bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limitation of gene flow by distance in the common yellow jasmine (Chrysojasminum fruticans, Oleaceae): implications for the study of its mating strategies
Authors: Puyoou Aurore , Gryta Hervé , Fuchs Anne-Laure , Blanchard Pierrick , Cheptou Pierre-Olivier , Civeyrel Laure , Dufay Mathilde , Dupin Julia , Jargeat Patricia , Lecompte Emilie , Besnard Guillaume 
Published: August 2023

Abstract
The common yellow jasmine (Chrysojasminum fruticans, Oleaceae) is a distylous shrub occurring in the wild in south-western Europe and the Mediterranean Basin. Little is known about the genetics of its populations and such information would be necessary to investigate its spread and mating strategies. Here, the organization of its genetic diversity was investigated among and between 13 populations from southern France, including a 35-year-old experimental plot (‘CEFE’, CNRS Montpellier). Markers (microsatellites and indels) were developed to screen polymorphisms in nuclear, chloroplast, and mitochondrial genomes. Low linkage disequilibrium was observed between chloroplast and mitochondrial haplotypes probably resulting from paternal leaks in their inheritance as reported in other species of tribe Jasmineae. Yet, analyses of 36 progenies issued from parents with distinct chloroplast and/or mitochondrial DNA haplotypes only revealed a maternal contribution. Natural populations of C. fruticans are moderately to highly differentiated at the regional scale with a strong isolation-by-distance pattern detected on nuclear data, indicating limited gene flow. An isolated site (‘Moulis’), located on the marginal distribution area, was remarkably genetically depauperate and highly differentiated from other populations. Further studies on the variation of mating strategies in C. fruticans should consider populations with contrasting patterns of genetic diversity. The artificial ‘CEFE’ population also offers opportunities for experiments in a closed system.
Are there sex differences in cardiovascular outcomes in non-dialysis CKD patients?
Authors: Provenzano Pasquale Fabio , Caridi Grazia , Parlongo Giovanna , Leonardis Daniela , Puntorieri Elvira , Tripepi Giovanni , Zoccali Carmine , Mallamaci Francesca 
Published: August 2023

ABSTRACT

Background
Sex differences for cardiovascular (CV) risk and outcomes in chronic kidney disease (CKD) patients not on dialysis have been scarcely or never investigated. We therefore studied this important aspect in a cohort of CKD stage 2–5 in the south of Italy.

Methods
We tested the relationship between sex and fatal and non-fatal major CV events in a cohort of 759 stage 2–5 CKD patients followed up for a median time of 36 months.

Results
Out of 759 patients, 455 were males (60%) and the remaining 304 patients were females (40%). During the follow-up, 42 patients died, and 118 had fatal and non-fatal CV events. On univariate Cox regression analyses, the male sex failed to be associated with all-cause mortality but was strongly related to the incidence rate of fatal and non-fatal major CV events [hazard ratio (HR) 1.75, 95% confidence interval (CI) 1.18–2.60, P = .006]. Data adjustment for a series of major potential confounders did not materially affect the strength of this relationship (HR 1.78, 95% CI 1.03–3.09). Further analysis testing the effect of age on major CV outcomes by sex showed an effect modification by this risk factor on the same outcome (P = .037) because the HR of male versus female CV events increased progressively with aging.

Conclusion
Male patients in stage G2–5 CKD had a higher risk for CV events compared with female patients. Age was shown to be a risk modifier for the association between sex and CV events and this risk increased linearly across a wide age spectrum in CKD patients.
Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish
Authors: Thorstensen Matt J , Weinrauch Alyssa M , Bugg William S , Jeffries Ken M , Anderson W Gary 
Published: August 2023

AbstractThe lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America, but a lack of genomic resources has hindered molecular research in the species. To support such research, we created a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach, anterior intestine, pyloric cecum, spiral valve and rectum. The transcriptomes for each tissue were sequenced and assembled individually from a mean of 98.3 million (±38.9 million SD) reads each. In addition, an overall transcriptome was assembled and annotated with all data used for each tissue-specific transcriptome. All assembled transcriptomes and their annotations were made publicly available as a scientific resource. The non-gut transcriptomes provide important resources for many research avenues. However, we focused our analysis on messenger ribonucleic acid (mRNA) observations in the gut because the gut represents a compartmentalized organ system with compartmentalized functions, and seven of the sequenced tissues were from each of these portions. These gut-specific analyses were used to probe evidence of microbiome regulation by studying heterogeneity in microbial genes and genera identified from mRNA annotations. Gene set enrichment analyses were used to reveal the presence of photoperiod and circadian-related transcripts in the pyloric cecum, which may support periodicity in lake sturgeon digestion. Similar analyses were used to identify different types of innate immune regulation across the gut, while analyses of unique transcripts annotated to microbes revealed heterogeneous genera and genes among different gut tissues. The present results provide a scientific resource and information about the mechanisms of compartmentalized function across gut tissues in a phylogenetically ancient vertebrate.Database URL: https://figshare.com/projects/Lake_Sturgeon_Transcriptomes/133143
Correlates and prognostic implications of LVEF reduction after transcatheter edge-to-edge repair for primary mitral regurgitation
Authors: Shechter Alon , Kaewkes Danon , Lee Mirae , Makar Moody , Patel Vivek , Koren Ofir , Koseki Keita , Nagasaka Takashi , Skaf Sabah , Chakravarty Tarun , Makkar Raj R , Siegel Robert J 
Published: August 2023

Abstract

Aims
To explore the characteristics and outcomes of patients undergoing transcatheter edge-to-edge repair (TEER) for primary mitral regurgitation (MR) according to the presence of left ventricular ejection fraction (LVEF) reduction post-procedure.

Methods and results
We retrospectively analysed 317 individuals [median age 83 (interquartile range, 75–88) years, 197 (62.1%) males] treated with an isolated, first-time TEER that was concluded by a successful clip deployment. Stratified by LVEF change at 1-month compared with baseline, the cohort was evaluated for residual MR and heart failure (HF) indices up to 1-year, as well as all-cause mortality and HF hospitalizations at 2-years. Overall, 212 (66.9%) patients displayed LVEF reduction, which was mainly driven by lowered total stroke volume and diffuse hypocontractility. While post-procedural MR, transmitral mean pressure gradient, and functional status were comparable in the two study groups, patients with LVEF reduction exhibited a greater decline in filling pressures intra-procedurally; left ventricular mass index, pulmonary arterial systolic pressure, and serum natriuretic peptide level at 1-month; and walking limitation at 1-year. Also, by 2 years, they were less likely to die (13.3% vs. 5.7%, P = 0.019), be readmitted for HF (17.1% vs. 9.0%, P = 0.033), and experience either of the two (23.8% vs. 12.7%, P = 0.012). Lastly, LVEF reduction was the only 1-month echocardiographic parameter to independently confer an attenuated risk for the composite of deaths or HF hospitalizations (HR 0.28, 95% CI 0.10–0.78, P = 0.016).

Conclusion
LVEF reduction at 1-month post-TEER for primary MR is associated with better clinical outcomes, possibly reflecting a more pronounced unloading effect of the procedure.
Transcatheter recanalization of chronic total occlusion in congenital heart disease: case reports and lessons from percutaneous coronary interventions
Authors: Hribernik Ines , Bentham James 
Published: August 2023

Abstract

Background
Chronic complete vascular occlusion causes significant morbidity and mortality in patients with congenital heart disease (CHD). The diversity of lesions, lack of dedicated equipment, and small number of procedures performed by individual operator continue to pose a challenge to congenital interventional cardiologists.

Case summary
We report two cases of percutaneous recanalization in CHD using percutaneous coronary intervention (PCI) equipment for chronic total occlusion (CTO).

Discussion
Careful pre-procedural planning, access site choice, use of catheter guiding systems for support, and selection of penetrating guidewires and techniques used in CTO-PCIs are key steps to a successful outcome.
The dose-dependent effect of estrogen on bone mineral density in trans girls
Authors: Boogers Lidewij Sophia , van der Loos Maria Anna Theodora Catharina , Wiepjes Chantal Maria , van Trotsenburg Adrianus Sarinus Paulus , den Heijer Martin , Hannema Sabine Elisabeth 
Published: August 2023

Abstract

Objective
Treatment in transgender girls can consist of puberty suppression (PS) with a gonadotropin-releasing hormone agonist (GnRHa) followed by gender-affirming hormonal treatment (GAHT) with estrogen. Bone mineral density (BMD) Z-scores decrease during PS and remain relatively low during GAHT, possibly due to insufficient estradiol dosage. Some adolescents receive high-dose estradiol or ethinyl estradiol (EE) to limit growth allowing comparison of BMD outcomes with different dosages.

Design
Retrospective study.

Methods
Adolescents treated with GnRHa for ≥1 year prior to GAHT followed by treatment with a regular estradiol dose (gradually increased to 2 mg), 6 mg estradiol or 100-200 µg EE were included to evaluate height-adjusted BMD Z-scores (HAZ scores) on DXA.

Results
Eighty-seven adolescents were included. During 2.3 ± 0.7 years PS, lumbar spine HAZ scores decreased by 0.69 [95% confidence interval (CI) −0.82 to −0.56)]. During 2 years HT, lumbar spine HAZ scores hardly increased in the regular group (0.14, 95% CI −0.01 to 0.28, n = 59) vs 0.42 (95% CI 0.13 to 0.72) in the 6 mg group (n = 13), and 0.68 (95% CI 0.20 to 1.15) in the EE group (n = 15). Compared with the regular group, the increase with EE treatment was higher (0.54, 95% CI 0.05 to 1.04). After 2 years HT, HAZ scores approached baseline levels at start of PS in individuals treated with 6 mg or EE (difference in 6 mg group −0.20, 95% CI −0.50 to 0.09; in EE 0.17, 95% CI −0.16 to 0.50) but not in the regular group (−0.64, 95% CI −0.79 to −0.49).

Conclusion
Higher estrogen dosage is associated with a greater increase in lumbar spine BMD Z-scores. Increasing dosage up to 2 mg estradiol is insufficient to optimize BMD and approximately 4 mg may be required for adequate serum concentrations.
Spatial methods for measuring access to health care
Authors: Beks Hannah , Wood Sarah M , Clark Robyn A , Vincent Versace L 
Published: August 2023

Abstract
Access to health care is a universal human right and key indicator of health system performance. Spatial access encompasses geographic factors mediating with the accessibility and availability of health services. Equity of health service access is a global issue, which includes access to the specialized nursing workforce. Nursing research applying spatial methods is in its infancy. Given the use of spatial methods in health research is a rapidly developing field, it is timely to provide guidance to inspire greater application in cardiovascular research. Therefore, the objective of this methods paper is to provide an overview of spatial analysis methods to measure the accessibility and availability of health services, when to consider applying spatial methods, and steps to consider for application in cardiovascular nursing research.
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience
Authors: Mendes de Farias Tarcisio , Wollbrett Julien , Robinson-Rechavi Marc , Bastian Frederic 
Published: August 2023

Abstract

Background
Enhancing interoperability of bioinformatics knowledge bases is a high-priority requirement to maximize data reusability and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange value once the knowledge base is (re)used, and without interoperability, the utility lies dormant.

Results
In this article, we discuss several approaches to boost interoperability depending on the interoperable parts. The findings are driven by several real-world scenario examples that were mostly implemented by Bgee, a well-established gene expression knowledge base. To better justify the findings are transferable, for each Bgee interoperability experience, we also highlight similar implementations by major bioinformatics knowledge bases. Moreover, we discuss ten general main lessons learned. These lessons can be applied in the context of any bioinformatics knowledge base to foster data reusability.

Conclusions
This work provides pragmatic methods and transferable skills to promote reusability of bioinformatics knowledge bases by focusing on interoperability.
Chromosome-level genome and recombination map of the male buffalo
Authors: Wang Xiaobo , Li Zhipeng , Feng Tong , Luo Xier , Xue Lintao , Mao Chonghui , Cui Kuiqing , Li Hui , Huang Jieping , Huang Kongwei , Rehman Saif-ur , Shi Deshun , Wu Dongdong , Ruan Jue , Liu Qingyou 
Published: August 2023

Abstract

Background
The swamp buffalo (Bubalus bubalis carabanesis) is an economically important livestock supplying milk, meat, leather, and draft power. Several female buffalo genomes have been available, but the lack of high-quality male genomes hinders studies on chromosome evolution, especially Y, as well as meiotic recombination.

Results
Here, a chromosome-level genome with a contig N50 of 72.2 Mb and a fine-scale recombination map of male buffalo were reported. We found that transposable elements (TEs) and structural variants (SVs) may contribute to buffalo evolution by influencing adjacent gene expression. We further found that the pseudoautosomal region (PAR) of the Y chromosome is subject to stronger purification selection. The meiotic recombination map showed that there were 2 obvious recombination hotspots on chromosome 8, and the genes around them were mainly related to tooth development, which may have helped to enhance the adaption of buffalo to inferior feed. Among several genomic features, TE density has the strongest correlation with recombination rates. Moreover, the TE subfamily, SINE/tRNA, is likely to play a role in driving recombination into SVs.

Conclusions
The male genome and sperm sequencing will facilitate the understanding of the buffalo genomic evolution and functional research.
Health, wellbeing and nutritional impacts after 2 years of free school meals in New Zealand
Authors: McKelvie-Sebileau Pippa , Swinburn Boyd , Glassey Rachael , Tipene-Leach David , Gerritsen Sarah 
Published: August 2023

AbstractIn 2020, a government-funded healthy school lunch program was introduced in a quarter of New Zealand schools, selected due to high levels of socio-economic barriers. This study assesses the impact of the introduction of the school lunch program from family (whānau), student and school principal perspectives. Across four schools, we conducted five focus groups (two with secondary students and three with family members) and four school principal interviews. Participating schools represented a range of contexts: primary and secondary, schools with cooks in on-site kitchens and schools receiving meals delivered by external caterers. Thematic analysis was used to develop themes describing the health, wellbeing and nutritional impact of the program. Family participants were 82% Indigenous Māori and self-identified as having ‘borderline’ (73.5%) or no financial security (8.8%). Seven positive impact themes were identified: improved food security, enhanced equity, increased appreciation of healthy foods for students, enhanced mana (wellbeing) for all, reduced financial hardship/stress for families, opportunities for nutritional learning and recognition that appreciation and uptake happen over time. Four negative impact themes were identified: low uptake that created food waste, perception that healthy food is not palatable for students, lack of knowledge of the program and loss of agency for students. This is the largest intervention in nutrition and food security for children implemented in New Zealand since the 1930's. The first 2 years have offered wellbeing and financial benefits for students and families, particularly when school environments promote uptake. More involvement of students and family members in the program planning is essential.
The Whole is Greater Than the Sum of Its Parts: Large-scale Phenomena Arising from Small-scale Biophysical Processes
Authors: Wheeler Jeanette D , Chan Kit Yu Karen 
Published: August 2023

Synopsis
The symposium “Large-scale biological phenomena arising from small-scale biophysical processes” at the SICB 2023 Annual General Meeting focused on the cross-disciplinary exploration of emergent phenomena in biology. Interactions between cells or organisms at small scales within a system can govern patterns occurring at larger scales in space, time, or biological complexity. This theme recurs in many sub-disciplines of biology, including cell and developmental biology, evolution, and ecology. This symposium, and the associated special issue introduced here, showcases a wide range of cross-disciplinary collaborations among biologists, physicists, and engineers. Technological advancements in microscopy and microfluidics, as well as complementary advances in mathematical modeling and associated theory demonstrate the timeliness of this issue. This introduction seeks to provide useful background information to place the studies within this issue in a broader biophysical context and highlight similarities in ideas and approaches across systems and sub-disciplines. We hope to demonstrate that cross-disciplinary research linking small-scale biophysics to larger-scale emergent phenomena can help us understand problems ranging from single-cell behaviors to tissue formation and function, evolution of form, and the dynamics of communities.
Late erosion of Amplatzer Septal Occluder device 9 years after the implantation: a case report
Authors: Koumallos Nikolaos , Aggeli Costantina , Milas Theodoros , Tsioufis Kostantinos 
Published: August 2023

Abstract
Cardiac erosion is a rare but life-threatening complication after the interventional closure of an atrial septal defect. We present the case of a patient who developed cardiac erosion 9 years after the placement of an Amplatzer Septal Occluder. The patient presented to our hospital with symptoms of tamponade. Surgical exploration revealed a tear in the roof of the left atrium. To our knowledge, this is one of the most delayed presentations reported. In these cases, diagnosis is difficult and a level of clinical suspicion is demanded.
The added value of text from Dutch general practitioner notes in predictive modeling
Authors: Seinen Tom M , Kors Jan A , van Mulligen Erik M , Fridgeirsson Egill , Rijnbeek Peter R 
Published: August 2023

Abstract

Objective
This work aims to explore the value of Dutch unstructured data, in combination with structured data, for the development of prognostic prediction models in a general practitioner (GP) setting.

Materials and methods
We trained and validated prediction models for 4 common clinical prediction problems using various sparse text representations, common prediction algorithms, and observational GP electronic health record (EHR) data. We trained and validated 84 models internally and externally on data from different EHR systems.

Results
On average, over all the different text representations and prediction algorithms, models only using text data performed better or similar to models using structured data alone in 2 prediction tasks. Additionally, in these 2 tasks, the combination of structured and text data outperformed models using structured or text data alone. No large performance differences were found between the different text representations and prediction algorithms.

Discussion
Our findings indicate that the use of unstructured data alone can result in well-performing prediction models for some clinical prediction problems. Furthermore, the performance improvement achieved by combining structured and text data highlights the added value. Additionally, we demonstrate the significance of clinical natural language processing research in languages other than English and the possibility of validating text-based prediction models across various EHR systems.

Conclusion
Our study highlights the potential benefits of incorporating unstructured data in clinical prediction models in a GP setting. Although the added value of unstructured data may vary depending on the specific prediction task, our findings suggest that it has the potential to enhance patient care.
Prospective Evaluation of the Cost of Performing Breast Imaging Examinations Using a Time-Driven Activity-Based Costing Method: A Single-Center Study
Authors: Ali Aamir , Phillips Jordana , Ljuboja Damir , Shehab Syed , Pisano Etta D , Kaplan Robert S , Sarwar Ammar 
Published: August 2023

Abstract

Objective
Measuring the cost of performing breast imaging is difficult in healthcare systems. The purpose of our study was to evaluate this cost using time-driven activity-based costing (TDABC) and to evaluate cost drivers for different exams.

Methods
An IRB-approved, single-center prospective study was performed on 80 female patients presenting for breast screening, diagnostic or biopsy exams from July 2020 to April 2021. Using TDABC, data were collected for each exam type. Included were full-field digital mammography (FFDM), digital breast tomosynthesis (DBT), contrast-enhanced mammography (CEM), US and MRI exams, and stereotactic, US-guided and MRI-guided biopsies. For each exam type, mean cost and relative contributions of equipment, personnel and supplies were calculated.

Results
Screening MRI, CEM, US, DBT, and FFDM costs were $249, $120, $83, $28, and $30. Personnel was the major contributor to cost (60.0%–87.0%) for all screening exams except MRI where equipment was the major contributor (62.2%). Diagnostic MRI, CEM, US, and FFDM costs were $241, $123, $70, and $43. Personnel was the major contributor to cost (60.5%–88.6%) for all diagnostic exams except MRI where equipment was the major contributor (61.8%). Costs of MRI-guided, stereotactic and US-guided biopsy were $1611, $826, and $356. Supplies contributed 40.5%–49.8% and personnel contributed 30.7%–55.6% to the total cost of biopsies.

Conclusion
TDABC provides assessment of actual costs of performing breast imaging. Costs and contributors varied across screening, diagnostic and biopsy exams and modalities. Practices may consider this methodology in understanding costs and making changes directed at cost savings.