bluuebunny/crossref_metadata_2025_split huggingface dataset:
Winners and losers over 35 years of dragonfly and damselfly distributional change in Germany
Authors: Bowler D.E , Eichenberg D. , Conze K.J. , Suhling F. , Baumann K. , Bönsel A. , Bittner T. , Drews A. , Günther A. , Isaac N.J.B. , Petzold F. , Seyring M. , Spengler T. , Trockur B. , Willigalla C. , Bruelheide H. , Jansen F. , Bonn A. 
Published: August 2020

AbstractRecent studies suggest insect declines in parts of Europe; however, the generality of these trends across different taxa and regions remains unclear. Standardized data are not available to assess large-scale, long-term changes for most insect groups but opportunistic citizen science data is widespread for some taxa. We compiled over 1 million occurrence records of Odonata (dragonflies and damselflies) from different regional databases across Germany. We used occupancy-detection models to estimate annual distributional changes between 1980 and 2016 for each species. We related species attributes to changes in the species’ distributions and inferred possible drivers of change. Species showing increases were generally warm-adapted species and/or running water species while species showing decreases were cold-adapted species using standing water habitats such as bogs. We developed a novel approach using time-series clustering to identify groups of species with similar patterns of temporal change. Using this method, we defined five typical patterns of change for Odonata – each associated with a specific combination of species attributes. Overall, trends in Odonata provide mixed news – improved water quality, coupled with positive impacts of climate change, could explain the positive trend status of many species. At the same time, declining species point to conservation challenges associated with habitat loss and degradation. Our study demonstrates the great value of citizen science data for assessing large-scale distributional change and conservation decision-making.
GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets
Authors: Kratochvíl Miroslav , Hunewald Oliver , Heirendt Laurent , Verissimo Vasco , Vondrášek Jiří , Satagopam Venkata P. , Schneider Reinhard , Trefois Christophe , Ollert Markus 
Published: August 2020

AbstractBackgroundThe amount of data generated in large clinical and phenotyping studies that use single-cell cytometry is constantly growing. Recent technological advances allow to easily generate data with hundreds of millions of single-cell data points with more than 40 parameters, originating from thousands of individual samples. The analysis of that amount of high-dimensional data becomes demanding in both hardware and software of high-performance computational resources. Current software tools often do not scale to the datasets of such size; users are thus forced to down-sample the data to bearable sizes, in turn losing accuracy and ability to detect many underlying complex phenomena.ResultsWe present GigaSOM.jl, a fast and scalable implementation of clustering and dimensionality-reduction for flow and mass cytometry data. The implementation of GigaSOM.jl in the high-level and high-performance programming language Julia makes it accessible to the scientific community, and allows for efficient handling and processing of datasets with billions of data points using distributed computing infrastructures. We describe the design of GigaSOM.jl, measure its performance and horizontal scaling capability, and showcase the functionality on a large dataset from a recent study.ConclusionsGigaSOM.jl facilitates utilization of the commonly available high-performance computing resources to process the largest available datasets within minutes, while producing results of the same quality as the current state-of-art software. Measurements indicate that the performance scales to much larger datasets. The example use on the data from an massive mouse phenotyping effort confirms the applicability of GigaSOM.jl to huge-scale studies.Key pointsGigaSOM.jl improves the applicability of FlowSOM-style single-cell cytometry data analysis by increasing the acceptable dataset size to billions of single cells.Significant speedup over current methods is achieved by distributed processing and utilization of efficient algorithms.GigaSOM.jl package includes support for fast visualization of multidimensional data.
Assembly defects of the human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia
Authors: Sekulovski Samoil , Devant Pascal , Panizza Silvia , Gogakos Tasos , Pitiriciu Anda , Heitmeier Katharina , Ramsay Ewan Phillip , Barth Marie , Schmidt Carla , Weitzer Stefan , Tuschl Thomas , Baas Frank , Martinez Javier , Trowitzsch Simon 
Published: August 2020

AbstractIntrons of human transfer RNA precursors (pre-tRNAs) are excised by the tRNA splicing endonuclease TSEN in complex with the RNA kinase CLP1. Mutations in TSEN/CLP1 occur in patients with pontocerebellar hypoplasia (PCH), however, their role in the disease is unclear. Here, we show that intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers independently of CLP1. Splice site recognition involves the mature domain and the anticodon-intron base pair of pre-tRNAs. The 2.1-Å resolution X-ray crystal structure of a TSEN15–34 heterodimer and differential scanning fluorimetry analyses show that PCH mutations cause thermal destabilization. While endonuclease activity in recombinant mutant TSEN is unaltered, we observe assembly defects and reduced pre-tRNA cleavage activity resulting in an imbalanced pre-tRNA pool in PCH patient-derived fibroblasts. Our work defines the molecular principles of intron excision in humans and provides evidence that modulation of TSEN stability may contribute to PCH phenotypes.
RAD: a web application to identify region associated differentially expressed genes
Authors: Guo Yixin , Xue Ziwei , Yuan Ruihong , Pastor William A. , Liu Wanlu 
Published: August 2020

AbstractWith the advance of genomic sequencing techniques, chromatin accessible regions, transcription factor binding sites and epigenetic modifications can be identified at genome-wide scale. Conventional analyses focus on the gene regulation at proximal regions; however, distal regions are usually neglected, largely due to the lack of reliable tools to link the distal regions to coding genes. In this study, we introduce RAD (Region Associated Differentially expressed genes), a user-friendly web tool to identify both proximal and distal region associated differentially expressed genes. RAD maps the up- and down-regulated genes associated with any genomic regions of interest (gROI) and helps researchers to infer the regulatory function of these regions based on the distance of gROI to differentially expressed genes. RAD includes visualization of the results and statistical inference for significance.AvailabilityRAD is implemented with Python 3.7 and run on a Nginx server. RAD is freely available athttp://labw.org/radas online web service.
Acidic monosaccharides become incorporated into calcite single crystals
Authors: Lang Arad , Mijowska Sylwia , Polishchuk Iryna , Fermani Simona , Falini Giuseppe , Katsman Alexander , Marin Frédéric , Pokroy Boaz 
Published: August 2020

ABSTRACTCarbohydrates, along with proteins and peptides, are known to represent a major class of biomacromolecules involved in calcium carbonate biomineralization. However, in spite of multiple physical or biochemical characterizations, the explicit role of saccharide macromolecules (long chains of carbohydrate molecules) is not yet understood in mineral deposition. In the present study we investigated the influence of two common acidic monosaccharides (MSs), which are the simplest form of carbohydrates and are represented here by glucuronic and galacturonic acids, on the formation of calcite crystalsin vitro. We show that the size, morphology and microstructure of calcite crystals are altered when they are grown in the presence of these MSs. More importantly, MSs were found to become incorporated into the calcite crystalline lattice and induce anisotropic lattice distortions, a widely studied phenomenon in other biomolecules related to CaCO3biomineralization but never before reported in the case of single MSs. Changes in the calcite lattice induced by MS incorporation were precisely determined by the technique of high-resolution synchrotron powder X-ray diffraction. We believe that the results of this research may deepen our understanding of the interaction of saccharide polymers with an inorganic host and shed light on the implications of carbohydrates for biomineralization processes.
Performance, but not size, of hindleg weaponry is sexually dimorphic in the giant mesquite bug (Thasus neocalifornicus)
Authors: Graham Zackary A. , Kaiser Nicole , Palaoro Alexandre V. 
Published: August 2020

ABSTRACTIn many species, males possess specialized weaponry that have evolved to confer a benefit during aggressive interactions. Because male weaponry is typically an exaggerated or extreme version of pre-existing body parts, females often possess reduced or weaponry. Although much research has investigated sexual dimorphism in the sizes of such weapons, other weapon components, such as weapon performance or alternative weapon forms can also explain the evolution of weapon sexual dimorphisms. Here, we investigated the allometry and variation of multiple weapon components of hindleg weaponry in the male and female giant mesquite bugs,Thasus necalifornicus. Despite theory predicating greater allocation in male weaponry, we found that females allocated more into the lengths of their hindlegs compared to males. Despite this allocation, males possess relatively wider hindlegs, which likely increase area of muscle mass. Indeed, the squeezing performance of male hindlegs was much greater than that of female hindlegs. Lastly, we also described the allometry and variation in a male weapon component, prominent tibial spines, which likely are used to damage competitors during aggressive interaction. Overall, our findings highlight the intricacies of weapon sexual dimorphism and demonstrate the importance of measuring multiple weapon components and not a single measure.
Climate risk to European fisheries and coastal communities
Authors: Payne Mark R. , Kudahl Manja , Engelhard Georg H. , Peck Myron A. , Pinnegar John K. 
Published: August 2020

AbstractWith the majority of the global human population living in coastal regions, correctly characterising the climate risk that ocean-dependent communities and businesses are exposed to is key to prioritising the finite resources available to support adaptation. We apply a climate risk analysis across the European fisheries sector for the first time to identify the most at-risk fishing fleets and coastal regions and then link the two analyses together. We employ a novel approach combining biological traits with physiological metrics to differentiate climate hazards between 556 populations of fish and use these to assess the relative climate risk for 380 fishing fleets and 105 coastal regions in Europe. Countries in southeast Europe as well as the UK have the highest risks to both fishing fleets and coastal regions overall while, in other countries, the risk-profile is greater at either the fleet level or at the regional level. European fisheries face a diversity of challenges posed by climate change and climate adaptation, therefore, needs to be tailored to each country, region and fleet’s specific situation. Our analysis supports this process by highlighting where and what adaptation measures might be needed and informing where policy and business responses could have the greatest impact.Significance StatementWe present a novel climate risk analysis for i) 105 ocean-dependent communities and ii) 380 fishing fleets in Europe. Our unique approach provides a perspective over the climate risks in this diverse and populous continent that is unprecedented in both its breadth and detail. We show that countries in southeast Europe as well as the UK have the highest climate risk overall, both in terms of fishing fleets and coastal communities. Substantial variation in climate risk is seen even within countries, emphasizing that climate adaptation interventions need to be tailored to the specific characteristics of the fleet or community. A focus on sustainable fisheries management and diversification of fish portfolios can reduce climate risks across the board.
Equal performance but distinct behaviors:Astatotilapia burtonisex differences in a novel object recognition task and spatial maze
Authors: Wallace Kelly J. , Hofmann Hans A. 
Published: August 2020

AbstractSex differences in behavior and cognition can be driven by differential selection pressures from the environment and in the underlying neuromolecular mechanisms of decision-making. The highly social cichlid fishAstatotilapia burtoniexhibits dynamic and complex social hierarchies, yet explicit cognitive testing (outside of social contexts) and investigations of sex differences in cognition have yet to be fully explored. Here we assessed male and femaleA. burtoniin two cognitive tasks: a novel object recognition task and a spatial task. We hypothesized that males outperform females in a spatial learning task and exhibit more neophilic/exploratory behavior in across both tasks. In the present study we find that both sexes prefer the familiar object in a novel object recognition task, but the time at which they exhibit this preference differs between the sexes. Females more frequently learned the spatial task, exhibiting longer decision latencies and quicker error correction, suggesting a potential speed-accuracy tradeoff.Furthermore, the sexes differ in space use in both tasks and in a principal component analysis of the spatial task. A model selection analysis finds that preference, approach, and interaction duration in the novel object recognition task that reach a threshold of importance averaged across all models. This work highlights the need to explicitly test for sex differences in cognition to better understand how individuals navigate dynamic social environments.
Bioconcentration of glyphosate in wetland biofilms
Authors: Beecraft Laura , Rooney Rebecca 
Published: August 2020

AbstractWetland biofilms were exposed to the herbicide glyphosate viain situfield exposures and controlled microcosm experiments to measure bioconcentration and metabolism of glyphosate by biofilm organisms. Glyphosate concentrations in biofilms were orders of magnitude higher than the surrounding water, bioconcentration factors averaged 835 and 199 in field- and lab-exposed biofilms, respectively. Glyphosate in water where it had been detected in biofilms at field-exposed sites ranged from below detection (<0.001 ppm) up to 0.13 ppm. Glyphosate bioconcentration in biofilms was inversely proportional to levels in the surrounding water, and the retention kinetics were similar to both adsorption and enzymatic models. Microorganisms present in both the water and biofilms metabolized glyphosate to its primary breakdown product aminomethyl phosphonic acid (AMPA), with increased rates of breakdown in and around the biofilms. Photosynthetic efficiency of the algae within the biofilms was not affected by 24 h glyphosate controlled exposures. Our results demonstrate the role of biofilms in improving wetland water quality by removing contaminants like glyphosate, but also as a potential exposure route to higher trophic levels via consumption. Due to bioconcentration of pesticides, exposure risk to organisms consuming or living in biofilms may be much higher than indicated by concentrations in ambient water samples.
Repeat Exposure to Hypercapnic Seawater Modifies Performance and Oxidative Status in a Tolerant Burrowing Clam
Authors: Gurr Samuel J. , Trigg Shelly A. , Vadopalas Brent , Roberts Steven B. , Putnam Hollie M. 
Published: August 2020

AbstractModerate oxidative stress is a hypothesized driver of enhanced stress tolerance and lifespan. Whereas thermal stress, irradiance, and dietary restriction show evidence of dose-dependent benefits for many taxa, stress acclimation remains understudied in marine invertebrates, despite being threatened by climate change stressors such as ocean acidification. To test for life-stage and stress-intensity dependence in eliciting enhanced tolerance under subsequent stress encounters, we initially conditioned pediveliger Pacific geoduck (Panopea generosa) larvae to (i) ambient and moderately elevatedpCO2(920 μatm and 2800 μatm, respectively) for 110 days, (ii) secondarily applied a 7-day exposure to ambient, moderate, and severely elevatedpCO2(750 μatm, 2800 μatm, and 4900 μatm, respectively), followed by 7 days in ambient conditions, and (iii) implemented a modified-reciprocal 7-day tertiary exposure to ambient (970 μatm) and moderatepCO2(3000 μatm). Initial conditioning to moderatepCO2stress followed by secondary and tertiary exposure to severe and moderatepCO2stress increased respiration rate, organic biomass, and shell size suggesting a stress-intensity-dependent effect on energetics. Additionally, stress-acclimated clams had lower antioxidant capacity compared to clams under initial ambient conditions, supporting the hypothesis that stress over postlarval-to-juvenile development affects oxidative status later in life. We posit two subcellular mechanisms underpinning stress-intensity-dependent effects on mitochondrial pathways and energy partitioning: i) stress-induced attenuation of mitochondrial function and ii) adaptive mitochondrial shift under moderate stress. Time series and stress intensity-specific approaches can reveal life-stages and magnitudes of exposure, respectively, that may elicit beneficial phenotypic variation.Summary statementHypercapnic conditions during postlarval development improves physiological performance and oxidative status. This novel investigation of adaptive stress acclimation highlights the plasticity of bioenergetic and subcellular responses inPanopea generosa.
Melting dsDNA donor molecules potentiates precision genome editing inC. elegans
Authors: Ghanta Krishna S. , Mello Craig C. 
Published: August 2020

ABSTRACTCRISPR genome editing has revolutionized genetics in many organisms. In the nematodeCaenorhabditis elegansone injection into each of the two gonad arms of an adult hermaphrodite exposes hundreds of meiotic germ cells to editing mixtures, permitting the recovery of multiple indels or small precision edits from each successfully injected animal. Unfortunately, particularly for long insertions, editing efficiencies can vary widely, necessitating multiple injections, and often requiring co-selection strategies. Here we show that melting double stranded DNA (dsDNA) donor molecules prior to injection increases the frequency of precise homology-directed repair (HDR) by several fold for longer edits. We describe troubleshooting strategies that enable consistently high editing efficiencies resulting, for example, in up to 100 independent GFP knock-ins from a single injected animal. These efficiencies makeC. elegansby far the easiest metazoan to genome edit, removing barriers to the use and adoption of this facile system as a model for understanding animal biology.
Modeling the evolutionary architectures of human enhancer sequences reveals distinct origins, functions, and associations with human-trait variation
Authors: Fong Sarah L. , Capra John A. 
Published: August 2020

ABSTRACTMotivationDespite the importance of gene regulatory enhancers in human biology and evolution, we lack a comprehensive evolutionary model of enhancer sequence architecture and function. This substantially limits our understanding of the genetic basis for divergence between species and our ability to interpret the effects of non-coding variants on human traits.ResultsTo explore enhancer sequence evolution and its relationship to regulatory function, we traced the evolutionary origins of human sequences with enhancer activity defined by eRNA from diverse tissues and cellular contexts. The majority of enhancers are sequences of a single evolutionary age (“simple” enhancer architectures), likely indicating constraint against genomic rearrangements. A minority of enhancers are composites of sequences of multiple evolutionary ages (“complex” enhancer architectures). Compared to simple enhancers, complex enhancers are older, more pleiotropic, and more active across species. Genetic variants within complex enhancers are also less likely to have effects on human traits and biochemical activity. Transposable-element-derived sequences have made diverse contributions to enhancer architectures; some have nucleated enhancers with simple architectures, while others have remodeled older sequences to create complex regulatory architectures.ConclusionsBased on these results, we propose a framework for modeling enhancer sequence architecture and evolution. Applying this framework to human enhancer sequences reveals multiple, distinct trajectories of human regulatory sequence evolution. Considering these evolutionary histories can aid interpretation of the effects of variants on enhancer function.
KH domain containing RNA-binding proteins coordinate with microRNAs to regulateCaenorhabditis elegansdevelopment
Authors: Haskell D , Zinovyeva A 
Published: August 2020

ABSTRACTmicroRNAs (miRNAs) and RNA binding proteins (RBPs) regulate gene expression at the post-transcriptional level, but the extent to which these key regulators of gene expression coordinate and the precise mechanisms of their coordination are not well understood. RNA binding proteins often have recognizable RNA binding domains that correlate with specific protein function. Recently, several RBPs containing K Homology (KH) RNA binding domains were shown to work with miRNAs to regulate gene expression, raising the possibility that KH domains may be important for coordinating with miRNA pathways in gene expression regulation. To ascertain whether additional KH domain proteins functionally interact with miRNAs duringCaenorhabditis elegansdevelopment, we knocked down twenty-four genes encoding KH-domain proteins in several miRNA sensitized genetic backgrounds. Here, we report that a majority of the KH domain-containing genes genetically interact with multiple miRNAs and Argonautealg-1. Interestingly, two KH domain genes, predicted splicing factorssfa-1andasd-2, genetically interacted with all of the miRNA mutants tested, while other KH domain genes exhibited functional interactions only with specific miRNAs. Our domain architecture and phylogenetic relationship analyses of theC. elegansKH domain-containing proteins revealed potential groups that may share both structure and function. Collectively, we show that manyC. elegansKH domain RBPs functionally interact with miRNAs, suggesting direct or indirect coordination between these two classes of post-transcriptional gene expression regulators.