bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of Juvenile Cutthroat Trout Translocated as Embryos from Five Populations into a Common Habitat
Authors: Andrews Tessa C. , Shepard Bradley B. , Litt Andrea R. , Kruse Carter G. , Lee Nelson M. , Clancey Patrick , Zale Alexander V. , Taper Mark L. , Kalinowski Steven T. 
Published: July 2016

Abstract
The distributions of most native trout species in western North America have been severely reduced, and conservation of many of these species will require translocation into vacant habitats following removal of nonnative species. A critical question managers have is “Does it matter which donor sources are used for these translocations?” We present a case study that addressed this question for a large native trout translocation project in Montana. We introduced embryos from five source populations of Westslope Cutthroat Trout Oncorhynchus clarkii lewisi to a large, fishless watershed in Montana following removal of nonnative fish with piscicides. Source populations providing embryos for translocations were three nearby (&lt;120 km) wild populations, the state of Montana's captive Westslope Cutthroat Trout hatchery conservation population (initiated 32 years ago using fish from wild populations located &gt;350 km from the translocation site), and a population in captivity for one generation comprised of individuals from the three wild populations used as single sources for this project, which were variably crossed (59% within populations and 41% between populations) to provide embryos. We used remote-site incubators at six different sites to introduce approximately 35,000 embryos from 400 genotyped parents. We later resampled and genotyped 1,450 of these individuals at age 1 and age 2. Juvenile survival for the more genetically diverse Montana Westslope Cutthroat Trout conservation population was twice as high as for other source populations, even though these other source populations were geographically closer to the translocation site than populations used to make the Montana Westslope Cutthroat Trout conservation population. Body weight for progeny from the two captive populations was higher than for progeny from wild source populations, and some differences were observed in body condition among source populations. Continued monitoring over several generations will be necessary to determine the eventual contributions of each source population and the relevance of these initial findings.
Received October 9, 2015; accepted February 27, 2016 Published online July 20, 2016
ntHash: recursive nucleotide hashing
Authors: Mohamadi Hamid , Chu Justin , Vandervalk Benjamin P. , Birol Inanc 
Published: July 2016

Abstract

Motivation
Hashing has been widely used for indexing, querying and rapid similarity search in many bioinformatics applications, including sequence alignment, genome and transcriptome assembly, k-mer counting and error correction. Hence, expediting hashing operations would have a substantial impact in the field, making bioinformatics applications faster and more efficient.

Results
We present ntHash, a hashing algorithm tuned for processing DNA/RNA sequences. It performs the best when calculating hash values for adjacent k-mers in an input sequence, operating an order of magnitude faster than the best performing alternatives in typical use cases.

Availability and implementation
ntHash is available online at http://www.bcgsc.ca/platform/bioinfo/software/nthash and is free for academic use.

Contacts
hmohamadi@bcgsc.ca or ibirol@bcgsc.ca

Supplementary information
Supplementary data are available at Bioinformatics online.
TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization
Authors: Kou Qiang , Xun Likun , Liu Xiaowen 
Published: July 2016

Summary: Top-down mass spectrometry enables the observation of whole complex proteoforms in biological samples and provides crucial information complementary to bottom-up mass spectrometry. Because of the complexity of top-down mass spectra and proteoforms, it is a challenging problem to efficiently interpret top-down tandem mass spectra in high-throughput proteome-level proteomics studies. We present TopPIC, a tool that efficiently identifies and characterizes complex proteoforms with unknown primary structure alterations, such as amino acid mutations and post-translational modifications, by searching top-down tandem mass spectra against a protein database.
Availability and Implementation: http://proteomics.informatics.iupui.edu/software/toppic/
Contact: xwliu@iupui.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
LEVER: software tools for segmentation, tracking and lineaging of proliferating cells
Authors: Winter Mark , Mankowski Walter , Wait Eric , Temple Sally , Cohen Andrew R. 
Published: July 2016

The analysis of time-lapse images showing cells dividing to produce clones of related cells is an important application in biological microscopy. Imaging at the temporal resolution required to establish accurate tracking for vertebrate stem or cancer cells often requires the use of transmitted light or phase-contrast microscopy. Processing these images requires automated segmentation, tracking and lineaging algorithms. There is also a need for any errors in the automated processing to be easily identified and quickly corrected. We have developed LEVER, an open source software tool that combines the automated image analysis for phase-contrast microscopy movies with an easy-to-use interface for validating the results and correcting any errors.
Availability and Implementation: LEVER is available free and open source, licensed under the GNU GPLv3. Details on obtaining and using LEVER are available at http://n2t.net/ark:/87918/d9rp4t.
Contact: acohen@coe.drexel.edu
Online interactive analysis of protein structure ensembles with Bio3D-web
Authors: Skjærven Lars , Jariwala Shashank , Yao Xin-Qiu , Grant Barry J. 
Published: July 2016

Summary: Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. Major functionality is provided for identifying protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations and the quantitative comparison of their predicted structural dynamics.
Availability: Bio3D-web is based on the Bio3D and Shiny R packages. All major browsers are supported and full source code is available under a GPL2 license from http://thegrantlab.org/bio3d-web.
Contact: bjgrant@umich.edu or lars.skjarven@uib.no
Preoperative Evaluation Clinic Visit Is Associated with Decreased Risk of In-hospital Postoperative Mortality
Authors: Blitz Jeanna D. , Kendale Samir M. , Jain Sudheer K. , Cuff Germaine E. , Kim Jung T. , Rosenberg Andrew D. 
Published: July 2016

Abstract

Background
As specialists in perioperative medicine, anesthesiologists are well equipped to design and oversee the preoperative patient preparation process; however, the impact of an anesthesiologist-led preoperative evaluation clinic (PEC) on clinical outcomes has yet to be fully elucidated. The authors compared the incidence of in-hospital postoperative mortality in patients who had been evaluated in their institution’s PEC before elective surgery to the incidence in patients who had elective surgery without being seen in the PEC.

Methods
A retrospective review of an administrative database was performed. There were 46 deaths from 64,418 patients (0.07%): 22 from 35,535 patients (0.06%) seen in PEC and 24 from 28,883 patients (0.08%) not seen in PEC. After propensity score matching, there were 13,964 patients within each matched set; there were 34 deaths (0.1%). There were 11 deaths from 13,964 (0.08%) patients seen in PEC and 23 deaths from 13,964 (0.16%) patients not seen in PEC. A subanalysis to assess the effect of a PEC visit on deaths as a result of failure to rescue (FTR) was also performed.

Results
A visit to PEC was associated with a reduction in mortality (odds ratio, 0.48; 95% CI, 0.22 to 0.96, P = 0.04) by comparison of the matched cohorts. The FTR subanalysis suggested that the proportion of deaths attributable to an unanticipated surgical complication was not significantly different between the two groups (P = 0.141).

Conclusions
An in-person assessment at the PEC was associated with a reduction in in-hospital mortality. It was difficult to draw conclusions about whether a difference exists in the proportion of FTR deaths between the two cohorts due to small sample size.
A Population-based Study Evaluating the Association between Surgery in Early Life and Child Development at Primary School Entry
Authors: O’Leary James D. , Janus Magdalena , Duku Eric , Wijeysundera Duminda N. , To Teresa , Li Ping , Maynes Jason T. , Crawford Mark W. 
Published: July 2016

Abstract

Background
It is unclear whether exposure to surgery in early life has long-term adverse effects on child development. The authors aimed to investigate whether surgery in early childhood is associated with adverse effects on child development measured at primary school entry.

Methods
The authors conducted a population-based cohort study in Ontario, Canada, by linking provincial health administrative databases to children’s developmental outcomes measured by the Early Development Instrument (EDI). From a cohort of 188,557 children, 28,366 children who underwent surgery before EDI completion (age 5 to 6 yr) were matched to 55,910 unexposed children. The primary outcome was early developmental vulnerability, defined as any domain of the EDI in the lowest tenth percentile of the population. Subgroup analyses were performed based on age at first surgery (less than 2 and greater than or equal to 2 yr) and frequency of surgery.

Results
Early developmental vulnerability was increased in the exposed group (7,259/28,366; 25.6%) compared with the unexposed group (13,957/55,910; 25.0%), adjusted odds ratio, 1.05; 95% CI, 1.01 to 1.08. Children aged greater than or equal to 2 yr at the time of first surgery had increased odds of early developmental vulnerability compared with unexposed children (odds ratio, 1.05; 95% CI, 1.01 to 1.10), but children aged less than 2 yr at the time of first exposure were not at increased risk (odds ratio, 1.04; 95% CI, 0.98 to 1.10). There was no increase in odds of early developmental vulnerability with increasing frequency of exposure.

Conclusions
Children who undergo surgery before primary school age are at increased risk of early developmental vulnerability, but the magnitude of the difference between exposed and unexposed children is small.
Inappropriate dose of multitargeted tyrosine kinase inhibitors: the original sin
Authors: Kotecki Nuria , Penel Nicolas 
Published: July 2016

Purpose of review
The use of antiangiogenic tyrosine kinase inhibitors (TKIs) is challenging and often requires dose adaptation and transient or definitive treatment interruption. We believe that the inappropriate recommended dose of TKI is related to no optimal study designs in the early development of the drug.

Recent findings
As an example of this, we described herein some pitfalls made in the successive development of sunitinib, sorafenib, regorafenib, and pazopanib, but there are several other examples of early drugs development illustrating this issue.

Summary
Regarding the antiangiogenic TKI mechanism of action, we strongly feel that innovative approaches are needed such as extended dose-limiting toxicity period or a better definition of the induced toxicity. Furthermore, before classic phase II/III trials, an intermediate step may be needed to better define the recommended phase II dose, such as a randomized phase I/II trial with several expansion cohorts.
Polycystic ovary syndrome in adolescents: a review of past year evidence
Authors: Javed Asma , Chelvakumar Gayathri , Bonny Andrea E. 
Published: July 2016

Purpose of review
Despite the fact that polycystic ovary syndrome (PCOS) is a common disorder, much remains unknown or controversial regarding the cause, diagnosis, and management of this disorder, particularly in adolescents where normal pubertal events can overlap with the PCOS phenotype.

Recent findings
We put forth a critical assessment of recent literature on PCOS in adolescents, with particular focus on new information regarding the pathogenesis, diagnosis, associated morbidities, and management.

Summary
Although the evidence is increasing, there is still a critical need for large, prospective studies of adolescents with PCOS. Given the current level of evidence, a definitive diagnosis of PCOS is not necessary to effectively identify and treat manifestations of this syndrome in adolescents. Currently, ovarian imaging is not recommended in the diagnostic evaluation of PCOS in adolescents until high-quality data for defining polycystic ovarian morphology are available in this age group. Weight loss remains the safest and most effective treatment option for obese or overweight adolescents with PCOS. Clinicians should be mindful of the significant associated psychological morbidity and effectively screen and manage these conditions in adolescents with manifestations of PCOS.
How much do we really know about von Willebrand disease?
Authors: Swystun Laura L. , Lillicrap David 
Published: July 2016

Purpose of review
In the last nine decades, large advances have been made toward the characterization of the pathogenic basis and clinical management of von Willebrand disease (VWD), the most prevalent inherited bleeding disorder. Pathological variations at the von Willebrand factor (VWF) locus present as a range of both quantitative and qualitative abnormalities that make up the complex clinical spectrum of VWD. This review describes the current understanding of the pathobiological basis of VWD.

Recent findings
The molecular basis of type 2 (qualitative abnormalities) and type 3 VWD (total quantitative deficiency) have been well characterized in recent decades. However, knowledge of type 1 VWD (partial quantitative deficiency) remains incomplete because of the allelic and locus heterogeneity of this trait, and is complicated by genetic variability at the VWF gene, interactions between the VWF gene and the environment, and the involvement of external modifying loci. Recent genome wide association studies and linkage analyses have sought to identify additional genes that modify the type 1 VWD phenotype.

Summary
Understanding the pathogenic basis of VWD will facilitate the development of novel treatment regimens for this disorder, and improve the ability to provide complementary molecular diagnostics for type 1 VWD.
Revealing neuro-computational mechanisms of reinforcement learning and decision-making with the hBayesDM package
Authors: Ahn Woo-Young , Haines Nathaniel , Zhang Lei 
Published: July 2016

AbstractReinforcement learning and decision-making (RLDM) provide a quantitative framework and computational theories, with which we can disentangle psychiatric conditions into basic dimensions of neurocognitive functioning. RLDM offer a novel approach to assess and potentially diagnose psychiatric patients, and there is growing enthusiasm on RLDM and Computational Psychiatry among clinical researchers. Such a framework can also provide insights into the brain substrates of particular RLDM processes as exemplified by model-based functional magnetic resonance imaging (fMRI) or electroencephalogram (EEG). However, many researchers often find the approach too technical and have difficulty adopting it for their research. Thus, there remains a critical need to develop a user-friendly tool for the wide dissemination of computational psychiatric methods. We introduce an R package called hBayesDM (hierarchicalBayesian modeling ofDecision-Making tasks), which offers computational modeling on an array of RLDM tasks and social exchange games. The hBayesDM package offers state-of-the-art hierarchical Bayesian modeling, where both individual and group parameters (i.e., posterior distributions) are estimated simultaneously in a mutually constraining fashion. At the same time, it is extremely user-friendly: users can perform computational modeling, output visualization, and Bayesian model comparisons–each with a single line of coding. Users can also extract trial-by-trial latent variables (e.g., prediction errors) required for model-based fMRI/EEG. With the hBayesDM package, we anticipate that anyone with minimal knowledge of programming can take advantage of cutting-edge computational modeling approaches and investigate the underlying processes of and interactions between multiple decision-making (e.g., goal-directed, habitual, and Pavlovian) systems. In this way, it is our expectation that the hBayesDM package will contribute to the dissemination of advanced modeling approaches and enable a wide range of researchers to easily perform computational psychiatric research within their populations.
Genome urbanization: Clusters of topologically co-regulated genes delineate functional compartments in the genome ofS. cerevisiae
Authors: Tsochatzidou Maria , Malliarou Maria , Papanikolaou Nikolas , Roca Joaquim , Nikolaou Christoforos 
Published: July 2016

AbstractThe eukaryotic genome evolves under the dual constraint of maintaining co-ordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable DNA topological tension. DNA supercoiling is resolved and, in some cases, even harnessed by the genome through the function of DNA topoisomerases, as has been shown in the concurrent transcriptional activation and suppression of genes upon transient deactivation of topoisomerase II (topoII). By analyzing a genome wide run-on experiment upon thermal inactivation of topoII inS.cerevisiae. we were able to define 116 gene clusters of consistent response (either positive or negative) to topological stress. A comprehensive analysis of these topologically co-regulated gene clusters revealed pronounced preferences regarding their functional, regulatory and structural attributes. Genes that negatively respond to topological stress, are positioned in gene-dense pericentromeric regions, are more conserved and associated to essential functions, while up-regulated gene clusters are preferentially located in the gene-sparse nuclear periphery, associated with secondary functions and under complex regulatory control. We propose that evolves with a core of essential genes occupying a compact genomic “old town”, whereas more recently acquired, condition-specific genes tend to be located in a more spacious “suburban” genomic periphery.
Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses
Authors: Jacox Edwin , Weller Mathias , Tannier Eric , Scornavacca Celine 
Published: July 2016

AbstractMotivationGene trees reconstructed from sequence alignments contain poorly supported branches when the phylogenetic signal in the sequences is weak. When a species tree is available, the signal of gains and losses of genes can be used to correctly resolve the unsupported parts of the gene history. Unfortunately, finding the best (i.e. most parsimonious) resolution has been shown to be NP-hard if transfers are considered as possible gene scale events, in addition to gene originations, duplications and losses.ResultsWe propose an exact, parameterized algorithm solving this problem in single-exponential time, where the parameter is the number of connected branches of the gene tree that show low support from the sequence alignment or, equivalently, the maximum number of children of any node of the gene tree once the low-support branches have been collapsed. We propose a way to choose among optimal solutions based on the available information. We show the usability of this principle on several simulated and biological data sets. The results show a comparable or better quality than several other tested methods having similar goals, but with a lower running time and a guarantee on the optimality of the solution.AvailabilityOur algorithm has been integrated into the ecceTERA phylogeny package, available athttp://mbb.univ-montp2.fr/MBB/download_sources/16_ecceTERAand which can be run online athttp://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera.Contactceline.scornavacca@umontpellier.fr
Maternal immune activation dysregulation of the fetal brain transcriptome and relevance to the pathophysiology of autism spectrum disorder
Authors: Lombardo Michael V. , Moon Hyang Mi , Su Jennifer , Palmer Theo D. , Courchesne Eric , Pramparo Tiziano 
Published: July 2016

AbstractMaternal immune activation (MIA) via infection during pregnancy is known to increase risk for autism spectrum disorder (ASD). However, it is unclear how MIA disrupts fetal brain gene expression in ways that may explain this increased risk. Here we examine how MIA dysregulates fetal brain gene expression near the end of the first trimester of human gestation in ways relevant to ASD-associated pathophysiology. MIA downregulates expression of ASD-associated genes, with the largest enrichments in genes known to harbor rare highly penetrant mutations. MIA also downregulates expression of many genes also known to be persistently downregulated in ASD cortex later in life and which are canonically known for roles in affecting prenatally-late developmental processes at the synapse. Transcriptional and translational programs that are downstream targets of highly ASD-penetrantFMR1andCHD8genes are also heavily affected by MIA. MIA strongly upregulates expression of a large number of genes involved in translation initiation, cell cycle, DNA damage, and proteolysis processes that affect multiple key neural developmental functions. Upregulation of translation initiation is common to and preserved in gene network structure with the ASD cortical transcriptome throughout life and has downstream impact on cell cycle processes. The cap-dependent translation initiation gene,EIF4E, is one of the most MIA-dysregulated of all ASD-associated genes and targeted network analyses demonstrate prominent MIA-induced transcriptional dysregulation ofmTORandEIF4E-dependent signaling. This dysregulation of translation initiation via alteration of theTsc2-mTor-Eif4e-axis was further validated across MIA rodent models. MIA may confer increased risk for ASD by dysregulating key aspects of fetal brain gene expression that are highly relevant to pathophysiology affecting ASD.
Identification of a novel putative interaction partner of the nucleoporin ALADIN
Authors: Jühlen Ramona , Landgraf Dana , Huebner Angela , Koehler Katrin 
Published: July 2016

AbstractIt has been shown that the nucleoporin ALADIN employs a significant role in the redox homeostasis of the cell but the function in steroidogenesis contributing to adrenal atrophy in triple A syndrome remains largely unknown. In an attempt to identify new interaction partners of ALADIN, co-immunoprecipitation followed by proteome analysis was conducted in different expression models using the human adrenocortical tumour cell line NCI-H295R. Our results suggest an interaction of ALADIN with the microsomal protein PGRMC2. PGRMC2 is shown to be activity regulator of CYP P450 enzymes and therefore, to be a possible target for adrenal dysregulation in triple A syndrome. We show that there is a sexual dimorphism regarding the expression ofPgrmc2in adrenals and gonads of WT andAaasKO mice. FemaleAaasKO mice are sterile due to delayed oocyte maturation and meiotic spindle assembly. A participation in meiotic spindle assembly confirms the recently investigated involvement of ALADIN in mitosis and emphasises an interaction with PGRMC2 which is a regulator of cell cycle. By identification of a novel interaction partner of ALADIN we provide novel aspects for future research of the function of ALADIN during cell cycle and for new insights into the pathogenesis of triple A syndrome.