bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic analysis of 1,298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas
Authors: Machado Fabricio Brum , Moharana Kanhu C. , Almeida-Silva Fabricio , Gazara Rajesh K. , Pedrosa-Silva Francisnei , Coelho Fernanda S. , Grativol Clícia , Venancio Thiago M. 
Published: December 2019

AbstractSoybean (Glycine max[L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the past five years generated an enormous amount of RNA-seq data, encompassing various tissues, developmental conditions, and genotypes. In this study, we have collected data from 1,298 publicly available soybean transcriptome samples, processed the raw sequencing reads, and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52,737/56,044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground, and seed/seed-related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1,349 genes showed heavily biased expression patterns towards particular tissues. A transcript-level analysis revealed that 95% (70,963/74,490) of the known transcripts overlap with those reported here, whereas 3,256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user-friendly web interface athttp://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.
Germlinede novomutation rates on exons versus introns in humans
Authors: Rodriguez-Galindo Miguel , Casillas Sònia , Weghorn Donate , Barbadilla Antonio 
Published: December 2019

AbstractA main assumption of molecular population genetics is that genomic mutation rate does not depend on sequence function. Challenging this assumption, a recent study has found a reduction in the mutation rate in exons compared to introns in somatic cells. This reduction was ascribed to an enhanced exonic mismatch repair system activity. If this reduction happens also in the germline, it can compromise studies of population genomics, including the detection of the footprint of selection when using introns as proxies of neutrality. Here we compiled and analyzed published germlinede novomutation (DNM) data to test if the exonic mutation rate is also reduced in germ cells. We detected ascertainment bias in studies using DNM data from diseased probands and investigated the impact of extended nucleotide context onde novomutation rate. After controlling for these factors, we found no reduction in the mutation rate in exons compared to introns in the germline genome, in contrast to what has been previously described in somatic cells. Therefore, there is no evidence of an enhanced mismatch repair system activity in exons with respect to adjacent introns in germline cells.
Anin vitroquantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias
Authors: Wilson Jennifer L. , Lu Dan , Corr Nick , Fullerton Aaron , Lu James 
Published: December 2019

AbstractMyelosuppression is one of the most common and severe adverse events associated with anti-cancer therapies and can be a source of drug attrition. Current mathematical modeling methods for assessing cytopenia risk rely on indirect measurements of drug effects and primarily focus on single lineage responses to drugs. However, anti-cancer therapies have diverse mechanisms with varying degrees of effect across hematopoietic lineages. To improve predictive understanding of drug-induced myelosuppression, we developed a quantitative systems pharmacology (QSP) model of hematopoiesisin vitrofor quantifying the effects of anti-cancer agents on multiple hematopoietic cell lineages. We calibrated the system parameters of the model to cell kinetics data without treatment and then validated the model by showing that the inferred mechanisms of anti-proliferation and/or cell-killing are consistent with the published mechanisms for three classes of drugs with different mechanisms of action. Using a set of compounds as a sample set, we then analyzed novel compounds to predict their mechanisms and magnitude of myelosuppression. Further, these quantitative mechanisms are valuable for the development of translationalin vivomodels to predict clinical cytopenia effects.Author SummaryReduced bone marrow activity and levels of mature blood cells is an undesirable side effect of many anti-cancer therapies. Selecting promising lead compounds for further development requires understanding of potential myelosuppressive effects. However, existing preclinical experiments and modeling formulations fail to consider drug effects on multiple blood cell types or the mechanistic differences between how drugs induced myelosuppression. Here we developed a quantitative systems pharmacology (QSP) model that estimates a drug candidate’s effect on multiple precursor and mature blood cell lineages and further distinguishes how the drug affects these populations - through cell-killing or anti-proliferation mechanisms. This modeling formalism is valuable for vetting compounds for therapeutic development and for further translational modeling to anticipate the clinical effects of compounds.
Handling and Packaging of Medical Bags at the Acute Disaster Site Under High Temperature Conditions
Authors: Ando Wataru , Imamura Yumika , Nagashima Hideyuki , Kondo Kouji , Nakamura Kazunori , Otori Katsuya 
Published: December 2019

AbstractThe handling of medical bags in high temperature disaster sites has not been fully evaluated. In this study, medical bags were assessed in the closed, semi-opened, and opened state, with and without heat insulating material (HIM) and a coolant. The bags were heated for 300 minutes at 35 or 40°C, and the internal temperature was measured. closed and semi-opened bags were able to limit temperature increases in the central part of the bag at both 35 and 40°C to a greater extent than opened bags. When coolant and HIM were used in closed and semi-opened bags, the internal temperature was significantly lower than that seen in the opened state at 40°C (P < 0.01 and P < 0.001, respectively). In conclusion, in high temperature disaster sites, medical bags should be maintained in a semi-opened or closed state using a HIM and coolant.
Soil solution in Swiss forest stands: a 20 year’s time series
Authors: Braun Sabine 
Published: December 2019

AbstractThe chemistry of the soil solution is influenced by atmospheric deposition of air pollutants, by exchange processes between the soil matrix and the soil solution and by processes between the rhizosphere and the soil. At sites of the Intercantonal Long-term Forest Observation Programme in Switzerland the soil solution has been monitored since 1998 in a number of forest plots growing from 9 to 47 sites in a wide range of soil conditions and air pollution impacts. The results show various site-specific developments of soil acidification. At sites with already advanced acidification (pH < 4.2), the acidification indicators remained rather stable at high levels, possibly due to the high buffering capacity of the aluminum buffer (pH 4.2 – 3.8). In contrast, in less acidified sites the acidification still progressed further which is reflected by e.g. the ongoing decrease of the base cation to aluminum ratio. Main driver of the acidification is the high N deposition which provokes cation loss and impedes sustainable nutrient balances for tree nutrition in the majority of plots examined. On an average for the years 2005-2017, N leaching rates were 9.4 kg N ha-1yr-1, ranging from 0.04 to 53 kg N ha-1yr-1. Three plots with high N input show very low N leaching, suggesting that N leaching may not always be a good eutrophication indicator. Both N deposition and N leaching have decreased since the year 2000 but the latter trend is partly also due to increased drought.
Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity
Authors: Ghosh Arpan C. , Tattikota Sudhir G. , Liu Yifang , Comjean Aram , Hu Yanhui , Barrera Victor , Ho Sui Shannan J. , Perrimon Norbert 
Published: December 2019

AbstractPDGF/VEGF ligands regulate a plethora of biological processes in multicellular organisms via autocrine, paracrine and endocrine mechanisms. Here, we investigated organ-specific roles of Drosophila PDGF/VEGF-like factors (Pvfs). We combine genetic approaches and single-nuclei sequencing to demonstrate that muscle-derived Pvf1 signals to the Drosophila hepatocyte-like cells/oenocytes to suppress lipid synthesis by activating the Pi3K/Akt1/mTOR signaling cascade in the oenocytes. Additionally, we show that this signaling axis regulates the rapid expansion of adipose tissue lipid stores observed in newly eclosed flies. Flies emerge after pupation with limited adipose tissue lipid stores and lipid levels are progressively restored via lipid synthesis. We find that pvf1 expression in the adult muscle increase rapidly during this stage and that muscle-to-oenocyte Pvf1 signaling inhibits restoration of adipose tissue lipid stores as the process reaches completion. Our findings provide the first evidence in a metazoan of a PDGF/VEGF ligand acting as a myokine that regulates systemic lipid homeostasis by activating mTOR in hepatocyte-like cells.HighlightsMuscle specific Pvf1 protects mature adult flies from obesitySingle-nuclei RNA sequencing reveals that PvR, the receptor for Pvf1, is highly expressed in the Drosophila hepatocyte-like cells/oenocytes.PvR is required specifically in oenocytes to protect adult flies from obesityMuscle-to-oenocyte Pvf1 signaling activates PvR/Pi3K/Akt1/mTOR in the oenocytes to suppress lipid synthesisMuscle-derived Pvf1 helps terminate the rapid expansion of adipose tissue lipid stores in newly eclosed flies
Effect of oral administration of 1,3-1,6 β-glucans in DWV naturally infected newly emerged bees (Apis mellifera L.)
Authors: Antonio Felicioli , Mario Forzan , Simona Sagona , Paola D’agostino , Baido Diego , Baldassare Fronte , Maurizio Mazzei 
Published: December 2019

AbstractHoneybee pathogens have an important role in honeybee colony mortality and colony losses, most of them are widely spread and necessitate worldwide solutions to contrast honeybee’s decline. Possible accepted solutions to cope with the spread of honeybee’s pathogen are focused on the study of experimental protocols to enhance the insect’s immune defences. Honeybee’s artificial diet capable to stimulate the immune system is a promising field of investigation as ascertained by the introduction of 1,3-1,6 β-glucans as a dietary supplement. In this work, by collecting faecal samples of honeybees exposed to different dietary conditions of 1,3-1,6 β-glucans (0.5% and 2% w/w), it has been possible to investigate the DWV viral load kinetic without harming the insects. Virological data obtained by a one-step TaqMan RT-PCR highlights the ability of 1,3-1,6 β-glucans to reduce the viral load at 24thday of rearing. Furthermore, results indicated that the diet supplemented with 1,3-1,6 β-glucans was associated with a dose-dependent activation of phenoloxidase. Control group showed a higher survival rate than honeybees exposed to different dietary conditions of 1,3-1,6 β-glucans while no differences have been observed concerning syrup daily consumption.
GCNG: Graph convolutional networks for inferring cell-cell interactions
Authors: Yuan Ye , Bar-Joseph Ziv 
Published: December 2019

AbstractSeveral methods have been developed for inferring gene-gene interactions from expression data. To date, these methods mainly focused on intra-cellular interactions. The availability of high throughput spatial expression data opens the door to methods that can infer such interactions both within and between cells. However, the spatial data also raises several new challenges. These include issues related to the sparse, noisy expression vectors for each cell, the fact that several different cell types are often profiled, the definition of a neighborhood of cell and the relatively small number of extracellular interactions. To enable the identification of gene interactions between cells we extended a Graph Convolutional Neural network approach for Genes (GCNG). We encode the spatial information as a graph and use the network to combine it with the expression data using supervised training. Testing GCNG on spatial transcriptomics data we show that it improves upon prior methods suggested for this task and can propose novel pairs of extracellular interacting genes. Finally, we show that the output of GCNG can also be used for down-stream analysis including functional assignment.Supporting website with software and data:https://github.com/xiaoyeye/GCNG.
Two distinct bacterial biofilm components trigger metamorphosis in the colonial hydrozoanHydractinia echinata
Authors: Guo Huijuan , Rischer Maja , Westermann Martin , Beemelmanns Christine 
Published: December 2019

AbstractIn the marine environment bacterial-induced metamorphosis of larvae is a widespread cross-kingdom communication phenomenon and critical for the persistence of many marine invertebrates. However, the identities of most inducing bacterial signals and the underlying cellular mechanisms remain enigmatic. Larvae ofHydractinia echinataprovide an excellent model for investigating bacteria-stimulated settlement as they transform upon detection of the signal into the colonial adult stage within 24 h. AlthoughH. echinataserved as cell biological model system for decades, the influence of bacterial signals on the morphogenic transition remained largely unexplored. Using a bioassay-guided analysis, we first identified that specific bacterial (lyso)phospholipids, naturally present in bacterial biofilms, elicit metamorphosis inHydractinialarvae in a dose-response matter. In particular, lysophospholipids as single compounds or in combinations at 50 µM concentrations induced metamorphosis in up to 50% of all larvae phospholipid within 48 h. By using fluorescence-labeled bacterial phospholipids, we demonstrated their incorporation into the larval membranes, where interactions with internal signaling cascades could occur. In addition, two structurally distinct exopolysaccharides, the newly identified Rha-Man polysaccharide fromPseudoalteromonassp. P1-9 and curdlan fromAlcaligenes faecaliscaused up to 75% of all larvae to transform within 24 h. We also found that combinations of (lyso)phospholipids and curdlan induced the transformation in almost all larvae within 24 h, thereby exceeding the morphogenic activity observed for single compounds and axenic bacterial biofilms. Our results demonstrate that multiple and structurally distinct bacterial-derived metabolites converge to induce high transformation rates ofHydractinialarvae, which might ensure optimal habitat selection despite the general widespread occurrence of both compound classes.Significance StatementBacterial biofilms profoundly influence the recruitment and settlement of marine invertebrates, critical steps for diverse marine processes such as coral reef formation, marine fisheries and the fouling of submerged surfaces. Yet, the complex composition of biofilms often makes it challenging to characterize the individual signals and regulatory mechanisms. Developing tractable model systems to characterize these co-evolved interactions is the key to understand fundamental processes in evolutionary biology. Here, we characterized for the first time two types of bacterial signaling molecules that induce the morphogenic transition and analyzed their abundance and combinatorial activity. This study highlights the crucial role of the converging activity of multiple bacterial signals in development-related cross-kingdom signaling.AreasMajor: Chemical Biology, Microbiology, Developmental Biology
A novel mouse model expressing human forms for complement receptorsCR1andCR2
Authors: Jackson Harriet M. , Foley Kate E. , O’Rourke Rita , Stearns Timothy M. , Fathalla Dina , Morgan B Paul , Howell Gareth R. 
Published: December 2019

AbstractThe complement cascade is increasingly implicated in development of a variety of diseases with strong immune contributions such as Alzheimer’s disease and Systemic Lupus Erythematosus. Mouse models have been used to determine function of central components of the complement cascade such as C1q and C3. However, species differences in their gene structures mean that mice do not adequately replicate human complement regulators, includingCR1andCR2. Genetic variation inCR1andCR2have been implicated in modifying disease states but the mechanisms are not known. To decipher the roles of humanCR1andCR2in health and disease, we engineered C57BL/6J (B6) mice to replace endogenous murineCr2with human complement receptors,CR1andCR2(B6.CR2CR1). CR1 has an array of allotypes in human populations and using traditional recombination methods (Flp-frtandCre-loxP) two of the most common alleles (referred to asCR1longandCR1short) are replicated within this mouse model, along with a CR1 knockout allele (CR1KO). Transcriptional profiling of spleens and brains identifies genes and pathways differentially expressed between mice homozygous for eitherCR1long,CR1shortorCR1KO. Gene set enrichment analysis predicts hematopoietic cell number and cell infiltration are modulated byCR1long, but notCR1shortorCR1KO. Therefore, this mouse model provides a novel tool for determining the relationship between human-relevantCR1alleles and disease.Summary StatementWe present the creation and validation of a novel mouse model that expresses human forms of complement cascade regulators CR1 and CR2.
Costs and benefits of multiple mating in a species with first‐male sperm precedence
Authors: Rodrigues Leonor R. , Figueiredo Alexandre R. T. , Van Leeuwen Thomas , Olivieri Isabelle , Magalhães Sara 
Published: December 2019

Abstract

Different patterns of sperm precedence are expected to entail different costs and benefits of mating for each sex that translate into distinct predictions regarding mating system evolution. Still, most studies addressing these costs and benefits have focused on species with mixed paternity or last male precedence, neglecting first‐male sperm precedence. We attempted to understand whether this latter pattern of sperm precedence translates into different costs and benefits for each sex in the haplodiploid spider mite Tetranychus urticae, a species in which female multiple mating is prevalent but most offspring are sired by first males.

First, we assessed the stability of the sperm precedence pattern. To do so, we measured offspring paternity after exposing females to a different number of matings and mating intervals. Next, to determine the potential costs or benefits of multiple mating for females under different contexts, we measured the fecundity and survival of females that re‐mated at different time points. To measure the potential costs of multiple mating for males, we analysed male survival in the presence of different numbers of virgin or mated females. We also tested whether males can reduce offspring production of their competitors, by reducing the production of fertilized offspring of mated females.

We found no change in the pattern of sperm precedence, independently of the mating interval between matings and the number of matings. Females paid a cost of mating, as multiply‐mated females laid fewer eggs than once‐mated females. However, while males had reduced survival when exposed to an intermediate number of virgin females, they paid no additional costs of mating with mated females. Moreover, females that mated multiple times produced fewer fertilized offspring than females that mated once. Thus, males that copulated with mated females reduced the fitness of other males, potentially leading to a relative fitness benefit for themselves.

Our results show that complex costs and benefits may arise in males in species with first‐male sperm precedence. How these costs and benefits affect the maintenance of selection for polyandry remains an open question.
Plant nutrient supply alters the magnitude of indirect interactions between insect herbivores: From foliar chemistry to community dynamics
Authors: Han Peng , Becker Christine , Le Bot Jacques , Larbat Romain , Lavoir Anne‐Violette , Desneux Nicolas 
Published: December 2019

Abstract

Density‐ and trait‐mediated indirect interactions (DMIIs and TMIIs respectively) are important drivers of community dynamics but how plant nutrients (bottom‐up effects) affect the magnitude of such indirect interactions has been scarcely addressed.

To assess the impact of bottom‐up forces on indirect interactions, we carried out laboratory and greenhouse experiments manipulating plant nutrient supplies in a four‐species diamond food web consisting of a plant (tomato), two phytophagous insects (a leafminer and an aphid) and a predator (a mirid bug) attacking both herbivores.

Multiple negative indirect effects of the leafminer occurred towards the aphid. The presence of its eggs negatively affected aphid population growth through increased predator abundance (DMIIs), and larval herbivory slowed down aphid development and negatively modulated aphid behaviours, for example they spent less time feeding (TMIIs), likely owing to enhanced plant chemical defences and/or decreased plant nutritional quality. Moreover, the low plant nutrient supply further magnified TMIIs.

Synthesis. Abiotic factors modulated predator‐ and plant‐mediated indirect interactions among herbivorous community members. Our study highlights the importance of using a holistic approach, from foliar chemistry to community dynamics, for disentangling interspecific interactions in a simple food web.
A systematic review of clinical practice guidelines on uncomplicated birth
Authors: Zhao Y , Lu H , Zang Y , Li X 
Published: December 2019

BackgroundClinical practice guidelines on uncomplicated birth provide clinical practice guidance and help to reduce unnecessary, non‐evidence‐based and potentially harmful intrapartum care practices. Little is known about the trustworthiness and consistency of these guidelines.ObjectivesTo appraise guidelines relevant to uncomplicated birth, and summarise consensus and non‐consensus recommendations.Search strategyEight literature databases and the websites of guideline development institutions and organisations of obstetricians, gynaecologists and midwives were searched from January 2008 to October 2018.Selection criteriaGuidelines that: reported in Chinese or English; labelled guideline, or recommendation, or consensus, or practice parameter, or position paper/stand; with uncomplicated birth being the primary objectives or comprised chapter(s); and were the most recently published or updated versions.Data collection and analysisTwo reviewers independently assessed guideline quality using the AGREE II instrument, and synthesised consensus and non‐consensus recommendations using the content analysis approach.Main resultsEleven guidelines met the inclusion criteria. The WHO and NICE guidelines were deemed to have the highest methodological quality. Twenty‐three discrepant recommendations and 39 groups of unanimous recommendations (containing 113 individual ones) were identified, among which 14 recommendations including eating and drinking as desired, prophylactic uterotonics, routine amniotomy and episiotomy were included in five or more guidelines. Perineal massage, uterine massage, active or expectant management at the third stage and use of hands‐on or hands‐poised technique were identified as the main discrepant recommendations.ConclusionsTwo guidelines with higher methodological quality and key clinical guideline recommendations, including both consensus and non‐consensus ones, on uncomplicated birth were identified.Tweetable abstractClinical guidelines of uncomplicated birth agree and disagree on several key recommendations.