bluuebunny/crossref_metadata_2025 huggingface dataset:
Cytomegalovirus Viremia in HIV-1 Subtype C Positive Women at Delivery in Botswana and Adverse Birth/Infant Health Outcomes
Authors: Moraka Natasha O. , Moyo Sikhulile , Mayondi Gloria , Leidner Jean , Ibrahim Maryanne , Smith Christiana , Weinberg Adriana , Li Shaobing , Thami Prisca K. , Kammerer Betsy , Ajibola Gbolahan , Musonda Rosemary , Shapiro Roger , Gaseitsiwe Simani , Lockman Shahin
Published: April 2019

Background:

We evaluated the association between maternal cytomegalovirus (CMV) viremia during pregnancy and adverse birth and infant health outcomes in HIV-infected mothers and their HIV-exposed uninfected infants.

Methods:

HIV-positive women and their infants were followed prospectively from pregnancy through 2 years postpartum in the “Tshipidi” study in Botswana. We analyzed the association between detectable CMV DNA in maternal blood at delivery and adverse birth outcomes (stillbirth, preterm delivery, small for gestational age, or birth defect), as well as infant hospitalization and mortality through 24 months.

Results:

We measured CMV DNA in blood samples from 350 (77.1%) of 454 HIV-positive women from the Tshipidi study. The median maternal CD4 count was 422 cells/mL, and median HIV-1 RNA at entry was 3.2 log10 copies/mL. Fifty-one (14.6%) women had detectable CMV DNA. In unadjusted analyses, detectable CMV DNA was associated with higher maternal HIV-1 RNA [odds ratio (OR) 1.4, 95% confidence interval (CI): 1.1 to 1.9], presence of a birth defect (OR 9.8, 95% CI: 1.6 to 60.3), and occurrence of any adverse birth outcome (OR 2.0, 95% CI: 1.04 to 3.95). In multivariable analysis, we observed a trend toward association between detectable maternal CMV DNA and occurrence of any adverse birth outcome (adjusted OR 1.9, 95% CI: 0.96 to 3.8). Maternal CMV viremia was not associated with infant hospitalization and/or death by 24 months.

Conclusions:

Approximately 1 in 6 HIV-positive women in Botswana had detectable CMV DNA in blood at delivery. The presence of maternal CMV viremia had a borderline association with adverse birth outcomes but not with 24-month morbidity or mortality in HIV-exposed uninfected children.
Core Competencies Required for Gastroenterology Nursing Specialists in China
Authors: Ren Hongfei , Liu Changqing , Wang Rui , Zhang Mingguang , Ma Fang , Li Rongrong , Zhu Xiaofei , Yang Xiaoli , Zhang Qiongying , Li Luohong
Published: April 2019

Healthcare professionals responsible for patients with gastrointestinal diseases need a particular level of nursing knowledge and abilities to ensure excellent care. This study aims to propose a set of core competencies for the gastroenterology nursing specialists (GNS) in China. This research integrates quantitative and qualitative research methods. Literature review, semistructured interview, and the Delphi approach were used to develop the core competency items of GNS in China. SPSS 16.0 was used to analyze the data. Finally, 28 of 30 experts participated in the study resulting in a consensual list containing 7 domains (clinical nursing practice, communication and collaboration, education and counseling, critical thinking, leadership, ethical and legal practice, and professional development), 23 aspects, and 66 competencies required for GNS. The authority coefficient (Cr) of the consensus was 0.77, and the Kendall (W) value of each level of competencies all scored above 0.5. Results of the study can serve as a foundation of work performance evaluation for GNS as well as promote nurses' professional development.
Understanding the Barriers to Reporting Sexual Harassment in Surgical Training
Authors: Freedman-Weiss Mollie R. , Chiu Alexander S. , Heller Danielle R. , Cutler Abigail S. , Longo Walter E. , Ahuja Nita , Yoo Peter S.
Published: April 2019

Objective:

To investigate the occurrence, nature, and reporting of sexual harassment in surgical training and to understand why surgical trainees who experience harassment might not report it. This information will inform ways to overcome barriers to reporting sexual harassment.

Summary/ Background Data:

Sexual harassment in the workplace is a known phenomenon with reports of high frequency in the medical field. Aspects of surgical training leave trainees especially vulnerable to harassing behavior. The characteristics of sexual harassment and reasons for its underreporting have yet to be studied on the national level in this population.

Methods:

An electronic anonymous survey was distributed to general surgery trainees in participating program; all general surgery training programs nationally were invited to participate.

Results:

Sixteen general surgery training programs participated, yielding 270 completed surveys (response rate of 30%). Overall, 48.9% of all respondents and 70.8% of female respondents experienced at least 1 form of sexual harassment during their training. Of the respondents who experienced sexual harassment, 7.6% reported the incident. The most common cited reasons for nonreporting were believing that the action was harmless (62.1%) and believing reporting would be a waste of time (47.7%).

Conclusion:

Sexual harassment occurs in surgical training and is rarely reported. Many residents who are harassed question if the behavior they experienced was harassment or feel that reporting would be ineffectual—leading to frequent nonreporting. Surgical training programs should provide all-level education on sexual harassment and delineate the best mechanism for resident reporting of sexual harassment.
Efficacy of Educational Interventions in Improving Measures of Living-donor Kidney Transplantation Activity: A Systematic Review and Meta-analysis
Authors: Sandal Shaifali , Dendukuri Nandini , Wang Shouao , Guadagno Elena , Ekmekjian Taline , Alam Ahsan
Published: April 2019

Background.

To address patient-level barriers to living-donor kidney transplantation (LDKT), centers have implemented educational interventions. Recently, some have highlighted several gaps in knowledge and lack of evidence of efficacy of these interventions. No review has synthesized the available data.

Methods.

We conducted a systematic review and meta-analysis of studies conducted to increase measures of LDKT. Outcomes of interest were LDKT rates, donor evaluation, donor contact/inquiry, total transplantation rates, and change in knowledge scores and pursuit behaviors. A literature search was conducted across 7 databases from inception until 2017. Educational interventions were a decision/teaching aid alone or with personalized sessions. Comparator was another intervention or nonspecific education. Random effects meta-analysis was performed to pool risk ratios (RRs) across studies.

Results.

Of the 1813 references, 15 met the inclusion criteria; 9 were randomized control trials. When compared with nonspecific education, interventions increased LDKT rates (RR = 2.54; 95% confidence interval [CI], 1.49-4.35), donor evaluation (RR = 3.82; 95% CI, 1.91-7.64), and donor inquiry/contact (RR = 2.41; 95% CI, 1.53-3.80), but not total transplants (RR = 1.24; 95% CI, 0.96-1.61). Significant increased mean knowledge scores postintervention was noted, and most showed favorable trends in pursuit behaviors. Quality across the studies was mixed and sometimes difficult to assess. The biggest limitations were small sample size, selection bias, and short follow-ups.

Conclusions.

Educational interventions improve measures of LDKT activity; however, current literature is heterogeneous and at risk of selection bias. Prospective studies with diverse patient populations, longer follow-ups, and robust outcomes are needed to inform clinical practice.
HLA Class I–sensitized Renal Transplant Patients Have Antibody Binding to SLA Class I Epitopes
Authors: Martens Gregory R. , Ladowski Joseph M. , Estrada Jose , Wang Zheng-Yu , Reyes Luz M. , Easlick Juliet , Smith Clarkson , Butler James R. , Sidner Richard A. , Eckhoff Devin E. , Tector Matthew , Tector Joseph
Published: April 2019

Background.

Highly sensitized patients are difficult to match with suitable renal allograft donors and may benefit from xenotransplant trials. We evaluate antibody binding from sensitized patients to pig cells and engineered single allele cells to identify anti-human leukocyte antigen (HLA) antibody cross-species reactivity with swine leukocyte antigen (SLA). These novel testing strategies assess HLA/SLA epitopes and antibody-binding patterns and introduce genetic engineering of SLA epitopes.

Methods.

Sensitized patient sera were grouped by calculated panel reactive antibody and luminex single antigen reactivity profile and were tested with cloned GGTA1/CMAH/B4GalNT2 glycan knockout porcine cells. Pig reactivity was assessed by direct flow cytometric crossmatch and studied following elution from pig cells. To study the antigenicity of individual class I HLA and SLA alleles in cells, irrelevant sera binding to lymphoblastoid cells were minimized by CRISPR/Cas9 elimination of endogenous class I and class II HLA, B-cell receptor, and Fc receptor genes. Native HLA, SLA, and mutants of these proteins after mutating 144K to Q were assessed for antibody binding.

Results.

Those with predominately anti-HLA-B&C antibodies, including Bw6 and Bw4 sensitization, frequently have low pig reactivity. Conversely, antibodies eluted from porcine cells are more commonly anti-HLA-A. Single HLA/SLA expressing engineered cells shows variable antigenicity and mutation of 144K to Q reduces antibody binding for some sensitized patients.

Conclusions.

Anti-HLA antibodies cross-react with SLA class I in predictable patterns, which can be identified with histocompatibility strategies, and SLA class I is a possible target of genetic engineering.
Peptidylarginine Deiminase inhibition abolishes the production of large extracellular vesicles fromGiardia intestinalis, affecting host-pathogen interactions by hindering adhesion to host cells
Authors: Gavinho Bruno , Rossi Izadora Volpato , Evans-Osses Ingrid , Lange Sigrun , Ramirez Marcel Ivan
Published: April 2019

Giardia intestinalisis an anaerobic protozoan that is an important etiologic agent of inflammation-driven diarrhea worldwide. Although self-limiting, a deep understanding of the factors involved in the pathogenicity that produces the disruption of the intestinal barrier remains unknown. There is evidence that under diverse conditions, the parasite is capable of shedding extracellular vesicles (EVs) which could modulate the physiopathology of giardiasis. Here we describe new insights ofG. intestinalisEV production, revealing its capacity to shed two different enriched EV populations (large and small extracellular vesicles) and identified a relevant adhesion function associated only with the larger population. Our work also aimed at assessing the influences of two recently identified inhibitors of EV release in mammalian cells, namely peptidylarginine deiminase (PAD) inhibitor and cannabidiol (CBD), on EV release fromGiardiaand their putative effects on host-pathogen interactions. PAD-inhibitor Cl-amidine and CBD were both able to effectively reduce EV shedding, the PAD-inhibitor specifically affecting the release of large extracellular vesicles and interfering within vitrohost-pathogen interactions. The strong efficacy of the PAD-inhibitor onGiardiaEV release indicates a phylogenetically conserved pathway of PAD-mediated EV release, most likely affecting theGiardiaarginine deiminase (GiADI) homolog of mammalian PADs. While there is still much to learn aboutG. intestinalisinteraction with its host, our results suggest that large and small EVs may be differently involved in protozoa communication, and that EV-inhibitor treatment may be a novel strategy for recurrent giardiasis treatment.
Robust Pavlovian-to-Instrumental and Pavlovian-to-Metacognitive Transfers in human reinforcement learning
Authors: Ting Chih-Chung , Palminteri Stefano , Engelmann Jan B. , Lebreton Maël
Published: April 2019

In simple instrumental-learning tasks, humans learn to seek gains and to avoid losses equally well. Yet, two effects of valence are observed. First, decisions in loss-contexts are slower, which is consistent with the Pavlovian-instrumental transfer (PIT) hypothesis. Second, loss contexts decrease individuals’ confidence in their choices – a bias akin to a Pavlovian-to-metacognitive transfer (PMT). Whether these two effects are two manifestations of a single mechanism or whether they can be partially dissociated is unknown. Here, across six experiments, we attempted to disrupt the PIT effects by manipulating the mapping between decisions and actions and imposing constraints on response times (RTs). Our goal was to assess the presence of the metacognitive bias in the absence of the RT bias. Were observed both PIT and PMT despite our disruption attempts, establishing that the effects of valence on motor and metacognitive responses are very robust and replicable. Nonetheless, within- and between-individual inferences reveal that the confidence bias resists the disruption of the RT bias. Therefore, although concomitant in most cases, PMT and PIT seem to be – partly – dissociable. These results highlight new important mechanistic constraints that should be incorporated in learning models to jointly explain choice, reaction times and confidence.
Distributed Code for Semantic Relations Predicts Neural Similarity
Authors: Chiang Jeffrey N. , Peng Yujia , Lu Hongjing , Holyoak Keith J. , Monti Martin M.
Published: April 2019

The ability to generate and process semantic relations is central to many aspects of human cognition. Theorists have long debated whether such relations are coded as atomistic links in a semantic network, or as distributed patterns over some core set of abstract relations. The form and content of the conceptual and neural representations of semantic relations remains to be empirically established. The present study combined computational modeling and neuroimaging to investigate the representation and comparison of abstract semantic relations in the brain. By using sequential presentation of verbal analogies, we decoupled the neural activity associated with encoding the representation of the first-order semantic relation between words in a pair from that associated with the second-order comparison of two relations. We tested alternative computational models of relational similarity in order to distinguish between rival accounts of how semantic relations are coded and compared in the brain. Analyses of neural similarity patterns supported the hypothesis that semantic relations are coded, in the parietal cortex, as distributed representations over a pool of abstract relations specified in a theory-based taxonomy. These representations, in turn, provide the immediate inputs to the process of analogical comparison, which draws on a broad frontoparietal network. This study sheds light not only on the form of relation representations but also on their specific content.

Significance

Relations provide basic building blocks for language and thought. For the past half century, cognitive scientists exploring human semantic memory have sought to identify the code for relations. In a neuroimaging paradigm, we tested alternative computational models of relation processing that predict patterns of neural similarity during distinct phases of analogical reasoning. The findings allowed us to draw inferences not only about the form of relation representations, but also about their specific content. The core of these distributed representations is based on a relatively small number of abstract relation types specified in a theory-based taxonomy. This study helps to resolve a longstanding debate concerning the nature of the conceptual and neural code for semantic relations in the mind and brain.
Validation of new bioinformatic tools to identify expanded repeats: a non-reference intronic pentamer expansion inRFC1causes CANVAS
Authors: Rafehi Haloom , Szmulewicz David J , Bennett Mark F , Sobreira Nara LM , Pope Kate , Smith Katherine R , Gillies Greta , Diakumis Peter , Dolzhenko Egor , Eberle Michael A , Barcina María García , Breen David P , Chancellor Andrew M , Cremer Phillip D , Delatycki Martin B. , Fogel Brent L , Hackett Anna , Halmagyi G. Michael , Kapetanovic Solange , Lang Anthony , Mossman Stuart , Mu Weiyi , Patrikios Peter , Perlman Susan L , Rosemargy Ian , Storey Elsdon , Watson Shaun RD , Wilson Michael A , Zee David , Valle David , Amor David J , Bahlo Melanie , Lockhart Paul J
Published: April 2019

Genomic technologies such as Next Generation Sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have proven inefficient at identifying pathogenic repeat expansions. Here, we apply a collection of bioinformatics tools that can be utilized to identify either known or novel expanded repeat sequences in NGS data. We performed genetic studies of a cohort of 35 individuals from 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Analysis of whole genome sequence (WGS) data with five independent algorithms identified a recessively inherited intronic repeat expansion [(AAGGG)exp] in the gene encoding Replication Factor C1 (RFC1). This motif, not reported in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)11short tandem repeat. Genetic analyses confirmed the pathogenic expansion in 18 of 22 CANVAS families and identified a core ancestral haplotype, estimated to have arisen in Europe over twenty-five thousand years ago. WGS of the fourRFC1negative CANVAS families identified plausible variants in three, with genomic re-diagnosis of SCA3, spastic ataxia of the Charlevoix-Saguenay type and SCA45. This study identified the genetic basis of CANVAS and demonstrated that these improved bioinformatics tools increase the diagnostic utility of WGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders.
Resting Eyes Closed Beta-Phase High Gamma-Amplitude Coupling Deficits in Children with Attention Deficit Hyperactivity Disorder
Authors: Ibanez-Soria David , Kroupi Eleni , Rojas Andrés , Castellano Marta , Picardo Jacobo , García-Banda Gloria , Saez Belen , Servera Mateu , Ruffini Giulio , Soria-Frisch Aureli
Published: April 2019

Objective

Attention-deficit hyperactivity disorder (ADHD) is the neurobehavioral disorder with the largest prevalence rate in childhood. ADHD is generally assessed based on physical examination of the child and interviews, and therefore prone to subjectivity. This fact may lead to a high risk of mis- and over-diagnosis, a problem that can be addressed through the use of objective markers.

Methods

Here we propose to use phase-amplitude coupling as a digital biomarker in ADHD. We investigated the hypothesis that coupling between the phase of slow brain rhythms and the amplitude of fast rhythms is altered in the ADHD population. We tested this hypothesis measuring phase-amplitude coupling (PAC) in the 4 to 200Hz range in electroencephalographic (EEG) signals recorded in the central-frontal area in children during eyes closed resting state.

Results

Using automatic clustering, we observed statistically significant beta-gamma PAC deficits in the ADHD population in the frontal-left hemisphere.

Conclusions

These findings suggests alterations in the beta-gamma coupling in the ADHD population. We discuss the hypothesis that these alterations may be indicators of working memory and attention deficits.

Significance

The study of the coupling between the different brain rhythms can potentially contribute to the understanding and clinical diagnosis of ADHD.
The speciation and hybridization history of the genusSalmonella
Authors: Criscuolo Alexis , Issenhuth-Jeanjean Sylvie , Didelot Xavier , Thorell Kaisa , Hale James , Parkhill Julian , Thomson Nicholas R. , Weill François-Xavier , Falush Daniel , Brisse Sylvain
Published: April 2019

Bacteria and archaea make up most of natural diversity but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genusSalmonella, an ecologically diverse bacterial lineage, within whichS. entericasubsp.entericais responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified eleven distinct phylogroups, three of which were previously undescribed. Strains assigned toS. entericasubsp.salamaeare polyphyletic, with two distinct lineages that we designate Salamae A and Salamae B. Strains of subspecieshoutenaeare subdivided into two groups, Houtenae A and B and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages but detected more subtle signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence may not apply inSalmonella.

Data summary

Illumina sequence data were submitted to the European Nucleotide Archive under project number PRJEB2099 and are available from INSDC (NCBI/ENA/DDBJ) under accession numbers ERS011101 to ERS011146. The MLST sequence and profile data generated in this study have been publicly available on theSalmonellaMLST web site between 2010 and the migration of theSalmonellaMLST website to EnteroBase (https://enterobase.warwick.ac.uk/), and subsequently from there.
PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria
Authors: Bayliss Sion C. , Thorpe Harry A. , Coyle Nicola M. , Sheppard Samuel K. , Feil Edward J.
Published: April 2019

Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement And Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino-acid or nucleotide identity thresholds and uses the clustering information to rapidly classify paralogous gene families into either putative fission/fusion events or gene duplications. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation and estimates sequence divergence for each gene family. We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.

Availability

PIRATE is implemented in Perl and is freely available under an GNU GPL 3 open source license fromhttps://github.com/SionBayliss/PIRATE.

Supplementary Information

Supplementary data is available online.
Genetic Associations with Mathematics Tracking and Persistence in Secondary School
Authors: Harden K. Paige , Domingue Benjamin W. , Belsky Daniel W. , Boardman Jason D. , Crosnoe Robert , Malanchini Margherita , Nivard Michel , Tucker-Drob Elliot M. , Mullan Harris Kathleen
Published: April 2019

Maximizing the flow of students through the science, technology, engineering, and math (STEM) pipeline is important to promoting human capital development and reducing economic inequality1. A critical juncture in the STEM pipeline is the highly-cumulative sequence of secondary school math courses2–5. Students from disadvantaged schools are less likely to complete advanced math courses, but debate continues about why6,7. Here, we address this question using studentpolygenic scores, which are DNA-based indicators of propensity to succeed in education8. We integrated genetic and official school transcript data from over 3,000 European-ancestry students from U.S. high schools. We used polygenic scores as a molecular tracer to understand how the flow of students through the high school math pipeline differs in socioeconomically advantaged versus disadvantaged schools. Students with higher education polygenic scores were tracked to more advanced math already at the beginning of high school and persisted in math for more years. Molecular tracer analyses revealed that the dynamics of the math pipeline differed by school advantage. Compared to disadvantaged schools, advantaged schools tracked more students with high polygenic scores into advanced math classes at the start of high school, and they buffered students with low polygenic scores from dropping out of math. Across all schools, even students with exceptional polygenic scores (top 2%) were unlikely to take the most advanced math classes, suggesting substantial room for improvement in the development of potential STEM talent. These results link new molecular genetic discoveries to a common target of educational-policy reforms.
Differential coupling of adult-born granule cells to parvalbumin and somatostatin interneurons
Authors: Groisman Ayelén I. , Yang Sung M. , Schinder Alejandro F.
Published: April 2019

The dentate gyrus of the hippocampus is dominated by a strong GABAergic tone that maintains sparse levels of activity. Adult neurogenesis disrupts this balance through the continuous addition of new granule cells (GCs) that display high excitability while develop and connect within the preexisting host circuit. The dynamics of the connectivity map for developing GCs in the local inhibitory networks remains unknown. We used optogenetics to study afferent and efferent synaptogenesis between new GCs and GABAergic interneurons expressing parvalbumin (PV-INs) and somatostatin (SST-INs). Inputs from PV-INs targeted the soma and remained immature until they grew abruptly in >4-week-old GCs. This transition was accelerated by exposure to enriched environment. Inputs from SST-INs were dendritic and developed slowly until reaching maturity by 8 weeks. Synaptic outputs from GCs onto PV-INs matured faster than those onto SST-INs, but also required several weeks. In the mature dentate network, PV-INs exerted an efficient control of GC spiking and were involved in both feedforward and feedback loops, a mechanism that would favor lateral inhibition and sparse coding. Our results reveal a long-lasting transition where adult-born neurons remain poorly coupled to inhibition, which might enable a parallel streaming channel from the entorhinal cortex to CA3 pyramidal cells.
Nanog regulates Pou3f1 expression and represses anterior fate at the exit from pluripotency
Authors: Barral Antonio , Rollan Isabel , Sanchez-Iranzo Hector , Jawaid Wajid , Badia-Careaga Claudio , Menchero Sergio , Gomez Manuel J. , Torroja Carlos , Sanchez-Cabo Fatima , Göttgens Berthold , Manzanares Miguel , de Aja Julio Sainz
Published: April 2019

Pluripotency is regulated by a network of transcription factors that maintains early embryonic cells in an undifferentiated state while allowing them to proliferate. NANOG is a critical factor for maintaining pluripotency and its role in primordial germ cell differentiation has been well described. However, Nanog is expressed during gastrulation across all the posterior epiblast, and only later in development its expression is restricted to primordial germ cells. In this work, we unveiled a previously unknown mechanism by which Nanog specifically represses the anterior epiblast lineage. Analysis of transcriptional data from both embryonic stem cells and gastrulating mouse embryos revealed Pou3f1 expression to be negatively correlated with that of Nanog during the early stages of differentiation. We have functionally demonstrated Pou3f1 to be a direct target of NANOG by using a dual transgene system for the controlled expression of Nanog. Use of Nanog null ES cells further demonstrated a role for Nanog in repressing anterior neural genes. Deletion of a NANOG binding site (BS) located nine kilobases downstream of the transcription start site of Pou3f1 revealed this BS to have a specific role in the regionalization of the expression of this gene in the embryo. Our results indicate an active role of Nanog inhibiting the neural fate by repressing Pou3f1 at the onset of gastrulation.
The full-length transcriptome ofC. elegansusing direct RNA sequencing
Authors: Roach Nathan P. , Sadowski Norah , Alessi Amelia F. , Timp Winston , Taylor James , Kim John K.
Published: April 2019

Current transcriptome annotations have largely relied on short read lengths intrinsic to most widely used high-throughput cDNA sequencing technologies. For example, in the annotation of theCaenorhabditis eleganstranscriptome, more than half of the transcript isoforms lack full-length support and instead rely on inference from short reads that do not span the full length of the isoform. We applied nanopore-based direct RNA sequencing to characterize the developmental polyadenylated transcriptome ofC. elegans. Taking advantage of long reads spanning the full length of mRNA transcripts, we provide support for 20,902 splice isoforms across 14,115 genes, without the need for computational reconstruction of gene models. Of the isoforms identified, 2,188 are novel splice isoforms not present in the Wormbase WS265 annotation. Furthermore, we identified 16,325 3’ untranslated region (3’UTR) isoforms, 2,304 of which are novel and do not fall within 10 bp of existing 3’UTR datasets and annotations. Combining 3’UTRs and splice isoforms we identified 25,944 full-length isoforms. We also determined that poly(A) tail lengths of transcripts vary across development, as do the strengths of previously reported correlations between poly(A) tail length and expression level, and poly(A) tail length and 3’UTR length. Finally, we have formatted this data as a publically accessible track hub, enabling researchers to explore this dataset easily in a genome browser.
Prediction of the Effect of Naturally Occurring Missense Mutations on CellularN-Acetyl-GlucosaminidaseEnzymatic Activity
Authors: Ford Colby T. , Uppal Aneeta , Nodzak Conor M. , Shi Xinghua
Published: April 2019

In 2015, the Critical Assessment of Genome Interpretation (CAGI) proposed a challenge to devise a computational method for predicting the phenotypic consequences of genetic variants of a lysosomal hydrolase enzyme known asα-N-acetylglucosaminidase (NAGLU). In 2014, the Human Gene Mutation Database released that 153 NAGLU mutations associated with MPS IIIB and 90 of them are missense mutations. The ExAC dataset catalogued 189 missense mutations NAGLU based on exome sequence data from about 60,000 individual and 24 of them are known to be disease associated. Biotechnology company, BioMarin, has quantified the relative functionality of NAGLU for the remaining subset of 165 missense mutations. For this particular challenge, we examined the subset missense mutations within the ExAC dataset and predicted the probability of a given mutation being deleterious and relating this measure to the capacity of enzymatic activity. In doing so, we hoped to learn the degree to which changes in amino acid physicochemical properties are tolerable for NAGLU function.

Amino acid substitution (AAS) prediction methods are mainly based on the sequence and structure information. Simple comparisons between different AAS methods are not only difficult, but also irrational because each method was tested on various datasets and based on varied versions of databases. Currently, several AAS prediction methods have been introduced. PolyPhen-2, an updated version of PolyPhen, is a tool used to predict possible impacts of an amino acid substitution on the structure and function. Users are required to provide protein or SNP identifiers, protein sequences, substitution positions, etc. A score is provided, ranging from 0 to 1, corresponding to the probability of a mutation resulting in no functionality for the enzyme

Once the probability scores were generated, the dataset was then run through multiple machine learning algorithms to generate an applicable model for predicting the enzymatic activity of MPS IIIB-related mutations. This prediction was generated using the PolyPhen-2 probability score and other information about the mutation (amino acid type, location, allele frequency, etc.) as input feature variables. This generated a predicted aggregate score for each mutation, which was then reported back to CAGI. The results of the analysis are significant enough to hold confidence that the scores are decent predictors of enzymatic activity given a mutation in the NAGLU amino acid sequence.
Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci
Authors: Gutierrez-Arcelus Maria , Baglaenko Yuriy , Arora Jatin , Hannes Susan , Luo Yang , Amariuta Tiffany , Teslovich Nikola , Rao Deepak A. , Ermann Joerg , Jonsson Helena , Naverrete Cristina , Gregersen Peter K. , Esko Tonu , Brenner Michael B. , Raychaudhuri Soumya
Published: April 2019

Understanding how genetic regulatory variation affects gene expression in different T cell states is essential to deciphering autoimmunity. We conducted a high-resolution RNA-seq time course analysis of stimulated memory CD4+T cells from 24 healthy individuals. We identified 186 genes with dynamic allele-specific expression, where the balance of alleles changes over time. These genes were four fold enriched in autoimmune loci. We found pervasive dynamic regulatory effects within six HLA genes, particularly for a major autoimmune risk gene,HLA-DQB1. EachHLA-DQB1allele had one of three distinct transcriptional regulatory programs. Using CRISPR/Cas9 genomic editing we demonstrated that a single nucleotide variant at the promoter is causal for T cell-specific control ofHLA-DQB1expression. Our study in CD4+T cells shows that genetic variation incisregulatory elements may affect gene expression in a lymphocyte activation status-dependent manner contributing to the inter-individual complexity of immune responses.
Integrated RNA and metabolite profiling of urine liquid biopsies for prostate cancer biomarker discovery
Authors: Lee Bongyong , Mahmud Iqbal , Marchica John , Dereziński Paweł , Qi Feng , Wang Fubo , Joshi Piyush , Valerio Felipe , Rivera Inoel , Patel Vipul , Pavlovich Christian P. , Garrett Timothy , Schroth Gary P. , Sun Yinghao , Perera Ranjan J.
Published: April 2019

Sensitive and specific diagnostic and prognostic biomarkers for prostate cancer (PCa) are urgently needed. Urine samples are a non-invasive means to obtain abundant and readily accessible “liquid biopsies”. Herein we used urine liquid biopsies to identify and characterize a novel group of urine-enriched RNAs and metabolites in PCa patients and normal individuals with or without benign prostatic disease. Differentially expressed RNAs were identified in urine samples by deep sequencing and metabolites in urine were measured by mass spectrometry. The mRNA and metabolite profiles were distinct in patients with benign and malignant disease. Integrated analysis of urinary gene expression and metabolite signatures unveiled an aberrant glutamate metabolism and tricarboxylic acid (TCA) cycle node in prostate cancer-derived cells. Functional validation supports a role for glutamate metabolism and glutamate oxaloacetate transaminase 1 (GOT1)-dependent redox balance in prostate cancer, which can be exploited for novel biomarkers and therapies.
Improved bacteria population structure analysis on thousands of genomes using unsupervised methods
Authors: Schlum Katrina , Jun Se-Ran , Udaondo Zulema , Ussery David W. , Emrich Scott J.
Published: April 2019

Over ten thousand genomes ofEscherichia coliare now available, and this number will continue to grow for this and other important microbial species. The first approach often used to better understand microbes is phylogenetic group analysis followed by pan-genome analysis of highly related genomes. Here, we combine sequence-based features with unsupervised clustering on up to 2,231E. coligenomes and a total of 1,367Clostridium difficilegenomes. We show that Non-negative Matrix Factorization (NMF) can identify “mixed”/cryptic genomes, and can better determine inter-related genome groups and their distinguishing features (genes) relative to prior methods.
Spatial density estimates of Eurasian lynx (Lynx lynx) in the French Jura and Vosges Mountains
Authors: Gimenez Olivier , Gatti Sylvain , Duchamp Christophe , Germain Estelle , Laurent Alain , Zimmermann Fridolin , Marboutin Eric
Published: April 2019

Obtaining estimates of animal population density is a key step in providing sound conservation and management strategies for wildlife. For many large carnivores however, estimating density is difficult because these species are elusive and wide-ranging. Here, we focus on providing the first density estimates of the Eurasian lynx (Lynx lynx) in the French Jura and Vosges mountains. We sampled a total of 413 camera trapping sites (with 2 cameras per site) between January 2011 and April 2016 in seven study areas across seven counties of the French Jura and Vosges mountains. We obtained 592 lynx detections over 19,035 trap days in the Jura mountain and 0 detection over 6,804 trap days in the Vosges mountain. Based on coat patterns, we identified a total number of 92 unique individuals from photographs, including 16 females, 13 males and 63 individuals of unknown sex. Using spatial capture-recapture (SCR) models, we estimated abundance in the study areas between 5 (SE = 0.1) and 29 (0.2) lynx and density between 0.24 (SE = 0.02) and 0.91 (SE = 0.03) lynx per 100 km2. We also provide a comparison with non-spatial density estimates and discuss the expected discrepancies. Our study is yet another example of the advantage of combining SCR methods and non-invasive sampling techniques to estimate density for elusive and wide-ranging species, like large carnivores. While the estimated densities in the French Jura mountain are comparable to other lynx populations in Europe, the fact that we detected no lynx in the Vosges mountain is alarming. Connectivity should be encouraged between the French Jura mountain, the Vosges mountain and the Palatinate Forest in Germany where a reintroduction program is currently ongoing. Our density estimates will help in setting a baseline conservation status for the lynx population in France.
Quality control of large genome datasets using genome fingerprints
Authors: Robinson Max , Joshi Arpita , Vidyarthi Ansh , Maccoun Mary , Rangavajjhala Sanjay , Glusman Gustavo
Published: April 2019

The 1000 Genomes Project (TGP) is a foundational resource which serves the biomedical community as a standard reference cohort for human genetic variation. There are now seven public versions of these genomes. The TGP Consortium produced the first by mapping its final data release against human reference sequence GRCh37, then “lifted over’’ these genomes to the improved reference sequence (GRCh38) when it was released, and remapped the original data to GRCh38 with two similar pipelines. As ‘best practice’ quality validation, the pipelines that generated these versions were benchmarked against the Genome In A Bottle Consortium’s ‘platinum quality’ genome (NA12878). The New York Genome Center recently released the results of independently resequencing the cohort at greater depth (30X), a phased version informed by the inclusion of related individuals, and independently remapped the original variant calls to GRCh38. We evaluated all seven versions using genome fingerprinting, which supports ultrafast genome comparison even across reference versions. We noted multiple issues including discrepancies in cohort membership, disagreement on the overall level of variation, evidence of substandard pipeline performance on specific genomes and in specific regions of the genome, cryptic relationships between individuals, inconsistent phasing, and annotation distortions caused by the history of the reference genome itself. We therefore recommend global quality assessment by rapid genome comparisons, using genome fingerprints and other metrics, alongside benchmarking as part of ‘best practice’ quality assessment of large genome datasets. Our observations also help inform the decision of which version to use, to support analyses by individual researchers.
SUPPRESSOR OF MAX2 1-LIKE 5 promotes secondary phloem formation during radial stem growth
Authors: Wallner Eva-Sophie , Jouannet Virginie , Greb Thomas
Published: April 2019

As a prerequisite for constant growth, plants can produce vascular tissues at different sites in their postembryonic body. In particular, the formation of vascular tissues during longitudinal and radial expansion of growth axes differs fundamentally with respect to its anatomical configuration. This raises the question to which level regulatory mechanisms of vascular tissue formation are shared throughout plant development. Here, we show that, similar as primary phloem formation during longitudinal growth, the cambium-based formation of secondary phloem depends on the function of SMXL genes. Using promoter reporter lines, we observe that SMXL4 and SMXL5 activities are associated with different stages of secondary phloem formation in Arabidopsis stems and the specific loss of SMXL5 function results in the absence of secondary phloem. Interestingly, the additional disruption of SMXL4 activity increases cell proliferation rates in the cambium region without that secondary phloem is formed. Based on genome-wide transcriptional profiling and expression analyses of phloem-related markers we conclude that early steps of phloem formation are impaired in smxl4;smxl5 double mutants and that additional cambium-derived cells fail in establishing any phloem-related feature. Our results show that molecular mechanisms determining primary and secondary phloem share important features but differ slightly with SMXL5 playing a more dominant role in the formation of secondary phloem.
Electric-induced reversal of morphogenesis inHydra
Authors: Braun Erez , Ori Hillel
Published: April 2019

Morphogenesis involves the dynamic interplay of biochemical, mechanical and electrical processes. Here we ask: to what extent can the course of morphogenesis be modulated and controlled by an external electric field? We show that above a critical amplitude, an external electric field can halt morphogenesis inHydraregeneration. Moreover, above this critical amplitude, the electric field can even lead to reversal dynamics: a fully developedHydrafolds back into its incipient spheroid morphology. The potential to renew morphogenesis is re-exposed when the field is reduced back to amplitudes below criticality. These dynamics are accompanied by modulations of theWnt3activity, a central component of the head organizer inHydra. Reversal of morphogenesis is shown to be triggered by enhanced epithelial electrical excitations, accompanied by intensified calcium activity, indicating that electrical processes play an instructive role to a level that can direct developmental trajectories. Reversal of morphogenesis by external fields, calls for extending its framework beyond programmatic, forward-driven, hierarchical processes.
Extensive Ribosome and RF2 Rearrangements during Translation Termination
Authors: Svidritskiy Egor , Demo Gabriel , Loveland Anna B. , Xu Chen , Korostelev Andrei A.
Published: April 2019

Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, we resolved a cryo-EM ensemble of E. coli 70S•RF2 structures at up to 3.3 Å in a single sample. Five structures suggest a highly dynamic termination pathway. Upon peptidyl-tRNA hydrolysis, the CCA end of deacyl-tRNA departs from the peptidyl transferase center. The catalytic GGQ loop of RF2 is rearranged into a long β-hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit. Ribosomal intersubunit rotation destabilizes the catalytic RF2 domain on the 50S subunit and disassembles the central intersubunit bridge B2a, resulting in RF2 departure. Our structures visualize how local rearrangements and spontaneous inter-subunit rotation poise the newly-made protein and RF2 to dissociate in preparation for ribosome recycling.
Conformational catalysis of cataract-associated aggregation in a human eye lens crystallin occurs via interface stealing
Authors: Serebryany Eugene , Jacobs William M. , Razban Rostam M. , Shakhnovich Eugene I.
Published: April 2019

Human γD-crystallin (HγD) is an abundant and highly stable two-domain protein in the core region of the eye lens. Destabilizing mutations and post-translational modifications in this protein are linked to onset of aggregation that causes cataract disease (lens turbidity). Wild-type HγD greatly accelerates aggregation of the cataract-related W42Q variant, without itself aggregating. The mechanism of this “inverse prion” catalysis of aggregation remained unknown. Here we provide evidence that an early unfolding intermediate with an opened domain interface enables transient dimerization of the C-terminal domains of wild-type and mutant, or mutant and mutant, HγD molecules, which deprives the mutant’s N-terminal domain of intramolecular stabilization by the native domain interface and thus accelerates its misfolding to a distinct, aggregation-prone intermediate. A detailed kinetic model predicts universal power-law scaling relationships for lag time and rate of the resulting aggregation, which are in excellent agreement with the data. The mechanism reported here, which we term interface stealing, can be generalized to explain how common domain-domain interactions can have surprising consequences, such as conformational catalysis of unfolding, in multidomain proteins.

Significance

Most known proteins in nature consist of multiple domains. Interactions between domains may lead to unexpected folding and misfolding phenomena. This study of human γD-crystallin, a two-domain protein in the eye lens, revealed one such surprise: conformational catalysis of misfolding via intermolecular domain interface “stealing.” An intermolecular interface between the more stable domains outcompetes the native intramolecular domain interface. Loss of the native interface in turn promotes misfolding and subsequent aggregation, especially in cataract-related γD-crystallin variants. This phenomenon is likely a contributing factor in the development of cataract disease, the leading worldwide cause of blindness. However, interface stealing likely occurs in many proteins composed of two or more interacting domains.