bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rhinovirus Detection in the Nasopharynx of Children Undergoing Cardiac Surgery Is Not Associated With Longer PICU Length of Stay: Results of the Impact of Rhinovirus Infection After Cardiac Surgery in Kids (RISK) Study
Authors: Roeleveld Peter Paul , Van Rijn Anneloes L. , de Wilde Rob B. P. , van Zwet Erik W. , Wink Jeroen , Rozendaal Lieke , Hogenbirk Karin , Hazekamp Mark G. , Man Wing Ho , Sidorov Igor , Kraakman Margriet E. M. , Claas Eric C. J. , de Jonge Evert , Kroes Aloys C. M. , de Vries Jutte J. C. 
Published: October 2020

Objectives:
To determine whether children with asymptomatic carriage of rhinovirus in the nasopharynx before elective cardiac surgery have an increased risk of prolonged PICU length of stay.

Study Design:
Prospective, single-center, blinded observational cohort study.

Setting:
PICU in a tertiary hospital in The Netherlands.

Patients:
Children under 12 years old undergoing elective cardiac surgery were enrolled in the study after informed consent of the parents/guardians.

Interventions:
The parents/guardians filled out a questionnaire regarding respiratory symptoms. On the day of the operation, a nasopharyngeal swab was obtained. Clinical data were collected during PICU admission, and PICU/hospital length of stay were reported. If a patient was still intubated 3 days after operation, an additional nasopharyngeal swab was collected. Nasopharyngeal swabs were tested for rhinovirus and other respiratory viruses with polymerase chain reaction.

Measurements and Main RESULTS:
Of the 163 included children, 74 (45%) tested rhinovirus positive. Rhinovirus-positive patients did not have a prolonged PICU length of stay (median 2 d each; p = 0.257). Rhinovirus-positive patients had a significantly shorter median hospital length of stay compared with rhinovirus-negative patients (8 vs 9 d, respectively; p = 0.006). Overall, 97 of the patients (60%) tested positive for one or more respiratory virus. Virus-positive patients had significantly shorter PICU and hospital length of stay, ventilatory support, and nonmechanical ventilation. Virus-negative patients had respiratory symptoms suspected for a respiratory infection more often. In 31% of the children, the parents reported mild upper respiratory complaints a day prior to the cardiac surgery, this was associated with postextubation stridor, but no other clinical outcome measures.

Conclusions:
Preoperative rhinovirus polymerase chain reaction positivity is not associated with prolonged PICU length of stay. Our findings do not support the use of routine polymerase chain reaction testing for respiratory viruses in asymptomatic children admitted for elective cardiac surgery.
Growth and Neurodevelopment Outcomes in HIV-, Tenofovir-, and Efavirenz-Exposed Breastfed Infants in the PMTCT Option B+ Program in Malawi
Authors: Kapito-Tembo Atupele P. , Bauleni Andy , Wesevich Austin , Ongubo Dennis , Hosseinipour Mina C. , Dube Queen , Mwale Patrick , Corbett Amanda , Mwapasa Victor , Phiri Sam 
Published: October 2020

Background:
Pregnant and breastfeeding women in Option B+ in Malawi received antiretroviral drugs (ARVs) containing efavirenz (EFV) and tenofovir disoproxil fumarate (TDF). However, effects on growth, renal, bone metabolism, and neurodevelopment of long-term exposure to low doses of these drugs through breast milk in HIV-exposed infants are unclear.

Methods:
Prospective cohorts of TDF-and-EFV–exposed and TDF-and-EFV–unexposed breastfed infants of HIV-infected and HIV-uninfected mothers in Option B+ were recruited in 2:1 ratio, respectively, followed from birth to 18 months. Infants with low birth weight, premature birth, and congenital abnormalities were excluded. Anthropometrics were assessed at birth, 6 weeks, 3, 6, 12, and 18 months. Neurodevelopment assessments used the Bayley Scales of Infant and Toddler Development III from 6 weeks. Creatinine, alkaline phosphatase, and phosphorus were assessed at 3, 6, and 12 months.

Results:
Of 260 HIV-and-ARV–exposed and 125 HIV-and-ARV–unexposed infants enrolled at birth, 87% and 57%, 78% and 59%, 77% and 54%, 73% and 51%, and 65% and 43% completed 6-weeks, 3, 6, 12, and 18 months visits, respectively. There were no significant differences in the mean Z-scores for length-for-age, weight-for-age, weight-for-length, mid-upper arm circumference-for-age, and head circumference-for-age between groups except at 6-weeks for length-for-age. No bone fractures occurred. Neurodevelopment outcomes were similar between groups. Of creatinine, alkaline phosphatase, and serum phosphate measurements, 1.7%, 2.6%, and 3.3% reached any toxicity levels grades 1–4, respectively, with no differences between groups.

Conclusion:
Long-term exposure to EFV and TDF through breastfeeding in infants of HIV-infected mothers does not seem to result in significant growth, neurodevelopment, renal, or bone adverse outcomes. Data support safety of breastfeeding through 18 months within the Option B+ program.
SARS-CoV-2 RNA detection using pooling of self-collected samples: Simple protocol may foster asymptomatic surveillance
Authors: Lopez-Lopes Giselle Ibette , de Cassia Compagnoli Carmona Rita , Silva Valéria Oliveira , Ahagon Cintia Mayumi , do Prado Lincoln Spinazola , dos Santos Fabiana Pereira , da Silva Daniela Bernardes Borges , de Oliveira Santos Katia Corrêa , Benega Margarete Aparecida , Ribeiro Willian Nery , Cilli Audrey , Matsuda Elaine Monteiro , Sardinha Afonso Ana Maria , Sampaio Tavares Timenetsky Maria do Carmo , de Macedo Brígido Luís Fernando 
Published: October 2020

1AbstractBackgroundSurveillance of COVID infection and isolation of infected individuals is one of the available tools to control the spread of SAR-CoV-2. Asymptomatic and pre symptomatic are responsible for substantial transmission. RNA or antigen tests are necessary to identify non-symptomatic individuals. We tested the feasibility of using samples pooling offering different collection alternatives (swab/throat wash/saliva) to volunteers of a public health institute.MethodsWe evaluated pool samples from frozen material from previously tested samples and a prospective collection from asymptomatic volunteers. Some collections were paired for comparison. Pools and some individual samples were extracted with QIAamp Viral RNA Mini Kit (Qiagen, USA) and/or Lucigen Quick Extract DNA extraction solution (BioSearch, USA) and submitted to rtPCR (Allplex, Seegene, Korea).ResultsA total of 240 samples from 130 new collections and 37 samples with known result were evaluated. Pool CT was generally higher than individual samples. Lucigen extraction showed higher CT, including false negative results for samples with high CT at Qiagen extraction. Paired Swab and TW samples showed comparable results. No volunteer from negative pools reported any symptom in the 2-3 days after collection.ConclusionsClinical samples pooling to detect SARS-CoV-2 RNA is feasible and an economical way to test for COVID-19, especially in surveillance strategies targeting more infectiousness, higher viremia individuals. The use of Lucigen reagents show lower sensibility that may lead to false negative results with lower viremia samples. Combining throat wash with saliva may provide and interesting self-collection alternative, but more comparative work is needed.
In vivoassessment of neurodegeneration in Spinocerebellar Ataxia type 7
Authors: Parker Jacob A. , Merchant Shabbir H. , Attaripour-Isfahani Sanaz , Cho Hyun Joo , McGurrin Patrick , Brooks Brian P. , La Spada Albert R. , Hallett Mark , Huryn Laryssa A. , Horovitz Silvina G. 
Published: October 2020

AbstractSpinocerebellar Ataxia type 7 (SCA7) is a neurodegenerative disease characterized by progressive cerebellar ataxia and retinal degeneration. Increasing loss of visual function complicates the use of clinical scales to track the progression of motor symptoms, hampering our ability to develop accurate biomarkers of disease progression, and thus test the efficacy of potential treatments. In this cross-sectional study, we aimed to identify imaging measures of neurodegeneration, which may more accurately reflect SCA7 severity and progression. We analyzed diffusion tensor imaging (DTI) data collected from a cohort of 13 SCA7 patients and 14 healthy volunteers using two recent methodological advances: 1) a diffusion tensor-based image registration technique, and 2) a dual-compartment DTI model to control for the potential increase in extracellular CSF-like water due to neurodegeneration. These methodologies allowed us to assess both volumetric and microstructural abnormalities in both white and gray matter brain-wide in SCA7 patients for the first time. To measure tissue volume, we performed diffusion tensor-based morphometry (DTBM) using the tensor-based registration. To assess tissue microstructure, we computed the parenchymal mean diffusivity (pMD) and parenchymal fractional anisotropy (pFA) using the dual compartment model. This model also enabled us to estimate the parenchymal volume fraction (pVF), a measure of parenchymal tissue volume within a given voxel. While DTBM and pVF revealed tissue loss primarily in the brainstem, cerebellum, thalamus, and a subset of cerebral white matter tracts in patients, pMD and pFA detected microstructural abnormalities brain-wide (p< 0.05, FWE corrected; Hedge’sg> 1). This distinction was meaningful in terms of motor symptom severity, as we found that patient scores on the Scale for the Assessment and Rating of Ataxia correlated most strongly with cerebellar pVF (r= - 0.66,p= 0.015) and global white matter pFA (r= −0.64,p= 0.018). Since this contrast between focal tissue loss and global microstructural abnormality has previously been described in neuropathology, we believe the approach employed here is well suited for thein-vivoassessment of neurodegeneration. Moving forward, this approach could be applied to characterize the full spatiotemporal pattern of neurodegeneration in SCA7, and potentially develop an accurate imaging biomarker of disease progression.HighlightsDTI study reveals brain-wide differences between SCA7 patients and controls.DTI dual-compartment model controls for increased CSF-like free water in patients.Tensor-based deformations show SCA7 tissue loss extends beyond cerebellum.Focal atrophy, but global microstructural abnormalities were observed in SCA7.Ataxia most correlated with cerebellar atrophy, global microstructural abnormality.
Sex differences in the human brain transcriptome of cases with schizophrenia
Authors: Hoffman Gabriel E. , Ma Yixuan , Montgomery Kelsey S. , Bendl Jaroslav , Jaiswal Manoj Kumar , Kozlenkov Alex ,   the CommonMind Consortium, Peters Mette A. , Dracheva Stella , Fullard John F. , Chess Andrew , Devlin Bernie , Sieberts Solveig K. , Roussos Panos 
Published: October 2020

AbstractWhile schizophrenia differs between males and females in age of onset, symptomatology and the course of the disease, the molecular mechanisms underlying these differences remain uncharacterized. In order to address questions about the sex-specific effects of schizophrenia, we performed a large-scale transcriptome analysis of RNA-seq data from 437 controls and 341 cases from two distinct cohorts from the CommonMind Consortium. Analysis across the cohorts identifies a reproducible gene expression signature of schizophrenia that is highly concordant with previous work. Differential expression across sex is reproducible across cohorts and identifies X- and Y-linked genes, as well as those involved in dosage compensation. Intriguingly, the sex expression signature is also enriched for genes involved in neurexin family protein binding and synaptic organization. Differential expression analysis testing a sex-by-diagnosis interaction effect did not identify any genome-wide signature after multiple testing corrections. Gene coexpression network analysis was performed to reduce dimensionality and elucidate interactions among genes. We found enrichment of co-expression modules for sex-by-diagnosis differential expression signatures, which were highly reproducible across the two cohorts and involve a number of diverse pathways, including neural nucleus development, neuron projection morphogenesis, and regulation of neural precursor cell proliferation. Overall, our results indicate that the effect size of sex differences in schizophrenia gene expression signatures is small and underscore the challenge of identifying robust sex-by-diagnosis signatures, which will require future analyses in larger cohorts.
In-depth analysis of proteomic and genomic fluctuations during the time course of human embryonic stem cells directed differentiation into beta cells
Authors: Budnik Bogdan , Straubhaar Juerg , Neveu John , Shvartsman Dmitry 
Published: October 2020

AbstractPluripotent stem cells (PSC) endocrine differentiation at a large scale allows sampling of transcriptome and proteome with phosphoproteome (proteoform) at specific time points. We describe the dynamic time course of changes in cells undergoing directed beta-cell differentiation and show target proteins or previously unknown phosphorylation of critical proteins in pancreas development, NKX6-1, and Chromogranin A (CHGA). We describe fluctuations in the correlation between gene expression, protein abundance, and phosphorylation, which follow differentiation protocol perturbations of cell fates at all stages to identify proteoform profiles. Our computational modeling recognizes outliers on a phenomic landscape of endocrine differentiation, and we outline several new biological pathways involved. We have validated our proteomic data by analyzing two independent single-cell RNA sequencing datasets for in-vitro pancreatic islet productions using the same cell starting material and differentiation protocol and corroborating our findings for several proteins suggest as targets for future research.Moreover, our single-cell analysis combined with proteoform data places new protein targets within the specific time point and at the specific pancreatic lineage of differentiating stem cells. We also suggest that non-correlating proteins abundances or new phosphorylation motifs of NKX6.1 and CHGA point to new signaling pathways that may play an essential role in beta-cell development. We present our findings for the research community’s use to improve endocrine differentiation protocols and developmental studies.
Dissecting phenotypic transitions in metastatic disease via photoconversion-based isolation
Authors: Sela Yogev , Li Jinyang , Kuri Paola , Merrell Allyson , Li Ning , Lengner Chris , Rompolas Pantelis , Stanger Ben Z. 
Published: October 2020

AbstractCancer patients presenting with surgically resectable disease often harbor occult metastases, a potential source of relapse that is targetable only through systemic therapy. Studies of this occult fraction have been limited by a lack of tools with which to isolate discrete cells based on spatial grounds. We developed PIC-IT, photoconversion-based isolation technique allowing efficient recovery of cell clusters of any size including solitary disseminated tumor cells (DTCs), which are largely inaccessible otherwise. In a murine pancreatic cancer model, transcriptional profiling of spontaneously arising DTCs revealed phenotypic heterogeneity, functionally reduced propensity to proliferate and enrichment for inflammatory-response phenotype associated with NF-κB /AP-1 signaling. Pharmacological inhibition of NF-κB depleted DTCs but had no effect on macrometastases, suggesting DTCs are particularly dependent on this pathway. PIC-IT enables systematic investigation of the earliest stages of metastatic colonization. Moreover, this new technique can be applied to other biological systems in which isolation and characterization of spatially distinct cell populations is not currently feasible.
Benchmarking non-targeted metabolomics using yeast derived libraries
Authors: Rampler Evelyn , Hermann Gerrit , Grabmann Gerlinde , El Abiead Yasin , Schoeny Harald , Baumgartinger Christoph , Köcher Thomas , Koellensperger Gunda 
Published: October 2020

AbstractNon-targeted analysis by high-resolution mass spectrometry (HRMS) is the essential discovery tool in metabolomics. Up to date, standardization and validation remain a challenge. Community wide accepted, cost-effective benchmark materials are lacking. In this work, we propose yeast (Pichia pastoris) extracts, derived from fully controlled fermentations for this purpose. We established an open-source metabolite library of > 200 metabolites, reproducibly recovered in ethanolic extracts by orthogonal LCHRMS methods, different fermentations (over three years) and different laboratories. More specifically, compound identification was based on accurate mass, matching retention times, and MS/MS spectra as compared to authentic standards and internal databases. The library includes metabolites from the classes of 1) organic acids and derivatives (2) nucleosides, nucleotides and analogues, (3) lipids and lipid-like molecules, (4) organic oxygen compounds, (5) organoheterocyclic compounds, (6) organic nitrogen compounds and (7) benzoids at expected concentrations ranges of sub-nM to µM. As yeast is a eukaryotic organism, key regulatory elements are highly conserved between yeast and all annotated metabolites were also reported in the Human metabolome data base (HMDB). A large fraction of metabolites was found to be stable for several years when stored at −80°C. Thus, the yeast benchmark material enabled not only to test for the chemical space and coverage upon method implementation and developments, but enabled in-house routines for instrumental performance tests. Finally, the benchmark material opens new avenues for batch to batch corrections in large scale non-targeted metabolomics studies.
Glycan-induced protein dynamics in human norovirus P dimers depend on virus strain and deamidation status
Authors: Dülfer Jasmin , Yan Hao , Brodmerkel Maxim N , Creutznacher Robert , Mallagaray Alvaro , Peters Thomas , Caleman Carl , Marklund Erik G , Uetrecht Charlotte 
Published: October 2020

AbstractNoroviruses are the major cause of gastroenteritis and re-emerge worldwide every year, with GII.4 currently being the most frequent human genotype. The norovirus capsid protein VP1 is essential for host immune response. The P domain mediates cell attachment via histo blood-group antigens (HBGAs) in a strain-dependent manner but how these glycan-interactions actually relate to cell entry remains unclear. Here, hydrogen/deuterium exchange mass spectrometry (HDX-MS) is used to investigate glycan-induced protein dynamics in P dimers of different strains, which exhibit high structural similarity but different prevalence in humans. While the almost identical strains GII.4 Saga and GII.4 MI001 share glycan-induced dynamics, the dynamics differ in the emerging GII.17 Kawasaki 308 and rare GII.10 Vietnam 026 strain. We also further examine structural effects of N373 deamidation upon glycan binding in partially deamidated GII.4 P dimers, which are likely present during infection. Such mixed species exhibit increased exposure to solvent in the P dimer upon glycan binding as opposed to pure wildtype. Furthermore, deamidated P dimers display increased flexibility and a monomeric population. Our results indicate that glycan binding induces strain-dependent structural dynamics, which are further altered by N373 deamidation, and hence hint at a role of deamidation in modulating cell attachment and entry in GII.4 strains.
Health care financing and income inequality in Nigeria
Authors: Oburota Chukwuedo Susan , Olaniyan Olanrewaju 
Published: October 2020

PurposeThe purpose of this paper is to decompose the inequities induced by the Nigerian health care financing sources and their effect on the income distribution. Inequities in health care financing sources are of immense policy concern particularly in developing countries such as Nigeria, where high-level income inequality exists, and the cost of medical care is generally financed out-of-pocket (OOP) due to limited access to health insurance.Design/methodology/approachThe Ducloset al.decomposition model provided the theoretical framework for the study. Data were obtained from two waves of the Nigeria General Household Survey (GHS) panel, 2012–13 and 2015–16. The analysis covered 3,999 households in 2012–13 and 4,051 households in 2015–16. Two measures of health care financing: OOP payment and health insurance contribution (HIC) were used. The ability to pay measure was household consumption expenditure.FindingsThe major inequity issue induced by the OOP payments was vertical inequity. HICs created the problems of vertical inequity, horizontal inequity and reranking among households. Overall both health care financing options were associated with the worsening of income inequality both at the national and sectorial levels in the country. The operations of the NHIS need to be improved to ensuring improved health care coverage for the poor.Originality/valueThis paper fulfills an identified need to determine the income redistributive effects (REs) of the social health insurance (SHI) contribution at the national, urban and rural locations overtime.
Transformative place management (TPM) in commercial settings and business performance
Authors: Losada-Otálora Mauricio , Siqueira Jose Ribamar 
Published: October 2020

Purpose
This study aims to introduce transformative place management – TPM – (defined as the deliberate efforts of place managers in commercial settings to provide a pool of restorative resources to improve the consumers’ emotional well-being) by merging the REPLACE framework and transformative service research. Additionally, this research analyzes the direct and indirect impacts of restorative resources as a form of TPM on consumers’ emotional well-being and place attachment, considering the moderating role of employee emotional labor.

Design/methodology/approach
A total of 240 customers were surveyed in an experience-based store in a developing country by using a questionnaire. Then, a moderated mediation model was applied to analyze the moderating role of employee emotional labor in the relationship between TPM and place attachment through consumers’ well-being.

Findings
TPM that provides restorative resources to consumers influences place attachment by improving consumer well-being. However, surface acting by employees reduces the ability of TPM to increase place attachment through the improvement of consumers’ emotional well-being. Deep acting, on the other hand, does not enhance the effect of TPM on place attachment through consumers’ emotional well-being.

Originality/value
This paper proposes new developments in the transformative service research (TSR) paradigm by introducing TPM. By showing how the place of consumption increases the well-being of customers, this paper helps TSR researchers to accomplish the purpose of transforming the lives of consumers through relevant research. Although marketing researchers and environmental psychologists have theoretically anticipated the positive effects on well-being from consumption settings, this paper explains how commercial places promote customer well-being through the provision of restorative resources. Also, this paper shows how the place of consumption transforms consumers’' lives and identifies some of the boundary conditions at which such a transformation occurs.