bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating Cross-National Abortion Behavior and Its Relationship with Attitudes
Authors: Adamczyk Amy 
Published: January 2025

Abstract
This chapter investigates abortion behavior and its relationship with attitudes, laws, and other factors. It begins by examining the country-level forces associated with cross-national abortion rates. Neither legislation nor public abortion disapproval is significantly associated with rates. Rather, economic and educational development and gender equality are critical for decreasing abortion rates by limiting unintended pregnancies. From there, the chapter examines the key characteristics associated with women’s abortion decisions in a set of economically, politically, and religiously diverse countries. Using longitudinal data from young American women, the pathways through which personal religious beliefs shape abortion decisions are investigated. Interviews from the United States and China are used to examine how stigma and shame connect to abortion behavior in these countries. Finally, the circumstances and characteristics of the women the Chinese and American public think typically obtains abortions are compared to those of the women who get abortions in these countries.
The Regulatory Framework
Authors: Malcolm Rosalind , Pointing John 
Published: January 2025

Abstract
The enforcement of statutory nuisance legislation is primarily the responsibility of local authorities under powers and duties set down in section 80 of the Environmental Protection Act 1990 (EPA 1990). English local authorities enforcing the Act comprise district councils outside Greater London and London borough councils in Greater London. Unitary authorities in non-metropolitan counties are responsible for enforcement.
SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline
Authors: Potente Sara , Boscarino Diego , Paladin Dino , Marchini Sergio , Beltrame Luca , Romualdi Chiara 
Published: January 2025

Abstract
Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy number alterations (CNAs). However, there remains a gap for a standardized workflow specifically designed for sWGS analysis. To address this need, in this work we present SAMURAI, a bioinformatics pipeline specifically designed for analyzing CNAs from sWGS data in a standardized and reproducible manner. SAMURAI is built using established community standards, ensuring portability, scalability, and reproducibility. The pipeline features a modular design with independent blocks for data preprocessing, copy number analysis, and customized reporting. Users can select workflows tailored for either solid or liquid biopsy analysis (e.g. circulating tumor DNA), with specific tools integrated for each sample type. The final report generated by SAMURAI provides detailed results to facilitate data interpretation and potential downstream analyses. To demonstrate its robustness, SAMURAI was validated using simulated and real-world data sets. The pipeline achieved high concordance with ground truth data and maintained consistent performance across various scenarios. By promoting standardization and offering a versatile workflow, SAMURAI empowers researchers in diverse environments to reliably analyze CNAs from sWGS data. This, in turn, holds promise for advancements in precision medicine.
Longitudinal urine metabolic profiling and gestational age prediction in human pregnancy
Authors: Shen Xiaotao , Chen Songjie , Liang Liang , Avina Monika , Zackriah Hanyah , Jelliffe-Pawlowski Laura , Rand Larry , Snyder Michael P 
Published: January 2025

Abstract
Pregnancy is a vital period affecting both maternal and fetal health, with impacts on maternal metabolism, fetal growth, and long-term development. While the maternal metabolome undergoes significant changes during pregnancy, longitudinal shifts in maternal urine have been largely unexplored. In this study, we applied liquid chromatography–mass spectrometry-based untargeted metabolomics to analyze 346 maternal urine samples collected throughout pregnancy from 36 women with diverse backgrounds and clinical profiles. Key metabolite changes included glucocorticoids, lipids, and amino acid derivatives, indicating systematic pathway alterations. We also developed a machine learning model to accurately predict gestational age using urine metabolites, offering a non-invasive pregnancy dating method. Additionally, we demonstrated the ability of the urine metabolome to predict time-to-delivery, providing a complementary tool for prenatal care and delivery planning. This study highlights the clinical potential of urine untargeted metabolomics in obstetric care.
Sequali: efficient and comprehensive quality control of short- and long-read sequencing data
Authors: Vorderman Ruben H P 
Published: January 2025

Abstract

Motivation
Quality control of sequencing data is the first step in many sequencing workflows. Short- and long-read sequencing technologies have many commonalities with regard to quality control. Several quality control programs exist; however, none possess a feature set that is adequate for both technologies. Quality control programs aimed at Oxford Nanopore Technologies sequencing lack vital features, such as adapter searching, overrepresented sequence analysis, and duplication analysis.

Results
Sequali was developed to provide sequencing quality control for both short- and long-read sequencing technologies. It features adapter search, overrepresented sequence analysis, and duplication analysis and supports FASTQ and uBAM inputs. It is significantly faster than comparable sequencing quality control programs for both short- and long-read sequencing technologies.

Availability and Implementation
Sequali is an open-source Python application using C extensions and is freely available under the AGPL-3.0 license at https://github.com/rhpvorderman/sequali. The source code for each release is archived at zenodo: https://zenodo.org/doi/10.5281/zenodo.10822485.
Introducing Sofosbuvir/Velpatasvir + Ribavirin as a Generic Retreatment Regimen for Hepatitis C: Evaluation of a Government Program in Rwanda
Authors: Serumondo Janvier , Barebwanuwe Peter , Sheferaw Ephrem Daniel , Iyonizera Jeannette , Berabose Charles , Umuraza Sabine , Ntuyenabo Calliope , Kwizera Kelly Reine , Dushimiyimana Donatha , Umutesi Justine , Kabakambira Jean Damascene , Buya Bobo , Azania Amy , Boeke Caroline E , Ngwije Alida , Ramers Christian B , Rwibasira Gallican 
Published: January 2025

Abstract
Sofosbuvir/velpatasvir/voxilaprevir is recommended for hepatitis C virus (HCV) retreatment in those who fail initial treatment but is unavailable in resource-limited settings. We describe a government sofosbuvir/velpatasvir + ribavirin (SOF/VEL + RBV) × 24 weeks retreatment program in Rwanda (November 2021–October 2022). Of 231 participants, 174 were cured (75.3% intention-to-treat analysis). SOF/VEL + RBV may be considered for HCV retreatment in resource-limited settings.
International validation of a pre-transplant risk assessment tool for graft survival in pediatric kidney transplant recipients
Authors: Oomen Loes , de Wall Liesbeth L , Tönshoff Burkhard , Krupka Kai , Harambat Jerome , Hogan Julien , Couchoud Cécile , Savoye Emilie , de Jong Huib , Cornelissen Elisabeth A M , Bouts Antonia H M , Keijzer-Veen Mandy G , Feitz Wout F J , Bootsma-Robroeks Charlotte M H H T 
Published: January 2025

Abstract

Background
A pre-transplant prediction model using commonly available factors is valuable for optimizing donor selection, communication, and counselling for pediatric kidney transplant (PKT) recipients. This study aims to externally validate a Dutch PKT prediction model and assess its international applicability.

Methods
Data from the Dutch-, CERTAIN-, and CRISTAL registries, covering PKT from 2005 to 2021, were used. The Dutch prediction model was externally validated in a German and French cohort and then adapted to these specific countries. An international prediction model was also developed using all available data. Models were based on 80% derivation cohorts and internally validated using areas under the receiver operating characteristics curve (ROC-AUC) and calibration plots.

Results
Of 3266 transplantations, 2475 (273 Dutch, 356 German and 1622 French, 224 other) were used for analysis. Cohorts differed significantly in baseline characteristics and outcomes. Internal validation of the Dutch model showed ROC-AUCs of 0.77 and 0.75 at 10 and 15 years. External validation in German and French cohorts yielded 10-year ROC-AUCs of 0.63 and 0.60, respectively.
Internal validation of the international prediction model showed AUCs of 0.61 and 0.60 at 10 and 15 years with poor calibration, indicating inferior performance. The adapted national models showed better internal validation performance, with 10-year ROC-AUCs of 0.77, 0.76, and 0.73 in Dutch, French, and German cohorts, respectively.

Conclusions
The Dutch PKT prediction tool requires country-specific adaptations for use in other countries, given the diversity of clinical practice across Europe. A country-specific model is preferable to an international model in the current landscape.
Left ventricular force with resting volumetric transthoracic echocardiography identifies different phenotypes in heart failure with preserved ejection fraction
Authors: Wang Y , Quirino C , Zagatina A , Padang R , Kane G C , Villarraga H R , Cortigiani L , Vazquez J P , Boshchenko A , Ryabova T , Manganelli F , Amor M , Yin L , Pellikka P A , Picano E 
Published: January 2025

Abstract

Background
Heart failure and preserved ejection fraction (HFpEF) is a heterogeneous entity including patients with different phenotypes of reduced, normal, and supernormal left ventricular (LV) function.

Objectives
To assess the value of resting LV elastance with transthoracic echocardiography (TTE) to identify HFpEF phenotypes.

Methods
In a prospective, observational, multicenter study, 2380 HFpEF patients were recruited from July 2016 to May 2024 by 35 certified laboratories of 15 countries. HFpEF was diagnosed according to the European Society of Cardiology (ESC) guidelines. Systolic blood pressure (SBP) was measured. We assessed wall motion score index (WMSI), LV end-diastolic volume (EDV), end-systolic volume (ESV), EF, force (SBP/ESV), stroke volume (SV), arterial elastance (AE, SBP/SV), ventricular-arterial coupling (VAC, as SV/ESV), and left atrial volume index (LAVI). Global longitudinal strain (GLS) was available in 1164 (48.9%) patients. In 271 (11.4%) patients, N-terminal pro-brain natriuretic peptide (NT-proBNP) was assessed. Patients were divided into three groups based on rest force: low rest force group (&lt; 25% percentile, Group 1), median rest force group (≥ 25% percentile & ≤ 75% percentile, Group 2), and high rest force group (&gt; 75% percentile, Group 3).

Results
330 (13.9%) patients presented with ischemic RWMA. The 3 groups showed a gradient with descending values (Group 3&gt;2&gt;1) for SBP, EF, GLS, AE, and VAC, with the opposite gradient (Group 1&gt; 2&gt; 3) for EDV, EDVi, ESV, ESVi, SV, SVi, and LAVI values (all P&lt;0.01). Patients in Group 3 have higher NTproBNP level and higher percentage of B-line compared to groups 1 and 2 (P&lt;0.05). The 3 groups were similar for values of coronary flow velocity, systolic pulmonary artery pressure, and E/e’ (see table). Univariable linear regression analysis showed that NTproBNP was correlated with force (r = 0.271, p &lt; 0.001), VAC (r = 0.194, p = 0.001), LAVI (r = 0.327, p &lt; 0.001), LVEDV (r = -0.245, p &lt; 0.001), LVEDVi (r = -0.261, p &lt; 0.001), LVESVi (r = -0.190, p = 0.002) and LVESV (r = -0.187, p = 0.002) (see figure). However, multivariable linear regression analysis showed that NTproBNP was independently associated with LAVI (β= 0.211, p &lt; 0.001) and force (β= 1.804, p = 0.002).

Conclusions
HFpEF patients present with different LV contractile phenotypes, easily identified with resting LV force and volumetric TTE. LV force is linearly correlated with cardiac natriuretic peptide levels. The dominant hemodynamic feature of hypocontractile phenotype is a preload recruitment with dilation of LV EDV and normal SV, while the hypercontractile phenotype is characterized by a small LV with reduced SV.

heat map
Cardiac damage associated with aortic stenosis: comparison between patients treated with surgery and transcatheter aortic valve replacement
Authors: Roman R , Islas F , Gil C , O Neill P , Luque M , Carnero M , Jimenez P , Perez-Camargo D , Nombela L , Rivadeneira M , Gutierrez E , De Agustin J A , Olmos C 
Published: January 2025

Abstract

Background and Purpose
Current evidence shows that surgical aortic valve replacement (SAVR) and transcatheter aortic valve replacement (TAVR) are comparable and equally beneficial in patients with severe aortic stenosis (AS) across different risk profiles.
Our aim was to analyse potential differences in cardiac damage related to AS between patients undergoing SAVR and those treated with TAVR in a contemporary cohort of patients with AS.

Methods
Retrospective analysis of a prospective cohort of patients with AS who underwent SAVR or TAVR in a tertiary care center from 2017 to 2022. Clinical and echocardiographic parameters prior to surgery were compared.
Additionally, patients were classified into different categories of available cardiac damage staging systems (1,2).

Results
874 patients were included, of which 524 underwent TAVR and 350 were treated with SAVR. A comparison of epidemiological and echocardiographic features is displayed in the Table.
Patients who underwent TAVR were significantly older and more commonly female.
Regarding echocardiographic features, patients treated with TAVR had lower left ventricular ejection fraction and higher LV mass and left atrium volumes, as well as higher E/’e values. Pulmonary systolic arterial pressures were higher; beside, this group of patients showed lower TAPSE and right ventricular arterial coupling (Figure 1).
When applying two different cardiac damage staging systems in the two cohorts, those patients treated with TAVR had significantly more cardiac damage, with a higher proportion of patients classified into advance stages (Figure 2).

Conclusions
In a contemporary cohort of patients with severe AS, those treated with TAVR had significantly more advance cardiac damage, particularly at the expense of right ventricular damage, compared to those who underwent SAVR.
Earlier treatment before significant cardiac damage takes place may help to improve outcomes.
Echocardiographic characteristics
Cardiac damage staging systems
Rational and design of EACVI-MMVD study: an international registry on multimodality imaging for mixed and multiple valvular heart disease
Authors: Unger A , Mandoli G E , Neglia D , Romero Dorta E , Kagiyama N , Borodzicz-Jazdzyk S , Velegraki E , Coisne A , Uygur B , Afana A , Florence J , Delgado V , Petersen S , Pezel T 
Published: January 2025

Abstract

Background
Despite the high frequency of multiple (combination of stenotic or regurgitant lesions occurring on ≥2 cardiac valves) and mixed (combination of stenotic and regurgitant lesions on the same valve) valvular heart disease (MMVD) in clinical practice, comprehensive insights into its clinical presentation, management strategies, impact of multimodality imaging, and outcomes are not well established.

Objective
The "EACVI-MMVD Study" will be the first prospective international study assessing all consecutive patients with MMVD to assess its proportion, and describe baseline epidemiological, cardiovascular imaging, management, and prognosis data.

Methods
International prospective, multicentre, observational study led by the Heart Imagers of Tomorrow (HIT) of the European Association of Cardiovascular Imaging (EACVI) to include all consecutive patients with at least 2 moderate-to-severe VHD involving ≥2 different valves, according to the current ESC guidelines, and/or mixed VHD, defined as at least moderate stenosis and at least moderate regurgitation of a single valve, according to the current ESC guidelines. The recruitment is ongoing over 6 months, involving more than 100 centres across 30 countries. Inclusion and exclusion criteria are provided in Table 1.

Results
The primary outcome will be the proportion of MMVD cases assessed in echocardiographic labs over 6 months. We will then describe the clinical presentation, management strategies, cardiovascular imaging data, and 1-year prognosis of these MMVD patients (Figure 1). Physicians will determine baseline evaluation, which may include the full spectrum of multimodality imaging, such as transthoracic and transoesophageal echocardiography, stress echocardiography, computed tomography, and cardiovascular magnetic resonance. Optionally, three dedicated core laboratories will analyse cardiovascular imaging data from participating centres.

Conclusion
The EACVI-MMVD study will be the first and largest international multicentre study evaluating the prevalence of MMVD in clinical practice and determining the impact of multimodality imaging in MMVD patients.
Table1 Inclusion and exclusion criteria
Figure 1 Overview of the study
Predicting valvular heart disease prognosis from large echocardiography record datasets by machine learning
Authors: Lin W W , Wang Y H , Chen H M , Huang H N , Lee W L , Yang C T 
Published: January 2025

Abstract
Echocardiography is the best choice for diagnosing valvular heart disease. The treatment guidelines of the AHA and ESC provide clinicians with how to select patients for interventional treatment at the appropriate time. However, these treatment guidelines often vary according to different places and ethnic groups. There are 15,000 echocardiography examinations in our hospital every year. Each patient has approximately 50 measured parameters, plus physiological measurements such as height, weight, blood pressure, heart rate, clinical diagnoses and comorbidities, and the image data are stored in DICOM format. Starting in 2012, we formatted and stored this information in structural reports, and by 2023 we had a total of 170,000 records. We analyzed the 3 years prognosis and survival rate of patients with severe aortic stenosis who received different treatments in our hospital from 2012 to 2015. After the clinical data are divided into 9 categories, both unsupervised and supervised learnings are uses to train the best feasible model based on training data. Unsupervised and supervised learnings use 7 and 2 algorithms, respectively, through recursive features to eliminate and filter important features out. The judgement based on the model accuracy for supervised learning and the comparison of four different features’ impact on accuracy for unsupervised learning. The highest accuracy for supervised learning is 1, while the highest accuracy of the unsupervised model is about 0.44. The accuracy of feature selection is not much different from the original data. This study shows the XGBoost algorithm possess the highest accuracy. In the future, we will use wearable devices to continuously monitor patients’ vital signs. Coupled with the remote monitoring of Internet of Things (IOT) technology and fast computer calculations, we may integrate them into big databases to create personalized and precision diagnosis and recommendations for valvular heart disease.
Important features selected by XGBoost
Dynamic ventricular-arterial coupling during supine ergometry is related to outcome in asymptomatic severe aortic stenosis
Authors: Armenis I , Leontiadis E , Tsiapras D , Kyrzopoulos S , Iakovou I , Athanassopoulos G D 
Published: January 2025

Abstract

Background
Ventricular-arterial coupling (VAC) represents a key pathophysiological component for the preservation of left ventricular (LV) contractile efficiency. Increased age, hypertension and evolving atherosclerosis may induce VAC mismatch in asymptomatic severe aortic stenosis (AS).

Purpose
Purpose of the study was to assess the effect of supine ergometry (Ex) on VAC in AS and to interrogate potential relationship with the clinical outcome.

Methods
Forty eight AS patients, followed-up on valve clinic in a tertiary center (age 66±12 years), were referred for Ex. AS-related cardiac events (independent decision for surgery, occurrence of AS-related symptoms) during a follow-up of 33±21 months occurred in 19 patients (EV group).
The following parameters were estimated noninvasively both at rest-R/Ex: LV ejection fraction (EF:%), strain (SR:%), transmitral E/e ratio, peak transtricuspid systolic pressure, AV mean gradient (meanGR: mmHg), valvuloarterial impedance (Za: mm Hg·ml-1m2), effective arterial elastance (Ea: mmHg/ml), LV endsystolic elastance (Ees: mmHg/ml) and VAC as the ratio Ea/Ees.

Results
Event (EV) and non-event (nEV) groups had similar % target heart rate at Ex (96±17 vs 100±12), age (66±12 vs 66±12 years), women/men ratio (9/19 vs 14/29), EF-R (55±8 vs 56±7%), SR-R (15.0±4.0 vs 14.5±3.5%), SR-Ex (16±5 vs 17±4%) but lower EF-Ex (59±9 vs 64±6%, p=0.03).
EV group had greater meanGR at R (45±16 vs 37±12mmHg, p=0.03), but similar Za both at R and Ex (2.3±1.0 vs 2.0±0.8mm Hg·ml-1m2 and 2.7±0.8 vs 2.7±1.0mm Hg·ml-1m2).
EV group had lower Ees at Ex (4.0±2.0 vs 5.6±2.3mmHg/ml, p=0.026) but similar Ees at R (3.0±1.3 vs 3.3±1.5 mmHg/ml) as well Ea both at R and Ex (2.4±1.0 vs 2.6±1.0 mmHg/ml and 2.7±1.0 vs 3.1±1.1 mmHg/ml).
Despite similar VAC at R (0.84±0.24 vs 0.79±0.25), EV group showed worsening VAC during Ex (0.75±0.29 vs 0.58±0.12, p=0.01).
Binary logistic regression analysis for events, including the different parameters between groups (meanGR, VAC Ex, EF Ex), selected only the VAC Ex (exp(b)=0.01, p=0.02) as independent predictor.
ROC event cut off for VAC Ex was 0.69 (area 0.68, p=0.05, sensitivity 0.6 specificity=0.9, figure 1).
Kaplan Meier analysis for the greater values of the VAC Ex than 0.69 showed an increased hazard ratio for events (log rank=6.9 p=0.009, figure 2).

Conclusion
In asymptomatic patients with AS, noninvasive VAC at Ex provides an independent prognostic yield for cardiac outcome from conventional indices of either LV function or hydraulic aortic valve performance.