bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy
Authors: Rodríguez-Gijón Alejandro , Nuy Julia K. , Mehrshad Maliheh , Buck Moritz , Schulz Frederik , Woyke Tanja , Garcia Sarahi L. 
Published: January 2021

AbstractOur view of genome size in Archaea and Bacteria has remained skewed as the data used to paint its picture has been dominated by genomes of microorganisms that can be cultivated under laboratory settings. However, the continuous effort to catalog the genetic make-up of Earth’s microbiomes specifically propelled by recent extensive work on uncultivated microorganisms, provides a unique opportunity to revise our perspective on genome size distribution. Capitalizing on a recently released extensive catalog of tens of thousands of metagenome-assembled genomes, we provide a comprehensive overview of genome size distributions. We observe that the known phylogenetic diversity of environmental microorganisms possesses significantly smaller genomes than the collection of laboratory isolated microorganisms. Aquatic microorganisms average 3.1 Mb, host-associated microbial genomes average 3.0 Mb, terrestrial microorganism average 3.7 Mb and isolated microorganisms average 4.3 Mb. While the environment where the microorganisms live can certainly be linked to genome size, in some cases, evolutionary phylogenetic history can be a stronger predictor. Moreover, ecological strategies such as auxotrophies have a direct impact on genome size. To better understand the ecological drivers of genome size, we expand on the known and the overlooked factors that influence genome size in different environments, phylogenetic groups and trophic strategies.
Selection for feed efficiency elicits different postprandial plasma metabolite profiles in response to poor hygiene of housing conditions in growing pigs
Authors: Fraga Alícia Zem , Louveau Isabelle , Campos Paulo Henrique Reis Furtado , Hauschild Luciano , Le Floc’h Nathalie 
Published: January 2021

AbstractSelection for residual feed intake (RFI), a measure of feed efficiency, may affect the ability of pigs to adapt their metabolism in response to poor environmental conditions. This study was conducted to compare postprandial plasma concentrations of insulin, energy related metabolites, and amino acids measured after a 6-week challenge consisting of exposure to good or poor hygiene of housing conditions of 24 growing pigs divergently selected for low-RFI (LRFI) and high-RFI (HRFI). Blood indicators of immune responses were assessed from samples collected before (week 0 or W0), and 3 (W3) and 6 weeks (W6) after pigs transfer to their respective housing hygiene conditions. Plasma haptoglobin concentrations and blood neutrophil granulocyte numbers were greater in poor than in good conditions at W3. Plasma concentrations of total immunoglobulin G were greater (p= 0.04) in poor than in good hygiene conditions at W6. At W6, pigs were fitted with an intravenous catheter for serial blood samplings. Low-RFI pigs had greater insulin (p< 0.001) and lower triglyceride (p= 0.04) average plasma concentrations than HRFI pigs in both conditions. In poor hygiene conditions, the peaks of insulin and glucose occured earlier and that of insulin was greater in LRFI than in HRFI pigs. Irrespective of genetic line, average plasma concentrations of histidine, isoleucine, leucine, methionine, threonine, valine, and alanine were greater in poor compared with good conditions. Only HRFI pigs had greater lysine, asparagine, proline, and tyrosine plasma concentrations in poor than in good hygiene conditions. Conversely, arginine, tryptophan, proline, and tyrosine plasma concentrations were lower only for LRFI pigs housed in poor hygiene conditions. The impact of poor hygiene of housing conditions on insulin, triglycerides, and AA profiles differed between RFI lines. More specifically, our results suggest that, contrary to HRFI, LRFI pigs increased or maintained their utilization of Trp, Arg, and Lys when housed in poor hygiene conditions. This difference may contribute to the better capacity of LRFI to cope with the poor hygiene of housing conditions.
A national analysis of trends in COVID-19 infection and clinical management in Veterans Health Administration medical facilities
Authors: Aboumrad Maya , Shiner Brian , Riblet Natalie , Huizenga Hugh , Neupane Nabin , Young-Xu Yinong 
Published: January 2021

ABSTRACTOBJECTIVEWe explored longitudinal trends in sociodemographic characteristics, reported symptoms, laboratory findings, pharmacological and non-pharmacological treatment, comorbidities, and 30-day in-hospital mortality among hospitalized patients with coronavirus disease 2019 (COVID-19).METHODSThis retrospective cohort study included 43,267 patients diagnosed with COVID-19 in the Veterans Health Administration between 03/01/20 and 08/31/20 and followed until 09/30/20. We focused our analysis on patients that were subsequently hospitalized, and categorized them into groups based on the month of hospitalization. We summarized our findings through descriptive statistics. We used a nonparametric rank-sum test for trend to examine any differences in the distribution of our study variables across the six months.RESULTSDuring our study period, 8,240 patients were hospitalized, and 1,081 (13.1%) died within 30 days of admission. Hospitalizations increased over time, but the proportion of patients that died consistently declined from March (N=221/890, 24.8%) to August (N=111/1,396, 8.0%). Patients hospitalized in March compared to August were younger on average, mostly black, and symptomatic. They also had a higher frequency of baseline comorbidities, including hypertension and diabetes, and were more likely to present with abnormal laboratory findings including low lymphocyte counts and elevated creatinine. Lastly, receipt of mechanical ventilation and Hydroxychloroquine declined from March to August, while treatment with Dexamethasone and Remdesivir increased.CONCLUSIONWe found evidence of declining COVID-19 severity and fatality over time within a national health care system.
Novel method for the extraction of DNA from Lamniformes tooth and denticle enamel Suitable for PCR
Authors: Swig Bryan , Collier Ralph S. 
Published: January 2021

AbstractExtraction of high-quality genomic DNA from Lamniformes tooth fragment and dermal denticle enamel is discussed as a method of identifying individual sharks. We describe a procedure that permits isolation of genomic DNA of satisfactory size and quality for PCR analysis, as well as for most routine cloning applications. This method should allow for the non-invasive collection of genomic samples from Lamniformes.
Investigating the effect of Ser256 phosphorylation on gating of aquaporin-2: Molecular Dynamics study
Authors: Priyadarshini Pragya , Singh Balvinder 
Published: January 2021

AbstractRegulation of water transport via aquaporins is crucial for osmoregulation and water homeostasis of an organism. This transport of water is regulated either by gating or trafficking wherein AQPs are transported from intracellular storage sites to plasma membrane. It has been proposed that water movement via AQP2 is regulated by post-translational modification. We aimed to explore the structural and functional changes occurring in AQP2 due to Ser256 phosphorylation. We have carried out molecular dynamics simulations to investigate molecular basis of effect of phosphorylation on water permeability of AQP2. MD simulations show that there are mild variations in the pore sizes of different monomers of the phosphorylated and unphosphorylated AQP2. Analysis of inter and intra-monomeric interactions such as hydrogen bond, electrostatic and hydrophobic interactions has been carried out. Structures of the phosphorylated AQP2 do not show any blocking of mouth of pore of the monomers during the course of MD simulations. Further, water permeability calculations do corroborate the above finding. This molecular dynamics study suggests that phosphorylation of C-terminal Ser-256 residue of AQP2 may not be directly responsible for gating mechanism.
Time-resolved FRET screening identifies small molecular modifiers of mutant Huntingtin conformational inflexibility in patient-derived cells
Authors: Wilbertz Johannes H. , Frappier Julia , Muller Sandra , Gratzer Sabine , Englaro Walter , Stanek Lisa M. , Calamini Barbara 
Published: January 2021

AbstractHuntington’s disease (HD) is the most common monogenic neurodegenerative disease and is fatal. CAG repeat expansions in mutant Huntingtin (mHTT) exon 1 encode for polyglutamine (polyQ) stretches and influence age of onset and disease severity, depending on their length. mHTT is more structured compared to wild-type (wt) HTT, resulting in a decreased N-terminal conformational flexibility. mHTT inflexibility may contribute to both gain of function toxicity, due to increased mHTT aggregation propensity, but also to loss of function phenotypes, due to decreased interactions with binding partners. High-throughput-screening techniques to identify mHTT flexibility states and potential flexibility modifying small molecules are currently lacking. Here, we propose a novel approach for identifying small molecules that restore mHTT’s conformational flexibility in human patient fibroblasts. We applied an antibody-based time-resolved Förster resonance energy transfer (TR-FRET) immunoassay, measuring endogenous HTT flexibility using two validated HTT-specific antibodies. The ratio of TR-FRET signal at 4°C and 20°C differs between wtHTT and mHTT and allowed to perform a high-throughput screening using HTT flexibility as a read-out. We identified several small molecules that can partially rescue mHTT inflexibility, presumably by altering HTT post-translational modifications. This novel screening approach has the potential to identify previously unknown HD drugs and drug targets.
Changing Patterns and Drivers of Increased Pesticides Use in Smallholder Vegetable Production Systems in Tanzania
Authors: Kapeleka Jones A. , Sauli Elingarami , Sadik Omowunmi , Ndakidemi Patrick A. 
Published: January 2021

AbstractPesticides use has become a key component of smallholder horticulture production. Therefore, dynamics in pesticides handling need to be ascertained. This study assessed drivers of pesticides use and determinants of changing patterns of pesticides handling practices in smallholder vegetable systems. Data were collected from 385 farmers from Iringa, Arusha, Manyara, and Kilimanjaro regions in Tanzania through an in-depth survey and field observations. A binary probit model was used to derive factors fostering increased pesticides use. Results showed that 47.9 % of all pesticides were wrongly used. Most farmers (88.6%) lacked knowledge of pest control and 88.9% were unaware of safety practices. Disposal methods of empty pesticides foster occupational and environmental exposure (58%). There was an increasing trend in pesticides use (58.4%), accompanied by changing pesticides formulations. Over 60 pesticides with 29 different formulations were used. Mixing pesticides (71.2%), high dose rates with increased frequency of application were observed. Pesticides under Class II WHO hazard (68.9%) dominated. Extremely hazardous (Class Ia) and highly hazardous (Class Ib) were also used. Binary probit model showed that number of crops grown, pesticides mixing, and region contributed positively to the likelihood of increased pesticides use while farmers’ perception of effectiveness of pesticides, lack of access to safe use information, poor use of safety gears and inability to read pesticides labels had a negative impact. The fate of pesticides use in smallholder vegetable production systems is therefore the culmination of serious health and environmental implications. Excessive pesticides use escalated by increased number of crops, improper use of PPE, and pesticides mixing practices subjects the general population to pesticides environmental exposure thereby jeopardizing sustainability of smallholder vegetable production in Tanzania. Regular training to farmers and extension officers on current and emerging issues on pests and pesticide safe use is vital.
The viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape
Authors: Vandermeulen Charlotte , O’Grady Tina , Galvan Bartimee , Cherkaoui Majid , Desbuleux Alice , Coppin Georges , Olivet Julien , Ameur Lamya Ben , Kataoka Keisuke , Ogawa Seishi , Thiry Marc , Mortreux Franck , Calderwood Michael A. , Hill David E. , Van Weyenbergh Johan , Charloteaux Benoit , Vidal Marc , Dequiedt Franck , Twizere Jean-Claude 
Published: January 2021

SUMMARYWhile viral infections are known to hijack the transcription and translation of the host cell, the extent to which encoded viral proteins coordinate these perturbations remains unclear. Here we demonstrate that the oncoviral proteins Tax and HBZ interact with specific components of the spliceosome machinery, including the U2 auxiliary factor large subunit (U2AF2), and the complementary factor for APOBEC-1 (A1CF), respectively. Tax and HBZ perturb the splicing landscape in T-cells by altering cassette exons in opposing manners, with Tax inducing exon inclusion while HBZ induces exon exclusion. Among Tax- and HBZ-dependent splicing changes, we identify events that are also altered in Adult T cell leukemia (ATL) patients, and in well-known cancer census genes. Our interactome mapping approach, applicable to other viral oncogenes, has identified spliceosome perturbation as a novel mechanism coordinately used by Tax and HBZ to reprogram the transcriptome.HighlightsTax and HBZ interact with RNA-binding proteins as well as transcription factorsHTLV-1 encoded proteins Tax and HBZ alter the splicing landscape in T-cellsTax and HBZ expression affect alternative splicing of 33 and 63 cancer genes, respectivelyOpposing roles for Tax and HBZ in deregulation of gene expressionGraphical abstract
Δ9-tetrahydrocannabinol inhibits Hedgehog-dependent patterning during development
Authors: Lo Hsiao-Fan , Hong Mingi , Szutorisz Henrietta , Hurd Yasmin L. , Krauss Robert S. 
Published: January 2021

AbstractMany birth defects are thought to arise from a multifactorial etiology; i.e., interaction between genetic and environmental risk factors. The Hedgehog (HH) signaling pathway regulates myriad developmental processes, and pathway inhibition is associated with birth defects, including holoprosencephaly (HPE). Cannabinoids are HH pathway inhibitors, but little is known of their effects on HH-dependent processes in mammalian embryos, and their mechanism of action is unclear. We report here that the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC) induces two hallmark HH loss-of-function phenotypes (HPE and ventral neural tube patterning defects) inCdonmutant mice, which have a subthreshold deficit in HH signaling. THC therefore acts as a “conditional teratogen”, dependent on a complementing but insufficient genetic insult. In vitro findings indicate that THC is a direct, albeit relatively weak, inhibitor of the essential HH pathway component, Smoothened. In contrast, the canonical THC receptor, cannabinoid receptor-type 1, is not required for THC to inhibit HH signaling. Cannabis consumption during pregnancy may contribute to the combination of risk factors underlying specific developmental disorders. These findings therefore have significant public health relevance.
Individual differences in representational similarity of first and second languages in the bilingual brain
Authors: Nichols Emily S. , Gao Yue , Fregni Sofia , Liu Li , Joanisse Marc F. 
Published: January 2021

AbstractCurrent theories of bilingualism disagree on the extent to which separate brain regions are used to maintain or process one’s first and second language. The present study took a novel multivariate approach to address this question. We examined whether bilinguals maintain distinct neural representations of two languages; specifically, we tested whether brain areas that are involved in processing word meaning in either language are reliably representing each language differently, and whether language representation is influenced by individual differences in proficiency level and age of acquisition of L2. Thirty-one English-Mandarin bilingual adults performed a picture-word matching task in both languages. We then used representational similarity analysis to examine which brain regions reliably showed different patterns of activity for each language. As a group, there were no regions that reliably represented languages distinctly. However, both proficiency and age of acquisition predicted dissimilarity between language representations in several brain areas within the language network as well as several regions of the ventral visual pathway, demonstrating that top-down language knowledge and individual language experience shapes concept representation in the processing stream. The results support the model of an integrated language system in bilinguals, along with a novel description of how representations for each language change with proficiency level and L2 age of acquisition.
Voxelwise encoding models show that cerebellar language representations are highly conceptual
Authors: LeBel Amanda , Jain Shailee , Huth Alexander G. 
Published: January 2021

AbstractThere is a growing body of research demonstrating that the cerebellum is involved in language understanding. Early theories assumed that the cerebellum is involved in low-level language processing. However, those theories are at odds with recent work demonstrating cerebellar activation during cognitive tasks. Using natural language stimuli and an encoding model framework, we performed an fMRI experiment where subjects passively listened to five hours of natural language stimuli which allowed us to analyze language processing in the cerebellum with higher precision than previous work. We used this data to fit voxelwise encoding models with five different feature spaces that span the hierarchy of language processing from acoustic input to high-level conceptual processing. Examining the prediction performance of these models on separate BOLD data shows that cerebellar responses to language are almost entirely explained by high-level conceptual language features rather than low-level acoustic or phonemic features. Additionally, we found that the cerebellum has a higher proportion of voxels that represent social semantic categories, which include “social” and “people” words, and lower representations of all other semantic categories, including “mental”, “concrete”, and “place” words, than cortex. This suggests that the cerebellum is representing language at a conceptual level with a preference for social information.Significance StatementRecent work has demonstrated that, beyond its typical role in motor planning, the cerebellum is implicated in a wide variety of tasks including language. However, little is known about the language representations in the cerebellum, or how those representations compare to cortex. Using voxelwise encoding models and natural language fMRI data, we demonstrate here that language representations are significantly different in the cerebellum as compared to cortex. Cerebellum language representations are almost entirely semantic, and the cerebellum contains over-representation of social semantic information as compared to cortex. These results suggest that the cerebellum is not involved in language processing per se, but cognitive processing more generally.
Metagenomic methylation patterns resolve complex microbial genomes
Authors: Wilbanks Elizabeth G. , Doré Hugo , Ashby Meredith H. , Heiner Cheryl , Roberts Richard J. , Eisen Jonathan A. 
Published: January 2021

AbstractThe plasticity of bacterial and archaeal genomes makes examining their ecological and evolutionary dynamics both exciting and challenging. The same mechanisms that enable rapid genomic change and adaptation confound current approaches for recovering complete genomes from metagenomes. Here, we use strain-specific patterns of DNA methylation to resolve complex bacterial genomes from the long-read metagenome of a marine microbial consortia, the “pink berries” of the Sippewissett Marsh. Unique combinations of restriction-modification (RM) systems encoded by the bacteria produced distinctive methylation profiles that accurately binned and classified metagenomic sequences. We linked the methylation patterns of each metagenome-assembled genome with encoded DNA methyltransferases and discovered new restriction modification (RM) defense systems, including novel associations of RM systems with RNase toxins. Using this approach, we finished the largest and most complex circularized bacterial genome ever recovered from a metagenome (7.9 Mb with >600 IS elements), the finished genome ofThiohalocapsasp. PB-PSB1 the dominant bacteria in the consortia. From these methylation-binned genomes, we identified instances of lateral gene transfer between sulfur-cycling symbionts (Thiohalocapsasp. PB-PSB1 andDesulfofustissp. PB-SRB1), phage infection, and strain-level structural variation.
Measuring competitiveness through the global competitiveness project framework: the Brazilian experience
Authors: De Montreuil Carmona Linda Jessica , Gomes Giancarlo 
Published: January 2021

Purpose
The purpose of this paper is twofold: first, to validate the global competitiveness project (GCP) framework in the Brazilian context; second, to describe the competitiveness levels on a sample of Brazilian firms, searching for heterogeneities of size, age and industry.

Design/methodology/approach
The study used the theoretical-empirical GCP framework, comprising the dimensions: human capital, product, domestic market, networks, technology, decision-making, competitive strategy, marketing, internationalization and online presence (Lafuente, Szerb and Rideg, 2016; Lafuente et al., 2019) and applied descriptive statistics, correlation analysis, confirmatory factor analysis and cluster analysis, on a survey data set of 55 Brazilian firms from different sizes, ages and industries.

Findings
The GCP framework was found robust, reliable and useful in emerging economies as the Brazilian. Three clusters of competitiveness were identified. Heterogeneities were detected in knowledge-intensive business services results. This work allows a better understanding of competitiveness through the identification and measurement of dimensions, which can help managers to identify/audit capacities to plan/improve firm performance.

Practical implications
Findings may support managers to identify, estimate and manage their competitiveness pillars, and thus increase their competitiveness levels with a focus on strategic long-term goals.

Originality/value
This paper contributes to knowledge production in two ways: to the validation of the framework in the Brazilian scenario and the understanding of the dynamics of competitiveness of firms.