bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demonstration of Synaptic Behaviors and Resistive Switching Characterizations by Proton Exchange Reactions in Silicon Oxide
Authors: Chang Yao-Feng , Fowler Burt , Chen Ying-Chen , Zhou Fei , Pan Chih-Hung , Chang Ting-Chang , Lee Jack C. 
Published: February 2016

AbstractWe realize a device with biological synaptic behaviors by integrating silicon oxide (SiOx) resistive switching memory with Si diodes. Minimal synaptic power consumption due to sneak-path current is achieved and the capability for spike-induced synaptic behaviors is demonstrated, representing critical milestones for the use of SiO2–based materials in future neuromorphic computing applications. Biological synaptic behaviors such as long-term potentiation (LTP), long-term depression (LTD) and spike-timing dependent plasticity (STDP) are demonstrated systematically using a comprehensive analysis of spike-induced waveforms and represent interesting potential applications for SiOx-based resistive switching materials. The resistive switching SET transition is modeled as hydrogen (proton) release from (SiH)2 to generate the hydrogen bridge defect and the RESET transition is modeled as an electrochemical reaction (proton capture) that re-forms (SiH)2. The experimental results suggest a simple, robust approach to realize programmable neuromorphic chips compatible with large-scale CMOS manufacturing technology.
Genetic analysis of arsenic accumulation in maize using QTL mapping
Authors: Fu Zhongjun , Li Weihua , Xing Xiaolong , Xu Mengmeng , Liu Xiaoyang , Li Haochuan , Xue Yadong , Liu Zonghua , Tang Jihua 
Published: February 2016

AbstractArsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars.
Chemical control of xylem differentiation by thermospermine, xylemin and auxin
Authors: Yoshimoto Kaori , Takamura Hiroyoshi , Kadota Isao , Motose Hiroyasu , Takahashi Taku 
Published: February 2016

AbstractThe xylem conducts water and minerals from the root to the shoot and provides mechanical strength to the plant body. The vascular precursor cells of the procambium differentiate to form continuous vascular strands, from which xylem and phloem cells are generated in the proper spatiotemporal pattern. Procambium formation and xylem differentiation are directed by auxin. In angiosperms, thermospermine, a structural isomer of spermine, suppresses xylem differentiation by limiting auxin signalling. However, the process of auxin-inducible xylem differentiation has not been fully elucidated and remains difficult to manipulate. Here, we found that an antagonist of spermidine can act as an inhibitor of thermospermine biosynthesis and results in excessive xylem differentiation, which is a phenocopy of a thermospermine-deficient mutant acaulis5 in Arabidopsis thaliana. We named this compound xylemin owing to its xylem-inducing effect. Application of a combination of xylemin and thermospermine to wild-type seedlings negates the effect of xylemin, whereas co-treatment with xylemin and a synthetic proauxin, which undergoes hydrolysis to release active auxin, has a synergistic inductive effect on xylem differentiation. Thus, xylemin may serve as a useful transformative chemical tool not only for the study of thermospermine function in various plant species but also for the control of xylem induction and woody biomass production.
Diagnosis of adults Xp11.2 translocation renal cell carcinoma by immunohistochemistry and FISH assays: clinicopathological data from ethnic Chinese population
Authors: Qu Yuanyuan , Gu Chengyuan , Wang Hongkai , Chang Kun , Yang Xiaoqun , Zhou Xiaoyan , Dai Bo , Zhu Yao , Shi Guohai , Zhang Hailiang , Ye Dingwei 
Published: February 2016

AbstractThis study aimed to assess the utility of transcription factor E3 (TFE3) break-apart fluorescence in situ hybridization (FISH) assay in diagnosis of Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) and to compare the clinicopathological features between adult Xp11.2 RCC and non-Xp11.2 RCC. 76 pathologically suspected Xp11.2 RCCs were recruited from our institution. Both TFE3 immunohistochemistry (IHC) and TFE3 FISH assay were performed for the entire cohort. The progression-free survival (PFS) and overall survival (OS) curves were estimated using the Kaplan-Meier method. FISH analysis confirmed 30 Xp11.2 RCCs, including 28 cases with positive TFE3 immunostaining and 2 cases with negative immunostaining. The false-positive and false-negative rates were 6.7% (2/30) and 4.3% (2/46), respectively, for TFE3 IHC compared with FISH assay. Xp11.2 RCC was significantly associated with higher pathological stage and Fuhrman nuclear grade compared with non-Xp11.2 RCC (P < 0.05). The median PFS and OS for TFE3 FISH-positive group were 13.0 months (95% CI, 8.4–17.6 months) and 50.0 months (95% CI, 27.6–72.4 months), respectively, while the median PFS and OS had not been reached for TFE3 FISH-negative group. In conclusion, TFE3 break-apart FISH assay is a highly useful and standard diagnostic method for Xp11.2 RCC. Adult Xp11.2 RCC is clinically aggressive and often presents at advanced stage with poor prognosis.
Non-Radiative Carrier Recombination Enhanced by Two-Level Process: A First-Principles Study
Authors: Yang Ji-Hui , Shi Lin , Wang Lin-Wang , Wei Su-Huai 
Published: February 2016

AbstractNon-radiative recombination plays an important role in the performance of optoelectronic semiconductor devices such as solar cells and light-emitting diodes. Most textbook examples assume that the recombination process occurs through a single defect level, where one electron and one hole are captured and recombined. Based on this simple picture, conventional wisdom is that only defect levels near the center of the bandgap can be effective recombination centers. Here, we present a new two-level recombination mechanism: first, one type of carrier is captured through a defect level forming a metastable state; then the local defect configuration rapidly changes to a stable state, where the other type of carrier is captured and recombined through another defect level. This novel mechanism is applied to the recombination center "Equation missing" in CdTe. We show that this two-level process can significantly increase the recombination rate (by three orders of magnitude) in agreement with experiments. We expect that this two-level recombination process can exist in a wide range of semiconductors, so its effect should be carefully examined in characterizing optoelectronic materials.
Knockout of BRD7 results in impaired spermatogenesis and male infertility
Authors: Wang Heran , Zhao Ran , Guo Chi , Jiang Shihe , Yang Jing , Xu Yang , Liu Yukun , Fan Liqing , Xiong Wei , Ma Jian , Peng Shuping , Zeng Zhaoyang , Zhou Yanhong , Li Xiayu , Li Zheng , Li Xiaoling , Schmitt David C. , Tan Ming , Li Guiyuan , Zhou Ming 
Published: February 2016

AbstractBRD7 was originally identified as a novel bromodomain gene and a potential transcriptional factor. BRD7 was found to be extensively expressed in multiple mouse tissues but was highly expressed in the testis. Furthermore, BRD7 was located in germ cells during multiple stages of spermatogenesis, ranging from the pachytene to the round spermatid stage. Homozygous knockout of BRD7 (BRD7−/−) resulted in complete male infertility and spermatogenesis defects, including deformed acrosomal formation, degenerative elongating spermatids and irregular head morphology in postmeiotic germ cells in the seminiferous epithelium, which led to the complete arrest of spermatogenesis at step 13. Moreover, a high ratio of apoptosis was determined by TUNEL analysis, which was supported by high levels of the apoptosis markers annexin V and p53 in knockout testes. Increased expression of the DNA damage maker λH2AX was also found in BRD7−/− mice, whereas DNA damage repair genes were down−regulated. Furthermore, no or lower expression of BRD7 was detected in the testes of azoospermia patients exhibiting spermatogenesis arrest than that in control group. These data demonstrate that BRD7 is involved in male infertility and spermatogenesis in mice, and BRD7 defect might be associated with the occurrence and development of human azoospermia.
Intensity‐tunable guided mode resonance reflectance filter with dual channels
Authors: Li Ye , Wang Qi , Zhang Dawei , Wang Jianyu , Chen Peng , Dai Bo , Huang Yuanshen , Tao Chunxian , Sheng Bin 
Published: February 2016

An intensity‐tunable reflectance filter with an unetched grating that is based on guided mode resonance is proposed. The unetched grating is designed for simplifying the fabrication proceeds and avoiding the errors of etching. The dual resonant wavelength channels are calculated by rigorous coupled‐wave analysis to be at 747.3 and 786.5 nm. Theoretical and experimental data indicate that the intensity of the spectral reflectance at the peak wavelength of 747.3 nm increases monotonically with variation of the azimuthal angle from 0° to 90°. Conversely, the intensity of the spectral reflectance decreases monotonically under the same conditions at the resonant wavelength of 786.5 nm. It is found experimentally that the intensity can be tuned via the azimuthal angles, and this agrees well with the results of the theoretical analysis. In addition, the influence of the structural parameters on the value of the wavelength separation between the dual resonance channels is analysed, and the electric field distributions at the resonant wavelengths are presented.
SweepFinder2: increased sensitivity, robustness and flexibility
Authors: DeGiorgio Michael , Huber Christian D. , Hubisz Melissa J. , Hellmann Ines , Nielsen Rasmus 
Published: February 2016

Abstract
Summary: SweepFinder is a widely used program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection. Moreover, SweepFinder2 has increased flexibility that enables the user to specify test sites, set the distance between test sites and utilize a recombination map.
Availability and implementation: SweepFinder2 is a freely-available (www.personal.psu.edu/mxd60/sf2.html) software package that is written in C and can be run from a Unix command line.
Contact: mxd60@psu.edu
EPS: an empirical Bayes approach to integrating pleiotropy and tissue-specific information for prioritizing risk genes
Authors: Liu Jin , Wan Xiang , Ma Shuangge , Yang Can 
Published: February 2016

Abstract
Motivation: Researchers worldwide have generated a huge volume of genomic data, including thousands of genome-wide association studies (GWAS) and massive amounts of gene expression data from different tissues. How to perform a joint analysis of these data to gain new biological insights has become a critical step in understanding the etiology of complex diseases. Due to the polygenic architecture of complex diseases, the identification of risk genes remains challenging. Motivated by the shared risk genes found in complex diseases and tissue-specific gene expression patterns, we propose as an Empirical Bayes approach to integrating Pleiotropy and Tissue-Specific information (EPS) for prioritizing risk genes.
Results: As demonstrated by extensive simulation studies, EPS greatly improves the power of identification for disease-risk genes. EPS enables rigorous hypothesis testing of pleiotropy and tissue-specific risk gene expression patterns. All of the model parameters can be adaptively estimated from the developed expectation–maximization (EM) algorithm. We applied EPS to the bipolar disorder and schizophrenia GWAS from the Psychiatric Genomics Consortium, along with the gene expression data for multiple tissues from the Genotype-Tissue Expression project. The results of the real data analysis demonstrate many advantages of EPS.
Availability and implementation: The EPS software is available on https://sites.google.com/site/liujin810822.
Contact: eeyang@hkbu.edu.hk
Supplementary information: Supplementary data are available at Bioinformatics online.
A quantitative model for oxygen uptake and release in a family of hemeproteins
Authors: Bustamante Juan P. , Szretter María E. , Sued Mariela , Martí Marcelo A. , Estrin Darío A. , Boechi Leonardo 
Published: February 2016

Abstract
Motivation: Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time.
Results: We present a physical–chemical model, which uses data obtained exclusively from computer simulations, to describe the uptake and release of oxygen in a family of hemeproteins, called truncated hemoglobins (trHbs). Through a rigorous statistical analysis we demonstrate that our model successfully recaptures all the reported experimental oxygen association and dissociation kinetic rate constants, thus allowing us to establish the key factors that determine the rates at which these hemeproteins uptake and release oxygen. We found that internal tunnels as well as the distal site water molecules control ligand uptake, whereas oxygen stabilization by distal site residues controls ligand release. Because these rates largely determine the functions of these hemeproteins, these approaches will also be important tools in characterizing the trHbs members with unknown functions.
Contact: lboechi@ic.fcen.uba.ar
Supplementary information: Supplementary data are available at Bioinformatics online.
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap
Authors: Wang Hao , McManus Joel , Kingsford Carl 
Published: February 2016

Abstract
Summary: Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30 bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. We present a technique and software that addresses this problem by assigning reads to potential origins proportional to estimated transcript abundance. This yields a more accurate estimate of ribosome profiles compared with a naïve mapping.
Availability and implementation: Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomap.
Contact: carlk@cs.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
KiT: a MATLAB package for kinetochore tracking
Authors: Armond Jonathan W. , Vladimirou Elina , McAinsh Andrew D. , Burroughs Nigel J. 
Published: February 2016

Abstract
Summary: During mitosis, chromosomes are attached to the mitotic spindle via large protein complexes called kinetochores. The motion of kinetochores throughout mitosis is intricate and automated quantitative tracking of their motion has already revealed many surprising facets of their behaviour. Here, we present ‘KiT’ (Kinetochore Tracking)—an easy-to-use, open-source software package for tracking kinetochores from live-cell fluorescent movies. KiT supports 2D, 3D and multi-colour movies, quantification of fluorescence, integrated deconvolution, parallel execution and multiple algorithms for particle localization.
Availability and implementation: KiT is free, open-source software implemented in MATLAB and runs on all MATLAB supported platforms. KiT can be downloaded as a package from http://www.mechanochemistry.org/mcainsh/software.php. The source repository is available at https://bitbucket.org/jarmond/kit and under continuing development.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: jonathan.armond@warwick.ac.uk
Informational and emotional elements in online support groups: a Bayesian approach to large-scale content analysis
Authors: Deetjen Ulrike , Powell John A 
Published: February 2016

Objective This research examines the extent to which informational and emotional elements are employed in online support forums for 14 purposively sampled chronic medical conditions and the factors that influence whether posts are of a more informational or emotional nature.Methods Large-scale qualitative data were obtained from Dailystrength.org. Based on a hand-coded training dataset, all posts were classified into informational or emotional using a Bayesian classification algorithm to generalize the findings. Posts that could not be classified with a probability of at least 75% were excluded.Results The overall tendency toward emotional posts differs by condition: mental health (depression, schizophrenia) and Alzheimer’s disease consist of more emotional posts, while informational posts relate more to nonterminal physical conditions (irritable bowel syndrome, diabetes, asthma). There is no gender difference across conditions, although prostate cancer forums are oriented toward informational support, whereas breast cancer forums rather feature emotional support. Across diseases, the best predictors for emotional content are lower age and a higher number of overall posts by the support group member.Discussion The results are in line with previous empirical research and unify empirical findings from single/2-condition research. Limitations include the analytical restriction to predefined categories (informational, emotional) through the chosen machine-learning approach.Conclusion Our findings provide an empirical foundation for building theory on informational versus emotional support across conditions, give insights for practitioners to better understand the role of online support groups for different patients, and show the usefulness of machine-learning approaches to analyze large-scale qualitative health data from online settings.
Development and validation of a predictive model for detection of colorectal cancer in primary care by analysis of complete blood counts: a binational retrospective study
Authors: Kinar Yaron , Kalkstein Nir , Akiva Pinchas , Levin Bernard , Half Elizabeth E , Goldshtein Inbal , Chodick Gabriel , Shalev Varda 
Published: February 2016

AbstractObjective The use of risk prediction models grows as electronic medical records become widely available. Here, we develop and validate a model to identify individuals at increased risk for colorectal cancer (CRC) by analyzing blood counts, age, and sex, then determine the model’s value when used to supplement conventional screening.Materials and Methods Primary care data were collected from a cohort of 606 403 Israelis (of whom 3135 were diagnosed with CRC) and a case control UK dataset of 5061 CRC cases and 25 613 controls. The model was developed on 80% of the Israeli dataset and validated using the remaining Israeli and UK datasets. Performance was evaluated according to the area under the curve, specificity, and odds ratio at several working points.Results Using blood counts obtained 3–6 months before diagnosis, the area under the curve for detecting CRC was 0.82 ± 0.01 for the Israeli validation set. The specificity was 88 ± 2% in the Israeli validation set and 94 ± 1% in the UK dataset. Detecting 50% of CRC cases, the odds ratio was 26 ± 5 and 40 ± 6, respectively, for a false-positive rate of 0.5%. Specificity for 50% detection was 87 ± 2% a year before diagnosis and 85 ± 2% for localized cancers. When used in addition to the fecal occult blood test, our model enabled more than a 2-fold increase in CRC detection.Discussion Comparable results in 2 unrelated populations suggest that the model should generally apply to the detection of CRC in other groups. The model’s performance is superior to current iron deficiency anemia management guidelines, and may help physicians to identify individuals requiring additional clinical evaluation.Conclusions Our model may help to detect CRC earlier in clinical practice.
A method for comparing non-nested models with application to astrophysical searches for new physics
Authors: Algeri Sara , Conrad Jan , van Dyk David A. 
Published: February 2016

AbstractSearches for unknown physics and decisions between competing astrophysical models to explain data both rely on statistical hypothesis testing. The usual approach in searches for new physical phenomena is based on the statistical likelihood ratio test and its asymptotic properties. In the common situation, when neither of the two models under comparison is a special case of the other i.e. when the hypotheses are non-nested, this test is not applicable. In astrophysics, this problem occurs when two models that reside in different parameter spaces are to be compared. An important example is the recently reported excess emission in astrophysical γ-rays and the question whether its origin is known astrophysics or dark matter. We develop and study a new, simple, generally applicable, frequentist method and validate its statistical properties using a suite of simulations studies. We exemplify it on realistic simulated data of the Fermi-Large Area Telescope γ-ray satellite, where non-nested hypotheses testing appears in the search for particle dark matter.
annotatr: Genomic regions in context
Authors: Cavalcante Raymond G. , Sartor Maureen A. 
Published: February 2016

AbstractMotivation:Analysis of next-generation sequencing data often results in a list of genomic regions. These may include differentially methylated CpGs/regions, transcription factor binding sites, interacting chromatin regions, or GWAS-associated SNPs, among others. A common analysis step is to annotate such genomic regions to genomic annotations (promoters, exons, enhancers, etc.). Existing tools are limited by a lack of annotation sources and flexible options, the time it takes to annotate regions, an artificial one-to-one region-to-annotation mapping, a lack of visualization options to easily summarize data, or some combination thereof.Results:We developed the annotatr Bioconductor package to flexibly and quickly summarize and plot annotations of genomic regions. The annotatr package reports all intersections of regions and annotations, giving a better understanding of the genomic context of the regions. A variety of graphics functions are implemented to easily plot numerical or categorical data associated with the regions across the annotations, and across annotation intersections, providing insight into how characteristics of the regions differ across the annotations. We demonstrate that annotatr is up to 27x faster than comparable R packages. Overall, annotatr enables a richer biological interpretation of experiments.Availability:http://bioconductor.org/packages/annotatr/Contact:rcavalca@umich.eduSupplementary information:Supplementary data are available atBioinformaticsonline.