bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smooth-threshold multivariate genetic prediction incorporating gene–environment interactions
Authors: Ueki Masao , Tamiya Gen ,   for Alzheimer’s Disease Neuroimaging Initiative
Published: August 2021

AbstractWe propose a genetic prediction modeling approach for genome-wide association study (GWAS) data that can include not only marginal gene effects but also gene–environment (GxE) interaction effects—i.e., multiplicative effects of environmental factors with genes rather than merely additive effects of each. The proposed approach is a straightforward extension of our previous multiple regression-based method, STMGP (smooth-threshold multivariate genetic prediction), with the new feature being that genome-wide test statistics from a GxE interaction analysis are used to weight the corresponding variants. We develop a simple univariate regression approximation to the GxE interaction effect that allows a direct fit of the STMGP framework without modification. The sparse nature of our model automatically removes irrelevant predictors (including variants and GxE combinations), and the model is able to simultaneously incorporate multiple environmental variables. Simulation studies to evaluate the proposed method in comparison with other modeling approaches demonstrate its superior performance under the presence of GxE interaction effects. We illustrate the usefulness of our prediction model through application to real GWAS data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI).
Social Health in the National Social Life, Health, and Aging Project
Authors: Waite Linda J , Duvoisin Rebeccah , Kotwal Ashwin A 
Published: August 2021

Abstract

Objectives
In this article, we present the theoretical framework that guided the development of the National Social Life, Health, and Aging Project (NSHAP) including the measures of social health. We discuss the literature that links social measures to other outcomes, and we discuss in detail how researchers might construct common measures of social health, including those that reflect social relationships, sexuality, social networks, social resources, and social participation.

Methods
The NSHAP includes multiple detailed measures of social health, collected in the rounds of data collection carried out in 2005, 2010, and 2015, allowing for study of changes over time and as people age among a nationally representative sample of the community-dwelling population of older adults in the United States.

Results
We define indicators of social health, describe measures of each in the 2015 round of NSHAP, and show the distribution of the measures by gender and age. We present scales of dimensions of social health that have been developed elsewhere and describe their properties.

Discussion
We briefly discuss the distribution of these measures by age and gender in the 2015 round of NSHAP. Simple analyses of these categorized measures reveal differences by age and gender that deserve closer attention in future investigations using the NSHAP data.
Myeloid cell-mediated targeting of LIF to dystrophic muscle causes transient increases in muscle fiber lesions by disrupting the recruitment and dispersion of macrophages in muscle
Authors: Flores Ivan , Welc Steven S , Wehling-Henricks Michelle , Tidball James G 
Published: August 2021

Abstract
Leukemia inhibitory factor (LIF) can influence development by increasing cell proliferation and inhibiting differentiation. Because of its potency for expanding stem cell populations, delivery of exogenous LIF to diseased tissue could have therapeutic value. However, systemic elevations of LIF can have negative, off-target effects. We tested whether inflammatory cells expressing a LIF transgene under control of a leukocyte-specific, CD11b promoter provide a strategy to target LIF to sites of damage in the mdx mouse model of Duchenne muscular dystrophy, leading to increased numbers of muscle stem cells and improved muscle regeneration. However, transgene expression in inflammatory cells did not increase muscle growth or increase numbers of stem cells required for regeneration. Instead, transgene expression disrupted the normal dispersion of macrophages in dystrophic muscles, leading to transient increases in muscle damage in foci where macrophages were highly concentrated during early stages of pathology. The defect in inflammatory cell dispersion reflected impaired chemotaxis of macrophages to C-C motif chemokine ligand-2 and local increases of LIF production that produced large aggregations of cytolytic macrophages. Transgene expression also induced a shift in macrophage phenotype away from a CD206+, M2-biased phenotype that supports regeneration. However, at later stages of the disease when macrophage numbers declined, they dispersed in the muscle, leading to reductions in muscle fiber damage, compared to non-transgenic mdx mice. Together, the findings show that macrophage-mediated delivery of transgenic LIF exerts differential effects on macrophage dispersion and muscle damage depending on the stage of dystrophic pathology.
Distantly supervised biomedical relation extraction using piecewise attentive convolutional neural network and reinforcement learning
Authors: Zhu Tiantian , Qin Yang , Xiang Yang , Hu Baotian , Chen Qingcai , Peng Weihua 
Published: August 2021

AbstractObjectiveThere have been various methods to deal with the erroneous training data in distantly supervised relation extraction (RE), however, their performance is still far from satisfaction. We aimed to deal with the insufficient modeling problem on instance-label correlations for predicting biomedical relations using deep learning and reinforcement learning.Materials and MethodsIn this study, a new computational model called piecewise attentive convolutional neural network and reinforcement learning (PACNN+RL) was proposed to perform RE on distantly supervised data generated from Unified Medical Language System with MEDLINE abstracts and benchmark datasets. In PACNN+RL, PACNN was introduced to encode semantic information of biomedical text, and the RL method with memory backtracking mechanism was leveraged to alleviate the erroneous data issue. Extensive experiments were conducted on 4 biomedical RE tasks.ResultsThe proposed PACNN+RL model achieved competitive performance on 8 biomedical corpora, outperforming most baseline systems. Specifically, PACNN+RL outperformed all baseline methods with the F1-score of 0.5592 on the may-prevent dataset, 0.6666 on the may-treat dataset, and 0.3838 on the DDI corpus, 2011. For the protein-protein interaction RE task, we obtained new state-of-the-art performance on 4 out of 5 benchmark datasets.ConclusionsThe performance on many distantly supervised biomedical RE tasks was substantially improved, primarily owing to the denoising effect of the proposed model. It is anticipated that PACNN+RL will become a useful tool for large-scale RE and other downstream tasks to facilitate biomedical knowledge acquisition. We also made the demonstration program and source code publicly available at http://112.74.48.115:9000/.
Evaluation of performance of pelvic CT-MR deformable image registration using two software programs
Authors: Ishida Tomoya , Kadoya Noriyuki , Tanabe Shunpei , Ohashi Haruna , Nemoto Hikaru , Dobashi Suguru , Takeda Ken , Jingu Keiichi 
Published: August 2021

Abstract
We assessed the accuracy of deformable image registration (DIR) accuracy between CT and MR images using an open-source software (Elastix, from Utrecht Medical Center) and a commercial software (Velocity AI Ver. 3.2.0 from Varian Medical Systems, Palo Alto, CA, USA) software. Five male patients’ pelvic regions were studied using publicly available CT, T1-weighted (T1w) MR, and T2-weighted (T2w) MR images. In the cost function of the Elastix, we used six DIR parameter settings with different regularization weights (Elastix0, Elastix0.01, Elastix0.1, Elastix1, Elastix10, and Elastix100). We used MR Corrected Deformable algorithm for Velocity AI. The Dice similarity coefficient (DSC) and mean distance to agreement (MDA) for the prostate, bladder, rectum and left and right femoral heads were used to evaluate DIR accuracy. Except for the bladder, most algorithms produced good DSC and MDA results for all organs. In our study, the mean DSCs for the bladder ranged from 0.75 to 0.88 (CT-T1w) and from 0.72 to 0.76 (CT-T2w). Similarly, the mean MDA ranges were 2.4 to 4.9 mm (CT-T1w), 4.6 to 5.3 mm (CT-T2w). For the Elastix, CT-T1w was outperformed CT-T2w for both DSCs and MDAs at Elastix0, Elastix0.01, and Elastix0.1. In the case of Velocity AI, no significant differences in DSC and MDA of all organs were observed. This implied that the DIR accuracy of CT and MR images might differ depending on the sequence used.
WALLABY pre-pilot survey: two dark clouds in the vicinity of NGC 1395
Authors: Wong O I , Stevens A R H , For B-Q , Westmeier T , Dixon M , Oh S-H , Józsa G I G , Reynolds T N , Lee-Waddell K , Román J , Verdes-Montenegro L , Courtois H M , Pomarède D , Murugeshan C , Whiting M T , Bekki K , Bigiel F , Bosma A , Catinella B , Dénes H , Elagali A , Holwerda B W , Kamphuis P , Kilborn V A , Kleiner D , Koribalski B S , Lelli F , Madrid J P , McQuinn K B W , Popping A , Rhee J , Roychowdhury S , Scott T C , Sengupta C , Spekkens K , Staveley-Smith L , Wakker B P 
Published: August 2021

ABSTRACT
We present the Australian Square Kilometre Array Pathfinder (ASKAP) WALLABY pre-pilot observations of two ‘dark’ H i sources (with H i masses of a few times 108 $\rm {M}_\odot$ and no known stellar counterpart) that reside within 363 kpc of NGC 1395, the most massive early-type galaxy in the Eridanus group of galaxies. We investigate whether these ‘dark’ H i sources have resulted from past tidal interactions or whether they are an extreme class of low surface brightness galaxies. Our results suggest that both scenarios are possible, and not mutually exclusive. The two ‘dark’ H i sources are compact, reside in relative isolation, and are more than 159 kpc away from their nearest H i-rich galaxy neighbour. Regardless of origin, the H i sizes and masses of both ‘dark’ H i sources are consistent with the H i size–mass relationship that is found in nearby low-mass galaxies, supporting the possibility that these H i sources are an extreme class of low surface brightness galaxies. We identified three analogues of candidate primordial ‘dark’ H i galaxies within the TNG100 cosmological, hydrodynamic simulation. All three model analogues are dark matter dominated, have assembled most of their mass 12–13 Gyr ago, and have not experienced much evolution until cluster infall 1–2 Gyr ago. Our WALLABY pre-pilot science results suggest that the upcoming large-area H i surveys will have a significant impact on our understanding of low surface brightness galaxies and the physical processes that shape them.
Blue straggler stars in open clusters using Gaia: dependence on cluster parameters and possible formation pathways
Authors: Jadhav Vikrant V , Subramaniam Annapurni 
Published: August 2021

ABSTRACT
Blue straggler stars (BSSs) are the most massive stars in a cluster formed via binary or higher order stellar interactions. Though the exact nature of such formation scenarios is difficult to pin down, we provide observational constraints on the different possible mechanism. In this quest, we first produce a catalogue of BSSs using Gaia DR2 data. Among the 670 clusters older than 300 Myr, we identified 868 BSSs in 228 clusters and 500 BSS candidates in 208 clusters. In general, all clusters older than 1 Gyr and massive than 1000 M⊙ have BSSs. The average number of BSSs increases with cluster age and mass, and there is a power-law relation between the cluster mass and the maximum number of BSSs in the cluster. We introduce the term fractional mass excess ($\mathcal {M}_{e}$) for BSSs. We find that at least 54 per cent of BSSs have $\mathcal {M}_{e}$ &lt; 0.5 (likely to have gained mass through a binary mass transfer (MT)), 30 per cent in the 1.0 &lt; $\mathcal {M}_{e}$ &lt;0.5 range (likely to have gained mass through a merger), and up to 16 per cent with $\mathcal {M}_{e}$ &gt; 1.0 (likely from multiple mergers/MT). We also find that the percentage of low $\mathcal {M}_{e}$ BSSs increases with age, beyond 1–2 Gyr, suggesting an increase in formation through MT in older clusters. The BSSs are radially segregated, and the extent of segregation depends on the dynamical relaxation of the cluster. The statistics and trends presented here are expected to constrain the BSS formation models in open clusters.
STEP survey – II. Structural analysis of 170 star clusters in the SMC
Authors: Gatto M , Ripepi V , Bellazzini M , Tosi M , Cignoni M , Tortora C , Leccia S , Clementini G , Grebel E K , Longo G , Marconi M , Musella I 
Published: August 2021

ABSTRACT
We derived surface brightness profiles in the g band for 170 Small Magellanic Cloud (SMC) star clusters (SCs) mainly located in the central region of the galaxy. We provide a set of homogeneous structural parameters obtained by fitting Elson–Fall–Freeman and King models. Through a careful analysis of their colour–magnitude diagrams we also supply the ages for a subsample of 134 SCs. For the first time, such a large sample of SCs in the SMC is homogeneously characterized in terms of their sizes, luminosities, and masses, widening the probed region of the parameter space, down to hundreds of solar masses. We used these data to explore the evolution of the SC’s structural parameters with time. In particular, we confirm the existence of a physical mechanism that induces an increase of the core radius after 0.3–1.0 Gyr. We suggest that cluster mass could be the main parameter driving the inner expansion, as none of the SCs having log (M/M⊙) ≤ 3.5 dex analysed in this work undergoes to such an expansion. We also detected a mass–size relationship almost over the entire range of SCs masses investigated here. Finally, our data suggest that globally the SMC SC system is dynamically evolved.
A phage-encoded nucleoid associated protein compacts both host and phage DNA and derepresses H-NS silencing
Authors: Son Bokyung , Patterson-West Jennifer , Arroyo-Mendoza Melissa , Ramachandran Revathy , Iben James R , Zhu Jingen , Rao Venigalla , Dimitriadis Emilios K , Hinton Deborah M 
Published: August 2021

AbstractNucleoid Associated Proteins (NAPs) organize the bacterial chromosome within the nucleoid. The interaction of the NAP H-NS with DNA also represses specific host and xenogeneic genes. Previously, we showed that the bacteriophage T4 early protein MotB binds to DNA, co-purifies with H-NS/DNA, and improves phage fitness. Here we demonstrate using atomic force microscopy that MotB compacts the DNA with multiple MotB proteins at the center of the complex. These complexes differ from those observed with H-NS and other NAPs, but resemble those formed by the NAP-like proteins CbpA/Dps and yeast condensin. Fluorescent microscopy indicates that expression of motB in vivo, at levels like that during T4 infection, yields a significantly compacted nucleoid containing MotB and H-NS. motB overexpression dysregulates hundreds of host genes; ∼70% are within the hns regulon. In infected cells overexpressing motB, 33 T4 late genes are expressed early, and the T4 early gene repEB, involved in replication initiation, is up ∼5-fold. We postulate that MotB represents a phage-encoded NAP that aids infection in a previously unrecognized way. We speculate that MotB-induced compaction may generate more room for T4 replication/assembly and/or leads to beneficial global changes in host gene expression, including derepression of much of the hns regulon.
Entanglements of structure elements revealed in RNA 3D models
Authors: Popenda Mariusz , Zok Tomasz , Sarzynska Joanna , Korpeta Agnieszka , Adamiak Ryszard W , Antczak Maciej , Szachniuk Marta 
Published: August 2021

AbstractComputational methods to predict RNA 3D structure have more and more practical applications in molecular biology and medicine. Therefore, it is crucial to intensify efforts to improve the accuracy and quality of predicted three-dimensional structures. A significant role in this is played by the RNA-Puzzles initiative that collects, evaluates, and shares RNAs built computationally within currently nearly 30 challenges. RNA-Puzzles datasets, subjected to multi-criteria analysis, allow revealing the strengths and weaknesses of computer prediction methods. Here, we study the issue of entangled RNA fragments in the predicted RNA 3D structure models. By entanglement, we mean an arrangement of two structural elements such that one of them passes through the other. We propose the classification of entanglements driven by their topology and components. It distinguishes two general classes, interlaces and lassos, and subclasses characterized by element types—loops, dinucleotide steps, open single-stranded fragments—and puncture multiplicity. Our computational pipeline for entanglement detection, applied for 1,017 non-redundant models from RNA-Puzzles, has shown the frequency of different entanglements and allowed identifying 138 structures with intersected assemblies.
One-loop $W$ boson contributions to the decay $H\rightarrow Z\gamma$ in the general $R_\xi$ gauge
Authors: Phan Khiem Hong , Hue Le Tho , Tran Dzung Tri 
Published: August 2021

Abstract
One-loop $W$ boson contributions to the decay $H\rightarrow Z\gamma$ in the general $R_\xi$ gauge are presented. The analytical results are expressed in terms of well-known Passarino–Veltman functions such that their numerical evaluations can be generated using $\texttt{LoopTools}$. In the limit $d\rightarrow 4$, we have shown that these analytical results are independent of the unphysical parameter $\xi$ and consistent with previous results. The gauge parameter independence is also checked numerically for consistence. Our results are also well stable with different values of $\xi =0,\ 1,\ 100$ and $\xi \rightarrow \infty$.
Prioritization of persons with special needs in Covid-19 vaccinations in the Philippines
Authors: Maboloc Christopher Ryan 
Published: August 2021

Abstract
The World Health Organization (WHO) has stated that vaccinations against Covid-19 are safer than not getting vaccinated. Covid-19 is a severe respiratory disease caused by the coronavirus. In the Philippines, the Department of Health (DOH) has implemented a prioritization policy framework for its Covid-19 vaccination program. However, upon consideration of the sectors listed in the guidelines, persons with special needs like those with autism spectrum disorder (ASD) appear to be omitted or at the very least not specified in the Vaccination Prioritization Policy. This is a policy gap that needs to be corrected.
Post-lockdown infection rates of COVID-19 following the reopening of public businesses
Authors: Bruckhaus Alexander , Martinez Aubrey , Garner Rachael , La Rocca Marianna , Duncan Dominique 
Published: August 2021

AbstractBackgroundThe Coronavirus Disease 2019 (COVID-19) pandemic warranted a myriad of government-ordered business closures across the USA in efforts to mitigate the spread of the virus. This study aims to discover the implications of government-enforced health policies of reopening public businesses amidst the pandemic and its effect on county-level infection rates.MethodsEighty-three US counties (n = 83) that reported at least 20 000 cases as of 4 November 2020 were selected for this study. The dates when businesses (restaurants, bars, retail, gyms, salons/barbers and public schools) partially and fully reopened, as well as infection rates on the 1st and 14th days following each businesses’ reopening, were recorded. Regression analysis was conducted to deduce potential associations between the 14-day change in infection rate and mask usage frequency, median household income, population density and social distancing.ResultsOn average, infection rates rose significantly as businesses reopened. The average 14-day change in infection rate was higher for fully reopened businesses (infection rate = +0.100) compared to partially reopened businesses (infection rate = +0.0454). The P-value of the two distributions was 0.001692, indicating statistical significance (P &lt; 0.01).ConclusionThis research provides insight into the transmission of COVID-19 and promotes evidence-driven policymaking for disease prevention and community health.
High-Quality Complete Genome Resource of Pathogenic Bacterium Pectobacterium atrosepticum Strain Green1 Isolated from Potato (Solanum tuberosum L.) in Greenland
Authors: Czajkowski Robert , Rabalski Lukasz , Kosinski Maciej , de Neergaard Eigil , Harding Susanne 
Published: August 2021

Pectobacterium atrosepticum is a narrow-host-range, pectinolytic, plant-pathogenic bacterium causing blackleg of potato (Solanum tuberosum L.) worldwide. Till present, several P. atrosepticum genomes have been sequenced and characterized in detail; however, all of these genomes have come from P. atrosepticum isolates from plants grown in temperate zones, not from hosts cultivated under different climatic conditions. Herewith, we present the first complete, high-quality genome of the P. atrosepticum strain Green1 isolated from potato plants grown under a subarctic climate in Greenland. The genome of P. atrosepticum strain Green1 consists of one chromosome of 4,959,719 bp, with a GC content of 51% and no plasmids. The genome contains 4,531 annotated features, including 4,179 protein-coding genes, 22 ribosomal RNA genes, 70 transfer RNA genes, 8 noncoding RNA genes, 2 CRISPRs, and 126 pseudogenes. We believe that the information in this first high-quality, complete, closed genome of P. atrosepticum strains isolated from host plants grown in a subarctic agricultural region will provide resources for comparative genomic studies and for analyses targeting climatic adaptation and ecological fitness mechanisms present in P. atrosepticum. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .