bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association between white matter changes and development of malignant middle cerebral artery infarction
Authors: Wu Meng-Ni , Fang Pen-Tzu , Hung Chih-Hsien , Hsu Chung-Yao , Chou Ping-Song , Yang Yuan-Han 
Published: April 2021

Abstract
Disrupted blood–brain barrier (BBB) in patients with ischemic stroke plays a critical role in malignant middle cerebral artery infarction (MMI) development.
Cerebral white matter changes (WMC), particularly in the deep subcortical area or in severe one, may be also underlain by disrupted BBB. It is unclear whether the presence of WMC with potential premorbid disruption of BBB makes patients susceptible to MMI. Therefore, this study aimed to clarify any putative relationship between the MMI and WMC in terms of their severity and locations.
In this case–control study, patients with infarction in the middle cerebral artery territory were retrospectively reviewed. Brain magnetic resonance images were analyzed according to Fazekas scale, and identified WMC were divided into periventricular WMC (PV-WMC) and deep subcortical WMC (deep-WMC). Patients were scored as having WMC, PV-WMC, deep-WMC, severe PV-WMC, and severe deep-WMC according to the severity and locations. Patients were defined as having MMI if either a progressive conscious disturbance or signs of uncal herniation was recorded in combination with a midline shift >5 mm identified on the follow-up computed tomography.
Among 297 patients admitted between July 2009 and February 2015, 92 patients were eligible for final analysis. Compared to patients without MMI, patients with MMI had a higher score of National Institutes of Health Stroke Scale, a larger infarct volume, and an increasingly greater proportion of severe PV-WMC, deep-WMC, and severe deep-WMC, respectively. After adjustment for sex, age, infarct volume, and history of hypertension, severe deep-WMC (odds ratio [OR] = 6.362, 95% confidence interval [CI] = 1.444–28.023, P = .0144) and severe PV-WMC (odds ratio = 5.608, 95% confidence interval = 1.107–28.399, P = .0372) were significantly associated with MMI development.
MMI and WMC are significantly associated such that MMI development is more likely when PV-WMC or deep-WMC is more severe. We hypothesize that Fazekas scale-defined severe deep-WMC and PV-WMC may be considered as clinically approachable predictors of MMI development. These findings support that the WMC with potential premorbid disrupted BBB may make patients susceptible to MMI, and further prospective study should be conducted to clarify this hypothesis.
Analysis of risk factors for cesarean scar diverticulum
Authors: Liu Songjun , Chen Linlin , Zhu Guang , Shao Yupei , Yu Shuqian , Li Wu , Lv Wen 
Published: April 2021

Abstract
The purpose of this study was to explore the relevant factors that affect the risk of cesarean scar diverticulum (CSD).
A retrospective, case-control study was designed among women with a history of cesarean section (CS) who were admitted in Zhejiang Tongde Hospital from January 2017 to December 2019. Women with missing information were excluded. The basic clinical characteristics and the risk factors for CSD were assessed using univariate analysis and multivariate logistic regression analysis.
A total of 216 women were analyzed, including 87 patients with CSD and 129 cases without CSD as control. Significant differences in number of CS, trial of labor (elective or urgent CS), CS interval, uterine position, intraoperative hemorrhage, and dysmenorrhea between CSD group and control group (P < .05). Multivariate logistic regression analysis showed that number of CS, trial of labor, interval of CS, and uterine position were independent risk factors of CSD.
In women with a history of CS, multiple cesarean deliveries, elective CS, cesarean interval of less than 5 years, and retroflexed position of the uterus may be associated with an elevated risk of CSD.
Baseline Characteristics, Evaluation, and Management of Women With Complaints of Recurrent Urinary Tract Infections
Authors: Dieter Alexis A. , Mueller Margaret G. , Andy Uduak U. , Kirby Anna C. , Dwarica Denicia S. , Amundsen Cindy L. , Gregory W. Thomas , Desai Shivani , Clayton Laura , Squires Natalie A. , Allen Antoinette , Casper Kaitlyn P. , Murphy Mary J. , Shepherd Jonathan P. 
Published: April 2021

Objective
The aims of this study were to determine the proportion of women presenting for recurrent urinary tract infections (UTIs) who met the diagnostic criteria (culture-proven UTI ≥3 in 1 year or ≥2 in 6 months) and to assess advanced testing utilization, preventive therapy use, and risk factors.

Methods
This is a retrospective chart review of women seen as new urogynecology consults for recurrent UTI (rUTI) between April 1, 2017, and April 1, 2018, followed through April 1, 2019. Exclusion criteria included catheter use, cancer treatment within 2 years, and prior organ transplant, urinary diversion, conduit, or bladder augmentation.

Results
Of 600 women, 71% had follow-up with a median of 179 days. Urinary tract infection symptoms included frequency (50%), dysuria (46%), urgency (43%), and malodorous urine (7%). One third met the rUTI diagnostic criteria. Two hundred thirty-four (39%) underwent advanced testing, and 9% (21/234) of women who underwent advanced testing had a change in clinical care. Preventive therapy use increased after consultation (P < 0.001), with vaginal estrogen (47%) being most common. Compared with women not meeting the rUTI criteria, women meeting the rUTI criteria were more likely to be older (adjusted odds ratio [aOR], 1.03/year; 95% confidence interval [CI], 1.02–1.04), have a prior history of gynecologic cancer (aOR, 4.07; 95% CI, 1.02–16.25), or report UTI symptoms of dysuria (aOR, 2.27; 95% CI, 1.57–3.27), or malodorous urine (aOR, 2.96; 95% CI, 1.47–5.94) and, while equally likely to be receiving preventive treatment prior to consultation, were more likely after consultation (OR, 3.06; 95% CI, 2.05–4.55).

Discussion
Thirty-seven percent of women seen for rUTI met the diagnostic criteria. Advanced imaging rarely changed care. Education about diagnostic criteria and preventive therapy is warranted.
COVID-19 vaccine acceptance in older Syrian refugees: preliminary findings from an ongoing study
Authors: Salibi Noura , Abdulrahim Sawsan , Haddad Maria El , Bassil Stephanie , Khoury Zeina El , Ghattas Hala , McCall Stephen J. 
Published: April 2021

AbstractThis study assesses COVID-19 vaccine intentions among a sample of Syrian refugees (≥50 years) beneficiaries of a humanitarian organization in Lebanon, and explores factors associated with vaccine refusal. The findings are part of an ongoing rotating 4-wave panel study. The sample was limited to participants from the first panel who completed a phone interview between January-February, 2021. Out 1,037 beneficiaries, almost a third (29%) reported no intention to vaccinate. Reasons for refusal were: newness of the vaccine (35%); preference to maintain precaution measures (21%); belief that COVID-19 vaccine is not essential (21%); and other reasons (23%). COVID-19 vaccine refusal was significantly associated with perceptions regarding vaccine safety (OR: 5.97; 95%CI: 4.03-8.84) and effectiveness (OR: 6.80; 95%CI:4.44-10.42) but did not differ by age, presence of chronic conditions, self-reported adherence to COVID-19 measures, and perceptions of susceptibility to and severity of COVID-19. Addressing vaccine hesitancy among Syrian refugees in Lebanon necessitates disseminating accurate, accessible, and culturally appropriate information about vaccine safety and effectiveness.
The initial impact of a national BNT162b2 mRNA COVID-19 vaccine rollout
Authors: Zaqout Ahmed , Daghfal Joanne , Alaqad Israa , Hussein Saleh A.N. , Aldushain Abdullah , Almaslamani Muna A. , Abukhattab Mohammed , Omrani Ali S. 
Published: April 2021

AbstractObjectiveWe herein report the initial impact of a national BNT162b2 rollout on SARS-CoV-2 infections in Qatar.MethodsWe included all individuals who by 16 March 2021 had completed ≥14 days of follow up after the receipt of BNT162b2. We calculated incidence rates (IR) and their 95% confidence intervals (CI), during days 1–7, 8–14, 15–21, 22–28, and >28 days post-vaccination. Poisson regression was used to calculate incidence rate ratios (IRR) relative to the first 7-day post-vaccination period.ResultsWe included 199,219 individuals with 6,521,124 person-days of follow up. SARS-CoV-2 infection was confirmed in 1,877 (0.9%), of which 489 (26.1%) were asymptomatic and 123 (6.6%) required oxygen support. The median time from first vaccination to SARS-CoV-2 confirmation was 11.9 days (IQR 7.7–18.2). Compared with the first 7-day post-vaccination period, SARS-CoV-2 infections were lower by 65.8–84.7% during days 15–21, days 22–28, and >28 days (P <0.001 for each). For severe COVID-19, the incidence rates were 75.7– 93.3% lower (P <0.001 for each) during the corresponding time periods.ConclusionOur results are consistent with an early protective effect of BNT162b2 against all degrees of SARS-CoV-2 severity.
Physician Perceptions of Surveillance: Wearables, Apps, and Bots for COVID-19
Authors: Linares Alexandra R. , Bramstedt Katrina A. , Chilukuri Mohan M. , Doraiswamy P. Murali 
Published: April 2021

AbstractObjectiveTo characterize the global physician community’s opinions on the use of digital tools for COVID-19 public health surveillance and self-surveillance.MethodsCross-sectional, random, stratified survey done on Sermo, a physician networking platform, between September 9-15, 2020. We aimed to sample 1,000 physicians divided among the USA, EU, and rest of the world. The survey questioned physicians on the risk-benefit ratio of digital tools, as well as matters of data privacy and trust.ResultsThe survey was completed by 1004 physicians with a mean (SD) age of 49.14 (12) years. Enthusiasm was highest for self-monitoring smart watches (66%) and contact tracing apps (66%) and slightly lower (48-56%) for other tools. Trust was highest for health providers (68%) and lowest for technology companies (30%). Most respondents (69.8%) felt that loosening privacy standards to fight the pandemic would lead to misuse of privacy in the future.ConclusionThe survey provides foundational insights about how physicians think of surveillance. Collaborations between public health and technology researchers to strengthen evidence of effectiveness and build public trust may be useful.
SARS-CoV-2 subgenomic RNA kinetics in longitudinal clinical samples
Authors: Verma Renu , Kim Eugene , Martinez-Colón Giovanny Joel , Jagannathan Prasanna , Rustagi Arjun , Parsonnet Julie , Bonilla Hector , Khosla Chaitan , Holubar Marisa , Subramanian Aruna , Singh Upinder , Maldonado Yvonne , Blish Catherine A. , Andrews Jason R. 
Published: April 2021

AbstractBackgroundGiven the persistence of viral RNA in clinically recovered COVID-19 patients, subgenomic RNAs (sgRNA) have been reported as potential molecular viability markers for SARS-CoV-2. However, few data are available on their longitudinal kinetics, compared with genomic RNA (gRNA), in clinical samples.MethodsWe analyzed 536 samples from 205 patients with COVID-19 from placebo-controlled, outpatient trials of Peginterferon Lambda-1a (Lambda; n=177) and favipiravir (n=359). Nasal swabs were collected at three time points in the Lambda (Day 1, 4 and 6) and favipiravir (Day 1, 5, and 10) trials. N-gene gRNA and sgRNA were quantified by RT-qPCR. To investigate the decay kinetics in vitro, we measured gRNA and sgRNA in A549ACE2+ cells infected with SARS-CoV-2, following treatment with remdesivir or DMSO control.ResultsAt six days in the Lambda trial and ten days in the favipiravir trial, sgRNA remained detectable in 51.6% (32/62) and 49.5% (51/106) of the samples, respectively. Cycle threshold (Ct) values for gRNA and sgRNA were highly linearly correlated (Pearson’s r=0.87) and the rate of increase did not differ significantly in Lambda (1.36 cycles/day vs 1.36 cycles/day; p = 0.97) or favipiravir (1.03 cycles/day vs 0.94 cycles/day; p=0.26) trials. From samples collected 15-21 days after symptom onset, sgRNA was detectable in 48.1% (40/83) of participants. In SARS-CoV-2 infected A549ACE2+ cells treated with remdesivir, the rate of Ct increase did not differ between gRNA and sgRNA.ConclusionsIn clinical samples and in vitro, sgRNA was highly correlated with gRNA and did not demonstrate different decay patterns to support its application as a viability marker.SummaryWe observed prolonged detection of subgenomic RNA in nasal swabs and equivalent decay rates to genomic RNA in both longitudinal nasal swabs and in remdesivir-treated A549ACE2+ cells infected with SARS-CoV-2. Taken together, these findings suggest that subgenomic RNA from SARS-CoV-2 is comparably stable to genomic RNA and that its detection is therefore not a more reliable indicator of replicating virus.
Optimal use of COVID19 Ag-RDT screening at border crossings to prevent community transmission: a modeling analysis
Authors: Chevalier Joshua M , Sy Karla Therese L , Girdwood Sarah J , Khan Shaukat , Albert Heidi , Toporowski Amy , Hannay Emma , Carmona Sergio , Nichols Brooke E 
Published: April 2021

ABSTRACTBackgroundCountries around the world have implemented restrictions on mobility, especially cross-border travel to reduce or prevent SARS-CoV-2 community transmission. Rapid antigen testing (Ag-RDT), with on-site administration and rapid turnaround time may provide a valuable screening measure to ease cross-border travel while minimizing risk of local transmission. To maximize impact, we developed an optimal Ag-RDT screening algorithm for cross-border entry.MethodsUsing a previously developed mathematical model, we determined the daily number of imported COVID-19 cases that would generate no more than a relative 1% increase in cases over one month for different effective reproductive numbers (Rt) of the recipient country. We then developed an algorithm- for differing levels of Rt, arrivals per day, mode of travel, and SARS-CoV-2 prevalence amongst travelers-to determine the minimum proportion of people that would need Ag-RDT testing at border crossings to ensure no greater than the relative 1% community spread increase.FindingsWhen daily international arrivals and/or COVID-19 prevalence amongst arrivals increases, the proportion of arrivals required to test using Ag-RDT increases. At very high numbers of international arrivals/COVID-19 prevalence, Ag-RDT testing is not sufficient to prevent increased community spread, especially for lower levels of Rt. In these cases, Ag-RDT screening would need to be supplemented with other measures to prevent an increase in community transmission.InterpretationAn efficient Ag-RDT algorithm for SARS-CoV-2 testing depends strongly on Rt, volume of travel, proportion of land and air arrivals, test sensitivity, and COVID-19 prevalence among travelers.FundingUSAID, Government of the Netherlands
Phylogenomics Sheds Light on the population structure ofMycobacterium bovisfrom a Multi-Host Tuberculosis System
Authors: Reis Ana C. , Salvador Liliana C.M. , Robbe-Austerman Suelee , Tenreiro Rogério , Botelho Ana , Albuquerque Teresa , Cunha Mónica V. 
Published: April 2021

AbstractMolecular analyses ofMycobacterium bovisbased on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought insights into the epidemiology of animal tuberculosis (TB) in Portugal, showing high genotypic diversity of circulating strains that mostly cluster within the European 2 clonal complex. The genetic relatedness ofM. bovisisolates from cattle and wildlife have also suggested sustained transmission within this multi-host system. However, while previous surveillance highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric and provided valuable information on the prevalence and spatial occurrence of TB, links at the wildlife-livestock interfaces were established mainly via genotype associations. Therefore, evidence at a local fine scale of transmission events linking wildlife hosts and cattle remains lacking. Here, we explore the advantages of whole genome sequencing (WGS) applied to cattle, red deer and wild boar isolates to reconstruct the evolutionary dynamics ofM. bovisand to identify putative pathogen transmission events. Whole genome sequences of 44 representativeM. bovisisolates, obtained between 2003 and 2015 from three TB hotspots, were compared through single nucleotide polymorphism (SNP) variant calling analyses. Consistent with previous results combining classical genotyping with Bayesian population admixture modelling, SNP-based phylogenies support the branching of thisM. bovispopulation into five genetic clades, three with geographic specificities, as well as the establishment of a SNPs catalogue specific to each clade, which may be explored in the future as phylogenetic markers. The core genome alignment of SNPs was integrated within a spatiotemporal metadata framework to reconstruct transmission networks, which together with inferred secondary cases, further structured thisM. bovispopulation by host species and geographic location.WGS ofM. bovisisolates from Portugal is reported for the first time, refining the spatiotemporal context of transmission events and providing further support to the key role of red deer and wild boar on the persistence of animal TB in this Iberian multi-host system.
Endophytic microbiome variation at the level of a single plant seed
Authors: Bintarti AF , Sulesky-Grieb A , Stopnisek N , Shade A 
Published: April 2021

AbstractLike other plant compartments, the seed harbors a microbiome. The members of the seed microbiome are the first to colonize a germinating seedling, and they initiate the trajectory of microbiome assembly for the next plant generation. Therefore, the members of the seed microbiome are important for the dynamics of plant microbiome assembly and the vertical transmission of potentially beneficial symbionts. However, it remains challenging to assess the microbiome at the individual seed level (and, therefore, for the future individual plant) due to low endophytic microbial biomass, seed exudates that can select for particular members, and high plant and plastid contamination of resulting reads. Here, we report a protocol for extracting metagenomic DNA from an individual seed (common bean, Phaseolus vulgaris L.) with minimal disruption of host tissue, which we expect to be generalizable to other medium-and large-seed plant species. We applied this protocol to quantify the 16S rRNA V4 and ITS2 amplicon composition and variability for individual seeds harvested from replicate common bean plants grown under standard, controlled conditions to maintain health. Using metagenomic DNA extractions from individual seeds, we compared seed-to-seed, pod-to-pod, and plant-to-plant microbiomes, and found highest microbiome variability at the plant level. This suggests that several seeds from the same plant could be pooled for microbiome assessment, given experimental designs that apply treatments at the maternal plant level. This study adds protocols and insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems.
A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons
Authors: Mikl Martin , Eletto Davide , Lee Minkyoung , Lafzi Atefeh , Mhamedi Farah , Sain Simona Baghai , Handler Kristina , Moor Andreas E. 
Published: April 2021

AbstractAsymmetric subcellular localization of mRNA is a common cellular phenomenon that is thought to contribute to spatial gene regulation. In highly polar neurons, subcellular transcript localization and translation are thought to enhance cellular efficiency and timely responses to external cues. Although mRNA localization has been observed in many tissues and numerous examples of the functional importance of this process exist, we still lack a systematic understanding of how the transcript sorting machinery works in a sequence-specific manner.Here, we addressed these gaps by combining subcellular transcriptomics and rationally designed sequence libraries. We developed a massively parallel reporter assay (MPRA) for mRNA localization and tested ~50,000 sequences for their ability to drive RNA localization to neurites of neuronal cell lines. By scanning the 3’UTR of >300 genes we identified many previously unknown localization regions and mapped the localization potential of endogenous sequences. Our data suggest two ways the localization potential can be encoded in the 3’UTR: focused localization motifs and broadly encoded localization potential based on small contributions.We identified sequence motifs enriched in dendritically localized transcripts and tested the potential of these motifs to affect the localization behavior of an mRNA. This assay revealed sequence elements with the ability to bias localization towards neurite as well as soma. Depletion of RNA binding proteins predicted or experimentally shown to bind these motifs abolished the effect on localization, suggesting that these motifs act by recruiting specific RNA-binding proteins.Based on our dataset we developed machine learning models that accurately predict the localization behavior of novel sequences. Testing this predictor on native mRNA sequencing data showed good agreement between predicted and observed localization potential, suggesting that the rules uncovered by our MPRA also apply to the localization of native transcripts.Applying similar systematic high-throughput approaches to other cell types will open the door for a comparative perspective on RNA localization across tissues and reveal the commonalities and differences of this crucial regulatory mechanism.