bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting CTCF-mediated chromatin loops using CTCF-MP
Authors: Zhang Ruochi , Wang Yuchuan , Yang Yang , Zhang Yang , Ma Jian 
Published: April 2018

Abstract

Motivation
The three dimensional organization of chromosomes within the cell nucleus is highly regulated. It is known that CCCTC-binding factor (CTCF) is an important architectural protein to mediate long-range chromatin loops. Recent studies have shown that the majority of CTCF binding motif pairs at chromatin loop anchor regions are in convergent orientation. However, it remains unknown whether the genomic context at the sequence level can determine if a convergent CTCF motif pair is able to form a chromatin loop.

Results
In this article, we directly ask whether and what sequence-based features (other than the motif itself) may be important to establish CTCF-mediated chromatin loops. We found that motif conservation measured by ‘branch-of-origin’ that accounts for motif turn-over in evolution is an important feature. We developed a new machine learning algorithm called CTCF-MP based on word2vec to demonstrate that sequence-based features alone have the capability to predict if a pair of convergent CTCF motifs would form a loop. Together with functional genomic signals from CTCF ChIP-seq and DNase-seq, CTCF-MP is able to make highly accurate predictions on whether a convergent CTCF motif pair would form a loop in a single cell type and also across different cell types. Our work represents an important step further to understand the sequence determinants that may guide the formation of complex chromatin architectures.

Availability and implementation
The source code of CTCF-MP can be accessed at: https://github.com/ma-compbio/CTCF-MP

Supplementary information
Supplementary data are available at Bioinformatics online.
Novo&Stitch: accurate reconciliation of genome assemblies via optical maps
Authors: Pan Weihua , Wanamaker Steve I , Ah-Fong Audrey M V , Judelson Howard S , Lonardi Stefano 
Published: April 2018

Abstract

Motivation
De novo genome assembly is a challenging computational problem due to the high repetitive content of eukaryotic genomes and the imperfections of sequencing technologies (i.e. sequencing errors, uneven sequencing coverage and chimeric reads). Several assembly tools are currently available, each of which has strengths and weaknesses in dealing with the trade-off between maximizing contiguity and minimizing assembly errors (e.g. mis-joins). To obtain the best possible assembly, it is common practice to generate multiple assemblies from several assemblers and/or parameter settings and try to identify the highest quality assembly. Unfortunately, often there is no assembly that both maximizes contiguity and minimizes assembly errors, so one has to compromise one for the other.

Results
The concept of assembly reconciliation has been proposed as a way to obtain a higher quality assembly by merging or reconciling all the available assemblies. While several reconciliation methods have been introduced in the literature, we have shown in one of our recent papers that none of them can consistently produce assemblies that are better than the assemblies provided in input. Here we introduce Novo&Stitch, a novel method that takes advantage of optical maps to accurately carry out assembly reconciliation (assuming that the assembled contigs are sufficiently long to be reliably aligned to the optical maps, e.g. 50 Kbp or longer). Experimental results demonstrate that Novo&Stitch can double the contiguity (N50) of the input assemblies without introducing mis-joins or reducing genome completeness.

Availability and implementation
Novo&Stitch can be obtained from https://github.com/ucrbioinfo/Novo_Stitch.
An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins
Authors: Braun Edward L 
Published: April 2018

Abstract

Motivation
The relative rates of amino acid interchanges over evolutionary time are likely to vary among proteins. Variation in those rates has the potential to reveal information about constraints on proteins. However, the most straightforward model that could be used to estimate relative rates of amino acid substitution is parameter-rich and it is therefore impractical to use for this purpose.

Results
A six-parameter model of amino acid substitution that incorporates information about the physicochemical properties of amino acids was developed. It showed that amino acid side chain volume, polarity and aromaticity have major impacts on protein evolution. It also revealed variation among proteins in the relative importance of those properties. The same general approach can be used to improve the fit of empirical models such as the commonly used PAM and LG models.

Availability and implementation
Perl code and test data are available from https://github.com/ebraun68/sixparam.

Supplementary information
Supplementary data are available at Bioinformatics online.
An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification
Authors: Zhao Yixiu , Zeng Xiangrui , Guo Qiang , Xu Min 
Published: April 2018

Abstract

Motivation
Cellular Electron CryoTomography (CECT) is an emerging 3D imaging technique that visualizes subcellular organization of single cells at sub-molecular resolution and in near-native state. CECT captures large numbers of macromolecular complexes of highly diverse structures and abundances. However, the structural complexity and imaging limits complicate the systematic de novo structural recovery and recognition of these macromolecular complexes. Efficient and accurate reference-free subtomogram averaging and classification represent the most critical tasks for such analysis. Existing subtomogram alignment based methods are prone to the missing wedge effects and low signal-to-noise ratio (SNR). Moreover, existing maximum-likelihood based methods rely on integration operations, which are in principle computationally infeasible for accurate calculation.

Results
Built on existing works, we propose an integrated method, Fast Alignment Maximum Likelihood method (FAML), which uses fast subtomogram alignment to sample sub-optimal rigid transformations. The transformations are then used to approximate integrals for maximum-likelihood update of subtomogram averages through expectation–maximization algorithm. Our tests on simulated and experimental subtomograms showed that, compared to our previously developed fast alignment method (FA), FAML is significantly more robust to noise and missing wedge effects with moderate increases of computation cost. Besides, FAML performs well with significantly fewer input subtomograms when the FA method fails. Therefore, FAML can serve as a key component for improved construction of initial structural models from macromolecules captured by CECT.

Availability and implementation
http://www.cs.cmu.edu/mxu1
PrimAlign: PageRank-inspired Markovian alignment for large biological networks
Authors: Kalecky Karel , Cho Young-Rae 
Published: April 2018

Abstract

Motivation
Cross-species analysis of large-scale protein–protein interaction (PPI) networks has played a significant role in understanding the principles deriving evolution of cellular organizations and functions. Recently, network alignment algorithms have been proposed to predict conserved interactions and functions of proteins. These approaches are based on the notion that orthologous proteins across species are sequentially similar and that topology of PPIs between orthologs is often conserved. However, high accuracy and scalability of network alignment are still a challenge.

Results
We propose a novel pairwise global network alignment algorithm, called PrimAlign, which is modeled as a Markov chain and iteratively transited until convergence. The proposed algorithm also incorporates the principles of PageRank. This approach is evaluated on tasks with human, yeast and fruit fly PPI networks. The experimental results demonstrate that PrimAlign outperforms several prevalent methods with statistically significant differences in multiple evaluation measures. PrimAlign, which is multi-platform, achieves superior performance in runtime with its linear asymptotic time complexity. Further evaluation is done with synthetic networks and results suggest that popular topological measures do not reflect real precision of alignments.

Availability and implementation
The source code is available at http://web.ecs.baylor.edu/faculty/cho/PrimAlign.

Supplementary information
Supplementary data are available at Bioinformatics online.
Antimicrobial Stewardship Training for Infectious Diseases Fellows: Program Directors Identify a Curriculum Need
Authors: Luther Vera P , Shnekendorf Rachel , Abbo Lilian M , Advani Sonali , Armstrong Wendy S , Barsoumian Alice E , Beeler Cole B , Bystritsky Rachel , Cherabuddi Kartikeya , Cohen Seth , Hamilton Keith W , Ince Dilek , Justo Julie Ann , Logan Ashleigh , Lynch John B , Nori Priya , Ohl Christopher A , Patel Payal K , Pottinger Paul S , Schwartz Brian S , Stack Conor , Zhou Yuan 
Published: April 2018

Abstract
A needs assessment survey of infectious diseases (ID) training program directors identified gaps in educational resources for training and evaluating ID fellows in antimicrobial stewardship. An Infectious Diseases Society of America–sponsored core curriculum was developed to address that need.
Daily Stress Reactivity Across the Life span: Longitudinal and Cross-Sectional Effects of Age
Authors: Blaxton Jessica , Bergeman C S , Wang Lijuan 
Published: April 2018

Abstract

Objective
Exploration of development requires the use of research designs and process-oriented methodologies that can capture daily fluctuations within individuals, systematic changes within individuals, and differences between individuals. We examine the stress–affect relationship in this way to assess how the relationship between daily stress and negative affect (NA) as well as the relationship between daily stress and positive affect (PA) differs between individuals and changes over time depending on age and stress differences.

Method
Participants (N = 966) completed daily “burst” assessments of stress, NA, and PA. Three-level multilevel models depicted how cross-sectional age, within-person age changes, and global stress differences impact the daily stress–affect relationship.

Results
Findings illustrate that cross-sectional age and the aging process uniquely buffer the stress–NA relationship whereas global stress exacerbates it. Furthermore, older adults as well as adults with low global stress experience a weaker relationship between daily stress and PA as they age, but midlife adults and adults with high global stress experience a stronger relationship.

Discussion
These results depict differences in aging trajectories for both midlife and older adults and thus inform intervention and preventative care strategies aimed toward promoting stress regulation.
Validity and Reliability of the Major Depression Inventory for Persons With Dual Sensory Loss
Authors: Hovaldt Hanna Birkbak , Nielsen Tine , Dammeyer Jesper 
Published: April 2018

Abstract

Background and Objectives
Research has shown that dual sensory loss is a risk factor for depression in older adults. However, validated measures of depression for people with dual sensory loss are lacking. The purpose of the present study was to investigate the construct validity and reliability of the Major Depression Inventory for use among elderly persons with acquired dual sensory loss.

Research Design and Methods
A cross-sectional questionnaire survey was conducted in a national sample of people ≥50 years of age with functional acquired dual sensory loss. Of the invited participants, 302 (66%) returned the questionnaire and 207 complete cases were included for analysis. Rasch models and graphical log-linear Rasch models were used for item analysis. Lack of differential item functioning was tested relative to severity of vision and hearing impairment, mode of questionnaire completion, age, sex, comorbidity, instrumental activities of daily living, social position, and cohabitation status.

Results
The 10-item Major Depression Inventory did not fit the Rasch model. An 8-item version, excluding the items “feeling sad” and “sleep problems,” fit a graphical log-linear Rasch model. No evidence of differential item functioning was discovered, thus the 8-item Major Depression Inventory was measurement invariant across severity of impairments and mode of completing the questionnaire. The overall reliability was 0.81 and ranged from acceptable to good for all subgroups of participants, except males with severe hearing impairment and low functional status. Consequently, the 8-item version of the Major Depression Inventory was considered construct valid and reliable within the frame of reference.

Discussion and Implications
An 8-item version of the Major Depression Inventory can be used to screen for depressive symptoms in elderly persons with acquired dual sensory loss.
The 2017 August 21 American total solar eclipse through the eyes of GPS
Authors: Kundu Bhaskar , Panda Dibyashakti , Gahalaut Vineet K , Catherine J K 
Published: April 2018

SUMMARY
We explored spatio-temporal variation in total electron contents (TEC) in the ionosphere caused by the recent 2017 August 21 total solar eclipse, which was observed over the United States of America. The path of the total solar eclipse passes through the continental parts of the United States of America, starting in the northwestern state of Oregon and ending in the southeastern state of South Carolina, approximately covering 4000 km length. Across this length, EarthScope Plate Boundary Observatory (PBO) has been operating a dense Global Navigation Satellite Systems (GNSS) networks. During the course of passage of the solar eclipse, the sudden decline in solar radiation by temporarily obscuration by the Moon caused a drop of ∼6–9 × 1016 electrons m2 in the ionosphere with time-delay at the cGPS sites. The significant drop in TEC at cGPS sites captured the average migration velocity of shadow along the eclipse path (0.74 km s−1), from which we estimated the Moon's orbital velocity (∼1 km s−1). Further, this event also caused some marginal increase in TEC during the eclipse in the Earth's ionosphere in the magnetically conjugate region at the tip of South America and Antarctica, consistent with the model predictions of SAMI3 by Naval Research Laboratory.
Impacts of temperature and food availability on the condition of larval Arctic cod (Boreogadus saida) and walleye pollock (Gadus chalcogrammus)
Authors: Koenker Brittany L , Copeman Louise A , Laurel Benjamin J 
Published: April 2018

AbstractThe Arctic marine environment is rapidly changing with rising sea surface temperatures, declining sea ice habitat and projected increases in boreal species invasions. The success of resident Arctic fish will depend on both their thermal tolerance and their ability to cope with changing trophic interactions. Larval fish energetic condition is closely associated with mortality rates and therefore provides an indicator of overall well-being or fitness. In this study, we experimentally determined larval morphometric and lipid-based condition in an Arctic gadid (Arctic cod, Boreogadus saida) and a boreal gadid (walleye pollock, Gadus chalcogrammus) in response to different temperatures and food rations. Our results suggest that larval condition is highly sensitive to both factors but varies in a species- and ontogenetic-dependent manner. Results indicated that condition metrics based on length–weight relationships were not as sensitive as those based on lipid storage. Further, condition metrics changed with ontogeny and were best used within a developmental stage rather than across developmental stages. As expected, larval condition in first-feeding Arctic cod was higher at colder temperatures (2–5°C) than in the boreal gadid (5–12°C). However, at more developed larval stages the peak condition for Arctic cod was at warmer temperatures (7°C), while walleye pollock had the same thermal optimum as during earlier stages. Arctic cod were more sensitive to food ration at first feeding than walleye pollock, however; at later larval stages both species had a negative condition response to low food ration, especially at elevated temperatures (5 vs. 7°C). The lower thermal tolerance of Arctic cod, coupled with a higher sensitivity to food availability indicates that Arctic cod are particularly vulnerable to on-going environmental change. Arctic cod is a lipid-rich keystone species and therefore a reduction in their energetic condition during summer has the potential to affect the health of higher trophic levels throughout the Alaskan Arctic.
An inexact regularized Newton framework with a worst-case iteration complexity of $ {\mathscr O}(\varepsilon^{-3/2}) $ for nonconvex optimization
Authors: Curtis Frank E , Robinson Daniel P , Samadi Mohammadreza 
Published: April 2018

Abstract
An algorithm for solving smooth nonconvex optimization problems is proposed that, in the worst-case, takes ${\mathscr O}(\varepsilon ^{-3/2})$ iterations to drive the norm of the gradient of the objective function below a prescribed positive real number $\varepsilon $ and can take ${\mathscr O}(\varepsilon ^{-3})$ iterations to drive the leftmost eigenvalue of the Hessian of the objective above $-\varepsilon $. The proposed algorithm is a general framework that covers a wide range of techniques including quadratically and cubically regularized Newton methods, such as the Adaptive Regularization using Cubics (arc) method and the recently proposed Trust-Region Algorithm with Contractions and Expansions (trace). The generality of our method is achieved through the introduction of generic conditions that each trial step is required to satisfy, which in particular allows for inexact regularized Newton steps to be used. These conditions center around a new subproblem that can be approximately solved to obtain trial steps that satisfy the conditions. A new instance of the framework, distinct from arc and trace, is described that may be viewed as a hybrid between quadratically and cubically regularized Newton methods. Numerical results demonstrate that our hybrid algorithm outperforms a cubically regularized Newton method.
Venous Thromboembolism After Intraventricular Hemorrhage: Results From the CLEAR III Trial
Authors:   CLEAR III Trial Investigators, Shah Jharna N , Murthy Santosh B , Dlugash Rachel , McBee Nichol , Awad Issam , Hanley Daniel F , Ziai Wendy C 
Published: April 2018

Abstract

BACKGROUND
Venous thromboembolism (VTE) after intracerebral hemorrhage is well studied, but data on patients with spontaneous intraventricular hemorrhage (IVH) are limited.

OBJECTIVE
To study the factors associated with VTE, association between VTE and clinical outcomes in IVH, and safety of VTE chemoprophylaxis in IVH treated with intraventricular catheters and thrombolysis.

METHODS
Retrospective cohort study of patients enrolled in the CLEAR III trial, a multicenter, randomized trial comparing external ventricular drainage, with administration of intraventricular alteplase vs placebo, for obstructive IVH. Predictor variable was incident VTE in the first 30 d. Outcome measures were factors associated with VTE, and death/severe disability (modified Rankin Score 4-6) at 6 mo.

RESULTS
Of the 500 patients with IVH, VTE occurred in 59 patients (11.8%) within the first 30 d. VTE chemoprophylaxis was initiated in 412 (82.4%) patients, but before VTE diagnosis in only 401 (80.2%) at median of 4 d (interquartile range, 1-8) from IVH onset, and was not associated with intracranial bleeding or catheter tract hemorrhage. In the multivariate logistic regression analysis, infection within 30 d (odds ratio, 1.80; confidence interval, 1.03-3.17) was significantly associated with higher odds of VTE occurrence. Starting VTE chemoprophylaxis after 72 h was additionally associated with VTE occurrence after the first week.

CONCLUSION
Infection and delay in timely initiation of VTE chemoprophylaxis were associated with VTE occurrence. VTE chemoprophylaxis in IVH appears safe and should not be delayed beyond standard care policies for ICH including when intraventricular catheter placement and thrombolytic therapy are performed.
Association of Smokeless Tobacco Use and Oral Cancer: A Systematic Global Review and Meta-Analysis
Authors: Asthana Smita , Labani Satyanarayana , Kailash Uma , Sinha Dhirendra N , Mehrotra Ravi 
Published: April 2018

Abstract

Introduction
Smokeless tobacco products have been linked to precancerous and cancers of oral cavity for long. Evidence was available on the association between smokeless tobacco (SLT) products and oral cancers at regional but not at global level. Present meta-analysis is aimed to evaluate the risk of oral cancer with the use of SLT products among “ever” versus “never” users.

Method
Studies published for the period (1960–2016) are retrieved using Pubmed, Indmed, EMBASE, and Google Scholar search engines for the subject “ever” versus “never” users of SLT products and estimated the risk association with oral cancer. Summary odds ratios (relative risk) are estimated and meta-analysis was performed using random-effects model.

Results
Thirty-seven studies from four of six WHO regions, Southeast Asia region (SEAR), the Eastern Mediterranean Region (EMR), Europe, and region of Americas (North and South) are included in the analysis. Significant risk with SLT products with oral cancer was found for SEAR (4.44, 95% CI = 3.51 to 5.61) and for EMR (1.28, 95% CI = 1.04 to 1.56). Significantly higher risk (p &lt; .001) was found for females (5.83, 95% CI = 2.93 to 11.58). Product wise analysis for different SLT products revealed various levels of risk viz. gutkha (8.67, 95% CI = 3.59 to 20.93), pan tobacco / betel liquid (7.18, 95% CI = 5.48 to 9.41), oral snuff (4.18, 50% CI = 2.37 to 7.38), Mainpuri tobacco (3.32, 95% CI = 1.32 to 8.36), and snus (0.86, 95% CI = 0.58 to 1.29).

Conclusion
A significant positive association was observed between SLT use and the risk of oral cancer, in SEAR, EMRs, and among women users.

Implications
The present meta-analysis demonstrates SLT product use and the risk of oral cancer at global level. Moreover, the present analysis provided data on the risk associated with individual SLT product. The results fulfil the gap in the data on independent effect of individual SLT product use on the outcome of oral cancer at global level, conclusively. Chewing SLT products was associated with higher risk of oral cancer than other types of SLT. This can serve as a useful tool for policy makers in forming strict policies in controlling SLT menace. Hence, we propose that in addition to smoking, efforts should be directed towards SLT product cessation as well in reducing oral cancer incidence.
Identifying and managing depression in patients with coronary artery disease
Authors: Pragle Aimee Salzer , Salahshor Susan 
Published: April 2018

ABSTRACTCoronary artery disease (CAD) is the leading cause of death among adults in the United States. Despite advances in cardiac care, patients who have CAD and a diagnosis of depression have higher rates of morbidity and mortality. This article examines the epidemiology, clinical presentation, screening tools, and treatment recommendations for these patients.