bluuebunny/crossref_metadata_2025_split huggingface dataset:
Take-home tests as an assessment for learning strategy
Authors: Hobbs Garry Bryn , Mourão Sandie 
Published: June 2024

Abstract
This article reports on an intervention study conducted to improve young Thai learners’ motivation and attitudes towards take-home tests. The traditional use of summative tests in education has often led to increased pressure and demotivation among students. Based on formative assessment practices and motivational strategies, the study aimed to improve students’ motivation and engagement when taking tests. The intervention involved regular, short take-home tests and motivational strategies over 25 weeks and collected data using a mixed methods approach. Results showed notable improvement in students’ intrinsic motivation, writing motivation and homework completion rate of take-home tests over the course of the intervention. The article highlights the importance of incorporating formative assessment practices, goal setting, collaborative learning and visual aids to promote student ownership of learning and increase their motivation to complete tests. The study contributes to the ongoing dialogue on effective assessment methods and student motivation in an educational context.
Health-related quality of life in elderly cardiac patients undergoing cardiac rehabilitation and the association with exercise capacity: the EU-CaRE study
Authors: Kjesbu Ingunn E , Sibilitz Kirstine L , Petersen Janne , Houben Vital J G , Wilhelm Matthias , Pena-Gil Carlos , Iliou Marie Christine , Zeymer Uwe , Ardissino Diego , Van’t Hof Arnoud W J , van der Velde Astrid E , de Kluiver Ed P , Prescott Eva 
Published: June 2024

Abstract

Aims
The ability to be physically active is pivotal to the quality of life in elderly patients. This study aims to describe the association between exercise capacity and health-related quality of life (HRQoL), anxiety, and depression following an exercise-based cardiac rehabilitation (CR) programme in elderly cardiac patients.

Methods and results
Patients aged ≥65 years with acute and chronic coronary syndrome or heart valve surgery were consecutively included from eight CR centres in seven European countries. Exercise capacity [VO2peak(mL/kg/min)] was assessed with a cardiopulmonary exercise test (97%) or a 6-min walk test. Outcome variables included HRQoL [36-item Short-Form Health Survey physical and mental component scores (PCS and MCS)], anxiety (Generalized Anxiety Disorder-7), and depression (Patient Health Questionnaire-9). Mixed models were used to address the association between baseline and the development in VO2peak, and outcome variables stratified on sex, and adjusted for baseline values, age, and CR centre. A total of 1633 patients were included (T0), 1523 (93%) completed end-of-CR assessment (T1), and 1457 (89%) were available for 1-year follow-up (T2). Women had higher percentage of predicted VO2peak but poorer scores in HRQoL, anxiety, and depression at all time points. All scores improved in both sexes at follow-up. We found significant associations between VO2peak at baseline as well as development in VO2peak and all outcome variables at T1 and T2 in men (all P &lt; 0.001). In women, VO2peak was only associated with PCSs (P &lt; 0.001).

Conclusion
Improvements in exercise capacity were strongly associated with improvements in HRQoL and mental health, however, with stronger associations in men. The results highlight the importance of physical fitness for HRQol and mental health. The findings from this study might be useful to better target individual CR programmes.
Physiological responses of a black locust plantation to drought stress based on a throughfall exclusion experiment in semi-arid northwestern China
Authors: Liu Binbin , Tang Xianhui , Wang Lele , Zhang Pengyi , He Junhao , Yue Chao 
Published: June 2024

Abstract
Drought poses a significant threat on the ecosystem stability of extensive areas of black locust (Robinia pseudoacacia L.) plantations in northwestern China. However, limited understanding of the physiological responses of black locust to drought has impeded the development of proactive measures to alleviate potential adverse effects of drought. This study investigated the physiological impacts of varying drought intensities, manipulated by a throughfall exclusion experiment, on a 20-year-old black locust plantation in northwestern China. The experiment involved 40% throughfall exclusion for moderate drought, 80% exclusion for extreme drought, and no exclusion for control. One year after the implementation of the experiment, both predawn (Ψpd) and midday (Ψmd) leaf water potentials were significantly lower under drought treatments compared to those in control (P &lt; .01). Stomatal conductance (gs) exhibited a strong reduction, leading to decreased leaf transpiration and photosynthesis under drought. However, the reduction in gs did not effectively prevent the decrease in Ψmd. Instead, both Ψpd and Ψmd became more negative with increasing drought stress, but their difference remaining relatively constant (being ~1.1 MPa) across treatments. These results suggest that black locust adopts a balanced water regulatory strategy between isohydry and anisohydry to cope with drought stress. These results contribute to an enhanced understanding of the crucial physiological responses of black locust under drought stress, offering valuable insights for future management strategies aimed at sustaining the ecosystem stability of black locust plantations in an increasingly arid climate.
Exploring the Adaptation of Native Shrub Species to Different Levels of Shading: Augmenting their Sustainable Exploitation Framework
Authors: Karapatzak Eleftherios , Koularmanis Konstantinos , Papanastasi Katerina , Fotakis Dimitrios , Grigoriadou Katerina , Maloupa Eleni 
Published: June 2024

Abstract
The environmental adaptation potential of regional wild germplasm resources should be investigated in a species-specific manner in terms of the sustainable exploitation of underutilized native species. In the current work, three fruit/ornamental shrub species (Rosa canina L., Sambucus nigra L. and Cornus sanguinea L.) originating from regional wild germplasm of Greece with a previously set domestication framework have been investigated in terms of their environmental adaptation to different levels of shading. To this end, targeted experimentation was conducted on ex situ adapted material by applying different shading levels (0%, 30% and 60% shading) in purpose-built netting tunnels. Rosa canina showed similar growth patterns among the shading levels applied but with increased chlorophyll fluorescence patterns and increased abaxial leaf stomatal density with increased shading. Sambucus nigra showed similar results to R. canina in photosynthetic efficiency and leaf stomatal density but with additional effects on plant growth patterns. Cornus sanguinea, on the other hand, was not affected by shading level in the measured parameters. These results outline the adaptation potential in a species-specific manner of the studied species to shading in terms of adding novel exploitation options for agroecosystems, agroforestry, and landscape management in peri-urban green spaces and peri-urban forest understory enrichment to mitigate climate change impacts in temperate and semi-arid climates.
Study Implications: This study explores the adaptation potential to increasing levels of shading of ex situ adapted germplasm of wild origin of three underutilized shrub species with known multifaceted value. The work builds on the sustainable utilization framework of the focal species in terms of novel exploitation options in landscape management for peri-urban green spaces and peri-urban forest understory enrichment for enhancing biodiversity and soil erosion protection. Therefore, this work offers an example of an underlying research line towards systematized screening and utilization of wild plant species for climate change impact mitigation in agroecosystems, agroforestry, and landscape management in temperate semi-arid climates.
Whole-genome sequencing analysis of soybean diversity across different countries and selection signature of Korean soybean accession
Authors: Cho Youngbeom , Kim Jae-Yoon , Kim Seon-Kyu , Kim Seon-Young , Kim Namshin , Lee Jinhyuk , Park Jong-Lyul 
Published: June 2024

Abstract
Soybean is an important agricultural crop known for its high protein and oil content, contributing to essential nutritional and health benefits for humans. Domesticated in China over 5,000 years ago, soybean has since adapted to diverse environments and spread worldwide. This study aimed to investigate the genomic characteristics and population structures of 2,317 publicly available soybean whole-genome sequences from diverse geographical regions, including China, Korea, Japan, Europe, North America, and South America. We used large-scale whole-genome sequencing data to perform high-resolution analyses to reveal the genetic characteristics of soybean accessions. Soybean accessions from China and Korea exhibited landrace characteristics, indicating higher genetic diversity and adaptation to local environments. On the other hand, soybean accessions from Japan, the European Union, and South America were found to have low genetic diversity due to artificial selection and breeding for agronomic traits. We also identified key variants and genes associated with the ability to adapt to different environments. In Korean soybean accessions, we observed strong selection signals for isoflavone synthesis, an adaptive trait critical for improving soybean adaptability, survival, and reproductive success by mitigating environmental stress. Identifying specific genomic regions showing unique patterns of selective sweeps for genes such as HIDH, CYP73A11, IFS1, and CYP81E11 associated with isoflavone synthesis provided valuable insights into potential adaptation mechanisms. Our research has significantly improved our understanding of soybean diversity at the genetic level. We have identified key genetic variants and genes influencing adaptability, laying the foundation for future advances in genomics-based breeding programs and crop improvement efforts.
OrthoPhyl—streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales
Authors: Middlebrook Earl A , Katani Robab , Fair Jeanne M 
Published: June 2024

Abstract
There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (&gt;1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.
Do I Have Symptoms of Dementia: A Discursive Study of Awareness and Shame Among People With Advanced Dementia
Authors: Kłosińska Urszula , Leszko Magdalena 
Published: June 2024

AbstractBackground and ObjectivesThis study explores the narrated experiences of individuals with advanced stages of late-onset dementia, focusing on their diagnosis awareness. Such framing is motivated by 2 reasons. Firstly, there is a lack of consensus regarding the prevalence of anosognosia among people with dementia. Secondly, research on anosognosia often neglects to address the important issues of shame and stigma associated with receiving a dementia diagnosis.Research Design and MethodsFor this qualitative study, a total of 27 participants ranging in age from 66 to 94 were involved. The data collected were analyzed using textual-oriented discourse analysis.ResultsOur findings indicated that individuals with dementia struggled to comprehend the medical terminology used to describe their experiences within biomedical standards. The interviewees utilized 5 negative discourses on dementia, which shaped their attitudes toward the condition and people diagnosed with it. These discourses depicted dementia as an illness, negative aging, a devaluation, a burden, and a life tragedy. Moreover, study participants did not outright reject the diagnosis but rather negotiated its acceptance within the context of shame associated with dementia.Discussion and ImplicationsThe concept of anosognosia can serve as a mechanism of social control and stigmatization of people with dementia within the dominant biomedical discourse.
RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci
Authors: Shrestha Anish M S , Gonzales Mark Edward M , Ong Phoebe Clare L , Larmande Pierre , Lee Hyun-Sook , Jeung Ji-Ung , Kohli Ajay , Chebotarov Dmytro , Mauleon Ramil P , Lee Jae-Sung , McNally Kenneth L 
Published: June 2024

Abstract

Background
As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources.

Results
We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs.

Conclusions
RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf.
CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites
Authors: Müller Teresa , Mautner Stefan , Videm Pavankumar , Eggenhofer Florian , Raden Martin , Backofen Rolf 
Published: June 2024

Abstract

Background
RNA–RNA interactions are key to a wide range of cellular functions. The detection of potential interactions helps to understand the underlying processes. However, potential interactions identified via in silico or experimental high-throughput methods can lack precision because of a high false-positive rate.

Results
We present CheRRI, the first tool to evaluate the biological relevance of putative RNA–RNA interaction sites. CheRRI filters candidates via a machine learning–based model trained on experimental RNA–RNA interactome data. Its unique setup combines interactome data and an established thermodynamic prediction tool to integrate experimental data with state-of-the-art computational models. Applying these data to an automated machine learning approach provides the opportunity to not only filter data for potential false positives but also tailor the underlying interaction site model to specific needs.

Conclusions
CheRRI is a stand-alone postprocessing tool to filter either predicted or experimentally identified potential RNA–RNA interactions on a genomic level to enhance the quality of interaction candidates. It is easy to install (via conda, pip packages), use (via Galaxy), and integrate into existing RNA–RNA interaction pipelines.
Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation
Authors: Alves Rafael Moysés , de Abreu Vinicius A C , Oliveira Rafaely Pantoja , Almeida João Victor dos Anjos , de Oliveira Mauro de Medeiros , Silva Saura R , Paschoal Alexandre R , de Almeida Sintia S , de Souza Pedro A F , Ferro Jesus A , Miranda Vitor F O , Figueira Antonio , Domingues Douglas S , Varani Alessandro M 
Published: June 2024

Abstract

Background
Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family.

Findings
The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species.

Conclusions
The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.
Extended haplotype with rs41524547-G defines the ancestral origin of SCA10
Authors: McFarland Karen N , Tiwari Anjana , Hashem Vera , Zhang Linwei , Zeng Desmond , Vincent Justin , Arredondo Maria J , Johnson Kristy L , Gan Shi Rui , Yabe Ichiro , Skov Laurits , Rasmussen Astrid , Ashizawa Tetsuo 
Published: June 2024

Abstract
Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal dominant ataxia caused by a large expansion of the (ATTCT)n repeat in ATXN10. SCA10 was described in Native American and Asian individuals which prompted a search for an expanded haplotype to confirm a common ancestral origin for the expansion event. All patients with SCA10 expansions in our cohort share a single haplotype defined at the 5′-end by the minor allele of rs41524547, located ~35 kb upstream of the SCA10 expansion. Intriguingly, rs41524547 is located within the miRNA gene, MIR4762, within its DROSHA cleavage site and just outside the seed sequence for mir4792-5p. The world-wide frequency of rs41524547-G is less than 5% and found almost exclusively in the Americas and East Asia—a geographic distribution that mirrors reported SCA10 cases. We identified rs41524547-G(+) DNA from the 1000 Genomes/International Genome Sample Resource and our own general population samples and identified SCA10 repeat expansions in up to 25% of these samples. The reduced penetrance of these SCA10 expansions may be explained by a young (pre-onset) age at sample collection, a small repeat size, purity of repeat units, or the disruption of miR4762-5p function. We conclude that rs41524547-G is the most robust at-risk SNP allele for SCA10, is useful for screening of SCA10 expansions in population genetics studies and provides the most compelling evidence to date for a single, prehistoric origin of SCA10 expansions sometime prior to or during the migration of individuals across the Bering Land Bridge into the Americas.
Diagnosis of Inflammatory Bowel Disease–Associated Peripheral Arthritis: A Systematic Review
Authors: Falloon Katherine , Dossaji Zahra , Mude Pooja , Abushamma Suha , Ananthakrishnan Ashwin , Barnes Edward L , Bhalla Jaideep , Bhattacharya Abhik , Cheemalavagu Shashank , Colombel Jean-Fred , Cross Raymond K , Ermann Joerg , Ha Christina , Herfarth Hans , Horst Sara , Hou Jason , Husni M Elaine , Kline Theresa M , Kuhn Kristine A , Long Millie D , Loftus Edward V , Lukin Dana J , Patel Aditi , Rubin David T , Scherl Ellen J , Shah Samir A , Siaton Bernadette C , Sleiman Joseph , Qazi Taha , Weisman Michael H , Cohen Benjamin L , Feagan Brian G , Rieder Florian 
Published: June 2024

Abstract

Background
Inflammatory bowel disease (IBD)–associated peripheral spondyloarthritis (pSpA) decreases quality of life and remains poorly understood. Given the prevalence of this condition and its negative impact, it is surprising that evidence-based disease definitions and diagnostic strategies are lacking. This systematic review summarizes available data to facilitate development and validation of diagnostics, patient-reported outcomes, and imaging indices specific to this condition.

Methods
A literature search was conducted. Consensus or classification criteria, case series, cross-sectional studies, cohort studies, and randomized controlled trials related to diagnosis were included.

Results
A total of 44 studies reporting data on approximately 1500 patients with pSpA were eligible for analysis. Data quality across studies was only graded as fair to good. Due to large heterogeneity, meta-analysis was not possible. The majority of studies incorporated patient-reported outcomes and a physical examination. A total of 13 studies proposed or validated screening tools, consensus, classification, or consensus criteria. A total of 28 studies assessed the role of laboratory tests, none of which were considered sufficiently accurate for use in diagnosis. A total of 17 studies assessed the role of imaging, with the available literature insufficient to fully endorse any imaging modality as a robust diagnostic tool.

Conclusions
This review highlights existing inconsistency and lack of a clear diagnostic approach for IBD-associated pSpA. Given the absence of an evidence-based approach, a combination of existing criteria and physician assessment should be utilized. To address this issue comprehensively, our future efforts will be directed toward pursuit of a multidisciplinary approach aimed at standardizing evaluation and diagnosis of IBD-associated pSpA.