bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Advanced Renal Dysfunction on Posttransplant Outcomes After Living Donor Liver Transplantation in the United States
Authors: Bittermann Therese , Abt Peter L. , Olthoff Kim M. , Kaur Navpreet , Heimbach Julie K. , Emamaullee Juliet 
Published: March 2021

Background.
Survival after living donor liver transplantation (LDLT) in the United States is excellent. However, the significance of pretransplant kidney disease on outcomes in this population is poorly understood.

Methods.
This was a retrospective cohort study of 2806 LDLT recipients nationally between January 2010 and June 2020. Recipients with estimated glomerular filtration rate <40 mL/min/1.73 m2 (eGFR-low) or requiring dialysis were compared. Multivariable survival analyses evaluated (1) eGFR-low as a predictor of post-LDLT survival and (2) the survival of LDLT versus deceased donor liver transplant (DDLT) alone with eGFR-low.

Results.
From 2010 to 2020, 140 (5.0%) patients had eGFR-low and 18 (0.6%) required dialysis pre-LDLT. The number of LDLTs requiring dialysis between 2017 and 2020 outnumbered the prior 7 y. Overall LDLT experience was greater at centers performing LDLT in recipients with renal dysfunction (P < 0.001). LDLT recipients with eGFR-low had longstanding renal dysfunction: mean eGFR 3–6 mo before LDLT 42.7 (±15.1) mL/min/1.73 m2. Nearly half (5/12) of eGFR-low recipients with active kidney transplant (KT) listing at LDLT experienced renal recovery. Five patients underwent early KT after LDLT via the new “safety net” policy. Unadjusted survival after LDLT was worse with eGFR-low (hazard ratio 2.12 versus eGFR ≥40 mL/min/1.73 m2; 95% confidence interval, 1.47-3.05; P < 0.001), but no longer so when accounting for mean eGFR 3–6 mo pre-LDLT (hazard ratio, 1.27; 95% confidence interval, 0.82-1.95; P = 0.3). The adjusted survival of patients with eGFR-low receiving LDLT versus deceased donor liver transplant alone was not different (P = 0.08).

Conclusions.
Overall, outcomes after LDLT with advanced renal dysfunction are acceptable. These findings are relevant given the recent “safety net” KT policy.
Can you have a migraine aura without knowing it?
Authors: Hadjikhani Nouchine , Vincent Maurice 
Published: March 2021

Purpose of review
This review covers several aspects our understanding of episodic manifestations and unusual symptoms that may be associated with migraine aura.

Recent findings
The episodic manifestation of migraine aura is typically visual in nature, although five other types are currently recognized: sensory, speech and/or language, motor, brainstem, and retinal. Other transitory perceptions or experiences such as emotional, olfactory, or auditory have been reported as possible migraine auras. As underlined by the much higher reported prevalence of aura manifestation in individuals with professional knowledge of its possible manifestations, it appears that a number of migraine auras may remain unnoticed, unreported, or misdiagnosed.

Summary
Aura manifestations may be more common, complex, symptom-rich and variable than previously thought. Clinicians should proactively ask questions beyond those addressing visual symptoms when examining individuals with a potential diagnosis of migraine with aura.
Ambulatory EEG to Classify the Epilepsy Syndrome
Authors: González Otárula Karina A. , Balaguera Pedro , Schuele Stephan 
Published: March 2021

Summary:
Recording of interictal epileptiform discharges to classify the epilepsy syndrome is one of the most common indications for ambulatory EEG. Ambulatory EEG has superior sampling compared with standard EEG recordings and advantages in terms of cost-effectiveness and convenience compared with a prolonged inpatient EEG study. Ambulatory EEG allows for EEG recording in all sleep stages and transitional states, which can be very helpful in capturing interictal epileptiform discharges. In the absence of interictal epileptiform discharges or in patients with atypical events, the characterization of an epilepsy syndrome may require recording of the habitual events. Diagnostic ambulatory EEG can be a useful alternative to inpatient video-EEG monitoring in a selected number of patients with frequent events who do not require medication taper or seizure testing for surgical localization.
Conidial fusion in the asexual fungusVerticillium dahliae
Authors: Vangalis Vasileios , Knop Michael , Typas Milton A. , Papaioannou Ioannis A. 
Published: March 2021

AbstractCell-to-cell fusion is a fundamental biological process across the tree of life. In filamentous fungi, somatic fusion (or anastomosis) is required for the normal development of their syncytial hyphal networks, and it can initiate non-sexual genetic exchange processes, such as horizontal genetic transfer and the parasexual cycle. Although these could be important drivers of the evolution of asexual fungi, this remains a largely unexplored possibility due to the lack of suitable resources for their study in these puzzling organisms. In this study, we report that the spores of the important asexual plant-pathogenic fungusVerticillium dahliaeoften engage in cell fusion via Conidial Anastomosis Tubes (CATs). We optimized appropriate procedures for their highly reproducible quantification and live-cell imaging, which were used to characterize their physiology and cell biology, and to start elucidating their underlying genetic machinery. Formation of CATs was shown to depend on growth conditions and require functional Fus3 and Slt2 MAP kinases, as well as the NADPH oxidase NoxA, whereas the GPCR Ste2 and the mating-type protein MAT1-2-1 were dispensable. We show that nuclei and other organelles can migrate through CATs, which often leads to the formation of transient dikaryons. Their nuclei have possible windows of opportunity for genetic interaction before degradation of one by a presumably homeostatic mechanism. We establish here CAT-mediated fusion inV. dahliaeas an experimentally convenient system for the cytological analysis of fungal non-sexual genetic interactions. We expect that it will facilitate the dissection of sexual alternatives in asexual fungi.
Exploring the microdiversity within marine bacterial taxa: Towards an integrated biogeography in the Southern Ocean
Authors: Schwob G , Segovia NI , González-Wevar CA , Cabrol L , Orlando J , Poulin E 
Published: March 2021

AbstractThe phylogeography traditionally correlates the genetic relationships among individuals within a macroorganism species, to their spatial distribution. Most microbial phylogeographic studies so far have been restricted to narrow geographical regions, mainly focusing on isolated strains, either obtained by culture or single-strain natural enrichments. However, the laborious culture-based methodology imposes a low number of studied individuals, leading to poor resolution of haplotype frequency estimation, making difficult a realistic evaluation of the genetic structure of natural microbial populations in the environment.To tackle this limitation, we present a new approach to unravel the phylogeographic patterns of bacteria combining (i) community-wide survey by 16S rRNA gene metabarcoding, (ii) intra-species resolution through the oligotyping method, and (iii) genetic and phylogeographic indices, as well as migration parameters, estimated from populational molecular data as traditionally developed for macroorganisms as models.As a proof-of-concept, we applied this methodology to the bacterial genusSpirochaeta, classically reported as a gut endosymbiont of various invertebrates inhabiting the Southern Ocean (SO), but also described in marine sediment and in open waters. For this purpose, we centered our sampling into three biogeographic provinces of the SO; maritime Antarctica (King George Island), sub-Antarctic Islands (Kerguelen archipelago) and Patagonia in southern South America. Each targeted OTU was chaLRracterized by substantial intrapopulation microdiversity, a significant genetic differentiation and a robust phylogeographic structure among the three distant biogeographic provinces. Patterns of gene flow inSpirochaetapopulations support the role of the Antarctic Polar Front (APF) as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current (ACC) appears as the main driver of connectivity between geographically distant sub-Antarctic areas such as Patagonia and Kerguelen archipelago, and between Kerguelen archipelago and maritime Antarctica. Additionnally, we found that historical processes (drift and dispersal limitation) together govern up to 86% of the spatial turnover amongSpirochaetapopulations. Overall, our approach represents a substantial first attempt to bridge the gap between microbial and macrobial ecology by unifying the way to study phylogeography. We revealed that strong congruency with macroorganisms patterns at the populational level shaped by the same oceanographic structures and ecological processes.
Autism spectrum disorder: understanding the impact of SNPs on biological pathways in the fetal and adult cortex
Authors: Golovina E. , Fadason T. , Lints T.J. , Walker C. , Vickers M.H. , O’Sullivan J.M. 
Published: March 2021

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by significant and complex genetic etiology. GWAS studies have identified genetic variants associated with ASD, but the functional impacts of these variants remain unknown. Here, we integrated four distinct levels of biological information (GWAS, eQTL, spatial genome organization and protein-protein interactions) to identify potential regulatory impacts of ASD-associated SNPs (p< 5×10-8) on biological pathways within fetal and adult cortical tissues. We found 80 and 58 SNPs that mark regulatory regions (i.e. expression quantitative trait loci or eQTLs) in the fetal and adult cortex, respectively. These eQTLs were also linked to other psychiatric disorders (e.g. schizophrenia, ADHD, bipolar disorder). Functional annotation of ASD-associated eQTLs revealed that they are involved in diverse regulatory processes. In particular, we found significant enrichment of eQTLs within regions repressed by Polycomb proteins in the fetal cortex compared to the adult cortex. Furthermore, we constructed fetal and adult cortex-specific protein-protein interaction networks and identified that ASD-associated regulatory SNPs impact on immune pathways, fatty acid metabolism, ribosome biogenesis, aminoacyl-tRNA biosynthesis and spliceosome in the fetal cortex. By contrast in the adult cortex, they largely affect immune pathways. Overall, our findings highlight potential regulatory mechanisms and pathways important for the etiology of ASD in early brain development and adulthood. This approach, in combination with clinical studies on ASD, will contribute to individualized mechanistic understanding of ASD development.
Loss ofTsc1in cerebellar Purkinje cells induces transcriptional and translation changes in FMRP target transcripts
Authors: Dalal Jasbir , Winden Kellen D. , Salussolia Catherine L. , Sundberg Maria , Singh Achint , Zhou Pingzhu , Pu William T , Miller Meghan T. , Sahin Mustafa 
Published: March 2021

AbstractTuberous sclerosis complex (TSC) is a genetic disorder that is associated with multiple neurological manifestations. Previously, we demonstrated thatTsc1loss in cerebellar Purkinje cells (PCs) can cause altered social behavior in mice. Here, we performed detailed transcriptional and translational analyses ofTsc1-deficient PCs to understand the molecular alterations in these cells. We found that target transcripts of the Fragile X Mental Retardation Protein (FMRP) are reduced in mutant PCs with evidence of increased degradation. Surprisingly, we observed unchanged ribosomal binding for many of these genes using Translating Ribosome Affinity Purification (TRAP). Finally, we found that the FMRP target, SHANK2, was reduced in PC synapses, suggesting that compensatory increases in ribosomal binding efficiency may be unable to overcome reduced transcript levels. These data further implicate dysfunction of FMRP and its targets in TSC and suggest that treatments aimed at restoring the function of these pathways may be beneficial.
Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans
Authors: Dong Xiaofeng , Penrice-Randal Rebekah , Goldswain Hannah , Prince Tessa , Randle Nadine , Salguero Javier , Tree Julia , Vamos Ecaterina , Nelson Charlotte , Stewart James P. ,   ISARIC4C Investigators,   COVID-19 Genomics UK (COG-UK) Consortium, Semple Malcolm G. , Baillie J. Kenneth , Openshaw Peter J. M. , Turtle Lance , Matthews David A. , Carroll Miles W. , Darby Alistair C. , Hiscox Julian A. 
Published: March 2021

AbstractIntroductionSARS-CoV-2 has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgRNAs has a unique 5’ sequence, the leader-transcriptional regulatory sequence gene junction (leader-TRS-junction), that can be identified using sequencing.ResultsHigh resolution sequencing has been used to investigate the biology of SARS-CoV-2 and the host response in cell culture models and from clinical samples. LeTRS, a bioinformatics tool, was developed to identify leader-TRS-junctions and be used as a proxy to quantify sgmRNAs for understanding virus biology. This was tested on published datasets and clinical samples from patients and longitudinal samples from animal models with COVID-19.DiscussionLeTRS identified known leader-TRS-junctions and identified novel species that were common across different species. The data indicated multi-phasic abundance of sgmRNAs in two different animal models, with spikes in sgmRNA abundance reflected in human samples, and therefore has implications for transmission models and nucleic acid-based diagnostics.
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
Authors: Hippen Ariel A. , Falco Matias M. , Weber Lukas M. , Erkan Erdogan Pekcan , Zhang Kaiyang , Doherty Jennifer Anne , Vähärautio Anna , Greene Casey S. , Hicks Stephanie C. 
Published: March 2021

AbstractMotivationSingle-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a ‘low-quality’ cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA (mtDNA) encoded genes and (ii) if a small number of genes are detected. Current best practices use these QC metrics independently with either arbitrary, uniform thresholds (e.g. 5%) or biological context-dependent (e.g. species) thresholds, and fail to jointly model these metrics in a data-driven manner. Current practices are often overly stringent and especially untenable on lower-quality tissues, such as archived tumor tissues.ResultsWe propose a data-driven QC metric (miQC) that jointly models both the proportion of reads mapping to mtDNA genes and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset. We demonstrate how our QC metric easily adapts to different types of single-cell datasets to remove low-quality cells while preserving high-quality cells that can be used for downstream analyses.AvailabilitySoftware available athttps://github.com/greenelab/miQC. The code used to download datasets, perform the analyses, and reproduce the figures is available athttps://github.com/greenelab/mito-filtering.ContactStephanie C. Hicks (shicks19@jhu.edu) and Anna Vähärautio (anna.vaharautio@helsinki.fi)
High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes
Authors: Trigodet Florian , Lolans Karen , Fogarty Emily , Shaiber Alon , Morrison Hilary G. , Barreiro Luis , Jabri Bana , Eren A. Murat 
Published: March 2021

AbstractBy offering extremely long contiguous characterization of individual DNA molecules, rapidly emerging long-read sequencing strategies offer comprehensive insights into the organization of genetic information in genomes and metagenomes. However, successful long-read sequencing experiments demand high concentrations of highly purified DNA of high molecular weight (HMW), which limits the utility of established DNA extraction kits designed for short-read sequencing. Challenges associated with input DNA quality intensify further when working with complex environmental samples of low microbial biomass, which requires new protocols that are tailored to study metagenomes with long-read sequencing. Here, we use human tongue scrapings to benchmark six HMW DNA extraction strategies that are based on commercially available kits, phenol-chloroform (PC) extraction, and agarose encasement followed by agarase digestion. A typical end goal of HMW DNA extractions is to obtain the longest possible reads during sequencing, which is often achieved by PC extractions as demonstrated in sequencing of cultured cells. Yet our analyses that consider overall read-size distribution, assembly performance, and the number of circularized elements found in sequencing results suggest that non-PC methods may be more appropriate for long-read sequencing of metagenomes.
Collective behavior emerges from genetically controlled simple behavioral motifs in zebrafish
Authors: Aspiras Ariel C. , Harpaz Roy , Chambule Sydney , Tseng Sierra , Engert Florian , Fishman Mark C. , Bahl Armin 
Published: March 2021

AbstractSince Darwin, coordinated movement of animal groups has been believed to be essential to species survival, but it is not understood how changes in the genetic makeup of individuals might alter behavior of the collective. Here we find that even at the early larval stage, zebrafish regulate their proximity and alignment with each other. Two simple visual responses, one that measures relative visual field occupancy and the other global visual motion, suffice to account for the group behavior that emerges. We analyze how mutations in genes known to affect social behavior of humans perturb these simple reflexes in larval zebrafish and thereby affect their collective behaviors. We use model simulations to show that changes in reflexive responses of individual mutant animals predict well the distinctive collective patterns that emerge in a group. Hence group behaviors reflect in part genetically defined primitive sensorimotor “motifs”, which are evident even in young larvae.
Self-reported food safety knowledge and practices of early-school-aged children – a result of analysis in towns near the Warsaw city
Authors: Tomaszewska Marzena , Neffe-Skocińska Katarzyna , Trząskowska Monika , Trafialek Joanna , Wadolowska Lidia , Hamulka Jadwiga 
Published: March 2021

PurposeThe purpose of this study is to evaluate the knowledge and practices of selected group of Polish children in early school age in terms of issues such as: (1) the principles of food preparation, storage and eating meals; (2) personal hygiene; and (3) basic information about microorganisms.Design/methodology/approachThe auditorium survey method was used. The questionnaire consisted of 15 questions related to the children's knowledge of personal hygiene, the principles of food preparation and storage and the physiology of microorganisms and 13 questions related to the children's personal and food hygiene practice. In total, 169 questionnaires were collected. The study group of children had incomplete knowledge and often reported inappropriate food hygiene practices.FindingsThe subjects of food preparation and storage and knowledge of microbes were particular problem areas. By contrast, aspects related to handwashing, the appropriate practices while coughing or sneezing and washing fruit before consumption were positively evaluated. The children demonstrated the most knowledge in the field of personal hygiene. However, a very low percentage of correct answers was noted for the question about handwashing at school. None of the 13 questions related to this practice received more than 90% correct answers. The boys and girls demonstrated a comparable level of knowledge and practice in the area of food safety. It was showed that the place of school influenced answers to a greater extent compared to gender.Originality/valueThe results of the study play an important role in the prevention of food poisoning and are useful for the teachers, staff of training institutions and parents. They can also inspire institutions in countries with a high incidence of food poisoning to search for the causes in the inappropriate hygienic practices of young children.
Authentic leadership and employee health: a conditional process model
Authors: Hildenbrand Kristin , Daher Pascale , Akaighe Godbless 
Published: March 2021

PurposeThe purpose of this paper is to examine the effect of authentic leadership (AL) on employees' health via employees' perception of climate of authenticity (PCA) across two studies. In study 2, the authors additionally explore the moderating role of employees' neuroticism.Design/methodology/approachThe hypotheses were tested across two studies using two-wave survey data. In study 1 (n = 104), the mediation hypothesis was tested. Study 2 (n = 146) extended study 1 and examined the moderated mediation model.FindingsAcross both studies, AL is positively related to employee health, and employees' perceived climate of authenticity mediates this relationship. Study 2 additionally shows that employees' neuroticism moderates this indirect effect such that perceived climate of authenticity instigated by AL is particularly conducive for employees high in neuroticism as opposed to those low in neuroticism.Practical implicationsFindings emphasize the health-promoting effect of AL. It is recommended that organizations cascade, through their leaders, emotional display rules that encourage genuine emotional expression.Originality/valueThis paper addresses gaps in the leadership literature through investigating perceived climate of authenticity, a mediating variable that lies at the heart of AL, and integrating the role of employees' personality in the leadership process.