bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrothermal sulphur bacteria enhance mercury availability for coastal marine organisms
Authors: Ruiz Eliot , Lacoue-Labarthe Thomas , Brault-Favrou Maud , Pascal Pierre-Yves 
Published: April 2022

AbstractThe hydrothermal compounds massively released into the sea by the geothermal power plant of Bouillante (Guadeloupe, Lesser Antilles) support the growth of sulphur-oxidising bacteria like around black smokers. Opportunistic animals of the bay were previously shown to actively seek and consume the bacterial biofilm. To investigate the role of these bacterial mats in enhancing the transfer of Hg, a highly toxic heavy metal, its concentrations were assessed in sediments, bacteria, and 6 low trophic levels animals from the Bouillante Bay and a Control Site nearby containing only natural sources of Hg. Concentrations of Hg in all samples from Bouillante were greater than those from the Control Site (2 to 627 times higher). A comparison with the Hg concentrations reported in the literature for similar samples types reveals that they are abnormally high in most Bouillante samples. Although bacterial biofilm contained high levels of Hg, the link between bacteria contribution to diet and Hg concentration was more complex than expected, which might be due to interspecific differences in Hg uptake and elimination rates. Species not consuming bacteria (i.e. filter feeders) still presented higher levels of Hg, suggesting that significant amounts of Hg are released along with discharge waters from the Bouillante geothermal plant, and are integrated through diffusion. Differences in Hg concentrations between tissues do not indicate that Hg contained in samples from animals was under the form of MeHg, lowering the biomagnification potential of Hg in the Bouillante Bay trophic food web. Overall, the Bouillante case study emphasises for the first time an important role played by sulphur bacteria mats as a vector of hydrothermal inorganic Hg, and potentially other trace metals emitted in vents area, through dietary pathways.
Genome Report: Chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris)
Authors: Armstrong Ellie E. , Campana Michael G. , Solari Katherine A. , Morgan Simon R. , Ryder Oliver A. , Naude Vincent N. , Samelius Gustaf , Sharma Koustubh , Hadly Elizabeth A. , Petrov Dmitri A. 
Published: April 2022

AbstractThe big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. Here, we assemble genomes from three members of the genus, the tiger (Panthera tigris), the snow leopard (Panthera uncia), and the African leopard (Panthera pardus pardus), at chromosome or near-chromosome level. We used a combination of short- and long-read technologies, as well as proximity ligation data from Hi-C technology, to achieve high continuity and contiguity for each individual. We hope these genomes will aid in further evolutionary and conservation research of this iconic group of mammals.
Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis
Authors: Gegner Hagen M. , Naake Thomas , Dugourd Aurélien , Müller Torsten , Czernilofsky Felix , Kliewer Georg , Jäger Evelyn , Helm Barbara , Kunze-Rohrbach Nina , Klingmüller Ursula , Hopf Carsten , Müller-Tidow Carsten , Dietrich Sascha , Saez-Rodriguez Julio , Huber Wolfgang , Hell Rüdiger , Poschet Gernot , Krijgsveld Jeroen 
Published: April 2022

AbstractMetabolomic and proteomic analyses of human plasma and serum samples harbour the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, processing time, and differing operating procedures. To better understand the impact of pre-analytical factors that are relevant to implement a unified proteomic and metabolomic approach in a clinical setting, we assessed the influence of temperature, sitting times, and centrifugation speed on the plasma and serum metabolomes and proteomes from six healthy volunteers.We used targeted metabolic profiling (497 metabolites) and data-independent acquisition (DIA) proteomics (572 proteins) on the same samples generated with well-defined pre-analytical conditions to evaluate criteria for pre-analytical SOPs for plasma and serum samples. Time and temperature showed the strongest influence on the integrity of plasma and serum proteome and metabolome. While rapid handling and low temperatures (4°C) are imperative for metabolic profiling, the analysed proteome showed variability when exposed to temperatures of 4°C for more than 2 hours, highlighting the need for compromises in a combined analysis. We formalised a quality control scoring system to objectively rate sample stability and tested this score using external data sets from other pre-analytical studies.Stringent and harmonised standard operating procedures (SOPs) are required for pre-analytical sample handling when combining proteomics and metabolomics of clinical samples to yield robust and interpretable data on a longitudinal scale and across different clinics. To ensure an adequate level of practicability in a clinical routine for metabolomics and proteomics studies we suggest to keep blood samples up to 2 hours on ice (4°C) prior to snap-freezing as a compromise between stability and operability. Finally, we provide the methodology as an open source R package allowing the systematic scoring of proteomics and metabolomics datasets to assess the stability of plasma and serum samples.
Domestic dog lineages reveal genetic drivers of behavioral diversification
Authors: Dutrow Emily V. , Serpell James A. , Ostrander Elaine A. 
Published: April 2022

SummarySelective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing an innovative framework for understanding relationships between breeds and the behaviors that define them, utilizing genetic data for over 4,000 domestic, semi-feral and wild canids and behavioral survey data for over 46,000 dogs. We identify ten major canine genetic lineages and their behavioral correlates, and show that breed diversification is predominantly driven by non-coding regulatory variation. We determine that lineage-associated genes converge in neurodevelopmental co-expression networks, identifying a sheepdog-associated enrichment for interrelated axon guidance functions. This work presents a scaffold for canine diversification that positions the domestic dog as an unparalleled system for revealing the genetic origins of behavioral diversity.
Elevated arginine levels in liver tumors promote metabolic reprogramming and tumor growth
Authors: Mossmann Dirk , Park Sujin , Ryback Brendan , Weißenberger Diana , Colombi Marco , Hindupur Sravanth K. , Dazert Eva , Coto-Llerena Mairene , Caner Ercan , Cenzano Veronica J. , Piscuoglio Salvatore , Bosch Fatima , Terracciano Luigi M. , Sauer Uwe , Hall Michael N. 
Published: April 2022

AbstractArginine auxotropy, due to reduced expression of urea cycle genes, is common in cancer. However, little is known about the levels of arginine in these cancers. Here, we report that arginine levels are elevated in hepatocellular carcinoma (HCC) despite reduced expression of urea cycle enzymes. Liver tumors accumulate high levels specifically of arginine via increased uptake and, more importantly, via suppression of arginine-to-polyamine conversion due to reduced arginase 1 (ARG1) and agmatinase (AGMAT) expression. Furthermore, the high levels of arginine are required for tumor growth. Mechanistically, high levels of arginine promote tumorigenesis via transcriptional regulation of metabolic genes, including upregulation of asparagine synthetase (ASNS). ASNS-derived asparagine further enhances arginine uptake, creating a positive feedback loop to sustain high arginine levels and oncogenic metabolism. Thus, arginine is a novel second messenger-like molecule that reprograms metabolism to promote tumor growth.
Comparative Analysis of Dimension Reduction Methods for Cytometry by Time-of-Flight Data
Authors: Wang Kaiwen , Yang Yuqiu , Wu Fangjiang , Song Bing , Wang Xinlei , Wang Tao 
Published: April 2022

ABSTRACTWhile experimental and informatic techniques around single cell sequencing (scRNA-seq) are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged behind. CyTOF data are dramatically different from scRNA-seq data in many aspects. This calls for the evaluation and development of computational methods specific for CyTOF data. Dimension reduction (DR) is one of the critical steps of single cell data analysis. Here, we benchmark the performances of 21 DR methods on 110 real and 425 synthetic CyTOF samples. We find that less well-known methods like SAUCIE, SQuaD-MDS, and scvis are the overall best performers. In particular, SAUCIE and scvis are well balanced, SQuaD-MDS excels at structure preservation, whereas UMAP has great downstream analysis performance. We also find that t- SNE (along with SQuad-MDS/t-SNE Hybrid) possesses the best local structure preservation. Nevertheless, there is a high level of complementarity between these tools, so the choice of method should depend on the underlying data structure and the analytical needs.
Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury
Authors: Malagola E. , Vasciaveo A. , Ochiai Y. , Kim W. , Middelhoff M. , Nienhüser H. , Deng L. , Belin B. , LaBella J. , Zamechek LB. , Wong M.H. , Li L. , Guha C. , Cheng CW. , Yan KS. , Califano A. , Wang T.C. 
Published: April 2022

SummaryThe currently accepted intestinal epithelial cell organization model proposes that crypt base columnar (CBC) cells marked by high levels ofLgr5expression represent the sole intestinal stem cell (ISC) compartment. However, previous studies have indicated that Lgr5+cells are dispensable for intestinal regeneration, leading to two major hypotheses: one favoring the presence of a quiescent reserve stem cell population, the other calling for differentiated cell plasticity. To investigate these possibilities, we studied crypt epithelial cell organization, during homeostasis and regeneration, in unbiased fashion, via high-resolution single-cell profiling. These studies, combined within vivolineage tracing, show thatLgr5is not a specific ISC marker and that stemness potential exists beyond the crypt base in the isthmus region, whose cells, contrary to differentiated cells, participate in tissue homeostasis and support intestinal regeneration. Our results provide a novel model of organization for the intestinal crypt epithelium in which stemness potential is not restricted to CBC cells and suggesting that neither de-differentiation nor reserve stem cell populations are drivers of intestinal regeneration.
Projecting clumped transcriptomes onto single cell atlases to achieve single cell resolution
Authors: Johansen Nelson , Quon Gerald 
Published: April 2022

AbstractMulti-modal single cell RNA assays capture RNA content as well as other data modalities, such as spatial cell position or the electrophysiological properties of cells. Compared to dedicated scRNA-seq assays however, they may unintentionally capture RNA from multiple adjacent cells, exhibit lower RNA sequencing depth compared to scRNA-seq, or lack genome-wide RNA measurements. We present scProjection, a method for mapping individual multi-modal RNA measurements to deeply sequenced scRNA-seq atlases to extract cell type-specific, single cell gene expression profiles. We demonstrate several use cases of scProjection, including the identification of spatial motifs from spatial transcriptome assays, distinguishing RNA contributions from neighboring cells in both spatial and multi-modal single cell assays, and imputing expression measurements of un-measured genes from gene markers. scProjection therefore combines the advantages of both multi-modal and scRNA-seq assays to yield precise multi-modal measurements of single cells.
The global effects of alcohol consumption on Gross Domestic Product in high- and low-income countries: a systematic review and meta-analysis
Authors: Mahesarajah Swettha , Pazoki Raha 
Published: April 2022

ABSTRACTAims and objectivesThis study aims to measure the disease burden and the economic burden associated with alcohol consumption in both high- and low-income countries. To emphasise the necessity of making this issue a worldwide priority, the percentage of GDP attributable to alcohol-related costs will be stated.DesignSystematic review and meta-analysisData sourcesA systematic search concerning health and social costs was conducted primarily through PubMed and subsequent citation chaining of appropriate systematic reviews. Other electronic databases such as Google Scholar was also freely searched.Eligibility criteria for selecting studiesObservational studies examining alcohol-related harm, alcohol-related disease, and alcohol-related expenditure with all studies measuring alcohol-related harm using the alcohol-attributable fraction (AAF).Results9 cross-sectional studies were obtained assessing the consequences of alcohol on the respective country’s economy with all studies utilising a prevalence-based approach. 5 studies were eligible for a meta-analysis in the statistically programming software, R. The pooled estimate of the economic burden of alcohol in 5 countries equated to be 0.01% of GDP. Though inconsistencies in cost estimations resulted in an underestimation, our results provide evidence to suggest that alcohol negatively affects both individuals and society. The available literature on the topic of the economic impact of alcohol is inadequate; especially when investigating concerns in poorer regions of the world.ConclusionThough the current estimate of global GDP attributable to alcohol use is low, the evidence suggesting the global increase of alcohol consumption is paramount to avoid future calamities. Cooperative leadership from the World Health Organisation (WHO), International Monetary Fund, and the World Bank are requisite to control the harmful patterns of alcohol consumption seen across the globe.STRENGTHS AND LIMITATIONS OF THIS STUDYThis is the first systematic review assessing the detrimental consequences of alcohol on economic health with the inclusion of both lower-middle income and high-income countries.This study provides a pooled estimate of the global estimate of the percentage of GDP attributable to alcohol related costs using statistical package, R which has not been done before.The obtainment of research conducted in low-income countries proved to be difficult, and as a result no low-middle income countries were used when calculating the pooled estimate. Therefore, the accuracy of the provided estimate was decreased.
Different Routes for Direct Interspecies Electron Transfer with Diverse Electron-Accepting Partners
Authors: Holmes Dawn E. , Zhou Jinjie , Smith Jessica A. , Wang Caiqin , Liu Xinying , Lovley Derek R. 
Published: April 2022

AbstractDirect interspecies electron transfer (DIET) may be most important in methanogenic environments, but studies to date that have examined the mechanisms for electron transfer from electron-donating partners have primarily focused on co-cultures in which fumarate was the terminal electron acceptor. To better understand DIET with methanogens, the transcriptome of Geobacter metallireducens during DIET-based growth with Geobacter sulfurreducens reducing fumarate was compared with the transcriptome of G. metallireducens grown in co-culture with diverse Methanosarcina species. The transcriptome of G. metallireducens co-cultured with G. sulfurreducens was significantly different from those with Methanosarcina. Furthermore, the transcriptome of G. metallireducens grown with Methanosarcina barkeri, which lacks outer-surface cytochromes, was different from the transcriptome of G. metallireducens co-cultured with Methanosarcina acetivorans or Methanosarcina subterranea, which have an outer-surface c-type cytochrome that serves as an electrical connect for DIET. Differences in G. metallireducens expression patterns for c-type cytochrome genes were particularly notable. The impact of deleting G. metallireducens c-type cytochrome genes depended upon the electron-accepting partner. Multiple cytochromes that G. metallireducens required for DIET with G. sulfurreducens and for Fe(III) oxide reduction were not required for DIET with the Methanosarcina species. Porin-cytochrome complexes and e-pili were required for optimal DIET with all partners. Shewanella oneidensis, another electroactive microbe with abundant outer-surface c-type cytochromes, did not grow via DIET. The results demonstrate that the presence of outer-surface cytochromes does not necessarily confer the capacity for DIET, and also emphasize the substantial impact of the physiology of the electron-accepting partner on the physiology of the electron-donating DIET partner.
The Image Data Explorer: interactive exploration of image-derived data
Authors: Muller Coralie , Serrano-Solano Beatriz , Sun Yi , Tischer Christian , Hériché Jean-Karim 
Published: April 2022

AbstractMany bioimage analysis projects produce quantitative descriptors of regions of interest in images. Associating these descriptors with visual characteristics of the objects they describe is a key step in understanding the data at hand. However, as many bioimage data and their analysis workflows are moving to the cloud, addressing interactive data exploration in remote environments has become a pressing issue. To address it, we developed the Image Data Explorer (IDE) as a web application that integrates interactive linked visualization of images and derived data points with exploratory data analysis methods, annotation, classification and feature selection functionalities. The IDE is written in R using the shiny framework. It can be easily deployed on a remote server or on a local computer. The IDE is available at https://git.embl.de/heriche/image-data-explorer and a cloud deployment is accessible at https://shiny-portal.embl.de/shinyapps/app/01_image-data-explorer.
Characterizing dynamic neural representations of scene attractiveness
Authors: Kaiser Daniel 
Published: April 2022

AbstractAesthetic experiences during natural vision are varied: they can arise from viewing scenic landscapes, interesting architecture, or attractive people. Recent research in the field of neuroaesthetics has taught us a lot about where in the brain such aesthetic experiences are represented. Much less is known about when such experiences arise during the cortical processing cascade. Particularly, the dynamic neural representation of perceived attractiveness for rich natural scenes is not well understood. Here, I present data from an EEG experiment, in which participants provided attractiveness judgments for a set of diverse natural scenes. Using multivariate pattern analysis, I demonstrate that scene attractiveness is mirrored in early brain signals that arise within 200ms of vision, suggesting that the aesthetic appeal of scenes is first resolved during perceptual processing. In more detailed analyses, I show that even such early neural correlates of scene attractiveness are partly related to inter-individual variation in aesthetic preferences and that they generalize across scene contents. Together, these results characterize the time-resolved neural dynamics that give rise to aesthetic experiences in complex natural environments.
Novel trans-translation-associated gene regulation revealed by prophage excision-triggered switching of ribosome rescue pathway
Authors: Onodera Haruka , Niwa Tatsuya , Taguchi Hideki , Chadani Yuhei 
Published: April 2022

AbstractEscherichia coli has multiple pathways to release a nonproductive ribosome complex stalled at the 3’ end of nonstop mRNAs: SsrA RNA-mediated trans-translation and stop codon-independent termination by ArfA/RF2 or ArfB (YaeJ). The arfA mRNA lacks a stop codon and thus its expression is repressed by trans-translation. Therefore, ArfA is considered to complement the ribosome rescue activity of trans-translation, but the situations in which ArfA is expressed to rescue the nonproductive complexes have not been elucidated. Here, we demonstrated that the excision of the CP4-57 prophage adjacent to the E. coli ssrA gene leads to the inactivation of SsrA RNA and switches the primary rescue pathway from trans-translation to the ArfA/RF2 pathway. A comparative quantitative proteomic analysis revealed that the switching of the rescue pathway rearranges not only the proteome landscape in E. coli cells but also the phenotype, such as motility. Among the proteins with significantly increased abundance in the ssrA-inactivated cells, we found ZntR, whose mRNA is transcribed together as the upstream part of the nonstop arfA mRNA. Further analysis revealed that the translation of the nonstop ORF of arfA triggered the repression of the upstream zntR ORF, via trans-translation-coupled exonucleolytic (RUTEX) degradation by a polynucleotide phosphorylase. These results provide a novel example of trans-translation-dependent regulation, and shed new light on the physiological roles of prophages in gene expression.
Neural dynamics and architecture of the heading direction circuit in a vertebrate brain
Authors: Petrucco Luigi , Lavian Hagar , Wu You Kure , Svara Fabian , Štih Vilim , Portugues Ruben 
Published: April 2022

AbstractAnimals can use different strategies to navigate. They may guide their movements by relying on external cues in their environment or, alternatively, by using an internal cognitive map of the space around them and their position within it. An essential part of this representation are heading cells, neurons whose activity depends on the heading direction of the animal. Although those cells have been found in vertebrates, the full network has never been observed and there is very little mechanistic understanding of how these cells acquire their response properties. In this study, we use volumetric functional imaging in larval zebrafish to observe, for the first time in a vertebrate, a full network that encodes allocentric heading direction. This network of approximately one hundred inhibitory neurons is arranged in an anatomical circle in the anterior hindbrain. Its activity is driven purely by the integration of internally generated signals, indicating that a simple vertebrate brain can encode maps of how an animal moves within its surroundings. Single cell reconstructions of electron micrographs allow us to uncover how the connectivity pattern of neurons within the network supports the implementation of a ring attractor network. The neurons we identify share features with neurons in the dorsal tegmentum nucleus of rodents and the fly central complex, showing that similar connectivity and mechanistic principles underlie the generation of cognitive maps of heading direction across the animal kingdom.