bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pontoscolex corethrurus:a Homeless Invasive Tropical Earthworm?
Authors: Ortíz-Ceballos Angel I. , Ortiz-Gamino Diana , Andrade-Torres Antonio , Pérez-Rodríguez Paulino , López-Ortega Maurilio 
Published: May 2019

SummaryThe presence of earthworm species in crop fields is as old as agriculture itself. The earthwormsPontoscolex corethrurus(invasive) andBalanteodrilus pearsei(native) are associated with the emergence of agriculture and sedentism in the region Amazon and Maya, respectively. Both species have shifted their preference from their natural habitat to the cropland niche; however, they contrast in terms of intensification of agricultural land use (anthropic impact to the symbiotic soil microbiome).P. corethrurusinhabits conventional agroecosystems (pesticides, herbicides, and fertilizers are applied to soil), whileB. pearseithrives in traditional agroecosystems (biological management of soil); that is,P. corethrurushas not yet been recorded in soils whereB. pearseidwells. The demographic behavior of these two earthworm species was assessed in the laboratory over 100 days, according to their origin (OE;P. corethrurusandB. pearsei) food quality (FQ; soil only, maize stubble, andMucuna pruriens), and soil moisture (SM; 25, 33, and 42%). The results showed that OE, FQ, SM, and the OE x FQ interaction were highly significant for the survival, growth, and reproduction of earthworms.P. corethrurusshowed a lower survival rate (> mortality).P. corethrurussurvivors fed a diet of low-to-intermediate nutritional quality (soil and corn stalks, respectively) showed a greater capacity to grow and reproduce; however, it was surpassed by the native earthworm when fed a high-quality diet (M. pruriens). Besides,P. corethrurusdisplayed a low cocoon hatching (emergence of juveniles). These results suggest that the presence of the invasive species was associated with the absence of natural mutualistic bacteria (gut, nephridia, and cocoons), and with a negative interaction with the soil microbiota where the native species dwells. These results are consistent with the absence ofP. corethrurusin milpa and pasture-type agricultural niches managed by peasants (agroecologists) to grow food regularly a biological management of soil. The results reported here and the published information jointly (e.g., designation of the neotype and ambiguity of the place of origin) jointly suggest thatP. corethrurusis an invasive species that is neither wild nor domesticated, that is, its eco-evolutionary phylogeny needs to be derived based on its symbionts.
Genetic characterization of a recombinant myxoma virus leap into the Iberian hare (Lepus granatensis)
Authors: Águeda-Pinto Ana , de Matos Ana Lemos , Abrantes Mário , Kraberger Simona , Risalde Maria A. , Gortázar Christian , McFadden Grant , Varsani Arvind , Esteves Pedro J. 
Published: May 2019

AbstractMyxomatosis is a lethal disease of wild European and domestic rabbits (Oryctolagus cuniculus) caused by a Myxoma virus (MYXV) infection, a leporipoxvirus that is found naturally in someSylvilagusrabbit species in South America and California. The introduction of MYXV in the early 1950s into feral European rabbit populations in Australia and Europe demonstrate the best documented field example of host-virus coevolution following a cross-species transmission. Recently, a new cross-species jump of MYXV has been suggested in both Great Britain and Spain, where European brown hares (Lepus europaeus) and Iberian hares (Lepus granatensis) were found dead with lesions consistent with those observed in myxomatosis. To investigate the possibility of a new cross-species transmission event by MYXV, tissue samples collected from a wild Iberian hare found dead in Spain (Toledo region) were analyzed and deep sequenced. Our results report a new MYXV strain (MYXV Toledo) in the tissues of this species. The genome of this new strain encodes three disrupted genes (M009L,M036LandM152R) and a novel 2.8 KB recombinant region that resulted from an insertion of four novel poxviral genes towards the 5’ end of its genome. From the open reading frames inserted into the MYXV Toledo strain, a new orthologue of a poxvirus host range gene family member was identified which is related to the MYXV geneM064R. Overall, we confirmed the identity of a new MYXV strain in Iberian hares that we hypothesize was able to more effectively counteract the host defenses in hares and start an infectious process in this new host.
A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium
Authors: Barupal Dinesh K , Zhang Ying , Shen Tong , Fan Sili , Roberts Bryan S , Fitzgerald Patrick , Wancewicz Benjamin , Valdiviez Luis , Wohlgemuth Gert , Byram Gregory , Choy YingYng , Haffner Bennett , Showalter Megan R. , Vaniya Arpana , Bloszies Clayton S , Folz Jacob S , Kind Tobias , Fiehn Oliver 
Published: May 2019

AbstractMouse knockouts allow studying gene functions. Often, multiple phenotypes are impacted when a gene is inactivated. The International Mouse Phenotyping Consortium (IPMC) has generated thousands of mouse knockouts and catalogued their phenotype data. We have acquired metabolomics data from 220 plasma samples of 30 mouse gene knockouts and corresponding wildtype mice from IMPC. To acquire comprehensive metabolomics data, we have used liquid chromatography (LC) combined with mass spectrometry (MS) for detecting polar and lipophilic compounds in an untargeted approach. We have also used targeted methods to measure bile acids, steroids and oxylipins. In addition, we have used gas chromatography GC-TOFMS for measuring primary metabolites. The metabolomics dataset reports 832 unique structurally identified metabolites from 124 chemical classes as determined by ChemRICH software. The GCMS and LCMS raw data files, intermediate and finalized data matrices, R-Scripts, annotation databases and extracted ion chromatograms are provided in this data descriptor. The dataset can be used for subsequent studies to link genetic variants with molecular mechanisms and phenotypes.Data SetThe dataset is available at the MetabolomicsWorkbench repository (accession ID: ST001154)Data Set Licenselicense under which the data set is made available (CC0).
Proteomics Standards Initiative Extended FASTA Format (PEFF)
Authors: Binz Pierre-Alain , Shofstahl Jim , Vizcaíno Juan Antonio , Barsnes Harald , Chalkley Robert J. , Menschaert Gerben , Alpi Emanuele , Clauser Karl , Eng Jimmy K. , Lane Lydie , Seymour Sean L. , Sánchez Luis Francisco Hernández , Mayer Gerhard , Eisenacher Martin , Perez-Riverol Yasset , Kapp Eugene A. , Mendoza Luis , Baker Peter R. , Collins Andrew , Van Den Bossche Tim , Deutsch Eric W. 
Published: May 2019

AbstractMass spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs), in biological samples. However, most workflows require that such variations be included in the search space used to analyze the data, and doing so remains challenging with most analysis tools. In order to facilitate the search for known sequence variants and PTMs, the Proteomics Standards Initiative (PSI) has designed and implemented the PSI Extended FASTA Format (PEFF). PEFF is based on the very popular FASTA format but adds a uniform mechanism for encoding substantially more metadata about the sequence collection as well as individual entries, including support for encoding known sequence variants, PTMs, and proteoforms. The format is very nearly backwards compatible, and as such, existing FASTA parsers will require little or no changes to be able to read PEFF files as FASTA files, although without supporting any of the extra capabilities of PEFF. PEFF is defined by a full specification document, controlled vocabulary terms, a set of example files, software libraries, and a file validator. Popular software and resources are starting to support PEFF, including the sequence search engine Comet and the knowledge bases neXtProt and UniProtKB. Widespread implementation of PEFF is expected to further enable proteogenomics and top-down proteomics applications by providing a standardized mechanism for encoding protein sequences and their known variations. All the related documentation, including the detailed file format specification and example files, are available athttp://www.psidev.info/peff.
The swim-up technique separates bovine sperm by metabolic rates, motility and tail length
Authors: Magdanz Veronika , Boryshpolets Sergii , Ridzewski Clara , Eckel Barbara , Reinhardt Klaus 
Published: May 2019

AbstractSwim-up is a sperm purification method that is being used daily in andrology labs around the world as a simple step forin vitrosperm selection. This method accumulates the most motile sperm in the upper fraction and leaves sperm with low or no motility in the lower fraction but the underlying reasons are not fully understood. In this article, we compare metabolic rate, motility and sperm tail length of bovine sperm cells of the upper and lower fraction. The metabolic assay platform reveals oxygen consumption rates and extracellular acidification rates simultaneously and thereby delivers the metabolic rates in real time. Our study confirms the upper fraction of bull sperm has improved motility compared to the cells in the lower fraction and shows higher metabolic rates. This pattern was consistent across media of two different levels of viscosity. Sperm with longer flagella are selected in the upper fraction. We conclude that the motility-based separation of the swim-up technique is based on metabolic differences. Metabolic assays could serve as additional or alternative, label-free method to evaluate sperm quality, which is likely particularly useful in cases of asthenozoospermia and teratospermia. Furthermore, metabolic measurements of sperm cells can reveal differences in metabolic pathways in different environments.
Glomerulosclerosis and kidney failure in a mouse model of monoclonal immunoglobulin light-chain deposition disease
Authors: Bender Sébastien , Ayala Maria Victoria , Bonaud Amélie , Javaugue Vincent , Carrion Claire , Oblet Christelle , Rinsant Alexia , Quellard Nathalie , Kaaki Sihem , Oruc Zeliha , Boyer François , Paquet Agnès , Pons Nicolas , Hervé Bastien , Ashi Mohamad Omar , Jaccard Arnaud , Delpy Laurent , Touchard Guy , Cogné Michel , Bridoux Frank , Sirac Christophe 
Published: May 2019

AbstractLight chain deposition disease (LCDD) is a rare disorder characterized by glomerular and peritubular amorphous deposits of a monoclonal immunoglobulin (Ig) light chain (LC), leading to nodular glomerulosclerosis and nephrotic syndrome. We developed a transgenic model using site-directed insertion of the variable domain of a pathogenic human LC gene into the mouse Ig kappa locus, ensuring its production by all plasma cells. High free LC levels were achieved after backcrossing with mice presenting increased plasma cell differentiation and no Ig heavy chain (HC) production. Our mouse model recapitulates the characteristic features of LCDD, including progressive glomerulosclerosis, nephrotic-range proteinuria and finally, kidney failure. The variable domain of the LC bears alone the structural properties involved in its pathogenicity. RNA sequencing conducted on plasma cells demonstrated that LCDD LC induces endoplasmic reticulum stress, likely accounting for the high efficiency of proteasome inhibitor-based therapy. Accordingly, reduction of circulating pathogenic LC was efficiently achieved and not only preserved renal function, but partially reversed kidney lesions. Finally, transcriptome analysis of pre-sclerotic glomeruli revealed that proliferation and extracellular matrix remodelling represented the first steps of glomerulosclerosis, paving the way for future therapeutic strategies in LCDD and other kidney diseases featuring diffuse glomerulosclerosis, particularly diabetic nephropathy.
In vivo functional diversity of midbrain dopamine neurons within identified axonal projections
Authors: Farassat Navid , Costa Kauê M. , Albert Stefan , Kovacheva Lora , Shin Josef , Somayaji Mahalakshmi , Schneider Gaby , Roeper Jochen 
Published: May 2019

AbstractThe functional diversity of midbrain dopamine (DA) neurons ranges across multiple scales, from differences in intrinsic properties and synaptic connectivity to selective task engagement in behaving animals. Distinct in vitro biophysical features of DA neurons have been associated with different axonal projection targets. However, it is unknown how this translates to different firing patterns of projection-defined DA subpopulations in the intact brain. We combined retrograde tracing with single-unit recording and juxtacellular labelling in mouse brain to create the first single cell-resolved in vivo functional topography of the midbrain DA system. We identified surprising differences in burst firing among those DA neurons projecting to dorsolateral striatum, which were organized along the medio-lateral substantia nigra (SN) axis. Furthermore, burst properties also differentiated DA neurons in the medial SN that projected either to dorsal or ventral striatum. In contrast, DA neurons projecting to lateral shell of nucleus accumbens displayed identical firing properties, irrespective of whether they were located in the SN or ventral tegmental area (VTA), thus breaching classical anatomical boundaries. Finally, we found robust differences in mean firing rates and pause durations among VTA DA neurons projecting to either lateral or medial shell of nucleus accumbens. Together, our data set establishes a high-resolution functional landscape of midbrain DA neurons, which will facilitate the identification of selective functions and pathophysiological changes within the midbrain DA system.
Multilevel selection in groups of groups
Authors: Pruitt Jonathan N. , Fisher David N. , Costa-Pereira Raul , Pinter-Wollman Noa 
Published: May 2019

AbstractNatural selection occurs at many levels. We evaluated selection acting on collectives at a level of multilevel selection analysis not yet quantified: within and between clusters of groups. We did so by monitoring the performance of natural colonies of social spiders with contrasting foraging aggressiveness in clusters of various sizes. Within-clusters, growth rates were suppressed when colonies were surrounded by more rival groups, conveying that competition is greater. When colonies were surrounded by few rivals, the more aggressive colonies in a cluster were more successful. In contrast, relatively non-aggressive colonies performed better when surrounded by many rivals. Patterns of selection between-clusters depended on the performance metric considered, but cluster-wide aggressiveness was always favored in small clusters. Together, selection both within-and between natural clusters of colonies was detectable, but highly contingent on the number of competing colonies.
Pupillary dilation responses as a midlife indicator of risk for Alzheimer’s Disease: Association with Alzheimer’s disease polygenic risk
Authors: Kremen William S. , Panizzon Matthew S. , Elman Jeremy A. , Granholm Eric L. , Andreassen Ole A. , Dale Anders M. , Gillespie Nathan A. , Gustavson Daniel E. , Logue Mark W. , Lyons Michael J. , Neale Michael C. , Reynolds Chandra A. , Whitsel Nathan , Franz Carol E. 
Published: May 2019

ABSTRACTPathological changes in Alzheimer’s disease (AD) begin decades before dementia onset. Because locus coeruleus tau pathology is the earliest occurring AD pathology, targeting indicators of locus coeruleus (dys)function may improve midlife screening for earlier identification of AD risk. Pupillary responses during cognitive tasks are driven by the locus coeruleus and index cognitive effort. Several findings suggest task-associated pupillary response as an early marker of AD risk. Requiring greater effort suggests being closer to one’s compensatory capacity, and adults with mild cognitive impairment (MCI) have greater pupil dilation during digit span tasks than cognitively normal individuals, despite equivalent task performance. Higher AD polygenic risk scores (AD-PRSs) are associated with increased odds of MCI and tau positivity. We hypothesized that AD-PRSs would be associated with pupillary responses in cognitively normal middle-aged adults. We demonstrated that pupillary responses during digit span tasks were heritable (h2=.30-.36) in 1119 men ages 56-66. We then examined associations between AD-PRSs and pupillary responses in a cognitively normal subset who all had comparable span capacities (n=539). Higher AD-PRSs were associated with greater pupil dilation/effort in a high (9-digit recall) cognitive load condition; Cohen’s d=.36 for the upper versus lower quartile of the AD-PRS distribution. Results held up after controlling for APOE genotype. The results support pupillary response—and by inference, locus coeruleus dysfunction—as a genetically-mediated biomarker of early MCI/AD risk. In some studies, cognition predicted disease progression earlier than biomarkers. Pupillary responses might improve screening and early identification of genetically at-risk individuals even before cognitive performance declines.
When do individuals maximize their inclusive fitness?
Authors: Lehmann Laurent , Rousset François 
Published: May 2019

AbstractAdaptation is often described in behavioral ecology as individuals maximizing their inclusive fitness. Under what conditions does this hold and how does this relate to the gene-centered perspective of adaptation? We unify and extend the literature on these questions to class-structured populations. We demonstrate that the maximization (in the best-response sense) of class-specific inclusive fitness obtains in uninvadable population states (meaning that all deviating mutant go extinct). This defines a genuine actor-centered perspective on adaptation. But this inclusive fitness is assigned to all bearers of a mutant allele in a given class and depends on distributions of demographic and genetic contexts. These distributions, in turn, usually depend on events in previous generations and are thus not under individual control. This prevents, in general, from envisioning individuals themselves as autonomous fitness-maximizers, each with its own inclusive fitness. For weak selection, however, the dependence on earlier events can be neglected. We then show that each individual in each class appears to maximize its own inclusive fitness when all other individuals exhibit fitness-maximizing behavior. This defines a genuine individual-centered perspective of adaptation and justifies formally, as a first-order approximation, the long-heralded view of individuals appearing to maximize their own inclusive fitness.
Single-cell chromatin accessibility analysis of mammary gland development reveals cell state transcriptional regulators and cellular lineage relationships
Authors: Chung Chi-Yeh , Ma Zhibo , Dravis Christopher , Preissl Sebastian , Poirion Olivier , Luna Gidsela , Hou Xiaomeng , Giraddi Rajshekhar R. , Ren Bing , Wahl Geoffrey M. 
Published: May 2019

SummaryIt has only recently become possible to obtain single-cell level resolution of the epigenetic changes that occur during organ development. We reasoned that precision single-cell chromatin accessibility mapping of mammary gland development could provide needed insight into the epigenetic reprogramming and transcriptional regulators involved in normal mammary gland development. Here, we provide the first single-cell resource of chromatin accessibility for murine mammary development from the peak of fetal mammary stem cell (fMaSC) functional activity in late embryogenesis to the differentiation of adult basal and luminal cells. We find that the chromatin landscape within individual cells predicts both gene accessibility and transcription factor activity, and we present a web application as a scientific resource for facilitating future analyses. Strikingly, these single-cell chromatin profiling data reveal that fMaSCs can be separated into basal-like and luminal-like lineages, providing evidence of early lineage segregation prior to birth. Such distinctions were not evident in analyses of single-cell transcriptomic data.
A VEGF reaction-diffusion mechanism that selects variable densities of endothelial tip cells
Authors: Bedell W. , Stroock A. D. 
Published: May 2019

AbstractThe patterned differentiation of endothelial cells into tip and stalk cells represents an important step in the process of angiogenic sprouting. Vascular biologists hypothesize that changes in the density and overall structure of the vasculature can be traced in part to changes in the number of tip cells selected in the endothelium prior to sprout formation. However, the dominant hypotheses for tip cell selection invoke lateral inhibition via Notch; this juxtacrine mechanism predicts that a fixed fraction of endothelial cells become tip cells through a pattern-forming instability. Here, we present and analyze a hypothetical mechanism for tip cell selection that is based on endothelial competition for diffusible vascular endothelial growth factor (VEGF); this mechanism predicts that variable densities of tip cells emerge depending on the local (paracrine) production rate of VEGF. First, we hypothesize a network of VEGF signaling and trafficking based on previous experimental findings that could allow internalization of VEGF to occur with positive feedback. We formalize the hypothesis into a set of nonlinear ordinary differential equations and perform linear stability analysis to elucidate a general criterion for tip cell pattern formation under the mechanism. We use numerical integration to explore the nonlinear dynamics and final steady-states of tip cell patterns under this mechanism; the observed density of tip cells can be tuned from 10% to 84%. We conclude with proposals of future experiments and computational studies to explore how competitive consumption of diffusible VEGF may play a role in determining vascular structure.Statement of SignificanceThe patterned differentiation of endothelial cells into tip and stalk cells represents an important step in the process of blood vessel growth. Vascular biologists hypothesize that changes in the density and overall structure of the vasculature can be traced in part to changes in the number of tip cells selected during angiogenesis. However, the dominant hypotheses for tip cell selection predict that a locally fixed fraction of endothelial cells become tip cells following stimulation by vascular endothelial growth factor (VEGF). Here, we present and analyze a hypothetical mechanism for tip cell selection based on endothelial competition for diffusible VEGF; this mechanism predicts that variable densities of tip cells emerge depending on the local production rate of VEGF.