bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualization of Assembly Intermediates and Budding Vacuoles of Singapore Grouper Iridovirus in Grouper Embryonic Cells
Authors: Liu Yang , Tran Bich Ngoc , Wang Fan , Ounjai Puey , Wu Jinlu , Hew Choy L. 
Published: January 2016

AbstractIridovirid infection is associated with the catastrophic loss in aquaculture industry and the population decline of wild amphibians and reptiles, but none of the iridovirid life cycles have been well explored. Here, we report the detailed visualization of the life cycle of Singapore grouper iridovirus (SGIV) in grouper cells by cryo-electron microscopy (cryoEM) and tomography (ET). EM imaging revealed that SGIV viral particles have an outer capsid layer and the interaction of this layer with cellular plasma membrane initiates viral entry. Subsequent viral replication leads to formation of a viral assembly site (VAS), where membranous structures emerge as precursors to recruit capsid proteins to form an intermediate, double-shell, crescent-shaped structure, which curves to form icosahedral capsids. Knockdown of the major capsid protein eliminates the formation of viral capsids. As capsid formation progresses, electron-dense materials known to be involved in DNA encapsidation accumulate within the capsid until it is fully occupied. Besides the well-known budding mechanism through the cell periphery, we demonstrate a novel budding process in which viral particles bud into a tubular-like structure within vacuoles. This budding process may denote a new strategy used by SGIV to disseminate viral particles into neighbor cells while evading host immune response.
Temporally Coordinated Deep Brain Stimulation in the Dorsal and Ventral Striatum Synergistically Enhances Associative Learning
Authors: Katnani Husam A. , Patel Shaun R. , Kwon Churl-Su , Abdel-Aziz Samer , Gale John T. , Eskandar Emad N. 
Published: January 2016

AbstractThe primate brain has the remarkable ability of mapping sensory stimuli into motor behaviors that can lead to positive outcomes. We have previously shown that during the reinforcement of visual-motor behavior, activity in the caudate nucleus is correlated with the rate of learning. Moreover, phasic microstimulation in the caudate during the reinforcement period was shown to enhance associative learning, demonstrating the importance of temporal specificity to manipulate learning related changes. Here we present evidence that extends upon our previous finding by demonstrating that temporally coordinated phasic deep brain stimulation across both the nucleus accumbens and caudate can further enhance associative learning. Monkeys performed a visual-motor associative learning task and received stimulation at time points critical to learning related changes. Resulting performance revealed an enhancement in the rate, ceiling and reaction times of learning. Stimulation of each brain region alone or at different time points did not generate the same effect.
One-pot system for synthesis, assembly, and display of functional single-span membrane proteins on oil–water interfaces
Authors: Yunker Peter J. , Asahara Haruichi , Hung Kuo-Chan , Landry Corey , Arriaga Laura R. , Akartuna Ilke , Heyman John , Chong Shaorong , Weitz David A. 
Published: January 2016

Significance
Single-span membrane proteins (ssMPs) are anchored by single hydrophobic helices to cell surfaces, where they mediate cell–cell communications. Unfortunately, hydrophobic helices also cause aggregation in solution, rendering ssMPs nonfunctional. We discovered that in vitro-synthesized ssMPs localize on an oil drop’s surface, preventing aggregation of ssMPs in solution and promoting assembly of functional structures on the drop’s surface. We use this approach to synthesize and display apoptosis-inducing ssMPs and show that these “death drops” are functional and can kill cultured cancer cells. Our results illustrate a one-pot method for rapid synthesis and assembly of functional ssMPs, which is facilitated by the hydrophobic interaction rather than limited by it. Such functionalized oil drops represent a platform to communicate with cells.
Wetting hysteresis induced by nanodefects
Authors: Giacomello Alberto , Schimmele Lothar , Dietrich Siegfried 
Published: January 2016

Significance
Drops may fail to slide even on extremely smooth surfaces. This fact is due to the ubiquitous imperfections of surfaces: defects of molecular size—here too small to be noticed and experimentally characterizable—can hinder a macroscopic drop. To understand these far-reaching nanoscale phenomena, we combine a molecular description of the liquid with advanced techniques for the study of rare events. This approach allows us to bridge the diverse scales involved, demonstrating that even weak nanometer-sized surface defects can give rise to measurable differences between advancing and receding liquid fronts, i.e., contact angle hysteresis. The present results also shed new light on the unexpectedly long life of surface nanobubbles.
EGFR phosphorylates FAM129B to promote Ras activation
Authors: Ji Haitao , Lee Jong-Ho , Wang Yugang , Pang Yilin , Zhang Tao , Xia Yan , Zhong Lianjin , Lyu Jianxin , Lu Zhimin 
Published: January 2016

Significance
Ras activation has been detected in many types of human cancers, and its activity can be regulated by its association with GTPase-activating proteins (GAPs). However, the underlying mechanism of Ras regulation by GAP is incompletely understood. Here we show that FAM129B phosphorylation by EGFR reduced the association of p120-RasGAP with H-Ras, thereby enhancing H-Ras activation, the Warburg effect, and tumorigenesis. Given that FAM129B is overexpressed in human cancer and that approaches to directly target Ras have not been successful, disruption of Ras activation by interfering with FAM129B function can be an alternative approach for treating human cancers with activated Ras.
Uterine ALK3 is essential during the window of implantation
Authors: Monsivais Diana , Clementi Caterina , Peng Jia , Titus Mary M. , Barrish James P. , Creighton Chad J. , Lydon John P. , DeMayo Francesco J. , Matzuk Martin M. 
Published: January 2016

Significance
In the assisted reproductive technology (ART) clinic, pregnancy is defined by the rise of human chorionic gonadotropin upon embryo implantation. Achieving embryo implantation is a major roadblock to the success of ART; it is estimated that only 50% of transferred embryos implant in patients seeking ART, and that half of these embryos are subsequently lost. Thus, understanding the molecular pathways during the window of implantation will improve ART success. In this study, we conditionally deleted activin-like kinase 3 (ALK3) in mice and demonstrate that bone morphogenetic protein (BMP) signaling via ALK3 defines uterine receptivity. This mouse model will be a valuable research tool for studying implantation failure in women, and the results herein will contribute to our knowledge regarding female infertility.
Introduction to the Special Issue: Advances in island plant biology since Sherwin Carlquist's Island Biology
Authors: Traveset Anna , Fernández-Palacios José María , Kueffer Christoph , Bellingham Peter J. , Morden Clifford , Drake Donald R. 
Published: January 2016

Abstract
Sherwin Carlquist's seminal publications—in particular his classic Island Biology , published in 1974—formulated hypotheses specific to island biology that remain valuable today. This special issue brings together some of the most interesting contributions presented at the First Island Biology Symposium hosted in Honolulu on 7–11 July 2014. We compiled a total of 18 contributions that present data from multiple archipelagos across the world and from different disciplines within the plant sciences. In this introductory paper, we first provide a short overview of Carlquist's life and work and then summarize the main findings of the collated papers. A first group of papers deals with issues to which Carlquist notably contributed: long-distance dispersal, adaptive radiation and plant reproductive biology. The findings of such studies demonstrate the extent to which the field has advanced thanks to (i) the increasing availability and richness of island data, covering many taxonomic groups and islands; (ii) new information from the geosciences, phylogenetics and palaeoecology, which allows us a more realistic understanding of the geological and biological development of islands and their biotas; and (iii) the new theoretical and methodological advances that allow us to assess patterns of abundance, diversity and distribution of island biota over large spatial scales. Most other papers in the issue cover a range of topics related to plant conservation on islands, such as causes and consequences of mutualistic disruptions (due to pollinator or disperser losses, introduction of alien predators, etc.). Island biologists are increasingly considering reintroducing ecologically important species to suitable habitats within their historic range and to neighbouring islands with depauperate communities of vertebrate seed dispersers, and an instructive example is given here. Finally, contributions on ecological networks demonstrate the usefulness of this methodological tool to advancing conservation management and better predicting the consequences of disturbances on species and interactions in the fragile insular ecosystems.
Characterizing rate limiting steps in transcription from RNA production times in live cells
Authors: Häkkinen Antti , Ribeiro Andre S. 
Published: January 2016

AbstractMotivation: Single-molecule measurements of live Escherichia coli transcription dynamics suggest that this process ranges from sub- to super-Poissonian, depending on the conditions and on the promoter. For its accurate quantification, we propose a model that accommodates all these settings, and statistical methods to estimate the model parameters and to select the relevant components.Results: The new methodology has improved accuracy and avoids overestimating the transcription rate due to finite measurement time, by exploiting unobserved data and by accounting for the effects of discrete sampling. First, we use Monte Carlo simulations of models based on measurements to show that the methods are reliable and offer substantial improvements over previous methods. Next, we apply the methods on measurements of transcription intervals of different promoters in live E. coli, and show that they produce significantly different results, both in low- and high-noise settings, and that, in the latter case, they even lead to qualitatively different results. Finally, we demonstrate that the methods can be generalized for other similar purposes, such as for estimating gene activation kinetics. In this case, the new methods allow quantifying the inducer uptake dynamics as opposed to just comparing them between cases, which was not previously possible. We expect this new methodology to be a valuable tool for functional analysis of cellular processes using single-molecule or single-event microscopy measurements in live cells.Availability and implementation: Source code is available under Mozilla Public License at http://www.cs.tut.fi/%7Ehakkin22/censored/.Contact: andre.ribeiro@tut.fi or andre.sanchesribeiro@tut.fiSupplementary information: Supplementary data are available at Bioinformatics online.
Robust quantitative scratch assay
Authors: Vargas Andrea , Angeli Marc , Pastrello Chiara , McQuaid Rosanne , Li Han , Jurisicova Andrea , Jurisica Igor 
Published: January 2016

Abstract
The wound healing assay (or scratch assay) is a technique frequently used to quantify the dependence of cell motility—a central process in tissue repair and evolution of disease—subject to various treatments conditions. However processing the resulting data is a laborious task due its high throughput and variability across images. This Robust Quantitative Scratch Assay algorithm introduced statistical outputs where migration rates are estimated, cellular behaviour is distinguished and outliers are identified among groups of unique experimental conditions. Furthermore, the RQSA decreased measurement errors and increased accuracy in the wound boundary at comparable processing times compared to previously developed method (TScratch).
Availability and implementation: The RQSA is freely available at: http://ophid.utoronto.ca/RQSA/RQSA_Scripts.zip. The image sets used for training and validation and results are available at: (http://ophid.utoronto.ca/RQSA/trainingSet.zip, http://ophid.utoronto.ca/RQSA/validationSet.zip, http://ophid.utoronto.ca/RQSA/ValidationSetResults.zip, http://ophid.utoronto.ca/RQSA/ValidationSet_H1975.zip, http://ophid.utoronto.ca/RQSA/ValidationSet_H1975Results.zip, http://ophid.utoronto.ca/RQSA/RobustnessSet.zip, http://ophid.utoronto.ca/RQSA/RobustnessSet.zip). Supplementary Material is provided for detailed description of the development of the RQSA.
Contact: juris@ai.utoronto.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
SPMM: estimating infection duration of multivariant HIV-1 infections
Authors: Love Tanzy M. T. , Park Sung Yong , Giorgi Elena E. , Mack Wendy J. , Perelson Alan S. , Lee Ha Youn 
Published: January 2016

AbstractMotivation: Illustrating how HIV-1 is transmitted and how it evolves in the following weeks is an important step for developing effective vaccination and prevention strategies. It is currently possible through DNA sequencing to account for the diverse array of viral strains within an infected individual. This provides an unprecedented opportunity to pinpoint when each patient was infected and which viruses were transmitted.Results: Here we develop a mathematical tool for early HIV-1 evolution within a subject whose infection originates either from a single or multiple viral variants. The shifted Poisson mixture model (SPMM) provides a quantitative guideline for segregating viral lineages, which in turn enables us to assess when a subject was infected. The infection duration estimated by SPMM showed a statistically significant linear relationship with that by Fiebig laboratory staging (P = 0.00059) among 37 acutely infected subjects. Our tool provides a functional approach to understanding early genetic diversity, one of the most important parameters for deciphering HIV-1 transmission and predicting the rate of disease progression.Availability and implementation: SPMM, webserver, is available at http://www.hayounlee.org/web-tools.html.Contact: hayoun@usc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project
Authors: Prokopenko Dmitry , Hecker Julian , Silverman Edwin K. , Pagano Marcello , Nöthen Markus M. , Dina Christian , Lange Christoph , Fier Heide Loehlein 
Published: January 2016

AbstractMotivation: Population stratification is one of the major sources of confounding in genetic association studies, potentially causing false-positive and false-negative results. Here, we present a novel approach for the identification of population substructure in high-density genotyping data/next generation sequencing data. The approach exploits the co-appearances of rare genetic variants in individuals. The method can be applied to all available genetic loci and is computationally fast. Using sequencing data from the 1000 Genomes Project, the features of the approach are illustrated and compared to existing methodology (i.e. EIGENSTRAT). We examine the effects of different cutoffs for the minor allele frequency on the performance of the approach. We find that our approach works particularly well for genetic loci with very small minor allele frequencies. The results suggest that the inclusion of rare-variant data/sequencing data in our approach provides a much higher resolution picture of population substructure than it can be obtained with existing methodology. Furthermore, in simulation studies, we find scenarios where our method was able to control the type 1 error more precisely and showed higher power.Availability and implementation:Contact: dmitry.prokopenko@uni-bonn.deSupplementary information: Supplementary data are available at Bioinformatics online.
MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data
Authors: Trieu Tuan , Cheng Jianlin 
Published: January 2016

Abstract
Motivation: The three-dimensional (3D) conformation of chromosomes and genomes play an important role in cellular processes such as gene regulation, DNA replication and genome methylation. Several methods have been developed to reconstruct 3D structures of individual chromosomes from chromosomal conformation capturing data such as Hi-C data. However, few methods can effectively reconstruct the 3D structures of an entire genome due to the difficulty of handling noisy and inconsistent inter-chromosomal contact data.
Results: We generalized a 3D chromosome reconstruction method to make it capable of reconstructing 3D models of genomes from both intra- and inter-chromosomal Hi-C contact data and implemented it as a software tool called MOGEN. We validated MOGEN on synthetic datasets of a polymer worm-like chain model and a yeast genome at first, and then applied it to generate an ensemble of 3D structural models of the genome of human B-cells from a Hi-C dataset. These genome models not only were validated by some known structural patterns of the human genome, such as chromosome compartmentalization, chromosome territories, co-localization of small chromosomes in the nucleus center with the exception of chromosome 18, enriched center-toward inter-chromosomal interactions between elongated or telomere regions of chromosomes, but also demonstrated the intrinsically dynamic orientations between chromosomes. Therefore, MOGEN is a useful tool for converting chromosomal contact data into 3D genome models to provide a better view into the spatial organization of genomes.
Availability and implementation: The software of MOGEN is available at: http://calla.rnet.missouri.edu/mogen/.
Contact: chengji@missouri.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ChromothripsisDB: a curated database of chromothripsis
Authors: Yang Jian , Deng Gaofeng , Cai Haoyang 
Published: January 2016

Abstract
Summary: Chromothripsis is a single catastrophic event that can lead to massive genomic rearrangements confined to one or a few chromosomes. It provides an alternative paradigm in cancer development and changes the conventional view that cancer develops in a stepwise progression. The mechanisms underlying chromothripsis and their specific impact on tumorigenesis are still poorly understood, and further examination of a large number of identified chromothripsis samples is needed. Unfortunately, this data are difficult to access, as they are scattered across multiple publications, come in different formats and descriptions, or are hidden in figures and supplementary materials. To improve access to this data and promote meta-analysis, we developed ChromothripsisDB, a manually curated database containing a unified description of all published chromothripsis cases and relevant genomic aberrations. Currently, 423 chromothripsis samples representing 107 research articles are included in our database. ChromothripsisDB represents an extraordinary resource for mining the existing knowledge of chromothripsis, and will facilitate the identification of mechanisms involved in this phenomenon.
Availability and implementation: ChromothripsisDB is freely available at http://cgma.scu.edu.cn/ChromothripsisDB.
Contact: haoyang.cai@scu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Development of a large urban longitudinal HIV clinical cohort using a web-based platform to merge electronically and manually abstracted data from disparate medical record systems: technical challenges and innovative solutions
Authors: Greenberg Alan E , Hays Harlen , Castel Amanda D , Subramanian Thilakavathy , Happ Lindsey Powers , Jaurretche Maria , Binkley Jeff , Kalmin Mariah M , Wood Kathy , Hart Rachel ,   on behalf of the DC Cohort Executive Committee
Published: January 2016

Objective Electronic medical records (EMRs) are being increasingly utilized to conduct clinical and epidemiologic research in numerous fields. To monitor and improve care of HIV-infected patients in Washington, DC, one of the most severely affected urban areas in the United States, we developed a city-wide database across 13 clinical sites using electronic data abstraction and manual data entry from EMRs.
Materials and Methods To develop this unique longitudinal cohort, a web-based electronic data capture system (Discovere®) was used. An Agile software development methodology was implemented across multiple EMR platforms. Clinical informatics staff worked with information technology specialists from each site to abstract data electronically from each respective site’s EMR through an extract, transform, and load process.
Results Since enrollment began in 2011, more than 7000 patients have been enrolled, with longitudinal clinical data available on all patients. Data sets are produced for scientific analyses on a quarterly basis, and benchmarking reports are generated semi-annually enabling each site to compare their participants’ clinical status, treatments, and outcomes to the aggregated summaries from all other sites.
Discussion Numerous technical challenges were identified and innovative solutions developed to ensure the successful implementation of the DC Cohort. Central to the success of this project was the broad collaboration established between government, academia, clinics, community, information technology staff, and the patients themselves.
Conclusions Our experiences may have practical implications for researchers who seek to merge data from diverse clinical databases, and are applicable to the study of health-related issues beyond HIV.
Tibet's Ali: Asia's Atacama?
Authors: Ye Quan-Zhi , Su Meng , Li Hong , Zhang Xinmin 
Published: January 2016

Abstract
The Ngari (Ali) prefecture of Tibet, one of the highest areas in the world, has recently emerged as a promising site for future astronomical observation. Here, we use 31 yr of reanalysis data from the Climate Forecast System Reanalysis to examine the astroclimatology of Ngari, using the recently-erected Ali Observatory at Shiquanhe (5047 m above mean sea level) as the representative site. We find the percentage of photometric night, median atmospheric seeing and median precipitable water vapour of the Shiquanhe site to be 57 per cent, 0.8 arcsec and 2.5 mm, comparable some of the world's best astronomical observatories. Additional calculation supports the Shiquanhe region as one of the better sites for astronomical observations over the Tibetan Plateau. Based on the studies taken at comparable environment at Atacama, extraordinary observing condition may be possible at the few vehicle-accessible 6000 m heights in the Shiquanhe region. Such possibility should be thoroughly investigated in future.
Young tidal dwarf galaxies cannot be used to probe dark matter in galaxies
Authors: Flores H. , Hammer F. , Fouquet S. , Puech M. , Kroupa P. , Yang Y. , Pawlowski M. 
Published: January 2016

Abstract
The location of dark-matter free, tidal dwarf galaxies (TDGs) in the baryonic Tully–Fisher (bTF) diagram has been used to test cosmological scenarios, leading to various and controversial results. Using new high-resolution 3D spectroscopic data, we re-investigate the morpho-kinematics of these galaxies to verify whether or not they can be used for such a purpose. We find that the three observed TDGs are kinematically not virialized and show complex morphologies and kinematics, leading to considerable uncertainties about their intrinsic rotation velocities and their locations on the bTF. Only one TDG can be identify as a (perturbed) rotation disc that it is indeed a sub-component of NGC5291N and that lies at &lt;1σ from the local bTF relation. It results that the presently studied TDGs are young, dynamically forming objects, which are not enough virialized to robustly challenge cosmological scenarios.