bluuebunny/crossref_metadata_2025_split huggingface dataset:
Who Bears the Burden of Long-Lived Molecular Biology Databases?
Authors: Imker Heidi J. 
Published: February 2019

ABSTRACTIn the early 1990s the life sciences quickly adopted online databases to facilitate wide-spread dissemination and use of scientific data. From 1991, the journalNucleic Acids Researchhas published an annual Database Issue dedicated to articles describing molecular biology databases. Analysis of these articles reveals a set of long-lived databases which have now remained available for more than 15 years. Given the pervasive challenge of sustaining community resources, these databases provide an opportunity to examine what factors contribute to persistence by addressing two questions 1) which organizations fund these long-lived databases? and 2) which organizations maintain these long-lived databases? Funding and operating organizations for 67 databases were determined through review of Database Issue articles. The results reveal a diverse set of contributing organizations with financial and operational support spread across six categories: academic, consortium/collective, government, industry, philanthropic, and society/association. The majority of databases reported support from more than one funding organization, of which government organizations were most common source of funds. Operational responsibilities were more distributed, with academic organizations serving as the most common hosts. Although overall there is evidence of diversification, the most acknowledged funding and operating organizations contribute to disproportionately large percentages of the long-lived databases investigated here.
Sex and area differences in the association between adiposity and lipid profile in Malawi
Authors: Soares Ana Luiza G , Banda Louis , Amberbir Alemayehu , Jaffar Shabbar , Musicha Crispin , Price Alison , Nyrienda Moffat J , Lawlor Deborah A , Crampin Amelia C 
Published: February 2019

ABSTRACTBackgroundEvidence from high-income countries shows that higher adiposity results in an adverse lipid profile, but it is unclear whether this association is similar in Sub-Saharan African (SSA) populations. This study aimed to assess the association between total and central adiposity measures and lipid profile in Malawi, exploring differences by sex and area of residence (rural/urban).MethodsData from 12,847 rural and 12,096 urban Malawian residents were used. The associations of body mass index (BMI) and waist-hip ratio (WHR) with fasting lipids (total cholesterol (TC), low density lipoprotein-cholesterol (LDL-C), high density lipoprote in-cholesterol (HDL-C) and triglycerides (TG)) were assessed by area and sex.ResultsA great proportion of adults have high BMI and WHR, and this was associated with adverse lipid profiles; higher BMI and WHR were linearly associated with increased TC, LDL-C and TG and reduced HDL-C. BMI was more strongly related to fasting lipids than was WHR. The associations of adiposity with adverse lipid profile were stronger in urban compared with rural residents.ConclusionsThe consistent associations observed of higher adiposity with adverse lipid profiles in females and males living in rural and urban areas of Malawi highlight the emerging adverse cardio-metabolic epidemic in this poor population. Our findings underline the potential utility of BMI in estimating cardiovascular risk and highlight the need for greater investment to understand the long-term health outcomes of obesity and adverse lipid profiles and the extent to which lifestyle changes and treatments effectively prevent and modify adverse cardio-metabolic outcomes.Key messagesHigher body mass index (BMI) and waist to hip ratio (WHR) are associated with increased total cholesterol (TC), low density lipoprotein-cholesterol (LDL-C) and triglycerides (TG) and reduced high density lipoprotein-cholesterol (HDL-C) in a large sub-Saharan African population.Total adiposity is more strongly associated with adverse lipid profile than central adiposity.Despite the higher BMI and the less favourable lipid profile in urban residents, stronger associations between BMI and TC, LDL-C and TG are observed in rural than urban residents.
Rabies-induced behavioural changes are key to rabies persistence in dog populations: investigation using a network-based model
Authors: Brookes Victoria J. , Dürr Salome , Ward Michael P. 
Published: February 2019

ABSTRACTCanine-rabies was endemic pre-urbanisation, yet little is known about how it persists in small populations of dogs typically seen in rural and remote regions. Our objectives were to simulate rabies outbreaks in such populations (50—90 dogs) using a network-based model, and investigate the influence of rabies-induced behavioural changes.Such changes – increased bite frequency and either roaming or paralysis that increased the number or duration of contacts, respectively – were essential for disease propagation. Spread occurred in approximately 50% of model simulations and in these, a very low case rates (2.0—2.6 cases/month) over long durations (95% range 20—473 days) were predicted. Consequently, disease detection is a challenge, risking human infection and spread to other communities via dog movements. Even with 70% pre-emptive vaccination, spread occurred in >30% of model simulations (in these, median case rate was 1.5/month with 95% range of 15—275 days duration).We conclude that the social disruption caused by rabies-induced behavioural change is the key to explaining how rabies persists in small populations of dogs. We predict that vaccination of substantially greater than the recommended 70% of dog populations is required to prevent rabies emergence in currently free rural areas.
Temporal Trends without Seasonal Effects on Gestational Diabetes Incidence Relate to Reductions in Indices of Insulin Secretion: The Cambridge Baby Growth Study
Authors: Petry Clive J. , Fisher Benjamin G. , Ong Ken K. , Hughes Ieuan A. , Acerini Carlo L. , Dunger David B. 
Published: February 2019

AbstractAimsThe incidence of gestational diabetes has been reported to have risen over the first decade of this century. Some studies have also found it to vary with seasons of the year. We therefore investigated temporal and seasonal trends on gestational diabetes incidence in a single centre cohort study from Cambridge, U.K., and attempted to explain trends using associations with risk factors.Materials and MethodsUsing a cosinor model we tested whether there were both temporal and seasonal trends in gestational diabetes incidence in 1,074 women recruited to the Cambridge Baby Growth Study in 2001-2009 who underwent oral glucose tolerance tests around week 28 of pregnancy. We also undertook risk factor analyses.ResultsThere was a temporal increase in gestational diabetes incidence over the course of recruitment to this study (p=2.1×10−3) but no seasonal effect (p=0.7). HOMA B (p=3.0×10−3; n=1,049) and the insulin disposition index (p=3.0×10−3; n=1,000) showed negative temporal trends. There was no negative association with HOMA S. Risk factor analyses showed a concomitant temporal slight increase in the index of multiple deprivation (p=4.6×10−10, n=1,068). This index was positively associated with HOMA B (p=6.1×10−5, n=955) but not directly with gestational diabetes (p=0.6, n=1,032), HOMA S (p=0.2, n=955) or the insulin disposition index (p=0.4, n=955).ConclusionsIn this population there were temporal but not seasonal increases in gestational diabetes incidence between the years 2001 and 2009, which appeared to be related more to reductions in insulin secretion than sensitivity. Possible mediators of this link include confounding factors related to deprivation.
Genetic Diversity and Phylogenetic Relationships of Annual and PerennialGlycineSpecies
Authors: Hwang Eun-Young , Wei He , Schroeder Steven G. , Fickus Edward W. , Quigley Charles V. , Elia Patrick , Costa Larissa , Araya Susan , Ferreira Marcio Elias , Cregan Perry B. , Song Qijian 
Published: February 2019

ABSTRACTWe estimated average genetic diversity of twoGlycineannual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11G. canescensaccessions. Among the perennials,G. canescensshowed the highest nucleotide diversity and the other perennials exceptG. tomentellahad higher nucleotide diversity than the two annuals. Phylogenetic analysis of theGlycineshowed a similar genome grouping with the previous report exceptG. cyrtolobaandG. stenophitaformed a sister clade in the study. Divergence analysis supported the phylogenetic relationships,G. falcatawas the most divergent fromG. max, followed byG. cyrtoloba,G. syndetika,G. tomentellaD3,G. stenophitaandG. canescens. Neutrality selection tests within species showed that most genes were subjected to a recent directional selection due to a selective sweep or rapid population expansion. Although most gene sequence had negative and significant Tajima’s D, the sequences were homogeneous in the levels of polymorphism and divergence betweenG. maxand otherGlycinespecies based on the HKA test, thus,Glycineperennials may have experienced very similar evolutionary selection as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennialGlycinespecies and their origins from the warmer and drier climates of Australia suggested the perennials as potential sources of heat and drought resistance that will be of value in the face of climate change.
IFNγ induces epigenetic programming of human T-bethiB cells and promotes TLR7/8 and IL-21 induced differentiation
Authors: Zumaquero Esther , Stone Sara L. , Scharer Christopher D. , Jenks Scott A. , Nellore Anoma , Mousseau Betty , Rosal-Vela Antonio , Botta Davide , Bradley John E. , Wojciechowski Wojciech , Ptacek Travis , Danila Maria I. , Edberg Jeffrey C. , Bridges S. Louis , Kimberly Robert P. , Chatham W. Winn , Schoeb Trenton R. , Rosenberg Alexander , Boss Jeremy M. , Sanz Ignacio , Lund Frances E. 
Published: February 2019

AbstractAlthough B cells expressing the IFNγR or the IFNγ-inducible transcription factor T-bet drive autoimmunity in Systemic Lupus Erythematosus (SLE)-prone mouse models, the role for IFNγ signaling in human antibody responses is unknown. We show that elevated levels of IFNγ in SLE patients correlate with expansion of the T-bet expressing IgDnegCD27negCD11c+CXCR5neg(DN2) pre-antibody secreting cell (pre-ASC) subset. We demonstrate that naïve B cells form T-bethipre-ASCs following stimulation with either Th1 cells or with IFNγ, IL-2, anti-Ig and TLR7/8 ligand and that IL-21 dependent ASC formation is significantly enhanced by IFNγ or IFNγ-producing T cells. IFNγ promotes ASC development by synergizing with IL-2 and TLR7/8 ligands to induce genome-wide epigenetic reprogramming of B cells, which results in increased chromatin accessibility surrounding IRF4 and BLIMP1 binding motifs and epigenetic remodeling ofIL21RandPRDM1loci. Finally, we show that IFNγ signals poise B cells to differentiate by increasing their responsiveness to IL-21.
A lipid-structured model for macrophage populations in atherosclerotic plaques
Authors: Ford Hugh Z. , Byrne Helen M. , Myerscough Mary R. 
Published: February 2019

AbstractAtherosclerosis is a chronic inflammatory disease driven by the accumulation of pro-inflammatory, lipid-loaded macrophages at sites inside artery walls. These accumulations lead to the development of atherosclerotic plaques. The rupture of plaques that contain lipid-rich necrotic cores can trigger heart attacks and strokes via occlusion of blood vessels. We construct and analyse a system of partial integro-differential equations that model lipid accumulation by macrophages, including generating apoptotic cells and a necrotic core. The model includes the following cell behaviours: recruitment of macrophages into the plaque; macrophage ingestion of low density lipoproteins LDL and of apoptotic cells and necrotic material; lipid offloading to high density lipoproteins (HDL); macrophage emigration; and macrophage apoptosis and necrosis of apoptotic cells. With this model, we study how changes in parameters predict the characteristic features of plaque pathology. In particular, we find the qualitative form of lipid distribution across the macrophage population and show that high lipid loads can occur in the absence of LDL ingestion. We also demonstrate the importance of macrophage emigration in the model in mitigating and resolving inflammation and plaque lipid accumulation.ContributionsHZF: conceptualisation, formal analysis, investigation, methodology, visualisation, writing— original draft preparation, writing—review and editing.HMB: conceptualisation, funding acquisition, methodology, project administration, resources, supervision, writing—review and editing.MRM: conceptualisation, funding acquisition, methodology, project administration, resources, supervision, writing—original draft, writing—review and editing.
Characterizing grapevine (Vitis spp.) inflorescence architecture using X-ray imaging: implications for understanding cluster density
Authors: Li Mao , Klein Laura L. , Duncan Keith E. , Jiang Ni , Londo Jason P. , Miller Allison J. , Topp Christopher N. 
Published: February 2019

SummaryWe characterized grapevine inflorescence architecture (the rachis and all branches without berries) to describe variation among 10 wild Vitis species, assess phylogenetic signals underlying inflorescence architecture traits, and interpret this variation in the context of breeding objectives.Three-dimensional X-ray tomography scans of grapevine inflorescences were used to measure geometric traits and inflorescence topology using persistent homology, a mathematical approach that can comprehensively measure and compare shapes. We simulated potential space available for berry growth within a given inflorescence architecture by evaluating expanding spheres attached to pedicels, referred to as “berry potential.” Lastly, we performed phylogenetic analysis and mapped trait variation.We detected wide variation in inflorescence architecture features among Vitis species. Hierarchical clustering and correlation analyses revealed relationships among traits. Multivariate analyses identify traits contributing the most to variation and distinguish between species with high accuracy. Phylogenetic analyses revealed 12 morphological traits with strong phylogenetic signal.Morphometric analysis uncovered novel differences in inflorescence architecture among clades and between Vitis species. Cluster density is an important trait for assessing crop quality and forecasting yield; analyses presented here can be used to tease apart subtle, heritable features and environmental influences on this major agronomic trait.
Programming conventional electron microscopes for solving ultrahigh-resolution structures of small and macro-molecules
Authors: zhou Heng , Luo Feng , Luo Zhipu , Li Dan , Liu Cong , Li Xueming 
Published: February 2019

AbstractMicrocrystal electron diffraction (MicroED) is becoming a powerful tool in determining the crystal structures of biological macromolecules and small organic compounds. However, wide applications of this technique are still limited by the special requirement for radiation-tolerated movie-mode camera and the lacking of automated data collection method. Herein, we develop a stage-camera synchronization scheme to minimize the hardware requirements and enable the use of the conventional electron cryo-microscope with single-frame CCD camera, which ensures not only the acquisition of ultrahigh-resolution diffraction data but also low cost in practice. This method renders the structure determination of both peptide and small organic compounds at ultrahigh resolution up to ~0.60 Å with unambiguous assignment of nearly all hydrogen atoms. The present work provides a widely applicable solution for routine structure determination of MicroED, and demonstrates the capability of the low-end 120kV microscope with a CCD camera in solving ultra-high resolution structures of both organic compound and biological macromolecules.
mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana
Authors: Bhat Susheel Sagar , Bielewicz Dawid , Grzelak Natalia , Gulanicz Tomasz , Bodi Zsuzsanna , Szewc Lukasz , Bajczyk Mateusz , Dolata Jakub , Smolinski Dariusz J. , Fray Rupert G. , Jarmolowski Artur , Szweykowska-Kulinska Zofia 
Published: February 2019

Abstractm6A, one of the most abundant mRNA modifications, has been associated with various metabolic processes in plants. Here we show that m6A also plays a role in miRNA biogenesis in Arabidopsis thaliana. Significant reductions in plant m6A/MTA levels results in lower accumulation of miRNAs whereas pri-miRNA levels tend to be higher in such plants. m6A-IP Seq and MTA-GFP RIP were used to show that many pri-miRNAs are m6A methylated and are bound by MTA, further demonstrating that pri-miRNAs can also be substrates for m6A methylation by MTA. We report that MTA interacts with RNA Pol II, supporting the assumption that m6A methylation is a co-transcriptional process, and also identify TGH, a known miRNA biogenesis related protein, as a novel protein that interacts with MTA. Finally, reduced levels of miR393b may partially explain the strong auxin insensitivity seen in Arabidopsis plants with reduced m6A levels.
Factors that influence scientific productivity from different countries: A causal approach through multiple regression using panel data
Authors: Lancho-Barrantes Bárbara S. , Ceballos Héctor G. , Cantú-Ortiz Francisco J. 
Published: February 2019

AbstractThe main purpose of the economic expenditure of countries in research and development is to achieve higher levels of scientific findings within research ecosystems, which in turn could generate better living standards for society. Therefore, the collection of scientific production constitutes a faithful image of the capacity, trajectory and scientific depth assignable to each country. The intention of this article is to contribute to the understanding of the factors that certainly influence in the scientific production and how could be improved. In order to achieve this challenge, we select a sample of 19 countries considered partners in science and technology. On the one hand we download social and economic variables (gross domestic expenditure on R&D (GERD) as a percentage of gross domestic product (GDP) and researchers in full-time equivalent (FTE)) and on the other hand variables related to scientific results (total scientific production, scientific production by subject areas and by different institutions, without overlook the citations received as an impact measure) all this data within a 17-year time window. Through a causal model with multiple linear regression using panel data, the experiment confirms that two independent (or explanatory) variables of five selected explain the amount of scientific production by 98% for the countries analyzed. An important conclusion that we highlight stays the importance of checking for compliance of statistical assumptions when using multiple regression in research studies. As a result, we built a reliable predictive model to analyze scenarios in which the increase in any of the independent variables causes a positive effect on scientific production. This model allows decision maker to make comparison among countries and helps in the formulation of future plans on national scientific policies.
A semi-parametric Bayesian approach, iSBA, for differential expression analysis of RNA-seq data
Authors: Bi Ran , Liu Peng 
Published: February 2019

AbstractRNA sequencing (RNA-seq) technologies have been popularly applied to study gene expression in recent years. Identifying differentially expressed (DE) genes across treatments is one of the major steps in RNA-seq data analysis. Most differential expression analysis methods rely on parametric assumptions, and it is not guaranteed that these assumptions are appropriate for real data analysis. In this paper, we develop a semi-parametric Bayesian approach for differential expression analysis. More specifically, we model the RNA-seq count data with a Poisson-Gamma mixture model, and propose a Bayesian mixture modeling procedure with a Dirichlet process as the prior model for the distribution of fold changes between the two treatment means. We develop Markov chain Monte Carlo (MCMC) posterior simulation using Metropolis Hastings algorithm to generate posterior samples for differential expression analysis while controlling false discovery rate. Simulation results demonstrate that our proposed method outperforms other popular methods used for detecting DE genes.
PRH1 mediates ARF7-LBD dependent auxin signaling to regulate lateral root development inArabidopsis thaliana
Authors: Zhang Feng , Tao Wenqing , Sun Ruiqi , Wang Junxia , Li Cuiling , Kong Xiangpei , Tian Huiyu , Ding Zhaojun 
Published: February 2019

AbstractThe development of lateral roots inArabidopsis thalianais strongly dependent on signaling directed by the AUXIN RESPONSE FACTOR7 (ARF7), which in turn activates LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors (LBD16,18,29and33). Here, the product ofPRH1,aPR-1homolog annotated previously as encoding a pathogen-responsive protein, was identified as a target of ARF7-mediated auxin signaling and also as participating in the development of lateral roots.PRH1was shown to be strongly induced by auxin treatment, and plants lacking a functional copy ofPRH1formed fewer lateral roots. The transcription ofPRH1was controlled by the binding of both ARF7 and LBDs to its promoter region. An interaction was detected between PRH1 and GATA23, a protein which regulates cell identity in lateral root founder cells.Author SummaryInArabidopsis thalianaAUXIN RESPONSE FACTOR7 (ARF7)-mediated auxin signaling plays a key role in lateral roots (LRs) development. TheLATERAL ORGAN BOUNDARIES DOMAIN (LBD)transcription factors (LBD16,18,29and33) act downstream of ARF7-mediated auxin signaling to control LRs formation. Here, thePR-1homologPRH1was identified as a novel target of both ARF7 and LBDs (especially the LBD29) during auxin induced LRs formation, as both ARF7 and LBDs were able to bind to thePRH1promoter. More interestingly, PRH1 has a physical interaction with GATA23, which has been also reported to be up-regulated by auxin and influences LR formation through its regulation of LR founder cell identity. Whether the interaction between GATA23 and PRH1 affects the stability and/or the activity of either (or both) of these proteins remains an issue to be explored. This study provides improves new insights about how auxin regulates lateral root development.