bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influenza immunization of pregnant women in resource-constrained countries: an update for funding and implementation decisions
Authors: Ortiz Justin R. , Neuzil Kathleen M. 
Published: August 2017

Purpose of review
In 2018, Gavi, the Vaccine Alliance, is expected to review the strategy of maternal influenza immunization for potential investment in low-income countries.

Recent findings
Clinical trial data confirm the efficacy of maternal influenza immunization to prevent influenza disease in both mothers and their infants during the first months of life. Trial and observational data indicate no significant adverse events in mothers or newborns. High-quality disease burden data, particularly for seasonal influenza in low-income and middle-income countries, are limited. Thus, the anticipated impact of maternal influenza immunization programs on severe illness is unclear. However, assessments of the public health value of investment in maternal influenza immunization should extend beyond calculations of disease prevention and include broader effects such as improving health systems for antenatal care delivery, preventing inappropriate antibacterial prescribing, building a platform for other vaccines to be used during pregnancy, and strengthening systems to regulate, procure, and distribute influenza vaccines in response to a future pandemic.

Summary
A global investment in a maternal influenza immunization strategy would prevent influenza disease in pregnant women and their infants. It would also provide additional public health value by strengthening antenatal care systems and improving country pandemic preparedness.
Relation of antifactor-Xa peak levels and venous thromboembolism after trauma
Authors: Karcutskie Charles A. , Dharmaraja Arjuna , Patel Jaimin , Eidelson Sarah A. , Martin Arch G. , Lineen Edward B. , Namias Nicholas , Schulman Carl I. , Proctor Kenneth G. 
Published: August 2017

BACKGROUND
No previous studies have established the optimal antifactor Xa (anti-Xa) level to guide thromboprophylaxis (TPX) dosing with enoxaparin in trauma patients. We hypothesize that achieving 0.2–0.4 IU/mL anti-Xa will decrease venous thromboembolism (VTE) rates after trauma.

METHODS
This was a retrospective review of 194 intensive care unit patients sustaining blunt or penetrating trauma from January 2015 to March 2017. All received initial enoxaparin (30 mg BID subcutaneous) and mechanical devices for TPX. Peak anti-Xa levels were drawn after each third dose. The enoxaparin dose was adjusted up to a maximum of 60 mg BID subcutaneous until a peak level of 0.2–0.4 IU/mL was achieved. Data are expressed as mean ± SD if parametric or median (IQR) if not.

RESULTS
The Greenfield Risk Assessment Profile score was 9 ± 4, Injury Severity Score 23 ± 14, and hospital length of stay 19 (11–38) days. The overall VTE rate was 7.2% (n = 14), with 10 deep venous thromboses (DVT) and 5 pulmonary emboli (PE). One patient had both a DVT and PE. The median time to VTE diagnosis was 14 (7–17) days. In those diagnosed with a VTE, 50.0% (n = 7) never reached 0.2–0.4 IU/mL anti-Xa and 42.8% (n = 6) were diagnosed with a VTE after achieving these levels. Prophylactic levels were achieved initially in 64 (33.0%) patients, and achieved later in 38 (19.6%) additional patients, giving an overall prophylactic rate of 52.6% (n = 102). There were no differences in VTE (6.9% vs. 7.6%, p = 0.841), DVT (3.9% vs. 6.5%, p = 0.413), or PE (3.9% vs. 1.1%, p = 0.213) rates between those who became prophylactic and those who did not.

CONCLUSIONS
There was no difference in VTE incidence between those achieving anti-Xa peak levels of 0.2–0.4 IU/mL and those who did not. Furthermore, these levels were never achieved in some trauma patients despite repeated dosing over a >10-day period.

LEVEL OF EVIDENCE
Therapeutic study, level IV.
Effects of the distant population density on spatial patterns of demographic dynamics
Authors: Tamura Kohei , Masuda Naoki 
Published: August 2017

Spatio-temporal patterns of population changes within and across countries have various implications. Different geographical, demographic and econo-societal factors seem to contribute to migratory decisions made by individual inhabitants. Focusing on internal (i.e. domestic) migration, we ask whether individuals may take into account the information on the population density in distant locations to make migratory decisions. We analyse population census data in Japan recorded with a high spatial resolution (i.e. cells of size 500×500
m
) for the entirety of the country, and simulate demographic dynamics induced by the gravity model and its variants. We show that, in the census data, the population growth rate in a cell is positively correlated with the population density in nearby cells up to a distance of 20 km as well as that of the focal cell. The ordinary gravity model does not capture this empirical observation. We then show that the empirical observation is better accounted for by extensions of the gravity model such that individuals are assumed to perceive the attractiveness, approximated by the population density, of the source or destination cell of migration as the spatial average over a circle of radius ≈1 km.
Rapid changes in Atlantic grey seal milk from birth to desertion
Authors: Lowe Amanda D. , Bawazeer Sami , Watson David G. , McGill Suzanne , Burchmore Richard J.S. , Pomeroy P.P (Paddy) , Kennedy Malcolm W. 
Published: August 2017

AbstractTrue seals have the shortest lactation periods of any group of placental mammal. Most are capital breeders that undergo short, intense lactations, during which they fast while transferring substantial proportions of their body reserves to their pups, which they then abruptly desert. Milk was collected from Atlantic grey seals (Halichoerus grypus) periodically from birth until near desertion. Milk protein profiles matured within 24 hours or less, indicating the most rapid transition from colostrum to mature phase lactation yet observed. There was an unexpected persistence of immunoglobulin G almost until weaning, potentially indicating prolonged trans-intestinal transfer of IgG. Among components of innate immune protection were found fucosyllactose and siallylactose that are thought to impede colonisation by pathogens and encourage an appropriate gut microbiome. These oligosaccharides decreased from early lactation to almost undetectable levels by weaning. Taurine levels were initially high, then fell, possibly indicative of taurine dependency in seals, and progressive depletion of maternal reserves. Metabolites that could signal changes in the mother’s metabolism of fats, such as nicotinamide and derivatives, rose from virtual absence, and acetylcarnitines fell. It is therefore possible that indicators of maternal metabolic strain exist that signal the imminence of desertion.
Inhibition of NHEJ repair by type II-A CRISPR-Cas systems
Authors: Bernheim Aude , Villamanan Alicia Calvo , Basier Clovis , Rocha Eduardo PC , Touchon Marie , Bikard David 
Published: August 2017

AbstractCRISPR-Cas systems introduce double strand breaks into DNA of invading genetic material and use DNA fragments to acquire novel spacers during adaptation. Double strand breaks are the substrate of several bacterial DNA repair pathways, paving the way for interactions between them and CRISPR-Cas systems. Here, we hypothesized that non-homologous end joining (NHEJ) interferes with type II CRISPR-Cas systems. We tested this idea by studying the patterns of co-occurrence of the two systems in bacterial genomes. We found that NHEJ and type II-A CRISPR-Cas systems only co-occur once among 5563 fully sequenced prokaryotic genomes. We investigated experimentally the possible molecular interactions causing this negative association using the NHEJ pathway fromBacillus subtilisand the type II-A CRISPR-Cas systems fromStreptococcus thermophilusandStreptococcus pyogenes. Our results suggest that the NHEJ system has no effect on type II-A CRISPR-Cas interference and adaptation. On the other hand, we provide evidence for the inhibition of NHEJ repair by the Csn2 protein from type II-A CRISPR-Cas system. Our findings give insights on the complex interactions between CRISPR- Cas systems and repair mechanisms in bacteria and contribute to explain the scattered distribution of CRISPR-Cas systems in bacterial genomes.
Oasis2.0: improved online analysis of small RNA-seq data
Authors: Rahman Raza-Ur , Gautam Abhivyakti , Bethune Jörn , Sattar Abdul , Fiosins Maksims , Magruder Daniel Sumner , Capece Vincenzo , Shomroni Orr , Bonn Stefan 
Published: August 2017

AbstractOasis 2 is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module. Oasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment.Availability and Implementation:Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available athttp://oasis.dzne.de
The intrinsically disordered C-terminal linker of FtsZ regulates protofilament dynamics and superstructurein vitro
Authors: Sundararajan Kousik , Goley Erin D. 
Published: August 2017

ABSTRACTThe bacterial tubulin FtsZ2polymerizes to form a discontinuous cytokinetic ring that drives bacterial cell division by directing local cell wall synthesis. FtsZ comprises a polymerizing GTPase domain, an intrinsically disordered C-terminal linker (CTL) and a C-terminal conserved α-helix (CTC). FtsZ protofilaments align circumferentially in the cell, with the CTC mediating attachment to membrane-associated division proteins. The dynamic turnover and treadmilling of clusters of FtsZ protofilaments guides cell wall synthesis and constriction. The nature and regulation of the interactions that result in the assembly of protofilaments into dynamic clusters is unknown. Here, we describe a role for the CTL ofCaulobacter crescentusFtsZ as an intrinsic regulator of lateral interactions between protofilamentsin vitro. FtsZ lacking its CTL (ΔCTL) shows dramatically increased propensity to form long multifilament bundles compared to wildtype (WT). ΔCTL has reduced GTP hydrolysis rate compared to WT. However, reducing protofilament turnover in WT is not sufficient to induce bundling. Surprisingly, binding of the membrane-anchoring protein FzlC disrupts ΔCTL bundling in a CTC-dependent manner. Moreover, the CTL affects the ability of FtsZ curving protein FzlA to promote formation of helical bundles. We conclude that the CTL of FtsZ influences polymer structure and dynamics both through intrinsic effects on lateral interactions and turnover and by influencing extrinsic regulation of FtsZ by binding partners. Our characterization of CTL function provides a biochemical handle for understanding the relationship between Z-ring structure and function in bacterial cytokinesis.
Kernel multitask regression for toxicogenetics
Authors: Bernard Elsa , Jiao Yunlong , Scornet Erwan , Stoven Veronique , Walter Thomas , Vert Jean-Philippe 
Published: August 2017

AbstractThe development of high-throughputin vitroassays to study quantitatively the toxicity of chemical compounds on genetically characterized human-derived cell lines paves the way topredictive toxicogenetics, where one would be able to predict the toxicity of any particular compound on any particular individual. In this paper we present a machine learning-based approach for that purpose, kernel multitask regression (KMR), which combines chemical characterizations of molecular compounds with genetic and transcriptomic characterizations of cell lines to predict the toxicity of a given compound on a given cell line. We demonstrate the relevance of the method on the recent DREAM8 Toxicogenetics challenge, where it ranked among the best state-of-the-art models, and discuss the importance of choosing good descriptors for cell lines and chemicals.
Learning causal biological networks with the principle of Mendelian randomization
Authors: Badsha Md. Bahadur , Qiuyan Fu Audrey 
Published: August 2017

AbstractAlthough large amounts of genomic data are available, it remains a challenge to reliably infer causal (i.e., regulatory) relationships among molecular phenotypes (such as gene expression), especially when many phenotypes are involved. We extend the interpretation of the Principle of Mendelian randomization (PMR) and present MRPC, a novel machine learning algorithm that incorporates the PMR in classical algorithms for learning causal graphs in computer science. MRPC learns a causal biological network efficiently and robustly from integrating genotype and molecular phenotype data, in which directed edges indicate causal directions. We demonstrate through simulation that MRPC outperforms existing general-purpose network inference methods and other PMR-based methods. We apply MRPC to distinguish direct and indirect targets among multiple genes associated with expression quantitative trait loci.
Generalization guides human exploration in vast decision spaces
Authors: Wu Charley M. , Schulz Eric , Speekenbrink Maarten , Nelson Jonathan D. , Meder Bjöorn 
Published: August 2017

AbstractFrom foraging for food to learning complex games, many aspects of human behaviour can be framed as a search problem with a vast space of possible actions. Under finite search horizons, optimal solutions are generally unobtainable. Yet how do humans navigate vast problem spaces, which require intelligent exploration of unobserved actions? Using a variety of bandit tasks with up to 121 arms, we study how humans search for rewards under limited search horizons, where the spatial correlation of rewards (in both generated and natural environments) provides traction for generalization. Across a variety of diifferent probabilistic and heuristic models, we find evidence that Gaussian Process function learning—combined with an optimistic Upper Confidence Bound sampling strategy—provides a robust account of how people use generalization to guide search. Our modelling results and parameter estimates are recoverable, and can be used to simulate human-like performance, providing insights about human behaviour in complex environments.
Development of subcortical volumes across adolescence in males and females: A multisample study of longitudinal changes
Authors: Herting Megan M. , Johnson Cory , Mills Kathryn L. , Vijayakumar Nandita , Dennison Meg , Liu Chang , Goddings Anne-Lise , Dahl Ronald E. , Sowell Elizabeth R. , Whittle Sarah , Allen Nicholas B. , Tamnes Christian K. 
Published: August 2017

AbstractThe developmental patterns of subcortical brain volumes in males and females observed in previous studies have been inconsistent. To help resolve these discrepancies, we examined developmental trajectories using three independent longitudinal samples of participants in the age-span of 8-22 years (total 216 participants and 467 scans). These datasets, including Pittsburgh (PIT; University of Pittsburgh, USA), NeuroCognitive Development (NCD; University of Oslo, Norway), and Orygen Adolescent Development Study (OADS; The University of Melbourne, Australia), span three countries and were analyzed together and in parallel using mixed-effects modeling with both generalized additive models and general linear models. For all regions and across all samples, males were found to have significantly larger volumes as compared to females, and significant sex differences were seen in age trajectories over time. However, direct comparison of sample trajectories and sex differences identified within samples were not consistent. The trajectories for the amygdala, putamen, and nucleus accumbens were most consistent between the three samples. Our results suggest that even after using similar preprocessing and analytic techniques, additional factors, such as image acquisition or sample composition may contribute to some of the discrepancies in sex specific patterns in subcortical brain changes across adolescence, and highlight region-specific variations in congruency of developmental trajectories.
OptoGap: an optogenetics-enabled assay for quantification of cell-cell coupling in multicellular cardiac tissue
Authors: Yu Jinzhu , Boyle Patrick M. , Klimas Aleksandra , Williams John C. , Trayanova Natalia , Entcheva Emilia 
Published: August 2017

AbstractIntercellular electrical coupling is an essential means of communication between cells. It is important to obtain quantitative knowledge of such coupling between cardiomyocytes and nonexcitable cells when, for example, pathological electrical coupling between myofibroblasts and cardiomyocytes yields increased arrhythmia risk or during the integration of donor (e.g. cardiac progenitor) cells with native cardiomyocytes in cell-therapy approaches. Currently, there is no direct method for assessing heterocellular coupling within multicellular tissue. Here we demonstrate experimentally and computationally a new contactless assay for electrical coupling, OptoGap, based on selective illumination of inexcitable cells that express optogenetic actuators and optical sensing of the response of coupled excitable cells, e.g. cardiomyocytes, that are light-insensitive. Cell-cell coupling is quantified by the energy required to elicit an action potential via junctional current from the light-stimulated cell(s). The proposed technique is experimentally validated against the standard indirect approach, GapFRAP, using light-sensitive cardiac fibroblasts and non-transformed cardiomyocytes in a two-dimensional setting. It’s potential applicability to the complex three-dimensional setting of the native heart is corroborated by computational modeling and proper calibration.Intercellular coupling is a fundamental form of communication between cells, essential for the synchronization of physiological processes in different organs. Pathologically altered coupling or the emergence ofde novocoupling between native and donor cells are problems of interest in many cardiac applications, e.g. during cell delivery and cell integration for cardiac repair therapy1,2. In particular, interactions between cardiomyocytes and fibroblasts are of interest, especially the pro-arrhythmic increase in coupling as the latter transition to myofibroblasts3-6.Electrical coupling in cardiac tissue is mediated primarily by low-resistance paths formed by gap-junctional proteins (connexins), that can link cardiomyocytes (CMs) to each other and to non-cardiomyocytes (nCMs), such as fibroblasts. Qualitative and quantitative methods, e.g. immunofluorescence, messenger RNA and Western blots, are often used to assay connexin expression levels as a surrogate measure of coupling, but they do not provide functional information. A method for direct quantification of cell-cell coupling within the multicellular tissue context is highly desirable.
Unexpected variation across mitochondrial gene trees and evidence for systematic error: How much gene tree variation is biological?
Authors: Richards Emilie J. , Brown Jeremy M. , Barley Anthony J. , Chong Rebecca A. , Thomson Robert C. 
Published: August 2017

ABSTRACTThe use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of these biological versus methodological factors in explaining gene tree variation is a major unresolved question in phylogenetics. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and that critical evaluation of the fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.
Detection of live mycobacteria with a solvatochromic trehalose probe for point-of-care tuberculosis diagnosis
Authors: Kamariza M. , Shieh P. , Rodriguez-Rivera F. P. , Ealand C. S. , Chu B. , Martinson N. , Kana B. D. , Bertozzi C. R. 
Published: August 2017

Abstract:Tuberculosis (TB) is the leading cause of death from an infectious bacterial disease. Poor diagnostic tools to detect active disease plague TB control programs and affect patient care. Accurate detection of liveMycobacterium tuberculosis(Mtb), the causative agent of TB, will improve TB diagnosis and patient treatment. We report that live mycobacteria can be specifically detected with a fluorogenic trehalose analog. We designed a 4-N,N-dimethylamino-1,8- naphthalimide-trehalose (DMN-Tre) conjugate that undergoes >700-fold fluorescence increase when transitioned from aqueous to hydrophobic environments. This enhancement occurs upon metabolic conversion of DMN-Tre to trehalose monomycolate and incorporation into the outer membrane. DMN-Tre labeling enabled the rapid, no-wash visualization of mycobacterial and corynebacterial species without nonspecific labeling of Gram-positive or –negative bacteria. DMN-Tre labeling was selective for live mycobacteria and was reduced by treatment with TB drugs. Lastly, DMN-Tre labeled Mtb in TB-positive sputum samples suggesting this operationally simple method may be deployable for TB diagnosis.
Using a skill-building tool to enhance employee engagement
Authors: Bandura Randall P. , Lyons Paul R. 
Published: August 2017

Purpose
This paper aims to provide some bounds to the concept of employee engagement, explain how it links to job performance and offer a practical training tool, skill-charting (SC), that can assist a manager and her/his employees attain higher levels of work engagement.

Design/methodology/approach
The discussion of SC and employee engagement is based on a literature review of recent research.

Findings
In the realm of opportunities for managers to encourage and enhance employee engagement, the learning and problem-solving tool, SC, presents a practical means to achieve positive results in several domains.

Originality/value
There are few instances in the literature where highly specific advice is offered to practitioners regarding how managers can quickly and directly stimulate, encourage and assist employees to reach higher levels of engagement. The approach suggested in this paper can be of much value to both manager and employees.