bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput miRNA-sequencing of the human placenta: expression throughout gestation
Authors: Gonzalez Tania L , Eisman Laura E , Joshi Nikhil V , Flowers Amy E , Wu Di , Wang Yizhou , Santiskulvong Chintda , Tang Jie , Buttle Rae A , Sauro Erica , Clark Ekaterina L , DiPentino Rosemarie , Jefferies Caroline A , Chan Jessica L , Lin Yayu , Zhu Yazhen , Afshar Yalda , Tseng Hsian-Rong , Taylor Kent , Williams John , Pisarska Margareta D 
Published: February 2021

AbstractBackgroundAltered placenta miRNA abundance may impact the maternal-fetal interface and pregnancy outcomes. Understanding miRNA changes across gestation is essential before miRNAs can be used as biomarkers or prognostic indicators during pregnancy.Materials & MethodsUsing next-generation sequencing, we characterize the normative human placenta miRNA transcriptome in first (N=113) and third trimester (N=47).ResultsThere are 801 miRNAs expressed in both first and third trimester, including 182 with similar expression across gestation (P≥0.05) and 182 significantly different (FDR<0.05). Of placenta-specific miRNA clusters, C14MC is more upregulated in first trimester and C19MC is more highly expressed overall.ConclusionThis work provides a rich atlas of healthy pregnancies to direct functional studies investigating the epigenetic differences in first and third trimester placentae.Lay AbstractThe human body produces microRNAs which affect the expression of genes and proteins. This study uses next generation sequencing to identify the microRNA profile of first and third trimester human placentae using a large cohort (N=113 first, N=47 third trimester). All pregnancies resulted in healthy babies. We identify microRNAs with significantly different expression between first and third trimester, as well as stably expressed microRNAs. This work provides a baseline for future studies which may use microRNAs to monitor maternal-fetal health throughout pregnancy.
Population genetics as a tool to elucidate pathogen reservoirs: Lessons fromPseudogymnoascus destructans, the causative agent of white-nose disease in bats
Authors: Fischer Nicola M. , Altewischer Andrea , Ranpal Surendra , Dool Serena , Kerth Gerald , Puechmaille Sébastien J. 
Published: February 2021

AbstractEmerging infectious diseases pose a major threat to human, animal, and plant health. The risk of species-extinctions increases when pathogens can survive in the absence of the host, for example in environmental reservoirs. However, identifying such reservoirs and modes of infection is often highly challenging. In this study, we investigated the presence and nature of an environmental reservoir for the ascomycete fungusPseudogymnoascus destructans, the causative agent of white-nose disease. We also characterised the modes and timing of transmission of the pathogen; key elements to better understand the disease dynamics. Using 18 microsatellite markers, we determined the genotypic and genic (based on allele frequencies) differentiation between 1,497P. destructansisolates collected from nine closely situated hibernacula in North-Eastern Germany. One hibernaculum was the focus of intensive sampling in which both the bats and walls of the site were sampled at regular intervals over five consecutive winter seasons (1,062 isolates). We found significant genic differentiation between sites and few multi-locus genotypes shared across hibernacula (genotypic differentiation). This demonstrates that each hibernaculum has an essentially unique population of the fungus. This would be expected if bats purge viableP. destructansover the summer, preventing the mixing and exchange of the pathogen in maternity colonies, where bats from all of the studied hibernacula meet. Results from the intensively sampled site show higher measures of genotypic richness on walls compared to bats, the absence of genic differentiation between bats and walls, and stable relative abundance of multi-locus genotypes over multiple winter seasons. This clearly implicates hibernacula walls as the main environmental reservoir of the pathogen, from which bats become re-infected annually.
Expanding the SiMPl plasmid toolbox for use with spectinomycin/streptomycin
Authors: Palanisamy Navaneethan , Ballestin Ballestin Jara , Di Ventura Barbara 
Published: February 2021

ABSTRACTWe recently developed the SiMPl plasmid toolbox, which is constituted by pairs of plasmids, generically indicated as pSiMPlx_N and pSiMPlx_C, which can be stably maintained inEscherichia coliwith a single antibiotic x. The method exploits the split intein gp41-1 to reconstitute the enzyme conferring resistance towards the antibiotic x, whereby each enzyme fragment is expressed from one of the plasmids in the pair. pSiMPl plasmids are currently available for use with ampicillin, kanamycin, chloramphenicol, hygromycin and puromycin. Here we introduce another pair for use with spectinomycin/streptomycin broadening the application spectrum of the SiMPl toolbox. To find functional splice sites in aminoglycoside adenylyltransferase we apply a streamlined strategy looking exclusively at the flexibility of native cysteine and serine residues, which we first validated splitting the enzymes conferring resistance towards ampicillin, kanamycin, chloramphenicol and hygromycin. This strategy could be used in the future to split other enzymes conferring resistance towards antibiotics.
Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH
Authors: Rensen Elena , Pietropaoli Stefano , Mueller Florian , Weber Christian , Souquere Sylvie , Isnard Pierre , Rabant Marion , Gibier Jean-Baptiste , Simon-Loriere Etienne , Rameix-Welti Marie-Anne , Pierron Gérard , Barba-Spaeth Giovanna , Zimmer Christophe 
Published: February 2021

AbstractThe current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The positive-sense single-stranded RNA virus contains a single linear RNA segment that serves as a template for transcription and replication, leading to the synthesis of positive and negative-stranded viral RNA (vRNA) in infected cells. Tools to visualize viral RNA directly in infected cells are critical to analyze its replication cycle, screen for therapeutic molecules or study infections in human tissue. Here, we report the design, validation and initial application of fluorescencein situhybridization (FISH) probes to visualize positive or negative RNA of SARS-CoV-2 (CoronaFISH). We demonstrate sensitive visualization of vRNA in African green monkey and several human cell lines, in patient samples and human tissue. We further demonstrate the adaptation of CoronaFISH probes to electron microscopy (EM). We provide all required oligonucleotide sequences, source code to design the probes, and a detailed protocol. We hope that CoronaFISH will complement existing techniques for research on SARS-CoV-2 biology and COVID-19 pathophysiology, drug screening and diagnostics.
Does Food Insecurity exist among Farm Households? Evidence from Ghana
Authors: Acheampong Patricia Pinamang , Obeng Elvis Agyei , Opoku Monica , Brobbey Lydia , Sakyiamah Bernard 
Published: February 2021

AbstractHousehold food security exists when households have physical, social and economic access to sufficient, safe and nutritious food at all times that meets their dietary needs and food preferences for an active and healthy life. Food security remains a serious challenge for many households in Ghana and the situation is even more prevalent among smallholder farmers. Using data collected from 2,603 farm households across Ghana and employing an ordered probit model the determinants of food security among farm households were assessed. The food security indicator-Food Consumption Score (FCS) which combines diet diversity, frequency of consumption and relative nutritional importance of different food groups was used for the analysis. Results indicated that farm households (76%) across Ghana were within the acceptable household food consumption groups. Nonetheless, 19% and 6% of farm households respectively were within the borderline and poor food consumption groups respectively. Further analysis revealed the determinants of food security to include experience, gender, improved variety adoption, access to credit and location. The suggestion is that government and private institutions should create an enabling environment to enhancing production capacities, economic and social resilience to improve on food security and nutrition.
Prioritization of antimicrobial targets by CRISPR-based oligo recombineering
Authors: Benns HJ. , Storch M. , Falco J. , Fisher FR. , Alves E. , Wincott CJ. , Baum J. , Baldwin GS. , Weerapana E. , Tate EW. , Child MA. 
Published: February 2021

SummaryNucleophilic amino acids are important in covalent drug development yet underutilized as antimicrobial targets. Over recent years, several chemoproteomic technologies have been developed to mine chemically-accessible residues via their intrinsic reactivity toward electrophilic probes. However, these approaches cannot discern which reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based Oligo Recombineering (CORe) platform to systematically prioritize reactive amino acids according to their contribution to protein function. Our approach directly couples protein sequence and function with biological fitness. Here, we profile the reactivity of >1,000 cysteines on ~700 proteins in the eukaryotic pathogenToxoplasma gondiiand prioritize functional sites using CORe. We competitively compared the fitness effect of 370 codon switches at 74 cysteines and identify functional sites in a diverse range of proteins. In our proof of concept, CORe performed >800 times faster than a standard genetic workflow. Reactive cysteines decorating the ribosome were found to be critical for parasite growth, with subsequent target-based screening validating the apicomplexan translation machinery as a target for covalent ligand development. CORe is system-agnostic, and supports expedient identification, functional prioritization, and rational targeting of reactive sites in a wide range of organisms and diseases.
Return of a lost structure in the evolution of felid dentition revisited: A DevoEvo perspective on the irreversibility of evolution
Authors: Lynch Vincent J. 
Published: February 2021

AbstractThere is a longstanding interest in whether the loss of complex characters is reversible (so-called “Dollo’s law”). Reevolution has been suggested for numerous traits but among the first was Kurtén (1963), who proposed that the presence of the second lower molar (M2) of the Eurasian lynx (Lynx lynx) was a violation of Dollo’s law because all other Felids lack M2. While an early and often cited example for the reevolution of a complex trait, Kurtén (1963) and Werdelin (1987) used anad hocparsimony argument to support their proposition that M2reevolved in Eurasian lynx. Here I revisit the evidence that M2reevolved in Eurasian lynx using explicit parsimony and maximum likelihood models of character evolution and find strong evidence that Kurtén (1963) and Werdelin (1987) were correct – M2reevolved in Eurasian lynx. Next, I explore the developmental mechanisms which may explain this violation of Dollo’s law and suggest that the reevolution of lost complex traits may arise from the reevolution of cis-regulatory elements and protein-protein interactions, which have a longer half-life after silencing that protein coding genes. Finally, I present a model developmental model to explain the reevolution M2in Eurasian lynx.
Mesothelial cell-derived antigen-presenting cancer-associated fibroblasts induce expansion of regulatory T cells in pancreatic cancer
Authors: Huang Huocong , Wang Zhaoning , Zhang Yuqing , Brekken Rolf A. 
Published: February 2021

SummaryMultiple recent single cell RNA sequencing (scRNA-seq) studies have identified a unique cancer-associated fibroblast (CAF) population in pancreatic ductal adenocarcinoma (PDA) called antigen-presenting CAFs (apCAFs). apCAFs are characterized by the expression of MHC II molecules, suggesting a function in regulating tumor immunity. Here we integrated multiple scRNA-seq studies and found that apCAFs are derived from mesothelial cells. Our data show that during PDA progression, mesothelial cells form apCAFs by down-regulating mesothelial features and gaining the fibroblastic features, a process induced by IL-1 and TGFβ. Moreover, apCAFs directly ligate and induce naïve CD4+T cells into regulatory T cells (Tregs) in an antigen-specific manner. Our study elucidates an important but neglected cell type in the regulation of PDA immunity and may lead to targeted therapeutic strategies that can overcome immune evasion in PDA.
An agent-based model for exploring the impacts of reciprocal trust on knowledge transfer within an organization
Authors: Li Hong , Li Changhong , Wang Zhan 
Published: February 2021

PurposeThe effective transfer of knowledge within an organization is critical for its sustainable competitive advantage. Based on the norm of reciprocity, it can be concluded that individuals’ primary motivation to transfer their treasured knowledge can be summarized as “trust,” that is, the individuals trust their selfless transfer behavior can be reciprocated by the recipients in the future.Design/methodology/approachIn this study, a simulation model based on knowledge transfer behavior and reciprocal trust between individuals is built through agent-based modeling and simulation to investigate the factors that influence the efficiency of knowledge transfer within an organization.FindingsExperiments are performed to test the impact of reciprocal trust and organizational structure on the efficiency of knowledge transfer.Originality/valueThe results indicate a significant role of key elements of reciprocal trust and organizational structure, which provides relevant practical guidance for both individuals and organization managers in the context of knowledge transfer.
Endolithic microbial composition in Helliwell Hills, a newly investigated Mars‐like area in Antarctica
Authors: Coleine Claudia , Biagioli Federico , de Vera Jean Pierre , Onofri Silvano , Selbmann Laura 
Published: February 2021

SummaryThe diversity and composition of Antarctic cryptoendolithic microbial communities in the Mars‐analogue site of Helliwell Hills (Northern Victoria Land, Continental Antarctica) are investigated, for the first time, applying both culture‐dependent and high‐throughput sequencing approaches. The study includes all the domains of the tree of life: Eukaryotes, Bacteria and Archaea to give a complete overview of biodiversity and community structure. Furthermore, to explore the geographic distribution of endoliths throughout the Victoria Land (Continental Antarctica), we compared the fungal and bacterial community composition and structure of endolithically colonized rocks, collected in >30 sites in 10 years of Italian Antarctic Expeditions. Compared with the fungi and other eukaryotes, the prokaryotic communities were richer in species, more diverse and highly heterogeneous. Despite the diverse community compositions, shared populations were found and were dominant in all sites. Local diversification was observed and included prokaryotes as members of Alphaproteobacteria and Crenarchaeota (Archaea), the last detected for the first time in these cryptoendolithic communities. Few eukaryotes, namely lichen‐forming fungal species as Lecidella grenii, were detected in Helliwell Hills only. These findings suggest that geographic distance and isolation in these remote areas may promote the establishment of peculiar locally diversified microorganisms.
Clinical validation of a new molecular test (Seegene Allplex™ Vaginitis) for the diagnosis of vaginitis: a cross‐sectional study
Authors: Vieira‐Baptista P , Silva AR , Costa M , Aguiar T , Saldanha C , Sousa C 
Published: February 2021

ObjectiveTo validate the use of Seegene Allplex™ Vaginitis assay in the diagnosis of candidiasis, bacterial vaginosis (BV) and trichomoniasis.DesignCross‐sectional, prospective study conducted in a single centre.SettingOutpatient clinic of a gynaecology department.PopulationConsecutive symptomatic and asymptomatic women (18–60 years of age).MethodsComparison of the assay test with the reference standards for the diagnosis of vaginitis (cultures for yeasts, Nugent for BV and nucleic acid amplification test for trichomoniasis).Main outcome measuresPerformance of the investigational assay, in comparison with the reference standards for the diagnosis of the presence of Candida spp., Trichomonas vaginalis and BV. Secondary objectives are the evaluation of the performance of the test in postmenopausal women and in symptomatic women.ResultsA diagnosis of vaginitis was established in 14.0%. The global prevalences of BV, Candida spp. and T. vaginalis were 22.3%, 13.2% and 2.4%, respectively. The sensitivity and specificity of the assay test for those three causes of vaginitis were as follows: BV 91.7% and 86.6%; any Candida spp. 91.1% and 95.6%; Candida albicans 88.1% and 98.2%, non‐albicans Candida 100% and 97.5%, and T. vaginalis 94.4 and 99.9%. The performance of the test was identical in the subgroup of women that reported vulvovaginal symptoms. The presence of multiple infections did not interfere with the performance of the test.ConclusionsThe Seegene Allplex™ Vaginitis assay has an excellent performance in the diagnosis of the BV and presence of Candida; the results were good for trichomoniasis, but the study was underpowered for this outcome.Tweetable abstractSeegene Allplex™ Vaginitis is an excellent option for screening and diagnosis of vaginitis.
Deciphering bacterial mechanisms of root colonization
Authors: Knights Hayley E. , Jorrin Beatriz , Haskett Timothy L. , Poole Philip S. 
Published: February 2021

SummaryBacterial colonization of the rhizosphere is critical for the establishment of plant–bacteria interactions that represent a key determinant of plant health and productivity. Plants influence bacterial colonization primarily through modulating the composition of their root exudates and mounting an innate immune response. The outcome is a horizontal filtering of bacteria from the surrounding soil, resulting in a gradient of reduced bacterial diversity coupled with a higher degree of bacterial specialization towards the root. Bacteria–bacteria interactions (BBIs) are also prevalent in the rhizosphere, influencing bacterial persistence and root colonization through metabolic exchanges, secretion of antimicrobial compounds and other processes. Traditionally, bacterial colonization has been examined under sterile laboratory conditions that mitigate the influence of BBIs. Using simplified synthetic bacterial communities combined with microfluidic imaging platforms and transposon mutagenesis screening approaches, we are now able to begin unravelling the molecular mechanisms at play during the early stages of root colonization. This review explores the current state of knowledge regarding bacterial root colonization and identifies key tools for future exploration.
Maternal celiac disease and the risk for long‐term infectious morbidity of the offspring
Authors: Abu‐Freha Naim , Wainstock Tamar , Philip Aerin , Sheiner Eyal 
Published: February 2021

AbstractProblemCeliac disease is an autoimmune disease, patients with celiac have increased risk for infections, and offspring of celiac mothers have increased morbidity. The aim of the study was to assess long‐term infectious morbidity among offspring of pregnant women with celiac disease.Method of StudyA population‐based cohort study was conducted, including all singleton deliveries between the years 1991–2014 at a tertiary medical center. The offsprings were subdivided into two groups: offsprings of mothers with and without celiac disease. Data on demographics, maternal, perinatal, and long‐term hospitalizations for infectious morbidity were compared between the two groups.ResultsDuring the study period there were 210 (0.09%) deliveries of mothers with celiac, and they were compared to 242170 (99.91%) deliveries of non‐celiac mothers. Cumulative infectious morbidity was significantly higher in offspring of mothers with celiac compared to offspring of mothers without celiac (Kaplan‐Meier, log‐rank p = .004). Specifically, among the offspring of mothers with celiac significantly higher rates of bacteremia was noted (1.0% vs. 0.1%; p = .001), and infections of the central nervous system (1% vs. 0.2%; p = .028). In the Cox multivariable model which accounted for confounding variables, being born to mothers with celiac disease was associated with significantly increased risk for long‐term infectious morbidity of the offspring (adjusted HR = 1.6, 95% CI 1.165–2.357, p = .005).ConclusionsMaternal celiac disease is an independent risk factor for long‐term infectious morbidity for the offspring.
Risk factors for postpartum depressive symptoms among fathers: A systematic review and meta‐analysis
Authors: Ansari Najmus Sehr , Shah Jyotsna , Dennis Cindy‐Lee , Shah Prakesh S. 
Published: February 2021

AbstractIntroductionThe transition to parenthood is a major life change that may affect the mental well‐being of both mothers and fathers and place them at an increased risk for depression. The objective of our study was to systematically review the literature and identify factors associated with postpartum depressive symptoms in fathers.Material and methodsSearches were conducted in PubMed, PsychInfo, Embase, and CINAHL to identify studies published until March 2020. Studies that reported factors associated with depression among fathers were included. The data from these studies were extracted independently by two authors with disagreements resolved by a third author and consensus. The odds ratio (OR) was used as a measure of association between the risk factor and the primary outcome: depression within the first 12 months following childbirth among fathers diagnosed using any method. Summary estimates were calculated using a random effects model. The associations between the risk factors and depressive symptoms were evaluated.ResultsThe search identified 1040 reports. After screening titles and abstracts, 62 full‐text articles were assessed for eligibility and 25 studies involving 13 972 fathers were included in the systematic review. Fathers with a prior mental health illness episode had higher odds of developing depressive symptoms than those with no mental health history (eight studies, n = 3515, pooled OR 6.77, 95% CI 5.07–9.04; I2 = 0%). Other significant risk factors included relationship dissatisfaction (eight studies, n = 6924, pooled OR 1.53, 95% CI 1.29–1.81; I2 = 93%), maternal depression (seven studies, n = 6661, pooled OR 1.66, 95% CI 1.27–2.17; I2 = 88%), financial instability (five studies, n = 3052, pooled OR 2.24, 95% CI 1.44–3.48; I2 = 74%), paternal unemployment (three studies, n = 1505, pooled OR 6.61, 95% CI 1.94–22.54; I2 = 59%), low education level (two studies, n = 1697, pooled OR 3.56, 95% CI 1.06–11.97; I2 = 88%), and perceived stress (two studies, n = 692, pooled OR 1.06, 95% CI 1.02–1.11; I2 = 5%). Lack of support and low parenting self‐efficacy were also associated with paternal postpartum depressive symptoms.ConclusionsA history of paternal mental illness, maternal depression, and diverse psychosocial factors were associated with depressive symptoms among fathers postnatally. These findings can guide the development of family‐level interventions for early identification and treatment and social media campaigns to promote help‐seeking behaviors and engagement in preventive strategies.