bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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.
A carbon dot-based hybrid fluorescent sensor for detecting free chlorine in water medium
Authors: Ding Yanjun , Ling Jiang , Cai Jifeng , Wang Suiping , Li Xingmei , Yang Minghui , Zha Lagabaiyla , Yan Jie
Published: January 2016

There are two fluorescence peaks for the CD–RhB nanohybrid and the fluorescence of CDs would be quenched with the addition of NaClO while the peak of RhB almost remains constant and an obvious color change (rose red to lilac) accompanies the process which is very convenient to distinguish by the naked eye.
FeCo2O4 submicron-tube arrays grown on Ni foam as high rate-capability and cycling-stability electrodes allowing superior energy and power densities with symmetric supercapacitors
Authors: Zhu Baogang , Tang Shaochun , Vongehr Sascha , Xie Hao , Zhu Jian , Meng Xiangkang
Published: January 2016

Homogeneous FeCo2O4 submicron-tube arrays grown on Ni foam as binder-free electrodes allow even symmetric devices to have superior energy densities.
Unravelling the hydrogen absorption process in Pd overlayers on a Au(111) surface
Authors: Quaino Paola M. , Nazmutdinov Renat , Peiretti Leonardo F. , Santos Elizabeth
Published: January 2016

Shedding light on the mechanism of hydrogen absorption occurring in nano-structured materials using the power of modern computational chemistry.
Long and short term impacts of CuO, Ag and CeO2nanoparticles on anaerobic digestion of municipal waste activated sludge
Authors: Ünşar E. Kökdemir , Çığgın A. S. , Erdem A. , Perendeci N. A.
Published: January 2016

In this study, long and short term inhibition impacts of Ag, CuO and CeO2nanoparticles (NPs) on anaerobic digestion (AD) of waste activated sludge (WAS) were investigated.
High-throughput quantum cascade laser (QCL) spectral histopathology: a practical approach towards clinical translation
Authors: Pilling Michael J. , Henderson Alex , Bird Benjamin , Brown Mick D. , Clarke Noel W. , Gardner Peter
Published: January 2016

Infrared microscopy has become one of the key techniques in the biomedical research field for interrogating tissue. In partnership with multivariate analysis and machine learning techniques, it has become widely accepted as a method that can distinguish between normal and cancerous tissue with both high sensitivity and high specificity. While spectral histopathology (SHP) is highly promising for improved clinical diagnosis, several practical barriers currently exist, which need to be addressed before successful implementation in the clinic. Sample throughput and speed of acquisition are key barriers and have been driven by the high volume of samples awaiting histopathological examination. FTIR chemical imaging utilising FPA technology is currently state-of-the-art for infrared chemical imaging, and recent advances in its technology have dramatically reduced acquisition times. Despite this, infrared microscopy measurements on a tissue microarray (TMA), often encompassing several million spectra, takes several hours to acquire. The problem lies with the vast quantities of data that FTIR collects; each pixel in a chemical image is derived from a full infrared spectrum, itself composed of thousands of individual data points. Furthermore, data management is quickly becoming a barrier to clinical translation and poses the question of how to store these incessantly growing data sets. Recently, doubts have been raised as to whether the full spectral range is actually required for accurate disease diagnosis using SHP. These studies suggest that once spectral biomarkers have been predetermined it may be possible to diagnose disease based on a limited number of discrete spectral features. In this current study, we explore the possibility of utilising discrete frequency chemical imaging for acquiring high-throughput, high-resolution chemical images. Utilising a quantum cascade laser imaging microscope with discrete frequency collection at key diagnostic wavelengths, we demonstrate that we can diagnose prostate cancer with high sensitivity and specificity. Finally we extend the study to a large patient dataset utilising tissue microarrays, and show that high sensitivity and specificity can be achieved using high-throughput, rapid data collection, thereby paving the way for practical implementation in the clinic.
Discoveries from a phenanthroline-based dynamic combinatorial library: catenane from a copper(i) or copper(ii) template?
Authors: Tong King-Lung , Yee Chi-Chung , Tse Yuen Cheong , Au-Yeung Ho Yu
Published: January 2016

We report here a DCL study of a phenanthroline-based building block focusing on catenane formation with copper templates.
Design, synthesis, biological evaluation and molecular docking of amide and sulfamide derivatives as Escherichia coli pyruvate dehydrogenase complex E1 inhibitors
Authors: He Haifeng , Feng Jiangtao , He Junbo , Xia Qin , Ren Yanliang , Wang Fang , Peng Hao , He Hongwu , Feng Lingling
Published: January 2016

Optimal binding mode of novel E. coli PDHc E1 inhibitor 9d.
A one-pot process for the microwave-assisted synthesis of 7-substituted pyrazolo[1,5-a]pyrimidine
Authors: Bassoude Ibtissam , Tber Zahira , Essassi El Mokhtar , Guillaumet Gérald , Berteina-Raboin Sabine
Published: January 2016

An efficient synthesis of 7-substituted pyrazolo[1,5-a]pyrimidines using a one-pot, two-step process via Pd-catalyzed direct CH-arylation followed by a saponification–decarboxylation reaction is reported.
Pt–MoO3–RGO ternary hybrid hollow nanorod arrays as high-performance catalysts for methanol electrooxidation
Authors: Wang An-Liang , Liang Chao-Lun , Lu Xue-Feng , Tong Ye-Xiang , Li Gao-Ren
Published: January 2016

Here we design and synthesize novel Pt–MoO3–RGO (reduced graphene oxide) ternary hybrid hollow nanorod arrays (HNRAs) as anode catalysts for methanol electrooxidation.
Unravelling the nature, evolution and spatial gradients of active species and active sites in the catalyst bed of unpromoted and K/Ba-promoted Cu/Al2O3 during CO2 capture-reduction
Authors: Hyakutake Tsuyoshi , van Beek Wouter , Urakawa Atsushi
Published: January 2016

Space- and time-resolved operando DRIFTS, XAFS, and XRD uncovered the involved surface chemical species and active sites, especially the unique functions of K and Cu, during the CO2 capture-reduction process.
Fluorescence mutation and structural evolution of a π-conjugated molecular crystal during phase transition
Authors: Xu Yuanxiang , Wang Kai , Zhang Yujian , Xie Zengqi , Zou Bo , Ma Yuguang
Published: January 2016

Two thermodynamically stable crystalline phases (B- and G-phases) were found for a twistable π-conjugated molecule, CN-DSB, condensed from its solution.
Multifractal vector fields and stochastic Clifford algebra
Authors: Schertzer Daniel , Tchiguirinskaia Ioulia
Published: January 2016

In the mid 1980s, the development of multifractal concepts and techniques was an important breakthrough for complex system analysis and simulation, in particular, in turbulence and hydrology. Multifractals indeed aimed to track and simulate the scaling singularities of the underlying equations instead of relying on numerical, scale truncated simulations or on simplified conceptual models. However, this development has been rather limited to deal with scalar fields, whereas most of the fields of interest are vector-valued or even manifold-valued. We show in this paper that the combination of stable Lévy processes with Clifford algebra is a good candidate to bridge up the present gap between theory and applications. We show that it indeed defines a convenient framework to generate multifractal vector fields, possibly multifractal manifold-valued fields, based on a few fundamental and complementary properties of Lévy processes and Clifford algebra. In particular, the vector structure of these algebra is much more tractable than the manifold structure of symmetry groups while the Lévy stability grants a given statistical universality.
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.
Inhibition of Hif1α prevents both trauma-induced and genetic heterotopic ossification
Authors: Agarwal Shailesh , Loder Shawn , Brownley Cameron , Cholok David , Mangiavini Laura , Li John , Breuler Christopher , Sung Hsiao H. , Li Shuli , Ranganathan Kavitha , Peterson Joshua , Tompkins Ronald , Herndon David , Xiao Wenzhong , Jumlongras Dolrudee , Olsen Bjorn R. , Davis Thomas A. , Mishina Yuji , Schipani Ernestina , Levi Benjamin
Published: January 2016

Significance

Heterotopic ossification (HO) is a debilitating condition in which bone forms inappropriately within soft tissues. Two vastly different patient populations are at risk for developing HO: those with musculoskeletal trauma or severe burns and those with a genetic mutation in the bone morphogenetic protein receptor
ACVR1
(Activin type 1 receptor). In this study, we demonstrate that both forms of HO share a common signaling pathway through hypoxia inducible factor-1α, and that pharmacologic inhibition or genetic knockout of this signaling pathway can mitigate and even abolish HO formation. These findings pave the way for pharmacologic inhibitors of hypoxia inducible factor-1α as therapeutic options for heterotopic ossification.
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.
Loss of the BBSome perturbs endocytic trafficking and disrupts virulence of
Trypanosoma brucei
Authors: Langousis Gerasimos , Shimogawa Michelle M. , Saada Edwin A. , Vashisht Ajay A. , Spreafico Roberto , Nager Andrew R. , Barshop William D. , Nachury Maxence V. , Wohlschlegel James A. , Hill Kent L.
Published: January 2016

Significance

We combine genetics, biochemistry, cell biology, and proteomics to define Bardet–Biedl Syndrome complex (BBSome) composition, location, and function in the deadly parasite
Trypanosoma brucei
. BBSome mutants have reduced infectivity in mice, and quantitative proteomics identified parasite surface proteome changes that may underlie reduced virulence. To our knowledge, this work presents the first comprehensive study of the BBSome in any microbial pathogen.
T. brucei
is also among the earliest organisms to have diverged from other eukaryotes, showing deep evolutionary origins of the BBSome. Localization to membranes and vesicles at the flagellar pocket, together with functional analyses and interaction with clathrin and ubiquitin, supports a model whereby the BBSome functions in postendocytic sorting of select surface proteins.
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.
Social Support Among Substance Using Women with Criminal Justice Involvement
Authors: Majer John , Salina Doreen , Jason Leonard
Published: January 2016

Social support types (abstinence, appraisal, belonging, tangible) were analyzed among a sample of women with criminal justice involvement and substance use disorders (n = 200). Hierarchical linear regression was conducted to examine social support types in relation to changes in abstinence self-efficacy while controlling for incarceration histories. Only abstinence social support and tangible social support predicted significant increases in abstinence self-efficacy, with tangible support accounting for more variance in the analytic model. Findings suggest women with criminal justice involvement who have substance use disorders have basic needs that if met would have an indirect effect on their recovery. Implications for treatment and research are discussed.
Social Worker Assessments of Competency to Stand Trial
Authors: Roesch Ronald
Published: January 2016

This article focuses on an expanding role for social workers conducting assessments of competency to stand trial. This pretrial assessment is the most common form of pretrial forensic evaluations. Although a handful of states explicitly allow social workers to conduct these evaluations, it is suggested that this is a role in which social workers could have a greater role as the field of forensic social work develops. It is suggested that this role can be enhanced through the development of forensic specialty guidelines. The article reviews competency laws and assessment procedures and provides an overview of forensic assessment instruments that can be used in the evaluation of competency to stand trial. The special circumstances surrounding evaluations of competency in juvenile court are also examined.
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

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.
Authors’ response to ‘Comment on: ERGC: An efficient Referential Genome Compression Algorithm’
Authors: Saha Subrata , Rajasekaran Sanguthevar
Published: January 2016

Contact:  subrata.saha@engr.uconn.edu or rajasek@engr.uconn.edu
Characterizing rate limiting steps in transcription from RNA production times in live cells
Authors: Häkkinen Antti , Ribeiro Andre S.
Published: January 2016

Motivation: 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.fi

Supplementary 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

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

Motivation: 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.edu

Supplementary 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

Motivation: 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.de

Supplementary 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

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

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

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

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 <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.
Flickering of accreting white dwarfs: the remarkable amplitude–flux relation and disc viscosity
Authors: Zamanov R. K. , Boeva S. , Latev  G. , Sokoloski J. L. , Stoyanov  K. A. , Genkov V. , Tsvetkova S. V. , Tomov T. , Antov A. , Bode M. F.
Published: January 2016

We analyse optical photometric data of short term variability (flickering) of accreting white dwarfs in cataclysmic variables (KR Aur, MV Lyr, V794 Aql, TT Ari, V425 Cas), recurrent novae (RS Oph and T CrB) and jet-ejecting symbiotic stars (CH Cyg and MWC 560). We find that the amplitude–flux relationship is visible over four orders of magnitude, in the range of fluxes from 1029 to 1033 erg s−1 Å−1, as a ‘statistically perfect correlation with correlation coefficient 0.96 and p-value ∼10−28. In the above range, the amplitude of variability for any of our 9 objects is proportional to the flux level with (almost) one and the same factor of proportionality for all nine accreting white dwarfs with ΔF = 0.36(±0.05)Fav, σrms = 0.086(±0.011)Fav, and σrms/ΔF = 0.24 ± 0.02. Overall, our results indicate that the viscosity in the accretion discs is practically the same for all nine objects in our sample, in the mass accretion rate range 2 × 10−11 − 2 × 10−7 M⊙ yr−1.
EXTraS discovery of an 1.2-s X-ray pulsar in M 31
Authors: Esposito P. , Israel G. L. , Belfiore A. , Novara G. , Sidoli L. , Rodríguez Castillo G. A. , De Luca A. , Tiengo A. , Haberl F. , Salvaterra R. , Read A. M. , Salvetti D. , Sandrelli S. , Marelli M. , Wilms J. , D'Agostino D.
Published: January 2016

During a search for coherent signals in the X-ray archival data of XMM–Newton, we discovered a modulation at 1.2 s in 3XMM J004301.4+413017 (3X J0043), a source lying in the direction of an external arm of M 31. This short period indicates a neutron star (NS). Between 2000 and 2013, the position of 3X J0043 was imaged by public XMM–Newton observations 35 times. The analysis of these data allowed us to detect an orbital modulation at 1.27 d and study the long-term properties of the source. The emission of the pulsar was rather hard (most spectra are described by a power law with Γ < 1) and, assuming the distance to M 31, the 0.3–10 keV luminosity was variable, from ∼3 × 1037 to 2 × 1038 erg s−1. The analysis of optical data shows that, while 3X J0043 is likely associated to a globular cluster in M 31, a counterpart with V ≳ 22 outside the cluster cannot be excluded. Considering our findings, there are two main viable scenarios for 3X J0043: a peculiar low-mass X-ray binary, similar to 4U 1822−37 or 4U 1626−67, or an intermediate-mass X-ray binary resembling Her X−1. Regardless of the exact nature of the system, 3X J0043 is the first accreting NS in M 31 in which the spin period has been detected.
Twin peak quasi-periodic oscillations as signature of oscillating cusp torus
Authors: Török G. , Goluchová K. , Horák J. , Šrámková E. , Urbanec M. , Pecháček T. , Bakala P.
Published: January 2016

Serious theoretical effort has been devoted to explain the observed frequencies of twin-peak quasi-periodic oscillations (HF QPOs) observed in low-mass X-ray neutron star binaries. Here we propose a new model of HF QPOs. Within its framework we consider an oscillating torus with cusp that changes location r0 of its centre around radii very close to innermost stable circular orbit. The observed variability is assigned to global modes of accreted fluid motion that may give strong modulation of both accretion disc radiation and the accretion rate. For a given space–time geometry, the model predicts that QPO frequencies are function of single parameter r0. We illustrate that the model can provide fits of data comparable to those reached by other models, or even better. In particular, it is compared to relativistic precession model. Moreover, we also illustrate that the model consideration is compatible with consideration of models of a rotating neutron star in the atoll source 4U 1636−53.
BioGRID: A Resource for Studying Biological Interactions in Yeast
Authors: Oughtred Rose , Chatr-aryamontri Andrew , Breitkreutz Bobby-Joe , Chang Christie S. , Rust Jennifer M. , Theesfeld Chandra L. , Heinicke Sven , Breitkreutz Ashton , Chen Daici , Hirschman Jodi , Kolas Nadine , Livstone Michael S. , Nixon Julie , O’Donnell Lara , Ramage Lindsay , Winter Andrew , Reguly Teresa , Sellam Adnane , Stark Chris , Boucher Lorrie , Dolinski Kara , Tyers Mike
Published: January 2016

The Biological General Repository for Interaction Datasets (BioGRID) is a freely available public database that provides the biological and biomedical research communities with curated protein and genetic interaction data. Structured experimental evidence codes, an intuitive search interface, and visualization tools enable the discovery of individual gene, protein, or biological network function. BioGRID houses interaction data for the major model organism species—including yeast, nematode, fly, zebrafish, mouse, and human—with particular emphasis on the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe as pioneer eukaryotic models for network biology. BioGRID has achieved comprehensive curation coverage of the entire literature for these two major yeast models, which is actively maintained through monthly curation updates. As of September 2015, BioGRID houses approximately 335,400 biological interactions for budding yeast and approximately 67,800 interactions for fission yeast. BioGRID also supports an integrated posttranslational modification (PTM) viewer that incorporates more than 20,100 yeast phosphorylation sites curated through its sister database, the PhosphoGRID.
Evaluating communication competency of tour guides using a modified importance-performance analysis (MIPA)
Authors: Sulaiman Al Jahwari Dawood , Sirakaya-Turk Ercan , Altintas Volkan
Published: January 2016

Purpose

The purpose of this research is to evaluate the communication competency of tour guides using a modified importance–performance analysis (MIPA). Tour guides are cultural ambassadors of a country; their communication skills can make or break tourists’ experiences with guided tours and memories of a destination.

Design/methodology/approach

Data were collected from 387 professional tour guides representing 38 per cent of all tour guides in Antalya, Turkey. The study further performs factor analysis using 32 communication competency items to determine underlying performance dimensions. This is followed by an MIPA to statistically identify the gap between factors that tour guides consider important and their perceptions of how they perform on these factors.

Findings

The study reveals that tour guides need improvement in verbal skills such as grammar, manner of speech and choice of words, as well as non-verbal behaviors such as approachability and the ability to remain friendly while maintaining a certain personal space.

Research limitations/implications

Due to the nature of this study and certain time limitations, the most effective method proved to be collecting data from a convenient sample of tour guides during their annual workshop. The theory of behavioral communication competency details theoretical and practical implications.

Practical implications

The study findings provide tour operators and the Association of Professional Tour Guides with a platform from which they can launch educational seminars and workshops to enhance tour guides’ communication competency.

Originality/value

The study contributes two main findings: This research provides a first-of-its-kind examination of professional tour guides’ communication competency using MIPA. The study improves the efficacy of traditional importance–performance analysis (IPA) models by enhancing them with a gap analysis through a t-test and effect size analysis including a gap analysis takes the arbitrariness out of the process of determining the location of items within the IPA grid. Tourism service providers can use these findings to offer educational seminars that can increase the skill sets of tour guides.
Accelerated HF‐rTMS Protocol has a Rate‐Dependent Effect on dACC Activation in Alcohol‐Dependent Patients: An Open‐Label Feasibility Study
Authors: Herremans Sarah C. , De Raedt Rudi , Van Schuerbeek Peter , Marinazzo Daniele , Matthys Frieda , De Mey Johan , Baeken Chris
Published: January 2016

Background

The application of accelerated high‐frequency (HF) repetitive transcranial magnetic stimulation (rTMS) could be a potential treatment option for alcohol‐dependent patients and may result in a faster clinical response. In this open‐label HF‐rTMS feasibility study, we wanted to replicate previous findings of baseline brain activation as a predictor of relapse, and to evaluate how this intervention influences the relapse neurocircuit of “treatment‐seeking” alcohol‐dependent patients, by means of functional magnetic resonance imaging (fMRI) cue‐exposure paradigms. Because relapsing patients have a diminished resilience of the emotion regulation/cognitive control system, before HF‐rTMS treatment, we expected lower neuronal activation of especially the ventromedial prefrontal cortex and anterior cingulate cortex (ACC) during the presentation of alcohol‐related cues in these patients. The relapse neurocircuit should be modified after accelerated HF‐rTMS treatment, only in those patients who did not relapse.

Methods

After being administered a single sham‐controlled HF‐rTMS session (20 Hz to 110% motor threshold), 19 alcohol‐dependent patients received an accelerated HF‐rTMS protocol, consisting of 14 right dorsolateral prefrontal cortical sessions spread over 3 days. Before and after stimulation, during fMRI patients were confronted with a block and an event‐related alcoholic cue‐exposure paradigm. Relapse was defined as the consumption of any amount of alcohol within 4 weeks after the stimulation. A region of interest analysis was performed to evaluate how HF‐rTMS exerts its effect.

Results

After 4 weeks, 13 of 19 patients had already consumed alcohol. When abstainers were compared to patients who had relapsed, we found higher dorsal ACC (dACC) activation at baseline, but only during the blocked cue‐exposure paradigm. The effects of HF‐rTMS on dACC blood oxygen level‐dependent response were negatively correlated with the baseline dACC activation. Due to susceptibility artifacts located at the ventral cortical aspects in 6 of our participants, reliable data were only obtained for the ACC.

Conclusions

Our data indicate that higher baseline dACC activation may serve as a protective mechanism regarding relapse. For the first time, it is demonstrated that accelerated HF‐rTMS treatment influences dACC activation in a rate‐dependent manner: the lower the baseline dACC activation, the more dACC activity was increased after HF‐rTMS treatment.
Urinary Neutrophil Gelatinase‐associated Lipocalin as a Marker for Identification of Acute Kidney Injury and Recovery in Dogs with Gentamicin‐induced Nephrotoxicity
Authors: Palm C.A. , Segev G. , Cowgill L.D. , LeRoy B.E. , Kowalkowski K.L. , Kanakubo K. , Westropp J.L.
Published: January 2016

Background

Acute kidney injury (AKI) is associated with high mortality rates in dogs, which may be a consequence of late recognition using traditional diagnostic tests. Neutrophil gelatinase‐associated lipocalin (NGAL) is a protein‐induced during kidney injury that may identifyAKIearlier than traditional tests.

Objectives/Hypothesis

To evaluate urinaryNGAL(uNGAL) anduNGAL‐to‐urinary creatinine ratio (UNCR) as early markers of kidney injury and recovery in anAKImodel in dogs. It was hypothesized that these markers would documentAKIearlier than serum creatinine concentration.

Animals

Five purpose‐bred dogs.

Methods

Prospective study. Acute kidney injury, defined as a > 50% increase in serum creatinine concentration above baseline, was induced in dogs by gentamicin administration (8–10 mg/kgSCq8h). Blood and urine collected for biochemical analyses anduNGALand urinary creatinine concentrations, respectively, duringAKIinduction and recovery.

Results

Acute kidney injury was diagnosed significantly earlier based on a 7‐fold increase inUNCRcompared to a > 50% increase in serum creatinine concentration (day 8; range, 2–10 mg/dl vs day 16; range, 14–19 mg/dl;P= .009). During recovery, the initial decrease inUNCRpreceded the decrease in serum creatinine concentration by a median of 2 days. TheuNGALchanges paralleledUNCRchanges, but the increase inuNGALwas triphasic; the initial peak occurred earlier thanUNCR(median, day 11 versus median, day 19).

Conclusions and Clinical Importance

TheUNCRwas early marker of gentamicin‐inducedAKIand its decrease documented onset of renal recovery. Additional studies are needed to validate this marker in dogs with naturally occurring renal injury.