bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative Wireless Device for Remote Continuous Blood Biomarker Monitoring
Authors: Phan Dinh-Tuan , Zeming Kerwin Kwek , Lian Sophie Wan Mei , Jin Lin , Dinh Ngoc-Duy , Chen Chia-Hung 
Published: May 2021

ABSTRACTTo perform precision medicine in real-time at home, a device capable of long-distance continuously monitoring target biomolecules in unprocessed blood under dynamic situations is essential. In this study, an integrative buffer-free wireless device is developed to measure drug concentrations in patient’s blood in real time for remote clinical healthcare. To demonstrate its capability, the drug molecules (i.e., small-molecule drug doxorubicin, DOX) are continuously measured in the unprocessed whole blood of live animals (e.g., rats). The dynamic changes of drug concentrations with sub-minute temporal resolution are recorded for an extended period of time (∼8 hours). As an advance in remote diagnosis, this device would benefit the public by enabling long-distance precision medicine to prevent pandemics in advance.
Mining endophytic microbiome information from plant and animal transcriptome data
Authors: Han Guomin , Wang Xianjin , Qiu Guiping 
Published: May 2021

AbstractEndophytic microorganisms play important physiological functions in plants and animals. In this paper, we developed a method to obtain endophytic microbiome information directly by analyzing transcriptome sequencing data files of plants and animals. Compared with the use of amplicon analysis or whole-genome sequencing of animal and plant tissues to analyze microbial composition information, this method can obtain endophytic microbiome information in addition to obtaining gene expression information of host plants and animals.
Bibliometric analysis of parental anxiety and postpartum depression across the perinatal period from 1920-2020: A protocol
Authors: Dol Justine , Campbell-Yeo Marsha , Dennis Cindy-Lee , Leahy-Warren Patricia 
Published: May 2021

ABSTRACTIntroductionThroughout the perinatal period from pregnancy to the first year postpartum, both men and women experience significant physical, psychological, and social changes which may increase their risk of a mental illness, including anxiety and depression. There has been significant growth in the frequency literature around anxiety and depression across the perinatal period over the past decades with significant variation in definition, measurement outcomes, and populations. To focus future research and identify gaps, it is important to explore current patterns and trends in the current literature.ObjectiveThe objective of this bibliometric analysis is to analyze the characteristics and trends in published research on anxiety and depression across the perinatal period from January 1, 1920 to end of 2020.Inclusion criteriaAll published literature in Web of Science on perinatal anxiety and depression from January 1, 1920 to December 31, 2020.MethodsWeb of Science will be used to analyze bibliometric information through their built-in analysis feature and citation report that generates a list of leading publications, publication years, document types, authors, source titles, countries/regions, organizations, and research areas. VOSViewer will be utilized to analyze and visualize the networks of linkages between the identified reports, including bibliometric networks, including co-authorship, co-occurrence, and co-citation, as well as co-occurrence between keywords.ConclusionThe findings from this study will provide useful information to guide future work on perinatal anxiety and depression. This bibliometric review will provide an overview of the work to date in perinatal mental health, identify key contributions to the field, and identify knowledge gaps and future directions.
The Core Human Fecal Metabolome
Authors: Haffner Jacob J. , Katemauswa Mitchelle , Kagone Thérèse S. , Hossain Ekram , Jacobson David , Flores Karina , Parab Adwaita R. , Obregon-Tito Alexandra J. , Tito Raul Y. , Reyes Luis Marin , Troncoso-Corzo Luzmila , Guija-Poma Emilio , Meda Nicolas , Carabin Hélène , Honap Tanvi P. , Sankaranarayanan Krithivasan , Lewis Cecil M. , McCall Laura-Isobel 
Published: May 2021

Summary ParagraphAmong the biomolecules at the center of human health and molecular biology is a system of molecules that defines the human phenotype known as the metabolome. Through an untargeted metabolomic analysis of fecal samples from human individuals from Africa and the Americas—the birthplace and the last continental expansion of our species, respectively—we present the characterization of the core human fecal metabolome. The majority of detected metabolite features were ubiquitous across populations, despite any geographic, dietary, or behavioral differences. Such shared metabolite features included hyocholic acid and cholesterol. However, any characterization of the core human fecal metabolome is insufficient without exploring the influence of industrialization. Here, we show chemical differences along an industrialization gradient, where the degree of industrialization correlates with metabolomic changes. We identified differential metabolite features like leucyl-leucine dipeptides and urobilin as major metabolic correlates of these behavioral shifts. Our results indicate that industrialization significantly influences the human fecal metabolome, but diverse human lifestyles and behavior still maintain a core human fecal metabolome. This study represents the first characterization of the core human fecal metabolome through untargeted analyses of populations along an industrialization gradient.
Adapting to extremes: reconstructing evolution in response to changing climate over time and space in the diverse Australian plant genus Acacia
Authors: Hua Xia , Cardillo Marcel , Bromham Lindell 
Published: May 2021

AbstractAimMacroevolutionary analysis is increasingly being used to study biodiversity responses to climate change, for example by using phylogenetic node ages to infer periods of diversification, or phylogenetic reconstruction of traits to infer adaptation to particular stresses. Here we apply a recently developed macroevolutionary method to investigate the responses of a diverse plant genus, Acacia, to increasing aridity and salinity in Australia from the Miocene to the present. We ask whether increase in tolerance of aridity and salinity coincided with periods of aridification, and if it allowed the radiation of Acacia into a wide range of niches.TaxonAcaciaLocationAustraliaMethodsWe applied the Niche Evolution Model (NEMo), which combines Environmental (or Ecological) Niche Modelling (ENM) with phylogenetic comparative methods (PCM) in a single statistical framework, to a large database of Acacia presence-only records and presence-absence survey sites in order to infer current environmental tolerances of Australia Acacia species and reconstruct the evolution of environmental tolerance to increasing aridity and salinity.ResultsWe find that patterns in evolution of Acacia, over time and across different habitat types, are consistent with the aridification history of Australia and suggests substantial ability to adapt to high aridity and salinity.Main conclusionsOur results suggest that many Acacia lineages have been able to exploit new environments created during the aridification of Australia through evolution of environmental tolerance, resulting in their current dominance of many habitats across the continent. This study demonstrates that phylogenetic studies of the evolution of responses to changing environment can move beyond application of simple trait-based models, allowing the underlying processes of speciation, adaptation and dispersal to be explicitly modelled in a macroecological and macroevolutionary context.Statement of significanceAcacia species are found throughout Australia, from rainforests to deserts, and are striking in their environmental adaptability, so they are a perfect case study for understanding evolution of tolerance to environmental extremes in a changing climate. We use the largest database of spatial distribution records yet assembled, using both surveys and atlas data, and a new analytical method that combines the strengths of environmental niche modelling with phylogenetic comparative methods, to demonstrate rapid evolution in aridity and salinity tolerance in response to aridification of the Australian continent during the Neogene and Quaternary.
Multiple ancestral duplications of the red-sensitive opsin gene (LWS) in teleost fishes and convergent spectral shifts to green vision in gobies
Authors: Cortesi Fabio , Camacho Daniel Escobar , Luehrmann Martin , Sommer Gina Maria , Musilova Zuzana 
Published: May 2021

AbstractPhotopigments, consisting of an opsin protein bound to a light-sensitive chromophore, are at the centre of vertebrate vision. The vertebrate ancestor already possessed four cone opsin classes involved in colour perception during bright-light conditions, which are sensitive from the ultraviolet to the red-wavelengths of light. Teleosts experienced an extra round of whole genome duplication (3R) at their origin, and while most teleosts maintained only one long-wavelength-sensitive opsin gene (LWS1), the second ancestral copy (LWS2) persisted in characins and osteoglossomorphs. Following 3R, teleost opsins have continued to expand and diversify, which is thought to be a consequence of the different light environment fishes inhabit, from clear streams to the relative darkness of the deep-sea. Although many recent and a few ancestral opsin duplicates can be found, none predating the 3R were thought to exist. In this study we report on a second, previously unnoticed ancestral duplication of the red-sensitive opsin (LWS3), which predates the teleost-specific genome duplication and only persists in gobiid fishes. This is surprising, since it implies thatLWS3has been lost at least 19-20 times independently along the teleost phylogeny. Mining 109 teleost genomes we also uncover a third lineage, the elopomorphs, that maintained theLWS2copy. We identify convergent amino acid changes that green-shift ancestral and recentLWScopies, leading to adaptive differentiation and the functional replacement of the original green-sensitiveRH2opsin. Retinal transcriptomes and in-situ hybridisation show thatLWS3is expressed to various extents in gobies and in the case of the whitebarred goby,Amblygobius phalaena, it occurs in a separate photoreceptor toLWS1. Our study highlights the importance of comparative studies to comprehend evolution of gene function.
Structural and mechanistic basis of reiterative transcription initiation
Authors: Liu Yu , Winkelman Jared T. , Yu Libing , Pukhrambam Chirangini , Firlar Emre , Kaelber Jason T , Zhang Yu , Nickels Bryce E. , Ebright Richard H. 
Published: May 2021

AbstractReiterative transcription initiation, observed at promoters that contain homopolymeric sequences at the transcription start site, generates RNA products having 5’ sequences non-complementary to the DNA template. Here, using crystallography and cryo-EM to define structures, protein-DNA-photocrosslinking to map positions of RNAP leading and trailing edges relative to DNA, and single-molecule DNA nanomanipulation to assess RNAP-dependent DNA unwinding, we show that RNA extension in reiterative transcription initiation: (1) occurs without DNA scrunching, (2) involves a short, 2-3 bp RNA-DNA hybrid, and (3) generates RNA that exits RNAP through the portal by which scrunched nontemplate-strand DNA exits RNAP in standard transcription initiation. The results establish that, whereas RNA extension in standard transcription initiation proceeds through a scrunching mechanism, RNA extension in reiterative transcription initiation proceeds through a slippage mechanism, with slipping of RNA relative to DNA within a short RNA-DNA hybrid, and with extrusion of RNA from RNAP through an alternative RNA exit.
DETECTION OF ITALIAN NURSES’ THOUGHTS ON SEXUAL HEALTH AND THEIR KNOWLEDGE ON THE HIV-TRANSMISSION: A WEB SURVEY
Authors: Costanzo Italo 
Published: May 2021

ABSTRACTINTRODUCTIONDespite the prevention of sexually transmitted infections included HIV and promotion of sexual health are fundamental parts of human health, the education system in Italy does not seem to provide healthcare professionals with specific knowledge requested by the most recent discoveries on HIV transmission.METHODSA web survey was randomly administered to Italian nurses to collect their thoughts about the academic education they received and analyse their knowledge on one of the newest discoveries related to HIV transmission.RESULTSMore than half of the participants never received any specific academic training on sexual health and sexually transmitted infections, and more than three-quarters of the respondents did not know that a gay couple where only one of the partners is HIV positive will not have to use condoms forever and for every sexual intercourse.CONCLUSIONSThe survey suggests that training on sexual health and sexually transmitted infections of Italian nurses need to be reinforced and it also highlights the need of updating nurses on the <undetectable equals untransmittable> campaign.KEY POINTKnowledge related to sexual health and HIV needs to be expanded in Italian nurses.
Sources of information waste in neuroimaging: mishandling structures, thinking dichotomously, and over-reducing data
Authors: Chen Gang , Taylor Paul A. , Stoddard Joel , Cox Robert W. , Bandettini Peter A. , Pessoa Luiz 
Published: May 2021

AbstractNeuroimaging relies on separate statistical inferences at tens of thousands of spatial locations. Such massively univariate analysis typically requires an adjustment for multiple testing in an attempt to maintain the family-wise error rate at a nominal level of 5%. First, we examine three sources of substantial information loss that are associated with the common practice under the massively univariate framework: (a) the hierarchical data structures (spatial units and trials) are not well maintained in the modeling process; (b) the adjustment for multiple testing leads to an artificial step of strict thresholding; (c) information is excessively reduced during both modeling and result reporting. These sources of information loss have far-reaching impacts on result interpretability as well as reproducibility in neuroimaging. Second, to improve inference efficiency, predictive accuracy, and generalizability, we propose a Bayesian multilevel modeling framework that closely characterizes the data hierarchies across spatial units and experimental trials. Rather than analyzing the data in a way that first creates multiplicity and then resorts to a post hoc solution to address them, we suggest directly incorporating the cross-space information into one single model under the Bayesian framework (so there is no multiplicity issue). Third, regardless of the modeling framework one adopts, we make four actionable suggestions to alleviate information waste and to improve reproducibility: 1) abandon strict dichotomization, 2) report full results, 3) quantify effects, and 4) model data hierarchies. We provide examples for all of these points using both demo and real studies, including the recent NARPS investigation.
Elucidating the diversity of microeukaryotes and epi-endophytes in the brown algal holobiome
Authors: Markussen Bjorbækmo Marit F. , Brodie Juliet , Krabberød Anders K. , Logares Ramiro , Attwood Stephanie , Fredriksen Stein , Fuss Janina , Wold-Dobbe Anders , Shalchian-Tabrizi Kamran , Bass David 
Published: May 2021

AbstractBackgroundBrown algae (Phaeophyceae) are essential species in coastal ecosystems where they form kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology. The bacterial microbial partners of brown algae have received far more attention than microbial eukaryotes. To our knowledge, this is the first study to investigate brown algal-associated eukaryotes (the eukaryome) using broadly targeting ‘pan-eukaryotic’ primers and high throughput sequencing (HTS). Using this approach, we aimed to unveil the eukaryome of seven large common brown algal species. We also aimed to assess whether these macroalgae harbour novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome, based on taxonomic affiliation and phylogenetic placement.ResultsOur sequence dataset was dominated by brown algal reads, from the host species and potential symbionts. We also detected a broad taxonomic diversity of eukaryotes in the brown algal holobiomes, with OTUs taxonomically assigned to ten of the eukaryotic major Kingdoms or supergroups. A total of 265 microeukaryotic and epi-endophytic operational taxonomic units (OTUs) were defined, using 97% similarity cut off during clustering, and were dominated by OTUs assigned to stramenopiles, Alveolata and Fungi. Almost one third of the OTUs we detected have not been found in previous molecular environmental surveys, and represented potential novel eukaryotic diversity. This potential novel diversity was particularly prominent in phylogenetic groups comprising heterotrophic and parasitic organisms, such as labyrinthulids and oomycetes, Cercozoa, and Amoebozoa.ConclusionsOur findings provide important baseline data for future studies of seaweed-associated microorganisms, and demonstrate that microeukaryotes and epi-endophytic eukaryotes should be considered as an integral part of brown algal holobionts. The potential novel eukaryotic diversity we found and the fact that the vast majority of macroalgae in marine habitats remain unexplored, demonstrates that brown algae and other seaweeds are potentially rich sources for a large and hidden diversity of novel microeukaryotes and epi-endophytes.
Hyperinflammation evokes different antiviral TMPRSS2 and ADAM17 expression responses in human gut xenograft versus host mouse gut although overall genomic responses are similar
Authors: Morris Lorna , Nisim-Eliraz Einat , Schouten Iftach , Bergey François , Dyer Nigel , Momiji Hiroshi , Nir Eilam , Marsiano Noga , Tezerji Raheleh Sheibani , Yagel Simcha , Rosenstiel Philip , Rand David , dos Santos Vitor A.P. Martins , Shpigel Nahum Y. ,   SysmedIBD research consortium
Published: May 2021

ABSTRACTThe global spread of the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the pandemic outbreak of coronavirus disease 2019 (COVID-19), an inflammatory disease that is primarily affecting the respiratory system. However, gastrointestinal symptoms in COVID-19 patients suggests that the gut may present another viral target organ. Disease development and severity is dependent on viral interaction with two cell surface human proteins, ACE2 and TMPRSS2, and on antiviral response which may lead to systemic hyperinflammatory syndrome and multiorgan dysfunction. Understanding the host response to SARS-CoV-2 infection and the pathology of the disease will be greatly enhanced by the development of appropriate animal models. Laboratory mice have been the mainstay of therapeutic and vaccine development, however, the virus does not grow in wild type mice and only induced mild disease in transgenic animals expressing human ACE2. As there are known differences between immune response in laboratory mice and humans we evaluated the response of human gut developed as xenografts and host mouse gut following systemic LPS injections as a hyperinflammation model system. The orthologous gene expression levels in the mouse and human gut were highly correlated (Spearman’s rank correlation coefficient: 0.28–0.76) and gene set enrichment analysis of significantly upregulated human and mouse genes revealed that a number of inflammatory and immune response pathways are commonly regulated in the two species. However, species differences were also observed, most importantly, in the inflamed human gut but not in the mouse gut, there was clear upregulation of mRNAs coding for TMPRSS2, ADAM17 and for RIG-I-like receptors, which are involved in the recognition of viruses and in antiviral innate immune response. Moreover, using species-specific immunofluorescence microscopy, we demonstrated the expression and localization of human ACE2 and TMPRSS2 proteins, which are essential elements of the molecular machinery that enables SARS-CoV-2 to infect and replicate in human gut cells. Our findings demonstrate that the intestinal immune response to inflammation in humans and mice are generally very similar. However, certain human-specific diseases, such as COVID-19, can only be successfully studied in an experimental model of human tissue, such as the gut xenograft.
Investigating VCAM-1 Targeted Nanoparticles and Annexin A1 Therapy using Dysfunctional-endothelium-on-a-chip
Authors: Bazban-Shotorbani Salime , Kamaly Nazila 
Published: May 2021

AbstractAtherosclerosis is an inflammation-driven disease of the arteries and one of the leading causes of global mortality. The initial pathological stage in atherosclerosis is dysfunctional endothelium (Dys-En), which results in loss of adherens-junctions between cells, thus enhancing permeability. Not only the enhanced permeability of Dys-En can be used as a nanoparticle targeting mechanism, but also the normalization and restoration of this phenomenon can be utilized as a potent anti-atherosclerotic therapy. This study aimed to recruit a robust biomicrofluidic model of Dys-En for 1) nanoparticle screening and 2) normalization assessments. The developed Dys-En-on-a-chip could successfully mimic the atherosclerotic flow condition, enhanced permeability, formation of actin stress fibers, and overexpression of vascular cell adhesion molecule 1 (VCAM-1), which are known as hallmarks of a Dys-En. The screening of VCAM-1 targeting nanoparticles with variable biophysicochemical properties showed that nanoparticle size plays the main role in nanoparticle targeting, and the design of nanoparticles in the range of 30-60 nm can highly increase their targeting to Dys-En. Moreover, treatment of Dys-En-on-a-chip with Annexin A1, as a novel pro-resolving mediator, resulted in restoration of adherens-junctions and normalization of the barrier integrity. This data validates the use of biomicrofluidic models for investigating treatment regimens with biologics and to identify optimal nanoparticle properties for effective atherosclerotic plaque targeting.