bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Cocoyam Modified Starch (Xanthosoma sagittifolium), Beetroot Juice, Cocoyam Modified Starch Adsorbing Beetroot on Plasma Selenium and Glutathione Peroxidase of Pre-Diabetic Rat
Authors: Hibaturrahman Said Naufal , Koyama Hiroshi , Kameo Satomi , Waspodo Priyo , Wardana Ata Aditya , Surono Ingrid Suryanti 
Published: March 2020

Abstract
This research was aimed to identify effect of cocoyam (Xanthosoma sagittifilum) and beetroot on plasma Glutathione Peroxidase (GPx) and selenium of pre-diabetic rats. The pre-diabetic rats were fed with cocoyam modified starch, beetroot juice and cocoyam modified starch adsorbing beetroot for 3 weeks. The plasma selenium and GPx were analyzed. The blood were withdrawn once in a week during 3 weeks. Selenium levels in pre-diabetic rats consumed each of feeding treatment were not significantly diffrent as compared to control feeding (AIN). Plasma GPx activity in pre-diabetic rats consumed cocoyam modified starch and cocoyam modified starch adsobing beetroot tended to have higher values than control in every week. Plasma GPx activity of pre-diabetic rats consumed beetroot juice tended to have higher values than control at the first and the second week.
Predicting incident delirium diagnoses using data from primary-care electronic health records
Authors: Bowman Kirsty , Jones Lindsay , Masoli Jane , Mujica-Mota Ruben , Strain David , Butchart Joe , Valderas José M , Fortinsky Richard H , Melzer David , Delgado João 
Published: March 2020

Abstract

Importance
risk factors for delirium in hospital inpatients are well established, but less is known about whether delirium occurring in the community or during an emergency admission to hospital care might be predicted from routine primary-care records.

Objectives
identify risk factors in primary-care electronic health records (PC-EHR) predictive of delirium occurring in the community or recorded in the initial episode in emergency hospitalisation. Test predictive performance against the cumulative frailty index.

Design
Stage 1: case-control; Stages 2 and 3: retrospective cohort.

Setting
clinical practice research datalink: PC-EHR linked to hospital discharge data from England.

Subjects
Stage 1: 17,286 patients with delirium aged ≥60 years plus 85,607 controls. Stages 2 and 3: patients ≥ 60 years (n = 429,548 in 2015), split into calibration and validation groups.

Methods
Stage 1: logistic regression to identify associations of 110 candidate risk measures with delirium. Stage 2: calibrating risk factor weights. Stage 3: validation in independent sample using area under the curve (AUC) receiver operating characteristic.

Results
fifty-five risk factors were predictive, in domains including: cognitive impairment or mental illness, psychoactive drugs, frailty, infection, hyponatraemia and anticholinergic drugs. The derived model predicted 1-year incident delirium (AUC = 0.867, 0.852:0.881) and mortality (AUC = 0.846, 0.842:0.853), outperforming the frailty index (AUC = 0.761, 0.740:0.782). Individuals with the highest 10% of predicted delirium risk accounted for 55% of incident delirium over 1 year.

Conclusions
a risk factor model for delirium using data in PC-EHR performed well, identifying individuals at risk of new onsets of delirium. This model has potential for supporting preventive interventions.
First explorations: ontogeny of central place foraging directions in two tropical seabirds
Authors: Collet Julien , Prudor Aurélien , Corbeau Alexandre , Mendez Loriane , Weimerskirch Henri 
Published: March 2020

Abstract
A widespread hypothesis for the ontogeny of behavior and decision-making is the early-exploration-later-canalization hypothesis. It postulates that juveniles are more exploratory and adults more consistent in their behavior. In addition, it is often assumed that naïve juveniles could overcome the costs of individual experience building by copying more the decisions of others than adults (early-conformism-later-self-defining hypothesis). Here, we compare the central place foraging movements of adults and postfledging juveniles in their first flights around the colony before dispersal and migration in two sympatric species of tropical seabirds: red-footed boobies and great frigatebirds. Using GPS records of individual movements, we analyzed the foraging directions of seabirds from the colony across successive trips. Juveniles of both species showed significant within-individual consistency in foraging direction but at lower levels than adults. Juveniles leaving the colony within the same time window showed significant but low between-individual resemblance in foraging direction at levels similar to adults. In both species, homing efficiency was lower in juveniles than in adults. Juvenile foraging directions were initially influenced by wind conditions, particularly in low wing loading frigatebirds. Wind conditions progressively lost influence on juvenile foraging directions during their first weeks of flights. In contrast, within-individual consistency, between-individual resemblance, and homing efficiency did not show signs of progression in juveniles. Our results support the early-exploration-later-canalization hypothesis but not the early-conformism-later-self-defining hypothesis. Relaxed constraints on self-feeding efficiency could favor high variability in postfledging tropical seabirds. Our simple approach could be applied to further test these hypotheses by comparing strategies across a wide range of central place foragers.
Heritability and correlations among learning and inhibitory control traits
Authors: Langley Ellis J G , Adams Gracie , Beardsworth Christine E , Dawson Deborah A , Laker Philippa R , van Horik Jayden O , Whiteside Mark A , Wilson Alastair J , Madden Joah R 
Published: March 2020

AbstractTo understand the evolution of cognitive abilities, we need to understand both how selection acts upon them and their genetic (co)variance structure. Recent work suggests that there are fitness consequences for free-living individuals with particular cognitive abilities. However, our current understanding of the heritability of these abilities is restricted to domesticated species subjected to artificial selection. We investigated genetic variance for, and genetic correlations among four cognitive abilities: inhibitory control, visual and spatial discrimination, and spatial ability, measured on &gt;450 pheasants, Phasianus colchicus, over four generations. Pheasants were reared in captivity but bred from adults that lived in the wild and hence, were subject to selection on survival. Pheasant chicks are precocial and were reared without parents, enabling us to standardize environmental and parental care effects. We constructed a pedigree based on 15 microsatellite loci and implemented animal models to estimate heritability. We found moderate heritabilities for discrimination learning and inhibitory control (h2 = 0.17–0.23) but heritability for spatial ability was low (h2 = 0.09). Genetic correlations among-traits were largely positive but characterized by high uncertainty and were not statistically significant. Principle component analysis of the genetic correlation matrix estimate revealed a leading component that explained 69% of the variation, broadly in line with expectations under a general intelligence model of cognition. However, this pattern was not apparent in the phenotypic correlation structure which was more consistent with a modular view of animal cognition. Our findings highlight that the expression of cognitive traits is influenced by environmental factors which masks the underlying genetic structure.
CeRNASeek: an R package for identification and analysis of ceRNA regulation
Authors: Zhang Mengying , Jin Xiyun , Li Junyi , Tian Yi , Wang Qi , Li Xinhui , Xu Juan , Li Yongsheng , Li Xia 
Published: March 2020

Abstract
Competitive endogenous RNA (ceRNA) represents a novel layer of gene regulation that controls both physiological and pathological processes. However, there is still lack of computational tools for quickly identifying ceRNA regulation. To address this problem, we presented an R-package, CeRNASeek, which allows identifying and analyzing ceRNA–ceRNA interactions by integration of multiple-omics data. CeRNASeek integrates six widely used computational methods to identify ceRNA–ceRNA interactions, including two global and four context-specific ceRNA regulation prediction methods. In addition, it provides several downstream analyses for predicted ceRNA–ceRNA pairs, including regulatory network analysis, functional annotation and survival analysis. With examples of cancer-related ceRNA prioritization and cancer subtyping, we demonstrate that CeRNASeek is a valuable tool for investigating the function of ceRNAs in complex diseases. In summary, CeRNASeek provides a comprehensive and efficient tool for identifying and analysis of ceRNA regulation. The package is available on the Comprehensive R Archive Network (CRAN) at https://CRAN.R-project.org/package=CeRNASeek.
A blind and independent benchmark study for detecting differentially methylated regions in plants
Authors: Kreutz Clemens , Can Nilay S , Bruening Ralf Schulze , Meyberg Rabea , Mérai Zsuzsanna , Fernandez-Pozo Noe , Rensing Stefan A 
Published: March 2020

Abstract

Motivation
Bisulfite sequencing (BS-seq) is a state-of-the-art technique for investigating methylation of the DNA to gain insights into the epigenetic regulation. Several algorithms have been published for identification of differentially methylated regions (DMRs). However, the performances of the individual methods remain unclear and it is difficult to optimally select an algorithm in application settings.

Results
We analyzed BS-seq data from four plants covering three taxonomic groups. We first characterized the data using multiple summary statistics describing methylation levels, coverage, noise, as well as frequencies, magnitudes and lengths of methylated regions. Then, simulated datasets with most similar characteristics to real experimental data were created. Seven different algorithms (metilene, methylKit, MOABS, DMRcate, Defiant, BSmooth, MethylSig) for DMR identification were applied and their performances were assessed. A blind and independent study design was chosen to reduce bias and to derive practical method selection guidelines. Overall, metilene had superior performance in most settings. Data attributes, such as coverage and spread of the DMR lengths, were found to be useful for selecting the best method for DMR detection. A decision tree to select the optimal approach based on these data attributes is provided. The presented procedure might serve as a general strategy for deriving algorithm selection rules tailored to demands in specific application settings.

Availability and implementation
Scripts that were used for the analyses and that can be used for prediction of the optimal algorithm are provided at https://github.com/kreutz-lab/DMR-DecisionTree. Simulated and experimental data are available at https://doi.org/10.6084/m9.figshare.11619045.

Contact
ckreutz@imbi.uni-freiburg.de

Supplementary information
Supplementary data are available at Bioinformatics online.
Juvenile-juvenile social signalling: a case for precocial sexual selection in the collared lizard,Crotaphytus collaris(Squamata: Crotaphytidae)?
Authors: Fox Stanley F , Rodríguez-Romero Felipe De Jesús , Crosby Andrea Acevedo 
Published: March 2020

AbstractSexual selection is widespread in animals, but quite naturally studied in adults. Juvenile males in most animals are not differentiated from females and coloration is usually drab. However, there is no reason to suspect that sexual differences cannot develop before puberty, influence social interactions, and then have fitness pay-offs later in life. Juvenile collared lizards (Crotaphytus collaris (Say, 1822)) show marked dichromatism: males develop bright dorsolateral orange bars whereas females do not. These juvenile orange bars (JOB) disappear at sexual maturity, when males develop different colour traits maintained by sexual selection. We conducted field experiments with juvenile males on their developing territories in which we utilized staged intruders of juvenile males (with JOB) and juvenile females (lacking JOB) and also juvenile male intruders whose JOB were manipulated. Residents reacted significantly more aggressively toward males vs. females, and also toward males whose JOB were emphasized with paint than those whose JOB were masked by paint. These JOB are used in signalling among juveniles and we suggest the social relations established then are retained until sexual maturation the next spring (after the JOB are lost) to benefit males that previously displayed strong JOB by increased matings in the spring as sexually mature yearlings as per a phenomenon we call precocial sexual selection.
Macrophage-induced reactive oxygen species promote myometrial contraction and labor-associated mechanisms†
Authors: Wendremaire Maeva , Hadi Tarik , Pezze Maria , Barrichon Marina , Lopez Tatiana , Neiers Fabrice , Sagot Paul , Garrido Carmen , Lirussi Frédéric 
Published: March 2020

AbstractAt labor, the myometrium is infiltrated by a massive influx of macrophages that secrete high levels of pro-inflammatory cytokines inducing the expression of specific labor-associated markers. However, the interactions between myocytes and macrophages and the role of macrophages in the myometrium at labor remain to be elucidated. In this work, we studied the role of myometrium-infiltrated macrophages and their interaction with myocytes in lipopolysaccharide-induced preterm labor. A co-culture model of human primary myometrial cells and macrophages was developed and validated. Collagen lattices were used to evaluate myocyte contraction. Differentiation steps were assessed by (i) phalloidin and vinculin staining for cytoskeleton reorganization, (ii) gap junction protein alpha 1 expression and scrape loading/dye transfer with Lucifer Yellow for gap junction intercellular communication, and (iii) calcium imaging for cell excitability. We demonstrated that macrophages favored lipopolysaccharide-induced contraction and early differentiation of myometrial cells. Transwell assays showed that previous activation of macrophages by lipopolysaccharide was essential for this differentiation and that macrophage/myocyte interactions involved macrophage release of reactive oxygen species (ROS). The effects of macrophage-released ROS in myometrial cell transactivation were mimicked by H2O2, suggesting that superoxide anion is a major intermediate messenger in macrophage/myocyte crosstalk during labor. These novel findings provide the foundation for innovative approaches to managing preterm labor, specifically the use of antioxidants to inhibit the initial stages of labor before the contractile phenotype has been acquired. In addition, the co-culture model developed by our team could be used in future research to decipher pathophysiological signaling pathways or screen/develop new tocolytics.
Neurofilaments: neurobiological foundations for biomarker applications
Authors: Gafson Arie R , Barthélemy Nicolas R , Bomont Pascale , Carare Roxana O , Durham Heather D , Julien Jean-Pierre , Kuhle Jens , Leppert David , Nixon Ralph A , Weller Roy O , Zetterberg Henrik , Matthews Paul M 
Published: March 2020

AbstractInterest in neurofilaments has risen sharply in recent years with recognition of their potential as biomarkers of brain injury or neurodegeneration in CSF and blood. This is in the context of a growing appreciation for the complexity of the neurobiology of neurofilaments, new recognition of specialized roles for neurofilaments in synapses and a developing understanding of mechanisms responsible for their turnover. Here we will review the neurobiology of neurofilament proteins, describing current understanding of their structure and function, including recently discovered evidence for their roles in synapses. We will explore emerging understanding of the mechanisms of neurofilament degradation and clearance and review new methods for future elucidation of the kinetics of their turnover in humans. Primary roles of neurofilaments in the pathogenesis of human diseases will be described. With this background, we then will review critically evidence supporting use of neurofilament concentration measures as biomarkers of neuronal injury or degeneration. Finally, we will reflect on major challenges for studies of the neurobiology of intermediate filaments with specific attention to identifying what needs to be learned for more precise use and confident interpretation of neurofilament measures as biomarkers of neurodegeneration.
Identification and Comparison of Tannins in Gall of Rhus chinensis Mill. and Gall of Quercus infectoria Oliv. by High-Performance Liquid Chromatography–Electrospray Mass Spectrometry
Authors: Ma Shangzhi , Qin Huiyu , Jiang Min , Wang Junqi , Wang Wei , Guo Gang , Zhou Liangxue , Chen Wen , Han Bo 
Published: March 2020

Abstract
Gall of Rhus chinensis Mill. (Chinese galls) and gall of Quercus infectoria Oliv. (Turkish galls) have similar applications and chemical compositions, and their extracts have been widely used for industrial production and for medicinal applications. In this study, high-performance liquid chromatography–electrospray mass spectrometry (HPLC-ESI-MS/MS) methods were established for profiling the components of Chinese galls and Turkish galls. Compounds representing 96.56 and 99.15% of the total peak area of Chinese galls and Turkish galls were identified. The results identified that the ellagic acid, galloyl-HHDP-glucose and pedunculagin act as the identifying markers for the comparison of Chinese galls and Turkish galls in HPLC-ESI-MS/MS. The peak area of tetragalloyl-glucoside, heptagalloyl-glucoside and pentagalloyl-glucoside can be used to distinguish these two phytomedicines. This work provides a reference for the study of the chemical composition of Chinese galls and Turkish galls, which not only introduce a simple and reliable method to prevent the adulteration or misuse of Chinese galls and Turkish galls but also lay the foundations for clarifying the material basis of their similar pharmacological action.
Longitudinal Care Cascade Outcomes Among People Eligible for Antiretroviral Therapy Who Are Newly Linking to Care in Zambia: A Multistate Analysis
Authors: Mody Aaloke , Glidden David V , Eshun-Wilson Ingrid , Sikombe Kombatende , Simbeza Sandra , Mukamba Njekwa , Somwe Paul , Beres Laura K , Pry Jake , Bolton-Moore Carolyn , Padian Nancy , Holmes Charles B , Sikazwe Izukanji , Geng Elvin H 
Published: March 2020

Abstract

Background
Retention in human immunodeficiency virus (HIV) care is dynamic, with patients frequently transitioning in and out of care. Analytical approaches (eg, survival analyses) commonly used to assess HIV care cascade outcomes fail to capture such transitions and therefore incompletely represent care outcomes over time.

Methods
We analyzed antiretroviral therapy (ART)-eligible adults newly linking to care at 64 clinics in Zambia between 1 April 2014 and 31 July 2015. We used electronic medical record data and supplemented these with updated care outcomes ascertained by tracing a multistage random sample of patients lost to follow-up (LTFU, &gt;90 days late for last appointment). We performed multistate analyses, incorporating weights from sampling, to estimate the prevalence of 9 care states over time since linkage with respect to ART initiation, retention in care, transfers, and mortality.

Results
In sum, 23 227 patients (58% female; median age 34 years [interquartile range 28–41]) were ART-eligible at enrollment. At 1 year, 75.2% had initiated ART and were in care: 61.8% were continuously retained, 6.1% had reengaged after LTFU, and 7.3% had transferred. Also, 10.1% were LTFU within 7 days of enrollment, and 15.2% were LTFU at 1 year (6.7% prior to ART). One year after LTFU, 51.6% of those LTFU prior to ART remained out of care compared to 30.2% of those LTFU after initiating ART. Overall, 6.9% of patients had died by 1 year with 3.0% dying prior to ART.

Conclusion
Multistate analyses provide more complete assessments of longitudinal HIV cascade outcomes and reveal treatment gaps at distinct timepoints in care that will still need to be addressed even with universal treatment.
Human Immunodeficiency Virus–2 (HIV-2): A Summary of the Present Standard of Care and Treatment Options for Individuals Living with HIV-2 in Western Europe
Authors: Berzow Dirk , Descamps Diane , Obermeier Martin , Charpentier Charlotte , Kaiser Rolf , Guertler Lutz , Eberle Josef , Wensing Annemarie , Sierra Saleta , Ruelle Jean , Gomes Perpetua , Mansinho Kamal , Taylor Ninon , Jensen Björn , Döring Matthias , Stürmer Martin , Rockstroh Jürgen , Camacho Ricardo 
Published: March 2020

AbstractHuman immunodeficiency virus–2 (HIV-2) is endemic in some countries in West Africa. Due to the lower prevalence in industrialized countries, there is limited experience and knowledge on the management of individuals living with HIV-2 in Europe. Compared to HIV-1, there are differential characteristics of HIV-2 regarding diagnostic procedures, the clinical course, and, most importantly, antiretroviral therapy.We integrated the published literature on HIV-2 (studies and reports on epidemiology, diagnostics, the clinical course, and treatment), as well as expert experience in diagnosing and clinical care, to provide recommendations for a present standard of medical care of those living with HIV-2 in Western European countries, including an overview of strategies for diagnosis, monitoring, and treatment, with suggestions for effective drug combinations for first- and second-line treatments, post-exposure prophylaxis, and the prevention of mother-to-child transmission, as well as listings of mutations related to HIV-2 drug resistance and C-C motif chemokine receptor type 5 and C-X-C motif chemokine receptor type 4 coreceptor tropism.
Applying conservation social science to study the human dimensions of Neotropical bird conservation
Authors: Dayer Ashley A , Silva-Rodríguez Eduardo A , Albert Steven , Chapman Mollie , Zukowski Benjamin , Ibarra J Tomás , Gifford Gemara , Echeverri Alejandra , Martínez-Salinas Alejandra , Sepúlveda-Luque Claudia 
Published: March 2020

AbstractAs the global human population increases, and many bird populations in the Neotropics and the rest of the world continue to decline, the study of the intersection of humans, birds, and conservation has become more relevant than ever. The field of conservation social science is an interdisciplinary field that applies the social sciences and humanities to examine research questions that have implications for biodiversity conservation, and encompasses disciplines as diverse as psychology, economics, and political ecology. An understanding of the human dimensions of biodiversity conservation issues can be an essential element in the success or failure of a conservation initiative, policy, or practice. The purpose of this article is to provide an understanding of the growing body of conservation social science relevant to Neotropical bird conservation research and to demonstrate its importance. We discuss how this research can contribute to addressing 5 major threats to bird conservation in the Neotropics, including future research needs, and we provide 3 case studies of bird conservation social science projects, demonstrating the insights that can be gained. We close with a discussion of how conservation biologists and ornithologists can most effectively work with conservation social scientists.