bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exome sequencing in patient‐parent trios suggests new candidate genes for early‐onset primary sclerosing cholangitis
Authors: Haisma Sjoukje‐Marije , Weersma Rinse K. , Joosse Maria E. , de Koning Barbara A. E. , de Meij Tim , Koot Bart G. P. , V. M. Wolters , Norbruis Obbe , Daly Mark J. , Stevens Christine , Xavier Ramnik J. , Koskela Jukka , Rivas Manuel A. , Visschedijk Marijn C. , Verkade Henkjan J. , Barbieri Ruggero , Jansen Dianne B. H. , Festen Eleonora A. M. , van Rheenen Patrick F. , van Diemen Cleo C. 
Published: February 2021

AbstractBACKGROUND & AIMSPrimary sclerosing cholangitis (PSC) is a rare bile duct disease strongly associated with inflammatory bowel disease (IBD). Whole‐exome sequencing (WES) has contributed to understanding the molecular basis of very early‐onset IBD, but rare protein‐altering genetic variants have not been identified for early‐onset PSC. We performed WES in patients diagnosed with PSC ≤ 12 years to investigate the contribution of rare genetic variants to early‐onset PSC.METHODSIn this multicentre study, WES was performed on 87 DNA samples from 29 patient‐parent trios with early‐onset PSC. We selected rare (minor allele frequency < 2%) coding and splice‐site variants that matched recessive (homozygous and compound heterozygous variants) and dominant (de novo) inheritance in the index patients. Variant pathogenicity was predicted by an in‐house developed algorithm (GAVIN), and PSC‐relevant variants were selected using gene expression data and gene function.RESULTSIn 22 of 29 trios we identified at least 1 possibly pathogenic variant. We prioritized 36 genes, harbouring a total of 54 variants with predicted pathogenic effects. In 18 genes, we identified 36 compound heterozygous variants, whereas in the other 18 genes we identified 18 de novo variants. Twelve of 36 candidate risk genes are known to play a role in transmembrane transport, adaptive and innate immunity, and epithelial barrier function.CONCLUSIONSThe 36 candidate genes for early‐onset PSC need further verification in other patient cohorts and evaluation of gene function before a causal role can be attributed to its variants.
Cats Felis catus as a threat to bats worldwide: a review of the evidence
Authors: Oedin Malik , Brescia Fabrice , Millon Alexandre , Murphy Brett P. , Palmas Pauline , Woinarski John C.Z. , Vidal Eric 
Published: February 2021

Abstract

Cats Felis catus, in all their forms (domestic, free‐roaming/stray and feral), have been identified as a major global threat to biodiversity, especially birds and small mammals. However, there has been little previous consideration of the extent and impact of predation of bats by cats, or of whether specific characteristics make certain species of bats particularly vulnerable to predation by cats.

We reviewed the impact of cats on bats, based on a collation of scientific literature and the International Union for Conservation of Nature (IUCN) Red List database. Our aim was to produce a synthesis of the extent to which cats prey upon and threaten bats. We also collated available data on cat diet, which provide information on predation rates of bats by cats.

Few studies (n = 44) have identified bat species preyed upon or threatened by cats, with a disproportionate number of studies from islands. In these studies, 86 bat species (about 7% of the global extant tally) are reported as preyed upon or threatened by cats, and about one quarter of these species are listed as Near Threatened or threatened (IUCN categories Critically Endangered, Endangered, or Vulnerable). In IUCN Red List assessments, cats are more frequently mentioned as a threat to threatened or Near Threatened bat species than to non‐threatened species (IUCN category Least Concern).

In studies reporting on the incidence of bats in cat dietary samples (scats, stomachs and guts), the frequency of occurrence of bats in samples averaged 0.7 ± 2.1% (mean ± standard deviation; n = 102). Many studies had sample sizes that were too small to be likely to detect bats.

All forms of cat are reported to kill bats, and such predation has been reported in all major terrestrial habitats. We conclude that predation by cats is an under‐appreciated threat to the world’s bat species.
Learning decision boundaries for cone penetration test classification
Authors: Erharter Georg H. , Oberhollenzer Simon , Fankhauser Anna , Marte Roman , Marcher Thomas 
Published: February 2021

AbstractIn geotechnical field investigations, cone penetration tests (CPT) are increasingly used for ground characterization of fine‐grained soils. Test results are different parameters that are typically visualized in CPT based data interpretation charts. In this paper we propose a novel methodology which is based on supervised machine learning that permits a redefinition of the boundaries within these charts to account for unique soil conditions. We train ensembles of randomly generated artificial neural networks to classify six soil types based on a database of hundreds of CPT tests from Austria and Norway. After training we combine the multiple unique solutions for this classification problem and visualize the new decision boundaries in between the soil types. The generated boundaries between soil types are comprehensible and are a step towards automatically adjusted CPT interpretation charts for specific local conditions.
ppGpp influences protein protection, growth and photosynthesis in Phaeodactylum tricornutum
Authors: Avilan Luisana , Lebrun Regine , Puppo Carine , Citerne Sylvie , Cuiné Stephane , Li‐Beisson Yonghua , Menand Benoît , Field Ben , Gontero Brigitte 
Published: February 2021

Summary

Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta‐ and tetraphosphate ((p)ppGpp). In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes.

Here, we studied the function of ppGpp in the diatom Phaeodactylum tricornutum using transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression.

We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent‐like state with reduced proliferation and ageing. Strikingly, using nontargeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments.

Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.
Work Hard or Play Hard? Degree Class, Student Leadership and Employment Opportunities*
Authors: Baert Stijn , Verhaest Dieter 
Published: February 2021

AbstractThis study investigates the impact on first hiring outcomes of two main curriculum vitae (CV) characteristics by which graduates with a tertiary education degree distinguish themselves from their peers: degree class and extra‐curricular activities. These characteristics were randomly assigned to 2,800 fictitious job applications that were sent to real vacancies in Belgium. Academic performance and extra‐curricular engagement enhance job interview rates by 7.0% (CI 95% [0.3%, 13.7%]) and 6.5% (CI 95% [−0.5%, 13.4%]), respectively. We did not find evidence for these CV characteristics to reinforce or reduce their effect.
Clinical manifestations of neonatal seizures
Authors: Nguyen Thuy , Wusthoff Courtney J. 
Published: February 2021

AbstractNeonatal seizures present a unique diagnostic challenge with clinical manifestations often subtle or absent to the bedside observer. Seizures can be overdiagnosed in newborns with unusual paroxysmal movements and underdiagnosed in newborns without clinical signs of seizures. Electroclinical “uncoupling” also adds to the diagnostic challenge. Reliable diagnosis requires additional tools; continuous electroencephalogram (EEG) monitoring is the gold standard for diagnosis of neonatal seizures. Certain high‐risk neonatal populations with known brain injury, such as stroke or hypoxic‐ischemic encephalopathy, are most likely to benefit from continuous EEG. Studies have shown that risk stratification for continuous EEG has positive impact on care, including rapid and accurate diagnosis and treatment of neonatal seizures, which leads to reduced use of antiseizure medicines and length of hospital stay. This review describes common clinical manifestations of neonatal seizures, and clinical situations in which EEG monitoring to screen for seizures should be considered.
Partial aggregation in ethics
Authors: Horton Joe 
Published: February 2021

AbstractIs there any number of people you should save from paralysis rather than saving one person from death? Is there any number of people you should save from a migraine rather than saving one person from death? Many people answer ‘yes’ and ‘no’, respectively. The aim of partially aggregative moral views is to capture and justify combinations of intuitions like these. These views contrast with fully aggregative moral views, which imply that the answer to both questions is ‘yes’, and with non‐aggregative moral views, which imply that the answer to both questions is ‘no’. In this article, I review the most natural and influential ways of developing partially aggregative views and explain the main problems they face.
Modeling and Managing Poliovirus Risks: We are Where we are…
Authors: Thompson Kimberly M. 
Published: February 2021

AbstractThis introduction for the third special issue on modeling poliovirus risks provides context for the current status of global polio eradication efforts and gives an overview of the individual papers included in the issue. Although risk analysis continues to support the Global Polio Eradication Initiative (GPEI), efforts to finish the job remained off track at the beginning of 2020 and prior to the COVID‐19 pandemic, as discussed in the special issue. The disruptions associated with COVID‐19 occurring now will inevitably change the polio eradication trajectory, and future studies will need to characterize the impacts of these disruptions on the polio endgame.
Etiological profile of diarrhea in solid organ transplant recipients at a tertiary care center in Southern India
Authors: Vyas Viral Dineshchandra , Parameswaran Sarojini Ashok , Paramasivan Piramanayagam , Sankaranarayanan Krishnan , Palaniswamy Kallipatti Ramasamy , Mohan Arumugam T , Srinivas Usha , Dhus Ubal , Muthuswamy Hariharan , Revathy Marimuthu S , Natarajan Murugan , Karunakaran Premkumar , Venkatesh Seshadri , Mahalingam Preethi , Patel Ankit 
Published: February 2021

AbstractBackgroundDiarrhea is one of the common gastrointestinal (GI) adverse events after solid organ transplantation. Diarrhea may be caused by infectious or non‐infectious etiology. The infectious etiology of diarrhea varies according to the location and duration of diarrhea. Non‐infectious etiologies include drugs, inflammatory bowel disease, neoplasia. The objective of this study was to evaluate the etiological profile of diarrhea in solid organ transplant recipients presenting to a tertiary care center in Southern India.MethodsThis was a retrospective analysis of prospectively collected data of all solid organ transplantation recipients referred to the Department of Medical Gastroenterology for evaluation of diarrhea from April 2012 till May 2014. All patients had stool evaluated by wet mount examination, modified acid fast (AFB) stain, trichrome stain, culture, and Clostridium difficile toxin assay. EDTA plasma was collected for quantitative Cytomegalovirus (CMV) detection by real‐time PCR. If the diarrhea was acute (<2 wk), and no etiological agent was identified, empirical antibiotic therapy was instituted and followed up. If persistent or chronic diarrhea (>2‐4 wk), endoscopic evaluation (upper GI endoscopy and/or colonoscopy with biopsies), depending on the clinical type of diarrhea was done. If no specific etiological diagnosis was established after endoscopic evaluation, breath test for SIBO and celiac serology were done. If no specific etiology was identified after the above investigations, dose of immunosuppressive drugs was reduced. If diarrhea responded to dose reduction, it was considered to be drug related.ResultsFifty‐eight episodes of diarrhea occurred in 55 solid organ transplant recipients during the study period. Renal transplant recipients constituted the majority (70%). Most (79%) of patients included in the study had their transplant > 6 mo ago. Infective diarrhea was the etiology in 46%, drug‐related diarrhea in 29.3%. No specific etiology was identified in 22.4% of patients. Parasites accounted for 69% of all infective diarrhea. Stool evaluation was the main investigation in establishing diagnosis in acute diarrhea. Endoscopic evaluation was required in two thirds of patients to establish diagnosis in chronic diarrhea.ConclusionGI infections and drug‐related diarrhea were the common causes of diarrhea in solid organ transplant recipients. Parasites were the most common infectious etiology of diarrhea. Step‐wise evaluation was able to identify the etiology in ~ 77% of patients. Overall, 98% of diarrheal episodes resolved.
Cytomegalovirus antiviral stewardship in the COVID‐19 Era: Increasing complexity of prophylaxis and treatment and potential mitigation strategies
Authors: Jorgenson Margaret R. , Descourouez Jillian L. , Wong Cynthia , Strayer Jill R. , Parajuli Sandesh , Rice John P. , Redfield Robert R. , Smith Jeannina A. , Mandelbrot Didier A. , Saddler Christopher M. 
Published: February 2021

AbstractCytomegalovirus (CMV) infection is one of the most common and significant complications after solid organ transplant (SOT). Severe acute respiratory coronavirus 2 (SARS‐CoV‐2), which causes the novel betacoronavirus 2019 disease (COVID‐19), has become the first global pandemic in 100 years. The world's attention has turned to address this unanticipated development; however, the viral infection that has long plagued outcomes after solid organ transplantation still requires vigilance. With physical distancing as the key intervention to reduce the healthcare burden, and the unease related to healthcare contact within the transplant population given the associated morbidity and mortality of COVID‐19 in transplant recipients, providers have struggled to evaluate and streamline essential in‐person healthcare contact, including laboratory visits. Owing to this, the COVID‐19 pandemic has placed a significant strain on the delivery of CMV prophylaxis and treatment after solid organ transplantation. In this piece, we will describe issues our CMV antiviral stewardship service has encountered in the care of the transplant recipient with CMV during the this unprecedented time and share our expert opinion to approaches to providing optimal, evidenced based care during a pandemic associated with a seemingly unrelated viral infection.
Multi‐omics analysis to visualize the dynamic roles of defense genes in the response of tea plants to gray blight
Authors: Wang Shuangshuang , Liu Lu , Mi Xiaozeng , Zhao Shiqi , An Yanlin , Xia Xiaobo , Guo Rui , Wei Chaoling 
Published: February 2021

SUMMARYGray blight (GB) is one of the most destructive diseases of tea plants, causing considerable damage and productivity losses; however, the dynamic roles of defense genes during pathogen infection remain largely unclear. To explore the numerous molecular interactions associated with GB stress in tea plants, we employed transcriptome, sRNAome and degradome sequencing from 1 to 13 days post‐inoculation (dpi) at 3‐day intervals. The transcriptomics results showed that differentially expressed genes (DEGs) related to flavonoid synthesis, such as chalcone synthase (CHS) and phenylalanine ammonia‐lyase (PAL), were particularly induced at 4 dpi. Consistent with this, the contents of catechins (especially gallocatechin), which are the dominant flavonoids in tea plants, also increased in the leaves of tea plants infected with GB. Combined analysis of the sRNAome and degradome revealed that microRNAs could mediate tea plant immunity by regulating DEG expression at the post‐transcriptional level. Co‐expression network analysis demonstrated that miR530b‐ethylene responsive factor 96 (ERF96) and miRn211‐thaumatin‐like protein (TLP) play crucial roles in the response to GB. Accordingly, gene‐specific antisense oligonucleotide assays suggested that suppressing ERF96 decreased the levels of reactive oxygen species (ROS), whereas suppressing TLP increased the levels of ROS. Furthermore, ERF96 was induced, but TLP was suppressed, in susceptible tea cultivars. Our results collectively demonstrate that ERF96 is a negative regulator and TLP is a positive regulator in the response of tea plants to GB. Taken together, our comprehensive integrated analysis reveals a dynamic regulatory network linked to GB stress in tea plants and provides candidate genes for improvement of tea plants.
SEC6 exocyst subunit contributes to multiple steps of growth and development of Physcomitrella (Physcomitrium patens)
Authors: Brejšková Lucie , Hála Michal , Rawat Anamika , Soukupová Hana , Cvrčková Fatima , Charlot Florence , Nogué Fabien , Haluška Samuel , Žárský Viktor 
Published: February 2021

SUMMARYSpatially directed cell division and expansion is important for plant growth and morphogenesis and relies on cooperation between the cytoskeleton and the secretory pathway. The phylogenetically conserved octameric complex exocyst mediates exocytotic vesicle tethering at the plasma membrane. Unlike other exocyst subunits of land plants, the core exocyst subunit SEC6 exists as a single paralog in Physcomitrium patens and Arabidopsis thaliana genomes. Arabidopsis SEC6 (AtSEC6) loss‐of‐function (LOF) mutation causes male gametophytic lethality. Our attempts to inactivate the P. patens SEC6 gene, PpSEC6, using targeted gene replacement produced two independent partial LOF (‘weak allele’) mutants via perturbation of the PpSEC6 gene locus. These mutants exhibited the same pleiotropic developmental defects: protonema with dominant chloronema stage; diminished caulonemal filament elongation rate; and failure in post‐initiation gametophore development. Mutant gametophore buds, mostly initiated from chloronema cells, exhibited disordered cell file organization and cross‐wall perforations, resulting in arrested development at the eight‐ to 10‐cell stage. Complementation of both sec6 moss mutant lines by both PpSEC6 and AtSEC6 cDNA rescued gametophore development, including sexual organ differentiation. However, regular sporophyte formation and viable spore production were recovered only by the expression of PpSEC6, whereas the AtSEC6 complementants were only rarely fertile, indicating moss‐specific SEC6 functions.
Previous experience, experimentation and export survival: Evidence from firm‐product‐destination level data
Authors: Esteve‐Pérez Silviano 
Published: February 2021

AbstractThis paper explores the role of a firm's product and/or market export experience and experimentation for survival of new product‐destination export spells, using firm‐level Spanish customs data over the period 1997–2015. Previous research has documented a positive impact of experience on export survival. This paper contributes to the extant literature by unravelling the distinct effect on export survival of ongoing accumulated experience (i.e., from the start of a product‐destination export spell), previous product and/or destination‐market experience and experimentation (repetition of product‐destination relationships). We find that 60% of new product‐country export spells end during their first year. Thereafter, the hazard rate remarkably falls with their elapsed duration (i.e., age). Exporting a new product endures a higher risk than entering a new market. Besides, experimentation (repeated product‐destination combinations) and previous experience (especially at product rather than at destination level) significantly lower the exit hazard. The results are consistent with previous studies that suggest that sunk costs to enter markets are relatively high, while experimentation and learning are more relevant at product level.
Feasibility of applying nonthermal plasma for dairy effluent treatment and optimization of process parameters
Authors: Suresh Ramya , Rajoo Baskar , Chenniappan Maheswari , Palanisamy Manikandan 
Published: February 2021

AbstractDairy industry effluent will pollute the environment if not properly treated. In the present work, the feasibility of nonthermal plasma (NTP) for the treatment of dairy industry effluent is assessed. The effect of energy yield and plasma intensity on reduction of Chemical Oxygen Demand (COD) removal is investigated. Box–Behnken design (BBD) is employed to optimize the operating parameters such as initial pH (5–9), reaction time (4–8 h), effluent flow rate (10–90 ml/min) and applied voltage (20–30 kV) where COD and energy yield are taken as responses. The optimum condition for COD removal and energy yield is same with a pH of 9, effluent flow rate of 10 ml/min and applied voltage of 30 kVp‐p, whereas reaction time differs as 8 and 4 h, respectively. COD reduction of 52% indicates that NTP process is a promising technology for dairy effluent treatment.