerge that may be useful for addressing today's primary agricultural development challenge: that of improving the lives and well-being of people in Africa. First, it is critical not to underestimate the temporal and spatial variability of the biological and physical conditions in which agriculture operates; second, it is critical not to underestimate the institutional challenges of agricultural development; third, ever-renewing agricultural technology is essential and simply transferring technology from other parts of the world or from international research centers will have limited value without local adaptive research; fourth, every country needs its own people with the capacity to conduct adaptive agricultural research and to design and implement agricultural policy; and fifth, people in assistance agencies, national organizations and in rural areas are the key to successful development assistance. These lessons all point to the need for countries to build their own capabilities to conduct agricultural research, establish policies, and design the institutions necessary for a dynamic agricultural sector to meet current and future needs.The conclusions question whether today's foundations, which have very few staff stationed in sub-Sahara Africa, will be able to achieve the depth and nuanced understanding of local actors and institutions to apply their resources optimally. Can they identify national actors who truly have the will to remake policies to ensure agricultural development? Are enough resources being devoted to educate the people needed to create and adapt agricultural technology for today and the future? Do the organizations which are receiving more than 90% of the foundations' funds have the incentive to create national capacity and work themselves out of a job? © 2012 Elsevier Ltd.


Jonkers I.,University of Groningen | Lis J.T.,Cornell University
Nature Reviews Molecular Cell Biology | Year: 2015

Recent advances in sequencing techniques that measure nascent transcripts and that reveal the positioning of RNA polymerase II (Pol II) have shown that the pausing of Pol II in promoter-proximal regions and its release to initiate a phase of productive elongation are key steps in transcription regulation. Moreover, after the release of Pol II from the promoter-proximal region, elongation rates are highly dynamic throughout the transcription of a gene, and vary on a gene-by-gene basis. Interestingly, Pol II elongation rates affect co-transcriptional processes such as splicing, termination and genome stability. Increasing numbers of factors and regulatory mechanisms have been associated with the steps of transcription elongation by Pol II, revealing that elongation is a highly complex process. Elongation is thus now recognized as a key phase in the regulation of transcription by Pol II. © 2015 Macmillan Publishers Limited.


Lai D.,Cornell University
Monthly Notices of the Royal Astronomical Society | Year: 2013

We study the interactions between a protostar and circumstellar disc under the influence of a binary companion to determine the evolution of the mutual misalignment between the stellar spin and disc angular momentum axes. Significant misalignments can be generated as the star-disc system evolves in time such that the frequency of disc precession (driven by the binary companion) and that of stellar precession (driven by the disc) cross each other. This resonance behaviour can be understood in a geometric way from the precession dynamics of spin and disc angular momenta. We show that such resonance crossing can occur under reasonable protostar-disc-binary conditions. The star-disc inclination is also affected by mass accretion and by magnetic star-disc interaction torques, which can either promote or reduce star-disc misalignment. In general, a variety of star-disc misalignment angles are produced within the lifetimes of protoplanetary discs. We discuss the implications of our results for stellar spin orientations in binaries, for the alignments/misalignments of protostellar and debris discs, and for the stellar obliquities in exoplanetary systems. In particular, even for systems where the Kozai effect is absent or suppressed, misaligned planets and hot Jupiters may still be produced during the protoplanetary disc phase. © 2014 The Author Published by Oxford University Press on behalf of the Royal Astronomical Society.


Pope S.B.,Cornell University
Journal of Fluid Mechanics | Year: 2010

An alternative foundation is developed for the large-eddy simulation (LES) of turbulent flows. It is based on self-conditioned fields, for example, the mean velocity field conditional on a discrete representation of the filtered velocity field. It is shown that the self-conditioned velocity field minimizes the residual kinetic energy, and that, with the ideal model, the method yields the correct one-time behaviour as determined by the Navier-Stokes equations. The approach is extended to the self-conditioned probability density function (PDF) of compositions. Compared to LES formulations based on the filtered velocity and the filtered density function, the self-conditioned field approach has several advantages: for laminar flow, and in the direct-numerical-simulation limit, the residual fluctuations are zero or exponentially small; full account is taken of the probability distribution of turbulent fields; there are no commutation issues; and there are no issues with filtering at walls, where the self-conditioned velocity is zero. The exact evolution equations for the self-conditioned velocity and composition PDF are derived. Basic models are presented, and the development of improved models is discussed. © 2010 Cambridge University Press.


Wang Y.,Cornell University
Genome Biology and Evolution | Year: 2013

Whole-genome duplications (WGDs) have recurred in the evolution of angiosperms, resulting in many duplicated chromosomal segments. Local gene duplications are also widespread in angiosperms. WGD-derived duplicates, that is, ohnologs, and local duplicates often show contrasting patterns of gene retention and evolution. However, many genes in angiosperms underwent multiple gene duplication events, possibly by different modes, indicating that different modes of gene duplication are not mutually exclusive. In two representative angiosperm genomes, Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), we found that 9.6% and 11.3% of unique ohnologs, corresponding to 15.5% and 17.1% of ohnolog pairs, were also involved in local duplications, respectively. Locally duplicated ohnologs are widely distributed in different duplicated chromosomal segments and functionally biased. Coding sequence divergence between duplicated genes is denoted by nonsynonymous (Ka) and synonymous (Ks) substitution rates. Locally duplicated ohnolog pairs tend to have higher Ka, Ka/Ks, and gene expression divergence than nonlocally duplicated ohnolog pairs. Locally duplicated ohnologs also tend to have higher interspecies sequence divergence. These observations indicate that locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs. This study highlights the necessity to take local duplications into account when analyzing the evolutionary dynamics of ohnologs. © 2013 The Author(s).


Madsen E.L.,Cornell University
Current Opinion in Biotechnology | Year: 2011

Biogeochemistry is the discipline that strives to understand intricate processes, often microbially mediated ones, that transform and recycle both organic and inorganic substances in soils, sediments, and waters. These processes, manifestations of diverse and highly evolved cellular mechanisms catalyzed by Bacteria and Archaea, maintain the biosphere. Progress in biogeochemistry relies upon the underlying science of environmental microbiology. Over the last 2 years, important discoveries have advanced the ecological, physiological, biochemical, and genomic bases for a variety of microbiological processes including anaerobic methane oxidation, photosynthesis, phosphorous uptake, biodegradation of organic pollutants, and numerous aspects of the nitrogen and sulfur cycles. Here recent literature is assessed and placed within a five-stage paradigm for making scientific progress in environmental microbiology, biogeochemistry, and biotechnology. © 2011 Elsevier Ltd.


Meinwald J.,Cornell University
Journal of Natural Products | Year: 2011

The chemistry of naturally occurring compounds has long been pursued in the search for medicines, dyes, pesticides, flavors, and fragrances. In addition, the deeper aim of understanding life itself as a chemical phenomenon has motivated generations of scientists. One consequence of such studies has been the realization that natural products often serve central roles as biological signaling agents. We consider natural products from the viewpoint of the organisms that produce and/or respond to them and suggest how a naturally occurring compound may acquire its role in chemical communication. © 2010 The American Chemical Society and American Society of Pharmacognosy.


Wicker S.B.,Cornell University
Communications of the ACM | Year: 2012

"Our view of reality is conditioned by our position in space and time-not by our personalities as we like to think. Thus every interpretation of reality is based upon a unique position. Two paces east or west and the whole picture is changed." -Lawrence Durrell, Balthazaar10 "...to be human is to be in place'." -Tim Cresswell, Place: A Short Introduction7 On April 20, 2011, U.K. researchers Alasdair Allan and Peter Warden caused a media frenzy by announcing their discovery of an iPhone file-consolidated.dba-that contained time-stamped user-location data.4 A FAQ published by Apple3 and congressional testimony by Apple's vice president for software technology. © 2012 ACM.


Rivera E.,Cornell University | Gomez H.,Instituto Nacional Of Enfermedades Neoplasicas
Breast Cancer Research | Year: 2010

Resistance to chemotherapy is a major obstacle to the eff ective treatment of many tumor types. Although many anticancer therapies can alter tumor growth, in most cases the eff ect is not long lasting. Consequently, there is a signifi cant need for new agents with low susceptibility to common drug resistance mechanisms in order to improve response rates and potentially extend survival. Approximately 30% of the women diagnosed with early-stage disease in turn progress to metastatic breast cancer, for which therapeutic options are limited. Current recommendations for fi rst-line chemotherapy include anthracycline-based regimens and taxanes (paclitaxel and docetaxel). They typically give response rates of 30 to 70% but the responses are often not durable, with a time to progression of 6 to 10 months. Patients with progression or resistance may be administered capecitabine, gemcitabine, vinorelbine, albumin-bound paclitaxel, or ixabepilone, while other drugs are being evaluated. Response rates in this setting tend to be low (20 to 30%); the median duration of responses is <6 months and the results do not always translate into improved longterm outcomes. The present article reviews treatment options in taxane-resistant metastatic breast cancer and the role of ixabepilone in this setting. © 2010 Rivera and Gomez; licensee BioMed Central Ltd.


Ahn S.M.,Cornell University
Annals of the New York Academy of Sciences | Year: 2010

Conventional bariatric operations, including Roux-en-Y gastric bypass (RYGB), laparoscopic adjustable gastric banding, and biliopancreatic diversion (BPD) appear to be a safe and effective treatment for many severely obese patients with type 2 diabetes mellitus (T2DM). These operations improve glucose homeostasis through a variety of mechanisms, however, not only due to reduced food intake and body weight. Research to elucidate the weight-independent antidiabetic mechanisms of gastrointestinal (GI) surgery and to clarify the molecular mechanisms responsible for the benefits of GI surgery on glucose homeostasis is a compelling research objective. We review the existing knowledge regarding the clinical outcomes and of the mechanisms of GI surgery to treat T2DM. © 2011 New York Academy of Sciences.


We consider the indifference-zone (IZ) formulation of the ranking and selection problem with independent normal samples. In this problem, we must use stochastic simulation to select the best among several noisy simulated systems, with a statistical guarantee on solution quality. Existing IZ procedures sample excessively in problems with many alternatives, in part because loose bounds on probability of correct selection lead them to deliver solution quality much higher than requested. Consequently, existing IZ procedures are seldom considered practical for problems with more than a few hundred alternatives. To overcome this, we present a new sequential elimination IZ procedure, called BIZ (Bayes-inspired indifference zone), whose lower bound on worst-case probability of correct selection in the preference zone is tight in continuous time, and nearly tight in discrete time. To the author's knowledge, this is the first sequential elimination procedure with tight bounds on worst-case preference-zone probability of correct selection for more than two alternatives. Theoretical results for the discrete-time case assume that variances are known and have an integer multiple structure, but the BIZ procedure itself can be used when these assumptions are not met. In numerical experiments, the sampling effort used by BIZ is significantly smaller than that of another leading IZ procedure, the KN procedure, especially on the largest problems tested (214 D161384 alternatives).


Derry L.A.,Cornell University
Earth and Planetary Science Letters | Year: 2010

Marked negative δ 13C excursions in Ediacaran-age carbonate sediments have been identified in several sections globally, but are not recognized in all sections of similar age. The presence of δ 13C carb values as low as -12‰ has been interpreted as recording fundamentally different processes in the global carbon cycle than those recognized today. The δ 13C carb anomalies are strongly correlated with δ 18O carb values but are not represented in δ 13C org records. While no primary depositional processes have been identified that can produce the correlated δ 18O-δ 13C arrays, simulations show that fluid-rock interaction with high-pCO 2 fluids is capable of producing such arrays at geologically reasonable pCO 2 and water-rock ratios. Variations in the Mg/Ca ratio and sulfate concentration of the altering fluid determine the extent of dolomite vs. calcite and anhydrite in the resulting mineral assemblage. Incorporation of an initially aragonitic mineralogy demonstrates that high Sr, low Mn/Sr and modest alteration of 87Sr/ 86Sr in ancient carbonates are all compatible with a burial diagenesis mechanism for generation of the δ 13C anomalies, and do not necessarily imply preservation of primary values. The profound Ediacaran negative δ 13C anomalies can be adequately explained by well-understood diagenetic processes, conflated with the difficulty of correlating Precambrian sections independently of chemostratigraphy. They are not a record of primary seawater variations and need not have independent stratigraphic significance. © 2010 Elsevier B.V.


Wilks D.S.,Cornell University
Quarterly Journal of the Royal Meteorological Society | Year: 2010

Relatively little attention has been given to the effects of serial correlation of forecasts and observations on the sampling properties of forecast verification statistics. An assumption of serial independence for low-quality forecasts may be reasonable. However, forecasts of sufficient quality for autocorrelated events must themselves be autocorrelated: as quality approaches the limit of perfect forecasts, the forecasts become increasingly similar to the corresponding observations.The effects of forecast serial correlation on the sampling properties of the Brier Score (BS) and Brier Skill Score (BSS), for probability forecasts of dichotomous events, are examined here. As in other settings, the effect of serial correlation is to inflate the variances of the sampling distributions of the two statistics, so that uncorrected confidence intervals are too narrow, and uncorrected hypothesis tests yield p-values that are too small. Expressions are given for 'effective sample size' corrections for the sampling variances of both BS and BSS, in which it can be seen that the effects of serial correlation on the sampling variances increase with increasing forecast accuracy, and with decreasing climatological event probability. The sampling variance of BSS is more robust to serial correlation than that of BS. Hypothesis tests based on BSS are seen to be more powerful (i.e. more sensitive) than those based on BS, and substantially so for lower-accuracy forecasts of lower-probability events, for both serially correlated and temporally independent forecasts. © 2010 Royal Meteorological Society.


Ganzel B.L.,Cornell University | Morris P.A.,New York University
Development and Psychopathology | Year: 2011

We previously used the theory of allostasis as the foundation for a model of the current stress process. This work highlighted the core emotional systems of the brain as the central mediator of the relationship between stress and health. In this paper, we extend this theoretical approach to consider the role of developmental timing. In doing so, we note that there are strong implicit models that underlie current developmental stress research in the social and life sciences. We endeavor to illustrate these models explicitly as we review the evidence behind each one and discuss their implications. We then extend these models to reflect recent findings from research in life span human neuroscience. The result is a new set of developmental allostatic models that provide fodder for future empirical research, as well as novel perspectives on intervention. © Cambridge University Press 2011.


Moussa I.D.,Cornell University
Catheterization and Cardiovascular Interventions | Year: 2011

The current evidence-base pertaining to PCI in coronary bifurcation lesions is not adequate to inform decision making in all patients, hence a gap still exists between the evidence-base and patient-centered decision-making. Although meta-analyses of the existing RCTs improve the statistical power of the data they do not remedy the problem of trial design. The reason for the gap between "evidence" and patient-centered decision-making is that the research methodology used in the RCTs does not simulate the questions asked in practice. The purpose of this review is to make the case for a counter perspective to the narrative that provisional stenting (PS) [stenting the main vessel (MV), with additional stenting of the side branch (SB) only in the case of an unsatisfactory result] is better than elective double stenting (EDS) of both branches in all patients. Namely, that neither approach should be the default strategy in all patients with bifurcation lesions and a decision as to which technique to use should be based on the patient's bifurcation anatomy. The majority of patients with bifurcation lesions will have anatomy that can be safely treated with PS; however, some patients have "at risk" bifurcation anatomy where PS may be associated with high risk of side branch occlusion. © 2011 Wiley-Liss, Inc.


Barbash D.A.,Cornell University
Genetics | Year: 2010

Within 10 years of the beginning of experimental genetic research on Drosophila melanogaster, in 1919, A. H. Sturtevant discovered its sibling species, D. simulans. He hybridized the two species and made fundamental discoveries about the genetic basis of hybrid incompatibility. The complete sterility of surviving F1 hybrids frustrated Sturtevant and his vision of comprehensively exploring the genetics of interspecific differences. But over the next 90 years, a combination of clever genetic tricks and close observation of natural variation has led to a wealth of discovery using these and other hybrids of D. melanogaster and D. simulans, resulting in an advanced understanding of speciation and the evolution of morphology, gene regulation, and behavior. Copyright © 2010 by the Genetics Society of America.


O'Rourke T.D.,Cornell University
Geotechnique | Year: 2010

A general classification for scale in geotechnical engineering is used to explore the modelling of large, geographically distributed systems and their response to geohazards. Both component and network performance are reviewed. With respect to components, prototypescale experiments of underground pipeline response to abrupt ground deformation are described, including control of soil properties, soil-pipeline interaction, and performance of high-density polyethylene pipelines. Direct shear (DS) apparatus size is shown to have a significant effect on DS strength, and the most reliable DS device is identified from comparative tests with different equipment. Mohr-Coulomb strength parameters for partially saturated sand are developed from DS test data and applied in finite element simulations of soil-pipeline interaction that show excellent agreement with prototypescale experimental results. Apparent cohesion measured during shear failure of partially saturated sand is caused by suction-induced dilatancy. With respect to networks, the modelling of liquefaction effects on the San Francisco water supply is described, and a case history of its successful application during the Loma Prieta earthquake is presented. The systematic analysis of pipeline repair records after the Northridge earthquake is used to identify zones of potential ground failure, and correlate pipeline damage rates with strong ground motion. Hydraulic network analyses are described for the seismic performance of the Los Angeles water supply, with practical applications for emergency response. The effects of Hurricane Katrina are reviewed with respect to the New Orleans hurricane protection system, Gulf of Mexico oil and gas production, and interaction between electric power and liquid fuel delivery systems. The sustainability of the Mississippi delta is discussed with regard to flood control, maintenance of wetlands and barrier islands, and catastrophic change in the course of the Mississippi River.


Lockenhoff C.E.,Cornell University
Annals of the New York Academy of Sciences | Year: 2011

Time and time perceptions are integral to decision making because any meaningful choice is embedded in a temporal context and requires the evaluation of future preferences and outcomes. The present review examines the influence of chronological age on time perceptions and horizons and discusses implications for decision making across the life span. Time influences and interacts with decision making in multiple ways. Specifically, this review examines the following topic areas: (1) processing speed and decision time, (2) internal clocks and time estimation, (3) mental representations of future time and intertemporal choice, and (4) global time horizons. For each aspect, patterns of age differences and implications for decision strategies and quality are discussed. The conclusion proposes frameworks to integrate different lines of research and identifies promising avenues for future inquiry. © 2011 New York Academy of Sciences..


Primary cilia are displayed during the G(0)/G(1) phase of many cell types. Cilia are resorbed as cells prepare to re-enter the cell cycle, but the causal and molecular link between these two cellular events remains unclear. We show that Tctex-1 phosphorylated at Thr 94 is recruited to ciliary transition zones before S-phase entry and has a pivotal role in both ciliary disassembly and cell cycle progression. However, the role of Tctex-1 in S-phase entry is dispensable in non-ciliated cells. Exogenously adding a phospho-mimic Tctex-1(T94E) mutant accelerates cilium disassembly and S-phase entry. These results support a model in which the cilia act as a brake to prevent cell cycle progression. Mechanistic studies show the involvement of actin dynamics in Tctex-1-regulated cilium resorption. Tctex-1 phosphorylated at Thr 94 is also selectively enriched at the ciliary transition zones of cortical neural progenitors, and has a key role in controlling G(1) length, cell cycle entry and fate determination of these cells during corticogenesis. © 2011 Macmillan Publishers Limited. All rights reserved


Loew E.R.,Cornell University
Current Biology | Year: 2014

Using two UV-sensitive visual pigments and the UV-filtering properties of four mycosporine-like amino acids, mantis shrimp create six spectrally distinct UV receptors. This is yet another example of the unique ways in which mantis shrimp have adapted to extract information from their visual world. © 2014 Elsevier Ltd.


Stover P.J.,Cornell University
Current Opinion in Clinical Nutrition and Metabolic Care | Year: 2010

PURPOSE OF REVIEW: To review the prevalence, causes and functional significance of vitamin B12 deficiency in vulnerable subpopulations including older adults and the developing embryo. RECENT FINDINGS: It is becoming increasingly recognized that the susceptibility to vitamin B12 deficiency may change throughout the life cycle, with the developing embryo and older adults exhibiting elevated risk. Recent data implicate low vitamin B12 status as a risk factor for birth defects resulting from improper neural tube development. The potential for vitamin supplementation and/or food fortification to ameliorate the risk of deficiency in these subpopulations is discussed. SUMMARY: The prevalence and impact of vitamin B12 deficiency varies throughout the life cycle, with older adults and potentially the developing embryo having the greatest risk and susceptibility. Additional research is needed to develop effective public health interventions that address the unique causes of this nutritional deficiency, which differ among at-risk subpopulations. © 2010 Wolters Kluwer Health | Lippincott Williams & Wilkins.


Mueller E.J.,Cornell University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

We calculate the single-particle spectral density of a normal (nonsuperfluid) two-component gas of fermions in the BCS-BEC crossover within a T-matrix approximation. We review how noncondensed pairs lead to a spectral density reminiscent of the ordered state, and explore how a gaplike feature in the spectrum evolves as one changes the polarization of the gas. As the gas is polarized, we find that this pseudogap becomes more diffuse and moves away from the Fermi level, reflecting the fact that fewer pairs are present but that they still play an important role in the excitations. © 2011 American Physical Society.


The unipolar induction DC circuit model, originally developed by Goldreich and Lynden-Bell for the Jupiter-Io system, has been applied to different types of binary systems in recent years. We show that there exists an upper limit to the magnetic interaction torque and energy dissipation rate in such a model. This arises because when the resistance of the circuit is too small, the large current flow severely twists the magnetic flux tube connecting the two binary components, leading to the breakdown of the circuit. Applying this limit, we find that in coalescing neutron star binaries, magnetic interactions produce negligible correction to the phase evolution of the gravitational waveform, even for magnetar-like field strengths. However, energy dissipation in the binary magnetosphere may still give rise to electromagnetic radiation prior to the final merger. For ultracompact white dwarf binaries, we find that unipolar induction does not provide adequate energy dissipation to explain the observed X-ray luminosities of several sources. For exoplanetary systems containing close-in Jupiters or super-Earths, the magnetic torque and energy dissipation induced by the orbital motion are negligible, except possibly during the early T Tauri phase, when the stellar magnetic field is stronger than 103 G. © 2012 The American Astronomical Society. All rights reserved.


BACKGROUND: The interaction of plants with endophytic symbiotic fungi in the genus Trichoderma alters the plant proteome and transcriptome and results in enhanced plant growth and resistance to diseases. In a previous study, we identified the numerous chitinolytic enzyme families and individual enzymes in maize which are implicated in plant disease resistance and other plant responses. RESULTS: We examined the differential expression of the entire suite of chitinolytic enzymes in maize plants in the presence and absence of T. harzianum. Expression of these enzymes revealed a band of chitinolytic enzyme activity that had greater mass than any known chitinase. This study reports the characterization of this large protein. It was found to be a heretofore undiscovered heterodimer between an exo- and an endo-enzyme, and the endo portion differed between plants colonized with T. harzianum and those grown in its absence and between shoots and roots. The heterodimeric enzymes from shoots in the presence and absence of T. harzianum were purified and characterized. The dimeric enzyme from Trichoderma-inoculated plants had higher specific activity and greater ability to inhibit fungal growth than those from control plants. The activity of specific chitinolytic enzymes was higher in plants grown from Trichoderma treated seeds than in control plants. CONCLUSIONS: This is the first report of a dimer between endo- and exochitinase. The endochitinase component of the dimer changed post Trichoderma inoculation. The dimer originating from Trichoderma inoculated plants had a higher antifungal activity than the comparable enzyme from control plants.


Douglas A.E.,Cornell University
Current Opinion in Insect Science | Year: 2014

Genome research is transforming our understanding of nutrient exchange between insects and intracellular bacteria. A key characteristic of these bacteria is their small genome size and gene content. Their fastidious and inflexible nutritional requirements are met by multiple metabolites from the insect host cell. Although the bacteria have generally retained genes coding the synthesis of nutrients required by the insect, some apparently critical genes have been lost, and compensated for by shared metabolic pathways with the insect host or supplementary bacteria with complementary metabolic capabilities. © 2014 Elsevier Inc. All rights reserved.


Fox T.D.,Cornell University
Genetics | Year: 2012

The mitochondrion is arguably the most complex organelle in the budding yeast cell cytoplasm. It is essential for viability as well as respiratory growth. Its innermost aqueous compartment, the matrix, is bounded by the highly structured inner membrane, which in turn is bounded by the intermembrane space and the outer membrane. Approximately 1000 proteins are present in these organelles, of which eight major constituents are coded and synthesized in the matrix. The import of mitochondrial proteins synthesized in the cytoplasm, and their direction to the correct soluble compartments, correct membranes, and correct membrane surfaces/topologies, involves multiple pathways and macromolecular machines. The targeting of some, but not all, cytoplasmically synthesized mitochondrial proteins begins with translation of messenger RNAs localized to the organelle. Most proteins then pass through the translocase of the outer membrane to the intermembrane space, where divergent pathways sort them to the outer membrane, inner membrane, and matrix or trap them in the intermembrane space. Roughly 25% of mitochondrial proteins participate in maintenance or expression of the organellar genome at the inner surface of the inner membrane, providing 7 membrane proteins whose synthesis nucleates the assembly of three respiratory complexes. © 2012 by the Genetics Society of America.


Benitez J.J.,Cornell University
Methods in enzymology | Year: 2010

Protein-protein interactions are fundamental biological processes. While strong protein interactions are amenable to many characterization techniques including crystallography, weak protein interactions are challenging to study because of their dynamic nature. Single-molecule fluorescence resonance energy transfer (smFRET) can monitor dynamic protein interactions in real time, but are generally limited to strong interacting pairs because of the low concentrations needed for single-molecule detection. Here, we describe a nanovesicle trapping approach to enable smFRET study of weak protein interactions at high effective concentrations. We describe the experimental procedures, summarize the application in studying the weak interactions between intracellular copper transporters, and detail the single-molecule kinetic analysis of bimolecular interactions involving three states. Both the experimental approach and the theoretical analysis are generally applicable to studying many other biological processes at the single-molecule level. Copyright 2010 Elsevier Inc. All rights reserved.


Pass R.,Cornell University
Proceedings of the Annual ACM Symposium on Theory of Computing | Year: 2011

We show that the security of some well-known cryptographic protocols, primitives and assumptions (e.g., the Schnorr identification scheme, commitments secure under adaptive selective-decommitment, the 'one-more' discrete logarithm assumption) cannot be based on any standard assumption using a Turing (i.e., black-box) reduction. These results follow from a general result showing that Turing reductions cannot be used to prove security of constant-round sequentially witness-hiding special-sound protocols for unique witness relations, based on standard assumptions; we emphasize that this result holds even if the protocol makes non-black-box use of the underlying assumption. © 2011 ACM.


Uhlmann E.L.,Organisational Behaviour Area | Pizarro D.A.,Cornell University | Diermeier D.,Northwestern University
Perspectives on Psychological Science | Year: 2015

Both normative theories of ethics in philosophy and contemporary models of moral judgment in psychology have focused almost exclusively on the permissibility of acts, in particular whether acts should be judged on the basis of their material outcomes (consequentialist ethics) or on the basis of rules, duties, and obligations (deontological ethics). However, a longstanding third perspective on morality, virtue ethics, may offer a richer descriptive account of a wide range of lay moral judgments. Building on this ethical tradition, we offer a person-centered account of moral judgment, which focuses on individuals as the unit of analysis for moral evaluations rather than on acts. Because social perceivers are fundamentally motivated to acquire information about the moral character of others, features of an act that seem most informative of character often hold more weight than either the consequences of the act or whether a moral rule has been broken. This approach, we argue, can account for numerous empirical findings that are either not predicted by current theories of moral psychology or are simply categorized as biases or irrational quirks in the way individuals make moral judgments. © The Author(s) 2014.


Skou S.,Copenhagen University | Gillilan R.E.,Cornell University | Ando N.,Massachusetts Institute of Technology
Nature Protocols | Year: 2014

With recent advances in data analysis algorithms, X-ray detectors and synchrotron sources, small-angle X-ray scattering (SAXS) has become much more accessible to the structural biology community. Although limited to ∼10 Å resolution, SAXS can provide a wealth of structural information on biomolecules in solution and is compatible with a wide range of experimental conditions. SAXS is thus an attractive alternative when crystallography is not possible. Moreover, advanced use of SAXS can provide unique insight into biomolecular behavior that can only be observed in solution, such as large conformational changes and transient protein-protein interactions. Unlike crystal diffraction data, however, solution scattering data are subtle in appearance, highly sensitive to sample quality and experimental errors and easily misinterpreted. In addition, synchrotron beamlines that are dedicated to SAXS are often unfamiliar to the nonspecialist. Here we present a series of procedures that can be used for SAXS data collection and basic cross-checks designed to detect and avoid aggregation, concentration effects, radiation damage, buffer mismatch and other common problems. Human serum albumin (HSA) serves as a convenient and easily replicated example of just how subtle these problems can sometimes be, but also of how proper technique can yield pristine data even in problematic cases. Because typical data collection times at a synchrotron are only one to several days, we recommend that the sample purity, homogeneity and solubility be extensively optimized before the experiment. © 2014 Nature America, Inc. All rights reserved.


Derry L.A.,Cornell University
Earth and Planetary Science Letters | Year: 2010

A graphical analysis of the correlations between δc and εTOC was introduced by Rothman et al. (2003) to obtain estimates of the carbon isotopic composition of inputs to the oceans and the organic carbon burial fraction. Applied to Cenozoic data, the method agrees with independent estimates, but with Neoproterozoic data the method yields results that cannot be accommodated with standard models of sedimentary carbon isotope mass balance. We explore the sensitivity of the graphical correlation method and find that the variance ratio between δc and δo is an important control on the correlation of δc and ε. If the variance ratio σc/σo≥1 highly correlated arrays very similar to those obtained from the data are produced from independent random variables. The Neoproterozoic data shows such variance patterns, and the regression parameters for the Neoproterozoic data are statistically indistinguishable from the randomized model at the 95% confidence interval. The projection of the data into δc-ε space cannot distinguish between signal and noise, such as post-depositional alteration, under these circumstances. There appears to be no need to invoke unusual carbon cycle dynamics to explain the Neoproterozoic δc-ε array. The Cenozoic data have σc/σo<1 and the δc vs. ε correlation is probably geologically significant, but the analyzed sample size is too small to yield statistically significant results. © 2010 Elsevier B.V.


Adler P.B.,Utah State University | Ellner S.P.,Cornell University | Levine J.M.,University of California at Santa Barbara
Ecology Letters | Year: 2010

Despite decades of research documenting niche differences between species, we lack a quantitative understanding of their effect on coexistence in natural communities. We perturbed an empirical sagebrush steppe community model to remove the demographic effect of niche differences and quantify their impact on coexistence. With stabilizing mechanisms operating, all species showed positive growth rates when rare, generating stable coexistence. Fluctuation-independent mechanisms contributed more than temporal variability to coexistence and operated more strongly on recruitment than growth or survival. As expected, removal of stabilizing niche differences led to extinction of all inferior competitors. However, complete exclusion required 300-400 years, indicating small fitness differences among species. Our results show an 'excess' of niche differences: stabilizing mechanisms were not only strong enough to maintain diversity but were much stronger than necessary given the small fitness differences. The diversity of this community cannot be understood without consideration of niche differences. © 2010 Blackwell Publishing Ltd/CNRS.


Douglas A.E.,Cornell University
Cold Spring Harbor Perspectives in Biology | Year: 2014

Eukaryotes have evolved and diversified in the context of persistent colonization by nonpathogenic microorganisms. Various resident microorganisms provide a metabolic capability absent from the host, resulting in increased ecological amplitude and often evolutionary diversification of the host. Some microorganisms confer primary metabolic pathways, such as photosynthesis and cellulose degradation, and others expand the repertoire of secondary metabolism, including the synthesis of toxins that confer protection against natural enemies. A further route by which microorganisms affect host fitness arises from their modulation of the eukaryotic-signaling networks that regulate growth, development, behavior, and other functions. These effects are not necessarily based on interactions beneficial to the host, but can be a consequence of either eukaryotic utilization of microbial products as cues or host- microbial conflict. By these routes, eukaryote-microbial interactions play an integral role in the function and evolutionary diversification of eukaryotes. © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.


Contraceptive choice in patients with systemic lupus erythematosus (SLE) and antiphospholipid syndrome (APS) is challenging but important. Long-acting forms of contraception such as the progesterone intrauterine device (IUD) or subdermal implant are preferable for most patients. Estrogen-containing hormonal contraceptives may be used in stable, inactive SLE patients but are contraindicated in patients with positive antiphospholipid antibodies (aPL). The levonorgestrel IUD is a good alternative for many APS patients and often decreases menstrual blood loss. It is prudent to avoid depot medroxyprogesterone acetate (DMPA) in corticosteroid-treated or other patients at risk for osteoporosis because of the inhibition of ovulation. Effective and safe contraception in patients with SLE and APS permits planning for pregnancy during inactive disease and while on pregnancy-compatible medications, preventing a poorly timed pregnancy that may jeopardize maternal and/or fetal health. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.


Cornwell E.Y.,Cornell University | Waite L.J.,University of Chicago
Journal of Health and Social Behavior | Year: 2012

Hypertension is one of the most prevalent chronic diseases among older adults, but rates of blood pressure control are low. In this article, we explore the role of social network ties and network-based resources (e.g., information and support) in hypertension diagnosis and management. We use data from the National Social Life, Health, and Aging Project to identify older adults with undiagnosed or uncontrolled hypertension. We find that network characteristics and emotional support are associated with hypertension diagnosis and control. Importantly, the risks of undiagnosed and uncontrolled hypertension are lower among those with larger social networks-if they discuss health issues with their network members. When these lines of communication are closed, network size is associated with greater risk for undiagnosed and uncontrolled hypertension. Health care utilization partially mediates associations with diagnosis, but the benefits of network resources for hypertension control do not seem to stem from health-related behaviors. © American Sociological Association 2012.


Casey B.J.,Cornell University
Annual Review of Psychology | Year: 2015

Adolescence is the transition from childhood to adulthood that begins around the onset of puberty and ends with relative independence from the parent. This developmental period is one when an individual is probably stronger, of higher reasoning capacity, and more resistant to disease than ever before, yet when mortality rates increase by 200. These untimely deaths are not due to disease but to preventable deaths associated with adolescents putting themselves in harm's way (e.g., accidental fatalities). We present evidence that these alarming health statistics are in part due to diminished self-control-the ability to inhibit inappropriate desires, emotions, and actions in favor of appropriate ones. Findings of adolescent-specific changes in self-control and underlying brain circuitry are considered in terms of how evolutionarily based biological constraints and experiences shape the brain to adapt to the unique intellectual, physical, sexual, and social challenges of adolescence. © 2015 by Annual Reviews. All rights reserved.


Tamayo D.,Cornell University
Monthly Notices of the Royal Astronomical Society | Year: 2014

Fomalhaut b is currently the least massive, directly imaged exoplanet candidate. New observation epochs have revealed this object to be moving on a highly eccentric orbit, which sets important new constraints. I consider scenarios where Fomalhaut b is the only object interacting with the debris disc, and ones involving an additional unseen planet. I also investigate the possibility that Fomalhaut b is merely a transient dust cloud in light of the revised eccentric orbit. I argue that the scenario best able to match the observational constraints is a super-Earth Fomalhaut b surrounded by a vast cloud of dust that is generated by a population of irregular satellites, with an undetected ∼Saturn-mass planet orbiting interior to the disc and driving the secular dynamics. Testable predictions are summarized that could differentiate between this scenario and other possibilities. © 2014 The Author Published by Oxford University Press on behalf of the Royal Astronomical Society.


Russo P.,Cornell University
Nature Reviews Urology | Year: 2013

In the past decade, the medical and oncological rationale for kidney-sparing surgical approaches for small renal masses has been clarified. Although radical nephrectomy is still necessary for many patients diagnosed with large renal tumours, accumulating evidence indicates that partial nephrectomy provides equivalent oncological outcomes while also preserving renal function and preventing the adverse cardiovascular effects of chronic kidney disease. Furthermore, approximately 45% of resected small renal tumours are benign or indolent, with limited - if any - metastatic potential. Patients who develop kidney cancer often have medical comorbidities that can affect kidney function, such as diabetes and hypertension, and histological examination of the non-tumour-bearing elements of the kidney demonstrate significant pathological changes in the vast majority of patients. For elderly patients or patients with comorbidities, active surveillance provides an alternative kidney-sparing approach, and is associated with extremely low rates of clinical disease progression and metastases. Despite these important advances in understanding, which support the use of partial nephrectomy for the treatment of small renal masses, the technique remains underused. © 2013 Macmillan Publishers Limited. All rights reserved.


Goldstein O.,Cornell University
Investigative ophthalmology & visual science | Year: 2013

To identify the causative mutations in two early-onset canine retinal degenerations, crd1 and crd2, segregating in the American Staffordshire terrier and the Pit Bull Terrier breeds, respectively. Retinal morphology of crd1- and crd2-affected dogs was evaluated by light microscopy. DNA was extracted from affected and related unaffected controls. Association analysis was undertaken using the Illumina Canine SNP array and PLINK (crd1 study), or the Affymetrix Version 2 Canine array, the "MAGIC" genotype algorithm, and Fisher's Exact test for association (crd2 study). Positional candidate genes were evaluated for each disease. Structural photoreceptor abnormalities were observed in crd1-affected dogs as young as 11-weeks old. Rod and cone inner segment (IS) and outer segments (OS) were abnormal in size, shape, and number. In crd2-affected dogs, rod and cone IS and OS were abnormal as early as 3 weeks of age, progressing with age to severe loss of the OS, and thinning of the outer nuclear layer (ONL) by 12 weeks of age. Genome-wide association study (GWAS) identified association at the telomeric end of CFA3 in crd1-affected dogs and on CFA33 in crd2-affected dogs. Candidate gene evaluation identified a three bases deletion in exon 21 of PDE6B in crd1-affected dogs, and a cytosine insertion in exon 10 of IQCB1 in crd2-affected dogs. Identification of the mutations responsible for these two early-onset retinal degenerations provides new large animal models for comparative disease studies and evaluation of potential therapeutic approaches for the homologous human diseases.


Cawley J.,Cornell University
Health Affairs | Year: 2010

In the past few decades, obesity rates among American children have skyrocketed. Although many factors have played a part in this unhealthy increase, this paper focuses on how economic policies may be contributing to our children's growing girth and how these policies might be altered to reverse this trend. It examines the economic causes and consequences of obesity, the rationales for government intervention, the cost-effectiveness of various policies, and the need for more research funding. © 2010 Project HOPE-The People-to-People Health Foundation, Inc.


Martinez-Millan M.,Cornell University
Botanical Review | Year: 2010

The Asteridae is a group of some 80,000 species of flowering plants characterized by their fused corollas and iridoid compounds. Recent phylogenetic analyses have helped delimit the group and have identified four main clades within it; Cornales, Ericales, Lamiids and Campanulids, with the last two collectively known as the Euasteridae. A search for the oldest fossils representing asterids yielded a total of 261 records. Each of these fossils was evaluated as to the reliability of its identification. The oldest accepted fossils for each clade were used to estimate minimum ages for the whole of the Asteridae. The results suggest that the Asteridae dates back to at least the Turonian, Late Cretaceous (89. 3 mya) and that by the Late Santonian-Early Campanian (83.5 mya) its four main clades were already represented in the fossil record. © The New York Botanical Garden 2010.


Schuldt J.P.,Cornell University
Health Communication | Year: 2013

The food industry has recently implemented numerous front-of-package nutrition labels to readily convey key aspects a food product's nutritional profile to consumers (e.g., calories and fat content). Although seemingly well-intentioned, such labels might lead consumers to perceive relatively poor nutrition foods in a healthier light. The present research explores whether one underresearched aspect of nutrition labels-namely, their color-might influence perceptions of a product's healthfulness. In Study 1, participants perceived a candy bar as healthier when it bore a green rather than a red calorie label, despite the fact that the labels conveyed the same calorie content. Study 2 examined the perceived healthfulness of a candy bar bearing a green versus white calorie label and assessed individual differences in the importance of healthy eating. Overall, results suggest that green labels increase perceived healthfulness, especially among consumers who place high importance on healthy eating. Discussion focuses on implications for health-related judgment and nutrition labeling. © 2013 Copyright Taylor & Francis Group, LLC.


Klasse P.J.,Cornell University
Progress in Molecular Biology and Translational Science | Year: 2015

The ratio of virus particles to infectious units is a classic measurement in virology and ranges widely from several million to below 10 for different viruses. Much evidence suggests a distinction be made between infectious and infecting particles or virions: out of many potentially infectious virions, few infect under regular experimental conditions, largely because of diffusion barriers. Still, some virions are inert from the start; others become defective through decay. And with increasing cell- and molecular-biological knowledge of each step in the replicative cycle for different viruses, it emerges that many processes entail considerable losses of potential viral infectivity. Furthermore, all-or-nothing assumptions about virion infectivity are flawed and should be replaced by descriptions that allow for spectra of infectious propensities. A more realistic understanding of the infectivity of individual virions has both practical and theoretical implications for virus neutralization, vaccine research, antiviral therapy, and the use of viral vectors. © 2015 Elsevier Inc. All rights reserved.


Fortier L.A.,Cornell University
The journal of knee surgery | Year: 2012

Microfracture of subchondral bone to enhance cartilage repair is a popular surgical technique used in human and animal patients. Clinical results with resolution or improvement in pain are promising and last on average for 2 to 3 years. Animal studies aimed at understanding microfracture indicate that the repair tissue continues to remodel toward chondrogenesis for at least a year, but longer term results are not available to gain insight into the mechanism of microfracture function or failure over time. Subchondral bone sclerosis and central lesional osteophyte formation following subchondral bone microfracture have been observed in animal models of microfracture, but studies do not provide any insight into the etiology of these pathologies. The continued maturation of microfracture repair tissue over time supports further investigation of microfracture or microfracture-augmented cartilage repair procedures with caution for the investigator and clinician to be observant for conditions that lead to subchondral bone sclerosis or central osteophyte formation, and what affect these boney reactions have on clinical outcome.


Forsyth A.,Cornell University
Journal of physical activity & health | Year: 2012

The Pedestrian and Bicycling Survey (PABS) is a questionnaire designed to be economical and straightforward to administer so that it can be used by local governments interested in measuring the amount and purposes of walking and cycling in their communities. In addition, it captures key sociodemographic characteristics of those participating in these activities. In 2009 and 2010 results from the 4-page mail-out/mail-back PABS were tested for reliability across 2 administrations (test-retest reliability). Two versions--early and refined--were tested separately with 2 independent groups of university students from 4 universities (N = 100 in group 1; N = 87 in group 2). Administrations were 7 to 9 days apart. Almost all survey questions achieved adequate to excellent reliability. Transportation surveys have not typically been tested for reliability making the PABS questionnaire an important new option for improving information collection about travel behavior, particularly walking and cycling.


Miao M.-S.,Beijing Computational Science Research Center | Miao M.-S.,University of California at Santa Barbara | Hoffmann R.,Cornell University
Accounts of Chemical Research | Year: 2014

ConspectusElectrides, in which electrons occupy interstitial regions in the crystal and behave as anions, appear as new phases for many elements (and compounds) under high pressure. We propose a unified theory of high pressure electrides (HPEs) by treating electrons in the interstitial sites as filling the quantized orbitals of the interstitial space enclosed by the surrounding atom cores, generating what we call an interstitial quasi-atom, ISQ.With increasing pressure, the energies of the valence orbitals of atoms increase more significantly than the ISQ levels, due to repulsion, exclusion by the atom cores, effectively giving the valence electrons less room in which to move. At a high enough pressure, which depends on the element and its orbitals, the frontier atomic electron may become higher in energy than the ISQ, resulting in electron transfer to the interstitial space and the formation of an HPE.By using a He lattice model to compress (with minimal orbital interaction at moderate pressures between the surrounding He and the contained atoms or molecules) atoms and an interstitial space, we are able to semiquantitatively explain and predict the propensity of various elements to form HPEs. The slopes in energy of various orbitals with pressure (s > p > d) are essential for identifying trends across the entire Periodic Table. We predict that the elements forming HPEs under 500 GPa will be Li, Na (both already known to do so), Al, and, near the high end of this pressure range, Mg, Si, Tl, In, and Pb. Ferromagnetic electrides for the heavier alkali metals, suggested by Pickard and Needs, potentially compete with transformation to d-group metals. © 2014 American Chemical Society.


Gibofsky A.,Cornell University
The American journal of managed care | Year: 2012

Rheumatoid arthritis (RA) is a common autoimmune systemic inflammatory disease affecting approximately 1% of the worldwide population. The interaction of genetic and environmental factors results in a cascade of immune reactions, which ultimately lead to the development of synovitis, joint damage, and structural bone damage. These, in turn, lead to pain, disability, and emotional, social, and economic challenges. A number of extraarticular manifestations and comorbidities are present in patients with RA, which result in increased mortality. The American College of Rheumatology and European League Against Rheumatism recently published updated disease classification criteria in an effort to identify RA earlier so that effective treatment can be employed to prevent irreversible changes.


Pope S.B.,Cornell University
Proceedings of the Combustion Institute | Year: 2013

A major goal of combustion research is to develop accurate, tractable, predictive models for the phenomena occurring in combustion devices, which predominantly involve turbulent flows. With the focus on gasphase, non-premixed flames, recent progress is reviewed, and the significant remaining challenges facing models of turbulent combustion are examined. The principal challenges are posed by the small scales, the many chemical species involved in hydrocarbon combustion, and the coupled processes of reaction and molecular diffusion in a turbulent flow field. These challenges, and how different modeling approaches face them, are examined from the viewpoint of low-dimensional manifolds in the high-dimensional space of chemical species. Most current approaches to modeling turbulent combustion can be categorized as flamelet-like or PDF-like. The former assume or imply that the compositions occurring in turbulent combustion lie on very-low-dimensional manifolds, and that the coupling between turbulent mixing and reaction can be parameterized by at most one or two variables. PDF-like models do not restrict compositions in this way, and they have proved successful in describing more challenging combustion regimes in which there is significant local extinction, or in which the turbulence significantly disrupts flamelet structures. Advances in diagnostics, the design of experiments, computational resources, and direct numerical simulations are all contributing to the continuing development of more accurate and general models of turbulent combustion. © 2012 The Combustion Institute. Published by Elsevier Inc. All rights reserved.


Ugine T.A.,Cornell University
Journal of invertebrate pathology | Year: 2013

Experiments were conducted with the fungal entomopathogen Metarhizium brunneum to determine the feasibility of using agar-based fungal bands versus two new types of oil-formulated fungal bands for Asian longhorned beetle management. We investigated conidial retention and survival on three types of bands attached to trees in New York and Pennsylvania: standard polyester fiber agar-based bands containing fungal cultures, and two types of bands made by soaking either polyester fiber or jute burlap with oil-conidia suspensions. Fungal band formulation did not affect the number or viability of conidia on bands over the 2-month test period, although percentage conidial viability decreased significantly with time for all band types. In a laboratory experiment testing the effect of the three band formulations on conidial acquisition and beetle survival, traditional agar-based fungal bands delivered the most conidia to adult beetles and killed higher percentages of beetles significantly faster (median survival time of 27d) than the two oil-formulated materials (36-37d). We also tested the effect of band formulation on conidial acquisition by adult beetles kept individually in cages with a single band for 24h, and significantly more conidia (3-7times) were acquired by beetles from agar-based bands compared to the two oil formulations. Copyright © 2013 Elsevier Inc. All rights reserved.


Fungal bands can deliver lethal conidial doses to adult Asian longhorned beetles. Because higher doses result in shorter survival times, developing a method to deliver more conidia to beetles walking across the fungal bands is desirable. We compared fungal bands made using standard flat material to bands made using a shaggy, textured material. The median survival time of adult beetles exposed to shaggy bands was reduced to 10 d versus 18 d for beetles exposed to flat bands. Beetles climbing across shaggy bands acquired 1.83×10(6) conidia per beetle, which was 14.6 times greater than beetles exposed to flat bands. Copyright © 2013. Published by Elsevier Inc.


Kok J.F.,U.S. National Center for Atmospheric Research | Kok J.F.,Cornell University
Atmospheric Chemistry and Physics | Year: 2011

The size distribution of mineral dust aerosols partially determines their interactions with clouds, radiation, ecosystems, and other components of the Earth system. Several theoretical models predict that the dust size distribution depends on the wind speed at emission, with larger wind speeds predicted to produce smaller aerosols. The present study investigates this prediction using a compilation of published measurements of the size-resolved vertical dust flux emitted by eroding soils. Surprisingly, these measurements indicate that the size distribution of naturally emitted dust aerosols is independent of the wind speed. The recently formulated brittle fragmentation theory of dust emission is consistent with this finding, whereas other theoretical models are not. The independence of the emitted dust size distribution with wind speed simplifies both the interpretation of geological records of dust deposition and the parameterization of dust emission in atmospheric circulation models. © 2011 Author(s).


This article tells the story of two indigenous, drought-tolerant grains, finger millet and sorghum, once grown in northern Malawi. Sorghum essentially disappeared from the landscape, replaced by maize. Finger millet persisted, despite being discouraged by colonial and postcolonial governments, but is now in decline. This case study of these two crops in northern Malawi uses data from in-depth interviews, focus groups, archival documents, and observations. I suggest that sorghum almost disappeared due to a combination of maize promotion, male migration, and pest problems. An upsurge of tobacco production, in part due to neoliberal policies, combined with gender dynamics that favor maize are reducing finger millet production. Drawing on theories of feminist political ecology, resilience, and indigenous knowledge, I argue that agrobiodiversity and related indigenous knowledge are situated in material and gendered practices. Efforts to improve social resilience in these vulnerable regions need to pay attention to processes and the intersectionality of gender, class, and other subjectivities at different scales that produce particular agricultural practices and knowledge in a given place. © 2014 © 2014 by Association of American Geographers.


Russell D.G.,Cornell University
Cell Host and Microbe | Year: 2011

Evolving under constant threat from invading microbes, macrophages have acquired multiple means of killing bacteria. In this issue of Cell Host & Microbe, Botella and colleagues (Botella et al., 2011) describe a novel antimicrobial mechanism based on elevated levels of intraphagosomal Zn 2+ and the corresponding induction of bacterial genes to ameliorate this host-derived stress. © 2011 Elsevier Inc.


Ginzburg Y.,New York Blood Center | Rivella S.,Cornell University
Blood | Year: 2011

β-thalassemia is a disease characterized by anemia and is associated with ineffective erythropoiesis and iron dysregulation resulting in iron overload. The peptide hormone hepcidin regulates iron metabolism, and insufficient hepcidin synthesis is responsible for iron overload in minimally transfused patients with this disease. Understanding the crosstalk between erythropoiesis and iron metabolism is an area of active investigation in which patients with and models of β-thalassemia have provided significant insight. The dependence of erythropoiesis on iron presupposes that iron demand for hemoglobin synthesis is involved in the regulation of iron metabolism. Major advances have been made in understanding iron availability for erythropoiesis and its dysregulation in β-thalassemia. In this review, we describe the clinical characteristics and current therapeutic standard in β-thalassemia, explore the definition of ineffective erythropoiesis, and discuss its role in hepcidin regulation. In preclinical experiments using interventions such as transferrin, hepcidin agonists, and JAK2 inhibitors, we provide evidence of potential new treatment alternatives that elucidate mechanisms by which expanded or ineffective erythropoiesis may regulate iron supply, distribution, and utilization in diseasessuch as β-thalassemia. © 2011 by The American Society of Hematology.


Genetic lesions such as BCR-ABL1, E2A-PBX1, and MLL rearrangements (MLLr) are associated with unfavorable outcomes in adult B-cell precursor acute lymphoblastic leukemia (B-ALL). Leukemia oncoproteins may directly or indirectly disrupt cytosine methylation patterning to mediate the malignant phenotype. We postulated that DNA methylation signatures in these aggressive B-ALLs would point toward disease mechanisms and useful biomarkers and therapeutic targets. We therefore conducted DNA methylation and gene expression profiling on a cohort of 215 adult patients with B-ALL enrolled in a single phase III clinical trial (ECOG E2993) and normal control B cells. In BCR-ABL1-positive B-ALLs, aberrant cytosine methylation patterning centered around a cytokine network defined by hypomethylation and overexpression of IL2RA(CD25). The E2993 trial clinical data showed that CD25 expression was strongly associated with a poor outcome in patients with ALL regardless of BCR-ABL1 status, suggesting CD25 as a novel prognostic biomarker for risk stratification in B-ALLs. In E2A-PBX1-positive B-ALLs, aberrant DNA methylation patterning was strongly associated with direct fusion protein binding as shown by the E2A-PBX1 chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq), suggesting that E2A-PBX1 fusion protein directly remodels the epigenome to impose an aggressive B-ALL phenotype. MLLr B-ALL featured prominent cytosine hypomethylation, which was linked with MLL fusion protein binding, H3K79 dimethylation, and transcriptional upregulation, affecting a set of known and newly identified MLL fusion direct targets with oncogenic activity such as FLT3 and BCL6. Notably, BCL6 blockade or loss of function suppressed proliferation and survival of MLLr leukemia cells, suggesting BCL6-targeted therapy as a new therapeutic strategy for MLLr B-ALLs. We conducted the first integrative epigenomic study in adult B-ALLs, as a correlative study to the ECOG E2993 phase III clinical trial. This study links for the first time the direct actions of oncogenic fusion proteins with disruption of epigenetic regulation mediated by cytosine methylation. We identify a novel clinically actionable biomarker in B-ALLs: IL2RA (CD25), which is linked with BCR-ABL1 and an inflammatory signaling network associated with chemotherapy resistance. We show that BCL6 is a novel MLL fusion protein target that is required to maintain the proliferation and survival of primary human adult MLLr cells and provide the basis for a clinical trial with BCL6 inhibitors for patients with MLLr. ©2012 AACR.


White W.M.,Cornell University
Annual Review of Earth and Planetary Sciences | Year: 2010

Mantle plumes-which are usually, but not always, chemically distinct from the mid-ocean ridge basalt (MORB)-may be rooted in the core-mantle boundary and begin with large voluminous heads triggering massive eruptions or be headless and arise in the mid-mantle. Geochemistry provides convincing evidence that mantle plumes are 100-300°C hotter than normal upper mantle and that upwelling rates within the melting region are faster than beneath mid-ocean ridges. 186Os/188Os hints at the possibility of material from Earth's core in the Hawaiian plume, but this is not seen in other oceanic island basalt (OIB) and has not been confirmed by 182W184W measurements. High 3He4He in plumes does not require a primordial deep-mantle reservoir. The geochemical signature of mantle plumes originates primarily through melting in the upper mantle, probably through creation and subduction of oceanic lithosphere, but the details remain obscure. Plumes are lithologically heterogeneous, consisting of stringers of mafic material embedded in a more dominant peridotite. Copyright © 2010 by Annual Reviews. All rights reserved.


Magnetic tunnel junctions with high-tunneling magnetoresistance values such as Fe|MgO|Fe capitalize on spin filtering in the oxide region based on the band symmetry of incident electrons. However, these structures rely on magnetic leads and oxide regions of the same cubic symmetry class. A new magnetic tunnel junction (FeCo|Mg3B2O6|FeCo) is presented that uses a reduced symmetry oxide region (orthorhombic) to provide spin filtering between the two cubic magnetic leads. Complex band structure analysis of Mg 3B2O6 based on density functional calculations shows that significant spin filtering could occur in this system. This new type of magnetic tunnel junction may have been fabricated already and can explain recent experimental studies of rf-sputtered FeCoB| MgO | FeCoB junctions where there is significant B diffusion into the MgO region. © 2010 American Chemical Society.


Rohlfs M.,University of Gottingen | Churchill A.C.L.,Cornell University
Fungal Genetics and Biology | Year: 2011

Fungi share a diverse co-evolutionary history with animals, especially arthropods. In this review, we focus on the role of secondary metabolism in driving antagonistic arthropod-fungus interactions, i.e., where fungi serve as a food source to fungal grazers, compete with saprophagous insects, and attack insects as hosts for growth and reproduction. Although a wealth of studies on animal-fungus interactions point to a crucial role of secondary metabolites in deterring animal feeding and resisting immune defense strategies, causal evidence often remains to be provided. Moreover, it still remains an unresolved puzzle as to what extent the tight regulatory control of secondary metabolite formation in some model fungi represents an evolved chemical defense system favored by selective pressure through animal antagonists. Given these gaps in knowledge, we highlight some co-evolutionary aspects of secondary metabolism, such as induced response, volatile signaling, and experimental evolution, which may help in deciphering the ecological importance and evolutionary history of secondary metabolite production in fungi. © 2010 Elsevier Inc.


Wilks D.S.,Cornell University
Monthly Weather Review | Year: 2011

Ensemble consistency is a name for the condition that an observation being forecast by a dynamical ensemble is statistically indistinguishable from the ensemble members. This statistical indistinguishability condition is meaningful only in a multivariate sense. That is, it pertains to the joint distribution of the ensemble members and the observation. The rank histogram has been designed to assess overall ensemble consistency, but mistakenly employing it to assess only restricted aspects of this joint distribution (e.g., the climatological distribution) leads to the incorrect conclusion that the verification rank histogram is not a useful diagnostic for good behavior of ensemble forecasts. The potential confusion is analyzed in the context of an idealized multivariate Gaussian model of forecast ensembles and their corresponding observations, and it is shown that the rank histogram does correctly assess the consistency of forecast ensembles. © 2011 American Meteorological Society.


Bamberger M.,Cornell University
New solutions : a journal of environmental and occupational health policy : NS | Year: 2012

Environmental concerns surrounding drilling for gas are intense due to expansion of shale gas drilling operations. Controversy surrounding the impact of drilling on air and water quality has pitted industry and lease-holders against individuals and groups concerned with environmental protection and public health. Because animals often are exposed continually to air, soil, and groundwater and have more frequent reproductive cycles, animals can be used as sentinels to monitor impacts to human health. This study involved interviews with animal owners who live near gas drilling operations. The findings illustrate which aspects of the drilling process may lead to health problems and suggest modifications that would lessen but not eliminate impacts. Complete evidence regarding health impacts of gas drilling cannot be obtained due to incomplete testing and disclosure of chemicals, and nondisclosure agreements. Without rigorous scientific studies, the gas drilling boom sweeping the world will remain an uncontrolled health experiment on an enormous scale.


Lotem A.,Tel Aviv University | Halpern J.Y.,Cornell University
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2012

A fundamental and frequently overlooked aspect of animal learning is its reliance on compatibility between the learning rules used and the attentional and motivational mechanisms directing them to process the relevant data (called here data-acquisition mechanisms). We propose that this coordinated action, which may first appear fragile and error prone, is in fact extremely powerful, and critical for understanding cognitive evolution. Using basic examples from imprinting and associative learning, we argue that by coevolving to handle the natural distribution of data in the animal's environment, learning and data-acquisition mechanisms are tuned jointly so as to facilitate effective learning using relatively little memory and computation. We then suggest that this coevolutionary process offers a feasible path for the incremental evolution of complex cognitive systems, because it can greatly simplify learning. This is illustrated by considering how animals and humans can use these simple mechanisms to learn complex patterns and represent them in the brain. We conclude with some predictions and suggested directions for experimental and theoretical work. © 2012 The Royal Society.


Weber M.G.,Cornell University | Keeler K.H.,University of Nebraska - Lincoln
Annals of Botany | Year: 2013

Background and Aims Understanding the evolutionary patterns of ecologically relevant traits is a central goal in plant biology. However, for most important traits, we lack the comprehensive understanding of their taxonomic distribution needed to evaluate their evolutionary mode and tempo across the tree of life. Here we evaluate the broad phylogenetic patterns of a common plant-defence trait found across vascular plants: extrafloral nectaries (EFNs), plant glands that secrete nectar and are located outside the flower. EFNs typically defend plants indirectly by attracting invertebrate predators who reduce herbivory. Methods Records of EFNs published over the last 135 years were compiled. After accounting for changes in taxonomy, phylogenetic comparative methods were used to evaluate patterns of EFN evolution, using a phylogeny of over 55 000 species of vascular plants. Using comparisons of parametric and non-parametric models, the true number of species with EFNs likely to exist beyond the current list was estimated. Key Results To date, EFNs have been reported in 3941 species representing 745 genera in 108 families, about 1-2% of vascular plant species and approx. 21% of families. They are found in 33 of 65 angiosperm orders. Foliar nectaries are known in four of 36 fern families. Extrafloral nectaries are unknown in early angiosperms, magnoliids and gymnosperms. They occur throughout monocotyledons, yet most EFNs are found within eudicots, with the bulk of species with EFNs being rosids. Phylogenetic analyses strongly support the repeated gain and loss of EFNs across plant clades, especially in more derived dicot families, and suggest that EFNs are found in a minimum of 457 independent lineages. However, model selection methods estimate that the number of unreported cases of EFNs may be as high as the number of species already reported. Conclusions EFNs are widespread and evolutionarily labile traits that have repeatedly evolved a remarkable number of times in vascular plants. Our current understanding of the phylogenetic patterns of EFNs makes them powerful candidates for future work exploring the drivers of their evolutionary origins, shifts, and losses. © 2012 The Author. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved.


Reppy J.D.,Cornell University
Physical Review Letters | Year: 2010

The torsional oscillator experiments described here examine the effect of disorder on the nonclassical rotational inertia (NCRI) of a solid He4 sample. The NCRI increases with increasing disorder, but the period changes responsible for this increase occur primarily at higher temperatures. Contrary to expectations based on a supersolid scenario, the oscillator period remains relatively unaffected at the lowest temperatures. This result points to a nonsuperfluid origin for the NCRI. © 2010 The American Physical Society.


Shuler M.L.,Cornell University
Annals of Biomedical Engineering | Year: 2012

We seek to construct physical and mathematical models of life. Such models allow us to test our understanding of how living systems function and how they respond to human imposed stimuli. One system is a genomically and chemically complete model of a minimal cell. This cell is a hypothetical bacterium with the fewest number of genes possible. Such a minimal cell provides a platform to ask about the essential features of a living cell and forms a platform to investigate "synthetic biology." A second system is "Body-on-a-Chip" which is a microfabricated microfluidic system with cells or tissue constructs representing various organs in the body. It can be constructed from human or animal cells and used in drug discovery development. That model is a physical representation of a physiologically based pharmacokinetic model. Both the computer and the physical models provide insight into the underlying biology and provide new tools to make use of that understanding to provide benefits to society. © 2012 Biomedical Engineering Society.


Karasev A.V.,University of Idaho | Gray S.M.,Cornell University
Annual Review of Phytopathology | Year: 2013

Potato virus Y (PVY) is one of the oldest known plant viruses, and yet in the past 20 years it emerged in the United States as a relatively new and very serious problem in potato. The virus exists as a complex of strains that induce a wide variety of foliar and tuber symptoms in potato, leading to yield reduction and loss of tuber quality. PVY has displayed a distinct ability to evolve through accumulation of mutations and more rapidly through recombination between different strains, adapting to new potato cultivars across different environments. Factors behind PVY emergence as a serious potato threat are not clear at the moment, and here an attempt is made to analyze various properties of the virus and its interactions with potato resistance genes and with aphid vectors to explain this recent PVY spread in potato production areas. Recent advances in PVY resistance identification and mapping of corresponding genes are described. An updated classification is proposed for PVY strains that takes into account the most current information on virus molecular genetics, serology, and host reactivity. © Copyright ©2013 by Annual Reviews. All rights reserved.


Kelley M.C.,Cornell University
Annales Geophysicae | Year: 2011

A recent breakthrough experiment by Ogawa et al. (2009) showed that Mesoscale Traveling Ionospheric Disturbances (MSTIDs), a common phenomenon at midlatitudes, originate in the auroral zone as gravity waves. Curiously, however, the latter do not seem to be related to magnetic activity. These atmospheric waves are common at high latitudes (Bristow and Greenwald, 1996; Bristow et al., 1996), and we argue here that, as they propagate to lower latitudes, Joule damping reduces the gravity wave spectrum to waves suffering the weakest damping. The direction of weakest damping corresponds to the direction predicted by the Perkins instability (Perkins, 1973) for nighttime MSTIDs. The daytime features reported by Ogawa et al. (2009) are very likely due to classical gravity wave interaction with the F-region ionosphere. © Author(s) 2011.


Lloyd J.P.,Cornell University
Astrophysical Journal Letters | Year: 2011

Studies of the planet abundance as a function of stellar mass have suggested a strong increase in the frequency of planet occurrence around stars more massive than 1.5 M ⊙, and that such stars are deficit in short-period planets. These planet searches have relied on giant stars for a sample of high mass stars, which are hostile to precision Doppler measurements due to rotation and activity while on the main sequence. This Letter considers the observed vsin i and observationally inferred mass for exoplanet hosting giants with the vsin i of distribution of field stars, which show discrepancies that can be explained by erroneous mass determinations of some exoplanet host stars. By comparison with an expected mass distribution constructed from integrating isochrones, it is shown that the exoplanet hosts are inconsistent with a population of massive stars. These stars are more likely to have originated from a main-sequence population of late F/early G dwarfs with mass 1.0-1.2 M ⊙, only slightly more massive than the typical FGK dwarfs with Doppler detected planets. The deficit of short-period planets is most likely explained by tidal capture. The planet abundance difference requires either a steeper increase in planet frequency with mass than previously thought or a high rate of false positives due to signals of stellar origin. The measurement of photospheric carbon isotope ratios is suggested as a method to discriminate whether this sample of giant stars is significantly more massive than the population of FGK dwarfs with Doppler detected planets. © 2011. The American Astronomical Society. All rights reserved.


Smith K.A.,Cornell University
Frontiers in Immunology | Year: 2014

Early reports on T cell antigen receptor (TCR) signaling uncovered a rapid increase in intracellular calcium concentration and the activation of calcium-dependent protein kinase as necessary for T cell activation. Cytolytic T cell clones were instrumental in the discovery of intracellular cytolytic granules, and the isolation of the perforin and granzyme molecules as the molecular effectors of cell-mediated lysis of target cells via apoptosis. Cytolytic T cell clones and TCR cDNA clones were also instrumental for the generation of TCR transgenic animals, which provided definitive evidence for negative selection of self-reactive immature thymocytes. In addition, studies of TCR complex signaling of immature thymocytes compared with mature T cells were consistent with the interpretation that negative selection occurs as a consequence of the incapacity of immature cells to produce IL-2, resulting in cytokine deprivation apoptosis. By comparison, taking advantage of cloned TCRs derived from T cell clones reactive with male-specific molecules, using TCR transgenic mice it was possible to document positive selection of female thymocytes when the male-specific molecules were absent. Focusing on the molecular mechanisms of T cell "help" for the generation of antibody-forming cells following the path opened by the elucidation of the IL-2 molecule, several groups were successful in the identification, isolation, and characterization of three new interleukin molecules (IL-4, IL-5, and IL-6) that promote the proliferation and differentiation of B cells. In addition, the identification of a B cell surface molecule (CD40) that augmented B cell antigen receptor-stimulated proliferation and differentiation led to the discovery of a T cell activation surface molecule that proved to be the CD40-ligand, thus finally providing a molecular explanation for "linked or cognate" recognition when T cells and B cells interact physically. Accordingly, the decade after the generation of the first T cell clones saw the elucidation of the molecular mechanisms of T cell cytotoxicity and T cell help, thereby expanding the number of molecules responsible for adaptive T cell immunity. © 2014 Smith.


Does free access to journal articles result in greater diffusion of scientific knowledge? Using a randomized controlled trial of open access publishing, involving 36 participating journals in the sciences, social sciences, and humanities, we report on the effects of free access on article downloads and citations. Articles placed in the open access condition (n=712) received significantly more downloads and reached a broader audience within the first year, yet were cited no more frequently, nor earlier, than subscription-access control articles (n=2533) within 3 yr. These results may be explained by social stratification, a process that concentrates scientific authors at a small number of elite research universities with excellent access to the scientific literature. The real beneficiaries of open access publishing may not be the research community but communities of practice that consume, but rarely contribute to, the corpus of literature. © FASEB.


Sammaritano L.R.,Cornell University
Autoimmunity Reviews | Year: 2012

Menopause represents a time of significant clinical and hormonal change. Given the incompletely understood interrelationship between gonadal hormones and the immune system, it is possible that menopause may affect, or be affected by, the presence of autoimmune disease. Menopause has significant effects on a number of organ systems including the cardiovascular, skeletal, central nervous and genitourinary systems. Premature ovarian failure is related to autoimmune factors in a proportion of cases, but is not generally associated with systemic autoimmune disorders unless secondary to treatment with alkylating agents such as cyclophosphamide. Gonadal hormones have been suggested to relate to both onset and activity in certain autoimmune diseases. For patients with systemic lupus erythematosus, disease activity is lower, and damage accrual higher, in the postmenopausal years, but the mechanisms responsible may relate to age, duration of disease, menopause changes, long-term effects of therapy, or some combination of these factors. Early menopause is a risk factor for rheumatoid arthritis, and post-menopausal status in RA is associated with greater damage and disability. Systemic sclerosis and giant cell arteritis may also be adversely affected by onset of menopause. Importantly, autoimmune disease and menopause may have an additive effect on risk for common comorbidities such as cardiovascular disease and osteoporosis. © 2011 Elsevier B.V.


Hidalgo D.A.,Cornell University
Plastic and Reconstructive Surgery | Year: 2011

Background: Limitations associated with traditional skin-muscle flaps and later with transconjunctival fat resection combined with carbon dioxide laser resurfacing have led to newer concepts in lower blepharoplasty that emphasize fat preservation, blending of the lid-cheek junction, simplified skin excision, and less morbid resurfacing techniques. Avoiding incision through the orbicularis muscle to preserve its innervation and reduce translamellar scarring is favored, as is a more liberal use of lateral canthal tightening procedures. This study investigates the use of a transconjunctival approach to resect and transpose fat combined with a skin flap technique that permits skin excision and simultaneous resurfacing with 30% trichloroacetic acid. The orbicularis is not violated and lateral canthal support is used as necessary. Methods: Lower blepharoplasty performed in 248 patients over a 4-year period was studied. The technique consisted of component procedures that varied based on individual anatomy. Results: Fat excision was performed in 91 percent, fat transposition was performed in 61 percent, skin excision was performed in 63 percent, trichloroacetic acid peels were performed in 62 percent, temporary tarsorrhaphy was performed in 31 percent, and lateral canthopexy was performed in 18 percent of patients. Average follow-up was 5.5 months. There were three complications and six revisions. Conclusions: Lower blepharoplasty that integrates component techniques tailored to individual anatomical problems and spares the orbicularis muscle is effective and associated with few complications and revisions. Fat transposition achieves effacement of the tear trough deformity. A skin flap approach effectively treats rhytides and is safe for simultaneous resurfacing with a mild peeling agent. Selective use of lateral canthal support improves lower eyelid tone and prevents malposition problems. Copyright © 2010 by the American Society of Plastic Surgeons.


Wriggers W.,Cornell University | Wriggers W.,D E Shaw Research
Acta Crystallographica Section D: Biological Crystallography | Year: 2012

Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs to be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed. © International Union of Crystallography 2012.


The role of the right hemisphere (RH) in metaphor comprehension is still controversial. Numerous neuroimaging studies have found that conventionality, sentential context, and task demand can influence the involvement of the RH in metaphor processing. The current meta-analysis used foci from 17 original functional magnetic resonance imaging studies to identify what factors modulate the involvement of the RH in metaphor processing. Activation likelihood estimation was used for quantification. We focused on the contrast of metaphorical meaning processing versus literal meaning processing and calculated the meta-analysis effects when (1) metaphorical meaning is conventional, (2) metaphorical meaning is novel, (3) metaphorical and literal meaning are presented in words, (4) metaphorical and literal meaning are presented in sentential context, (5) task is valence judgment, and (6) task is semantic relatedness judgment. The results indicated that the RH only showed significant effects in metaphor processing when the metaphorical meaning is novel, when metaphorical meaning is presented in sentential context, and when the task is semantic relatedness judgment. The effects were located in right fronto-temporal regions, including inferior frontal gyrus, middle frontal gyrus, insula, superior temporal gyrus, and middle temporal gyrus. These results suggest that conventionality, contextual complexity, and task demand can modulate the effect of figurativeness and influence the involvement of RH in metaphor comprehension. The main role of the RH in metaphor processing is related with activating broad semantic fields and integrating concepts that may have distant semantic relations, and hence provide support for the view that the RH is responsible for processing coarse semantic information in language comprehension. Hum Brain Mapp 35:107-122, 2014. © 2012 Wiley Periodicals, Inc.


Tumbar T.,Cornell University
Stem Cell Reviews and Reports | Year: 2012

Mouse epithelial skin stem cells constitute an important model system for understanding the dynamics of stem cell emergence and behavior in an intact vertebrate tissue. Recent published work defined discrete populations of epithelial stem cells in the adult skin epithelium, which reside in the hair follicle bulge and germ, isthmus, sebaceous gland and inter-follicular epidermis. Adult epidermal and hair follicle stem cells seem to adopt mostly symmetric or unidirectional fate decisions of either one of two possible fates: (1) differentiate and be lost from the tissue or (2) expand symmetrically to self-renew. Asymmetric divisions appear to be mostly implicated in differentiation and stratification of the epidermis. While mechanisms of adult stem cell homeostasis begin to be unraveled, the embryonic origin of the adult epithelial skin stem cells is poorly understood. Recent studies reported Sox9, Lgr6, and Runx1 expression in subpopulations of cells in the embryonic hair placode. These subpopulations seem to act as precursors of different classes of adult epithelial stem cells. In particular, Runx1 regulates a Wnt-mediated cross-talk between the nascent adult-type hair follicle stem cells and their environment, which is essential for timely stem cell emergence, proper maturation, long-term differentiation potential, and maintenance. The new data begin to define the basic dynamics and regulatory pathways governing the ontogeny of adult epithelial stem cells. © 2012 Springer Science+Business Media, LLC.


Escobedo F.A.,Cornell University
Soft Matter | Year: 2014

The role of entropic interactions, often subtle and sometimes crucial, on the structure and properties of soft matter has a well-recognized place in the classic and modern scientific literature. However, the lessons learned from many of those studies do not always form part of the standard arsenal of strategies that are taught or used for de novo studies relevant to the engineering of new materials. Fortunately, a growing number of examples exist where entropic effects have been designed a priori to achieve a desired or new outcome. This tutorial review describes some recent such examples, selected to illustrate the potential benefits of a more pro-active approach to harnessing the often overlooked power of entropy. This journal is © the Partner Organisations 2014.


Fan J.,Cornell University | Pavletich N.P.,Sloan Kettering Cancer Center
Genes and Development | Year: 2012

Replication protein A (RPA) is the main eukaryotic ssDNA-binding protein with essential roles in DNA replication, recombination, and repair. RPA maintains the DNA as single-stranded and also interacts with other DNA-processing proteins, coordinating their assembly and disassembly on DNA. RPA binds to ssDNA in two conformational states with opposing affinities for DNA and proteins. The RPA-protein interactions are compatible with a low DNA affinity state that involves DNA-binding domain A (DBD-A) and DBD-B but not with the high DNA affinity state that additionally engages DBD-C and DBD-D. The structure of the high-affinity RPA-ssDNA complex reported here shows a compact quaternary structure held together by a four-way interface between DBD-B, DBD-C, the intervening linker (BC linker), and ssDNA. The BC linker binds into the DNAbinding groove of DBD-B, mimicking DNA. The associated conformational change and partial occlusion of the DBD-A-DBA-B protein-protein interaction site establish a mechanism for the allosteric coupling of RPA-DNA and RPA-protein interactions. © 2012 by Cold Spring Harbor Laboratory Press.


Background: Banana (Musa spp.) is grown throughout the tropical and subtropical regions of the world. The fruits are a key staple food in many developing countries and a source of income for subsistence farmers. Bananas are also a major, multibillion-dollar export commodity for consumption primarily in developed countries, where few banana cultivars are grown. The fungal pathogen Mycosphaerella fijiensis causes black leaf streak disease (BLSD; aka black Sigatoka leaf spot) on the majority of edible banana cultivars grown worldwide. The fact that most of these cultivars are sterile and unsuitable for the breeding of resistant lines necessitates the extensive use of fungicides as the primary means of disease control. BLSD is a significant threat to the food security of resource-poor populations who cannot afford fungicides, and increases the environmental and health hazards where large-acreage monocultures of banana (Cavendish subgroup, AAA genome) are grown for export. Taxonomy: Mycosphaerella fijiensis M. Morelet is a sexual, heterothallic fungus having Pseudocercospora fijiensis (M. Morelet) Deighton as the anamorph stage. It is a haploid, hemibiotrophic ascomycete within the class Dothideomycetes, order Capnodiales and family Mycosphaerellaceae. Its taxonomic placement is based on DNA phylogeny, morphological analyses and cultural characteristics. Disease symptoms and host range: Mycosphaerella fijiensis is a leaf pathogen that causes reddish-brown streaks running parallel to the leaf veins, which aggregate to form larger, dark-brown to black compound streaks. These streaks eventually form fusiform or elliptical lesions that coalesce, form a water-soaked border with a yellow halo and, eventually, merge to cause extensive leaf necrosis. The disease does not kill the plants immediately, but weakens them by decreasing the photosynthetic capacity of leaves, causing a reduction in the quantity and quality of fruit, and inducing the premature ripening of fruit harvested from infected plants. Although Musa spp. are the primary hosts of M. fijiensis, the ornamental plant Heliconia psittacorum has been reported as an alternative host. New opportunities: Several valuable tools and resources have been developed to overcome some of the challenges of studying this host-pathogen system. These include a DNA-mediated fungal transformation system and the ability to conduct targeted gene disruptions, reliable quantitative plant bioassays, diagnostic probes to detect and differentiate M. fijiensis from related pathogens and to distinguish strains of different mating types, and a genome sequence that has revealed a wealth of gene sequences and molecular markers to be utilized in functional and population biology studies. © 2010 The Author. Molecular Plant Pathology © 2010 BSPP and Blackwell Publishing Ltd.


Rapuano B.E.,Cornell University
The International journal of oral & maxillofacial implants | Year: 2012

A number of environmental and patient-related factors contribute to implant failure. A significant fraction of these failures can be attributed to limited osseointegration resulting from poor bone healing responses. The overall goal of this study was to determine whether surface treatment of a titanium-aluminum-vanadium alloy (Ti-6Al-4V) implant material in combination with a biomimetic protein coating could promote the differentiation of attached osteoblastic cells. The specific aims of the study were to investigate whether osteoprogenitor cells cultured on a rigorously cleaned implant specimen showed a normal pattern of differentiation and whether preadsorbed fibronectin accelerated or enhanced osteoblast differentiation. Ti-6Al-4V disks were rigorously cleaned, passivated in nitric acid, and dry heat- sterilized; some of the disks were then coated with 1 nmol/L fibronectin. MC3T3 osteoprogenitor cells were then cultured on the pretreated disks for several weeks. Quantitative real-time polymerase chain reaction was performed to measure changes over time in the mRNA levels of osteoblast genes. Fibronectin increased the peak expression of all analyzed osteoblast gene markers. "Early" genes that normally mark the proliferative phase (0 to 10 days) of osteoblastic development showed peak expression within the first 10 days after cell attachment to the titanium alloy. In contrast, "late" genes that normally mark the differentiation (10 to 20 days) and mineralization (20 to 36 days) phases of osteoblastogenesis achieved peak expression only after approximately 3 to 4 weeks of culture. Osteoprogenitors cultured on a rigorously cleaned Ti-6Al-4V alloy were found to demonstrate a normal pattern of osteoblast differentiation. Preadsorbed fibronectin was observed to stimulate osteoblast differentiation during the mineralization phase of osteoblastogenesis.


Garrod R.T.,Cornell University | Pauly T.,Iowa State University
Astrophysical Journal | Year: 2011

We investigate the formation and evolution of interstellar dust-grain ices under dark-cloud conditions, with a particular emphasis on CO2. We use a three-phase model (gas/surface/mantle) to simulate the coupled gas-grain chemistry, allowing the distinction of the chemically active surface from the ice layers preserved in the mantle beneath. The model includes a treatment of the competition between barrier-mediated surface reactions and thermal-hopping processes. The results show excellent agreement with the observed behavior of CO2, CO, and water ice in the interstellar medium. The reaction of the OH radical with CO is found to be efficient enough to account for CO 2 ice production in dark clouds. At low visual extinctions, with dust temperatures ≳12K, CO2 is formed by direct diffusion and reaction of CO with OH; we associate the resultant CO2-rich ice with the observational polar CO2 signature. CH4 ice is well correlated with this component. At higher extinctions, with lower dust temperatures, CO is relatively immobile and thus abundant; however, the reaction of H and O atop a CO molecule allows OH and CO to meet rapidly enough to produce a CO:CO2 ratio in the range 2-4, which we associate with apolar signatures. We suggest that the observational apolar CO2/CO ice signatures in dark clouds result from a strongly segregated CO:H 2O ice, in which CO2 resides almost exclusively within the CO component. Observed visual-extinction thresholds for CO2, CO, and H2O are well reproduced by depth-dependent models. Methanol formation is found to be strongly sensitive to dynamical timescales and dust temperatures. © 2011. The American Astronomical Society. All rights reserved..


Bogdanove A.J.,Cornell University
Current Opinion in Plant Biology | Year: 2014

Recent advances in DNA targeting allow unprecedented control over gene function and expression. Targeting based on TAL effectors is arguably the most promising for systems biology and metabolic engineering. Multiple, orthogonal TAL-effector reagents of different types can be used in the same cell. Furthermore, variation in base preferences of the individual structural repeats that make up the TAL effector DNA recognition domain makes targeting stringency tunable. Realized applications range from genome editing to epigenome modification to targeted gene regulation to chromatin labeling and capture. The principles that govern TAL effector DNA recognition make TAL effectors well suited for applications relevant to plant physiology and metabolism. TAL effector targeting has merits that are distinct from those of the RNA-based DNA targeting CRISPR/Cas9 system. © 2014 Elsevier Ltd.


Csaki C.,Cornell University | Kuflik E.,Tel Aviv University | Volansky T.,Tel Aviv University
Physical Review Letters | Year: 2014

We present a new paradigm for supersymmetric theories with R-parity violation (RPV). At high scale, R parity is conserved in the visible sector but spontaneously broken in the supersymmetry-breaking sector. The breaking is then dynamically mediated to the visible sector and is manifested via nonrenormalizable operators at low energy. Consequently, RPV operators originate from the Kähler potential rather than the superpotential, and are naturally suppressed by the supersymmetry-breaking scale, explaining their small magnitudes. A new set of nonholomorphic RPV operators is identified and found to often dominate over the standard RPV ones. We study the relevant low-energy constraints arising from baryon-number violating processes, proton decay, and flavor changing neutral currents, which may all be satisfied if a solution to the standard model flavor puzzle is incorporated. The chiral structure of the RPV operators implies new and distinct collider signatures, indicating the need to alter current techniques in searching for RPV at the LHC. © 2014 American Physical Society.


Wagner A.B.,Cornell University
IEEE Transactions on Information Theory | Year: 2011

Distributed compression of a pair of Gaussian sources in which the goal is to reproduce a linear function of the sources at the decoder is considered. It has recently been noted that lattice codes can provide improved compression rates for this problem compared to conventional, unstructured codes. It is first shown that the state-of-the-art lattice scheme can be improved by including an additional linear binning stage. An outer bound on the rate-distortion region and a separate lower bound on the optimal sum rate are then established. The outer bound implies that for the special case of communicating the difference of two positively correlated Gaussian sources, the unimproved lattice scheme achieves within one bit of the rate region at any distortion level. The sum rate lower bound implies that unstructured codes achieve within one bit of the optimal sum rate whenever the weights of the two sources in the linear combination differ by more than a factor of two. © 2006 IEEE.


Agrawal A.A.,Cornell University | Weber M.G.,University of California at Davis
Ecology Letters | Year: 2015

Species comparisons are a cornerstone of biology and there is a long tradition of using the comparative framework to study the ecology and evolution of plant defensive traits. Early comparative studies led to the hypothesis that plant chemistry plays a central role in plant defence, and the evolution of plant secondary chemistry in response to insect herbivory remains a classic example of coevolution. However, recent comparative work has disagreed with this paradigm, reporting little connection between plant secondary chemicals and herbivory across distantly related plant taxa. One conclusion of this new work is that the importance of secondary chemistry in plant defence may have been generally overstated in earlier research. Here, we attempt to reconcile these contradicting viewpoints on the role of plant chemistry in defence by critically evaluating the use and interpretation of species correlations as a means to study defence-herbivory relationships. We conclude that the notion that plant primary metabolites (e.g. leaf nitrogen content) are the principal determinants of herbivory (or the target of natural selection by herbivores) is not likely to be correct. Despite the inference of recent community-wide studies of herbivory, strong evidence remains for a prime role of secondary compounds in plant defence against herbivores. © 2015 John Wiley & Sons Ltd/CNRS.


The vast majority of infant formulas in the United States contain the long-chain polyunsaturated fatty acids (PUFAs) docosahexaenoic acid (22:6n-3) and arachidonic acid (20:4n-6), which were first permitted by the US Food and Drug Administration in 2001. As a scientific case study, preclinical animal studies of these nutrients definitively influenced the design and interpretation of human clinical studies. Early studies were tied to the availability of test substances, and in hindsight suggest re-evaluation of the essential fatty acid concept in light of the totality of available evidence. Research in the 1950s established the essentiality of n-6 PUFAs for skin integrity; however, widespread recognition of the essentiality of n-3 PUFAs came decades later despite compelling evidence of their significance. Barriers to an understanding of the essentiality of n-3 PUFAs were as follows: 1) their role is in neural function, which is measured only with difficulty compared with skin lesions and growth faltering that are apparent for n-6 PUFAs; 2) the experimental use of vegetable oils as PUFA sources that contain the inefficiently used C18 PUFAs rather than the operative C20 and C22 PUFAs; 3) the shift from reliance on high-quality animal studies to define mechanisms that established the required nutrients in the first part of the 20th century to inherently challenging human studies. Advances in nutrition of premature infants require the best practices and opinions available, taking into account the totality of preclinical and clinical evidence. © 2016 American Society for Nutrition.


Widom B.,Cornell University
Annual Review of Physical Chemistry | Year: 2011

PrologueThis is an account mostly of what I have seen and worked on in physical chemistry, from my time in graduate school six decades ago to the present. It is a personal story about kinetics, thermodynamics, and statistical mechanicsin which subjects I continue to be educated, thanks to patient instruction by my students and associates. When I had the invitation from Steve Leone to write this article I said "yes"because (a) "yes"is my default setting; (b) it was a great honor to have been invited to do it; and (c) I was too busy at the time to think about what the consequences of saying "yes" would be. I must now do my best to fulfill my promise. © 2011 by Annual Reviews. All rights reserved.


Caudill M.A.,Cornell University
American Journal of Clinical Nutrition | Year: 2010

The addition of folic acid to the US food supply, along with the critical role of folate in certain health outcomes, has intensified worldwide interest in the bioavailability of folate. Bioavailability is a function of absorptive and postabsorptive processes, which in turn are influenced by diet, individuality, and complex diet-host interactions. As such, it is unlikely that a single bioavailability figure will accurately reflect food folate bioavailability from every diet for every person. Although there is broad agreement that naturally occurring food folate is not as bioavailable as folic acid, questions remain as to the extent of these differences, particularly within the context of a whole diet. This article 1) summarizes and integrates bioavailability estimates derived from studies that use whole-diet approaches; 2) highlights the influences of genetics, ethnicity-race, and sex as postabsorptive bioavailability modifiers; and 3) discusses the adequacy of the US folate Recommended Dietary Allowance in achieving folate sufficiency in select subpopulations. © 2010 American Society for Nutrition.


Haith D.A.,Cornell University
Environmental Science and Technology | Year: 2010

An ecological risk assessment was performed for runoff of 37 pesticides registered for use on grass surfaces (lawns and golf courses) in the U.S. The assessment was based on 100-yr simulations using TPQPond, a newly developed model of pesticide runoff and subsequent accumulation in a receiving pond. One-in-10 yr pond concentrations were compared with acute toxicity end points for fish, invertebrates, and algae. Simulations were performed for pesticides applied at label rates on lawns, fairways, and greens using weather data for nine U.S. locations. Runoff of 4 of the 37 pesticides produced potential acute risk to invertebrates or fish. Two chemicals posed a comparable danger to plants. Risk was highest with fairways and lowest for greens. Locations with long growing seasons and large amounts of precipitation produced the highest risks. The risk assessment followed the general protocols recommended by USEPA, but with different models, weather data, and scenarios. In spite of the differences, the results confirmed that most but not all of the pesticides which had survived the USEPA registration process were also demonstrated safe, with respect to acute risks, by this independent assessment. The five exceptions were explained by differences in models, simulation scenarios, and input data. These results do not mean that the studied pesticides are free of any ecological dangers. In particular, no attempt was made to evaluate chronic risk. © 2010 American Chemical Society.


Agrawal A.A.,Cornell University
Functional Ecology | Year: 2011

1. In this essay I summarize current trends in the evolutionary ecology of plant defence, while advocating for approaches that integrate community ecology with specific tests of classic evolutionary hypotheses. Several conclusions emerge. 2.The microevolution of defence is perhaps best studied by reciprocal transplant experiments of differentiated plant populations while simultaneously manipulating the presence of the herbivore(s) hypothesized to be the agent(s) of natural selection. 3. Although there is continued interest in the costs of defence, I argue that some empirical approaches to estimating costs (e.g. genetic engineering) may provide limited insight into evolutionary processes. 4.Essentially all plants employ several different lines of defence against herbivory. It is thus time to abandon searching for single silver bullet traits and the simple trade-off model (where traits are arbitrarily expected to negatively covary across genotypes or species). We still know very little about which trait combinations are most effective and have repeatedly evolved together. Thus, some of our prominent theories (e.g. a predicted trade-off between direct and indirect defence) need to be revised. 5.Studies of the macroevolution of plant defence are enjoying renewed interest due to available phylogenies and analytical methods. Although general trends are not currently surmisable, we will soon have strong case studies evaluating both biotic and abiotic drivers of convergent evolution in defence strategies and the role of defence evolution in the adaptive radiation of plant lineages. 6.The evolution of specificity is proposed as a final frontier in understanding complexity in plant-herbivore interactions. Although it is abundantly clear that plants can deploy highly specific defensive responses that are differentially perceived by herbivore species, how such responses evolve and are physiologically regulated remains an important gap. Relatively straightforward methodologies are now available to close the loop between plant perception of herbivory, hormonal responses, and production of defensive end-products across genotype or species. © 2010 The Author. Functional Ecology © 2010 British Ecological Society.


Asparagine-linked (N-linked) protein glycosylation has been observed in all domains of life, including most recently in bacteria and is now widely considered a universal post-translational modification. However, cell-based production of homogeneous glycoproteins for laboratory and preparative purposes remains a significant challenge due in part to the complexity of this process in vivo. To address this issue, an easily available and highly controllable Escherichia coli-based cell-free system for the production of N-linked glycoproteins was developed. The method was created by coupling existing in vitro translation systems with an N-linked glycosylation pathway reconstituted from defined components. The translation/glycosylation system yielded efficiently glycosylated target proteins at a rate of hundreds of micrograms/milliliters in half a day. This is the first time a prokaryote-based cell-free protein synthesis system has generated N-linked glycoproteins. © The Author 2011.


Elser V.,Cornell University
Acta Crystallographica Section A: Foundations of Crystallography | Year: 2013

Recent experiments at free-electron laser X-ray sources have been able to resolve the intensity distributions about Bragg peaks in nanocrystals of large biomolecules. Information derived from small shifts in the peak positions augment the Bragg samples of the particle intensity with samples of its gradients. Working on the assumption that the nanocrystal is entirely generated by lattice translations of a particle, an algorithm is developed that reconstructs the particle from intensities and intensity gradients. Unlike traditional direct phasing methods that require very high resolution data in order to exploit sparsity of the electron density, this method imposes no constraints on the contrast other than positivity and works well at low resolution. Successful reconstructions are demonstrated with simulated P1 lysozyme nanocrystal data down to a signal-to-noise ratio of 2 in the intensity gradients. © 2013 International Union of Crystallography Printed in Singapore - all rights reserved.


Padamsee H.S.,Cornell University
Annual Review of Nuclear and Particle Science | Year: 2014

Superconducting cavities have been operating routinely in a variety of accelerators with a range of demanding applications. With the success of completed projects, niobium cavities have become an enabling technology, offering upgrade paths for existing facilities and pushing frontier accelerators for nuclear physics, high-energy physics, materials science, and the life sciences. With continued progress in basic understanding of radio-frequency superconductivity, the performance of cavities has steadily improved to approach theoretical capabilities. Copyright © 2014 by Annual Reviews. All rights reserved.


Benedek N.A.,University of Texas at Austin | Fennie C.J.,Cornell University
Journal of Physical Chemistry C | Year: 2013

We use a combination of symmetry arguments and first-principles calculations to explore the connection between structural distortions and ferroelectricity in the perovskite family of materials. We explain the role of octahedral rotations in suppressing ferroelectricity in these materials and show that, as the tolerance factor decreases, rotations alone cannot fully suppress ferroelectricity. Our results show that it is cation displacements ("hidden" in Glazer notation) that accompany the rotations, rather than the rotations themselves, that play the decisive role in suppressing ferroelectricity in these cases. We use the knowledge gained in our analysis of this problem to explain the origin of ferroelectricity in R3c materials such as FeTiO3 and ZnSnO3 and to suggest strategies for the design and synthesis of new perovskite ferroelectrics. Our results have implications not only for the fundamental crystal chemistry of the perovskites but also for the discovery of new functional materials. © 2013 American Chemical Society.


Kinoshita T.,Cornell University
International Journal of Modern Physics A | Year: 2014

This paper presents the current status of the theory of electron anomalous magnetic moment ae ≡(g-2)/2, including a complete evaluation of 12,672 Feynman diagrams in the tenth-order perturbation theory. To solve this problem, we developed a code-generator which converts Feynman diagrams automatically into fully renormalized Feynman-parametric integrals. They are evaluated numerically by an integration routine VEGAS. The preliminary result obtained thus far is 9.16 (58) (α/π)5, where (58) denotes the uncertainty in the last two digits. This leads to ae(theory) = 1.159 652 181 78 (77) × 10-3, which is in agreement with the latest measurement ae (exp:2008) = 1.159 652 180 73 (28) × 10-3. It shows that the Feynman-Dyson method of perturbative QED works up to the precision of 10-12. © 2014 World Scientific Publishing Company.


Yang J.-S.,Sloan Kettering Institute | Yang J.-S.,Cornell University | Lai E.,Sloan Kettering Institute
Molecular Cell | Year: 2011

Since the establishment of a canonical animal microRNA biogenesis pathway driven by the RNase III enzymes Drosha and Dicer, an unexpected variety of alternative mechanisms that generate functional microRNAs have emerged. We review here the many Drosha-independent and Dicer-independent microRNA biogenesis strategies characterized over the past few years. Beyond reflecting the flexibility of small RNA machineries, the existence of noncanonical pathways has consequences for interpreting mutants in the core microRNA machinery. Such mutants are commonly used to assess the consequences of "total" microRNA loss, and indeed, they exhibit many overall phenotypic similarities. Nevertheless, ongoing studies reveal a growing number of settings in which alternative microRNA pathways contribute to distinct phenotypes among core microRNA biogenesis mutants. © 2011 Elsevier Inc.


Johnson P.A.,Cornell University
Reproduction in Domestic Animals | Year: 2012

Follicle development in the highly efficient laying hen is characterized by a well-organized follicular hierarchy. This is not the case in other chickens such as the broiler breeder hen that has excessive follicle development and lower reproductive efficiency. Although management practices can optimize egg production in less productive breeds of chickens, the factors that contribute to this difference are not known. Interactions between the oocyte and surrounding somatic cells are believed to be involved in promoting follicle selection. Anti-Müllerian hormone (AMH) has been shown to have a role in regulating rate of follicle development in mammals. In hens, the expression of AMH is restricted to the growing population of follicles and, similar to mammals, is markedly decreased at around the time of follicle selection. The oocyte factors, growth and differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15), have been identified in the hen, and their expression pattern has been characterized. Anti-Müllerian hormone expression in hens is decreased by a protein factor from the oocyte (not GDF9) and is also decreased by vitamin D. Associated with the decrease in AMH expression by vitamin D, follicle-stimulating hormone receptor mRNA is increased. These data suggest that information about AMH regulation may enhance our understanding of follicle selection, particularly in birds with aberrant follicle development. © 2012 Blackwell Verlag GmbH.


Heberle F.A.,Cornell University
Cold Spring Harbor perspectives in biology | Year: 2011

Cell membranes show complex behavior, in part because of the large number of different components that interact with each other in different ways. One aspect of this complex behavior is lateral organization of components on a range of spatial scales. We found that lipid-only mixtures can model the range of size scales, from approximately 2 nm up to microns. Furthermore, the size of compositional heterogeneities can be controlled entirely by lipid composition for mixtures such as 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/cholesterol or sphingomyelin (SM)/DOPC/POPC/cholesterol. In one region of special interest, because of its connection to cell membrane rafts, nanometer-scale domains of liquid-disordered phase and liquid-ordered phase coexist over a wide range of compositions.


Arguello J.R.,Cornell University
PloS one | Year: 2013

Chemical signaling between organisms is a ubiquitous and evolutionarily dynamic process that helps to ensure mate recognition, location of nutrients, avoidance of toxins, and social cooperation. Evolutionary changes in chemical communication systems progress through natural variation within the organism generating the signal as well as the responding individuals. A promising yet poorly understood system with which to probe the importance of this variation exists between D. melanogaster and S. cerevisiae. D. melanogaster relies on yeast for nutrients, while also serving as a vector for yeast cell dispersal. Both are outstanding genetic and genomic models, with Drosophila also serving as a preeminent model for sensory neurobiology. To help develop these two genetic models as an ecological model, we have tested if - and to what extent - S. cerevisiae is capable of producing polymorphic signaling through variation in metabolic volatiles. We have carried out a chemical phenotyping experiment for 14 diverse accessions within a common garden random block design. Leveraging genomic sequences for 11 of the accessions, we ensured a genetically broad sample and tested for phylogenetic signal arising from phenotypic dataset. Our results demonstrate that significant quantitative differences for volatile blends do exist among S. cerevisiae accessions. Of particular ecological relevance, the compounds driving the blend differences (acetoin, 2-phenyl ethanol and 3-methyl-1-butanol) are known ligands for D. melanogasters chemosensory receptors, and are related to sensory behaviors. Though unable to correlate the genetic and volatile measurements, our data point clear ways forward for behavioral assays aimed at understanding the implications of this variation.


Shakya B.,Cornell University
Physics of the Dark Universe | Year: 2013

The viability of neutralino dark matter as an explanation of the 130 GeV gamma ray signal from the Galactic Center recently observed by the Fermi Large Area Telescope is examined. It is found that the signal can be compatible with a sharp feature from internal bremsstrahlung from a mostly bino dark matter particle of mass around 145 GeV, augmented by a contribution from annihilation into gamma+Z via a small wino admixture. This scenario circumvents the problematic overproduction of lower energy continuum photons that plague line interpretations of this signal. Sleptons approximately degenerate in mass with the neutralino are required to enhance the internal bremsstrahlung feature. © 2013 Bibhushan Shakya.


Lloyd J.P.,Cornell University
Astrophysical Journal Letters | Year: 2013

High mass stars are hostile to Doppler measurements due to rotation and activity on the main-sequence, so RV searches for planets around massive stars have relied on evolved stars. A large number of planets have been found around evolved stars with M > 1.5 M⊙. To test the robustness of mass determinations, Lloyd compared mass distributions of planet hosting subgiants with distributions from integrating isochrones and concluded that it is unlikely the subgiant planet hosts are this massive, but rather that the mass inferences are systematically in error. The conclusions of Lloyd have been called in to question by Johnson et al., who show TRILEGAL-based mass distributions that disagree with the mass distributions in Lloyd, which they attribute to Malmquist bias. Johnson et al. argue that the very small spectroscopic observational uncertainties favor high masses, and there are a large number of high mass sub giants in RV surveys. However, in this Letter, it is shown that Malmquist bias does not impact the mass distributions, but the mass distribution is sensitive to Galaxy model. The relationship needed to reconcile the subgiant planet host masses with any model of the Galactic stellar population is implausible, and the conclusion of Lloyd that spectroscopic mass determinations of subgiants are likely to have been overestimated is robust. © 2013. Copyright Information.


Tidball K.G.,Cornell University
Ecology and Society | Year: 2012

This contribution builds upon contemporary work on principles of biological attraction as well as earlier work on biophilia while synthesizing literatures on restorative environments, community-based ecological restoration, and both community and social-ecological disaster resilience. It suggests that when humans, faced with a disaster, as individuals and as communities and populations, seek engagement with nature to further their efforts to summon and demonstrate resilience in the face of a crisis, they exemplify an urgent biophilia. This urgent biophilia represents an important set of human-nature interactions in SES characterized by hazard, disaster, or vulnerability, often appearing in the 'backloop' of the adaptive cycle. The relationships that human-nature interactions have to other components within interdependent systems at many different scales may be one critical source of resilience in disaster and related contexts. In other words, the affinity we humans have for the rest of nature, the process of remembering that attraction, and the urge to express it through creation of restorative environments, which may also restore or increase ecological function, may confer resilience across multiple scales. In making this argument, the paper also represents a novel contribution to further theorizing alternatives to anthropocentric understandings of human-nature relations, and strongly makes the case for humans as part of, not separate from, ecosystems. © 2012 by the author(s).


Wilks D.S.,Cornell University
International Journal of Climatology | Year: 2014

Canonical correlation analysis (CCA) is a higher-dimensional extension of univariate multiple regression that is often used to construct seasonal and other forecasts in a climatological context. Although its use is widespread, to date it has apparently been used only to produce nonprobabilistic forecasts. Here an analytic result for the prediction covariance matrix of vector CCA forecasts is presented, which is sufficient to define a full forecast probability distribution if a multivariate Gaussian distribution can reasonably be assumed for the forecast errors. The approach is illustrated by computing and verifying probabilistic seasonal forecasts for tropical Pacific sea-surface temperatures. © 2013 Royal Meteorological Society.


Non-steroidal anti-inflammatory drugs are prescribed for the treatment of patients with acute pain but use of such analgesics is associated with dose-dependent adverse events (AEs). Diclofenac submicron particle capsules have been developed using SoluMatrix technology to provide analgesia at lower doses than available solid oral dosing forms. Our study evaluated the analgesic efficacy and safety of lower-dose diclofenac submicron particle capsules in patients with acute pain following elective surgery. A phase 3, multicenter, double-blind study enrolled 428 patients, aged 18 to 65 years, with moderate-to-severe pain following bunionectomy under regional anesthesia. Patients experiencing a pain intensity rating of ≥ 40 mm on a 100-mm Visual Analog Scale were randomized to receive lower-dose diclofenac submicron particle capsules (35 or 18 mg, 3 times daily [TID]), celecoxib (200 mg, twice daily [BID], 400-mg loading dose), or placebo. The primary efficacy parameter was the overall (summed) pain intensity difference measured over 0 to 48 hours (SPID-48). Secondary efficacy parameters included pain intensity difference (PID) at scheduled assessments. Lower-dose diclofenac submicron particle capsules 35 mg TID (524.05; P < 0.001), 18 mg TID (393.25; P = 0.010), and celecoxib 200 mg BID (390.22; P = 0.011) demonstrated significant pain control compared with placebo (77.10) for the primary efficacy parameter, mean SPID-48. Diclofenac submicron particle capsules 35 mg TID (4.52) provided some pain control (higher mean PID) at 30 minutes following administration, in contrast to celecoxib 200 mg BID (0.80), diclofenac submicron particle capsules 18 mg TID (0.31), and placebo (0.12). Better pain control (PID) was noted across all active treatment groups at 5 hours compared with placebo (P ≤ 0.03), and pain relief was sustained throughout the treatment period. The most frequent non-procedure-related AEs were nausea, headache, dizziness, and vomiting. Lower-dose diclofenac submicron particle capsules provided effective analgesia in this phase 3 clinical study in patients with acute pain and are a potentially promising option for the treatment of patients with acute pain.


Vascular plants contain two gene families that encode monosaccharide transporter proteins. The classical monosaccharide transporter(-like) gene superfamily is large and functionally diverse, while the recently identified SWEET transporter family is smaller and, thus far, only found to transport glucose. These transporters play essential roles at many levels, ranging from organelles to the whole plant. Many family members are essential for cellular homeostasis and reproductive success. Although most transporters do not directly participate in long-distance transport, their indirect roles greatly impact carbon allocation and transport flux to the heterotrophic tissues of the plant. Functional characterization of some members from both gene families has revealed their diverse roles in carbohydrate partitioning, phloem function, resource allocation, plant defense, and sugar signaling. This review highlights the broad impacts and implications of monosaccharide transport by describing some of the functional roles of the monosaccharide transporter(-like) superfamily and the SWEET transporter family. © 2011 The Author.


Isolated Malpighian tubules of the yellow fever mosquito secrete NaCl and KCl from the peritubular bath to the tubule lumen via active transport of Na(+) and K(+) by principal cells. Lumen-positive transepithelial voltages are the result. The counter-ion Cl(-) follows passively by electrodiffusion through the paracellular pathway. Water follows by osmosis, but specific routes for water across the epithelium are unknown. Remarkably, the transepithelial secretion of NaCl, KCl and water is driven by a H(+) V-ATPase located in the apical brush border membrane of principal cells and not the canonical Na(+), K(+) -ATPase. A hypothetical cation/H(+) exchanger moves Na(+) and K(+) from the cytoplasm to the tubule lumen. Also remarkable is the dynamic regulation of the paracellular permeability with switch-like speed which mediates in part the post-blood-meal diuresis in mosquitoes. For example, the blood meal the female mosquito takes to nourish her eggs triggers the release of kinin diuretic peptides that (i) increases the Cl(-) conductance of the paracellular pathway and (ii) assembles V(1) and V(0) complexes to activate the H(+) V-ATPase and cation/H(+) exchange close by. Thus, transcellular and paracellular pathways are both stimulated to quickly rid the mosquito of the unwanted salts and water of the blood meal. Stellate cells of the tubule appear to serve a metabolic support role, exporting the HCO(3)(-) generated during stimulated transport activity. Septate junctions define the properties of the paracellular pathway in Malpighian tubules, but the proteins responsible for the permselectivity and barrier functions of the septate junction are unknown. © 2010 The Authors. Acta Physiologica © 2010 Scandinavian Physiological Society.


Weinstein A.M.,Cornell University
American Journal of Physiology - Renal Physiology | Year: 2015

Proximal tubule and loop of Henle function are coupled, with proximal transport determining loop fluid composition, and loop transport modulating glomerular filtration via tubuloglomerular feedback (TGF). To examine this interaction, we begin with published models of the superficial rat proximal convoluted tubule (PCT; including flow-dependent transport in a compliant tubule), and the rat thick ascending Henle limb (AHL). Transport parameters for this PCT are scaled down to represent the proximal straight tubule (PST), which is connected to the thick AHL via a short descending limb. Transport parameters for superficial PCT and PST are scaled up for a juxtamedullary nephron, and connected to AHL via outer and inner medullary descending limbs, and inner medullary thin AHL. Medullary interstitial solute concentrations are specified. End-AHL hydrostatic pressure is determined by distal nephron flow resistance, and the TGF signal is represented as a linear function of end-AHL cytosolic Cl concentration. These two distal conditions required iterative solution of the model. Model calculations capture inner medullary countercurrent flux of urea, and also suggest the presence of an outer medullary countercurrent flux of ammonia, with reabsorption in AHL and secretion in PST. For a realistically strong TGF signal, there is the expected homeostatic impact on distal flows, and in addition, a homeostatic effect on proximal tubule pressure. The model glycosuria threshold is compatible with rat data, and predicted glucose excretion with selective 1Na_:1glucose cotransporter (SGLT2) inhibition comports with observations in the mouse. Model calculations suggest that enhanced proximal tubule Na_ reabsorption during hyperglycemia is sufficient to activate TGF and contribute to diabetic hyperfiltration. © 2015 the American Physiological Society.


Roeder A.H.K.,Cornell University
Current Opinion in Plant Biology | Year: 2012

Computational modeling of growing plant tissues raises two basic questions about plant cell division: when does a cell decide to divide and where is the new wall placed? Although biologists and modelers commonly assume that a cell divides after it reaches a threshold size, two recent experiments show that models with variable division sizes better replicate the tissue. Similarly, comparing model predictions with living plant cells reveals that the choice of division plane is variable, although the shortest path dividing a cell in half (i.e. the minimal surface area) is the most probable division plane. © 2012 Elsevier Ltd.


A dramatic change in agricultural crops is needed in order to keep pace with the demands of an increasing human population, exponential need for renewable fuels, and uncertain climatic changes. Grasses make up the vast majority of agricultural commodities. How these grasses capture, transport, and store carbohydrates underpins all aspects of crop productivity. Sink-source dynamics within the plant direct how much, where, and when carbohydrates are allocated, as well as determine the harvestable tissue. Carbohydrate partitioning can limit the yield capacity of these plants, thus offering a potential target for crop improvement. Grasses have the ability to buffer this sink-source interaction by transiently storing carbohydrates in stem tissue when production from the source is greater than whole-plant demand. These reserves improve yield stability in grain crops by providing an alternative source when photosynthetic capacity is reduced during the later phases of grain filling, or during periods of environmental and biotic stresses. Domesticated grasses such as sugarcane and sweet sorghum have undergone selection for high accumulation of stem carbohydrates, which serve as the primary sources of sugars for human and animal consumption, as well as ethanol production for fuel. With the enormous expectations placed on agricultural production in the near future, research into carbohydrate partitioning in grasses is essential for maintaining and increasing yields in grass crops. This review highlights the current knowledge of non-structural carbohydrate dynamics in grass stems and discusses the impacts of stem reserves in essential agronomic grasses. © 2012 The Author.


Krasny M.E.,Cornell University
Ecology and Society | Year: 2014

University campus sustainability initiatives have proliferated over the last decade. We contend that such initiatives benefit from applying conceptual frameworks to help understand and guide their activities and from a focus on campus open space and natural areas management. Informed by an adaptive comanagement framework encompassing social learning, social capital, and shared action, we used semistructured interviews to examine student participation in the immediate response and longer-term policy formulation following a crisis that occurred in a campus natural area. Students exhibited social learning as demonstrated by reflection and the integration of new ideas through discussions with administrators and peers, as well as social capital through increased social trust, which led to a shift in perspective regarding norms of student-administrator interactions. Further, students participated in shared action, such as posting warning signs in dangerous areas, and importantly, through their contributions to longer-term campus natural area safety and recreational access policy. Three conditions explain student engagement in the adaptive comanagement process: the presence of a pre-existing student organization that had built bonding social capital and was committed to campus natural area stewardship, openness to multiple stakeholder viewpoints and commitment to action on the part of the university administration, and the presence of a crisis that spurred emotions and action. Based on these findings, we assert that student organizations can contribute to an adaptive comanagement process and that such a process is consistent with university and campus sustainability values related to the importance of student engagement, mental health, and learning. © 2014 by the author(s).


Cortes-Medellin G.,Cornell University
IEEE Transactions on Antennas and Propagation | Year: 2011

We are presenting a novel ultra-wideband, dual polarized, antenna design based on a non-planar quasi self-complementary (QSC) approach. An important characteristic of this QSC antenna is an input match better than -10 dB over a decade of bandwidth. We have demonstrated the concept by fabricating a QSC prototype antenna that works from 400 MHz to 4.0 GHz. We have measured the prototype performance in terms of input impedance and radiation patterns, from which the antenna directivity, beamwidth, polarization, and aperture efficiency for a 65° illumination angle were calculated. From these measurements we confirmed the ultra-wideband characteristics of the QSC feed prototype. In particular, we looked for the presence of resonances by measuring the radiation patterns with 3 MHz resolution, over the decade of bandwidth, in both polarizations, and none was found. The measured directivity of the QSC antenna feed is 10 dBi. The half beam-width, at -10 dB level, varies between 60° and 70°, with a frequency average value of 65°. The measured beam-integrated cross-polarization inside the -10 dB level of the patterns is better than -10 dB. The phase center location does not move with frequency. © 2011 IEEE.


Concerns exist about adequacy of vitamin D in pregnant women relative to both maternal and fetal adverse health outcomes. Further contributing to these concerns is the prevalence of inadequate and deficient vitamin D status in pregnant women, which ranges from 5 to 84% globally. Although maternal vitamin D metabolism changes during pregnancy, the mechanisms underlying these changes and the role of vitamin D during development are not well understood. Observational evidence links low maternal vitamin D status with an increased risk of non-bone health outcome in the mother (pre-eclampsia, gestational diabetes, obstructed labour and infectious disease), the fetus (gestational duration) and the older offspring (developmental programming of type 1 diabetes, inflammatory and atopic disorders and schizophrenia); but the totality of the evidence is contradictory (except for maternal infectious disease and offspring inflammatory and atopic disorders), lacking causality and, thus, inconclusive. In addition, recent evidence links not only low but also high maternal vitamin D status with increased risk of small-for-gestational age and schizophrenia in the offspring. Rigorous and well-designed randomised clinical trials need to determine whether vitamin D has a causal role in non-bone health outcomes in pregnancy. © 2012 The Author.


Erickson D.,Cornell University | Sinton D.,Kings College
Nature Photonics | Year: 2011

Since its emergence as a field, optofluidics has developed unique tools and techniques for enabling the simultaneous delivery of light and fluids with microscopic precision. In this Review, we describe the possibilities for applying these same capabilities to the field of energy. We focus in particular on optofluidic opportunities in sunlight-based fuel production in photobioreactors and photocatalytic systems, as well as optofluidically enabled solar energy collection and control. We then provide a series of physical and scaling arguments that demonstrate the potential benefits of incorporating optofluidic elements into energy systems. Throughout the Review we draw attention to the ways in which optofluidics must evolve to enable the up-scaling required to impact the energy field. © 2011 Macmillan Publishers Limited. All rights reserved.


For older adults aging in the community, living conditions can promote health, enhance coping, and reduce disablement-but they can also create stress and increase risks of illness, accidents, and decline. Although socioeconomic disparities in housing likely contribute to inequalities in interior conditions, I argue that living conditions are also shaped by social resources such as coresidential relationships, social network ties, and social support. In this article, I examine the distribution of a set of risky or stressful physical and ambient living conditions including structural disrepair, clutter, lack of cleanliness, noise, and odor. Using data from the National Social Life, Health, and Aging Project (NSHAP), I find that low-income and African American older adults have more disordered living conditions as do those with poorer physical and mental health. In addition, older adults who have a coresident partner, more nonresidential network ties, and more sources of instrumental support are exposed to fewer risky or harmful living conditions. This suggests that living conditions are an important, though overlooked, mechanism through which household composition, social networks, and social support affect health and well-being in later life. © The Author(s) 2013.


Piras G.,Cornell University
Journal of Statistical Software | Year: 2010

Sphet is a package for estimating and testing spatial models with heteroskedastic innovations. We implement recent generalized moments estimators and semiparametric methods for the estimation of the coeffcients variance-covariance matrix. This paper is a general description of sphet and all functionalities are illustrated by application to the popular Boston housing dataset. The package in its current version is limited to the estimators based on Arraiz, Drukker, Kelejian, and Prucha (2010); Kelejian and Prucha (2007, 2010). The estimation functions implemented in sphet are able to deal with virtually any sample size.


Hale J.T.,Cornell University
Cognitive Science | Year: 2011

This article examines cognitive process models of human sentence comprehension based on the idea of informed search. These models are rational in the sense that they strive to find a good syntactic analysis quickly. Informed search derives a new account of garden pathing that handles traditional counterexamples. It supports a symbolic explanation for local coherence as well as an algorithmic account of entropy reduction. The models are expressed in a broad framework for theories of human sentence comprehension. © 2010 Cognitive Science Society, Inc.


Ryan A.M.,Cornell University
Health Services Research | Year: 2010

Objective. To examine whether the CMS and Premier Inc. Hospital Quality Incentive Demonstration (PHQID), a hospital-based pay-for-performance (P4P) and public quality reporting program, caused participating hospitals (1) to avoid treating minority patients diagnosed with acute myocardial infarction (AMI), heart failure, and pneumonia and (2) to avoid providing coronary artery bypass graft (CABG) to minority patients diagnosed with AMI. Data Sources. One hundred percent Medicare inpatient claims, denominator files, and provider of service files from 2000 to 2006. Study Design. We test for differences in the conditional probability of receiving care at PHQID hospitals for AMI, heart failure, and pneumonia before and after implementation of the PHQID between white and minority patients. We also test for differences in the conditional probability that white and minority patients diagnosed with AMI receive CABG in hospitals participating, and not participating, in the PHQID before and after the implementation of the PHQID. Data Extraction Methods. Data were obtained from CMS. Principal Findings. We find little evidence that the PHQID reduced access for minority patients: only "Other Race" beneficiaries had a significant reduction in adjusted admissions to PHQID hospitals in the postperiod, and only for AMI. Only marginally significant (p<.10) evidence of a reduction in CABG was found, also occurring for Other Race beneficiaries. Conclusions. Despite minimal evidence of minority patient avoidance in the PHQID, monitoring of avoidance should continue for P4P programs. © 2010 Health Research and Educational Trust.


Population structure and kinship are widespread confounding factors in genome-wide association studies (GWAS). It has been standard practice to include principal components of the genotypes in a regression model in order to account for population structure. More recently, the linear mixed model (LMM) has emerged as a powerful method for simultaneously accounting for population structure and kinship. The statistical theory underlying the differences in empirical performance between modeling principal components as fixed versus random effects has not been thoroughly examined. We undertake an analysis to formalize the relationship between these widely used methods and elucidate the statistical properties of each. Moreover, we introduce a new statistic, effective degrees of freedom, that serves as a metric of model complexity and a novel low rank linear mixed model (LRLMM) to learn the dimensionality of the correction for population structure and kinship, and we assess its performance through simulations. A comparison of the results of LRLMM and a standard LMM analysis applied to GWAS data from the Multi-Ethnic Study of Atherosclerosis (MESA) illustrates how our theoretical results translate into empirical properties of the mixed model. Finally, the analysis demonstrates the ability of the LRLMM to substantially boost the strength of an association for HDL cholesterol in Europeans. © 2013 Gabriel E.


Mendle J.,Cornell University
Child Development Perspectives | Year: 2014

Few periods of the life span are as dynamic, tumultuous, and emotionally salient as puberty. The combination of biological and social change during this transition contributes to sweeping shifts in the prevalence and nature of psychopathology. In this article, I highlight the role of puberty in psychological well-being, reviewing both individual and population-wide trends in psychological symptoms and disorders. Emphasis is on three domains associated with maturation: typicality of symptoms, epidemiological shifts, and individual differences. © 2014 The Society for Research in Child Development.


Sevier C.S.,Cornell University
Antioxidants and Redox Signaling | Year: 2012

Significance: Members of the Erv/ALR/QSOX protein family contain an Erv sequence module and catalyze protein disulfide bond formation. Erv enzymes impact protein function within and outside cells that affects both normal and malignant cell growth. This protein family is named for its founding members: Erv1 (essential for respiratory and vegetative growth 1) and ALR (augmenter of liver regeneration), homologous mitochondrial proteins from yeast and mammals, respectively, and QSOX (quiescin sulfhydryl oxidase), an oxidase secreted from quiescent cells. This review will focus on a subset of Erv proteins that are localized within the secretory pathway: Erv2-like proteins, proteins present in the endoplasmic reticulum of fungi, and QSOX proteins, proteins localized within the secretory pathway and extracellular space and present in most eukaryotes, but not fungi. Recent Advances: A wealth of structural and biochemical data has been obtained for Erv2 and QSOX proteins. These data have identified a generally conserved catalytic mechanism and structure for the Erv2 and QSOX proteins with unique features for each enzyme. Critical Issues: Many fundamental questions remain about the activity for these proteins in living cells including the partners, pathways, and locations utilized by these enzymes in vivo. Future Directions: A more comprehensive understanding of the cellular roles for Erv2 and QSOX enzymes will require identification of their partners and substrates. Also, determining when Erv2 and QSOX function during growth and development, and how changes in levels of active Erv2 and QSOX impact cell function, is necessary to facilitate a better understanding of these intriguing enzymes. Antioxid. Redox Signal. 16, 800-808. © Copyright 2012, Mary Ann Liebert, Inc. 2012.


Dalziel B.D.,Cornell University
Proceedings. Biological sciences / The Royal Society | Year: 2013

The epidemic dynamics of infectious diseases vary among cities, but it is unclear how this is caused by patterns of infectious contact among individuals. Here, we ask whether systematic differences in human mobility patterns are sufficient to cause inter-city variation in epidemic dynamics for infectious diseases spread by casual contact between hosts. We analyse census data on the mobility patterns of every full-time worker in 48 Canadian cities, finding a power-law relationship between population size and the level of organization in mobility patterns, where in larger cities, a greater fraction of workers travel to work in a few focal locations. Similarly sized cities also vary in the level of organization in their mobility patterns, equivalent on average to the variation expected from a 2.64-fold change in population size. Systematic variation in mobility patterns is sufficient to cause significant differences among cities in infectious disease dynamics-even among cities of the same size-according to an individual-based model of airborne pathogen transmission parametrized with the mobility data. This suggests that differences among cities in host contact patterns are sufficient to drive differences in infectious disease dynamics and provides a framework for testing the effects of host mobility patterns in city-level disease data.


Wilson D.B.,Cornell University
Current Opinion in Microbiology | Year: 2011

Enzymatic hydrolysis of cellulose by microorganisms is a key step in the global carbon cycle. Despite its abundance only a small percentage of microorganisms can degrade cellulose, probably because it is present in recalcitrant cell walls. There are at least five distinct mechanisms used by different microorganisms to degrade cellulose all of which involve cellulases. Cellulolytic organisms and cellulases are extremely diverse possibly because their natural substrates, plant cell walls, are very diverse. At this time the microbial ecology of cellulose degradation in any environment is still not clearly understood even though there is a great deal of information available about the bovine rumen. Two major problems that limit our understanding of this area are the vast diversity of organisms present in most cellulose degrading environments and the inability to culture most of them. © 2011 Elsevier Ltd.


Dobzinski S.,Cornell University
Proceedings of the Annual ACM Symposium on Theory of Computing | Year: 2011

We show that every universally truthful randomized mechanism for combinatorial auctions with submodular valuations that provides an approximation ratio of m1/2-ε must use exponentially many value queries, where m is the number of items. In contrast, ignoring incentives there exist constant ratio approximation algorithms for this problem. Our approach is based on a novel direct hardness technique that completely skips the notoriously hard step of characterizing truthful mechanisms. The characterization step was the main obstacle for proving impossibility results in algorithmic mechanism design so far. We demonstrate two additional applications of our new technique: (1) an impossibility result for universally-truthful polynomial time flexible combinatorial public projects and (2) an impossibility result for truthful-in-expectation mechanisms for exact combinatorial public projects. The latter is the first result that bounds the power of polynomial-time truthful in expectation mechanisms in any setting. © 2011 ACM.


Laland K.N.,University of St. Andrews | Odling-Smee J.,University of Oxford | Myles S.,Cornell University | Myles S.,Acadia University
Nature Reviews Genetics | Year: 2010

Researchers from diverse backgrounds are converging on the view that human evolution has been shaped by gene-culture interactions. Theoretical biologists have used population genetic models to demonstrate that cultural processes can have a profound effect on human evolution, and anthropologists are investigating cultural practices that modify current selection. These findings are supported by recent analyses of human genetic variation, which reveal that hundreds of genes have been subject to recent positive selection, often in response to human activities. Here, we collate these data, highlighting the considerable potential for cross-disciplinary exchange to provide novel insights into how culture has shaped the human genome. © 2010 Macmillan Publishers Limited. All rights reserved.


Kirkland E.J.,Cornell University
Ultramicroscopy | Year: 2011

New aberration correctors present new challenges in optimizing (minimizing) the probe size in the STEM (Scanning Transmission Electron Microscope). A small probe is important for high resolution imaging and analytical microscopy. Some effects of aperture size, corrector accuracy, and higher order aberrations on probe size and image artifacts are calculated. Accumulated small errors in the aberration corrector can produce a significant decrease in image contrast, which may be important in quantitative image comparisons of theory and experiment. It is important to match the objective aperture to the accuracy of the corrector instead of just the (third order) spherical aberration of the objective as in the commonly used Scherzer conditions. © 2011 Elsevier B.V.


Bachlechner T.C.,Cornell University
Journal of High Energy Physics | Year: 2014

We study the distribution of metastable vacua and the likelihood of slow roll inflation in high dimensional random landscapes. We consider two examples of landscapes: a Gaussian random potential and an effective supergravity potential defined via a Gaussian random superpotential and a trivial Kähler potential. To examine these landscapes we introduce a random matrix model that describes the correlations between various derivatives and we propose an efficient algorithm that allows for a numerical study of high dimensional random fields. Using these novel tools, we find that the vast majority of metastable critical points in N dimensional random supergravities are either approximately supersymmetric with |F| < M susy or supersymmetric. Such approximately supersymmetric points are dynamical attractors in the landscape and the probability that a randomly chosen critical point is metastable scales as log(P) ∝N. We argue that random supergravities lead to potentially interesting inflationary dynamics. © 2014 The Author(s).


Chaturvedi R.K.,Indian Institute of Toxicology Research | Chaturvedi R.K.,Academy of Scientific and Innovative Research AcSIR | Beal M.F.,Cornell University
Free Radical Biology and Medicine | Year: 2013

Neurodegenerative disorders are debilitating diseases of the brain, characterized by behavioral, motor and cognitive impairments. Ample evidence underpins mitochondrial dysfunction as a central causal factor in the pathogenesis of neurodegenerative disorders including Parkinson's disease, Huntington's disease, Alzheimer's disease, Amyotrophic lateral sclerosis, Friedreich's ataxia and Charcot-Marie-Tooth disease. In this review, we discuss the role of mitochondrial dysfunction such as bioenergetics defects, mitochondrial DNA mutations, gene mutations, altered mitochondrial dynamics (mitochondrial fusion/ fission, morphology, size, transport/trafficking, and movement), impaired transcription and the association of mutated proteins with mitochondria in these diseases. We highlight the therapeutic role of mitochondrial bioenergetic agents in toxin and in cellular and genetic animal models of neurodegen-erative disorders. We also discuss clinical trials of bioenergetics agents in neurodegenerative disorders. Lastly, we shed light on PGC-1α, TORC-1, AMP kinase, Nrf2-ARE, and Sirtuins as novel therapeutic targets for neurodegenerative disorders. © 2013 Elsevier Inc. All rights reserved.


Polkovnikov A.,Boston University | Sengupta K.,Indian Association for The Cultivation of Science | Silva A.,Abdus Salam International Center For Theoretical Physics | Vengalattore M.,Cornell University
Reviews of Modern Physics | Year: 2011

This Colloquium gives an overview of recent theoretical and experimental progress in the area of nonequilibrium dynamics of isolated quantum systems. There is particularly a focus on quantum quenches: the temporal evolution following a sudden or slow change of the coupling constants of the system Hamiltonian. Several aspects of the slow dynamics in driven systems are discussed and the universality of such dynamics in gapless systems with specific focus on dynamics near continuous quantum phase transitions is emphasized. Recent progress on understanding thermalization in closed systems through the eigenstate thermalization hypothesis is also reviewed and relaxation in integrable systems is discussed. Finally key experiments probing quantum dynamics in cold atom systems are overviewed and put into the context of our current theoretical understanding. © 2011 American Physical Society.


Nixon K.C.,Cornell University | Carpenter J.M.,American Museum of Natural History
Cladistics | Year: 2012

Homology in cladistics is reviewed. The definition of important terms is explicated in historical context. Homology is not synonymous with synapomorphy: it includes symplesiomorphy, and Hennig clearly included both plesiomorphy and synapomorphy as types of homology. Homoplasy is error, in coding, and is analogous to residual error in simple regression. If parallelism and convergence are to be distinguished, homoplasy would be evidence of the former and analogy evidence of the latter. We discuss whether there is a difference between molecular homology and morphological homology, character state homology, nested homology (additive characters), and serial homology. We conclude by proposing a global definition of homology. © 2011 The Willi Hennig Society.


Beyenbach K.W.,Cornell University
Annals of the New York Academy of Sciences | Year: 2012

Female mosquitoes gorge on vertebrate blood, a rich nutrient source for developing eggs, but gorging meals increase the risk of predation. Mosquitoes are quick to reduce the flight payload with a potent diuresis. Diuretic peptides of the insect kinin family induce a tenfold reduction in the paracellular resistance of Malpighian tubules and increase the paracellular permeation of Cl-, the counterion of the transepithelial secretion of Na+ and K+. As a result, the transepithelial secretion of NaCl and KCl and water increases. Insect kinins signal the opening of the paracellular pathway via G protein-coupled receptors and the elevation of intracellular [Ca2+], which leads to the reorganization of the cytoskeleton associated with the septate junction (SJ). The reorganization may affect the septate junctional proteins that control the barrier and permselectivity properties of the paracellular pathway. The proteins involved in the embryonic formation of the SJ and in epithelial polarization are largely known for ectodermal epithelia, but the proteins that form and mediate the dynamic functions of the SJ in Malpighian tubules remain to be determined. © 2012 New York Academy of Sciences.


Liu R.H.,Cornell University
Journal of Food Science | Year: 2013

There is strong scientific evidence suggesting that regular consumption of fruits and vegetables is negatively associated with risk of developing chronic diseases. The 2010 Dietary Guidelines for Americans recommend at least 9 servings of fruits and vegetables a day based on a 2000 kcal diet. However, the average person in the United States consumes 3.6 servings of fruits and vegetables per day. In order to achieve the goal of at least 9 servings, we should continue educating Americans about the health benefits of fruits and vegetables and recommend consumers to eat a wide variety of fruits and vegetables. The key is to increase the amount up to 9 to 13 servings of fruits and vegetables a day in all forms. Fresh, cooked, and processed fruits and vegetables including frozen and canned, 100% fruit juices, 100% vegetable juices, and dried fruits are all considered as servings of fruits and vegetables. A wide variety of fruits and vegetables provide a range of nutrients and different bioactive compounds including phytochemicals (phenolics, flavonoids, and carotenoids), vitamins (vitamin C, folate, and provitamin A), minerals (potassium, calcium, and magnesium), and fibers. More and more evidence suggests that the health benefits of fruits and vegetables are attributed to the additive and synergistic interactions of the phytochemicals present in whole foods by targeting multiple signal transduction pathways. Therefore, consumers should obtain nutrients and bioactive compounds from a wide variety of whole foods for optimal nutrition and health well-being, not from expensive dietary supplements. © 2013 Institute of Food Technologists®.


Schroder U.,TU Braunschweig | Harnisch F.,Helmholtz Center for Environmental Research | Angenent L.T.,Cornell University
Energy and Environmental Science | Year: 2015

Microbial electrochemistry is the study and application of interactions between living microbial cells and electrodes (i.e. electron conductors, capacitive materials). For a long time this subfield of bioelectrochemistry has been the interest of mainly fundamental researchers. This has considerably changed during the last decade and microbial electrochemistry gained interest from applied researchers and engineers. These researchers took the microbial fuel cell (MFC), which is a system that converts the chemical energy of organic material in wastewater into electric power, from a concept to a technology. In addition, a plethora of derivative technologies, such as microbial electrolysis cells (MECs), microbial desalination cells (MDCs), photomicrobial fuel cells (photoMFCs), microbial electrosynthesis (MES), and biocomputing have been developed. The growing number of systems is often referred to in literature under the termini bioelectrochemical system (BES), microbial electrochemical technology (MET), or electrobiotechnology. Within this article we introduce a classification of technologies based on interfacing microbiology and electrochemistry. We argue that BESs comprise all systems based on bioelectrochemistry, with a further layer of termini through the use of METs. Primary METs are based on extracellular electron transfer (direct or mediated), whereas secondary METs include systems in which electrochemistry is connected-at least through ionic contact-with a microbial process via the electrochemical control or adaptation of environmental parameters, such as pH or metabolite concentration level. © 2015 The Royal Society of Chemistry.


Stover P.J.,Cornell University
Journal of Nutrigenetics and Nutrigenomics | Year: 2011

Folate-mediated 1-carbon metabolism is a network of interconnected metabolic pathways necessary for the synthesis of purine nucleotides, thymidylate and the remethylation of homocysteine to methionine. Disruptions in this pathway influence both DNA synthesis and stability and chromatin methylation, and result from nutritional deficiencies and common gene variants. The mechanisms underlying folate-associated pathologies and developmental anomalies have yet to be established. This review focuses on the relationships among folate-mediated 1-carbon metabolism, chromatin methylation and human disease, and the role of gene-nutrient interactions in modifying epigenetic processes. Copyright © 2012 S. Karger AG, Basel.


Reyna V.F.,Cornell University | Mills B.A.,University of Texas at Dallas
Journal of Experimental Psychology: General | Year: 2014

Fuzzy-trace theory is a theory of memory, judgment, and decision making, and their development. We applied advances in this theory to increase the efficacy and durability of a multicomponent intervention to promote risk reduction and avoidance of premature pregnancy and sexually transmitted infections. Seven hundred and thirty-four adolescents from high schools and youth programs in 3 states (Arizona, Texas, and New York) were randomly assigned to 1 of 3 curriculum groups: RTR (Reducing the Risk), RTR+ (a modified version of RTR using fuzzy-trace theory), and a control group. We report effects of curriculum on self-reported behaviors and behavioral intentions plus psychosocial mediators of those effects: namely, attitudes and norms, motives to have sex or get pregnant, self-efficacy and behavioral control, and gist/verbatim constructs. Among 26 outcomes, 19 showed an effect of at least 1 curriculum relative to the control group: RTR+ produced improvements for 17 outcomes and RTR produced improvements for 12 outcomes. For RTR+, 2 differences (for perceived parental norms and global benefit perception) were confined to age, gender, or racial/ethnic subgroups. Effects of RTR+ on sexual initiation emerged 6 months after the intervention, when many adolescents became sexually active. Effects of RTR+ were greater than RTR for 9 outcomes, and remained significantly greater than controls at 1-year follow-up for 12 outcomes. Consistent with fuzzy-trace theory, results suggest that by emphasizing gist representations, which are preserved over long periods and are key memories used in decision making, the enhanced intervention produced larger and more sustained effects on behavioral outcomes and psychosocial mediators of adolescent risk taking. © 2014 American Psychological Association.


Marsh D.,Cornell University
Journal of High Energy Physics | Year: 2012

Affleck-Dine baryogenesis is preconditioned on a certain structure of non-renormalizable operators in the Kähler potential. In this paper, we geometrically characterize the resulting constraint on the field space Kähler geometry and survey the Lagrangian for correlated predictions. The Affleck-Dine field backreacts on the inflaton, and by mapping the backreacted potential to an inflaton potential with a step, we find that current CMB data severely constrain some versions of the scenario. © SISSA 2012.


Lu Y.,Cornell University
Nature Materials | Year: 2014

Rechargeable lithium, sodium and aluminium metal-based batteries are among the most versatile platforms for high-energy, cost-effective electrochemical energy storage. Non-uniform metal deposition and dendrite formation on the negative electrode during repeated cycles of charge and discharge are major hurdles to commercialization of energy-storage devices based on each of these chemistries. A long-held view is that unstable electrodeposition is a consequence of inherent characteristics of these metals and their inability to form uniform electrodeposits on surfaces with inevitable defects. We report on electrodeposition of lithium in simple liquid electrolytes and in nanoporous solids infused with liquid electrolytes. We find that simple liquid electrolytes reinforced with halogenated salt blends exhibit stable long-term cycling at room temperature, often with no signs of deposition instabilities over hundreds of cycles of charge and discharge and thousands of operating hours. We rationalize these observations with the help of surface energy data for the electrolyte/lithium interface and impedance analysis of the interface during different stages of cell operation. Our findings provide support for an important recent theoretical prediction that the surface mobility of lithium is significantly enhanced in the presence of lithium halide salts. Our results also show that a high electrolyte modulus is unnecessary for stable electrodeposition of lithium.


Singh A.,Cornell University | Peppas N.A.,University of Texas at Austin
Advanced Materials | Year: 2014

For over two decades, immunologists and biomaterials scientists have co-existed in parallel world with the rationale of understanding the molecular profile of immune responses to vaccination, implantation, and treating incurable diseases. Much of the field of biomaterial-based immunotherapy has relied on evaluating model antigens such as chicken egg ovalbumin in mouse models but their relevance to humans has been point of much discussion. Nevertheless, such model antigens have provided important insights into the mechanisms of immune regulation and served as a proof-of-concept for plethora of biomaterial-based vaccines. After years of extensive development of numerous biomaterials for immunomodulation, it is only recently that an experimental scaffold vaccine implanted beneath the skin has begun to use the human model to study the immune responses to cancer vaccination by co-delivering patient-derived tumor lysates and immunomodulatory proteins. If successful, this scaffold vaccine will change the way we approached untreatable cancers, but more importantly, will allow a faster and more rational translation of therapeutic regimes to other cancers, chronic infections, and autoimmune diseases. Most materials reviews have focused on immunomodulatory adjuvants and micro-nano-particles. Here we provide an insight into emerging hydrogel and scaffold based immunomodulatory approaches that continue to demonstrate efficacy against immune associated diseases. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Soderlund D.M.,Cornell University
Archives of Toxicology | Year: 2012

Synthetic pyrethroid insecticides were introduced into widespread use for the control of insect pests and disease vectors more than three decades ago. In addition to their value in controlling agricultural pests, pyrethroids are at the forefront of efforts to combat malaria and other mosquito-borne diseases and are also common ingredients of household insecticide and companion animal ectoparasite control products. The abundance and variety of pyrethroid uses contribute to the risk of exposure and adverse effects in the general population. The insecticidal actions of pyrethroids depend on their ability to bind to and disrupt voltage-gated sodium channels of insect nerves. Sodium channels are also important targets for the neurotoxic effects of pyrethroids in mammals but other targets, particularly voltage-gated calcium and chloride channels, have been implicated as alternative or secondary sites of action for a subset of pyrethroids. This review summarizes information published during the past decade on the action of pyrethroids on voltage-gated sodium channels as well as on voltage-gated calcium and chloride channels and provides a critical re-evaluation of the role of these three targets in pyrethroid neurotoxicity based on this information. © 2011 Springer-Verlag.


Caro T.,University of California at Davis | Sherman P.W.,Cornell University
Trends in Ecology and Evolution | Year: 2011

Behavioural ecologists often see little connection between the current conservation crisis and the future of their discipline. This view is myopic because our abilities to investigate and interpret the adaptive significance and evolutionary histories of behaviours are increasingly being compromised in human-dominated landscapes because of species extinctions, habitat destruction, invasive species, pollution, and climate change. In this review, we argue that many central issues in behavioural ecology will soon become prohibitively difficult to investigate and interpret, thus impeding the rapid progress that characterizes the field. To address these challenges, behavioural ecologists should design studies not only to answer basic scientific questions but also to provide ancillary information for protection and management of their study organisms and habitats, and then share their biological insights with the applied conservation community. © 2010 Elsevier Ltd.


Hanrath T.,Cornell University
Journal of Vacuum Science and Technology A: Vacuum, Surfaces and Films | Year: 2012

The prospect of designing novel materials with electrical, optical, and magnetic properties by design has intrigued scientists and engineers for years. Building blocks for such artificial solids have emerged from recent advances in nanomaterial synthesis, characterization, and emerging understanding of their size-dependent properties. Colloidal semiconductor nanocrystal quantum dots (NQDs) stand out as an intellectually intriguing and experimentally advantageous system for the fundamental study of artificial solids and their technological development. The authors review the rapid evolution of artificial solids from an early theoretical concept towards the refined control of metamaterials with programmable electronic structure and their potential commercial applications, in particular, in next-generation energy technologies. The review is organized around the three independently adjustable parameters of artificial solids: (i) the electronic structure of NQD as artificial atom by tailoring the quantum confinement of the wave function, (ii) the interdot coupling as an artificial bond, and (iii) the self-assembly of NQDs into ordered superstructures as artificial crystals. The authors review elementary aspects of colloidal NQD synthesis as well as pertinent advances which have led to refined control over the NQD size, shape, and composition. Coupling between NQDs is reviewed in the context of an artificial bond; we summarize chemical and physical approaches to address the seemingly contradictory requirements of coupling nanostructures while preserving the effects of quantum-confinement. The authors review the self-assembly of NQDs into ordered superstructures in analogy to atomic crystal growth and discuss fundamental interactions between NQD and how they can be modulated to direct the growth of superlattices with predefined structures. Collectively, the experimental control over the properties of the artificial atom, bond, and crystal enable the systematic exploration of the electronic phase diagram of NQD solids. From an applied perspective, these advances have created an immensely fertile opportunity space technological applications of artificial solids in optoelectronic devices. The authors conclude with a perspective on three specific unresolved challenges ahead: (i) knowledge gaps concerning the detailed physiochemical nature of the NQD surface, (ii) limitations posed by the inherent inhomogeneity within the ensemble of NQDs, (iii) the true electronic structure of NQD solids, and (iv) the connection between NQD model systems in the laboratory and commercially deployable NQD technologies. © 2012 American Vacuum Society.


Wilks D.S.,Cornell University
Journal of Applied Meteorology and Climatology | Year: 2013

Eleven alternatives to the annually updated 30-yr average for specifying climate "normals" are considered for the purpose of projecting nonstationarity in the mean U.S. temperature climate during 2006-12. Comparisons are made for homogenized U.S. Historical Climatology Network station data, corresponding nonhomogenized station data, and spatially aggregated ("megadivision") data. The use of homogenized station data shows clear improvement over nonhomogenized station data and spatially aggregated data in terms of mean-squared specification errors on independent data. The best single method overall was the most recent 15-yr average as implemented by the Climate Prediction Center (CPC15), consistent with previous work using nonhomogenized and spatially aggregated data, although "hinge" functions with the change point fixed at 1975 performed well for the spring and summer seasons. A hybrid normals-specification method, using one of these piecewise continuous functions when the regressions are sufficiently strong and the CPC15 otherwise, exhibits a favorable trade-off between squared error and bias that may make it an optimal choice for some users. © 2013 American Meteorological Society.


Salem R.,Picoluz LLC | Foster M.A.,Johns Hopkins University | Gaeta A.L.,Cornell University
Advances in Optics and Photonics | Year: 2013

Manipulation and characterization of information using ultrafast optical signals is critical for numerous applications in telecommunications, biology, quantum information science, spectroscopy, and atomic and molecular physics. Femtosecond pulsed laser sources are available over a wide range of wavelengths and repetition rates, which enable the generation, transmission, and characterization of information at bandwidths beyond 1 THz. In this article, we review the concept of space-time duality as a system design tool for ultrafast optical processing and characterization. The combination of this design framework with recent advances in nonlinear optical devices enables the realization of highly complex signal processing systems that can generate, characterize, and manipulate arbitrary and non-repetitive optical waveforms at unprecedented processing speeds. © 2013 Optical Society of America.


Csaki C.,Cornell University | Hubisz J.,Syracuse University | Terning J.,University of California at Davis
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2016

We consider the phenomenology of a resonance that couples to photons but not gluons, and estimate its production rate at the LHC from photon-photon fusion in elastic pp scattering using the equivalent photon and narrow width approximations. The rate is sensitive only to the mass, the spin, the total width of the resonance, and its branching fraction to photons. Production cross sections of 3-6 fb at 13 TeV can be easily accommodated for a 750 GeV resonance with partial photon width of 15 GeV. This provides the minimal explanation of the reported diphoton anomaly in the early LHC Run II data. © 2016 American Physical Society.


Kim C.-J.,Cornell University
Nature Nanotechnology | Year: 2016

Chiral materials possess left- and right-handed counterparts linked by mirror symmetry. These materials are useful for advanced applications in polarization optics, stereochemistry and spintronics. In particular, the realization of spatially uniform chiral films with atomic-scale control of their handedness could provide a powerful means for developing nanodevices with novel chiral properties. However, previous approaches based on natural or grown films, or arrays of fabricated building blocks, could not offer a direct means to program intrinsic chiral properties of the film on the atomic scale. Here, we report a chiral stacking approach, where two-dimensional materials are positioned layer-by-layer with precise control of the interlayer rotation (θ) and polarity, resulting in tunable chiral properties of the final stack. Using this method, we produce left- and right-handed bilayer graphene, that is, a two-atom-thick chiral film. The film displays one of the highest intrinsic ellipticity values (6.5 deg μm1) ever reported, and a remarkably strong circular dichroism (CD) with the peak energy and sign tuned by θ and polarity. We show that these chiral properties originate from the large in-plane magnetic moment associated with the interlayer optical transition. Furthermore, we show that we can program the chiral properties of atomically thin films layer-by-layer by producing three-layer graphene films with structurally controlled CD spectra. © 2016 Nature Publishing Group


Chylek L.A.,Cornell University
Science Signaling | Year: 2013

Immune defenses depend on the ability of immunoreceptors to recognize foreign antigens and initiate intracellular signaling when a pathogen is detected. Signal initiation requires spatial reorganization of proteins and site-specifi c receptor phosphorylation, which leads to engagement of feedback loops. This Journal Club discusses recent work using combined experimental and computational approaches to investigate these processes in B cell antigen receptor (BCR) signaling. Specifi cally, the roles of different kinases in the presence and absence of BCR clustering were evaluated. Results indicated that spleen tyrosine kinase (SYK) can compensate for loss of Src-family kinase activity when receptors are spatially clustered, in part because receptor clustering enables SYK to trigger a positive feedback loop. This study and its implications suggest additional uses for computational models in studies of immunoreceptor signaling and highlight areas where extensions of current methodology are needed to better understand the complexities of biomolecular interactions. © 2013 American Association for the Advancement of Science. All Rights Reserved.


Wansink B.,Cornell University
Psychology and Marketing | Year: 2015

Most of our research on eating behavior has no impact on health or public policy. Part is due to the nontranslational way we often conduct our studies; part is due to us not having a useful framework that organizes our conclusions. This paper's first purpose is to offer an organizing framework that shows how nearly all effective interventions on food choice either make healthy choices more convenient (physically or cognitively), more attractive (comparatively or absolutely), or more normal (perceived or actual). This paper's second purpose is to introduce the notion of activism research-an approach to designing and executing studies in a way that makes consumer psychology research more actionable, useful, effective, and scalable. Together these two tools could help expand both the relevance and reach, and impact of what we do. © 2015 Wiley Periodicals, Inc.


Broder J.,Cornell University | Rusmevichientong P.,University of Southern California
Operations Research | Year: 2012

We consider a stylized dynamic pricing model in which a monopolist prices a product to a sequence of T customers who independently make purchasing decisions based on the price offered according to a general parametric choice model. The parameters of the model are unknown to the seller, whose objective is to determine a pricing policy that minimizes the regret, which is the expected difference between the seller's revenue and the revenue of a clairvoyant seller who knows the values of the parameters in advance and always offers the revenue-maximizing price. We show that the regret of the optimal pricing policy in this model is φ(√T), by establishing an Ω(√T) lower bound on the worst-case regret under an arbitrary policy, and presenting a pricing policy based on maximum-likelihood estimation whose regret is (√T) across all problem instances. Furthermore, we show that when the demand curves satisfy a "well-separated" condition, the T -period regret of the optimal policy is φ(log T). Numerical experiments show that our policies perform well. © 2012 INFORMS.


Sondermann H.,Cornell University | Shikuma N.J.,University of California at Santa Cruz | Yildiz F.H.,University of California at Santa Cruz
Current Opinion in Microbiology | Year: 2012

Cyclic dimeric guanosine monophosphate (c-di-GMP) is a common, bacterial second messenger that regulates diverse cellular processes in bacteria. Opposing activities of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) control c-di-GMP homeostasis in the cell. Many microbes have a large number of genes encoding DGCs and PDEs that are predicted to be part of c-di-GMP signaling networks. Other building blocks of these networks are c-di-GMP receptors which sense the cellular levels of the dinucleotide. C-di-GMP receptors form a more diverse family, including various transcription factors, PilZ domains, degenerate DGCs or PDEs, and riboswitches. Recent studies revealing the molecular basis of c-di-GMP signaling mechanisms enhanced our understanding of how this molecule controls downstream biological processes and how c-di-GMP signaling specificity is achieved. © 2012 Elsevier Ltd.


Boyle M.,Cornell University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2016

Gravitational-wave data is gauge dependent. While we can restrict the class of gauges in which such data may be expressed, there will still be an infinite-dimensional group of transformations allowed while remaining in this class, and almost as many different - though physically equivalent - waveforms as there are transformations. This paper presents a method for calculating the effects of the most important transformation group, the Bondi-Metzner-Sachs (BMS) group, consisting of rotations, boosts, and supertranslations (which include time and space translations as special cases). To a reasonable approximation, these transformations result in simple coupling between the modes in a spin-weighted spherical-harmonic decomposition of the waveform. It is shown that waveforms from simulated compact binaries in the publicly available SXS waveform catalog contain unmodeled effects due to displacement and drift of the center of mass, accounting for mode mixing at typical levels of 1%. However, these effects can be mitigated by measuring the average motion of the system's center of mass for a portion of the inspiral, and applying the opposite transformation to the waveform data. More generally, controlling the BMS transformations will be necessary to eliminate the gauge ambiguity inherent in gravitational-wave data for both numerical and analytical waveforms. Open-source code implementing BMS transformations of waveforms is supplied along with this paper in the supplemental materials. © 2016 American Physical Society.


Celik E.,Cornell University | Calik P.,Middle East Technical University
Biotechnology Advances | Year: 2012

Yeasts are widely used in production of recombinant proteins of medical or industrial interest. For each individual product, the most suitable expression system has to be identified and optimized, both on the genetic and fermentative level, by taking into account the properties of the product, the organism and the expression cassette. There is a wide range of important yeast expression hosts including the species Saccharomyces cerevisiae, Pichia pastoris, Hansenula polymorpha, Kluyveromyces lactis, Schizosaccharomyces pombe, Yarrowia lipolytica and Arxula adeninivorans, with various characteristics such as being thermo-tolerant or halo-tolerant, rapidly reaching high cell densities or utilizing unusual carbon sources. Several strains were also engineered to have further advantages, such as humanized glycosylation pathways or lack of proteases. Additionally, with a large variety of vectors, promoters and selection markers to choose from, combined with the accumulated knowledge on industrial-scale fermentation techniques and the current advances in the post-genomic technology, it is possible to design more cost-effective expression systems in order to meet the increasing demand for recombinant proteins and glycoproteins. In this review, the present status of the main and most promising yeast expression systems is discussed. © 2011 Elsevier Inc.


Gaby J.C.,Cornell University
Database : the journal of biological databases and curation | Year: 2014

We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.


Chassaing B.,Georgia State University | Ley R.E.,Cornell University | Gewirtz A.T.,Georgia State University
Gastroenterology | Year: 2014

METHODS: We generated C57BL/6 mice with LoxP sites flanking Tlr5. These mice were crossed with mice expressing Cre recombinase, regulated by the villin or CD11c promoters, to generate mice that lacked expression of TLR5 by IECs (TLR5ΔIEC) or DCs (TLR5ΔDC), respectively. Tlr5fl/fl siblings were used as controls. On weaning, mice were housed by sex and genotype or by sex only (genotypes cohoused). Mice were examined for basal phenotypes, including microbiota composition; we also analyzed responses to pathobiont challenge, administration of dextran sodium sulfate, and high-fat diets.RESULTS: Similar to previous findings from TLR5-null mice, TLR5ΔIEC mice had low-grade inflammation (mild splenomegaly, shortened colons, and increased fecal levels of lipocalin 2), metabolic syndrome, and an inability to clear pathobionts and were prone to developing colitis compared with their sibling controls under both housing conditions. Development of this inflammation in the TLR5ΔIEC mice was eliminated by administration of antibiotics and associated with alterations in localization of microbiota and levels of fecal lipopolysaccharide and flagellin. The composition of the microbiota clustered more closely according to genotype than housing. Loss of TLR5 from DCs did not associate with development of inflammation-associated phenotypes or alterations in the composition of the microbiota but resulted in complete loss of flagellin-induced production of interleukin-22.CONCLUSIONS: In mice, flagellin activation of TLR5 on DCs leads to production of interleukin-22. Expression of TLR5 on IECs regulates the composition and localization of the intestinal microbiota, preventing diseases associated with intestinal inflammation.BACKGROUND & AIMS: Mice lacking the receptor Toll-like receptor 5 (TLR5-null mice), which recognizes flagellin, have an altered intestinal microbiota composition compared with wild-type mice; they develop low-grade inflammation and metabolic syndrome and are prone to colitis. The relative roles of intestinal epithelial cell (IEC) vs dendritic cell (DC) TLR5 in mediating these phenotypes are not clear; modification of intestinal microbiota composition has been reported to reflect animal husbandry practices rather than loss of TLR5. We generated mice with specific disruption of Tlr5 in IECs or DCs by using a breeding scheme that allows comparison with cohoused siblings as controls. © 2014 AGA Institute.


Grigoriu M.,Cornell University
Journal of Computational Physics | Year: 2012

A method is proposed for solving equations with random entries, referred to as stochastic equations (SEs). The method is based on two recent developments. The first approximates the response surface giving the solution of a stochastic equation as a function of its random parameters by a finite set of hyperplanes tangent to it at expansion points selected by geometrical arguments. The second approximates the vector of random parameters in the definition of a stochastic equation by a simple random vector, referred to as stochastic reduced order model (SROM), and uses it to construct a SROM for the solution of this equation.The proposed method is a direct extension of these two methods. It uses SROMs to select expansion points, rather than selecting these points by geometrical considerations, and represents the solution by linear and/or higher order local approximations. The implementation and the performance of the method are illustrated by numerical examples involving random eigenvalue problems and stochastic algebraic/differential equations. The method is conceptually simple, non-intrusive, efficient relative to classical Monte Carlo simulation, accurate, and guaranteed to converge to the exact solution. © 2012 Elsevier Inc.


Vines J.,Cornell University
General Relativity and Gravitation | Year: 2015

We review a simple but instructive application of the formalism of covariant bitensors, to use a deviation vector field along a fiducial geodesic to describe a neighboring worldline, in an exact and manifestly covariant manner, via the exponential map. Requiring the neighboring worldline to be a geodesic leads to the usual linear geodesic deviation equation for the deviation vector, plus corrections at higher order in the deviation and relative velocity. We show how these corrections can be efficiently computed to arbitrary orders via covariant bitensor expansions, deriving a form of the geodesic deviation equation valid to all orders, and producing its explicit expanded form through fourth order. We also discuss the generalized Jacobi equation, action principles for the higher-order geodesic deviation equations, results useful for describing accelerated neighboring worldlines, and the formal general solution to the geodesic deviation equation through second order. © 2015, Springer Science+Business Media New York.


We provide a short review of the status of using atomic-or molecular-scale simulations to look at the phenomena associated with growing thin films of small organic semiconductor materials, such as surface diffusion, thin film growth, Ehrlich-Schwoebel step-edge barrier, etc. We offer a summary of the advantages and limitations of existing computational tools (Molecular Dynamics, kinetic Monte Carlo, ab initio methods, etc.) and hint at method development that may help to deepen our understanding of "functional π"-materials. We provide a deeper focus on computational, as well as related experimental, studies of fundamental questions related to the thin-film growth of a representative member of this class of materials, pentacene, on a variety of substrates from insulating oxides to metals, and show results for some other organic semiconductor members of the class, wherever possible. © 2011 American Chemical Society.


Han Y.,Cornell University
Nature Nanotechnology | Year: 2016

Next-generation electronics calls for new materials beyond silicon, aiming at increased functionality, performance and scaling in integrated circuits. In this respect, two-dimensional gapless graphene and semiconducting transition-metal dichalcogenides have emerged as promising candidates due to their atomic thickness and chemical stability. However, difficulties with precise spatial control during their assembly currently impede actual integration into devices. Here, we report on the large-scale, spatially controlled synthesis of heterostructures made of single-layer semiconducting molybdenum disulfide contacting conductive graphene. Transmission electron microscopy studies reveal that the single-layer molybdenum disulfide nucleates at the graphene edges. We demonstrate that such chemically assembled atomic transistors exhibit high transconductance (10 µS), on–off ratio (∼106) and mobility (∼17 cm2 V-1 s-1). The precise site selectivity from atomically thin conducting and semiconducting crystals enables us to exploit these heterostructures to assemble two-dimensional logic circuits, such as an NMOS inverter with high voltage gain (up to 70). © 2016 Nature Publishing Group


DellaValle D.M.,Cornell University
Current Sports Medicine Reports | Year: 2013

Iron is an essential micronutrient involved in oxidative metabolism and critical to exercise performance. The prevalence of iron deficiency (ID) is much higher in active women for a variety of reasons, and poor iron status has been shown to be detrimental to overall health as well as physical performance. Iron status can be assessed using a number of indicators; however clinical cut-offs for active populations remain controversial. Randomized, placebo-controlled supplementation trials of iron-depleted female athletes have shown that oral iron supplementation in doses of 100-mg FeSO4Idj1 (approximately 20 mg elemental iron) improves iron status and may improve measures of physical performance. It is recommended that female athletes most at risk of ID be screened at the beginning of and during the training season using hemoglobin and serum ferritin, and appropriate dietary and/or supplementation recommendations be made to those with compromised iron status. © 2013 by the American College of Sports Medicine.


Van Ittersum K.,Georgia Institute of Technology | Wansink B.,Cornell University
Journal of Consumer Research | Year: 2012

Despite the challenged contention that consumers serve more onto larger dinnerware, it remains unclear what would cause this and who might be most at risk. The results of five studies suggest that the neglected Delboeuf illusion may explain how the size of dinnerware creates two opposing biases that lead people to overserve on larger plates and bowls and underserve on smaller ones. A countercyclical sinus-shaped relationship is shown to exist between these serving biases and the relative gap between the edge of the food and the edge of the dinnerware. Although these serving biases are difficult to eliminate with attention and education, changing the color of one's dinnerware or tablecloth may help attenuate them. By showing that the Delboeuf illusion offers a mechanistic explanation for how dinnerware size can bias serving and intake, we open new theoretical opportunities for linking illusions to eating behavior and suggest how simple changes in design can improve consumer welfare. © 2011 by JOURNAL OF CONSUMER RESEARCH, Inc. All rights reserved.


Linster C.,Cornell University | Fontanini A.,State University of New York at Stony Brook
Current Opinion in Neurobiology | Year: 2014

Neuromodulation can be defined as a biophysical process that serves to modify - or modulate - the computation performed by a neuron or network as a function of task demands and behavioral state of the animal. These modulatory effects often involve substances extrinsic to the network under observation, such as acetylcholine (ACh), norepinephrine (NE), histamine, serotonin (5-HT), dopamine (DA), and a variety of neuropeptides. Olfactory and gustatory processes especially need to be adaptive and respond flexibly to changing environments, availability of resources and physiological needs. It is therefore crucial to understand the neuromodulatory processes that regulate the function of these systems. © 2014 Elsevier Ltd.


Alenghat T.,Cincinnati Childrens Hospital Medical Center | Artis D.,Cornell University
Trends in Immunology | Year: 2014

The trillions of beneficial commensal microorganisms that normally reside in the gastrointestinal tract have emerged as a critical source of environmentally-derived stimuli that can impact health and disease. However, the underlying cellular and molecular mechanisms that recognize commensal bacteria-derived signals and regulate mammalian homeostasis are just beginning to be defined. Highly coordinated epigenomic modifications allow mammals to alter the transcriptional program of a cell in response to environmental cues. These modifications may play a key role in regulating the dynamic relationship between mammals and their microbiota. We review recent advances in understanding the interplay between the microbiota and mammalian epigenomic pathways, and highlight emerging findings that implicate a central role for histone deacetylases (HDACs) in orchestrating host-microbiota interactions. © 2014 Elsevier Ltd.


Mick D.U.,University of Gottingen | Fox T.D.,Cornell University | Rehling P.,University of Gottingen | Rehling P.,Max Planck Institute for Biophysical Chemistry
Nature Reviews Molecular Cell Biology | Year: 2011

Mitochondria maintain genome and translation machinery to synthesize a small subset of subunits of the oxidative phosphorylation system. To build up functional enzymes, these organellar gene products must assemble with imported subunits that are encoded in the nucleus. New findings on the early steps of cytochrome c oxidase assembly reveal how the mitochondrial translation of its core component, cytochrome c oxidase subunit 1 (Cox1), is directly coupled to the assembly of this respiratory complex. © 2011 Macmillan Publishers Limited. All rights reserved.


Rivella S.,Cornell University
Blood Reviews | Year: 2012

Ineffective erythropoiesis is the hallmark of beta-thalassemia that triggers a cascade of compensatory mechanisms resulting in clinical sequelae such as erythroid marrow expansion, extramedullary hematopoiesis, splenomegaly, and increased gastrointestinal iron absorption. Recent studies have begun to shed light on the complex molecular mechanisms underlying ineffective erythropoiesis and the associated compensatory pathways; this new understanding may lead to the development of novel therapies. Increased or excessive activation of the Jak2/STAT5 pathway promotes unnecessary disproportionate proliferation of erythroid progenitors, while other factors suppress serum hepcidin levels leading to dysregulation of iron metabolism. Preclinical studies suggest that Jak inhibitors, hepcidin agonists, and exogenous transferrin may help to restore normal erythropoiesis and iron metabolism and reduce splenomegaly; however, further research is needed. © 2012 Elsevier Ltd.


Van Wijk K.J.,Cornell University
Annual Review of Plant Biology | Year: 2015

Plastids, mitochondria, and peroxisomes are key organelles with dynamic proteomes in photosynthetic eukaryotes. Their biogenesis and activity must be coordinated and require intraorganellar protein maturation, degradation, and recycling. The three organelles together are predicted to contain ∼200 presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar proteins, such as N-end degrons and tagging systems, have not been identified, but the substrate recognition mechanisms likely share similarities between organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, degrons, and protein lifetime. Intraorganellar proteolysis is complemented by autophagy of whole organelles or selected organellar content, as well as by cytosolic protein ubiquitination and degradation by the proteasome. This review summarizes (putative) plant organellar protease functions and substrate-protease relationships. Examples illustrate key proteolytic events. ©2015 by Annual Reviews. All rights reserved.


Le Clair A.,Cornell University
New Journal of Physics | Year: 2011

We calculate the ratio of the viscosity to the entropy density for both Bose and Fermi gases in the unitary limit using a new approach to the quantum statistical mechanics of gases based on the S-matrix. In the unitary limit the scattering length diverges and the S-matrix equals - 1. For the fermion case, we obtain η/s > 4.7 times the proposed lower bound of h/4 πk B, which came from the anti-Desitter space/conformal field theory correspondence (AdS/CFT) for gauge theories, consistent with the most recent experiments. For the bosonic case, we present evidence that the gas undergoes a phase transition to a strongly interacting Bose-Einstein condensate and is a more perfect fluid, with η/s < 1.3 times the bound. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.


Cornwell B.,Cornell University
Research on Aging | Year: 2011

Research on older adults' social integration usually focuses on time-indefinite access to social support, community involvement, and network connectedness. Little research has examined the actual amount of social contact older adults have on a typical day. The author uses nationally representative data on 92,698 adults-collected in the 2003-2009 American Time Use Surveys-to examine age-related trends in rates of everyday contact. Zero-inflated negative binomial regression analyses reveal nonlinear relationships between age and rates of social contact. Older adults have substantially lower rates of social contact than younger and middle-aged adults-especially among women. A significant portion, but not all, of the age-related variation in contact patterns is attributable to life-course factors like living arrangements. The author closes by considering several potential explanations for these trends and by urging social gerontologists to pay closer attention to the causes and consequences of microsocial contact patterns among older adults. © The Author(s) 2011.


Elser V.,Cornell University
New Journal of Physics | Year: 2011

We develop the analysis of x-ray intensity correlations from dilute ensembles of identical particles in a number of ways. Firstly, we show that the three-dimensional (3D) particle structure can be determined if the particles can be aligned with respect to a single axis having a known angle with respect to the incident beam. Secondly, we clarify the phase problem in this setting and introduce a data reduction scheme that assesses the integrity of the data even before particle reconstruction is attempted. Finally, we describe an algorithm that reconstructs intensity and particle density simultaneously, thereby making maximal use of the available constraints. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.


Krimmel B.A.,University of California at Davis | Pearse I.S.,Cornell University
Ecology Letters | Year: 2013

Plant-provided foods for predatory arthropods such as extrafloral nectar and protein bodies provide indirect plant defence by attracting natural enemies of herbivores, enhancing top-down control. Recently, ecologists have also recognised the importance of carrion as a food source for predators. Sticky plants are widespread and often entrap and kill small insects, which we hypothesised would increase predator densities and potentially affect indirect defence. We manipulated the abundance of this entrapped insect carrion on tarweed (Asteraceae: Madia elegans) plants under natural field conditions, and found that carrion augmentation increased the abundance of a suite of predators, decreased herbivory and increased plant fitness. We suggest that entrapped insect carrion may function broadly as a plant-provided food for predators on sticky plants. © 2012 Blackwell Publishing Ltd/CNRS.


Felzenszwalb P.F.,University of Chicago | Zabih R.,Cornell University
IEEE Transactions on Pattern Analysis and Machine Intelligence | Year: 2011

Optimization is a powerful paradigm for expressing and solving problems in a wide range of areas, and has been successfully applied to many vision problems. Discrete optimization techniques are especially interesting since, by carefully exploiting problem structure, they often provide nontrivial guarantees concerning solution quality. In this paper, we review dynamic programming and graph algorithms, and discuss representative examples of how these discrete optimization techniques have been applied to some classical vision problems. We focus on the low-level vision problem of stereo, the mid-level problem of interactive object segmentation, and the high-level problem of model-based recognition. © 2011 IEEE.


St. George S.,University of Minnesota | Ault T.R.,Cornell University
Quaternary Science Reviews | Year: 2014

Here we show how the seasonality and strength of climate signals recorded by tree-ring widths changes across the Northern Hemisphere, and outline major regional differences in the climate 'window' sensed by trees that both constrain and augment our ability to interpret these records as paleoclimatic proxies. After surveying nearly 2200 ring-width records, we find the spatial structure of tree-climate relations across the hemisphere matches behavior predicted several decades ago very closely, confirming the principles that guide dendroclimatology are robust despite the complexity of interactions between climate, ecology and tree biology. We also show that climate filtering conducted by individual trees creates major regional differences in information that may be recovered from the hemispheric network. This behavior can introduce geographic biases to dendroclimatic reconstructions, but it also may be useful to evaluate the success of reconstruction techniques that explicitly represent the physical processes linking climate to tree growth. © 2014 Elsevier Ltd.


Gibofsky A.,Cornell University
American Journal of Managed Care | Year: 2014

Rheumatoid arthritis (RA) is one of the more common autoimmune disorders, affecting approximately 1% of the population worldwide. The exact cause of RA is not known; however, initiation of disease seems to result from an interaction among genetic susceptibility, environmental triggers, and chance. RA is characterized by dysregulated inflammatory processes in the synovium of the joint that eventually leads to the destruction of both cartilaginous and bony elements of the joint, with resulting pain and disability. Systemic inflammation associated with RA is associated with a variety of extra-articular comorbidities, including cardiovascular disease, resulting in increased mortality in patients with RA. RA is also associated with several psychosocial disorders. Classification criteria for RA that were promulgated jointly by the American College of Rheumatology and the European League Against Rheumatism in 2010 emphasize early detection of RA so that effective management can be initiated before pathological changes become irreversible.


Hoffmann R.,Cornell University
Angewandte Chemie - International Edition | Year: 2013

In a different light: In a provocative look at nanoscience, Nobel Laureate Roald Hoffmann considers the structural and electronic perplexities of dimensionality, the consequences of bond severance in nanoobject formation, the implications of simple acid-base chemistry for stabilization of nanostructures, and what lessons might be learned from surface science on structural relaxation and reconstruction. © 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.


Boyle M.,Cornell University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

This paper defines an angular velocity for time-dependent functions on the sphere and applies it to gravitational waveforms from compact binaries. Because it is geometrically meaningful and has a clear physical motivation, the angular velocity is uniquely useful in helping to solve an important - and largely ignored - problem in models of compact binaries: the inverse problem of deducing the physical parameters of a system from the gravitational waves alone. It is also used to define the corotating frame of the waveform. When decomposed in this frame, the waveform has no rotational dynamics and is therefore as slowly evolving as possible. The resulting simplifications lead to straightforward methods for accurately comparing waveforms and constructing hybrids. As formulated in this paper, the methods can be applied robustly to both precessing and nonprecessing waveforms, providing a clear, comprehensive, and consistent framework for waveform analysis. Explicit implementations of all these methods are provided in accompanying computer code. © 2013 American Physical Society.


Gudas L.J.,New York Medical College | Gudas L.J.,Cornell University
Seminars in Cell and Developmental Biology | Year: 2013

Vitamin A (all-trans retinol) and its active metabolites, collectively called retinoids, exert potent effects on stem cell differentiation and thus, the formation of the entire organism, in part via the modulation of the epigenome. All-trans retinoic acid (RA), through binding to the retinoic acid receptors (RARs), alters interactions of the RARs with various protein components of the transcription complex at numerous genes in stem cells, and some of these protein components of the transcription complex then either place or remove epigenetic marks on histones or on DNA, altering chromatin structure and leading to an exit from the self-renewing, pluripotent stem cell state. Different epigenetic mechanisms, i.e. first, primarily H3K27me3 marks and then DNA methylation, may be employed by embryonic stem cells and other stem cells for control of early vs. late stages of cell differentiation. Creating these stable epigenetic changes requires the actions of many molecules, including tet1, polycomb protein complexes (PRCs), miRNAs, DNA methyltransferases (DNMTs), and telomerase reverse transcriptase. A more complete understanding of retinoid-dependent stem cell differentiation should reward us with new insights into the failure to maintain a differentiated state that is an essential part of neoplastic cell transformation and cancer. © 2013 Elsevier Ltd.


Chakravarti A.,Johns Hopkins University | Clark A.G.,Cornell University | Mootha V.K.,Massachusetts General Hospital
Cell | Year: 2013

Technologies for genome-wide sequence interrogation have dramatically improved our ability to identify loci associated with complex human disease. However, a chasm remains between correlations and causality that stems, in part, from a limiting theoretical framework derived from Mendelian genetics and an incomplete understanding of disease physiology. Here we propose a set of criteria, akin to Koch's postulates for infectious disease, for assigning causality between genetic variants and human disease phenotypes. © 2013 Elsevier Inc.


Cordes J.M.,Cornell University | Jenet F.A.,University of Texas at Brownsville
Astrophysical Journal | Year: 2012

We compare the detectability of gravitational bursts passing through the solar system with those passing near each millisecond pulsar in an N-pulsar timing array. The sensitivity to Earth-passing bursts can exploit the correlation expected in pulse arrival times while pulsar-passing bursts, though uncorrelated between objects, provide an N-fold increase in overall time baseline that can compensate for the lower sensitivity. Bursts with memory from mergers of supermassive black holes produce step functions in apparent spin frequency that are the easiest to detect in pulsar timing. We show that the burst rate and amplitude distribution, while strongly dependent on inadequately known cosmological evolution, may favor detection in the pulsar terms rather than the Earth timing perturbations. Any contamination of timing data by red spin noise makes burst detection more difficult because both signals grow with the length of the time data span T. Furthermore, the different bursts that could appear in one or more data sets of length T 10yr also affect the detectability of the gravitational wave stochastic background that, like spin noise, has a red power spectrum. A burst with memory is a worthwhile target in the timing of multiple pulsars in a globular cluster because it should produce a correlated signal with a time delay of less than about 10years in some cases. © 2012. The American Astronomical Society. All rights reserved..


Cohen J.I.,Cornell University
American Journal of Botany | Year: 2010

Premise of the study: Research on the subject of heterostyly is often traced back to 1877 when Charles Darwin published the landmark book The Different Forms of Flowers on Plants of the Same Species. This book synthesized heterostyly research at the time, much of which Darwin conducted, and it continues to be a major contribution to the study of the breeding system. In this book, Darwin discussed the ecology, morph-specific differences, self- and intramorph-incompatibility, evolution and origin, and floral development of heterostyly. Many of the hypotheses he proposed have been and continue to be tested. Key results: Throughout the 20th and 21st centuries, researchers have continued to identify new and different morph-specific floral characters, discover the mechanisms that underlie heteromorphic self-incompatibility, use phylogenies to examine the evolution of heterostyly, and determine novel floral developmental patterns in heterostylous species. From all of these studies, we have learned a great deal about the function, evolution, and development of heterostyly. Conclusions: However, almost 150 years after Darwin's publications on the subject of heterostyly, we still have a great deal to learn concerning the breeding system, and new technologies and techniques are allowing for new advances in heterostyly research to occur. © 2010 Botanical Society of America.


Grigoriu M.,Cornell University
Journal of Engineering Mechanics | Year: 2011

Current estimates of seismic structural fragilities are commonly made on the basis of finite collections of actual or virtual ground-acceleration records that are scaled to have the same scalar intensity measure, for example, peak ground acceleration or pseudospectral acceleration. This paper models seismic ground-acceleration records by samples of Gaussian processes X(t) and constructs scaled versions X̃(t) of X(t) by following current procedures. This analysis shows that X̃(t) and X(t) have different probability laws, so that fragilities on the basis of X̃(t) provide limited if any information on the seismic performance of structural systems, that is, fragilities on the basis of X(t). The usefulness of current fragility estimates on the basis of scaled seismic ground-acceleration records is questionable, and scaling ground motions is not recommended. © 2011 American Society of Civil Engineers.


Nepusz T.,University of London | Yu H.,Cornell University | Paccanaro A.,University of London
Nature Methods | Year: 2012

We introduce clustering with overlapping neighborhood expansion (ClusterONE), a method for detecting potentially overlapping protein complexes from protein-protein interaction data. ClusterONE-derived complexes for several yeast data sets showed better correspondence with reference complexes in the Munich Information Center for Protein Sequence (MIPS) catalog and complexes derived from the Saccharomyces Genome Database (SGD) than the results of seven popular methods. The results also showed a high extent of functional homogeneity. © 2012 Nature America, Inc. All rights reserved.


Just D.R.,Cornell University | Price J.,Brigham Young University
Journal of Human Resources | Year: 2013

There is growing interest in the situations in which incentives have a significant effect on positive behaviors, particularly in children. Using a randomized field experiment, we find that incentives increase the fraction of children eating a serving of fruits or vegetables during lunch by 80 percent and reduce the amount of waste by 33 percent. At schools with a larger fraction of low-income children, the increase in the fraction of children who eat a serving of fruits or vegetables is even larger, indicating that incentives successfully target the children who are likely to benefit the most from the increased consumption. © 2013 by the Board of Regents of the University of Wisconsin System.


Stoye J.,Cornell University
Theory and Decision | Year: 2011

This article provides unified axiomatic foundations for the most common optimality criteria in statistical decision theory. It considers a decision maker who faces a number of possible models of the world (possibly corresponding to true parameter values). Every model generates objective probabilities, and von Neumann-Morgenstern expected utility applies where these obtain, but no probabilities of models are given. This is the classic problem captured by Wald's (Statistical decision functions, 1950) device of risk functions. In an Anscombe-Aumann environment, I characterize Bayesianism (as a backdrop), the statistical minimax principle, the Hurwicz criterion, minimax regret, and the "Pareto" preference ordering that rationalizes admissibility. Two interesting findings are that c-independence is not crucial in characterizing the minimax principle and that the axiom which picks minimax regret over maximin utility is von Neumann-Morgenstern independence. © 2010 Springer Science+Business Media, LLC.


Bauer M.,University of Heidelberg | Neubert M.,Johannes Gutenberg University Mainz | Neubert M.,Cornell University
Physical Review Letters | Year: 2016

We show that by adding a single new scalar particle to the standard model, a TeV-scale leptoquark with the quantum numbers of a right-handed down quark, one can explain in a natural way three of the most striking anomalies of particle physics: the violation of lepton universality in B→K + - decays, the enhanced B→D(∗)τν decay rates, and the anomalous magnetic moment of the muon. Constraints from other precision measurements in the flavor sector can be satisfied without fine-tuning. Our model predicts enhanced B→K(∗)νν decay rates and a new-physics contribution to Bs-Bs mixing close to the current central fit value. © 2016 American Physical Society.


Soderlund D.M.,Cornell University
Pesticide Biochemistry and Physiology | Year: 2010

Pyrethroids disrupt nerve function by altering the rapid kinetic transitions between conducting and nonconducting states of voltage-gated sodium channels that underlie the generation of nerve action potentials. Recent studies of pyrethroid action on cloned insect and mammalian sodium channel isoforms expressed in Xenopus laevis oocytes show that in some cases pyrethroid modification is either absolutely dependent on or significantly enhanced by repeated channel activation. These use-dependent effects have been interpreted as evidence of preferential binding of at least some pyrethroids to the open, rather than resting, state of the sodium channel. This paper reviews the evidence for state-dependent modification of insect and mammalian sodium channels expressed in oocytes by pyrethroids and considers the implications of state-dependent effects for understanding the molecular mechanism of pyrethroid action and the development and testing of models of the pyrethroid receptor. © 2009 Elsevier Inc.


Lerman B.B.,Cornell University
Trends in Cardiovascular Medicine | Year: 2015

During the last 20 years, the molecular etiology for many ventricular tachyarrhythmias once referred to as "idiopathic," has been elucidated. These arrhythmias are due to mutations in ion channels or structural proteins and include ventricular tachyarrhythmias due to long and short QT syndromes, Brugada syndrome, and catecholaminergic polymorphic ventricular tachycardia (VT). However, the basis for the most common form of idiopathic ventricular arrhythmia, which originates from right or left ventricular outflow tracts, has remained elusive. Although traditionally considered a benign ventricular arrhythmia, it is now appreciated that some outflow tract arrhythmias also trigger polymorphic VT or sudden cardiac death or result in cardiomyopathy. The current understanding of outflow tract arrhythmias will be examined. © 2015 Elsevier Inc..


Gudas L.J.,Cornell University
Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids | Year: 2012

The vitamin A (retinol) metabolite, all-trans retinoic acid (RA), is a signaling molecule that plays key roles in the development of the body plan and induces the differentiation of many types of cells. In this review the physiological and pathophysiological roles of retinoids (retinol and related metabolites) in mature animals are discussed. Both in the developing embryo and in the adult, RA signaling via combinatorial Hox gene expression is important for cell positional memory. The genes that require RA for the maturation/differentiation of T cells are only beginning to be cataloged, but it is clear that retinoids play a major role in expression of key genes in the immune system. An exciting, recent publication in regeneration research shows that ALDH1a2 (RALDH2), which is the rate-limiting enzyme in the production of RA from retinaldehyde, is highly induced shortly after amputation in the regenerating heart, adult fin, and larval fin in zebrafish. Thus, local generation of RA presumably plays a key role in fin formation during both embryogenesis and in fin regeneration. HIV transgenic mice and human patients with HIV-associated kidney disease exhibit a profound reduction in the level of RARβ protein in the glomeruli, and HIV transgenic mice show reduced retinol dehydrogenase levels, concomitant with a greater than 3-fold reduction in endogenous RA levels in the glomeruli. Levels of endogenous retinoids (those synthesized from retinol within cells) are altered in many different diseases in the lung, kidney, and central nervous system, contributing to pathophysiology. This article is part of a Special Issue entitled Retinoid and Lipid Metabolism. © 2011 Elsevier B.V.


Brannon P.M.,Cornell University
Scandinavian Journal of Clinical and Laboratory Investigation | Year: 2012

Despite interest and expanding research on non-bone health outcomes, the evidence remains inconclusive concerning the causal role of vitamin D in the non-bone health outcomes. To improve our understanding of its role, research needs to address five key areas related to vitamin D: 1) its physiology and molecular pathways. 2) its relationship to health outcomes. 3) its exposure-response relationships, 4) its interactions with genotype and other nutrients and 5) its adverse effects. Its metabolism needs to be elucidated including extra-renal activation and catabolism, distribution and mobilization from body pools, kinetics of this distribution, and their regulation during pregnancy and lactation. Rigorous, well-designed randomized clinical trials need to evaluate the causal role of vitamin D in a diverse array of non-bone health and chronic disease outcomes across the life cycle and reproductive states. Critically needed is the determination of the exposure-response, inflection and threshold of serum 25(OH)D concentrations relative to functional and health outcomes. The dose-response relationships of standardized measures of serum 25(OH)D need to be understood in response to low and high doses of total vitamin D with careful consideration of confounding factors including catabolic rates. How do relevant genetic polymorphisms, dietary calcium and phosphate and potentially dietary cholesterol interact with vitamin D exposure on its bioavailability, transport, distribution in body pools, metabolism and action as well as on bone and non-bone health outcomes? The nature and mechanisms of U-shaped risk relationships with adverse health outcomes at higher exposure to vitamin D needs elucidated across the life cycle and reproductive stages. © 2012 Informa Healthcare.


Barrett C.B.,Cornell University
Science | Year: 2010

Food security is a growing concern worldwide. More than 1 billion people are estimated to lack sufficient dietary energy availability, and at least twice that number suffer micronutrient deficiencies. Because indicators inform action, much current research focuses on improving food insecurity measurement. Yet estimated prevalence rates and patterns remain tenuous because measuring food security, an elusive concept, remains difficult. © 2010 American Association for the Advancement for Science. All Rights Reserved.


Wansink B.,Cornell University
Physiology and Behavior | Year: 2010

Plate shapes and package sizes, lighting and layout, color and convenience: these are a few of hidden persuaders that can contribute to how much food a person eats. This review first posits that these environmental factors influence eating because they increase consumption norms and decrease consumption monitoring. Second, it suggests that simply increasing awareness and offering nutrition education will be disappointingly ineffective in changing mindless eating. Third, promising pilot results from the National Mindless Eating Challenge provide insights into helping move from mindless eating to mindlessly eating better. The paper represents an invited review by a symposium, award winner or keynote speaker at the Society for the Study of Ingestive Behavior [SSIB] Annual Meeting in Portland, July 2009. © 2010 Elsevier Inc.


Farina M.,Cornell University
Journal of Cosmology and Astroparticle Physics | Year: 2015

We study a natural implementation of Asymmetric Dark Matter in Twin Higgs models. The mirroring of the Standard Model strong sector suggests that a twin baryon with mass around 5 GeV is a natural Dark Matter candidate once a twin baryon number asymmetry comparable to the SM asymmetry is generated. We explore twin baryon Dark Matter in two different scenarios, one with minimal content in the twin sector and one with a complete copy of the SM, including a light twin photon. The essential requirements for successful thermal history are presented, and in doing so we address some of the cosmological issues common to many Twin Higgs models. The required interactions we introduce predict signatures at direct detection experiments and at the LHC.


MacK D.J.,Cornell University | Njardarson J.T.,University of Arizona
Angewandte Chemie - International Edition | Year: 2013

Building with berries! Several labdane natural products have been synthesized for the first time by the combination of a copper-catalyzed vinyl oxirane ring expansion reaction with an abundant, inexpensive, chiral natural source (juniper berries; see scheme). These expedient (1-5 step) syntheses have resulted in the structural confirmations of five natural products and one reassignment. Reagent-controlled oxidation and 1,3-diene isomerization results are also presented. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Grigoriu M.,Cornell University
International Journal for Numerical Methods in Engineering | Year: 2010

A practical method is developed for calculating statistics of the states of linear dynamic systems with deterministic properties subjected to non-Gaussian noise and systems with uncertain properties subjected to Gaussian and non-Gaussian noise. These classes of problems are relevant as most systems have uncertain properties, physical noise is rarely Gaussian, and the classical theory of linear random vibration applies to deterministic systems and can only deliver the first two moments of a system state if the noise is non-Gaussian. The method (1) is based on approximate representations of all or some of the random elements in the definition of linear random vibration problems by stochastic reduced-order models (SROMs), that is, simple random elements having a finite number of outcomes of unequal probabilities, (2) can be used to calculate statistics of a system state beyond its first two moments, and (3) establishes bounds on the discrepancy between exact and SROM-based solutions of linear random vibration problems. The implementation of the method has required to integrate existing and new numerical algorithms. Examples are presented to illustrate the application of the proposed method and assess its accuracy. © 2009 John Wiley & Sons, Ltd.


Verma R.,Cornell University
Journal of Operations Management | Year: 2013

Researchers in several academic disciplines have investigated the effect of the sequence of pleasure and pain on the customer in service, experience, or healthcare-related interactions. Specifically, past research from psychology, behavioral economics, and other related fields suggests that the sequence effect can significantly impact a customer's overall impression of a service interaction. In this article, we test the influence that the sequence of discrete events separated by several days or weeks plays on customers' assessment of service bundles. If the relative importance of the sequence effect for discrete bundles is known, then a service designer and event scheduler can optimize and develop a better sequence of interactions for the customers, leading to higher satisfaction, loyalty, and repurchase. Using an extensive multi-year ticket purchase database from a world-renowned performing arts venue, we develop and test econometric models to predict season ticket subscription repurchase. The estimated models show that sequence effects do indeed play a significant role in determining customer repurchase of subscriptions. These results have important implications for effective service design and capacity planning for a wide range of service industries. This article suggests both managerial implications and future research opportunities related to sequence effects in service operations. © 2012 Elsevier B.V.


Roboz G.J.,Cornell University
Hematology / the Education Program of the American Society of Hematology. American Society of Hematology. Education Program | Year: 2011

Approximately 12 000 adults are diagnosed with acute myeloid leukemia (AML) in the United States annually, the majority of whom die from their disease. The mainstay of initial treatment, cytosine arabinoside (ara-C) combined with an anthracycline, was developed nearly 40 years ago and remains the worldwide standard of care. Advances in genomics technologies have identified AML as a genetically heterogeneous disease, and many patients can now be categorized into clinicopathologic subgroups on the basis of their underlying molecular genetic defects. It is hoped that enhanced specificity of diagnostic classification will result in more effective application of targeted agents and the ability to create individualized treatment strategies. This review describes the current treatment standards for induction, consolidation, and stem cell transplantation; special considerations in the management of older AML patients; novel agents; emerging data on the detection and management of minimal residual disease (MRD); and strategies to improve the design and implementation of AML clinical trials.


Bowman D.D.,Cornell University
Parasites and Vectors | Year: 2012

In order to provide a background to current concerns relative to the possible resistance of heartworms to macrocyclic lactones, this review summarizes various studies in which lack of efficacies (LOEs) have been observed in dogs on macrocyclic lactone preventives relative to the United States of America. Some of these studies have been published in the peer-reviewed literature, others have appeared in various reports to the Center for Veterinary Medicine (CVM) of the Food and Drug Administration (FDA) of the USA as New Animal Drug Application (NADA) summaries, and one appeared as a letter to US veterinarians. This review also discusses reports relating to the potential problem of heartworm resistance in microfilariae and third-stage larvae, as well as molecular markers associated with resistance to macrocyclic lactones within Dirofilaria immitis. As more work is being done in this area of great concern relative to the protection of dogs from infection using this class of preventives, it seems timely to summarize what is known about heartworms, their potential resistance to treatment, and the means of selecting for resistance genes in populations of this helminth in the laboratory and in the field. © 2012 Bowman; licensee BioMed Central Ltd.


Zaleski-Ejgierd P.,Cornell University
Journal of physics. Condensed matter : an Institute of Physics journal | Year: 2012

An initial observation of the formation of WH under pressure from W gaskets surrounding hydrogen in diamond anvil cells led to a theoretical study of tungsten hydride phases. At P = 1 atm no stoichiometry is found to be stable with respect to separation into the elements, but as the pressure is raised WH(n) (n = 1-6, 8) stoichiometries are metastable or stable. WH and WH(4) are calculated to be stable at P > 15 GPa, WH(2) becomes stable at P > 100 GPa and WH(6) at P > 150 GPa. In agreement with experiment, the structure computed for WH is anti-NiAs. WH(2) shares with WH a hexagonal arrangement of tungsten atoms, with hydrogen atoms occupying octahedral and tetrahedral holes. For WH(4) the W atoms are in a distorted fcc arrangement. As the number of hydrogens rises, the coordination of W by H increases correspondingly, leading to a twelve-coordinated W in WH(6). In WH(8) H(2) units also develop. All of the hydrides considered should be metallic at high pressure, though the Fermi levels of WH(4) and WH(6) lie in a deep pseudogap. Prodded by these theoretical studies, experiments were then undertaken to seek phases other than WH, exploring a variety of experimental conditions that would favor further reaction. Though a better preparation and characterization of WH resulted, no higher hydrides have as yet been found.


The Cassini spacecraft has provided data on over twenty satellites orbiting Saturn. In this study we update the shape measurements derived from imaging data of nearly all the observed regular satellites (those with low eccentricities and inclinations) and briefly discuss some of the implications of their properties. In particular, the improved data show that Rhea's shape is hydrostatic. © 2010 Elsevier Inc.


Hess P.G.,Cornell University | Zbinden R.,CNRS Laboratory for Aerology
Atmospheric Chemistry and Physics | Year: 2013

The influence of stratospheric ozone on the interannual variability and trends in tropospheric ozone is evaluated between 30 and 90 N from 1990-2009 using ozone measurements and a global chemical transport model, the Community Atmospheric Model with chemistry (CAM-chem). Long-term measurements from ozonesondes, at 150 and 500 hPa, and the Measurements of OZone and water vapour by in-service Airbus aircraft programme (MOZAIC), at 500 hPa, are analyzed over Japan, Canada, the Eastern US and Northern and Central Europe. The measurements generally emphasize northern latitudes, although the simulation suggests that measurements over the Canadian, Northern and Central European regions are representative of the large-scale interannual ozone variability from 30 to 90 N at 500 hPa. CAM-chem is run with input meteorology from the National Center for Environmental Prediction; a tagging methodology is used to identify the stratospheric contribution to tropospheric ozone concentrations. A variant of the synthetic ozone tracer (synoz) is used to represent stratospheric ozone. Both the model and measurements indicate that on large spatial scales stratospheric interannual ozone variability drives significant tropospheric variability at 500 hPa and the surface. In particular, the simulation and the measurements suggest large stratospheric influence at the surface sites of Mace Head (Ireland) and Jungfraujoch (Switzerland) as well as many 500 hPa measurement locations. Both the measurements and simulation suggest the stratosphere has contributed to tropospheric ozone trends. In many locations between 30-90 N 500 hPa ozone significantly increased from 1990-2000, but has leveled off since (from 2000-2009). The simulated global ozone budget suggests global stratosphere-troposphere exchange increased in 1998-1999 in association with a global ozone anomaly. Discrepancies between the simulated and measured ozone budget include a large underestimation of measured ozone variability and discrepancies in long-term stratospheric ozone trends. This suggests the need for more sophisticated simulations including better representations of stratospheric chemistry and circulation. © 2013 Author(s).


Gilbert C.,Cornell University
Current Biology | Year: 2013

A new semi-automated method for high-throughput identification of visual neurons and their synaptic partners has been combined with optical recording of activity and behavioral analysis to give the first complete description of an elementary circuit for detecting visual motion. © 2013 Elsevier Ltd. All rights reserved.


Min J.K.,Cornell University | Shaw L.J.,Emory University | Berman D.S.,Cedars Sinai Medical Center
Journal of the American College of Cardiology | Year: 2010

In the past 5 years since the introduction of 64-detector row cardiac computed tomography angiography (CCTA), there has been an exponential growth in the quantity of scientific evidence to support the feasibility of its use in the clinical evaluation of individuals with suspected coronary artery disease (CAD). Since then, there has been considerable debate as to where CCTA precisely fits in the algorithm of evaluation of individuals with suspected CAD. Proponents of CCTA contend that the quality and scope of the available evidence to date support the replacement of conventional methods of CAD evaluation by CCTA, whereas critics assert that clinical use of CCTA is not yet adequately proven and should be restricted, if used at all. Coincident with the scientific debate underlying the clinical utility of CCTA, there has developed a perception by many that the rate of growth in cardiac imaging is disproportionately high and unsustainable. In this respect, all noninvasive imaging modalities and, in particular, more newly introduced ones, have undergone a higher level of scrutiny for demonstration of clinical and economic effectiveness. We herein describe the latest available published evidence supporting the potential clinical and cost efficiency of CCTA, drawing attention not only to the significance but also the limitations of such studies. These points may trigger discussion as to what future studies will be both necessary and feasible for determining the exact role of CCTA in the workup of patients with suspected CAD. © 2010 American College of Cardiology Foundation.


Hunter S.R.,Cornell University | Pasupathy R.,Virginia Polytechnic Institute and State University
INFORMS Journal on Computing | Year: 2013

Consider the context of selecting an optimal system from among a finite set of competing systems, based on a "stochastic" objective function and subject to multiple "stochastic" constraints. In this context, we characterize the asymptotically optimal sample allocation that maximizes the rate at which the probability of false selection tends to zero. Since the optimal allocation is the result of a concave maximization problem, its solution is particularly easy to obtain in contexts where the underlying distributions are known or can be assumed. We provide a consistent estimator for the optimal allocation and a corresponding sequential algorithm fit for implementation. Various numerical examples demonstrate how the proposed allocation differs from competing algorithms. © 2013 INFORMS.


Douglas A.E.,Cornell University
Annual Review of Entomology | Year: 2015

All insects are colonized by microorganisms on the insect exoskeleton, in the gut and hemocoel, and within insect cells. The insect microbiota is generally different from microorganisms in the external environment, including ingested food. Specifically, certain microbial taxa are favored by the conditions and resources in the insect habitat, by their tolerance of insect immunity, and by specific mechanisms for their transmission. The resident microorganisms can promote insect fitness by contributing to nutrition, especially by providing essential amino acids, B vitamins, and, for fungal partners, sterols. Some microorganisms protect their insect hosts against pathogens, parasitoids, and other parasites by synthesizing specific toxins or modifying the insect immune system. Priorities for future research include elucidation of microbial contributions to detoxification, especially of plant allelochemicals in phytophagous insects, and resistance to pathogens; as well as their role in among-insect communication; and the potential value of manipulation of the microbiota to control insect pests. © 2015 by Annual Reviews. All rights reserved.


Bander N.H.,Cornell University
Methods in Molecular Biology | Year: 2013

ADC success requires that all three components of the agent function in a near-flawless manner. Equally important is that the target be selected with stringent consideration as the target is the one factor in ADC development that is immutable and beyond the reach of the developer to refine/manipulate. This chapter reviews the critical factors of target selection that must be met if one is to succeed at ADC development. © Springer Science+Business Media, LLC 2013.


Chirik P.J.,Cornell University
Organometallics | Year: 2010

Metal sandwich compounds, more commonly known as metallocenes, are some of the most enduring molecules in organometallic chemistry. Beginning with Wilkinson's quest for titanocene, [(?5-C5H 5)2Ti], the synthesis and exploration of the electronic structure and reactivity of group 4 metal sandwich complexes have been an ongoing story for almost six decades. This review recounts the historical origins of group 4 metallocenes and highlights synthetic efforts to observe and stabilize formally d2 metal sandwich compounds. Specific attention is devoted to recent developments in the field, including dinitrogen coordination by various substituted titanocene derivatives as well as our group's interest in bis(indenyl)zirconium and -hafnium compounds. © 2010 American Chemical Society.


Locasale J.W.,Cornell University
Trends in Endocrinology and Metabolism | Year: 2012

The intake and metabolism of carbohydrates for the generation of energy and biomass is evolutionarily conserved, down to the most primitive of cells. Although a basal rate of glucose metabolism occurs in all cells, the processing rates of glucose can become dramatically enhanced when cells acquire malignant properties, or remain undifferentiated. This article investigates the consequences of how increased glucose metabolism affects cellular physiology by altering the physicochemical properties of the whole metabolic network. As a result, enhanced lactate production in the presence of oxygen (the Warburg effect) is required, and metabolism is consequently reconfigured, through multiple mechanisms, to confer numerous physiological and possibly regulatory properties to cells. © 2012 Elsevier Ltd.


Wong G.C.L.,University of Illinois at Urbana - Champaign | Pollack L.,Cornell University
Annual Review of Physical Chemistry | Year: 2010

Charges on biological polymers in physiologically relevant solution conditions are strongly screened by water and salt solutions containing counter-ions. However, the entropy of these counterions can result in surprisingly strong interactions between charged objects in water despite short screening lengths, via coupling between osmotic and electrostatic interactions. Widespread work in theory, experiment, and computation has been carried out to gain a fundamental understanding of the rich, yet sometimes counterintuitive, behavior of these polyelectrolyte systems. Examples of polyelectrolyte association in biology include DNA packaging and RNA folding, as well as aggregation and self-organization phenomena in different disease states. Copyright © 2010 by Annual Reviews. All rights reserved.


Wakshlag J.J.,Cornell University
The British journal of nutrition | Year: 2011

Evidence suggests that adipose tissue-derived adipokines induce mild inflammation and may play a role in insulin resistance associated with diabetes. The present study was designed to examine a series of adipokines and markers of inflammation in dogs before and after a successful weight loss. The study included fasting serum samples from twenty-five dogs before and after a weight-loss programme. Serum C-reactive protein (CRP) and monocyte chemoattractant protein-1 (MCP-1) were measured as indicators of chronic inflammation, while serum adipokines including total adiponectin, high-molecular-weight (HMW) adiponectin, resistin and leptin were also examined. Medians for CRP (before, 10.0 (interquartile range 5.4-15.0) μg/ml; after, 5.6 (interquartile range 3.8-7.0) μg/ml) and MCP-1 (before, 212 (interquartile range 157-288) ng/ml; after, 185 (interquartile range 143-215) ng/ml) decreased significantly after weight loss. Medians for resistin showed a mild, yet significant reduction (before, 67.1 (interquartile range 44.4-88.5) pg/ml; after, 60.5 (interquartile range 32.3-67.1) pg/ml), while leptin showed a dramatic decrease after weight loss (before, 18.9 (interquartile range 10.8-35.4) ng/ml; after, 6.6 (interquartile range 3.9-10.2) ng/ml). Serum total adiponectin and HMW adiponectin were unchanged on all analyses performed. These data suggest that weight loss can decrease chronic inflammation; however, the clinical implications of this decrease are not well elucidated in dogs. Surprisingly, there was no increase in total or HMW serum adiponectin after weight loss, as observed previously in human subjects. The lack of change in total and HMW adiponectin might explain why insulin resistance and type 2 diabetes are less prevalent in obese dogs when compared with humans and cats.


Shaik S.,Hebrew University of Jerusalem | Rzepa H.S.,Imperial College London | Hoffmann R.,Cornell University
Angewandte Chemie - International Edition | Year: 2013

What could be simpler than C2, a diatomic molecule that has the second strongest homonuclear bond? This molecule turns out to be a microcosm of the bonding issues that bother chemists, as is shown in this trialogue. Join the three authors in their lively debate, light a candle, as Faraday did, and see the excited states of C2! Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Henn B.M.,State University of New York at Stony Brook | Botigue L.R.,State University of New York at Stony Brook | Bustamante C.D.,Stanford University | Clark A.G.,Cornell University | Gravel S.,McGill University
Nature Reviews Genetics | Year: 2015

Next-generation sequencing technology has facilitated the discovery of millions of genetic variants in human genomes. A sizeable fraction of these variants are predicted to be deleterious. Here, we review the pattern of deleterious alleles as ascertained in genome sequencing data sets and ask whether human populations differ in their predicted burden of deleterious alleles-a phenomenon known as mutation load. We discuss three demographic models that are predicted to affect mutation load and relate these models to the evidence (or the lack thereof) for variation in the efficacy of purifying selection in diverse human genomes. We also emphasize why accurate estimation of mutation load depends on assumptions regarding the distribution of dominance and selection coefficients-quantities that remain poorly characterized for current genomic data sets. © 2015 Macmillan Publishers Limited. All rights reserved.


Concannon P.W.,Cornell University
Animal Reproduction Science | Year: 2011

Domestic dogs are monoestrous, typically non-seasonal, polytocous, spontaneous ovulators and have a spontaneous luteal phase slightly longer (by approx 5 day) than the 64. ±. 1 day luteal phases of a 65 ± 1 day pregnancy, a phase followed by an obligate anestrus before the next 2-3 week "heat" (proestrus-estrus). The resulting inter-estrus intervals of 5-12 months are variable among bitches, commonly 6-7 months, and range from highly variable to regular (to perhaps within. ±. 5-10 day of sequential 7 month cycle, for instance) within bitches, and across studies and do not vary significantly between pregnant and non-pregnant cycles. Hormone levels reported are those observed in this laboratory using previously reported assays and canine gonadotropin standards unless stated otherwise. Endocrine sequences for dog cycles are not unlike those of many other mammals, including selection of ovulatory follicles by increased LH pulsatility, the occurrence of estrus behavior and LH surge during a decline in the estrogen: progestin ratio, a pronounced preovulatory luteinization as in humans and rodents, and luteotrophic roles for both LH and prolactin. Non-pregnant bitches have a spontaneously prolonged luteal phase, often longer and with a more protracted decline in serum progesterone than in pregnancy as there is no uterine luteolytic mechanism. The obligate anestrus of 8-40 weeks is terminated by poorly understood interactions of environment (e.g. pheromones, possibly photoperiod) and a potential endogenous circannual cycle in sensitivities of hypothalamic dopaminergic, serotonergic and/or opioid pathways. © 2010.


Dispersal may affect predator-prey metapopulations by rescuing local sink populations from extinction or by synchronizing population dynamics across the metapopulation, increasing the risk of regional extinction. Dispersal is likely influenced by demographic stochasticity, however, particularly because dispersal rates are often very low in metapopulations. Yet the effects of demographic stochasticity on predator-prey metapopulations are not well known. To that end, I constructed three models of a twopatch predator-prey system. The models constitute a hierarchy of complexity, allowing direct comparisons. Two models included demographic stochasticity (pure jump process [PJP] and stochastic differential equations [SDE]), and the third was deterministic (ordinary differential equations [ODE]). One stochastic model (PJP) treated population sizes as discrete, while the other (SDE) allowed population sizes to change continuously. Both stochastic models only produced synchronized predator-prey dynamics when dispersal was high for both trophic levels. Frequent dispersal by only predators or prey in the PJP and SDE spatially decoupled the trophic interaction, reducing synchrony of the non-dispersive species. Conversely, the ODE generated synchronized predator-prey dynamics across all dispersal rates, except when initial conditions produced anti-phase transients. These results indicate that demographic stochasticity strongly reduces the synchronizing effect of dispersal, which is ironic because demographic stochasticity is often invoked post hoc as a driver of extinctions in synchronized metapopulations. © 2012 by the Ecological Society of America.


Without public trust of climate change science, policymaking in a democratic society cannot address the serious threats that we face. Recent calls for proposals to increase "climate literacy" from federal agencies such as NASA, NOAA (National Oceanic and Atmospheric Administration), and the National Science Foundation illustrate the urgency of this crisis. Although more climate change education is certainly needed, focusing solely on climate literacy will not garner public trust and may leave out high-impact media literacy education. Climate change deniers have been more effective "educators"than scientists and science educators because their messages are (a) empowering, built on the premise that every individual can quickly learn enough to enter public discourse on climate change; and (b) delivered through many forms of media. A more effective strategy for scientists and science educators should include not only discourse approaches that enable trust, with emphasis on empowerment through reasoning skills, but also approaches that embrace the maturing discipline of media literacy education. © 2011 by American Institute of Biological Sciences. All rights reserved.


Genes that are differentially expressed between the sexes (sex-biased genes) are among the fastest evolving genes in animal genomes. The majority of sex-biased expression is attributable to genes that are primarily expressed in sex-limited reproductive tissues, and these reproductive genes are often rapidly evolving because of intra- and intersexual selection pressures. Additionally, studies of multiple taxa have revealed that genes with sex-biased expression are also expressed in a limited number of tissues. This is worth noting because narrowly expressed genes are known to evolve faster than broadly expressed genes. Therefore, it is not clear whether sex-biased genes are rapidly evolving because they have sexually dimorphic expression, because they are expressed in sex-limited reproductive tissues, or because they are narrowly expressed. To determine the extend to which other confounding variables can explain the rapid evolution of sex-biased genes, I analyzed the rates of evolution of sex-biased genes in Drosophila melanogaster and Mus musculus in light of tissue-specific measures of expression. I find that genes with sex-biased expression in somatic tissues shared by both sexes are often evolving faster than non-sex-biased genes, but this is best explained by the narrow expression profiles of sex-biased genes. Sex-biased genes in sex-limited tissues in D. melanogaster, however, evolve faster than other narrowly expressed genes. Therefore, the rapid evolution of sex-biased genes is limited only to those genes primarily expressed in sex-limited reproductive tissues. © The Author 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.


Brannon P.M.,Cornell University | Picciano M.F.,U.S. National Institutes of Health
Annual Review of Nutrition | Year: 2011

Concerns exist about the adequacy of vitamin D in pregnant and lactating women. This review assesses the evidence that maternal vitamin D status influences maternal, fetal, and breast-fed infant bone health; maternal adverse outcomes (preeclampsia, gestational diabetes, obstructed labor, and infectious disease); fetal adverse outcomes (growth, gestational age, and developmental programming); and infant adverse outcomes. The evidence for all of these outcomes is contradictory (except for maternal infectious disease) and lacking causality; thus, it is inconclusive. The 2011 Dietary Reference Intakes for vitamin D and their implications for assessing vitamin D status are discussed. An estimated 5% to 29% of American pregnant women may have inadequate vitamin D status, with the higher prevalence in African Americans. Little is known about the prevalence of inadequacy in American lactating women. Research needs are also identified, especially the need for rigorous and well-designed randomized clinical trials to determine the role of vitamin D in nonbone health outcomes in pregnancy and lactation. Copyright © 2011 by Annual Reviews. All rights reserved.


Ecology Letters (2011) 14: 202-209 Interspecific interactions depend not only on the population densities of the interacting species, but on their phenotypes as well. Phenotypic variation can be plastic or heritable and both mechanisms can drive phenotypic change at rates comparable to or faster than those of ecological dynamics (e.g. changes in population abundances or spatial distributions). In this study, we compare the effects rapidly induced and rapidly evolving defences have on community dynamics by considering the fast phenotypic change limit using fast-slow systems theory. Our approach allows us to study phenotypically plastic and evolving systems with one overarching theory, thus capturing the effects rapidly induced defences have on ecological dynamics and how those effects differ from the effects of evolving defences. Our results show that rapidly induced defences tend to stabilize community dynamics and that some behaviours observed in rapidly evolving systems cannot be produced by phenotypic plasticity. © 2010 Blackwell Publishing Ltd/CNRS.


Cathles L.M.,Cornell University
Geochemistry, Geophysics, Geosystems | Year: 2012

The global warming impact of substituting natural gas for coal and oil is currently in debate. We address this question here by comparing the reduction of greenhouse warming that would result from substituting gas for coal and some oil to the reduction which could be achieved by instead substituting zero carbon energy sources. We show that substitution of natural gas reduces global warming by 40% of that which could be attained by the substitution of zero carbon energy sources. At methane leakage rates that are ∼1% of production, which is similar to today's probable leakage rate of ∼1.5% of production, the 40% benefit is realized as gas substitution occurs. For short transitions the leakage rate must be more than 10 to 15% of production for gas substitution not to reduce warming, and for longer transitions the leakage must be much greater. But even if the leakage was so high that the substitution was not of immediate benefit, the 40%-of-zero-carbon benefit would be realized shortly after methane emissions ceased because methane is removed quickly from the atmosphere whereas CO 2 is not. The benefits of substitution are unaffected by heat exchange to the ocean. CO 2 emissions are the key to anthropogenic climate change, and substituting gas reduces them by 40% of that possible by conversion to zero carbon energy sources. Gas substitution also reduces the rate at which zero carbon energy sources must eventually be introduced. © 2012. American Geophysical Union. All Rights Reserved.


Pimentel D.,Cornell University
Critical Reviews in Plant Sciences | Year: 2011

World malnutrition is a serious problem. Food security for the poor depends on an adequate supply of food and/or the ability to purchase food. The World Health Organization reports that more than 3.7 billion people worldwide are malnourished because of shortages of calories, protein, several vitamins, iron, and iodine. People can die because of shortages of any one or a combination of these nutrients. In the world today there are more than 6.8 billion humans. Based on current rates of increase, the world population is projected to double to more than 13 billion in about 58 years. At a time when the world population continues to expand at a rate of 1.2% per year, adding more than a quarter million people daily, providing adequate food becomes an increasingly difficult problem. The need to increase and make more rational food production, to conserve natural resources, and to reduce food (crop) losses to pests is critical. Also critical is a need to reduce human population numbers. Cropland, water and energy resources are inadquate to support the current 6.8 billion people on earth. © Taylor & Francis Group, LLC.


Koch D.L.,Cornell University | Subramanian G.,Engineering Mechanics Unit
Annual Review of Fluid Mechanics | Year: 2011

Experimental observations indicate that, at sufficiently high cell densities, swimming bacteria exhibit coordinated motions on length scales (10 to 100 μ) that are large compared with the size of an individual cell but too small to yield significant gravitational or inertial effects. We discuss simulations of hydrodynamically interacting self-propelled particles as well as stability analyses and numerical solutions of averaged equations of motion for low Reynolds number swimmers. It has been found that spontaneous motions can arise in such systems from the coupling between the stresses the bacteria induce in the fluid as they swim and the rotation of the bacteria due to the resulting fluid velocity disturbances. © 2011 by Annual Reviews. All rights reserved.


Hayes A.G.,Cornell University
Annual Review of Earth and Planetary Sciences | Year: 2016

Analogous to Earth's water cycle, Titan's methane-based hydrologic cycle supports standing bodies of liquid and drives processes that result in common morphologic features including dunes, channels, lakes, and seas. Like lakes on Earth and early Mars, Titan's lakes and seas preserve a record of its climate and surface evolution. Unlike on Earth, the volume of liquid exposed on Titan's surface is only a small fraction of the atmospheric reservoir. The volume and bulk composition of the seas can constrain the age and nature of atmospheric methane, as well as its interaction with surface reservoirs. Similarly, the morphology of lacustrine basins chronicles the history of the polar landscape over multiple temporal and spatial scales. The distribution of trace species, such as noble gases and higher-order hydrocarbons and nitriles, can address Titan's origin and the potential for both prebiotic and biotic processes. Accordingly, Titan's lakes and seas represent a compelling target for exploration. Copyright © 2016 by Annual Reviews. All rights reserved.


Schroeder F.C.,Cornell University
Chemistry and Biology | Year: 2015

The metabolome of the nematode Caenorhabditis elegans, like that of other model organisms, remained largely uncharacterized until recent studies demonstrated the importance of small molecule-based signaling cascades for many aspects of nematode biology. These studies revealed that nematodes are amazingly skilled chemists: using simple building blocks from primary metabolism and a strategy of modular assembly, nematodes create complex molecular architectures that serve as signaling molecules. These nematode-derived modular metabolites (NDMMs) are based on the dideoxysugars ascarylose and paratose, which serve as scaffolds for the attachment of moieties from lipid, amino acid, neurotransmitter, and nucleoside metabolism. Although preliminary biosynthetic studies have confirmed the primary metabolism origin of some of the building blocks incorporated into NDMMs, the mechanisms that underlie their highly specific assembly are not understood. I argue that identification of new variants of primary metabolism-derived structures that serve important signaling functions in C. Elegans and other nematodes provides a strong incentive for a comprehensive reanalysis of metabolism in higher animals, including humans. © 2015 Elsevier Ltd. All rights reserved.


Mookherjee M.,Cornell University | Mainprice D.,Montpellier University
Geophysical Research Letters | Year: 2014

Using first principle simulations we calculated the elasticity of chlorite. At a density ρ~ 2.60 g cm-3, the elastic constant tensor reveals significant elastic anisotropy: VP ~27%, VS1 ~56%, and VS2 ~43%. The shear anisotropy is exceptionally large for chlorite and enhances upon compression. Upon compression, the shear elastic constant component C44 and C55 decreases, whereas C66 shear component stiffens. The softening in C44 and C55 is reflected in shear modulus, G, and the shear wave velocity, VS. Our results on elastic anisotropy at conditions relevant to the mantle wedge indicates that a 10-20 km layer of hydrated peridotite with serpentine and chlorite could account for the observed shear polarization anisotropy and associated large delay times of 1-2 s observed in some subduction zone settings. In addition, chlorite could also explain the low VP/VS ratios that have been observed in recent high-resolution seismological studies. Key Points First report of high pressure elasticity of chlorite Unusual shear wave anisotropy for chlorite Shear elastic anisotropy explains seismological observations in subduction zones ©2014. American Geophysical Union. All Rights Reserved.


Niklas K.J.,Cornell University
American Journal of Botany | Year: 2014

Multicellularity has evolved at least once in every major eukaryotic clade (in all ploidy levels) and numerous times among the prokaryotes. According to a standard multilevel selection (MLS) model, in each case, the evolution of multicellularity required the acquisition of cell-cell adhesion, communication, cooperation, and specialization attended by a compulsory alignment-of-fitness phase and an export-of-fitness phase to eliminate cell-cell conflict and to establish a reproductively integrated phenotype. These achievements are reviewed in terms of generalized evolutionary developmental motifs (or "modules") whose overall logic constructs were mobilized and executed differently in bacteria, plants, fungi, and animals. When mapped onto a matrix of theoretically possible body plan morphologies (i.e., a morphospace), these motifs and the MLS model identify a "unicellular rArr; colonial ⇒ multicellular" transformation series of body plans that mirrors trends observed in the majority of algae (i.e., a polyphyletic collection of photoautotrophic eukaryotes) and in the land plants, fungi, and animals. However, an alternative, more direct route to multicellularity theoretically exists, which may account for some aspects of fungal and algal evolution, i.e., a "siphonous ⇒ multicellular" transformation series. This review of multicellularity attempts to show that natural selection typically acts on functional traits rather than on the mechanisms that generate them ("Many roads lead to Rome.") and that genome sequence homologies do not invariably translate into morphological homologies ("Rome isn't what it used to be."). © 2014 Botanical Society of America.


Chandon P.,Ican Inc | Wansink B.,Cornell University
Nutrition Reviews | Year: 2012

Food marketing is often singled out as the leading cause of the obesity epidemic. The present review examines current food marketing practices to determine how exactly they may be influencing food intake, and how food marketers could meet their business objectives while helping people eat healthier. Particular attention is paid to the insights provided by recently published studies in the areas of marketing and consumer research, and those insights are integrated with findings from studies in nutrition and related disciplines. The review begins with an examination of the multiple ways in which 1) food pricing strategies and 2) marketing communication (including branding and food claims) bias food consumption. It then describes the effects of newer and less conspicuous marketing actions, focusing on 3) packaging (including the effects of package design and package-based claims) and 4) the eating environment (including the availability, salience, and convenience of food). Throughout, this review underscores the promising opportunities that food manufacturers and retailers have to make profitable "win-win" adjustments to help consumers eat better. © 2012 International Life Sciences Institute.


Power A.G.,Cornell University
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2010

Agricultural ecosystems provide humans with food, forage, bioenergy and pharmaceuticals and are essential to human wellbeing. These systems rely on ecosystem services provided by natural ecosystems, including pollination, biological pest control, maintenance of soil structure and fertility, nutrient cycling and hydrological services. Preliminary assessments indicate that the value of these ecosystem services to agriculture is enormous and often underappreciated. Agroecosystems also produce a variety of ecosystem services, such as regulation of soil and water quality, carbon sequestration, support for biodiversity and cultural services. Depending on management practices, agriculture can also be the source of numerous disservices, including loss of wildlife habitat, nutrient runoff, sedimentation of waterways, greenhouse gas emissions, and pesticide poisoning of humans and non-target species. The tradeoffs that may occur between provisioning services and other ecosystem services and disservices should be evaluated in terms of spatial scale, temporal scale and reversibility. As more effective methods for valuing ecosystem services become available, the potential for 'win-win' scenarios increases. Under all scenarios, appropriate agricultural management practices are critical to realizing the benefits of ecosystem services and reducing disservices from agricultural activities. © 2010 The Royal Society.


Cornwell B.,Cornell University
Journals of Gerontology - Series B Psychological Sciences and Social Sciences | Year: 2015

Objectives. Research shows that socially disadvantaged groups - especially African Americans and people of low socioeconomic status (SES) - experience more unstable social environments. I argue that this causes higher rates of turnover within their personal social networks. This is a particularly important issue among disadvantaged older adults, who may benefit from stable networks. This article, therefore, examines whether social disadvantage is related to various aspects of personal network change. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. Method. Social network change was assessed using longitudinal egocentric network data from the National Social Life, Health, and Aging Project, a study of older adults conducted between 2005 and 2011. Data collection in Wave 2 included a technique for comparing respondents' confidant network rosters between waves. Rates of network losses, deaths, and additions were modeled using multivariate Poisson regression. Results. African Americans and low-SES individuals lost more confidants - especially due to death - than did whites and college-educated respondents. African Americans also added more confidants than whites. However, neither African Americans nor low-SES individuals were able to match confidant losses with new additions to the extent that others did, resulting in higher levels of confidant network shrinkage. These trends are partly, but not entirely, explained by disadvantaged individuals' poorer health and their greater risk of widowhood or marital dissolution. Discussion. Additional work is needed to shed light on the role played by race- and class-based segregation on group differences in social network turnover. Social gerontologists should examine the role these differences play in explaining the link between social disadvantage and important outcomes in later life, such as health decline. © The Author 2014.


The first off-lattice Monte Carlo kinetics model of interstellar dust grain surface chemistry is presented. The positions of all surface particles are determined explicitly, according to the local potential minima resulting from the pair-wise interactions of contiguous atoms and molecules, rather than by a pre-defined lattice structure. The model is capable of simulating chemical kinetics on any arbitrary dust grain morphology, as determined by the user-defined positions of each individual dust grain atom. A simple method is devised for the determination of the most likely diffusion pathways and their associated energy barriers for surface species. The model is applied to a small, idealized dust grain, adopting various gas densities and using a small chemical network. Hydrogen and oxygen atoms accrete onto the grain to produce H 2O, H2, O2, and H2O2. The off-lattice method allows the ice structure to evolve freely; the ice mantle porosity is found to be dependent on the gas density, which controls the accretion rate. A gas density of 2 × 104 cm-3, appropriate for dark interstellar clouds, is found to produce a fairly smooth and non-porous ice mantle. At all densities, H2 molecules formed on the grains collect within the crevices that divide nodules of ice and within micropores (whose extreme inward curvature produces strong local potential minima). The larger pores produced in the high-density models are not typically filled with H2. Direct deposition of water molecules onto the grain indicates that amorphous ices formed in this way may be significantly more porous than interstellar ices that are formed by surface chemistry. © 2013. The American Astronomical Society. All rights reserved.


Bondarescu R.,University of Zurich | Wasserman I.,Cornell University
Astrophysical Journal | Year: 2013

We describe how the nonlinear development of the R-mode instability of neutron stars influences spin up to millisecond periods via accretion. When nearly resonant interactions of the ℓ = m = 2 R-mode with pairs of "daughter modes" are included, the R-mode saturates at the lowest amplitude which leads to significant excitation of a pair of modes. The lower bound for this threshold amplitude is proportional to the damping rate of the particular daughter modes that are excited parametrically. We show that if dissipation occurs in a very thin boundary layer at the crust-core boundary, the R-mode saturation amplitude is too large for angular momentum gain from accretion to overcome loss to gravitational radiation. We find that lower dissipation is required to explain spin up to frequencies much higher than 300 Hz. We conjecture that if the transition from the fluid core to the crystalline crust occurs over a distance much longer than 1 cm, then a sharp viscous boundary layer fails to form. In this case, damping is due to shear viscosity dissipation integrated over the entire star. We estimate the lowest parametric instability threshold from first principles. The resulting saturation amplitude is low enough to permit spin up to higher frequencies. The requirement to allow continued spin up imposes an upper bound to the frequencies attained via accretion that plausibly may be about 750 Hz. Within this framework, the R-mode is unstable for all millisecond pulsars, whether accreting or not. © 2013. The American Astronomical Society. All rights reserved.


Cordes J.M.,Cornell University
Astrophysical Journal | Year: 2013

Markov processes are shown to be consistent with metastable states seen in pulsar phenomena, including intensity nulling, pulse-shape mode changes, subpulse drift rates, spin-down rates, and X-ray emission, based on the typically broad and monotonic distributions of state lifetimes. Markovianity implies a nonlinear magnetospheric system in which state changes occur stochastically, corresponding to transitions between local minima in an effective potential. State durations (though not transition times) are thus largely decoupled from the characteristic timescales of various magnetospheric processes. Dyadic states are common but some objects show at least four states with some transitions forbidden. Another case is the long-term intermittent pulsar B1931+24 that has binary radio-emission and torque states with wide, but non-monotonic duration distributions. It also shows a quasi-period of 38 ± 5 days in a 13 yr time sequence, suggesting stochastic resonance in a Markov system with a forcing function that could be strictly periodic or quasi-periodic. Nonlinear phenomena are associated with time-dependent activity in the acceleration region near each magnetic polar cap. The polar-cap diode is altered by feedback from the outer magnetosphere and by return currents from the equatorial region outside the light cylinder that may also cause the neutron star to episodically charge and discharge. Orbital perturbations of a disk or current sheet provide a natural periodicity for the forcing function in the stochastic-resonance interpretation of B1931+24. Disk dynamics may introduce additional timescales in observed phenomena. Future work can test the Markov interpretation, identify which pulsar types have a propensity for state changes, and clarify the role of selection effects. © 2013. The American Astronomical Society. All rights reserved.


Bass A.H.,Cornell University
Current Opinion in Neurobiology | Year: 2014

Animals that generate acoustic signals for social communication are faced with two essential tasks: generate a temporally precise signal and inform the auditory system about the occurrence of one's own sonic signal. Recent studies of sound producing fishes delineate a hindbrain network comprised of anatomically distinct compartments coding equally distinct neurophysiological properties that allow an organism to meet these behavioral demands. A set of neural characters comprising a vocal-sonic central pattern generator (CPG) morphotype is proposed for fishes and tetrapods that shares evolutionary developmental origins with pectoral appendage motor systems. © 2014 Elsevier Ltd.


Elser V.,Cornell University
Ultramicroscopy | Year: 2011

The high intensity of free-electron X-ray light sources may enable structure determinations of viruses or even individual proteins without the encumbrance of first forming crystals. This note compares two schemes of non-crystalline diffraction data collection that have been proposed: serial single-shot data from individual particles, and averaged cross-correlation data from particle ensembles. The information content of these schemes is easily compared and we show that the single-shot approach, although experimentally more challenging, is always superior in this respect. In fact, for 3D structure determination a constraint counting argument shows that the cross-correlation scheme suffers from data deficiency. © 2010 Elsevier B.V.


Artis D.,Cornell University | Spits H.,University of Amsterdam
Nature | Year: 2015

The innate immune system is composed of a diverse array of evolutionarily ancient haematopoietic cell types, including dendritic cells, monocytes, macrophages and granulocytes. These cell populations collaborate with each other, with the adaptive immune system and with non-haematopoietic cells to promote immunity, inflammation and tissue repair. Innate lymphoid cells are the most recently identified constituents of the innate immune system and have been the focus of intense investigation over the past five years. We summarize the studies that formally identified innate lymphoid cells and highlight their emerging roles in controlling tissue homeostasis in the context of infection, chronic inflammation, metabolic disease and cancer. © 2015 Macmillan Publishers Limited. All rights reserved.


Malemud C.J.,Cornell University
Future Medicinal Chemistry | Year: 2015

PI3K/Akt/mTOR signaling regulates diverse cellular processes. Abnormal PI3K/Akt/mTOR signaling is a characteristic feature of cancer. As such inhibition of PI3K/Akt/mTOR signaling using small molecule inhibitors has been a focus of recently developed anticancer drugs. Rheumatoid arthritis and psoriatic arthritis are autoimmune-mediated inflammatory diseases. PI3K signaling could now be targeted to determine its contribution to rheumatoid and psoriatic arthritis where deregulated proliferation and aberrant survival of activated immune cells, macrophages, monocytes, dendritic cells and synovial fibroblasts significantly overlap with abnormal growth of cancer cells. The results of some recent studies in psoriatic arthritis using PI3K signaling inhibitors suggests that small molecule inhibitor strategies directed at PI3K signaling may be a useful future therapy for immune-mediated arthritis. © 2015 Future Science Ltd.


Koutsourelakis P.S.,Cornell University
Probabilistic Engineering Mechanics | Year: 2010

The present paper advocates a probabilistic framework for assessing structural vulnerability against earthquakes. This is justified by the significant randomness that characterizes not only the earthquake excitation (amplitude, frequency content, duration), but also the structural system itself (i.e. stochastic variations in the material properties). Performance predictions can readily be summarized in the form of fragility curves which express the probability of exceeding various damage levels (from minor to collapse) with respect to a metric of the earthquake intensity. In this paper, a Bayesian framework is proposed for the derivation of fragility curves which can produce estimates irrespective of the amount of data available. It is particularly flexible when combined with Markov Chain Monte Carlo (MCMC) techniques and can efficiently provide credible intervals for the estimates. Furthermore, a general procedure based on logistic regression is illustrated that can lead in a principled manner to the derivation of fragility surfaces which express the probability of exceeding a damage level with respect to several measures of the earthquake load and can thus produce more accurate predictions. The methodologies presented are illustrated using data generated from computational simulations for a structure on top of a saturated sand deposit which is susceptible to liquefaction. © 2009 Elsevier Ltd. All rights reserved.


To determine the association between indicators of infant and young child feeding (IYCF) and anthropometric measures of nutritional status among children aged 0-23 months in a nationally representative data set. Data from the 2007 Bangladesh Demographic and Health Survey were used. Analyses were conducted using multiple linear regression and logistic regression analyses adjusted for the complex survey design of the survey, controlling for child, maternal and household characteristics, and including regional dummy variables. Bangladesh. Pairs (n 2096) of last born infants and their mothers. Exclusive breast-feeding under 6 months of age was associated with higher weight-for-height Z-score (effect size (ES) = 0·29; P < 0·05). Appropriate complementary feeding in children aged 6-8 months was associated with higher height-for-age Z-score (HAZ; ES = 0·63; P < 0·01) and higher weight-for-age Z-score (WAZ; ES = 0·30; P < 0·05). Higher dietary diversity index (DDI) was associated with higher HAZ (ES = 0·08; P < 0·01 for every 1 point higher DDI) and higher WAZ (ES = 0·04; P < 0·05). Children who achieved minimum diet diversity had higher HAZ (ES = 0·20; P < 0·05). Logistic regression models confirmed that exclusive breast-feeding was protective against wasting and DDI was protective against stunting and underweight. Our results highlight the importance of IYCF practices as determinants of child growth outcomes in this context, and reinforce the need for interventions that address the spectrum of IYCF practices, from exclusive breast-feeding to age-appropriate complementary feeding, especially diet diversity, in efforts to improve nutrition of infants and young children.


Wilson D.B.,Cornell University
Applied Microbiology and Biotechnology | Year: 2012

Cellulases are key enzymes used in many processes for producing liquid fuels from biomass. Currently there many efforts to reduce the cost of cellulases using both structural approaches to improve the properties of individual cellulases and genomic approaches to identify new cellulases as well as other proteins that increase the activity of cellulases in degrading pretreated biomass materials. Fungal GH-61 proteins are important new enzymes that increase the activity of current commercial cellulases leading to lower total protein loading and thus lower cost. Recent work has greatly increased our knowledge of these novel enzymes that appear to be oxido-reductases that target crystalline cellulose and increase its accessibility to cellulases. They appear to carry out the C1 activity originally proposed by Dr Reese. Cellobiose dehydrogenase appears to interact with GH-61 proteins in this function, providing a role for this puzzling enzyme. Cellulase research is making considerable progress and appears to be poised for even greater advances. © 2011 Springer-Verlag.


The Charophycean green algae (CGA) occupy a key phylogenetic position as the evolutionary grade that includes the sister group of the land plants (embryophytes), and so provide potentially valuable experimental systems to study the development and evolution of traits that were necessary for terrestrial colonization. The nature and molecular bases of such traits are still being determined, but one critical adaptation is thought to have been the evolution of a complex cell wall. Very little is known about the identity, origins and diversity of the biosynthetic machinery producing the major suites of structural polymers (i. e., cell wall polysaccharides and associated molecules) that must have been in place for land colonization. However, it has been suggested that the success of the earliest land plants was partly based on the frequency of gene duplication, and possibly whole genome duplications, during times of radical habitat changes. Orders of the CGA span early diverging taxa retaining more ancestral characters, through complex multicellular organisms with morphological characteristics resembling those of land plants. Examination of gene diversity and evolution within the CGA could help reveal when and how the molecular pathways required for synthesis of key structural polymers in land plants arose.


Jagota A.,Lehigh University | Hui C.-Y.,Cornell University
Materials Science and Engineering R: Reports | Year: 2011

The remarkable mechanical properties of natural contact surfaces have inspired a great deal of interest and research in recent years. The underlying driver of this interest is the surprising range of surface mechanical properties such as adhesion, friction, and compliance that can be attained primarily by design of near-surface architecture using generic materials properties. A considerable literature has developed spanning the range from biological studies of structure and properties, through models to understand these properties, to development of bio-mimetic and bio-inspired structures, along with theory to understand how structure leads to development of surface mechanical properties. The literature has matured sufficiently that common architectures and principles have emerged, for which we attempt here to present a unified view. The field remains vibrant so we hope that this review can at the same time help in its further progress. Our goal in this paper is to review the field from the point of view of scientists and engineers interested to learn about the architecture, properties, and mechanisms of contacting surfaces in nature and how these might be mimicked to create new materials with unique and interesting properties. We begin with a brief description of natural systems, their architectures and properties, and follow by a discussion of the main bio-mimetic and bio-inspired materials that have been developed recently. We then discuss surface mechanical properties - adhesion, friction, and compliance - how these are related to materials and architectural parameters, and how these properties are measured. Where possible, we provide quantitative models for the relationship between structure and properties. We conclude the paper with a discussion of outlook and future possibilities in this field. © 2011 Elsevier B.V. All rights reserved.


Douglas A.E.,Cornell University
Science Signaling | Year: 2011

The sustained health of an individual animal depends on the composition and activities of its resident microbiota. A major challenge is to identify the processes by which the microbiota and animal interact, recognizing that this research should lead ultimately to novel strategies to promote human health. Drosophila is emerging as a tractable model system to investigate these interactions. New evidence reveals that the gut microbiota promotes insulin signaling in Drosophila, leading to increased growth and development rates. Different gut bacteria and bacterial effectors were implicated: acetic acid produced by Acetobacter pomorum and branched-chain amino acids produced by Lactobacillus plantarum, respectively. These findings raise the possibility that multiple bacterial effectors may interact with signaling networks to shape animal health.


Buchon N.,Cornell University | Silverman N.,University of Massachusetts Medical School | Cherry S.,University of Pennsylvania
Nature Reviews Immunology | Year: 2014

Since the discovery of antimicrobial peptide responses 40 years ago, the fruit fly Drosophila melanogaster has proven to be a powerful model for the study of innate immunity. Early work focused on innate immune mechanisms of microbial recognition and subsequent nuclear factor-κ B signal transduction. More recently, D. melanogaster has been used to understand how the immune response is regulated and coordinated at the level of the whole organism. For example, researchers have used this model in studies investigating interactions between the microbiota and the immune system at barrier epithelial surfaces that ensure proper nutritional and immune homeostasis both locally and systemically. In addition, studies in D. melanogaster have been pivotal in uncovering how the immune response is regulated by both endocrine and metabolic signalling systems, and how the immune response modifies these systems as part of a homeostatic circuit. In this Review, we briefly summarize microbial recognition and antiviral immunity in D. melanogaster, and we highlight recent studies that have explored the effects of organism-wide regulation of the immune response and, conversely, the effects of the immune response on organism physiology. © 2015 Macmillan Publishers Limited.


Cleland T.A.,Cornell University
Progress in Brain Research | Year: 2014

Like other sensory systems, the olfactory system transduces specific features of the external environment and must construct an organized sensory representation from these highly fragmented inputs. As with these other systems, this representation is not accurate per se, but is constructed for utility, and emphasizes certain, presumably useful, features over others. I here describe the cellular and circuit mechanisms of the peripheral olfactory system that underlie this process of sensory construction, emphasizing the distinct architectures and properties of the two prominent computational layers in the olfactory bulb. Notably, while the olfactory system solves essentially similar conceptual problems to other sensory systems, such as contrast enhancement, activity normalization, and extending dynamic range, its peculiarities often require qualitatively different computational algorithms than are deployed in other sensory modalities. In particular, the olfactory modality is intrinsically high dimensional, and lacks a simple, externally defined basis analogous to wavelength or pitch on which elemental odor stimuli can be quantitatively compared. Accordingly, the quantitative similarities of the receptive fields of different odorant receptors (ORs) vary according to the statistics of the odor environment. To resolve these unusual challenges, the olfactory bulb appears to utilize unique nontopographical computations and intrinsic learning mechanisms to perform the necessary high-dimensional, similarity-dependent computations. In sum, the early olfactory system implements a coordinated set of early sensory transformations directly analogous to those in other sensory systems, but accomplishes these with unique circuit architectures adapted to the properties of the olfactory modality. © 2014 Elsevier B.V.


Cordes J.M.,Cornell University
Classical and Quantum Gravity | Year: 2013

Sources of noise in pulsar timing measurements are discussed along with spin stability of neutron stars. Estimates and scaling laws are given for spin noise, timing errors from fluctuations in pulsar magnetospheres, dispersion and scattering in the interstellar plasma, and in the matched filtering technique used to estimate arrival times. The composite noise spectrum is presented and an assessment of the detectability of gravitational waves (GWs) is given in terms of the sources of error and their mitigation. The scaling laws indicate that substantial improvement in sensitivity to GWs can be expected from implementation of new, wideband spectrometers at radio observatories, by using new algorithms to further reduce the levels of plasma propagation effects, and by increasing the number of millisecond pulsars used in pulsar timing arrays. © 2013 IOP Publishing Ltd.


Teukolsky S.A.,Cornell University
Classical and Quantum Gravity | Year: 2015

This review describes the events leading up to the discovery of the Kerr metric in 1963 and the enormous impact the discovery has had in the subsequent 50 years. The review discusses the Penrose process, the four laws of black hole mechanics, uniqueness of the solution, and the no-hair theorems. It also includes Kerr perturbation theory and its application to black hole stability and quasi-normal modes. The Kerr metric's importance in the astrophysics of quasars and accreting stellar-mass black hole systems is detailed. A theme of the review is the 'miraculous' nature of the solution, both in describing in a simple analytic formula the most general rotating black hole, and in having unexpected mathematical properties that make many calculations tractable. Also included is a pedagogical derivation of the solution suitable for a first course in general relativity. © 2015 IOP Publishing Ltd.


Reidy-Lagunes D.L.,Cornell University
JNCCN Journal of the National Comprehensive Cancer Network | Year: 2012

Well-differentiated neuroendocrine tumors (NETs) can be subdivided into carcinoid and pancreatic NETs (pancNETs). Although these tumors share many morphologic and clinical characteristics, carcinoid tumors appear to be far less sensitive to therapeutic agents than pancNETs, and recent advances approved for pancNETs have not been submitted for FDA approval in patients with carcinoid tumors. Treatment options for patients with advanced pancNETs are multidisciplinary and include surgical resection, liver-directed therapies, and systemic therapies. Cytotoxic therapies, such as temozolomide, fluorouracil, oxaliplatin, and streptozocin-based chemotherapy regimens, are active against some pancNETs, and can play a role in the palliation of patients with advanced disease and symptoms related to tumor bulk. Two therapies were recently approved for progressive well-differentiated pancNETs: sunitinib and everolimus. Both agents showed improved progression-free survival in patients with progressive pancNETs, but can also result in nontrivial toxicities, and therefore should only be considered in patients with progressing and advanced or symptomatic disease. This article discusses these recent trials and provides an update of systemic treatment options in patients with well-differentiated pancNETs. © JNCCN - Journal of the National Comprehensive Cancer Network.


Rondinelli J.M.,Drexel University | Fennie C.J.,Cornell University
Advanced Materials | Year: 2012

Electronic structure calculations based on density functional theory have uncovered a novel mechanism for inducing ferroelectric polarizations in cation ordered perovskites. We outline a materials selection strategy for designing this behavior. The guidelines are based on the octahedral rotations found in the two constituent oxides and the way the perovskite building blocks are interwoven to form the superlattice. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Barrett C.F.,Cornell University | Freudenstein J.V.,Ohio State University
Molecular Ecology | Year: 2011

In the spirit of recent calls for species delimitation studies to become more pluralistic, incorporating multiple sources of evidence, we adopted an integrative, phylogeographic approach to delimiting species and evolutionarily significant units (ESUs) in the Corallorhiza striata species complex. This rare, North American, mycoheterotrophic orchid has been a taxonomic challenge regarding species boundaries, displaying complex patterns of variation and reduced vegetative morphology. We employed plastid DNA, nuclear DNA and morphometrics, treating the C. striata complex as a case study for integrative species delimitation. We found evidence for the differentiation of the endangered C. bentleyi (eastern USA) + C. striata var. involuta (Mexico) from the remaining C. striata (= C. striata s.s.; USA, Canada, Mexico). Corallorhiza striata involuta and C. bentleyi, disjunct by thousands of kilometres (Mexico-Appalachia), were genetically identical but morphologically distinct. Evidence suggests the C. striata complex represents three species: C. bentleyi, C. involuta and a widespread C. striata s.s under operational criteria of diagnosability and common allele pools. In contrast, Bayesian coalescent estimation delimited four species, but more informative loci and a resultant species tree will be needed to place higher confidence in future analyses. Three distinct groupings were identified within C. striata s.s., corresponding to C. striata striata, C. striata vreelandii, and Californian accessions, but these were not delimited as species because of occupying a common allele pool. Each comprises an ESU, warranting conservation considerations. This study represents perhaps the most geographically comprehensive example of integrative species delimitation for any orchid and any mycoheterotroph. © 2011 Blackwell Publishing Ltd.


Avestimehr A.S.,Cornell University | Diggavi S.N.,University of California at Los Angeles | Tse D.N.C.,University of California at Berkeley
IEEE Transactions on Information Theory | Year: 2011

In a wireless network with a single source and a single destination and an arbitrary number of relay nodes, what is the maximum rate of information flow achievable? We make progress on this long standing problem through a two-step approach. First, we propose a deterministic channel model which captures the key wireless properties of signal strength, broadcast and superposition. We obtain an exact characterization of the capacity of a network with nodes connected by such deterministic channels. This result is a natural generalization of the celebrated max-flow min-cut theorem for wired networks. Second, we use the insights obtained from the deterministic analysis to design a new quantize-map-and-forward scheme for Gaussian networks. In this scheme, each relay quantizes the received signal at the noise level and maps it to a random Gaussian codeword for forwarding, and the final destination decodes the source's message based on the received signal. We show that, in contrast to existing schemes, this scheme can achieve the cut-set upper bound to within a gap which is independent of the channel parameters. In the case of the relay channel with a single relay as well as the two-relay Gaussian diamond network, the gap is 1 bit/s/Hz. Moreover, the scheme is universal in the sense that the relays need no knowledge of the values of the channel parameters to (approximately) achieve the rate supportable by the network. We also present extensions of the results to multicast networks, half-duplex networks, and ergodic networks. © 2011 IEEE.


Brutsaert W.,Cornell University
Water Resources Research | Year: 2013

There is still no general agreement on the relationship between the evaporation of open water from a small pan and the terrestrial evaporation from the surrounding landscape under drying conditions. A possible way out of this impasse is reviewed and applied to the harsh and extreme climatic conditions of the Tibetan Plateau. It is confirmed herein that during 1966-2000 with a pan evaporation trend of -4.57 mm a-2, the terrestrial evaporation trend was +0.7 mm a-2, in agreement with the experimental findings of Zhang et al. (2007). ©2013. American Geophysical Union. All Rights Reserved.


Starkov A.A.,Cornell University
Molecular and Cellular Neuroscience | Year: 2013

The activity of mitochondrial alpha-ketoglutarate dehydrogenase complex (KGDHC) is severely reduced in human pathologies where oxidative stress is traditionally thought to play an important role, such as familial and sporadic forms of Alzheimer's disease and other age-related neurodegenerative diseases. This minireview is focused on substantial data that were accumulated over the last 2 decades to support the concept that KGDHC can be a primary mitochondrial target of oxidative stress and at the same time a key contributor to it by producing reactive oxygen species. This article is part of a Special Issue entitled 'Mitochondrial function and dysfunction in neurodegeneration'. © 2012 Elsevier Inc.


Bernardo Carvalho A.,Federal University of Rio de Janeiro | Bernardo Carvalho A.,University of Washington | Clark A.G.,Cornell University
Genome Research | Year: 2013

Notwithstanding their biological importance, Y chromosomes remain poorly known in most species. A major obstacle to their study is the identification of Y chromosome sequences; due to its high content of repetitive DNA, in most genome projects, the Y chromosome sequence is fragmented into a large number of small, unmapped scaffolds. Identification of Y-linked genes among these fragments has yielded important insights about the origin and evolution of Y chromosomes, but the process is labor intensive, restricting studies to a small number of species. Apart from these fragmentary assemblies, in a few mammalian species, the euchromatic sequence of the Y is essentially complete, owing to painstaking BAC mapping and sequencing. Here we use female short-read sequencing and k-mer comparison to identify Y-linked sequences in two very different genomes, Drosophila virilis and human. Using this method, essentially all D. virilis scaffolds were unambiguously classified as Y-linked or not Y-linked. We found 800 new scaffolds (totaling 8.5 Mbp), and four new genes in the Y chromosome of D. virilis, including JYalpha, a gene involved in hybrid male sterility. Our results also strongly support the preponderance of gene gains over gene losses in the evolution of the Drosophila Y. In the intensively studied human genome, used here as a positive control, we recovered all previously known genes or gene families, plus a small amount (283 kb) of new, unfinished sequence. Hence, this method works in large and complex genomes and can be applied to any species with sex chromosomes. © 2013 Bashford-Rogers et al.