bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualizing genomic evolution in Caenorhabditis through WormSynteny
Authors: Bouvarel Lilly , Liu Dongyao , Zheng Chaogu 
Published: October 2024

AbstractUnderstanding the syntenic relationships among genomes is crucial to elucidate the genomic mechanisms that drive the evolution of species. The nematode Caenorhabditis is a good model for studying genomic evolution due to the well-established biology of Caenorhabditis elegans and the availability of > 50 genomes in the genus. However, effective alignment of more than ten species in Caenorhabditis has not been conducted before, and there is currently no tool to visualize the synteny of more than two species. In this study, we used Progressive Cactus, a recently developed multigenome aligner, to align the genomes of eleven Caenorhabditis species. Through the progressive alignment, we reconstructed nine ancestral genomes, analyzed the mutational types that cause genomic rearrangement during speciation, and found that insertion and duplication are the major driving forces for genome expansion. Dioecious species appear to expand their genomes more than androdioecious species. We then built an online interactive app called WormSynteny to visualize the syntenic relationship among the eleven species. Users can search the alignment dataset using C. elegans query sequences, construct synteny plots at different genomic scales, and use a set of options to control alignment output and plot presentation. We showcased the use of WormSynteny to visualize the syntenic conservation of one-to-one orthologues among species, tandem and dispersed gene duplication in C. elegans, and the evolution of exon and intron structures. Importantly, the integration of orthogroup information with synteny linkage in WormSynteny allows the easy visualization of conserved genomic blocks and disruptive rearrangement. In conclusion, WormSynteny provides immediate access to the syntenic relationships among the most widely used Caenorhabditis species and can facilitate numerous comparative genomics studies. This pilot study with eleven species also serves as a proof-of-concept to a more comprehensive larger-scale analysis using hundreds of nematode genomes, which is expected to reveal mechanisms that drive genomic evolution in the Nematoda phylum. Finally, the WormSynteny software provides a generalizable solution for visualizing the output of Progressive Cactus with interactive graphics, which would be useful for a broad community of genome researchers.
Lactuca super-pangenome reduces bias towards reference genes in lettuce research
Authors: van Workum Dirk-Jan M. , Mehrem Sarah L. , Snoek Basten L. , Alderkamp Marrit C. , Lapin Dmitry , Mulder Flip F. M. , Van den Ackerveken Guido , de Ridder Dick , Schranz M. Eric , Smit Sandra 
Published: October 2024

AbstractBackgroundBreeding of lettuce (Lactuca sativaL.), the most important leafy vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild relatives to provide the necessary genetic diversity. In this study, we constructed a super-pangenome based on fourLactucaspecies (representing the primary, secondary and tertiary gene pools) and comprising 474 accessions. We include 68 newly sequenced accessions to improve cultivar coverage and add important foundational breeding lines.ResultsWith the super-pangenome we find substantial presence/absence variation (PAV) and copy-number variation (CNV). Functional enrichment analyses of core and variable genes show that transcriptional regulators are conserved whereas disease resistance genes are variable. PAV-genome-wide association studies (GWAS) and CNV-GWAS are largely congruent with single-nucleotide polymorphism (SNP)-GWAS. Importantly, they also identify several major novel quantitative trait loci (QTL) for resistance againstBremia lactucaein variable regions not present in the reference lettuce genome. The usability of the super-pangenome is demonstrated by identifying the likely origin of non-reference resistance loci from the wild relativesLactuca serriola,Lactuca salignaandLactuca virosa.ConclusionsThe super-pangenome offers a broader view on the gene repertoire of lettuce, revealing relevant loci that are not in the reference genome(s). The provided methodology and data provide a strong basis for research into PAVs, CNVs and other variation underlying important biological traits of lettuce and other crops.
Exploring the health challenges of affected people in the 2023 Khoy earthquake: a content analysis
Authors: Akbarbegloo Masumeh , Heydari Ahad , Sanaeefar Mahnaz , Fallah-Aliabadi Saeed 
Published: October 2024

Abstract
Background
An earthquake has significant effects on health and livelihood of people. It is important to identify health needs and challenges of earthquake victims and use them to prepare for other possible earthquakes. Therefore, the purpose of this study is to explain the challenges and health needs of earthquake victims in Iran.

Methods
This was a qualitative study with 25 participation who were affected by the earthquake in Khoy City, and were selected using purposive sampling by snowball method technique in 2023. The study data was collected through open and semi-structured interviews. To analyze the data, the conventional content analysis with an inductive approach was used.

Results
The results show two main categories. The main categories “Management as a missing link in unexpected events” includes 9 subcategories: “The challenge of access to emergency resources and health facilities”, “Feeling of abandonment in medical personnel”, “Weakness in the structural safety and infrastructure of the health system”, “Logistical challenges”, “Risk management training”, “Crisis response management challenges”, “Weakness in the intelligent relief system”, “Management of secondary incidents”, and “Need to provide medical services and disease prevention”. Also, the main categories “Emotional actions of people in crisis” consist of 5 subcategories: “Overexcitement”, “Psychological vulnerability of children”, “Physical complaints caused by stress”, “Confusion caused by the lack of reliable information sources” and “Negative effects of living together with several families”.

Conclusion
To help deal with threats and other challenges in the earthquake crisis, countries should try to improve their capacity to manage natural disasters.
Trends in maternal body mass index, macrosomia and caesarean section in first-time mothers during the pandemic: a multicentre retrospective cohort study of 12 Melbourne public hospitals
Authors: Goldsack Andrew J. , Marzan Melvin B. , Rolnik Daniel L. , Lindquist Anthea C. , Said Joanne M. , Palmer Kirsten R. , Sheehan Penelope M. , Potenza Stephanie , Pritchard Natasha , Whitehead Clare L. , Ford Jolyon , Mol Ben W. , Walker Susan P. , Hui Lisa 
Published: October 2024

Abstract
Objective
To compare specific perinatal outcomes in nulliparas with a singleton infant in cephalic presentation at term, with and without exposure to the COVID-19 pandemic during pregnancy. We hypothesised that the pandemic conditions in Melbourne may have been an independent contributor to trends in maternal Body Mass Index ≥ 25 kg/m2, macrosomia and caesarean section.

Design
Multi-centre retrospective cohort study and interrupted time-series analysis.

Setting
Metropolitan Melbourne, Victoria.

Population
Singleton infants ≥ 20 weeks gestational age born between 1 January 2019 and 31 March 2022.

Main outcome measures
Rates of maternal Body Mass Index ≥ 25 kg/m2, macrosomia (birthweight ≥ 4000 g) and caesarean section.

Results
25 897 individuals gave birth for the first time to a singleton infant in cephalic presentation at term in the pre-pandemic cohort, and 25 298 in the pandemic-exposed cohort. Interrupted time-series analysis demonstrated no significant additional effect of the pandemic on pre-existing upward trends in maternal Body Mass Index ≥ 25 kg/m2, caesarean section or macrosomia. The rate of maternal Body Mass Index ≥ 25 kg/m2 was higher in the pandemic-exposed cohort compared with the pre-pandemic cohort, (45.82% vs. 44.58% respectively, p = 0.041) as was the overall rate of caesarean section (33.09% vs. 30.80%, p < 0.001). However, this increase in caesarean section was confined to individuals who had either an induction of labour or no labour. There was also a nonsignificant trend to higher rates of macrosomia in the pandemic-exposed cohort compared with the pre-pandemic cohort (8.55% vs. 7.99% respectively, p = 0.124).

Conclusions
While rates of Body Mass Index ≥ 25 kg/m2, pre-labour caesarean section, and caesarean section following induction of labour were higher among pandemic-exposed nulliparas, these findings represented a continuation of pre-existing upward trends, with no significant independent contribution from the pandemic. These trends are forecast to continue, with long term implications for population health.
Osseodensification versus piezoelectric internal sinus elevation (PISE) technique in delayed implant placement (a randomized controlled clinical trial)
Authors: Samir Mohammed , Bissar Mohamed Wagdy , Abuel-Ela Hala Ahmed 
Published: October 2024

AbstractTransalveolar sinus elevation is a minimally invasive technique aimed at augmenting the vertical bone height in the posterior maxilla, facilitating successful implant placement in areas with insufficient bone volume. This study compares the efficacy of osseodensification and piezoelectric internal sinus elevation (PISE) techniques in delayed implant placement. The primary objective was to radiographically assess vertical bone gain and bone density, while secondary objectives included clinical assessment of primary implant stability and post-operative satisfaction of both patients and operators. The study population of a total of 16 patients was randomly divided into two groups. Group 1 underwent osseodensification sinus lift using sticky bone as a graft material, whereas Group 2 received PISE with the same graft material. Results indicated that the osseodensification technique led to greater bone gain, improved bone density, and shorter surgical duration. Additionally, osseodensification was associated with enhanced rapid healing and higher patient satisfaction. Conversely, the PISE technique demonstrated superior primary stability of implants on the day of surgery. These findings suggest that while both techniques are effective, osseodensification may offer advantages in terms of bone gain, density, and patient satisfaction, making it a reliable method for enhancing rapid healing in delayed implant placement. the study was registered on clinicaltrials.gov at 26th September 2023 and clinical trials ID is NCT06055127.
Navigating transitions into, through, and beyond peer worker roles: insider insights from the Supporting Harm Reduction through Peer Support (SHARPS) study
Authors: Dumbrell Josh , Carver Hannah , Foster Rebecca , Pauly Bernie , Steele Wez , Roy Michael , Parkes Tessa 
Published: October 2024

Abstract
Background
Peer workers are individuals who draw on their personal experiences in a professional capacity to support clients. Existing research on the role of peer workers in mental health, homelessness, and substance use services has primarily focused on their impact on client outcomes. This paper describes the development of peer workers as they transition into, through, and beyond this role. Utilising data from the Supporting Harm Reduction through Peer Support (SHARPS) study, where Peer Navigators supported people experiencing homelessness and substance use challenges, this paper explores the sense-making involved in an intensive peer support worker role, adaptation to organisational culture, and engagement with opportunities for professional advancement.

Methods
Semi-structured interviews with three Peer Navigators were conducted by two SHARPS study researchers at four time points in 2018 and 2019 corresponding with the beginning, middle, and end of the intervention. These data were analysed along with entries from the three Peer Navigators’ reflective diaries. Analysis followed a multi-stage approach to thematic analysis utilising both inductive and deductive processes. The Peer Navigators’ personal reflections have also been incorporated into the recommendations.

Results
The foundational training provided to the Peer Navigators before taking up their role helped to ensure readiness and build confidence. This training illuminated the dynamics of supporting individuals with complex health and social challenges. Integrating into diverse organisational environments, the Peer Navigators adapted to new professional expectations and consistently advocated for harm reduction and psychologically informed approaches, sometimes encountering resistance from other professionals. Establishing effective relationships with participants and professionals was essential and involved dealing with challenges such as overcoming personal biases and navigating systemic obstacles. the Peer Navigators benefitted from the specially designed training to support career progress with personal and professional development opportunities which enabled successful transitions beyond the SHARPS study.

Conclusions
Pre-work training, coupled with support and adherence to key principles, enabled the Peer Navigators to integrate effectively into diverse organisations. Quality relationships were vital in achieving client outcomes and supporting the professional growth of the Peer Navigators. These findings are important for services employing peer workers and underscore the importance of a commitment to training and continuing professional development.
Transcriptional responses to direct and indirect TGFB1 stimulation in cancerous and noncancerous mammary epithelial cells
Authors: Janus Patryk , Kuś Paweł , Jaksik Roman , Vydra Natalia , Toma-Jonik Agnieszka , Gramatyka Michalina , Kurpas Monika , Kimmel Marek , Widłak Wiesława 
Published: October 2024

Abstract
Background
Transforming growth factor beta (TGFβ) is important for the morphogenesis and secretory function of the mammary gland. It is one of the main activators of the epithelial–mesenchymal transition (EMT), a process important for tissue remodeling and regeneration. It also provides cells with the plasticity to form metastases during tumor progression. Noncancerous and cancer cells respond differently to TGFβ. However, knowledge of the cellular signaling cascades triggered by TGFβ in various cell types is still limited.

Methods
MCF10A (noncancerous, originating from fibrotic breast tissue) and MCF7 (cancer, estrogen receptor-positive) breast epithelial cells were treated with TGFB1 directly or through conditioned media from stimulated cells. Transcriptional changes (via RNA-seq) were assessed in untreated cells and after 1–6 days of treatment. Differentially expressed genes were detected with DESeq2 and the hallmark collection was selected for gene set enrichment analysis.

Results
TGFB1 induces EMT in both the MCF10A and MCF7 cell lines but via slightly different mechanisms (signaling through SMAD3 is more active in MCF7 cells). Many EMT-related genes are expressed in MCF10A cells at baseline. Both cell lines respond to TGFB1 by decreasing the expression of genes involved in cell proliferation: through the repression of MYC (and the protein targets) in MCF10A cells and the activation of p63-dependent signaling in MCF7 cells (CDKN1A and CDKN2B, which are responsible for the inhibition of cyclin-dependent kinases, are upregulated). In addition, estrogen receptor signaling is inhibited and caspase-dependent cell death is induced only in MCF7 cells. Direct incubation with TGFB1 and treatment of cells with conditioned media similarly affected transcriptional profiles. However, TGFB1-induced protein secretion is more pronounced in MCF10A cells; therefore, the signaling is propagated through conditioned media (bystander effect) more effectively in MCF10A cells than in MCF7 cells.

Conclusions
Estrogen receptor-positive breast cancer patients may benefit from high levels of TGFB1 expression due to the repression of estrogen receptor signaling, inhibition of proliferation, and induction of apoptosis in cancer cells. However, some TGFB1-stimulated cells may undergo EMT, which increases the risk of metastasis.
Effects of platelet-rich plasma combined with exercise therapy for one year on knee osteoarthritis: retrospective cohort study
Authors: Kawahara Tsuneo , Iida Shuhei , Isoda Kazuma , Kim Sungdo 
Published: October 2024

Abstract
Background
Platelet-rich plasma (PRP) is a promising treatment for knee osteoarthritis (OA). However, exercise therapy and activities of daily living (ADL) guidance are recommended as core treatments in the Osteoarthritis Research Society International (OARSI) guidelines. However, the effects of PRP combined with exercise therapy are not fully understood. This study aimed to clarify the effectiveness of this treatment.

Methods
We assigned patients diagnosed with knee OA and treated between January 2021 and December 2022 to groups who underwent PRP + exercise (PE), PRP (P), or exercise (E) therapy. Outcomes were evaluated using Knee Injury and Osteoarthritis Outcome Scores (KOOS) before, and 1, 3, and 12 months after treatment. Within-group comparisons according to the time of each score were statistically assessed using a one-way analysis of variance, then differences were analyzed using Bonferroni multiple comparisons p < 0.05). Treatment responses were determined using Outcome Measures in Rheumatology (OMERACT)-OARSI Responder criteria.

Results
Pre-treatment KOOS did not significantly differ among the groups. Pain in the PE group improved within 1 month, symptoms, ADL, and quality of life (QOL) improved after 3, months and continued for 12 months. Pain and symptoms improved in the P group within 1 month, but ADLs and the QOL did not significantly change. Pain improved after 3 months in the E group and ADL, and QOL improved by 12 months. The response among the groups was the highest for the PE, with 50.0% at 1 and 3 months, and 65.0% at 12 months.

Conclusions
Therapy with PRP immediately relieved pain, whereas exercise conferred late, but enduring effects. Combining PRP with exercise conferred synergistic advantages that persisted for up to 12 months.
Measuring the impact of rare diseases in Tasmania, Australia
Authors: Scanlon Philippa , Ridler Garry , Say Genevieve , Kellett Miranda , Charlesworth Jac , Neil Amanda , Dickinson Joanne L. , Burdon Kathryn , Jose Matthew , Wallis Mathew 
Published: October 2024

Abstract
Background
An ongoing challenge with rare diseases is limited data and, consequently, limited knowledge about the collective prevalence and impact of these conditions on individuals, families, and the health system, particularly in rural and regional areas. Using existing datasets, this project aimed to examine the epidemiology of and hospital activity for Tasmanians with rare diseases.

Methods
Rare diseases were defined as non-infectious diseases with a prevalence of less than 1 in 2000. An initial resource set of 1028 ICD-10-AM diagnostic codes was used to identify a cohort of Tasmanians with rare diseases in Tasmanian Health datasets (1 January 2007 until 31 December 2020). Validating the resource set using a small group with known rare diseases revealed limitations in ascertainment, and so an expanded set of 1940 ICD-10-AM diagnostic codes was developed by cross-referencing ICD-10-AM codes with Orphanet data. Cohort hospital activity and admission costs were compared to statewide data for the final year of the study, 01 January 2020 to 31 December 2020.

Results
Using the resource set of 1028 ICD-10-AM diagnostic codes, the period prevalence of rare diseases in Tasmania across all age groups was estimated at 3.5%, with a point prevalence of 1.5% in December 2020. In 2020, 3384 individuals within the Tasmanian rare disease cohort, representing 0.6% of the Tasmanian population, accessed the public hospital system and accounted for 5.6% of all admissions. The mean length of stay for rare disease-related hospital admissions was 5.0 days, compared to 3.3 days for non-rare disease-related admissions. The mean cost per admission for the rare disease cohort was AUD$11,310, compared to AUD$6475 for all admissions statewide. In 2020, using the expanded resource set, the total cost of public hospital admissions in Tasmania was estimated to be AUD$979 million, with rare disease-related hospital admissions accounting for 9.1% of this cost, increasing to 19.0% when the costs for all admissions for the rare disease patients were included.

Conclusions
Patients with rare diseases had more admissions, longer length of stay, and a higher average cost per admission. Patients with rare diseases have a disproportionate impact on statewide hospital activity and costs in Tasmania.
Experiences of mothers of long-term surviving patients with cerebral adrenoleukodystrophy: a qualitative study
Authors: Koto Yuta , Hadano Nozomi , Sakai Norio 
Published: October 2024

Abstract
Background
Adrenoleukodystrophy (ALD) is an X-linked peroxisomal disorder. Its cerebral form presents as a learning and behavioral disorder that, if untreated, leads to rapid neurological regression, disability, and death within 10 years of diagnosis. Therefore, the disease significantly impacts patients’ quality of life, making quality of life assessment crucial for effective medical treatment and care. However, no disease-specific quality of life scale exists for ALD. Therefore, we conducted qualitative research to determine the experiences of patients and their families as a preliminary step toward developing one.

Results
Four mothers of patients with cerebral ALD were interviewed. Based on classification using the qualitative content analysis method, the verbatim transcripts were grouped into four themes: support needs for patients, support needs for families, the impact of treatment, and challenges within support systems.

Conclusions
Support for patients and family members is required after ALD is diagnosed. In addition to addressing symptoms, daily life support and caregiving burden should be considered. Furthermore, several challenges and opportunities exist for improving treatment and support systems. Therefore, combining appropriate supporters and support systems according to the progressive and hereditary characteristics of ALD is crucial.