Pensylvania State University

State College, PA, United States

Pensylvania State University

State College, PA, United States
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D'Avanzo P.,National institute for astrophysics | Perri M.,Science Data Center | Fugazza D.,National institute for astrophysics | Salvaterra R.,University of Insubria | And 22 more authors.
Astronomy and Astrophysics | Year: 2010

Context. Gamma-ray bursts (GRBs) have proven to be detectable to distances much larger than any other astrophysical object, providing the most effective way, complementing ordinary surveys of studying the high redshift universe. Aims. We present the results of an observational campaign devoted to the study of the high-z GRB 090205. Methods. We carried out optical/NIR spectroscopy and imaging of GRB 090205 with the ESO-VLT starting from hours after the event to several days later to detect the host galaxy. We compared the results obtained from our optical/NIR observations with the available Swift high-energy data of this burst. Results. Our observational campaign led to the detection of the optical afterglow and host galaxy of GRB 090205 and to the first measure of its redshift, z = 4.65. As in other high-z GRBs, GRB 090205 has a short duration in the rest frame with T90,rf = 1.6 s, which suggests that it might belong to the short GRB class. The X-ray afterglow of GRB 090205 has a complex and interesting behavior with a possible rebrightening at 500-1000 s from the trigger time and late flaring activity. Photometric observations of the GRB 090205 host galaxy imply that it is a starburst galaxy with a stellar population younger than ∼150 Myr. Moreover, the metallicity of Z > 0.27 ⊙ derived from the GRB afterglow spectrum is among the highest derived from GRB afterglow measurement at high-z, suggesting that the burst occurred in a rather enriched environment. Finally, a detailed analysis of the afterglow spectrum shows the existence of a line corresponding to Lyman-α emission at the redshift of the burst. GRB 090205 is thus hosted by a typical Lyman-α emitter (LAE) at z = 4.65. This makes the host galaxy of GRB 090205 the farthest GRB host galaxy, spectroscopically confirmed, detected to date. © 2010 ESO.

Strukov B.,Moscow State University | Davitadze S.,Moscow State University | Shnaidshtein I.,Moscow State University | Lemanov V.V.,RAS Ioffe Physical - Technical Institute | And 8 more authors.
Ferroelectrics | Year: 2011

A short review of the study of thermal properties of the nanostructured ferroelectrics is given. An application of the modern calorimetric technique to a comparative study of phase transitions in the ferroelectric nanostructured materials (polycrystalline and epitaxial thin films, superstructures, ferroelectric heterostructures, substrate-induced ferroelectricity) is considered. Copyright © Taylor &Francis Group, LLC.

Koehler K.,German Sport University Cologne | Koehler K.,Pensylvania State University | Abel T.,German Sport University Cologne | Wallmann-Sperlich B.,German Sport University Cologne | And 2 more authors.
Journal of Physical Activity and Health | Year: 2015

Background: Inactivity and overweight are major health concerns in children and adolescents with disabilities. Methods for the assessment of activity and energy expenditure may be affected negatively by the underlying disability, especially when motor function is impaired. The purpose of this study was to assess the validity of the SenseWear Armband in adolescents with cerebral palsy and hemiparesis. Methods: Ten volunteers (age: 13.4 ± 1.6 years) were equipped with SenseWear Armbands on the hemiparetic and nonhemiparetic side of the body. Energy expenditure was measured at rest and during treadmill exercise (speed range: 0.85 to 2.35 m/s). Indirect calorimetry served as independent reference method. Results: The mean error was between -0.6 and 0.8 kcal/min and there were no significant differences between SenseWear and indirect calorimetry at any speed. Differences between body sides in expenditure (mean: -0.2 to 0.0 kcal/min) and step count (mean: -3.4 to 9.7 steps/min) were not significant. Conclusions: The validity of the SenseWear Armband does not appear to be negatively affected by cerebral palsy during laboratory treadmill exercise. Future field studies are necessary to assess the validity and practicability of energy expenditure and physical activity assessment in children and adolescents with physical disabilities. © 2015 Human Kinetics, Inc.

Kim N.,Ulsan National Institute of Science and Technology | Joo J.,Inje University | Rothrock L.,Pensylvania State University | Wysk R.,North Carolina State University | Son Y.-J.,University of Arizona
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2011

In this paper, we propose a novel agent-based simulation modeling of human behaviors. A conceptual framework of human behavioral simulation is suggested using the ecological definition of affordances in order to mimic perception-based human actions interacting with the environment. A simulation example of a 'warehouse fire evacuation' is illustrated to demonstrate the applicability of the proposed framework. The perception-based human behaviors and planning algorithms are adapted and embedded within human agent models using the Static and Dynamic Floor Field Indicators, which represent the evacuee's prior knowledge of the floor layout and perceivable information of dynamic environmental changes, respectively. The proposed framework is expected to capture the natural manners in which humans participate in systems and enhance the simulation fidelity by incorporating cognitive intent into human behavior simulations. © 2011 Springer-Verlag.

Williams A.,University of Miami | Rawal S.,University of Miami | Ao Z.,University of Miami | Torres-Munoz J.,University of Miami | And 6 more authors.
IEEE EMBS Special Topic Conference on Point-of-Care (POC) Healthcare Technologies: Synergy Towards Better Global Healthcare, PHT 2013 | Year: 2013

The most important determinant of prognosis and management of cancer is the presence or absence of metastasis [1]. The road to metastasis involves tumor cells to become detached from the primary tumor and travel in the blood to distant sites, causing secondary tumors. These tumor cells traveling in blood are termed Circulating tumor cells (CTC). Capture of CTC from whole blood has been a challenging feat. The fact that these CTC are few in number, to effectively and efficiently isolate them from whole blood can be thought of as looking for a needle in a haystack. Our microfilter technology exploits the use of size based capture of the larger CTC from the smaller white blood cells and components of whole blood. The effective capture potential of the microfilter platform has driven the area of CTC analysis into a new age of research in the field of cancer. The ability to finally analyze CTC at a molecular level, leads to a deeper understanding of metastatic process, while providing an opportunity to evaluate, monitor and manage treatment options as well as the adherent possibility of having an "on-chip" drug sensitivity assay for focused treatment options. We have demonstrated through clinical trials the ability to effectively identify, enumerate and characterize CTC based on immunfluorescence and FISH assays and provide a companion endpoint for monitoring and evaluating treatment management. Our work on viable CTC capture has resulted in successfully capturing and culturing CTC from blood in mouse models that have been inoculated with breast cancer cell lines to form primary and secondary metastatic cancer sites. The future potential within the microfilter technology to capture viable CTC for culture, will catapult therapeutic interventions to a new level of personalized medicine in cancer management. © 2013 IEEE.

Chaudhuri S.,Pensylvania State University | Solar-Lezama A.,Massachusetts Institute of Technology
Proceedings of the ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI) | Year: 2010

We present smooth interpretation, a method to systematically approximate numerical imperative programs by smooth mathematical functions. This approximation facilitates the use of numerical search techniques like gradient descent for program analysis and synthesis. The method extends to programs the notion of Gaussian smoothing, a popular signal-processing technique that filters out noise and discontinuities from a signal by taking its convolution with a Gaussian function. In our setting, Gaussian smoothing executes a program according to a probabilistic semantics; the execution of program P on an input x after Gaussian smoothing can be summarized as follows: (1) Apply a Gaussian perturbation to x - the perturbed input is a random variable following a normal distribution with mean x. (2) Compute and return the expected output of P on this perturbed input. Computing the expectation explicitly would require the execution of P on all possible inputs, but smooth interpretation bypasses this requirement by using a form of symbolic execution to approximate the effect of Gaussian smoothing on P. The result is an efficient but approximate implementation of Gaussian smoothing of programs. Smooth interpretation has the effect of attenuating features of a program that impede numerical searches of its input space - for example, discontinuities resulting from conditional branches are replaced by continuous transitions. We apply smooth interpretation to the problem of synthesizing values of numerical control parameters in embedded control applications. This problem is naturally formulated as one of numerical optimization: the goal is to find parameter values that minimize the error between the resulting program and a programmer-provided behavioral specification. Solving this problem by directly applying numerical optimization techniques is often impractical due to the discontinuities in the error function. By eliminating these discontinuities, smooth interpretation makes it possible to search the parameter space efficiently by means of simple gradient descent. Our experiments demonstrate the value of this strategy in synthesizing parameters for several challenging programs, including models of an automated gear shift and a PID controller. © 2010 ACM.

PubMed | Pensylvania State University
Type: Journal Article | Journal: The Plant cell | Year: 2011

Auxin plays a fundamental role in organogenesis in plants. Multiple pathways for auxin biosynthesis have been proposed, but none of the predicted pathways are completely understood. Here, we report the positional cloning and characterization of the vanishing tassel2 (vt2) gene of maize (Zea mays). Phylogenetic analyses indicate that vt2 is a co-ortholog of TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1), which converts Trp to indole-3-pyruvic acid in one of four hypothesized Trp-dependent auxin biosynthesis pathways. Unlike single mutations in TAA1, which cause subtle morphological phenotypes in Arabidopsis thaliana, vt2 mutants have dramatic effects on vegetative and reproductive development. vt2 mutants share many similarities with sparse inflorescence1 (spi1) mutants in maize. spi1 is proposed to encode an enzyme in the tryptamine pathway for Trp-dependent auxin biosynthesis, although this biochemical activity has recently been questioned. Surprisingly, spi1 vt2 double mutants had only a slightly more severe phenotype than vt2 single mutants. Furthermore, both spi1 and vt2 single mutants exhibited a reduction in free auxin levels, but the spi1 vt2 double mutants did not have a further reduction compared with vt2 single mutants. Therefore, both spi1 and vt2 function in auxin biosynthesis in maize, possibly in the same pathway rather than independently as previously proposed.

PubMed | Pensylvania State University
Type: Journal Article | Journal: The Plant cell | Year: 2012

Understanding tissue-related gene expression patterns can provide important insights into gene, tissue, and organ function. Transcriptome analyses often have focused on housekeeping or tissue-specific genes or on gene coexpression. However, by analyzing thousands of single-gene expression distributions in multiple tissues of Arabidopsis thaliana, rice (Oryza sativa), human (Homo sapiens), and mouse (Mus musculus), we found that these organisms primarily operate by gene sharing, a phenomenon where, in each organism, most genes exhibit a high expression level in a few key tissues. We designed an analytical pipeline to characterize this phenomenon and then derived Arabidopsis and human gene-sharing networks, in which tissues are connected solely based on the extent of shared preferentially expressed genes. The results show that tissues or cell types from the same organ system tend to group together to form network modules. Tissues that are in consecutive developmental stages or have common physiological functions are connected in these networks, revealing the importance of shared preferentially expressed genes in conferring specialized functions of each tissue type. The networks provide predictive power for each tissue type regarding gene functions of both known and heretofore unknown genes, as shown by the identification of four new genes with functions in guard cell and abscisic acid response. We provide a Web interface that enables, based on the extent of gene sharing, both prediction of tissue-related functions for any Arabidopsis gene of interest and predictions concerning the relatedness of tissues. Common gene-sharing patterns observed in the four model organisms suggest that gene sharing evolved as a fundamental organizing principle of gene expression in diverse multicellular eukaryotes.

PubMed | Pensylvania State University
Type: Journal Article | Journal: The Plant cell | Year: 2013

The highly polymorphic S (for self-incompatibility) locus regulates self-incompatibility in Petunia inflata; the S-RNase regulates pistil specificity, and multiple S-locus F-box (SLF) genes regulate pollen specificity. The collaborative non-self recognition model predicts that, for any S-haplotype, an unknown number of SLFs collectively recognize all non-self S-RNases to mediate their ubiquitination and degradation. Using a gain-of-function assay, we examined the relationships between S2-SLF1 (for S2-allelic product of Type-1 SLF) and four S-RNases. The results suggest that S2-SLF1 interacts with S7- and S13-RNases, and the previously identified S1- and S3-RNases, but not with S5- or S11-RNase. An artificial microRNA expressed by the S2-SLF1 promoter, but not by the vegetative cell-specific promoter, Late Anther Tomato 52, suppressed expression of S2-SLF1 in S2 pollen, suggesting that SLF1 is specific to the generative cell. The S2 pollen with S2-SLF1 suppressed was compatible with S3-, S5-, S7-, S11-, and S13-carrying pistils, confirming that other SLF proteins are responsible for detoxifying S5- and S11-RNases and suggesting that S2-SLF1 is not the only SLF in S2 pollen that interacts with S3-, S7-, and S13-RNases. Petunia may have evolved at least two types of SLF proteins to detoxify any non-self S-RNase to minimize the deleterious effects of mutation in any SLF.

PubMed | Pensylvania State University
Type: Journal Article | Journal: The Plant cell | Year: 2010

Twenty-one-nucleotide microRNAs (miRNAs) and 24-nucleotide Pol IV-dependent small interfering RNAs (p4-siRNAs) are the most abundant types of small RNAs in angiosperms. Some miRNAs are well conserved among different plant lineages, whereas others are less conserved, and it is not clear whether less-conserved miRNAs have the same functionality as the well conserved ones. p4-siRNAs are broadly produced in the Arabidopsis genome, sometimes from active hot spot loci, but it is unknown whether individual p4-siRNA hot spots are retained as hot spots between plant species. In this study, we compare small RNAs in two closely related species (Arabidopsis thaliana and Arabidopsis lyrata) and find that less-conserved miRNAs have high rates of divergence in MIRNA hairpin structures, mature miRNA sequences, and target-complementary sites in the other species. The fidelity of miRNA biogenesis from many less-conserved MIRNA hairpins frequently deteriorates in the sister species relative to the species of first discovery. We also observe that p4-siRNA occupied loci have a slight tendency to be retained as p4-siRNA loci between species, but the most active A. lyrata p4-siRNA hot spots are generally not syntenic to the most active p4-siRNA hot spots of A. thaliana. Altogether, our findings indicate that many MIRNAs and most p4-siRNA hot spots are rapidly changing and evolutionarily transient within the Arabidopsis genus.

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