bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic variability and connectivity of the Mexican long-nosed bat between two distant roosts
Authors: Pourshoushtari Roxanne D , Ammerman Loren K 
Published: October 2020

AbstractGenetic variability generally is associated with adaptive potential of species and can be assessed using microsatellite markers. Mexican long-nosed bats (Leptonycteris nivalis) are endangered, migratory nectarivores thought to be experiencing population declines. Despite historical and current tracking efforts, migratory connections among roost sites remain elusive. Our objective was to assess the genetic variability and connectivity of two of the most geographically separated populations of L. nivalis currently known—a mating roost in central Mexico used from September to March, and a maternity roost in western Texas used by adult females and their young from June to August. Twelve loci developed for L. yerbabuenae and four for Glossophaga soricina amplified L. nivalis DNA; of those 16 loci, seven (all from L. yerbabuenae) were useful in genetic analyses of 113 individuals. High levels of genetic variation in L. nivalis from the two sites were not significantly different and no substructure was detected between these two roost sites separated by more than 1,200 km. Further, we recovered evidence of close relationship (parent–offspring) in nine pairs of juveniles captured at the northern roost and adults from the southern roost, confirming a connection between the two locations. For this endangered species, the level of variation detected, the lack of a recent bottleneck, and estimates of effective population size, are encouraging for future recovery. Management plans aimed at conserving Mexican long-nosed bats should recognize the need for managing these bats as a single population and conserving foraging and roosting habitat along migratory routes to reduce population fragmentation.
Delayed mortality of males in Thylamys bruchi, a semelparous marsupial from the Monte Desert, Argentina
Authors: Albanese M Soledad , Ojeda Ricardo A , Astié Andrea A 
Published: October 2020

AbstractMale-only obligate semelparity is a well-studied reproductive strategy in some Australian marsupials. This strategy has not been documented in South American species, although semelparity in both sexes occurs in some Neotropical didelphids. The fat-tailed mouse opossum, Thylamys bruchi, is an endemic species of the temperate Monte Desert, in Argentina. Seasonality and predictability of resources are two of the attributes associated with habitats where marsupial semelparity has evolved, and both are characteristic of the Monte Desert. We aimed to characterize the life-history strategy of T. bruchi to explore if it can be considered a semelparous species. We studied a fat-tailed mouse opossum population for 7 years with two different capture techniques (Sherman traps and nest boxes). Thylamys bruchi showed strong seasonality in abundance, with the highest captures during summer and autumn. Reproduction and weaning coincided with the most favorable period of the year with respect to climate and resource availability. Every year we observed a single cohort with little overlap until weaning of young. After breeding, all adults disappeared from the population; however, unlike any other didelphids, males showed delayed mortality and died, along with females, after weaning. We found no evidence of survival to a second breeding season for either sex. We therefore propose T. bruchi as a desert-dwelling marsupial with a semelparous reproductive strategy. Because the severity of winters may be acting as an important constraint on the energetic balance of adults in this population, we propose that challenging climatic conditions, coupled with the seasonality and high predictability of food resources, may have contributed to the evolution of the extreme reproductive strategy in this didelphid marsupial.
Shoulder septic arthritis following routine influenza vaccination
Authors: Damisa Josiah , Zulkeefli Zereda , Rohman Lebur , Burton David 
Published: October 2020

Abstract
The UK vaccination guidelines state that skin cleansing is not essential in socially clean patients. This report discusses a 69-year-old type 2 diabetic patient with a 4-week history of left shoulder pain with no precipitating factors other than a ‘flu vaccination without having had skin alcohol cleansing. She sustained a swollen left painful shoulder. Aspiration fluid grew Staphylococcus aureus and imaging confirmed diagnosis of septic arthritis. She underwent shoulder debridement and was started on antibiotics. Imaging 6 months later shows the sequelae of septic arthritis. The patient had ongoing stiffness and pain at 6 months. This report raises the question of whether there needs to be a revision of routine skin cleansing practice before vaccinations in certain groups of individuals.
Sulfoxidation regulation of transcription factor NAC42 influences its functions in relation to stress-induced fruit ripening in banana
Authors: Yan Huiling , Jiang Guoxiang , Wu Fuwang , Li Zhiwei , Xiao Lu , Jiang Yueming , Duan Xuewu 
Published: October 2020

AbstractRedox modification of functional or regulatory proteins has emerged as an important mechanism of post-translational modification. However, the role of redox modifications of transcription factors mediated by methionine sulfoxide reductase (Msr) in regulating physiological processes in plants remains unclear, especially in fruit ripening. In this study, we determined that MaNAC42, a transcriptional activator, is involved in the regulation of fruit ripening in banana under oxidative stress. Integrated analysis of ChIP-qPCR and EMSA data showed that MaNAC42 directly binds to promoters of genes related to oxidative stress and ripening. Ectopic overexpression of MaNAC42 in Arabidopsis delays dark-induced senescence in leaves, indicating that MaNAC42 plays a negative role in senescence. Furthermore, we found that MaNAC42 is a target of MaMsrB2, a methionine sulfoxide reductase B. Methionine oxidation in MaNAC42 (i.e. sulfoxidation) or mimicking sulfoxidation by mutating methionine to glutamine both lead to decreased DNA-binding capacity and transcriptional activity. On the other hand, MaMsrB2 can partially repair oxidized MaNAC42 and restore its DNA-binding capacity. Thus, our results suggest a novel regulatory mechanism of fruit ripening in banana involving MaMsrB2-mediated redox regulation of the ripening-related transcription factor MaNAC42.
Regulation of glucosinolate biosynthesis
Authors: Mitreiter Simon , Gigolashvili Tamara 
Published: October 2020

AbstractGlucosinolates are secondary defense metabolites produced by plants of the order Brassicales, which includes the model species Arabidopsis and many crop species. In the past 13 years, the regulation of glucosinolate synthesis in plants has been intensively studied, with recent research revealing complex molecular mechanisms that connect glucosinolate production with responses to other central pathways. In this review, we discuss how the regulation of glucosinolate biosynthesis is ecologically relevant for plants, how it is controlled by transcription factors, and how this transcriptional machinery interacts with hormonal, environmental, and epigenetic mechanisms. We present the central players in glucosinolate regulation, MYB and basic helix–loop–helix transcription factors, as well as the plant hormone jasmonate, which together with other hormones and environmental signals allow the coordinated and rapid regulation of glucosinolate genes. Furthermore, we highlight the regulatory connections between glucosinolates, auxin, and sulfur metabolism and discuss emerging insights and open questions on the regulation of glucosinolate biosynthesis.
Effect of gibberellin-sensitive Rht18 and gibberellin-insensitive Rht-D1b dwarfing genes on vegetative and reproductive growth in bread wheat
Authors: Tang Ting , Botwright Acuña Tina , Spielmeyer Wolfgang , Richards Richard A 
Published: October 2020

Abstract
Gibberellin (GA)-insensitive dwarfing genes Rht-B1b and Rht-D1b that are responsible for the ‘Green Revolution’ have been remarkably successful in wheat improvement globally. However, these alleles result in shorter coleoptiles and reduced vigour, and hence poor establishment and growth in some environments. Rht18, on the other hand, is a GA-sensitive, dominant gene with potential to overcome some of the early growth limitations associated with Rht-B1b and Rht-D1b. We assessed progeny from both a biparental and a backcross population that contained tall, single dwarf, and double dwarf lines, to determine whether Rht18 differs from Rht-D1b and hence verify its value in wheat improvement. Progeny with Rht18 had an almost identical height to lines with Rht-D1b, and both were ~26% shorter than the tall lines, with the double dwarf 13% shorter again. However, coleoptile length of Rht18 was 42% longer than that of Rht-D1b. We detected no differences in time to terminal spikelet and anthesis, and few differences in stem or spike growth. Both dwarfing genes diverted more dry matter to the spike than tall lines from prior to heading. No differences were detected between Rht18 and Rht-D1b that could prevent the adoption of Rht18 in wheat breeding to overcome some of the limitations associated with the ‘Green Revolution’ genes.
Distribution of Si ii λ6355 velocities of Type Ia supernovae and implications for asymmetric explosions
Authors: Zhang Keto D , Zheng WeiKang , de Jaeger Thomas , Stahl Benjamin E , Brink Thomas G , Han Xuhui , Kasen Daniel , Shen Ken J , Tang Kevin , Filippenko Alexei V 
Published: October 2020

ABSTRACT
The ejecta velocity is a very important parameter in studying the structure and properties of Type Ia supernovae (SNe Ia) and is a candidate key parameter in improving the utility of SNe Ia for cosmological distance determinations. Here, we study the velocity distribution of a sample of 311 SNe Ia from the kaepora data base. The velocities are derived from the Si ii λ6355 absorption line in optical spectra measured at (or extrapolated to) the time of peak brightness. We statistically show that the observed velocity has a bimodal Gaussian distribution (population ratio 201:110 or 65 per cent:35 per cent) consisting of two groups of SNe Ia: Group I with a lower but narrower scatter ($11\, 000 \pm 700\, \mathrm{km\, s}^{-1}$), and Group II with a higher but broader scatter ($12\, 300 \pm 1800\, \mathrm{km\, s}^{-1}$). The true origin of the two components is unknown. Naturally, there could exist two intrinsic velocity distributions observed. However, we try to use asymmetric geometric models through statistical simulations to reproduce the observed distribution assuming that all SNe Ia share the same intrinsic distribution. In the two cases we consider, 35 per cent of SNe Ia are considered to be asymmetric in Case 1, and all SNe Ia are asymmetric in Case 2. Simulations for both cases can reproduce the observed velocity distribution but require a significantly large portion ($\gt 35{{\ \rm per\ cent}}$) of SNe Ia to be asymmetric. In addition, the Case 1 result is consistent with recent SNe Ia polarization observations that higher Si ii λ6355 velocities tend to be more polarized.
Evolution of the Earth’s atmosphere during Late Veneer accretion
Authors: Sinclair Catriona A , Wyatt Mark C , Morbidelli Alessandro , Nesvorný David 
Published: October 2020

ABSTRACT
Recent advances in our understanding of the dynamical history of the Solar system have altered the inferred bombardment history of the Earth during accretion of the Late Veneer, after the Moon-forming impact. We investigate how the bombardment by planetesimals left-over from the terrestrial planet region after terrestrial planet formation, as well as asteroids and comets, affects the evolution of Earth’s early atmosphere. We develop a new statistical code of stochastic bombardment for atmosphere evolution, combining prescriptions for atmosphere loss and volatile delivery derived from hydrodynamic simulations and theory with results from dynamical modelling of realistic populations of impactors. We find that for an initially Earth-like atmosphere, impacts cause moderate atmospheric erosion with stochastic delivery of large asteroids, giving substantial growth (× 10) in a few ${{\ \rm per\ cent}}$ of cases. The exact change in atmosphere mass is inherently stochastic and dependent on the dynamics of the left-over planetesimals. We also consider the dependence on unknowns including the impactor volatile content, finding that the atmosphere is typically completely stripped by especially dry left-over planetesimals ($\lt 0.02 ~ {{\ \rm per\ cent}}$ volatiles). Remarkably, for a wide range of initial atmosphere masses and compositions, the atmosphere converges towards similar final masses and compositions, i.e. initially low-mass atmospheres grow, whereas massive atmospheres deplete. While the final properties are sensitive to the assumed impactor properties, the resulting atmosphere mass is close to that of current Earth. The exception to this is that a large initial atmosphere cannot be eroded to the current mass unless the atmosphere was initially primordial in composition.
Cosmic rates of black hole mergers and pair-instability supernovae from chemically homogeneous binary evolution
Authors: du Buisson L , Marchant P , Podsiadlowski Ph , Kobayashi C , Abdalla F B , Taylor P , Mandel I , de Mink S E , Moriya T J , Langer N 
Published: October 2020

ABSTRACT
During the first three observing runs of the Advanced gravitational-wave detector network, the LIGO/Virgo collaboration detected several black hole binary (BHBH) mergers. As the population of detected BHBH mergers grows, it will become possible to constrain different channels for their formation. Here we consider the chemically homogeneous evolution (CHE) channel in close binaries, by performing population synthesis simulations that combine realistic binary models with detailed cosmological calculations of the chemical and star-formation history of the Universe. This allows us to constrain population properties, as well as cosmological and aLIGO/aVirgo detection rates of BHBH mergers formed through this pathway. We predict a BHBH merger rate at redshift zero of $5.8 \textrm {Gpc}^{-3} \textrm {yr}^{-1}$ through the CHE channel, to be compared with aLIGO/aVirgo’s measured rate of ${53.2}_{-28.2}^{+55.8} \text{Gpc}^{-3}\text{yr}^{-1}$, and find that eventual merger systems have BH masses in the range $17{-}43 \,\textrm {M}_{\odot }$ below the pair-instability supernova (PISN) gap, and ${\gt}124 \textrm {M}_{\odot }$ above the PISN gap. We investigate effects of momentum kicks during black hole formation, and calculate cosmological and magnitude limited PISN rates. We also study the effects of high-redshift deviations in the star formation rate. We find that momentum kicks tend to increase delay times of BHBH systems, and our magnitude limited PISN rate estimates indicate that current deep surveys should be able to detect such events. Lastly, we find that our cosmological merger rate estimates change by at most ${\sim}8{{\ \rm per\ cent}}$ for mild deviations of the star formation rate in the early Universe, and by up to ${\sim}40\,\text{per cent}$ for extreme deviations.
Asteroseismic modelling of solar-type stars: a deeper look at the treatment of initial helium abundance
Authors: Nsamba Benard , Moedas Nuno , Campante Tiago L , Cunha Margarida S , Hernández Antonio García , Suárez Juan C , Monteiro Mário J P F G , Fernandes João , Jiang Chen , Akinsanmi Babatunde 
Published: October 2020

ABSTRACT
Detailed understanding of stellar physics is essential towards a robust determination of stellar properties (e.g. radius, mass, and age). Among the vital input physics used in the modelling of solar-type stars which remain poorly constrained, is the initial helium abundance. To this end, when constructing stellar model grids, the initial helium abundance is estimated either (i) by using the semi-empirical helium-to-heavy element enrichment ratio, (ΔY/ΔZ), anchored to the standard big bang nucleosynthesis value, or (ii) by setting the initial helium abundance as a free variable. Adopting 35 low-mass, solar-type stars with multiyear Kepler photometry from the asteroseismic ‘LEGACY’ sample, we explore the systematic uncertainties on the inferred stellar parameters (i.e. radius, mass, and age) arising from the treatment of the initial helium abundance in stellar model grids. The stellar masses and radii derived from grids with free initial helium abundance are lower compared to those from grids based on a fixed ΔY/ΔZ ratio. We find the systematic uncertainties on mean density, radius, mass, and age arising from grids which employ a fixed value of ΔY/ΔZ and those with free initial helium abundance to be ∼ 0.9 per cent, ∼ 2 per cent, ∼ 5 per cent, and ∼ 29 per cent, respectively. We report that the systematic uncertainties on the inferred masses and radii arising from the treatment of initial helium abundance in stellar grids lie within the expected accuracy limits of ESA’s PLATO, although this is not the case for the age.
Genome Variation Map: a worldwide collection of genome variations across multiple species
Authors: Li Cuiping , Tian Dongmei , Tang Bixia , Liu Xiaonan , Teng Xufei , Zhao Wenming , Zhang Zhang , Song Shuhui 
Published: October 2020

Abstract
The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. It aims to collect and integrate genome variations for a wide range of species, accepts submissions of different variation types from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Compared with the previous version, particularly, a total of 22 species, 115 projects, 55 935 samples, 463 429 609 variants, 66 220 associations and 56 submissions (as of 7 September 2020) were newly added in the current version of GVM. In the current release, GVM houses a total of ∼960 million variants from 41 species, including 13 animals, 25 plants and 3 viruses. Moreover, it incorporates 64 819 individual genotypes and 260 393 manually curated high-quality genotype-to-phenotype associations. Since its inception, GVM has archived genomic variation data of 43 754 samples submitted by worldwide users and served &gt;1 million data download requests. Collectively, as a core resource in the National Genomics Data Center, GVM provides valuable genome variations for a diversity of species and thus plays an important role in both functional genomics studies and molecular breeding.
The Zebrafish Information Network: major gene page and home page updates
Authors: Howe Douglas G , Ramachandran Sridhar , Bradford Yvonne M , Fashena David , Toro Sabrina , Eagle Anne , Frazer Ken , Kalita Patrick , Mani Prita , Martin Ryan , Moxon Sierra Taylor , Paddock Holly , Pich Christian , Ruzicka Leyla , Schaper Kevin , Shao Xiang , Singer Amy , Van Slyke Ceri E , Westerfield Monte 
Published: October 2020

Abstract
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, gene and mutant nomenclature, and reagents. New features at ZFIN include major updates to the home page and the gene page, the two most used pages at ZFIN. Data including disease models, phenotypes, expression, mutants and gene function continue to be contributed to The Alliance of Genome Resources for integration with similar data from other model organisms.
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data
Authors: Watanabe Yu , Aoki-Kinoshita Kiyoko F , Ishihama Yasushi , Okuda Shujiro 
Published: October 2020

Abstract
For the reproducibility and sustainability of scientific research, FAIRness (Findable, Accessible, Interoperable and Re-usable), with respect to the release of raw data obtained by researchers, is one of the most important principles underpinning the future of open science. In genomics and transcriptomics, the sharing of raw data from next-generation sequencers is made possible through public repositories. In addition, in proteomics, the deposition of raw data from mass spectrometry (MS) experiments into repositories is becoming standardized. However, a standard repository for such MS data had not yet been established in glycomics. With the increasing number of glycomics MS data, therefore, we have developed GlycoPOST (https://glycopost.glycosmos.org/), a repository for raw MS data generated from glycomics experiments. In just the first year since the release of GlycoPOST, 73 projects have already been registered by researchers around the world, and the number of registered projects is continuously growing, making a significant contribution to the future FAIRness of the glycomics field. GlycoPOST is a free resource to the community and accepts (and will continue to accept in the future) raw data regardless of vendor-specific formats.
RNA as the stone guest of protein aggregation
Authors: Louka Alexandra , Zacco Elsa , Temussi Piero Andrea , Tartaglia Gian Gaetano , Pastore Annalisa 
Published: October 2020

Abstract
The study of prions as infectious aggregates dates several decades. From its original formulation, the definition of a prion has progressively changed to the point that many aggregation-prone proteins are now considered bona fide prions. RNA molecules, not included in the original ‘protein-only hypothesis’, are also being recognized as important factors contributing to the ‘prion behaviour’, that implies the transmissibility of an aberrant fold. In particular, an association has recently emerged between aggregation and the assembly of prion-like proteins in RNA-rich complexes, associated with both physiological and pathological events. Here, we discuss the historical rising of the concept of prion-like domains, their relation to RNA and their role in protein aggregation. As a paradigmatic example, we present the case study of TDP-43, an RNA-binding prion-like protein associated with amyotrophic lateral sclerosis. Through this example, we demonstrate how the current definition of prions has incorporated quite different concepts making the meaning of the term richer and more stimulating. An important message that emerges from our analysis is the dual role of RNA in protein aggregation, making RNA, that has been considered for many years a ‘silent presence’ or the ‘stone guest’ of protein aggregation, an important component of the process.