bluuebunny/crossref_metadata_2025_split huggingface dataset:
circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs
Authors: Chen Li , Wang Feng , Bruggeman Emily C , Li Chao , Yao Bing 
Published: August 2019

AbstractMotivationCircular RNAs (circRNAs), a class of non-coding RNAs generated from non-canonical back-splicing events, have emerged to play key roles in many biological processes. Though numerous tools have been developed to detect circRNAs from rRNA-depleted RNA-seq data based on back-splicing junction-spanning reads, computational tools to identify critical genomic features regulating circRNA biogenesis are still lacking. In addition, rigorous statistical methods to perform differential expression (DE) analysis of circRNAs remain under-developed.ResultsWe present circMeta, a unified computational framework for circRNA analyses. circMeta has three primary functional modules: (i) a pipeline for comprehensive genomic feature annotation related to circRNA biogenesis, including length of introns flanking circularized exons, repetitive elements such as Alu elements and SINEs, competition score for forming circulation and RNA editing in back-splicing flanking introns; (ii) a two-stage DE approach of circRNAs based on circular junction reads to quantitatively compare circRNA levels and (iii) a Bayesian hierarchical model for DE analysis of circRNAs based on the ratio of circular reads to linear reads in back-splicing sites to study spatial and temporal regulation of circRNA production. Both proposed DE methods without and with considering host genes outperform existing methods by obtaining better control of false discovery rate and comparable statistical power. Moreover, the identified DE circRNAs by the proposed two-stage DE approach display potential biological functions in Gene Ontology and circRNA-miRNA–mRNA networks that are not able to be detected using existing mRNA DE methods. Furthermore, top DE circRNAs have been further validated by RT-qPCR using divergent primers spanning back-splicing junctions.Availability and implementationThe software circMeta is freely available at https://github.com/lichen-lab/circMeta.Supplementary informationSupplementary data are available at Bioinformatics online.
PyRanges: efficient comparison of genomic intervals in Python
Authors: Stovner Endre Bakken , Sætrom Pål 
Published: August 2019

Abstract

Summary
Complex genomic analyses often use sequences of simple set operations like intersection, overlap and nearest on genomic intervals. These operations, coupled with some custom programming, allow a wide range of analyses to be performed. To this end, we have written PyRanges, a data structure for representing and manipulating genomic intervals and their associated data in Python. Run single threaded on binary set operations, PyRanges is in median 2.3–9.6 times faster than the popular R GenomicRanges library and is equally memory efficient; run multi-threaded on 8 cores, our library is up to 123 times faster. PyRanges is therefore ideally suited both for individual analyses and as a foundation for future genomic libraries in Python.

Availability and implementation
PyRanges is available as open source under the MIT license at https://github.com/biocore-NTNU/pyranges and the documentation exists at https://biocore-NTNU.github.io/pyranges/

Supplementary information
Supplementary data are available at Bioinformatics online.
Invasive toads adopt marked capital breeding when introduced to a cooler, more seasonal environment
Authors: Vimercati Giovanni , Davies Sarah J , Measey John 
Published: August 2019

AbstractAmphibians from cold and seasonal environments show marked capital breeding and sustained resource allocation to growth when compared with conspecifics from warmer, less seasonal environments. Capital breeding fuels reproduction by using only stored energy, and larger sizes and masses confer higher fecundity, starvation resistance and heat and water retention. Invasive populations act as experiments to explore how resources are allocated in novel environments. We investigated resource allocation of the southern African toad Sclerophrys gutturalis in a native source population (Durban) and in an invasive population recently (< 20 years) established in a cooler, more seasonal climate (Cape Town). After dissection, lean structural mass (bones and muscles), gonadal mass, liver mass and body fat percentage were measured in 161 native and invasive animals sampled at the beginning and the end of the breeding season. As expected, female gonadal mass decreased throughout the breeding season only in the invaded range. Thus, invasive female toads adopt a more marked capital breeding strategy than native conspecifics. Conversely, males from both populations appear to be income breeders. Also, male and female toads from the invaded range allocate more resources to growth than their native counterparts. Such a novel allocation strategy might be a response to the low temperatures, reduced rainfall and heightened seasonality encountered by the invasive population.
Omega-3 polyunsaturated fatty acids impinge on CD4+ T cell motility and adipose tissue distribution via direct and lipid mediator-dependent effects
Authors: Cucchi Danilo , Camacho-Muñoz Dolores , Certo Michelangelo , Niven Jennifer , Smith Joanne , Nicolaou Anna , Mauro Claudio 
Published: August 2019

Abstract

Aims
Adaptive immunity contributes to the pathogenesis of cardiovascular metabolic disorders (CVMD). The omega-3 polyunsaturated fatty acids (n-3PUFA) are beneficial for cardiovascular health, with potential to improve the dysregulated adaptive immune responses associated with metabolic imbalance. We aimed to explore the mechanisms through which n-3PUFA may alter T cell motility and tissue distribution to promote a less inflammatory environment and improve lymphocyte function in CVMD.

Methods and results
Using mass spectrometry lipidomics, cellular, biochemical, and in vivo and ex vivo analyses, we investigated how eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), the main n-3PUFA, modify the trafficking patterns of activated CD4+ T cells. In mice subjected to allogeneic immunization, a 3-week n-3PUFA-enriched diet reduced the number of effector memory CD4+ T cells found in adipose tissue, and changed the profiles of eicosanoids, octadecanoids, docosanoids, endocannabinoids, 2-monoacylglycerols, N-acyl ethanolamines, and ceramides, in plasma, lymphoid organs, and fat tissues. These bioactive lipids exhibited differing chemotactic properties when tested in chemotaxis assays with activated CD4+ T cells in vitro. Furthermore, CD4+ T cells treated with EPA and DHA showed a significant reduction in chemokinesis, as assessed by trans-endothelial migration assays, and, when implanted in recipient mice, demonstrated less efficient migration to the inflamed peritoneum. Finally, EPA and DHA treatments reduced the number of polarized CD4+ T cells in vitro, altered the phospholipid composition of membrane microdomains and decreased the activity of small Rho GTPases, Rhoα, and Rac1 instrumental in cytoskeletal dynamics.

Conclusions
Our findings suggest that EPA and DHA affect the motility of CD4+ T cells and modify their ability to reach target tissues by interfering with the cytoskeletal rearrangements required for cell migration. This can explain, at least in part, the anti-inflammatory effects of n-3PUFA supporting their potential use in interventions aiming to address adipocyte low-grade inflammation associated with cardiovascular metabolic disease.
Emotional Functioning, Positive Relationships, and Language Use in Deaf Adults
Authors: Peñacoba Cecilia , Garvi Daniel , Gómez Lourdes , Álvarez Ana 
Published: August 2019

Abstract
This study aimed to explore emotional regulation, alexithymia, and interpersonal relations in a Spanish sample of 146 adult deaf participants and 146 typical hearing participants. For the deaf sample, the associations between type of language used and the above variables were also analyzed. Results showed that deaf participants scored higher on alexithymia and lower for positive relationships. However, no differences were found between deaf and typical hearing participants on emotional regulation. Regarding language use (Spanish Oral Language, SOL; Spanish Sign Language; or both), deaf participants used both languages in most contexts. Deaf participants who reported using SOL as their main mode of expression showed greater positive relationships than deaf participants who use both languages. Deaf participants who reported using both languages scored higher in emotional attention and emotional repair. These results evidence an association between the language use of deaf participants and alexithymia.
An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia
Authors: Dai Wenkui , Wang Heping , Zhou Qian , Li Dongfang , Feng Xin , Yang Zhenyu , Wang Wenjian , Qiu Chuangzhao , Lu Zhiwei , Xu Ximing , Lyu Mengxuan , Xie Gan , Li Yinhu , Bao Yanmin , Liu Yanhong , Shen Kunling , Yao Kaihu , Feng Xikang , Yang Yonghong , Zhou Ke , Li Shuaicheng , Zheng Yuejie 
Published: August 2019

Abstract

Background
The imbalanced respiratory microbiota observed in pneumonia causes high morbidity and mortality in childhood. Respiratory metagenomic analysis demands a comprehensive microbial gene catalogue, which will significantly advance our understanding of host–microorganism interactions.

Results
We collected 334 respiratory microbial samples from 171 healthy children and 76 children with pneumonia. The respiratory microbial gene catalogue we established comprised 2.25 million non-redundant microbial genes, covering 90.52% of prevalent genes. The major oropharyngeal microbial species found in healthy children were Prevotella and Streptococcus. In children with Mycoplasma pneumoniae pneumonia (MPP), oropharyngeal microbial diversity and associated gene numbers decreased compared with those of healthy children. The concurrence network of oropharyngeal microorganisms in patients predominantly featured Staphylococcus spp. and M. pneumoniae. Functional orthologues, which are associated with the metabolism of various lipids, membrane transport, and signal transduction, accumulated in the oropharyngeal microbiome of children with pneumonia. Several antibiotic resistance genes and virulence factor genes were identified in the genomes of M. pneumoniae and 13 other microorganisms reconstructed via metagenomic data. Although the common macrolide/β-lactam resistance genes were not identified in the assembled M. pneumoniae genome, a single-nucleotide polymorphism (A2063G) related to macrolide resistance was identified in a 23S ribosomal RNA gene.

Conclusions
The results of this study will facilitate exploration of unknown microbial components and host–microorganism interactions in studies of the respiratory microbiome. They will also yield further insights into the microbial aetiology of MPP.
Geo-clustered chronic affinity: pathways from socio-economic disadvantages to health disparities
Authors: Shin Eun Kyong , Kwon Youngsang , Shaban-Nejad Arash 
Published: August 2019

AbstractObjectiveOur objective was to develop and test a new concept (affinity) analogous to multimorbidity of chronic conditions for individuals at census tract level in Memphis, TN. The use of affinity will improve the surveillance of multiple chronic conditions and facilitate the design of effective interventions.MethodsWe used publicly available chronic condition data (Center for Disease Control and Prevention 500 Cities project), socio-demographic data (US Census Bureau), and demographics data (Environmental Systems Research Institute). We examined the geographic pattern of the affinity of chronic conditions using global Moran’s I and Getis-Ord Gi* statistics and its association with socio-economic disadvantage (poverty, unemployment, and crime) using robust regression models. We also used the most common behavioral factor, smoking, and other demographic factors (percent of the male population, percent of the population 67 years, and over and total population size) as control variables in the model.ResultsA geo-distinctive pattern of clustered chronic affinity associated with socio-economic deprivation was observed. Statistical results confirmed that neighborhoods with higher rates of crime, poverty, and unemployment were associated with an increased likelihood of having a higher affinity among major chronic conditions. With the inclusion of smoking in the model, however, only the crime prevalence was statistically significantly associated with the chronic affinity.ConclusionChronic affinity disadvantages were disproportionately accumulated in socially disadvantaged areas. We showed links between commonly co-observed chronic diseases at the population level and systematically explored the complexity of affinity and socio-economic disparities. Our affinity score, based on publicly available datasets, served as a surrogate for multimorbidity at the population level, which may assist policymakers and public health planners to identify urgent hot spots for chronic disease and allocate clinical, medical and healthcare resources efficiently.
Elevated Heterozygosity in Adults Relative to Juveniles Provides Evidence of Viability Selection on Eagles and Falcons
Authors: Doyle Jacqueline M , Willoughby Janna R , Bell Douglas A , Bloom Peter H , Bragin Evgeny A , Fernandez Nadia B , Katzner Todd E , Leonard Kolbe , DeWoody J Andrew 
Published: August 2019

AbstractViability selection yields adult populations that are more genetically variable than those of juveniles, producing a positive correlation between heterozygosity and survival. Viability selection could be the result of decreased heterozygosity across many loci in inbred individuals and a subsequent decrease in survivorship resulting from the expression of the deleterious alleles. Alternatively, locus-specific differences in genetic variability between adults and juveniles may be driven by forms of balancing selection, including heterozygote advantage, frequency-dependent selection, or selection across temporal and spatial scales. We use a pooled-sequencing approach to compare genome-wide and locus-specific genetic variability between 74 golden eagle (Aquila chrysaetos), 62 imperial eagle (Aquila heliaca), and 69 prairie falcon (Falco mexicanus) juveniles and adults. Although genome-wide genetic variability is comparable between juvenile and adult golden eagles and prairie falcons, imperial eagle adults are significantly more heterozygous than juveniles. This evidence of viability selection may stem from a relatively smaller imperial eagle effective population size and potentially greater genetic load. We additionally identify ~2000 single-nucleotide polymorphisms across the 3 species with extreme differences in heterozygosity between juveniles and adults. Many of these markers are associated with genes implicated in immune function or olfaction. These loci represent potential targets for studies of how heterozygote advantage, frequency-dependent selection, and selection over spatial and temporal scales influence survivorship in avian species. Overall, our genome-wide data extend previous studies that used allozyme or microsatellite markers and indicate that viability selection may be a more common evolutionary phenomenon than often appreciated.
Interpreting Crab Nebula’s synchrotron spectrum: two acceleration mechanisms
Authors: Lyutikov Maxim , Temim Tea , Komissarov Sergey , Slane Patrick , Sironi Lorenzo , Comisso Luca 
Published: August 2019

ABSTRACT
We outline a model of the Crab pulsar wind nebula with two different populations of synchrotron emitting particles, arising from two different acceleration mechanisms: (i) Component-I due to Fermi-I acceleration at the equatorial portion of the termination shock, with particle spectral index pI ≈ 2.2 above the injection break corresponding to γwindσwind ∼ 105, peaking in the ultraviolet (UV, γwind ∼ 102 is the bulk Lorentz factor of the wind, σwind ∼ 103 is wind magnetization); and (ii) Component-II due to acceleration at reconnection layers in the bulk of the turbulent Nebula, with particle index pII ≈ 1.6. The model requires relatively slow but highly magnetized wind. For both components, the overall cooling break is in the infrared at ∼0.01 eV, so that the Component-I is in the fast cooling regime (cooling frequency below the peak frequency). In the optical band, Component-I produces emission with the cooling spectral index of αo ≈ 0.5, softening towards the edges due to radiative losses. Above the cooling break, in the optical, UV, and X-rays, Component-I mostly overwhelms Component-II. We hypothesize that acceleration at large-scale current sheets in the turbulent nebula (Component-II) extends to the synchrotron burn-off limit of ϵs ∼ 100 MeV. Thus in our model acceleration in turbulent reconnection (Component-II) can produce both hard radio spectra and occasional gamma-ray flares. This model may be applicable to a broader class of high-energy astrophysical objects, like active galactic nuclei and gamma-ray burst jets, where often radio electrons form a different population from the high-energy electrons.
Rejuvenated galaxies with very old bulges at the origin of the bending of the main sequence and of the ‘green valley’
Authors: Mancini Chiara , Daddi Emanuele , Juneau Stéphanie , Renzini Alvio , Rodighiero Giulia , Cappellari Michele , Rodríguez-Muñoz Lucía , Liu Daizhong , Pannella Maurilio , Baronchelli Ivano , Franceschini Alberto , Bergamini Pietro , D’Eugenio Chiara , Puglisi Annagrazia 
Published: August 2019

ABSTRACT
We investigate the nature of star-forming galaxies with reduced specific star formation rate (sSFR) and high stellar masses, those ‘green valley’ objects that seemingly cause a reported bending, or flattening, of the star-forming main sequence. The fact that such objects host large bulges recently led some to suggest that the internal formation of bulges was a late event that induced the sSFRs of massive galaxies to drop in a slow downfall, and thus the main sequence to bend. We have studied in detail a sample of 10 galaxies at 0.45 &lt; z &lt; 1 with secure SFR from Herschel, deep Keck optical spectroscopy, and HST imaging from CANDELS allowing us to perform multiwavelength bulge to disc decomposition, and to derive star formation histories for the separated bulge and disc components. We find that the bulges hosted in these systems below main sequence are virtually all maximally old, with ages approaching the age of the Universe at the time of observation, while discs are young (〈 T50〉 ∼ 1.5 Gyr). We conclude that, at least based on our sample, the bending of the main sequence is, for a major part, due to rejuvenation, and we disfavour mechanisms that postulate the internal formation of bulges at late times. The very old stellar ages of our bulges suggest a number density of early-type galaxies at z = 1–3 higher than actually observed. If confirmed, this might represent one of the first direct validations of hierarchical assembly of bulges at high redshifts.
Evolution of relativistic thin discs with a finite ISCO stress – II. Late time behaviour
Authors: Mummery Andrew , Balbus Steven A 
Published: August 2019

ABSTRACT
We present solutions to the relativistic thin disc evolutionary equation using a modified description of the mean fluid flow within the disc. The model takes into account the effects of sub-circular velocities in the innermost disc regions, and resolves otherwise unsustainable behaviour present in simple finite innermost stable circular orbit (ISCO) stress disc models. We show that the behaviour of a relativistic thin disc evolving with a finite ISCO stress is comprised of three distinct stages which join the ordinarily distinct finite and vanishing ISCO stress solutions into a fully continuous model parametrization. The most important prediction of our model is the existence of an intermediate stage of ‘stalled accretion’, controlled by a single dimensionless parameter. The hallmarks of this evolutionary phase appear to have been seen in General Relativistic MHD simulations as well as in the late time X-ray observations of tidal disruption events, but dedicated simulations and extended observations are needed for a deeper understanding.
ATP/ADP modulates gp16–pRNA conformational change in the Phi29 DNA packaging motor
Authors: Cai Rujie , Price Ian R , Ding Fang , Wu Feifei , Chen Ting , Zhang Yunlong , Liu Guangfeng , Jardine Paul J , Lu Changrui , Ke Ailong 
Published: August 2019

AbstractPackaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA–gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a ‘Z’-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.
Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock
Authors: Schreiner William P , Pagliuso Delaney C , Garrigues Jacob M , Chen Jerry S , Aalto Antti P , Pasquinelli Amy E 
Published: August 2019

AbstractElevated temperatures activate a heat shock response (HSR) to protect cells from the pathological effects of protein mis-folding, cellular mis-organization, organelle dysfunction and altered membrane fluidity. This response includes activation of the conserved transcription factor heat shock factor 1 (HSF-1), which binds heat shock elements (HSEs) in the promoters of genes induced by heat shock (HS). The upregulation of protein-coding genes (PCGs), such as heat shock proteins and cytoskeletal regulators, is critical for cellular survival during elevated temperatures. While the transcriptional response of PCGs to HS has been comprehensively analyzed in a variety of organisms, the effect of this stress on the expression of non-coding RNAs (ncRNAs) has not been systematically examined. Here we show that in Caenorhabditis elegans HS induces up- and downregulation of specific ncRNAs from multiple classes, including miRNA, piRNA, lincRNA, pseudogene and repeat elements. Moreover, some ncRNA genes appear to be direct targets of the HSR, as they contain HSF-1 bound HSEs in their promoters and their expression is regulated by this factor during HS. These results demonstrate that multiple ncRNA genes respond to HS, some as direct HSF-1 targets, providing new candidates that may contribute to organismal survival during this stress.