bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accounting for overlapping annotations in genomic prediction models of complex traits
Authors: Mollandin Fanny , Gilbert Hélène , Croiseau Pascal , Rau Andrea 
Published: September 2022

Abstract
Background
It is now widespread in livestock and plant breeding to use genotyping data to predict phenotypes with genomic prediction models. In parallel, genomic annotations related to a variety of traits are increasing in number and granularity, providing valuable insight into potentially important positions in the genome. The BayesRC model integrates this prior biological information by factorizing the genome according to disjoint annotation categories, in some cases enabling improved prediction of heritable traits. However, BayesRC is not adapted to cases where markers may have multiple annotations.

Results
We propose two novel Bayesian approaches to account for multi-annotated markers through a cumulative (BayesRC+) or preferential (BayesRC$$\pi$$
π
) model of the contribution of multiple annotation categories. We illustrate their performance on simulated data with various genetic architectures and types of annotations. We also explore their use on data from a backcross population of growing pigs in conjunction with annotations constructed using the PigQTLdb. In both simulated and real data, we observed a modest improvement in prediction quality with our models when used with informative annotations. In addition, our results show that BayesRC+ successfully prioritizes multi-annotated markers according to their posterior variance, while BayesRC$$\pi$$
π
provides a useful interpretation of informative annotations for multi-annotated markers. Finally, we explore several strategies for constructing annotations from a public database, highlighting the importance of careful consideration of this step.

Conclusion
When used with annotations that are relevant to the trait under study, BayesRC$$\pi$$
π
and BayesRC+ allow for improved prediction and prioritization of multi-annotated markers, and can provide useful biological insight into the genetic architecture of traits.
Clinical course, viral etiology, and the diagnostic workup for patients with suspected myocarditis: a single-center prospective study
Authors: Khidr Shimaa S. , El-Mokhtar Mohamed Ahmed , Asaad Shery Refaat , Hetta Helal F. , Abdel-Rahim Mona Hussein , Youssef Amr Ahmed Aly , Hassan Ayman K. M. 
Published: September 2022

AbstractBackgroundMyocarditis is a highly heterogeneous disorder with a challenging diagnostic work-up. We aimed to focus on the possible diagnostic workup for this condition in settings where endomyocardial biopsy as a gold standard is not always feasible, detect the etiologic cardiotropic viruses in our locality, and follow the clinical course in patients admitted with clinically suspected myocarditis.MethodsThis is a prospective observational study. We recruited patients with clinically suspected myocarditis presenting at a university hospital from October 1st, 2020 until March 31st, 2021. All Patients had a diagnostic coronary angiography and were included only if they had a non-obstructive coronary artery disease. All patients also had cardiac magnetic resonance imaging (CMR) with contrast. Sera were obtained from all suspected patients for detection of antibodies against viruses using enzyme-linked immunosorbent assay, and viral genomes using polymerase chain reaction (PCR), and reverse transcription–PCR. Endomyocardial biopsy was done for patients with a typical CMR picture of myocarditis.ResultsOut of 2163 patients presenting to the hospital within the 6 months, only 51 met the inclusion criteria. Males represented 73%, with a mean age of 39 ± 16 years. CMR showed an ischemic pattern in 4 patients and thus they were excluded. We classified patients into two categories based on CMR results: group A (CMR-positive myocarditis), 12 patients (25.5%), and group B (CMR-negative myocarditis), 35 (74.5%) patients. On serological analysis, 66% of patients (n = 31/47) showed antibodies against the common cardiotropic viruses. Parvovirus B19 IgM in 22 patients (47%) and coxsackievirus IgM in 16 (34%) were the most observed etiologies. Regarding the outcome, 42.5% of patients recovered left ventricular ejection fraction and three patients died at 6 months’ clinical follow-up.ConclusionPatients with Clinically suspected myocarditis represented 2.2% of total hospital admissions in 6 months. CMR is only a good positive test for the diagnosis of acute myocarditis. Parvovirus B19 and coxsackievirus were the most common pathogens in our locality.Trial registration: Clinical trial registration no., NCT04312490; first registration: 18/03/2020. First recruited case 01/10/2020. URL:https://register.clinicaltrials.gov/prs/app/action/SelectProtocol?sid=S0009O3D&selectaction=Edit&uid=U0002DVP&ts=2&cx=9zdfin.
Immunomodulatory effects of metronomic vinorelbine (mVRL), with or without metronomic capecitabine (mCAPE), in hormone receptor positive (HR+)/HER2-negative metastatic breast cancer (MBC) patients: final results of the exploratory phase 2 Victor-5 study
Authors: Pepe F. F. , Cazzaniga M. E. , Baroni S. , Riva F. , Cicchiello F. , Capici S. , Cogliati V. , Maggioni C. , Cordani N. , Cerrito M. G. , Malandrin S. 
Published: September 2022

AbstractTregs are able of suppressing tumor-specific effector cells, such as lymphocytes CD8+, CD4+ and Natural Killer cells. Different drugs, especially different schedules of administration, like metronomic chemotherapy (mCHT), seem to be able to increase anticancer immunity, by acting on downregulation of Tregs. Most of the data available regarding the immunomodulating effect of mCHT have been obtained with Cyclophosphamide (CTX). Aim of the present study was to explore the effects of mVRL and mCAPE administration, alone or in combination, on T cells. Observation of 13 metastatic breast cancer patients lasted controlling for 56 days, where Treg frequencies and function, spontaneous anti-tumor T-cell responses were monitored, as well as the clinical outcome. No depletion in Treg absolute numbers, or percentage of T lymphocytes, was observed. Only in 5 patients, a modest and transient depletion of Tregs was observed during the first 14 days of treatment. To better describe the effect on Tregs, we subsequently looked at the variations in Memory, Naïve and Activated Treg subpopulations: we observed a trend in reduction for memory Treg (Treg MEM) and an increase for Treg Naïve (Treg NAIVE) and Treg Activated (Treg ACT) components. We finally analyzed the average trend of Treg in the Treg depleted patients and non-depleted ones, without fiding any significant differences. The trend of the Treg MEM appeared different, showing a reduction during the first 14 days, followed by an increase at the levels before treatment at Day 56 in the group of depleted patients and a progressive substantial reduction in the group of non-depleted patients along the entire course of treatment. Opposed to the data known, treatment with mVRL w/o mCAPE did not show any effect on Tregs.
Demographic Predictors of Complete Well-Being
Authors: Lee Matthew T. , McNeely Eileen , Weziak-Bialowolska Dorota , Ryan Karen A. , Mooney Kay D. , Cowden Richard G. , VanderWeele Tyler J. 
Published: September 2022

AbstractThis paper examines demographic differences in flourishing, defined as “complete well-being” and consisting of six domains: emotional health, physical health, purpose, character strengths, social connectedness, and financial security. Results are based on a random, cross-sectional sample of 2363 survey respondents drawn from employees of a large, national, self-insured employer based in the United States. We found that well-being across domains tends to increase with age, although there are some variations. Results are similar across most domains for men and women, although women score higher on character strengths, while men had higher scores on financial security. Racial and ethnic differences were striking. Black employees score higher than the reference group (White employees) on the emotional, purpose, and character strengths domains, but considerably lower on financial security. Hispanics also score lower on financial security (though not as low as Blacks), but higher than Whites on purpose, character strengths, and social connectedness. Asians reported higher well-being than Whites across all domains except purpose.
Configurations for positive public behaviors in response to the COVID-19 pandemic: a fuzzy set qualitative comparative analysis
Authors: Gu Junwang , Wu Chunmei , Wu Xuanhui , He Rong , Tao Jing , Ye Wenhui , Wu Ping , Hao Ming , Qiu Wei 
Published: September 2022

Abstract
Background
The COVID-19 crisis poses considerable threats to public health, and exploring the key configuration conditions of the public behavior response is very important for emergency risk management.

Objective
This study attempts to reveal differences in the conditional configuration and mechanism of public behavior based on the proposed framework, further make up for the deficiencies of existing research in explaining such issues as “How to promote the public’s protective behavior or reduce the public’s excessive behavior?” and finally provide new evidence and ideas for the government to improve the emergency management system.

Methods
A total of 735 valid cases were obtained using an online survey and revealed the conditional configuration and mechanism of public behavior differences through a fuzzy set qualitative comparative analysis based on the proposed public behavioral framework.

Results
The results show that critical factors including risk communication, trust, risk perception, and negative emotions alone did not constitute a necessary condition for public protective or excessive behavior. The different configurations of influencing factors reveal the complexity of public behavioral risk management, and taking adequate measures to increase public trust and reduce negative public emotions constitute the core path of risk management to enhance positive public behavior.

Conclusions
The configurations of various influencing factors reveal the complexity of public behavioral risk management. For behavioral risk management, governments should focus on adapting to multiple conditions according to their situations and, under the “overall perspective,” formulate policies based on local conditions and further form a differentiated risk management path. Practically speaking, for the government, taking adequate measures to increase public trust and reduce negative public emotions is the core path of risk management to enhance positive public behavior.
A comparative study of pre-trained language models for named entity recognition in clinical trial eligibility criteria from multiple corpora
Authors: Li Jianfu , Wei Qiang , Ghiasvand Omid , Chen Miao , Lobanov Victor , Weng Chunhua , Xu Hua 
Published: September 2022

AbstractBackgroundClinical trial protocols are the foundation for advancing medical sciences, however, the extraction of accurate and meaningful information from the original clinical trials is very challenging due to the complex and unstructured texts of such documents. Named entity recognition (NER) is a fundamental and necessary step to process and standardize the unstructured text in clinical trials using Natural Language Processing (NLP) techniques.MethodsIn this study we fine-tuned pre-trained language models to support the NER task on clinical trial eligibility criteria. We systematically investigated four pre-trained contextual embedding models for the biomedical domain (i.e., BioBERT, BlueBERT, PubMedBERT, and SciBERT) and two models for the open domains (BERT and SpanBERT), for NER tasks using three existing clinical trial eligibility criteria corpora. In addition, we also investigated the feasibility of data augmentation approaches and evaluated their performance.ResultsOur evaluation results using tenfold cross-validation show that domain-specific transformer models achieved better performance than the general transformer models, with the best performance obtained by the PubMedBERT model (F1-scores of 0.715, 0.836, and 0.622 for the three corpora respectively). The data augmentation results show that it is feasible to leverage additional corpora to improve NER performance.ConclusionsFindings from this study not only demonstrate the importance of contextual embeddings trained from domain-specific corpora, but also shed lights on the benefits of leveraging multiple data sources for the challenging NER task in clinical trial eligibility criteria text.
Long-term cardiovascular prognosis of patients with type 1 diabetes after myocardial infarction
Authors: Kerola Anne M. , Semb Anne Grete , Juonala Markus , Palomäki Antti , Rautava Päivi , Kytö Ville 
Published: September 2022

Abstract
Background
To explore long-term cardiovascular prognosis after myocardial infarction (MI) among patients with type 1 diabetes.

Methods
Patients with type 1 diabetes surviving 90 days after MI (n = 1508; 60% male, mean age = 62.1 years) or without any type of diabetes (n = 62,785) in Finland during 2005–2018 were retrospectively studied using multiple national registries. The primary outcome of interest was a combined major adverse cardiovascular event (MACE; cardiovascular death, recurrent MI, ischemic stroke, or heart failure hospitalization) studied with a competing risk Fine-Gray analyses. Median follow-up was 3.9 years (maximum 12 years). Differences between groups were balanced by multivariable adjustments and propensity score matching (n = 1401 patient pairs).

Results
Cumulative incidence of MACE after MI was higher in patients with type 1 diabetes (67.6%) compared to propensity score-matched patients without diabetes (46.0%) (sub-distribution hazard ratio [sHR]: 1.94; 95% confidence interval [CI]: 1.74–2.17; p < 0.0001). Probabilities of cardiovascular death (sHR 1.81; p < 0.0001), recurrent MI (sHR 1.91; p < 0.0001), ischemic stroke (sHR 1.50; p = 0.0003), and heart failure hospitalization (sHR 1.98; p < 0.0001) were higher in patients with type 1 diabetes. Incidence of MACE was higher in diabetes patients than in controls in subgroups of men and women, patients aged < 60 and ≥ 60 years, revascularized and non-revascularized patients, and patients with and without atrial fibrillation, heart failure, or malignancy.

Conclusions
Patients with type 1 diabetes have notably poorer long-term cardiovascular prognosis after an MI compared to patients without diabetes. These results underline the importance of effective secondary prevention after MI in patients with type 1 diabetes.
Anti-obesity therapy for cardiovascular disease prevention: potential expected roles of glucagon-like peptide-1 receptor agonists
Authors: Sawami Kosuke , Tanaka Atsushi , Node Koichi 
Published: September 2022

AbstractObesity is characterized by visceral fat accumulation and various metabolic disturbances that cause metabolic syndrome and obesity-related cardiovascular diseases (ORCVDs). Hence, treatments targeting obesity should also prevent ORCVDs. Nonetheless, lifestyle modification therapy alone is still insufficient to reduce the risk of ORCVDs, although most cardiovascular guidelines still list it as the only treatment for obesity. Additionally, conventional anti-obesity drugs, such as orlistat, phentermine-topiramate, and naltrexone-bupropion, can reduce body weight but have not demonstrated a clear reduction in the risk of ORCVDs. To overcome this unmet clinical need, newer anti-obesity drugs must exhibit not only sufficient and long-lasting weight loss but also obvious cardiovascular benefits. Given recent clinical findings and evidences, in this context glucagon-like peptide-1 receptor agonist is currently available as a candidate that is clinically positioned as a first-line anti-obesity agent for the effective prevention of ORCVDs in people with obesity.
Epidemiology and clinical features of imported malaria: a 14-year retrospective single-centre descriptive study in Prague, Czech Republic
Authors: Trojánek Milan , Grebenyuk Vyacheslav , Richterová Lenka , Zicklerová Ivana , Nohýnková Eva , Manďáková Zdenka , Kantor Jakub , Roháčová Hana , Stejskal František 
Published: September 2022

Abstract
Background
Malaria represents one of the most important imported tropical infectious diseases in European travellers. The objective of the study was to identify changes in the epidemiological features of imported malaria and to analyse the clinical findings and outcomes of imported malaria.

Methods
This single-centre descriptive study retrospectively analysed the medical records of all imported malaria cases in travellers treated at the Department of Infectious Diseases of University Hospital Bulovka in Prague from 2006 to 2019.

Results
The study included 203 patients with a median age of 37 years (IQR 30–48) and a male to female ratio of 3.72:1. Plasmodium falciparum was the predominant species (149/203), and its proportion significantly increased from 35/60 cases (58.3%) in 2006–2011 to 69/80 (86.3%) in 2016–2019 (p < 0.001). In contrast, the incidence of Plasmodium vivax malaria decreased from 19/60 cases (31.7%) in 2006–2011 to 5/80 (6.3%) in 2016–2019 (p < 0.001). Malaria was imported from sub-Saharan Africa in 161/203 cases (79.3%). The proportion of travellers from Southeast and South Asia decreased from 16/60 (26.7%) and 6/60 (10.0%) in 2006–2011 to 2/80 (2.5%) and no cases (0.0%) in 2016–2019, respectively (p < 0.001 and p = 0.006). Tourism was the most common reason for travel (82/203), however, the proportion of non-tourists significantly increased over time from 29/60 (48.3%) in 2006–2011 to 55/80 (68.8%) in 2016–2019, p = 0.015. Severe malaria developed in 32/203 (15.8%) patients who were significantly older (p = 0.013) and whose treatment was delayed (p < 0.001). Two lethal outcomes were observed during the study period.

Conclusions
This study demonstrated a significant increase in P. falciparum malaria, which frequently resulted in severe disease, especially in older patients and those with delayed treatment initiation. The rising proportion of imported malaria in non-tourists, including business travellers and those visiting friends and relatives, is another characteristic finding analogous to the trends observed in Western European and North American centres. The described changes in the aetiology and epidemiology of imported malaria may serve to optimize pre-travel consultation practices and improve post-travel diagnostics and medical care.
Comparison of two rating scales with the orofacial esthetic scale and practical recommendations for its application
Authors: Pattanaik Swaha , John Mike T. , Chung Seungwon , Keller San 
Published: September 2022

Abstract
Purpose
We compared measurement properties of 5-point and 11-point response formats for the orofacial esthetic scale (OES) items to determine whether collapsing the format would degrade OES score precision.

Methods
Data were collected from a consecutive sample of adult dental patients from HealthPartners dental clinics in Minnesota (N = 2,078). We fitted an Item Response Theory (IRT) model to the 11-point response format and the six derived 5-point response formats. We compared all response formats using test (or scale) information, correlation between the IRT scores, Cronbach’s alpha estimates for each scaling format, correlations based on the observed scores for the seven OES items and the eighth global item, and the relationship of observed and IRT scores to an external criterion using orofacial appearance (OA) indicators from the Oral Health Impact Profile (OHIP).

Results
The correlations among scores based on the different response formats were uniformly high for observed (0.97–0.99) and IRT scores (0.96–0.99); as were correlations of both observed and IRT scores and the OHIP measure of OA (0.66–0.68). Cronbach’s alpha based on any of the 5-point formats (α = 0.95) was nearly the same as that based on the 11-point format (α = 0.96). The weighted total information area for five of six derived 5-point response formats was 98% of that for the 11-point response format.

Conclusions
Our results support the use of scores based on a 5-point response format for the OES items. The measurement properties of scores based on a 5-point response format are comparable to those of scores based on the 11-point response format.
Predictors of problems reported on the EQ-5D-3L dimensions among people with impaired vision in northern Portugal
Authors: Macedo Antonio Filipe , Hellström Amanda , Massof Robert , Tuvesson Hanna , Rask Mikael , Ramos Pedro Lima , Safipour Jalal , Marteinsdottir Ina , Nilsson Evalill , Fagerström Cecilia , Årestedt Kristofer 
Published: September 2022

Abstract
Background
The EQ-5D index often fails to detect the effect of ophthalmic diseases and sight loss. Investigating predictors of individual EQ-5D health dimensions might reveal the underlying reasons. The aim of this study was to investigate predictors of health dimension ratings obtained with the EQ-5D-3L from participants with impaired vision representing a spectrum of eye diseases.

Methods
Observational cross-sectional study with participants recruited at four public hospitals in Portugal. Outpatients with visual acuity of 0.30 logMAR(6/12) or worse in the better-seeing eye were invited to participate. Participants completed two instruments: the EQ-5D-3L (measures participants’ perceived health-related quality-of-life) and the Massof Activity Inventory (measures visual ability–ability to perform vision-related activities). This study used logistic regression models to identify factors associated with responses to the EQ-5D-3L.

Results
The study included 492 participants, mean age 63.4 years (range = 18–93), 50% females. The most common diagnosis was diabetic retinopathy (37%). The mean visual acuity in the better seeing eye was 0.65 logMAR (SD = 0.48) and the mean visual ability was 0.62 logits (SD = 2.04), the correlation between the two was r = − 0.511 (p < 0.001). Mobility and self-care were the health dimensions with the fewest problems (1% reported extreme problems), anxiety and depression the dimension with the most problems (24% reported extreme problems). ROC curve analysis showed that the EQ-5D index was a poor predictor of cases of vision impairment whilst visual ability given was a good predictor of cases of vision impairment. Visual ability was an independent predictor of the response for all dimensions, higher ability was always associated with a reduced odds of reporting problems. The odds of reporting problems were increased for females in 3 out of 5 dimensions. Comorbidities, visual acuity and age-category were predictors of the odds of reporting problems for one dimension each.

Conclusions
The odds of reporting problems for the five health dimensions of the EQ-5D-3L were strongly influenced by the ability to perform vision-related activities (visual ability). The EQ-5D index showed poor performance at detecting vision impairment. These findings are informative and relevant for the clinic and for research evaluating the impact of eye diseases and disease treatments in ophthalmology.