bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diabetes mellitus is associated with increased prevalence of latent tuberculosis infection: Results from the National Health and Nutrition Examination Survey
Authors: Barron Marissa M. , Shaw Kate M. , Bullard Kai McKeever , Ali Mohammed K. , Magee Matthew J. 
Published: October 2017

ABSTRACTAimsWe aimed to determine the association between prediabetes and diabetes with latent TB using National Health and Nutrition Examination Survey data.MethodsWe performed a cross-sectional analysis of 2011-2012 National Health and Nutrition Examination Survey data. Participants ≥20 years were eligible. Diabetes was defined by glycated hemoglobin (HbA1c) as no diabetes (≤5.6% [38 mmol/mol]), prediabetes (5.7-6.4% [3946mmol/mol]), and diabetes (≥6.5% [48 mmol/mol]) combined with self-reported diabetes. Latent TB infection was defined by the QuantiFERON®-TB Gold In Tube (QFT-GIT) test. Adjusted odds ratios (aOR) of latent TB infection by diabetes status were calculated using logistic regression and accounted for the stratified probability sample.ResultsDiabetes and QFT-GIT measurements were available for 4,958 (89.2%) included participants. Prevalence of diabetes was 11.4% (95%CI 9.8-13.0%) and 22.1% (95%CI 20.523.8%) had prediabetes. Prevalence of latent TB infection was 5.9% (95%CI 4.9-7.0%). After adjusting for age, sex, smoking status, history of active TB, and foreign born status, the odds of latent TB infection were greater among adults with diabetes (aOR 1.90, 95%CI 1.15-3.14) compared to those without diabetes. The odds of latent TB in adults with prediabetes (aOR 1.15, 95%CI 0.90-1.47) was similar to those without diabetes.ConclusionsDiabetes is associated with latent TB infection among adults in the United States, even after adjusting for confounding factors. Given diabetes increases the risk of active TB, patients with co-prevalent diabetes and latent TB may be targeted for latent TB treatment.
The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach
Authors: Sergio Hleap Jose , Blouin Christian 
Published: October 2017

AbstractThe Glycoside Hydrolase Family 13 (GH13) is both evolutionary diverse and relevant to many industrial applications. Its members perform the hydrolysis of starch into smaller carbohydrates. Members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of GH13 protein structures given some phylogenetic and simulated dynamic information. We found that the TIM-barrel is not selectable since it is under purifying selection. We also show a method to rank important residues with higher inferred response to selection. These residues can be altered to effect change in properties. In this work, we define fitness as inferred thermodynamic stability. We show that under the developed framework, residues 112Y, 122K, 124D, 125W, and 126P are good candidates to increase the stability of the truncated protein 4E2O. Overall, this paper demonstrate the feasibility of a framework for the analysis of protein structures for any other fitness landscape.
Juicebox.js provides a cloud-based visualization system for Hi-C data
Authors: Robinson James , Turner Douglass , Durand Neva C. , Thorvaldsdottir Helga , Mesirov Jill P. , Aiden Erez Lieberman 
Published: October 2017

ABSTRACTContact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute.
Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot
Authors: Roca Jorjethe , Hori Naoto , Velmurugu Yogambigai , Narayanan Ranjani , Narayanan Prasanth , Thirumalai D. , Ansari Anjum 
Published: October 2017

ABSTRACTThe functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is important to elucidate the general principles governing their thermodynamics/folding mechanisms. Here, we combine experiments and simulations to examine the folding/unfolding pathways of the VPK pseudoknot, a variant of the Mouse Mammary Tumor Virus (MMTV) PK involved in ribosomal frameshifting. Fluorescent nucleotide analogs (2-aminopurine and pyrrolocytidine) placed at different stem/loop positions in the PK, and laser temperature-jump approaches serve as local probes allowing us to monitor the order of assembly of VPK with two helices with different intrinsic stabilities. The experiments and molecular simulations show that at 50 mM KCl the dominant folding pathway populates only the more stable partially folded hairpin. As the salt concentration is increased a parallel folding pathway emerges, involving the less stable hairpin structure as an alternate intermediate. Notably, the flux between the pathways is modulated by the ionic strength. The findings support the principle that the order of PK structure formation is determined by the relative stabilities of the hairpins, which can be altered by sequence variations or salt concentrations. Our study not only unambiguously demonstrates that PK folds by parallel pathways, but also establishes that quantitative description of RNA self-assembly requires a synergistic combination of experiments and simulations.SIGNIFICANCEThe assembly mechanism of RNA, vital to describing their functions, depends on both the sequence and the metal ion concentration. How the latter influences the folding trajectories remains an important unsolved problem. Here, we examine the folding pathways of an RNA pseudoknot (PK) with key functional roles in transcription and translation, using a combination of experiments and simulations. We demonstrate that the PK, consisting of two helices with differing stabilities, folds by parallel pathways. Surprisingly, the flux between them is modulated by monovalent salt concentration. Our work shows that the order of assembly of PKs is determined by the relative stability of the helices, implying that the folding landscape can be controlled by sequence and ion concentration.
Two spatially distinct Kinesin-14 Pkl1 and Klp2 generate collaborative inward forces against Kinesin-5 Cut7 inS. pombe
Authors: Yukawa Masashi , Yamada Yusuke , Yamauchi Tomoaki , Toda Takashi 
Published: October 2017

ABSTRACTKinesin motors play central roles in bipolar spindle assembly. In many eukaryotes, spindle pole separation is driven by Kinesin-5 that generates outward force. This outward force is balanced by antagonistic inward force elicited by Kinesin-14 and/or Dynein. In fission yeast, two Kinesin-14s, Pkl1 and Klp2, play an opposing role against Kinesin-5/Cut7. However, how these two Kinesin-14s coordinate individual activities remains elusive. Here we show that while deletion of eitherpkl1orklp2rescues temperature sensitivecut7mutants, onlypkl1deletion can bypass the lethality caused bycut7deletion. Pkl1 is tethered to the spindle pole body, while Klp2 is localized along the spindle microtubule. Forced targeting of Klp2 to the spindle pole body, however, compensates for Pkl1 functions, indicating that cellular localizations, rather than individual motor specificities, differentiate between the two Kinesin-14s. Interestingly, human Kinesin-14/HSET can replace either Pkl1 or Klp2. Moreover, overproducing HSET induces monopolar spindles, reminiscent of the phenotype of Cut7 inactivation. Taken together, this study has uncovered the biological mechanism of how two different Kinesin-14s exert their antagonistic roles against Kinesin-5 in a spatially distinct manner.SUMMARY STATEMENTProper force-balance generated by Kinesin-5 and Kinesin-14 is crucial for spindle bipolarity. Two fission yeast Kinesin-14s localize to different structures, thereby collaboratively producing inward forces against Kinesin-5-mediated outward force.Abbreviations usedGBPGFP-binding proteinMWP complexMsd1-Wdr8-Pkl1 complexSPBspindle pole bodytstemperature sensitiveγ-TuCthe γ-tubulin complex
Signposts in the fog: objects facilitate scene representations in left scene-selective cortex
Authors: Brandman Talia , Peelen Marius V. 
Published: October 2017

AbstractWe internally represent the structure of our surroundings even when there is little layout information available in the visual image, such as when walking through fog or darkness. One way in which we disambiguate such scenes is through object cues; for example, seeing a boat supports the inference that the foggy scene is a lake. Recent studies have investigated the neural mechanisms by which object and scene processing interact to support object perception. The current study examines the reverse interaction, by which objects facilitate the neural representation of scene layout. Photographs of indoor (closed) and outdoor (open) real-world scenes were blurred such that they were difficult to categorize on their own, but easily disambiguated by the inclusion of an object. fMRI decoding was used to measure scene representations in scene-selective parahippocampal place area (PPA) and occipital place area (OPA). Classifiers were trained to distinguish response patterns to fully visible indoor and outdoor scenes, presented in an independent experiment. Testing these classifiers on blurred scenes revealed a strong improvement in classification in left PPA and OPA when objects were present, despite the reduced low-level visual feature overlap with the training set in this condition. These findings were specific to left PPA/OPA, with no evidence for object-driven facilitation in right PPA/OPA, object-selective areas, and early visual cortex. These findings demonstrate separate roles for left and right scene-selective cortex in scene representation, whereby left PPA/OPA represents inferred scene layout, influenced by contextual object cues, and right PPA/OPA represents a scene’s visual features.
Temporal metacognition as the decoding of self-generated brain dynamics
Authors: Kononowicz Tadeusz W. , Roger Clémence , van Wassenhove Virginie 
Published: October 2017

SUMMARYMetacognition, the ability to know about one’s thought process, is self-referential. Here, we combined psychophysics and time-resolved neuroimaging to explore metacognitive inference on the accuracy of a self-generated behavior. Human participants generated a time interval and evaluated the signed magnitude of their temporal production. We show that both self-generation and self-evaluation relied on the power of beta oscillations (β; 15−40 Hz) with increases in early β power predictive of increases in duration. We characterized the dynamics of β power in a low dimensional space (β state-space trajectories) as a function of timing and found that the more distinct trajectories, the more accurate metacognitive inferences were. These results suggest that β states instantiates an internal variable determining the fate of the timing network’s trajectory, possibly as release from inhibition. Altogether, our study describes oscillatory mechanisms for timing, suggesting that temporal metacognition relies on inferential processes of self-generated dynamics.
Locus-Specific Enhancer Hubs And Architectural Loop Collisions Uncovered From Single Allele DNA Topologies
Authors: Allahyar Amin , Vermeulen Carlo , Bouwman Britta A.M. , Krijger Peter H.L. , Verstegen Marjon J.A.M. , Geeven Geert , Kranenburg Melissa van , Pieterse Mark , Straver Roy , Haarhuis Judith H.I. , Teunissen Hans , Renkens Ivo J. , Kloosterman Wigard P. , Rowland Benjamin D. , de Wit Elzo , de Ridder Jeroen , de Laat Wouter 
Published: October 2017

ABSTRACTChromatin folding is increasingly recognized as a regulator of genomic processes such as gene activity. Chromosome conformation capture (3C) methods have been developed to unravel genome topology through the analysis of pair-wise chromatin contacts and have identified many genes and regulatory sequences that, in populations of cells, are engaged in multiple DNA interactions. However, pair-wise methods cannot discern whether contacts occur simultaneously or in competition on the individual chromosome. We present a novel 3C method, Multi-Contact 4C (MC-4C), that applies Nanopore sequencing to study multi-way DNA conformations of tens of thousands individual alleles for distinction between cooperative, random and competing interactions. MC-4C can uncover previously missed structures in sub-populations of cells. It reveals unanticipated cooperative clustering between regulatory chromatin loops, anchored by enhancers and gene promoters, and CTCF and cohesin-bound architectural loops. For example, we show that the constituents of the active b-globin super-enhancer cooperatively form an enhancer hub that can host two genes at a time. We also find cooperative interactions between further dispersed regulatory sequences of the active proto-cadherin locus. When applied to CTCF-bound domain boundaries, we find evidence that chromatin loops can collide, a process that is negatively regulated by the cohesin release factor WAPL. Loop collision is further pronounced in WAPL knockout cells, suggestive of a “cohesin traffic jam”. In summary, single molecule multi-contact analysis methods can reveal how the myriad of regulatory sequences spatially coordinate their actions on individual chromosomes. Insight into these single allele higher-order topological features will facilitate interpreting the consequences of natural and induced genetic variation and help uncovering the mechanisms shaping our genome.
optSelect: using agent-based modeling and binary PSO techniques for ensemble feature selection and stability assessment
Authors: Uppal Karan , Lee Eva K. 
Published: October 2017

ABSTRACTMotivationRecent studies have shown that the ensemble feature selection approaches are essential for generating robust classifiers. Existing methods for aggregating feature lists from different methods require use of arbitrary thresholds for selecting the top ranked features and do not account for classification accuracy while selecting the optimal set. Here we present a two-stage ensemble feature selection framework for finding the optimal set of features without compromising on classification accuracy.Methods and ResultsWe present herein optSelect, a multi agent-based stochastic optimization approach for nested ensemble feature selection. Stage one involves function perturbation, where ranked list of features are generated using different methods and stage two involves data perturbation, where feature selection is performed within randomly selected subsets of the training data and the optimal set of features is selected within each set using the optSelect. The agents are assigned to different behavior states and move according to a binary PSO algorithm. A multi-objective fitness function is used to evaluate the classification accuracy of the agents. We evaluate the system performance using the random probe method and using five publicly available microarray datasets. The performance of optSelect is compared with single feature selection techniques and existing aggregation methods. The results show that the optSelect algorithm improves the classification accuracy compared to both individual and existing rank aggregation methods. The algorithm is incorporated into an R package, optSelect.Contactkuppal2@emory.edu
Electrostatic Tuning of a Potassium Channel in Electric Fish
Authors: Swapna Immani , Ghezzi Alfredo , Markham Michael R. , Halling D. Brent , Lu Ying , Gallant Jason R. , Zakon Harold H. 
Published: October 2017

AbstractMolecular and biophysical variation contributes to the evolution of adaptive phenotypes, particularly behavior, though it is often difficult to understandpreciselyhow. The adaptively significant electric organ discharge behavior of weakly electric fish is the direct result of biophysical membrane properties set by ion channels. Here we describe a voltage-gated potassium channel gene in African mormyrid electric fishes, that is under positive selection and highly expressed in the electric organ. The channel produced by this gene shortens electric organ action potentials by activating quickly and at hyperpolarized membrane potentials. Surprisingly, the source of these unique properties is a derived patch of negatively charged amino acids in an extracellular loop near the voltage sensor. Further, we demonstrate that this portion of the channel functions differently in vertebrates than the generally accepted model based on theshakerchannel, and suggest a role for this loop in the evolutionary tuning of voltage-dependent channels.
Understanding sequencing data as compositions: an outlook and review
Authors: Quinn Thomas P. , Erb Ionas , Richardson Mark F. , Crowley Tamsyn M. 
Published: October 2017

AbstractMotivationAlthough seldom acknowledged explicitly, count data generated by sequencing platforms exist as compositions for which the abundance of each component (e.g., gene or transcript) is only coherently interpretable relative to other components within that sample. This property arises from the assay technology itself, whereby the number of counts recorded for each sample is constrained by an arbitrary total sum (i.e., library size). Consequently, sequencing data, as compositional data, exist in a non-Euclidean space that renders invalid many conventional analyses, including distance measures, correlation coefficients, and multivariate statistical models.ResultsThe purpose of this review is to summarize the principles of compositional data analysis (CoDA), provide evidence for why sequencing data are compositional, discuss compositionally valid methods available for analyzing sequencing data, and highlight future directions with regard to this field of study.
Prevalence of somatisation as a determinant of burnout amongst staff working in drug and alcohol services
Authors: Mazoruk Sabina , Huxley Adam , Alexis-Garsee Camille , Schifano Fabrizio 
Published: October 2017

Purpose
The purpose of this paper is to explore the prevalence of somatisation as a determinant of burnout amongst drug and alcohol staff in the UK.

Design/methodology/approach
The study employed a cross-sectional design utilising a self-completion online questionnaire. Data were collected from substance misuse workers across England and Wales. In total, 165 responses were eligible for analysis, yielding a response rate of 5 per cent. Burnout and somatization were measured with Maslach’s Burnout Inventory and the Physical Symptoms Inventory.

Findings
The prevalence of somatic symptoms was relatively low in the sample studied. The reported levels of burnout were moderate. Personal accomplishment remained high in the sample. There was a strong association between burnout and incidence of stress-related somatic symptoms, with higher levels of burnout correlating with multiple symptoms.

Research limitations/implications
It was not possible to determine the extent of non-response bias, as at the time of the study there was no information available relating to the characteristics of drug and alcohol staff in the selected services. Therefore, as the response rate was very low (5 per cent) it was recognised that non-response bias might have affected the findings, in such way that non-respondents may have differed in their experiences of work stress, satisfaction, burnout and health outcomes.

Practical implications
Despite the limitations, the study provided practical information relating to burnout vulnerability and associated physical symptoms in this specific occupational group. These findings can support employers to address staff wellbeing with a view to prevent burnout and reduce existing levels of burnout and related somatic symptoms, and improve job performance, job satisfaction and staff retention through making appropriate adjustments, such as developing staff-wellbeing programmes. These adjustments could potentially contribute to improvement in substance misuse practice, through maintenance of healthy and satisfied workforce.

Originality/value
There are very few studies looking at burnout in drug and alcohol staff. This study is also novel in a way that it reveals correlations between a variety of specific stress-related physical symptoms and the three components of burnout.
A letter to teacher candidates at the dawn of the Trump Presidency
Authors: Smagorinsky Peter , Brasley Andie , Johnson Rebekah , Shurtz Lisa 
Published: October 2017

Purpose
This paper aims to describe a letter written to undergraduate students before their enrollment in a required foundations course, Service-Learning in English Education, taken before admission to the English education program at [the university]. The course, offered in the spring of 2017, came on the heels of Donald Trump’s election to the US Presidency, an event that followed from a campaign that raged against “politically correct” social developments that respect the dignity of people historically marginalized in US society.

Design/methodology/approach
The letter lays out the perils of teaching a diversity-oriented course in an era of disdain for diverse people and cultures. The letter explains how the course design attempts to give all interpretive authority to the students through their selection of course books and the book club design of promoting discussion outside professorial surveillance.

Findings
The paper includes the comments of three students regarding their response to the letter and course, and concludes that teaching a politicized course in a tempestuous time is risky yet possible.

Originality/value
This paper looks at one teacher educator’s approach to introducing diversity-related ideas in a Red State during an anti-diversity presidency.
Exploring #BlackLivesMatter and sociopolitical relationships through kinship writing
Authors: Muhammad Gholnecsar E. , Mason Chisholm Glenda , Starks Francheska D. 
Published: October 2017

PurposeThis study aims to explore the textual and sociopolitical relationships of kinship writing as 15 youth wrote politically charged poetry while participating in a four-week summer writing program grounded in a Black studies curriculum.Design/methodology/approachThe authors explore the following research questions: How do youth writers draw upon each other’s writing to compose sociopolitical kinship poems when writing about critical issues affecting Black lives? What topics and oppressions do youth choose to write about and how do they write about these topics?FindingsThe authors found that the youth wrote across multiple topics affecting Black lives in their kinship poems. These include the appropriation of black beauty, gun violence and police brutality, love and Black lives, the need for equality, negative depictions and misrepresentations of Black people, the neglect and omission of Black lives and suppression of freedom. The youth took up various critical issues in their poems, which addressed what they deemed as most urgent in the lives of Black people, and these selected topics were highly historicized. We also found that the youth used the content, styles and audience of the original poems to pen their own pieces.Research limitations/implicationsWriting with another peer afforded collaborative writing and spaces for youth to read and interrogate the world while building criticality through their writing.Originality/valueKinship writing is a genre in which one piece of writing has a relationship with another piece of writing. Kinship writing carries significance in the Black literary community as the history of Black education has been interlaced with ideals of social learning, community, family and kinship. This literary approach contributes to ways Black people used each other’s writings to offer healing, comfort and care in a turmoil filled world.