bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age and the Construction of Gendered and Raced Citizenship in the United States
Authors: Field Corinne T. , Syrett Nicholas L. 
Published: February 2020

Abstract
Focusing on the United States, Field and Syrett argue that the supposed universality of chronological age masks the processes through which legislators and government officials relied upon age to reinforce inequalities rooted in coverture and chattel slavery. Two case studies reveal how bureaucratic and legislative age requirements functioned in tandem to deny equal citizenship to women and formerly enslaved people. During the Civil War, Congress passed legislation to grant age-based Civil War pensions for minor children that appeared neutral in law but came to be administered in ways that denied equal benefits to the families of black Civil War soldiers on the grounds that they lacked adequate proof of age. State governments, meanwhile, continued to pass laws that differentiated between men and women in the realm of legal majority, using chronological age as a means to shore up gender inequality even as women gained new rights and opportunities. Recent conflicts over voter identification laws and age determination for child migrants reveal that chronological age remains a contested category through which government officials can deny equal treatment under the law by defining the criteria for what counts as adequate proof of age. Cracks in the modern regime of government-issued birth certificates reveal that age remains what it has always been: not a neutral fact, but a vector of power through which government officials and ordinary people construct and contest the boundaries of citizenship.
After the Catastrophe: A Reading of Manna’s Nakba and Survival
Authors: Saʾdi Ahmad H. 
Published: February 2020

Abstract
Adel Manna’s Nakba and Survival: The Story of the Palestinians Who Remained in Haifa and the Galilee, 1948–1956 appeared in Arabic and Hebrew 2016–2017. Manna’s book gives voice to the experience of the first generation of Palestinians living within the State of Israel. Here, four scholars of Palestinian and Israeli history review Nakba and Survival and weigh its importance for reckoning with the entangled history of the creation of Israel and the related dispossession of Palestinians during and after 1948.
Contextualizing Past Tenses in L2: Combined Effects and Interactions in the Present Perfect versus Simple Past Alternation
Authors: Deshors Sandra C 
Published: February 2020

AbstractThis multifactorial corpus-based exploration of past tenses focuses specifically on the present perfect (PP) versus simple past (SP) alternation in intermediate-to-advanced learner English produced by French and German native speakers. While existing work on past tenses in L2 has traditionally focused on the role of lexical aspect in the acquisition and uses of these past tenses, the current study focuses on the linguistic context of use of these tenses and identifies the linguistic features whose co-occurrence and combined effects cause native speakers and learners to differ in their uses of past tenses. Methodologically, the study uses a random forests approach including a surrogate logistic regression model and interactions between contextual linguistic features. Overall, the multifactorial results suggest that not all linguistic contexts facilitate native-like uses of the PP and SP equally as some contexts more than others are susceptible to cross-linguistic interference.
Sexual size dimorphism and sexual selection in artiodactyls
Authors: Cassini Marcelo H 
Published: February 2020

AbstractSexual size dimorphism is biased toward males in most mammalian species. The most common explanation is precopulatory intramale sexual selection. Large males win fights and mate more frequently. In artiodactyls, previous tests of this hypothesis consisted of interspecific correlations of sexual dimorphism with group size as a surrogate for the intensity of sexual selection (Is). However, group size is not a proper measure of sexual selection for several reasons as is largely recognized in other mammalian taxa. I conducted an interspecific test on the role of sexual selection in the evolution of sexual dimorphism using the variance in genetic paternity as a proxy for the Is. I reviewed the literature and found 17 studies that allowed estimating Is= V/(W2), where V and W are the variance and mean number of offspring per male, respectively. A phylogenetic generalized least squares analysis indicated that dimorphism (Wm/Wf) showed a significant positive regression with the intensity of sexual selection but not group size (multiple r2= 0.40; F3,17= 12.78, P = 0.002). This result suggests that sexual selection may have played a role in the evolution of sexual size dimorphism in Artiodactyla. An alternative hypothesis based on natural selection is discussed.
Ensemble learning for classifying single-cell data and projection across reference atlases
Authors: Wang Lin , Catalan Francisca , Shamardani Karin , Babikir Husam , Diaz Aaron 
Published: February 2020

Abstract

Summary
Single-cell data are being generated at an accelerating pace. How best to project data across single-cell atlases is an open problem. We developed a boosted learner that overcomes the greatest challenge with status quo classifiers: low sensitivity, especially when dealing with rare cell types. By comparing novel and published data from distinct scRNA-seq modalities that were acquired from the same tissues, we show that this approach preserves cell-type labels when mapping across diverse platforms.

Availability and implementation
https://github.com/diazlab/ELSA

Contact
aaron.diaz@ucsf.edu

Supplementary information
Supplementary data are available at Bioinformatics online.
DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species
Authors: Tang Qiang , Kang Juanjuan , Yuan Jiaqing , Tang Hua , Li Xianhai , Lin Hao , Huang Jian , Chen Wei 
Published: February 2020

Abstract

Motivation
DNA N4-methylcytosine (4mC) is a crucial epigenetic modification. However, the knowledge about its biological functions is limited. Effective and accurate identification of 4mC sites will be helpful to reveal its biological functions and mechanisms. Since experimental methods are cost and ineffective, a number of machine learning-based approaches have been proposed to detect 4mC sites. Although these methods yielded acceptable accuracy, there is still room for the improvement of the prediction performance and the stability of existing methods in practical applications.

Results
In this work, we first systematically assessed the existing methods based on an independent dataset. And then, we proposed DNA4mC-LIP, a linear integration method by combining existing predictors to identify 4mC sites in multiple species. The results obtained from independent dataset demonstrated that DNA4mC-LIP outperformed existing methods for identifying 4mC sites. To facilitate the scientific community, a web server for DNA4mC-LIP was developed. We anticipated that DNA4mC-LIP could serve as a powerful computational technique for identifying 4mC sites and facilitate the interpretation of 4mC mechanism.

Availability and implementation
http://i.uestc.edu.cn/DNA4mC-LIP/.

Contact
hlin@uestc.edu.cn or hj@uestc.edu.cn or chenweiimu@gmail.com

Supplementary information
Supplementary data are available at Bioinformatics online.
Dung mimicry inTyphonium(Araceae): explaining floral trait and pollinator divergence in a widespread species complex and a rare sister species
Authors: Sayers Thomas D J , Steinbauer Martin J , Farnier Kevin , Miller Rebecca E 
Published: February 2020

AbstractThe process of pollinator-driven evolution is best studied at the level of populations and among closely related plant species. Araceae provide a plant model for investigating plant–pollinator interactions, but few studies have investigated intraspecific variation in their pollination systems. Typhonium brownii (Araceae) is distributed widely across 2000 km from tropical to temperate latitudes in Australia, yet the existence of intraspecific variation and ecotypes has not been investigated. Typhonium brownii from five regions, potentially representing distinct taxa, and populations of the sister species, T. eliosurum, were studied to explore pollinator and floral trait divergence. We characterize significant intraspecific floral trait variation in T. brownii, indicating the existence of a species complex, despite the taxa trapping similar Coleoptera (Staphylinidae, Scarabaeidae). Although all T. brownii showed similar temperature increases in the appendix, there were significant shifts in the timing and pattern of thermogenic and anthesis rhythms between regions (taxa), and all T. brownii taxa had distinct scent compositions, with T. sp. aff. brownii being the most dissimilar to other taxa. In contrast, T. eliosurum inflorescences almost exclusively trapped Diptera (Sphaeroceridae, Psychodidae), had modest temperature increases confined to the staminate zone and had a distinct scent profile which differed from all T. brownii taxa; this scent was confirmed in field bioassays to be important for pollinator attraction. Prevalent volatile organic compounds (VOCs) emitted by T. eliosurum and T. brownii taxa included the common dung constituents skatole, indole and p-cresol. Typhonium eliosurum and T. brownii taxa further differed significantly in morphology and trapping mechanisms, particularly the fly-pollinated T. eliosurum. It is possible that a subset of ubiquitous VOCs identified in T. eliosurum and T. brownii taxa attract local communities of dung-seeking flies and beetles, and that floral morphological features are more important for trapping different insect orders in these dung mimics.
Medial temporal lobe connectivity and its associations with cognition in early Alzheimer’s disease
Authors: Berron David , van Westen Danielle , Ossenkoppele Rik , Strandberg Olof , Hansson Oskar 
Published: February 2020

Abstract
Human episodic memory critically depends on subregions of the medial temporal lobe, which are part of functional brain systems such as the anterior-temporal and the posterior-medial system. Here we analysed how Alzheimer’s pathology affects functional connectivity within these systems. Data from 256 amyloid-β-negative cognitively unimpaired, 103 amyloid-β-positive cognitively unimpaired, and 83 amyloid-β-positive individuals with mild cognitive impairment were analysed. Amyloid-β and tau pathology were measured using the CSF amyloid-β42/40 ratio and phosphorylated tau, respectively. We found that amyloid-β-positive cognitively unimpaired individuals were mainly characterized by decreased functional connectivity between the medial temporal lobe and regions in the anterior-temporal system, most prominently between left perirhinal/entorhinal cortices and medial prefrontal cortex. Furthermore, correlation analysis in this group revealed decreasing functional connectivity between bilateral perirhinal/entorhinal cortices, anterior hippocampus and posterior-medial regions with increasing levels of phosphorylated tau. The amyloid-β-positive individuals with mild cognitive impairment mostly exhibited reduced connectivity between the medial temporal lobe and posterior-medial regions, predominantly between the anterior hippocampus and posterior cingulate cortex. In addition, they showed hyperconnectivity within the medial temporal lobe and its immediate proximity. Lower medial temporal-cortical functional connectivity networks resulting from the group comparisons of cognitively unimpaired individuals were associated with reduced memory performance and more rapid longitudinal memory decline as shown by linear mixed-effects regression analysis. Finally, we found that reduced medial temporal-cortical connectivity in mildly cognitively impaired individuals was related to reduced entorhinal thickness and white matter integrity of the parahippocampal cingulum and the fornix. No such relationships were found in cognitively unimpaired individuals. In conclusion, our findings show that the earliest changes in preclinical Alzheimer’s disease might involve decreased connectivity within the anterior-temporal system, and early changes in connectivity might be related to memory impairment, but not to structural changes. With disease progression and increased tau pathology, medial temporal functional connectivity with posterior-medial regions seems to be increasingly impaired. In individuals with mild cognitive impairment, reduced functional connectivity is associated with structural brain changes as well as the emergence of locally increased connectivity patterns. Thus, functional connectivity between the medial temporal lobe and the anterior-temporal and posterior-medial system could serve as stage-specific functional markers in early Alzheimer’s disease.
Parabacteroides distasonis attenuates tumorigenesis, modulates inflammatory markers and promotes intestinal barrier integrity in azoxymethane-treated A/J mice
Authors: Koh Gar Yee , Kane Anne V , Wu Xian , Crott Jimmy W 
Published: February 2020

Abstract
Imbalance of the gut microbial community promotes inflammation and colorectal cancer (CRC). Previously, we demonstrated that freeze-dried Parabacteroides distasonis (Pd) suppressed obesity-driven colorectal tumorigenesis in mice. Here, we investigated if Pd could suppress the development of colon tumors in mice independent of obesity. Six-week-old male A/J mice were assigned to receive: (i) chow diet (CTR); (ii) chow with 0.04% wt/wt freeze-dried Pd (Pd-Early) or (iii) chow diet before switching to 0.04% Pd diet (Pd-Late). Mice remained on diet for 25 weeks with the switch for Pd-Late mice occurring after 19 weeks. All mice received 6 weekly injections of the colon carcinogen azoxymethane (AOM; 10 mg/kg I.P.) starting after 1 week on diet. Colon tumors were observed in 77, 55 and 40% in CTR, Pd-Early and Pd-Late mice, respectively (X2 = 0.047). Colonic expression of toll-like receptor 4, IL-4 and TNF-α was 40% (P &lt; 0.01), 58% (P = 0.05) and 55% (P &lt; 0.001) lower, respectively, in Pd-Early compared with CTR mice. Pd-Late mice displayed a 217% (P = 0.05) and 185% (P &lt; 0.001) increase in colonic IL-10 and TGF-β expression, respectively, compared with CTR mice and similar increases in protein abundances were detected (47–145%; P &lt; 0.05). Pd-Early and Pd-Late mice both demonstrated increased colonic expression of the tight junction proteins Zonula occludens-1 (P &lt; 0.001) and occludin (P &lt; 0.001) at the transcript (2–3-fold; P &lt; 0.01) and protein level (30–50%; P &lt; 0.05) relative to CTR. Our results support a protective role for Pd in colonic tumorigenesis and maintenance of intestinal epithelial barrier in AOM-treated mice.
Administrative and Related Barriers to Covering the Costs of Preexposure Prophylaxis at a Safety-net Clinic in Seattle, Washington
Authors: McMahan Vanessa M , McCanta Lanny , Tran Dominic , Herrera Luis , Viquez Luis , Swanson Fred , Crutsinger-Perry Beth , Baeten Jared M , Katz Aaron , Stekler Joanne D 
Published: February 2020

Abstract
One barrier to human immunodeficiency virus preexposure prophylaxis (PrEP) is lack or perceived lack of health insurance or financial assistance. We performed a medical records review at a safety-net PrEP clinic in Seattle, Washington, and found that barriers to obtaining financial assistance were commonly recorded in association with initiation and persistence on PrEP.
Antiretroviral Therapy Initiation Is Associated With Decreased Visceral and Subcutaneous Adipose Tissue Density in People Living With Human Immunodeficiency Virus
Authors: Debroy Paula , Lake Jordan E , Moser Carlee , Olefsky Maxine , Erlandson Kristine M , Scherzinger Ann , Stein James H , Currier Judith S , Brown Todd T , McComsey Grace A 
Published: February 2020

AbstractBackgroundAdipose tissue (AT) alterations are common in people living with human immunodeficiency virus (PLWH). Decreases in AT density suggest disrupted adipocyte function/hypertrophy. We assessed changes in AT density after antiretroviral therapy (ART) initiation and associations with immunometabolic parameters.MethodsIn a prospective randomized clinical trial of ART initiation, L4–L5 abdominal CT scans measured subcutaneous AT (SAT) and visceral AT (VAT) area and density in treatment-naive PLWH randomized to tenofovir-emtricitabine plus ritonavir-boosted atazanavir, ritonavir-boosted darunavir, or raltegravir. Linear regression models compared week 0 and week 96 levels, and 96-week changes, in SAT and VAT density (in Hounsfield units [HU]). Spearman correlations assessed relationships between AT density and immunometabolic parameters.ResultsOf the 228 participants, 89% were male and 44% were white non-Hispanic. Median age was 36 years, baseline HIV-1 RNA was 4.6 log10 copies/mL, and CD4+ T-cell count was 344 cells/μL. Over 96 weeks, SAT and VAT HU decreased significantly in all arms. Less dense week 96 SAT and VAT density correlated with higher high-density lipoprotein (HDL) cholesterol and adiponectin (r = 0.19–0.30) levels and lower interleukin 6, non-HDL cholesterol, triglyceride, leptin, and homeostatic model assessment of insulin resistance (r = −0.23 to −0.68) levels at week 96 after adjusting for baseline CD4+ T-cell count, HIV-1 RNA, and baseline AT area.ConclusionsFollowing virologic suppression, lower SAT and VAT density was associated with greater plasma measures of systemic inflammation, lipid disturbances, and insulin resistance independent of AT area, suggesting that changes in AT density with ART may lead to adverse health outcomes independent of AT quantity.Clinical Trials RegistrationNCT00851799.
About clique number estimates and exact enumeration in scale-free networks
Authors: Jursa Andrej , Markošová Mária , Rudolf Boris 
Published: February 2020

AbstractIn this article, we present several analytical methods for both correlated and uncorrelated scale-free networks to obtain the clique number upper bound estimate. To test these estimates, we developed several tools to construct networks with scale-free degree distribution. To compute an exact clique number of network in short time, we also developed a clique finder algorithm. As the empirical results show, the various estimate methods gives good upper bounding for the clique numbers. Our clique finder proves to be able to solve clique number problem of arbitrary graphs in a good computation time. To show this, we applied our clique finder on benchmark graphs from various known databases.
Cardioversion of atrial fibrillation and atrial flutter revisited: current evidence and practical guidance for a common procedure
Authors: Brandes Axel , Crijns Harry J G M , Rienstra Michiel , Kirchhof Paulus , Grove Erik L , Pedersen Kenneth Bruun , Van Gelder Isabelle C 
Published: February 2020

Abstract
Cardioversion is widely used in patients with atrial fibrillation (AF) and atrial flutter when a rhythm control strategy is pursued. We sought to summarize the current evidence on this important area of clinical management of patients with AF including electrical and pharmacological cardioversion, peri-procedural anticoagulation and thromboembolic complications, success rate, and risk factors for recurrence to give practical guidance.
The Evolution History of Fe–S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs
Authors: Lu Hui-Meng , Li Jing-Di , Zhang Yu-Dan , Lu Xiao-Li , Xu Chang , Huang Yuan , Gribskov Michael 
Published: February 2020

AbstractIron–sulfur (Fe–S) clusters play important roles in electron transfer, metabolic and biosynthetic reactions, and the regulation of gene expression. Understanding the biogenesis of Fe–S clusters is therefore relevant to many fields. In the complex process of Fe–S protein formation, the A-type assembly protein (ATAP) family, which consists of several subfamilies, plays an essential role in Fe–S cluster formation and transfer and is highly conserved across the tree of life. However, the taxonomic distribution, motif compositions, and the evolutionary history of the ATAP subfamilies are not well understood. To address these problems, our study investigated the taxonomic distribution of 321 species from a broad cross-section of taxa. Then, we identified common and specific motifs in multiple ATAP subfamilies to explain the functional conservation and nonredundancy of the ATAPs, and a novel, essential motif was found in Eumetazoa IscA1, which has a newly found magnetic function. Finally, we used phylogenetic analytical methods to reconstruct the evolution history of this family. Our results show that two types of ErpA proteins (nonproteobacteria-type ErpA1 and proteobacteria-type ErpA2) exist in bacteria. The ATAP family, consisting of seven subfamilies, can be further classified into two types of ATAPs. Type-I ATAPs include IscA, SufA, HesB, ErpA1, and IscA1, with an ErpA1-like gene as their last common ancestor, whereas type-II ATAPs consist of ErpA2 and IscA2, duplicated from an ErpA2-like gene. During the mitochondrial endosymbiosis, IscA became IscA1 in eukaryotes and ErpA2 became IscA2 in eukaryotes, respectively.
Development and piloting of a Checklist for healthy eating And Physical Activity in the Workplace (CEPAW)
Authors: Freak-Poli Rosanne , Brand Margaret , Boelsen-Robinson Tara , Huse Oliver , de Courten Maximilian , Peeters Anna 
Published: February 2020

Abstract
To develop and pilot a tool that assesses the infrastructure and policy workplace environment characteristics that may influence employee healthy eating and physical activity behaviours. A checklist was developed with reference to prior tools and piloted at eight worksites. Piloting of the tool demonstrated that it was generally feasible to use, took 1–2 hours to complete and appeared sensitive to differences between workplace environment characteristics. Refinement of the tool occurred after piloting. The final 21-item checklist contains sub-scores capturing policy, infrastructure, healthy eating and physical activity characteristics. This new checklist overcomes some limitations of pre-existing tools as it explicitly considers policy and is short, inexpensive and can be used by workplaces for self-assessment and by health promotion professionals in evaluation studies or as an intervention tool.
The health literacy of university students in North Cyprus
Authors: Sariyar Sultan , Firat Kiliç Hülya 
Published: February 2020

Abstract
Health literacy is individuals' motivation and ability to obtain, understand, evaluate and use health information. Health literacy is very important during university education when students have the ability to acquire and accumulate knowledge of the best way. The aim of this study was to determine the health literacy of university students. The sample of this descriptive cross-sectional study was composed of 365 students who were first-time visitors at the health center of a private university in Northern Cyprus between May and July 2017. An introductory information form and the Adult Health Literacy Scale (AHLS) were used as data collection tools. The mean AHLS score of the students was found as 13.91 ± 2.90. Health literacy was found to be lower for male students and students with more years of study. The students with low daily alcohol use had higher AHLS scores. The results of the study suggest that curricula should be revised to raise the health literacy of university students to the highest level. It is important to organize conferences, seminars and scientific activities to improving the health literacy of male students and students with more years of study. Due to the limitations of studies of health literacy in North Cyprus, future studies should be conducted with larger samples and different measurement tools.