bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advancing Equity in Blood Pressure Control: A Response to the Surgeon General’s Call-to-Action
Authors: Colvin Calvin L , Kalejaiye Ayoola , Ogedegbe Gbenga , Commodore-Mensah Yvonne 
Published: December 2021

AbstractHypertension is an established risk factor for cardiovascular disease. Although controlling blood pressure reduces cardiovascular and stroke mortality and target organ damage, poor blood pressure control remains a clinical and public health challenge. Furthermore, racial and ethnic disparities in the outcomes of hypertension are well documented. In October of 2020, the U.S. Department of Health and Human Services published The Surgeon General’s Call to Action to Control Hypertension. The Call to Action emphasized, among other priorities, the need to eliminate disparities in the treatment and control of high blood pressure and to address social determinants as root causes of inequities in blood pressure control and treatment. In support of the goals set in the Call to Action, this review summarizes contemporary research on racial, ethnic, and socioeconomic disparities in hypertension and blood pressure control; describes interventions and policies that have improved blood pressure control in minoritized populations by addressing the social determinants of health; and proposes next steps for achieving equity in hypertension and blood pressure control.
Alcohol Misuse among English Youth, Are Harms Attributable to Alcohol or to Underlying Disinhibitory Characteristics?
Authors: McArdle Paul , Coulton Simon , Kaner Eileen , Gilvarry Eilish , Drummond Colin 
Published: December 2021

Abstract

Introduction
Alcohol use by young people is associated with a range of psychological and physical harms. However, similar harms are also reported with disinhibitory conditions such as conduct problems that are said to precede and predispose to alcohol misuse. We explored whether alcohol use or indicators of underlying disinhibition predict psychological and physical harms in a cohort of young people.

Methods
We used data from a randomised controlled intervention trial that identified young people who consumed alcohol (n = 756), mean age = 15.6 years, attending emergency departments (EDs) in England. Disinhibition was measured by the self-report Strengths and Difficulties Questionnaire hyperactivity and conduct problem items, and alcohol-related harms by questions from the ESPAD, a major European school survey. We conducted a mediation analysis with a primary outcome of frequency of engaging in alcohol-related harms 12 months after screening in ED, exploring for the mediating influence of alcohol consumed at six months. We included age, gender, allocated group and baseline consumption as covariates and adjusted for the multi-level nature of the study, where young people were nested within EDs.

Results
Conduct problems and to a lesser extent hyperactivity predicted harms at twelve months. This effect was not mediated by alcohol consumed at 6 months.

Conclusions
Among young drinkers underlying behavioural attributes predict harm independently of alcohol use. This suggests that the harms associated with alcohol use are attributable more to underlying disinhibitory characteristics than the quantity of alcohol consumed.
Factors Associated with Adolescents’ Support for Product Information and Health Messaging on Alcohol Packaging: A Cross-Sectional Study in the United Kingdom
Authors: Peddireddy Snigdha , Boniface Sadie , Critchlow Nathan , Newberry Le Vay Jessica , Severi Katherine , Vohra Jyotsna 
Published: December 2021

Abstract

Aims
Adolescents in the UK are among the heaviest drinkers in Europe. The World Health Organization recommends alcohol product labelling to inform consumers about product information and health risks associated with alcohol use. This study investigates support for product information and health messaging on alcohol packaging among UK adolescents.

Methods
The 2019 UK Youth Alcohol Policy Survey was an online cross-sectional survey among 3388 adolescents aged 11–19. Participants indicated their support for seven forms of messaging on packaging (e.g. number of alcohol units, links to health conditions). Logistic regression models investigated associations between support for each of the seven forms and alcohol use, perceived risks of alcohol use, and previous exposure to messaging.

Results
Between 60 and 79% of adolescents were supportive of different aspects of product labelling. Compared to lower-risk drinkers, higher-risk drinkers (AUDIT-C 5+) had higher odds of supporting including the number of alcohol units (OR: 1.82, 95% CI: 1.31–2.54), calories (OR: 1.52, 95% CI: 1.04–1.68), and strength of the product (OR: 1.73, 95% CI: 1.19–2.52) but lower odds of supporting including information on alcohol-related health conditions (OR: 0.68, 95% CI: 0.53–0.87). Adolescents who perceived risks of alcohol use more strongly were more likely to support all forms of product information and messaging.

Conclusions
The majority of adolescents supported improved alcohol labelling. Higher-risk drinkers were supportive of improved product information but less supportive of health-related messaging. Adolescents who believe alcohol carries health risks were more likely to support messaging.
Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species
Authors: Tomaszewska Paulina , Vorontsova Maria S , Renvoize Stephen A , Ficinski Sarah Z , Tohme Joseph , Schwarzacher Trude , Castiblanco Valheria , de Vega José J , Mitchell Rowan A C , Heslop-Harrison J S (Pat) 
Published: December 2021

Abstract

Background and Aims
Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species.

Methods
Some 362 forage grass accessions from international germplasm collections were studied, and ploidy was determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the ‘brizantha’ and ‘humidicola’ agamic complexes and U. maxima.

Key Results
Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids.

Conclusions
We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for Urochloa brizantha, U. decumbens and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and assist in measuring and conserving biodiversity in grasslands.
protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data
Authors: Quast Jan-Philipp , Schuster Dina , Picotti Paola 
Published: December 2021

Abstract

Summary
We present a flexible, user-friendly R package called protti for comprehensive quality control, analysis and interpretation of quantitative bottom-up proteomics data. protti supports the analysis of protein-centric data such as those associated with protein expression analyses, as well as peptide-centric data such as those resulting from limited proteolysis-coupled mass spectrometry analysis. Due to its flexible design, it supports analysis of label-free, data-dependent, data-independent and targeted proteomics datasets. protti can be run on the output of any search engine and software package commonly used for bottom-up proteomics experiments such as Spectronaut, Skyline, MaxQuant or Proteome Discoverer, adequately exported to table format.

Availability and implementation
protti is implemented as an open-source R package. Release versions are available via CRAN (https://CRAN.R-project.org/package=protti) and work on all major operating systems. The development version is maintained on GitHub (https://github.com/jpquast/protti). Full documentation including examples is provided in the form of vignettes on our package website (jpquast.github.io/protti/).
A random forest classifier for protein–protein docking models
Authors: Barradas-Bautista Didier , Cao Zhen , Vangone Anna , Oliva Romina , Cavallo Luigi 
Published: December 2021

Abstract Herein, we present the results of a machine learning approach we developed to single out correct 3D docking models of protein–protein complexes obtained by popular docking software. To this aim, we generated 3×104 docking models for each of the 230 complexes in the protein–protein benchmark, version 5, using three different docking programs (HADDOCK, FTDock and ZDOCK), for a cumulative set of ≈7×106 docking models. Three different machine learning approaches (Random Forest, Supported Vector Machine and Perceptron) were used to train classifiers with 158 different scoring functions (features). The Random Forest algorithm outperformed the other two algorithms and was selected for further optimization. Using a features selection algorithm, and optimizing the random forest hyperparameters, allowed us to train and validate a random forest classifier, named COnservation Driven Expert System (CoDES). Testing of CoDES on independent datasets, as well as results of its comparative performance with machine learning methods recently developed in the field for the scoring of docking decoys, confirm its state-of-the-art ability to discriminate correct from incorrect decoys both in terms of global parameters and in terms of decoys ranked at the top positions.Supplementary informationSupplementary data are available at Bioinformatics Advances online.Software and data availability statementThe docking models are available at https://doi.org/10.5281/zenodo.4012018. The programs underlying this article will be shared on request to the corresponding authors.
CellMeSH: probabilistic cell-type identification using indexed literature
Authors: Mao Shunfu , Zhang Yue , Seelig Georg , Kannan Sreeram 
Published: December 2021

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) is widely used for analyzing gene expression in multi-cellular systems and provides unprecedented access to cellular heterogeneity. scRNA-seq experiments aim to identify and quantify all cell types present in a sample. Measured single-cell transcriptomes are grouped by similarity and the resulting clusters are mapped to cell types based on cluster-specific gene expression patterns. While the process of generating clusters has become largely automated, annotation remains a laborious ad hoc effort that requires expert biological knowledge.

Results
Here, we introduce CellMeSH—a new automated approach to identifying cell types for clusters based on prior literature. CellMeSH combines a database of gene–cell-type associations with a probabilistic method for database querying. The database is constructed by automatically linking gene and cell-type information from millions of publications using existing indexed literature resources. Compared to manually constructed databases, CellMeSH is more comprehensive and is easily updated with new data. The probabilistic query method enables reliable information retrieval even though the gene–cell-type associations extracted from the literature are noisy. CellMeSH is also able to optionally utilize prior knowledge about tissues or cells for further annotation improvement. CellMeSH achieves top-one and top-three accuracies on a number of mouse and human datasets that are consistently better than existing approaches.

Availability and implementation
Web server at https://uncurl.cs.washington.edu/db_query and API at https://github.com/shunfumao/cellmesh.

Supplementary information
Supplementary data are available at Bioinformatics online.
Variation in size and shape sexual dimorphism in the Sceloporus scalaris species group (Squamata: Phrynosomatidae) from the Transvolcanic Belt of Mexico
Authors: Cruz-Elizalde Raciel , Ramírez-Bautista Aurelio , Lozano Abraham , Velasco Julián A , Octavio-Aguilar Pablo , Berriozabal-Islas Christian 
Published: December 2021

Abstract
We attempted to identify the factors influencing size and shape dimorphism between sexes, as well as among populations and species in the Sceloporus scalaris group (Sceloporus aeneus, S. scalaris, S. bicanthalis and S. subniger). Our analysis focused on five morphological characteristics: snout–vent length, head length, head width, forearm length and tibia length. The effect of environmental variables (precipitation and temperature) on these variables was also tested. We found differences in morphological traits between sexes, and among populations of the same species. The oviparous species (S. aeneus and S. scalaris) were larger in overall body size than the viviparous species (S. bicanthalis and S. subniger). Differences in overall body size among populations were recorded only in S. aeneus and S. scalaris. Male-biased sexual size dimorphism occurred in oviparous but not viviparous lizards (except for one population of S. bicanthalis). An absence of sexual size dimorphism was also recorded in S. subniger and some populations of the remaining species. Two different shape patterns were found; the first was female-biased with larger relative body length in almost all populations, which could be explained by fecundity, and the second was male-biased with relatively larger head and limbs in a few populations, which may be explained by sexual selection. The patterns of sexual size and shape dimorphism show that environment, rather than phylogeny, may be determining the extent of sexual dimorphism. These types of studies show the importance of an integrated evaluation of interpopulation and interspecies variation to determine the factors that generate sexual dimorphism.
Urban housing affordability, economic disadvantage and racial disparities in gun violence: A neighbourhood analysis in four US cities
Authors: Stansfield Richard , Semenza Daniel 
Published: December 2021

Abstract
This study seeks to examine how urban affordability, and related issues of eviction and joblessness, are associated with gun violence in the United States. After discussing the theoretical importance of studying housing affordability, we provide a preliminary examination of how urban affordability moderates the relationship between other markers of economic disadvantage and gun violence. This study further considers whether these different indicators of disadvantage are associated with gun violence differently by majority Black and majority White neighbourhoods. This study rests on neighbourhood-level data from 4 large US cities. Through a series of fixed-effects models, our results reveal that changes in affordability are significantly associated with rising gun violence in general, particularly in majority Black neighbourhoods. Furthermore, joblessness and eviction are less influential in shaping gun violence in more affordable neighbourhoods, but more consequential in communities facing higher rent burdens. The study reiterates several recommendations about reducing unaffordability in urban communities, as well as recommending several avenues for future research on urban violence.
Tobacco carcinogen 4-[methyl(nitroso)amino]-1-(3-pyridinyl)-1-butanone (NNK) drives metabolic rewiring and epigenetic reprograming in A/J mice lung cancer model and prevention with diallyl sulphide (DAS)
Authors: Hudlikar Rasika R , Sargsyan Davit , Cheng David , Kuo Hsiao-Chen Dina , Wu Renyi , Su Xiaoyang , Kong Ah-Ng 
Published: December 2021

Abstract
Early detection of biomarkers in lung cancer is one of the best preventive strategies. Although many attempts have been made to understand the early events of lung carcinogenesis including cigarette smoking (CS) induced lung carcinogenesis, the integrative metabolomics and next-generation sequencing approaches are lacking. In this study, we treated the female A/J mice with CS carcinogen 4-[methyl(nitroso)amino]-1-(3-pyridinyl)-1-butanone (NNK) and naturally occurring organosulphur compound, diallyl sulphide (DAS) for 2 and 4 weeks after NNK injection and examined the metabolomic and DNA CpG methylomic and RNA transcriptomic profiles in the lung tissues. NNK drives metabolic changes including mitochondrial tricarboxylic acid (TCA) metabolites and pathways including Nicotine and its derivatives like nicotinamide and nicotinic acid. RNA-seq analysis and Reactome pathway analysis demonstrated metabolism pathways including Phase I and II drug metabolizing enzymes, mitochondrial oxidation and signaling kinase activation pathways modulated in a sequential manner. DNA CpG methyl-seq analyses showed differential global methylation patterns of lung tissues from week 2 versus week 4 in A/J mice including Adenylate Cyclase 6 (ADCY6), Ras-related C3 botulinum toxin substrate 3 (Rac3). Oral DAS treatment partially reversed some of the mitochondrial metabolic pathways, global methylation and transcriptomic changes during this early lung carcinogenesis stage. In summary, our result provides insights into CS carcinogen NNK’s effects on driving alterations of metabolomics, epigenomics and transcriptomics and the chemopreventive effect of DAS in early stages of sequential lung carcinogenesis in A/J mouse model.
Clinical assessment of olfactory function
Authors: Hummel Thomas , Podlesek Dino 
Published: December 2021

Abstract
Approximately 5% of the general population is affected by functional anosmia with approximately additional 15% exhibiting decreased olfactory function. Many of these individuals ask for help. Because the subjective rating of olfactory function is biased, assessment of olfactory function is important. Olfactory measurements are needed for patient counseling and the tracking of changes in the sense of smell over time. The present review provides an overview of frequently used psychophysical tests for olfactory function, discusses differences between threshold and suprathreshold aspects of olfactory function, and gives examples on how to apply psychophysical tests.
Interpretation of Relative Efficacy and Effectiveness for Influenza Vaccines
Authors: Lewis Nathaniel M , Chung Jessie R , Uyeki Timothy M , Grohskopf Lisa , Ferdinands Jill M , Patel Manish M 
Published: December 2021

Abstract

Background
Relative vaccine effectiveness (rVE) are metrics commonly reported to compare absolute VE (aVE) of 2 vaccine products.

Methods
Estimates of rVE for enhanced influenza vaccines (eIV) vs standard inactivated influenza vaccine (IIV) have been assessed across different seasons, influenza-specific endpoints, and nonspecific endpoints (eg, all-cause cardiovascular hospitalizations). To illustrate the challenges of comparability across studies, we conducted a scenario analysis to evaluate the effects of varying absolute VE (aVE) of IIV (ie, as compared with placebo) on the interpretation of rVE of eIV vs IIV.

Results
We show that estimates of rVE might not be comparable across studies because additional benefits commensurate with a given estimate of rVE are dependent on the aVE for the comparator vaccine, which can depend on factors such as host response to vaccine, virus type, and clinical endpoint evaluated.

Conclusions
These findings have implications for interpretation of rVE across studies and for sample size considerations in future trials.
Social positioning and the pursuit of power
Authors: Ornelas Martins Nuno 
Published: December 2021

Abstract
Tony Lawson has recently advanced a theory of social positioning, in terms of which various aspects of social reality are conceptualised. A central idea of the theory of social positioning is that social relations are ultimately power relationships, which structure how social phenomena are organised. This article further explores this idea, while also conceptualising various forms of power, such as coercion, manipulation, domination and subjectification, drawing on the theory of social positioning. In so doing, the theory of social positioning is also used to explain how institutionalisation influences the dynamics of empowerment and disempowerment, and its implications for human development and dehumanisation.
Bridging patients in cardiogenic shock with a paracorporeal pulsatile biventricular assist device to heart transplantation—a single-centre experience
Authors: Michel Sebastian , Buchholz Stefan , Buech Joscha , Veit Tobias , Fabry Thomas , Abicht Jan , Thierfelder Nikolaus , Mueller Christoph , Rosenthal Laura Lily , Pabst von Ohain Jelena , Haas Nikolaus , Hörer Jürgen , Hagl Christian 
Published: December 2021

Abstract

OBJECTIVES
We evaluated the outcome of patients in cardiogenic shock receiving a paracorporeal pulsatile biventricular assist device as a bridge to transplantation.

METHODS
We performed a retrospective single-centre analysis of all patients who received a Berlin Heart Excor® at our institution between 2004 and 2019.

RESULTS
A total of 97 patients (90 adults, 7 paediatric) were analysed. Eighty-four patients were in Interagency Registry for Mechanically Assisted Circulatory Support level 1 (80 adults, 4 paediatric). Diagnoses were dilated cardiomyopathy (n = 41), ischaemic cardiomyopathy (n = 17) or myocardial infarction (n = 4), myocarditis (n = 15), restrictive cardiomyopathy (n = 2), graft failure after heart transplant (n = 7), postcardiotomy heart failure (n = 5), postpartum cardiomyopathy (n = 3), congenital heart disease (n = 1), valvular cardiomyopathy (n = 1) and toxic cardiomyopathy (n = 1). All patients were in biventricular heart failure and had secondary organ dysfunction. The mean duration of support was 63 days (0–487 days). There was a significant decrease in creatinine values after assist device implantation (from 1.83 ± 0.79 to 1.12 ± 0.67 mg/dl, P = 0.001) as well as a decrease in bilirubin values (from 3.94 ± 4.58 to 2.65 ± 3.61 mg/dl, P = 0.084). Cerebral stroke occurred in 16 patients, bleeding in 15 and infection in 13 patients. Forty-eight patients died on support, while 49 patients could be successfully bridged to transplantation. Thirty-day survival and 1-year survival were 70.1% and 41.2%, respectively.

CONCLUSIONS
A pulsatile biventricular assist device is a reasonable therapeutic option in cardiogenic shock, when immediate high cardiac output is necessary to rescue the already impaired kidney and liver function of the patient.