bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association Between Repeated Tracheal Intubation Attempts and Adverse Events in Children in the Emergency Department
Authors: Funakoshi Hiraku , Kunitani Yuri , Goto Tadahiro , Okamoto Hiroshi , Hagiwara Yusuke , Watase Hiroko , Hasegawa Kohei 
Published: February 2021

Study Objectives
Studies have shown that multiple intubation attempts are associated with a higher risk of intubation-related adverse events. However, little is known about the relationship in children in the emergency department (ED).

Methods
This is an analysis of the data from 2 prospective, observational, multicenter registries of emergency airway management. The data were collected from consecutive patients who underwent emergency airway management in 19 EDs across Japan from March 2010 to November 2017. We included children 18 years or younger who underwent tracheal intubation in the ED. The primary exposure was the number of intubation attempts (1 vs ≥2). The primary outcome was an adverse event during or immediately after the intubation.

Results
A total of 439 children were eligible for the analysis. Of 279 children with first-pass success, 24 children (9%) had an adverse event. By contrast, of 160 children with ≥2 intubation attempts, 50 children patients (31%) had an adverse event. In the unadjusted model, multiple intubation attempts were significantly associated with a higher rate of adverse events (unadjusted odds ratio, 4.83; 95% confidence interval, 2.57–9.06; P < 0.001). This association remained significant after adjusting for 7 potential confounders and patient clustering within the hospital (adjusted odds ratio, 4.49; 95% confidence interval, 2.36–8.53; P < 0.001). Similar associations were found across different age groups and among children without cardiac arrest (all, P < 0.05).

Conclusions
In this analysis of large prospective multicenter data, multiple intubation attempts were associated with a significantly higher rate of intubation-related adverse events in children in the ED.
Costs of integrating hypertension care into HIV care in rural East African clinics
Authors: Shade Starley B. , Osmand Thomas , Kwarisiima Dalsone , Brown Lillian B. , Luo Alex , Mwebaza Betty , Mwesigye Aine Ronald , Kwizera Enos , Imukeka Haawa , Mwanga Florence , Ayieko James , Owaraganise Asiphas , Bukusi Elizabeth A. , Cohen Craig R. , Charlebois Edwin D. , Black Douglas , Clark Tamara D. , Petersen Maya L. , Kamya Moses R. , Havlir Diane V. , Jain Vivek 
Published: February 2021

Objective:
Sub-Saharan Africa faces twin epidemics of HIV and noncommunicable diseases including hypertension. Integrating hypertension care into chronic HIV care is a global priority, but cost estimates are lacking. In the SEARCH Study, we performed population-level HIV/hypertension testing, and offered integrated streamlined chronic care. Here, we estimate costs for integrated hypertension/HIV care for HIV-positive individuals, and costs for hypertension care for HIV-negative individuals in the same clinics.

Design:
Microcosting analysis of healthcare expenditures within Ugandan HIV clinics.

Methods:
SEARCH (NCT: 01864603) conducted community health campaigns for diagnosis and linkage to care for both HIV and hypertension. HIV-positive patients received hypertension/HIV care jointly including blood pressure monitoring and medications; HIV-negative patients received hypertension care at the same clinics. Within 10 Ugandan study communities during 2015–2016, we estimated incremental annual per-patient hypertension care costs using micro-costing techniques, time-and-motion personnel studies, and administrative/clinical records review.

Results:
Overall, 70 HIV-positive and 2355 HIV-negative participants received hypertension care. For HIV-positive participants, average incremental cost of hypertension care was $6.29 per person per year, a 2.1% marginal increase over prior estimates for HIV care alone. For HIV-negative participants, hypertension care cost $11.39 per person per year, a 3.8% marginal increase over HIV care costs. Key costs for HIV-positive patients included hypertension medications ($6.19 per patient per year; 98% of total) and laboratory testing ($0.10 per patient per year; 2%). Key costs for HIV-negative patients included medications ($5.09 per patient per year; 45%) and clinic staff salaries ($3.66 per patient per year; 32%).

Conclusion:
For only 2–4% estimated additional costs, hypertension care was added to HIV care, and also expanded to all HIV-negative patients in prototypic Ugandan clinics, demonstrating substantial synergy. Our results should encourage accelerated scale-up of hypertension care into existing clinics.
Risk of adverse coronavirus disease 2019 outcomes for people living with HIV
Authors: Mellor Maya M. , Bast Anne C. , Jones Nicholas R. , Roberts Nia W. , Ordóñez-Mena José M. , Reith Alastair J.M. , Butler Christopher C. , Matthews Philippa C. , Dorward Jienchi 
Published: February 2021

Objective:
To assess whether people living with HIV (PLWH) are at increased risk of coronavirus disease 2019 (COVID-19) mortality or adverse outcomes, and whether antiretroviral therapy (ART) influences this risk.

Design:
Rapid review with meta-analysis and narrative synthesis.

Methods:
We searched databases including Embase, Medline, medRxiv and Google Scholar up to 26 August 2020 for studies describing COVID-19 outcomes in PLWH and conducted a meta-analysis of higher quality studies.

Results:
We identified 1908 studies and included 19 in the review. In a meta-analysis of five studies, PLWH had a higher risk of COVID-19 mortality [hazard ratio 1.95, 95% confidence interval (CI): 1.62–2.34] compared with people without HIV. Risk of death remained elevated for PLWH in a subgroup analysis of hospitalized cohorts (hazard ratio 1.60, 95% CI: 1.12–2.27) and studies of PLWH across all settings (hazard ratio 2.08, 95% CI: 1.69–2.56). Eight other studies assessed the association between HIV and COVID-19 outcomes, but provided inconclusive, lower quality evidence due to potential confounding and selection bias. There were insufficient data on the effect of CD4+ T-cell count and HIV viral load on COVID-19 outcomes. Eleven studies reported COVID-19 outcomes by ART-regimen. In the two largest studies, tenofovir disoproxil fumarate-based regimens were associated with a lower risk of adverse COVID-19 outcomes, although these analyses are susceptible to confounding by co-morbidities.

Conclusion:
Emerging evidence suggests a moderately increased risk of COVID-19 mortality among PLWH. Further investigation into the relationship between COVID-19 outcomes and CD4+ T-cell count, HIV viral load, ART and the use of tenofovir disoproxil fumarate is warranted.
HIV-1LAI Nef blocks the development of hematopoietic stem/progenitor cells into T lymphoid cells
Authors: Zou Wei , Xing Juanjuan , Wang Fen , Chen Xinping , Liu Qian , Wang Jinyong , Zou Shijie , Chen Limin , Fu Xin , Zhou Zhengping , Wan Zhikai 
Published: February 2021

Objective:
Despite successful antiviral therapy, the recovery of CD4+ T cells may not be complete in certain HIV-1-infected individuals. In our previous work with humanized mice infected with CXCR4-tropic HIV-1LAI (LAI), viral protein Nef was found the major factor determining rapid loss of both CD4+ T cells and CD4+CD8+ thymocytes but its effect on early T-cell development is unknown. The objective of this study is to investigate the influence of LAI Nef on the development of hematopoietic stem/progenitor cells (HSPCs) into T lymphoid cells.

Design:
HSPC-OP9-DL1 cell co-culture and humanized mouse model was used to investigate the objective of our study in vitro and in vivo. RNA-seq was exploited to study the change of gene expression signature after nef expression in HSPCs.

Results:

Nef expression in HSPCs was found to block their development into T lymphoid cells both in vitro and in the mice reconstituted with nef-expressing HSPCs derived from human cord blood. More surprisingly, in humanized mice nef expression preferentially suppressed the production of CD4+ T cells. This developmental defect was not the result of CD34+ cell loss. RNA-seq analysis revealed that Nef affected the expression of 176 genes in HSPCs, including those involved in tumor necrosis factor, Toll-like receptor, and nucleotide-binding oligomerization domain-like receptor signaling pathways that are important for hematopoietic cell development.

Conclusion:
Our results demonstrate that Nef compromises the development of HSPCs into T lymphoid cells, especially CD4+ T cells. This observation suggests that therapeutics targeting Nef may correct HIV-1-associated hematopoietic abnormalities, especially defects in T-cell development.
Machine learning-based single cell and integrative analysis reveals that baseline mDC predisposition predicts protective Hepatitis B vaccine response
Authors: Aevermann Brian , Shannon Casey P. , Novotny Mark , Ben-Othman Rym , Cai Bing , Zhang Yun , Ye Jamie C. , Kobor Michael S. , Gladish Nicole , Lee Amy , Blimke Travis M , Hancock Robert E. , Llibre Alba , Duffy Darragh , Koff Wayne C. , Sadarangani Manish , Tebbutt Scott J. , Kollmann Tobias R. , Scheuermann Richard H. 
Published: February 2021

AbstractVaccination to prevent infectious disease is one of the most successful public health interventions ever developed. And yet, variability in individual vaccine effectiveness suggests a better mechanistic understanding of vaccine-induced immune responses could improve vaccine design and efficacy. We have previously shown that protective antibody levels could be elicited in a subset of recipients with only a single dose of the hepatitis B virus (HBV) vaccine. Why some, but not all, recipients responded in this way was not clear. Using single cell RNA sequencing of sorted innate immune cell subsets, we identified two distinct myeloid dendritic cell subsets (NDRG1-expressing mDC2 and CDKN1C-expressing mDC4), the ratio of which at baseline (pre-vaccination) predicted immune response to a single dose of HBV vaccine. Our results suggest that the participants in our vaccine study were in one of two different dendritic cell dispositional states at baseline – an NDRG2-mDC2 state in which the vaccine elicited an antibody response after a single immunization or a CDKN1C-mDC4 state in which the vaccine required two or three doses for induction of antibody responses. Genes expressed in these mDC subsets were used as an approach for feature selection prior to the construction of a predictive model using supervised canonical correlation machine learning. The resulting model showed an improved ability to predict serum antibody titers in response to vaccination. Taken together, these results suggest that the propensity of circulating dendritic cells toward either activation or suppression, their “dispositional endotype”, could dictate response to vaccination. The fact that these mDCs could be modulated via TLR stimulation could guide progress towards design of effective single dose vaccination strategies.
An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City
Authors: Zhang Sheng , Ponce Joan , Zhang Zhen , Lin Guang , Karniadakis George 
Published: February 2021

AbstractEpidemiological models can provide the dynamic evolution of a pandemic but they are based on many assumptions and parameters that have to be adjusted over the time when the pandemic lasts. However, often the available data are not sufficient to identify the model parameters and hence infer the unobserved dynamics. Here, we develop a general framework for building a trustworthy data-driven epidemiological model, consisting of a workflow that integrates data acquisition and event timeline, model development, identifiability analysis, sensitivity analysis, model calibration, model robustness analysis, and forecasting with uncertainties in different scenarios. In particular, we apply this framework to propose a modified susceptible–exposed–infectious–recovered (SEIR) model, including new compartments and model vaccination in order to forecast the transmission dynamics of COVID-19 in New York City (NYC). We find that we can uniquely estimate the model parameters and accurately predict the daily new infection cases, hospitalizations, and deaths, in agreement with the available data from NYC’s government’s website. In addition, we employ the calibrated data-driven model to study the effects of vaccination and timing of reopening indoor dining in NYC.
Contact patterns and HPV-genotype interactions yield heterogeneous HPV-vaccine impacts depending on sexual behaviours: an individual-based model
Authors: Bonneault Mélanie , Poletto Chiara , Flauder Maxime , Guillemot Didier , Delarocque-Astagneau Elisabeth , Thiébaut Anne CM , Opatowski Lulla 
Published: February 2021

AbstractHuman papillomaviruses are common sexually transmitted infections, caused by a large diversity of genotypes. In the context of vaccination against a subgroup of genotypes, better understanding the role of genotype interactions and human sexual behavior on genotype ecology is essential. Herein, we present an individual-based model that integrates realistic heterosexual partnership behaviors and simulates interactions between vaccine and non-vaccine genotypes. Genotype interactions were considered, assuming a previous vaccine-genotype infection shortened (competition) or extended (synergy) the duration of a secondary non-vaccine-genotype infection. Sexual behavior determined papillomavirus acquisition and transmission: only 19.5% of active individuals with 0–1 partner during the year, but >80% of those with ≥2 partners, were infected before vaccine introduction. Genotype interactions, despite being silent during the pre-vaccination era, markedly impacted genotype ecology after vaccination started, with a significant increase/decrease of non-vaccine prevalence for competitive/synergistic interactions. These changes were more pronounced in individuals with ≤3 partners (up to 30% of prevalence modification assuming 65% vaccine coverage) but barely visible for individuals with >3 partners (at most 0.30%). Results suggest that considering genotype interactions, in conjunction with heterogeneous sexual behaviors, is essential to anticipate the impact of existing and future anti-papillomavirus vaccines targeting a subgroup of genotypes.
The acoustic quality and health in urban environments (SALVE) project: Study design, rationale and methodology
Authors: Haselhoff Timo , Lawrence Bryce , Hornberg Jonas , Ahmed Salman , Sutcliffe Robynne , Gruehn Dietwald , Moebus Susanne 
Published: February 2021

AbstractSound pressure levels expressed in variations of decibel (dB) formulations are a common approach to describe the urban acoustic environment (AE). In recent years, different approaches gained traction to describe the urban AE, like the soundscape ecology approach, which focuses on the natural environment. To determine the feasibility of applying this approach to cities, a comprehensive dataset of high-quality sound recordings with high spatial and temporal resolution is essential.The acoustic quality and health in urban environments (SALVE) project aims to establish a spatially and temporally high-resolution dataset of the urban AE using land use categories. Since 2019, we assess the AE at selected places in the densely populated city of Bochum, Germany. For a high temporal resolution, we used automatic devices at 52 locations that recorded every 26 minutes for three minutes. For a high spatial resolution, we used manual devices to perform a five-minute recording four times a year at 730 selected locations. Altogether, we ended up with 1,500,493 minutes of sound recordings.Aim here is to outline our sampling design, methods used, and applied quality procedures in order to achieve a well-defined and high quality dataset presented for further scientific analysis. To the best of our knowledge, this represents one of the most extensive datasets currently available, which will provide a comprehensive database for future in-depth analyses of the associations between the urban AE, urban fabric and human health.HighlightsA conceptual sampling framework for measuring the urban acoustic environment is givenOne of the most extensive datasets of the urban acoustic environment is introducedExperiences and results of the field work of the SALVE-Project are presented
Scientific modelling can be accessible, interoperable and user friendly: An example for pasture and livestock modelling
Authors: Torres Alba Marquez , Balbi Stefano , Villa Ferdinando 
Published: February 2021

AbstractThis article describes the adaptation of a non-spatial model of pastureland dynamics, including vegetation life cycle, livestock management and nitrogen cycle, for use in a spatially explicit and modular modelling platform (k.LAB) dedicated to make data and models more interoperable. The aim is to deliver an existing, locally successful monolithic model, into a more modular, transparent and accessible approach to potential end users, regional managers, farmers and other stakeholders. This allows better usability and adaptability of the model beyond its originally intended geographical scope (the Cantabrian Region in the North of Spain). The original model, named Puerto, is developed in the R language and includes 1,491 lines of code divided into 13 script files and linked to 19 input tables. The spatiotemporal rewrite is structured around a set of 10 namespaces called PaL (Pasture and Livestock), which includes 198 interoperable but independent models. The end user chooses the spatial and temporal context of the analysis through an intuitive web-based user interface called k.Explorer. Each model can be called individually or in conjunction with the others, by querying any PaL-related concepts in a search bar. A scientific workflow is built as a response, which is run to produce result datasets and a report with information on the data sources and modelling processes used, delivering results with full transparency. We argue that this work demonstrates key steps needed to create more Findable, Accessible, Interoperable and Reusable (FAIR) models. This is particularly essential in environments as complex as agricultural systems, where multidisciplinary knowledge needs to be integrated across diverse spatial and temporal scales in order to understand complex and changing problems.
Improved transformation efficiency of group AStreptococcusby inactivation of a type I restriction modification system
Authors: Finn Meredith B. , Ramsey Kathryn M. , Dove Simon L. , Wessels Michael R. 
Published: February 2021

AbstractStreptococcus pyogenesor group AStreptococcus(GAS) is a leading cause of bacterial pharyngitis, skin and soft tissue infections, life-threatening invasive infections, and the post-infectious autoimmune syndromes of acute rheumatic fever and post-streptococcal glomerulonephritis. Genetic manipulation of this important pathogen is complicated by resistance of the organism to genetic transformation. Very low transformation efficiency is attributed to recognition and degradation of introduced foreign DNA by a type I restriction-modification system encoded by thehsdRSMlocus. DNA sequence analysis of this locus in ten GAS strains that had been previously transformed with an unrelated plasmid revealed that six of the ten harbored a spontaneous mutation inhsdR, S, orM. The mutations were all different, and at least five of the six were predicted to result in loss of function of the respectivehsdgene product. The unexpected occurrence of such mutations in previously transformed isolates suggested that the process of transformation selects for spontaneous inactivating mutations in the Hsd system. We investigated the possibility of exploiting the increased transformability ofhsdmutants by constructing a deletion mutation inhsdMin GAS strain 854, a clinical isolate representative of the globally dominant M1T1 clonal group. Mutant strain 854ΔhsdMexhibited a 5-fold increase in transformation efficiency compared to the wild type parent strain and no obvious change in growth or off-target gene expression. We conclude that genetic transformation of GAS selects for spontaneous mutants thehsdRSMrestriction modification system. We propose that use of a definedhsdMmutant as a parent strain for genetic manipulation of GAS will enhance transformation efficiency and reduce the likelihood of selecting spontaneoushsdmutants with uncharacterized genotypes.
Machine learning to predict the source of campylobacteriosis using whole genome data
Authors: Arning Nicolas , Sheppard Samuel K. , Clifton David A. , Wilson Daniel J. 
Published: February 2021

AbstractCampylobacteriosis is among the world’s most common foodborne illnesses, caused predominantly by the bacteriumCampylobacter jejuni. Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using machine learning. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity ofC. jejunistrains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential.Author summaryC. jejuniare the most common cause of food-borne bacterial gastroenteritis but the relative contribution of different sources are incompletely understood. We traced the origin of humanC. jejuniinfections using machine learning algorithms that compare the DNA sequences of bacteria sampled from infected people, contaminated chickens, cattle, sheep, wild birds and the environment. This approach achieved improvement in accuracy of source attribution by 33% over existing methods that use only a subset of genes within the genome and provided evidence for the relative contribution of different infection sources. Sometimes even very similar bacteria showed differences, demonstrating the value of basing analyses on the entire genome when developing this algorithm that can be used for understanding the global epidemiology and other important bacterial infections.