bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perceptions of preschoolers and parents on forest pollution
Authors: Demirkaya Hilmi , Köç Ahmet , Sunay Serap , Duygu Hüseyin , Mol Aslı , Günaydın Gülsevil , Günaydın Muhammedi Abdulkerim 
Published: October 2024

IntroductionAn examination of preschool children’s perceptions and attitudes towards the environment and forests has recently been conducted. However, little research has focused on preschool children’s and their parents’ perceptions of clean and dirty forests. Investigating these perceptions is essential to increase children’s interest in and sensitivity to the environment, thereby fostering their development as responsible individuals who protect the natural world.MethodsThis study aimed to address this knowledge gap by examining the perceptions of clean and dirty forests held by 40 5–6-year-old students and 40 parents, randomly selected from two preschools: one attended by children from high socioeconomic families and the other by children from low socioeconomic families, in a Mediterranean coastal city in southwestern Turkey. A semi-structured questionnaire was used to collect sociodemographic information and perceptions of clean and dirty forests. Additionally, drawing sheets were distributed to the students to illustrate their concepts of clean and dirty forests.ResultsThe results indicated that individuals with higher educational levels had more complex and conscious perceptions of clean forests. Children considered abstract concepts, such as supernatural forces and fossil fuels, while parents focused on awareness and conservation status. Conversely, parents and children with lower levels of education tended to concentrate on more concrete and everyday factors, such as litter and natural disasters. Individuals with higher socioeconomic status generally associated forest cleanliness with conscious behaviors and conservation, whereas those with lower socioeconomic status linked it more with polluting factors.DiscussionThis investigation provides valuable insights into the management and control of local forests by incorporating the perspectives of children and their parents, promoting responsible and sustainable tourism practices.
GTasm: a genome assembly method using graph transformers and HiFi reads
Authors: Luo Junwei , Zhang Ziheng , Ma Xinliang , Yan Chaokun , Luo Huimin 
Published: October 2024

MotivationGenome assembly aims to reconstruct the whole chromosome-scale genome sequence. Obtaining accurate and complete chromosome-scale genome sequence serve as an indispensable foundation for downstream genomics analyses. Due to the complex repeat regions contained in genome sequence, the assembly results commonly are fragmented. Long reads with high accuracy rate can greatly enhance the integrity of genome assembly results.ResultsHere we introduce GTasm, an assembly method that uses graph transformer network to find optimal assembly results based on assembly graphs. Based on assembly graph, GTasm first extracts features about vertices and edges. Then, GTasm scores the edges by graph transformer model, and adopt a heuristic algorithm to find optimal paths in the assembly graph, each path corresponding to a contig. The graph transformer model is trained using simulated HiFi reads from CHM13, and GTasm is compared with other assembly methods using real HIFI read set. Through experimental result, GTasm can produce well assembly results, and achieve good performance on NA50 and NGA50 evaluation indicators. Applying deep learning models to genome assembly can improve the continuity and accuracy of assembly results. The code is available from https://github.com/chu-xuezhe/GTasm.
Family planning knowledge, use, and associated factors among women with mental illness and epilepsy in Rwanda: a cross-sectional study
Authors: Mukangabire Pacifique , Umuziga M. Providence , Umubyeyi Benoite , Mukamana Donatilla , Gishoma Darius , Baziga Vedaste , Uwimana Philomene , Sebera Fidele , Bazirete Olive , Kanazayire Clementine 
Published: October 2024

IntroductionFamily planning knowledge and access to quality family planning services occupy a central position in the lives of all women of reproductive age. However, women with mental illness and epilepsy who are at a high risk of sexual violence, unwanted pregnancies, poor obstetric outcomes, and drug interaction consequences, need it the most. Understanding their family planning knowledge and utilization remains crucial for meeting their needs. The present study aims to assess knowledge, use of family planning, and associated factors among women living with mental illness and epilepsy who attend the Ndera Neuropsychiatric Hospital and affiliated branches.MethodologyA cross-sectional study was conducted between October 2022 and February 2023. The study involved a purposive sample of 289 women who attended the Ndera Neuropsychiatric Hospital and its two affiliated branches during the data collection period. Psychiatric nurses administered a structured questionnaire. Data were analyzed using descriptive statistics, and multiple logistic regression analysis was performed to assess the factors associated with the use of family planning methods.ResultsOut of 289 who participated in the study, the majority (96.9%) were aware of family planning methods, most (67.8%) had used one method once in their life course, a half (51.9%) were using a family planning method at the time of data collection, and a slight number (26%) expressed intentions of using a family planning method in the future. The most known and used methods were respectively the injectable (17.5%) and oral contraceptive pill (17.5%). Regarding the natural family planning methods, breastfeeding and withdrawal were less used. Being single (AOR = 66.4, 95% CI: 9.8, 44) or married (AOR = 51.4, 95% CI: 11.9–22), having a primary level of education (AOR = 5.6, 95% CI: 2.0, 15.9), knowing a contraceptive method (AOR = 5.8, 95% CI: 0.6, 49) and suffering from brief psychotic disorders (AOR = 2.7, 95% CI: 1.1, 6.6) predicted a higher utilization of family planning.ConclusionMost of the women with mental illness in this study were aware of family planning methods and had used one of the family planning methods in life. The national average is below when it comes to family planning awareness. It is important to improve family planning education and counseling for women who attend psychiatric outpatient clinics.
Obstetric violence and associated factors among women who gave birth at public hospitals in Addis Ababa city administration, Ethiopia
Authors: Simeneh Getinet Tilahun , Tesema Getaye Worku , Seifu Befikad Assefa , Tafesse Nebiyou , Hailemariam Abemelek Zegeye , Suleyiman Feruza Mehammed , Nigatu Digafe Tsegaye 
Published: October 2024

BackgroundObstetric violence during labor and delivery is one of the main reasons that women do not seek care from health caregivers in health facilities. Developing respectful maternity care services for women is the most important approach to ensure better newborn and maternal outcomes.ObjectiveThis study aimed to assess the magnitude of obstetric violence and associated factors among women who gave birth at public hospitals in Addis Adaba city administration, Ethiopia.MethodsAn institution-based cross-sectional study was carried out among 409 mothers who had given birth at two public hospitals (Gandhi Memorial Hospital and Abebech Gobena Mothers and Children's Health Hospital) in Addis Ababa, Ethiopia, from 1 to 30 May 2023. A systematic sampling method was applied and data were collected using a structured face-to-face interview questionnaire and entered into EpiData 3.1. The data were analyzed using Statistical Package for Social Science version 25. Bi-variable and multivariate analyses were performed. Statistical significance was declared at a P-value &lt;0.05.ResultsIn total, 318 mothers [77.8% with a 95% CI (73.64–81.96)] had experienced obstetric violence in the study settings. Being more educated [Adjusted Odds Ratio (AOR) = 6.43; 95% CI 2.92–14.17], having ≥4 antenatal care contacts (AOR = 3.59; 95% CI 1.91–6.75), being multiparous (AOR = 2.65; 95% CI 1.32–5.32), induction of labor (AOR = 3.39; 95% CI 1.69–6.79), vaginal delivery (AOR = 0.25; 95% CI 0.11–0.62), and female birth attendants AOR = 2.42, 95% CI (1.31–4.47) were significantly associated with obstetric violence.ConclusionMore than three-fourths of the participants experienced obstetric violence. Thus, stakeholders need to develop interventions by taking all risk factors of obstetric violence into account.
Increased thrombin generation in kidney transplant recipients with donor-specific antibodies directed against human leukocyte antigens
Authors: Lóczi Linda , P. Szabó Réka , Orbán-Kálmándi Rita , Hodossy-Takács Rebeka , Szilvási Anikó , Szalai Zoltán , Nagy Gábor , Antal-Szalmás Péter , Nemes Balázs , Bagoly Zsuzsa 
Published: October 2024

IntroductionThe development of de novo anti-HLA donor specific antibodies (DSAs) is associated with poor outcomes in kidney transplant recipients. It is surmised that an interaction between DSAs and the graft endothelium cause tissue injury, however, the exact underlying pathomechanism and optimal management of patients with DSAs remain undetermined.AimsWe hypothesized that in kidney transplant recipients the presence of DSAs induce hemostasis alterations, including hypercoagulability, as assessed by the thrombin generation assay (TGA). Patients and methods. In this observational cohort study, 27 kidney transplant recipients with DSAs (DSA+ group) and 16 without DSAs (DSA– group) were enrolled. Venous blood samples were obtained, and besides routine laboratory tests, von Willebrand factor antigen (VWF), FVIII activity, soluble E selectin (sEsel), soluble P selectin (sPsel), TGA, clot lysis assay (CLA), complement levels (C3, C4) were measured. To correlate results with potential changes in DSA status over time, patients were followed and reassessed 6 ± 1.5 months later.ResultsVWF and sPsel did not differ between groups, but both parameters were increased in the majority of patients. Endogenous thrombin potential (ETP) was significantly higher in the DSA+ group as compared to DSA– patients (median:1666; IQR:1438-2012 vs. 1230; IQR:1097-1659 nM*min, p=0.0019). Follow-up measurements indicated that the observed hemostasis alterations were not transient. CLA parameters, C3 and C4 did not differ between DSA+ and DSA– groups. The extent of anti-HLA II DSA positivity correlated positively with ETP, while tacrolimus levels negatively correlated with ETP and VWF/FVIII levels.ConclusionsIn patients with anti-HLA class II DSAs, thrombin generation was significantly increased as compared to DSA– kidney transplant recipients, suggesting that the presence of antibodies is associated with hypercoagulability. Tacrolimus levels were negatively associated with TGA parameters. Hypercoagulability, associated with the presence of DSAs, may potentially contribute to the pathomechanism of antibody-mediated graft injury, warranting future prospective studies.
A novel functional IKBKE variant activating NFAT in a patient with polyarthritis and a remittent fever
Authors: Yamada Saeko , Nagafuchi Yasuo , Yamada Mamiko , Suzuki Hisato , Natsumoto Bunki , Ota Mineto , Takazawa Ikuo , Hatano Hiroaki , Kono Masanori , Harada Hiroaki , Shoda Hirofumi , Okamura Tomohisa , Kosaki Kenjiro , Fujio Keishi 
Published: October 2024

BackgroundIKBKE is a negative regulator of T cell activation and one of the key activators of type I interferon (IFN) and NFκB signaling via non-classical pathways. The upstream single nucleotide polymorphism of IKBKE (rs2297550-G) is a genome-wide association study risk variant of systemic lupus erythematosus, and is associated with decreased IKBKE expression in T cells by expression quantitative trait locus analysis.Case presentationA 48-year-old female had a remittent fever, arthritis, and oral ulcers for 20 years. She had a poor response to corticosteroids or disease-modifying antirheumatic drugs, including the tumor necrosis factor-α antagonist, etanercept, and the anti-interleukin-6 receptor antibody, tocilizumab.MethodShe participated in the Initiative on Rare and Undiagnosed Disease (IRUD), and whole-exome sequencing (WES) was performed. Functional analyses were conducted by transfecting the identified variants into reporter cells to assess the activation of NFAT and NFκB signaling. Additionally, peripheral blood RNA- sequencing (RNA-seq) data were compared with those from healthy individuals to evaluate the gene expression profiles of immune cells.ResultWES identified a novel heterozygous c.1877G&gt;A, p(Cys626Tyr) variant in IKBKE. Functional analysis indicated that this variant led to increased activity of NFAT (p = 0.015) and decreased activity of NFκB and type I IFN (p = 0.00068 and 0.00044, respectively). The patient had a remarkably low proportion of Naïve CD4 T cells. RNA-seq of peripheral blood immune cell subsets revealed significant differences in gene expression, especially in T cells.ConclusionA novel functional heterozygous variant in IKBKE is described in a patient with a remittent fever and arthritis. The data suggest that IKBKE is an important negative regulator of inflammation, particularly in T cells, and this IKBKE variant might be the underlying cause of a novel autoinflammatory pathology.
Intestinal barrier damage contributes to a higher prevalence of frailty in aging people living with HIV: a retrospective case control study in a Chinese cohort
Authors: Xu Xiaolei , Ouyang Jing , Yan Jiangyu , Lu Yanqiu , Harypursat Vijay , Wu Hao , Chen Yaokai 
Published: October 2024

BackgroundIt has been previously demonstrated that intestinal barrier damage is one of the underlying mechanisms leading to frailty in non-HIV-infected aging populations. However, there is a paucity of direct evidence which demonstrates the association between intestinal barrier damage and frailty in people living with HIV (PLWH).MethodsThe present study is a retrospective case control study. Participants older than 50 years old were stratified into a frail/pre-frail group (case group) and non-frail group (control group) according to the Fried frailty phenotype. We collected and curated data concerning socio-demographic variables, psychological states and social functioning, and clinical information associated with the identification of biomarkers of intestinal barrier damage, microbial translocation, and levels of inflammatory cytokines of participants.ResultsThe case group had significantly higher levels of Reg-3α (p=0.042) and I-FABP (p=0.045) compared to the control group. We further observed, after adjusting for confounding factors by logistic regression analysis, that I-FABP levels remained significantly higher in the case group compared to the control group (p=0.033). Also, Fried Phenotype scores positively correlated with I-FABP levels (rs=0.21, p=0.01), LPS levels (rs=0.20, p=0.02), and sCD14 levels (rs=0.18, p=0.04). Moreover, the study confirmed both the positive correlation between inflammatory cytokines (IL-6 and IP-10) with frailty in aging PLWH, and between inflammatory cytokines (IL-6, IL-8 and IP-10) with biomarkers of intestinal barrier dysfunction in older PLWH.ConclusionThe present study indicates that the inflammation induced by intestinal barrier damage/dysfunction is likely to contribute to frailty in aging PLWH.
Assessing the impact of a potential canine vaccine for the control of Chagas disease: a mathematical modeling study
Authors: Fiatsonu Edem , Deka Aniruddha , Ndeffo-Mbah Martial L. 
Published: October 2024

IntroductionChagas disease, a zoonotic infection transmitted by triatomine bugs, poses serious public health risks in endemic areas. As dogs are important reservoirs in the disease’s spread, developing a canine vaccine could be transformative for controlling disease transmission to dogs and humans.MethodsWe developed a compartmental Susceptible-Infected model to simulate the transmission dynamics of Trypanosoma cruzi, considering interactions among dogs, humans, cats, rodents, and triatomine vectors. We used the model to assess the direct and indirect impacts of two vaccine mechanisms—all-or-nothing and leaky—on disease incidence across different host populations. The sensitivity of the model’s outcomes to changes in input parameters was analyzed using univariate sensitivity analysis.ResultsOur model showed that with a 90% vaccine efficacy, an all-or-nothing vaccine could reduce the cumulative incidence of T. cruzi in dogs by 91.3% over five years. The 60% and 30% vaccine efficacies would result in reductions of 63.47% and 33%, respectively, over 5 years. Similarly, the leaky vaccine achieved a 92.62% reduction in dog infections over 5 years with 90% efficacy. The indirect effects on human T. cruzi infection were notable; the all-or-nothing vaccine reduced human disease incidence by 14.37% at 90% efficacy, while the leaky vaccine achieved a 32.15% reduction over 5 years. Both vaccine mechanisms may substantially reduce T. cruzi incidence among dogs, and generate indirect benefit to other hosts, such as humans, by reducing their infection risk. The indirect benefits of vaccination were heavily influenced by the proportion of triatomine bugs blood meals taken from dogs.DiscussionThe study highlights the potential of targeted canine vaccination in controlling Chagas disease transmission and burden in endemic countries. It provides additional evidence for pursuing the development of a canine vaccine as a valuable tool for Chagas disease elimination.
Proteome-wide Mendelian randomization provides novel insights into the pathogenesis and druggable targets of osteoporosis
Authors: Yan Jingchuan , Huai Ying , Liang Qi , Lin Li , Liao Bo 
Published: October 2024

BackgroundWith the aging population, the prevalence and impact of osteoporosis are expected to rise, and existing anti-osteoporosis agents have limitations due to adverse events. This study aims to discover novel drug targets for osteoporosis.MethodsThe protein data were obtained from the latest proteome-wide association studies (PWAS) including 54, 219 participants. The osteoporosis data were extracted from a GWAS meta-analysis, characterized by heel bone mineral density (HBMD) comprising 426,824 individuals. Mendelian randomization (MR) was the primary approach used to establish genetic causality between specific traits. Summary-data-based MR (SMR), colocalization analysis, heterogeneity test, and external validation were applied to ensure the findings were reliable. The underlying mechanisms behind these causal associations were investigated by additional analyses. Finally, the druggability of the identified proteins was assessed.ResultsAfter Bonferroni correction, a total of 84 proteins were found to have a genetic association with osteoporosis. With strong colocalization evidence, proteins such as ACHE, HS6ST1, LRIG1, and LRRC37A2 were found to negatively influence HBMD, whereas CELSR2, CPE, FN1, FOXO1, and FSHB exhibited a positive association with HBMD. No significant heterogeneity was found. Additionally, CELSR2, FN1, FSHB, HS6ST1, LRIG1, and LRRC37A2 were replicated in the external validation. The effect of FSHB on HBMD was more pronounced in females compared to males. Interestingly, ACHE, LRIG1, FN1, and FOXO1 were observed to partially act on HBMD through BMI. Phewas analysis indicated that CPE and FOXO1 did not have genetic associations with any phenotypes other than osteoporosis. FN1 was highlighted as the most significant protein by protein-protein interaction network analysis.ConclusionIn conclusion, this study offers valuable insights into the role of specific proteins in the development of osteoporosis, and underscores potential therapeutic targets. Future studies should emphasize exploring these causal relationships and elucidating their underlying mechanisms.
Analysis of lactic acid bacteria species in Miang, a post-fermented tea in Thailand, and their potential use as probiotics
Authors: Horie Masanori , Ruengsomwong Supatjaree , Ohmiya Yoshihiro 
Published: October 2024

IntroductionMiang is one of the post-fermented teas made in Northern Thailand. Although lactic acid bacteria are involved in fermentation of Miang, details are still not clear. This study investigated the diversity of Lactobacillaceae bacteria, related to fermentation of Miang. Probiotic potential of isolated Lactobacillaceae bacteria was examined.MethodsLactobacillaceae bacteria were isolated from 52 Miang samples collected from three provinces in northern Thailand and identified by MALDI-TOF MS. Hemolytic activity, antibiotic susceptibility, antimicrobial activity and tolerance to gastrointestinal juice were examined for probiotic potential of isolates.ResultsA total of 1,181 Lactobacillaceae bacteria strains were isolated from Miang. The most abundant isolates were Lactiplantibacillus pentosus. Besides Lactiplantibacillus plantarum, Levilactobacillus brevis, Paucilactobacillus suebicus, Lacticaseibacillus pantheris, and Secundilactobacillus collinoides were also found with frequency. Of these isolates, 450 with a high score for MALDI-TOF identification were then screened for probiotic ability. Most isolates were resistant to aminoglycosides and clindamycin. Then, 35 isolates were tested for their antimicrobial activity against pathogens using the well diffusion method, and 31 isolates exhibited inhibition zones against Staphylococcus aureus, Staphylococcus epidermidis, Salmonella enterica serovar Typhimurium, S. enterica serovar Enteritidis, Listeria monocytogenes, Propionibacterium acnes, and Streptococcus mutans. All 31 isolates were non-hemolytic and readily tolerated simulated gastric juice at pH 3 and simulated intestinal juice at pH 8.DiscussionMiang contains lactic acid bacteria that could potentially be used as probiotics.
The HALP (hemoglobin, albumin, lymphocyte, and platelet) score is associated with hemorrhagic transformation after intravenous thrombolysis in patients with acute ischemic stroke
Authors: Chen Jiahao , Hu Rui , Shang Lejia , Li Xiaoqin , Lin Yisi , Yao Yu , Hu Chuanchen 
Published: October 2024

BackgroundHemorrhagic transformation (HT) after intravenous thrombolysis (IVT) with rt-PA can precipitate rapid neurological deterioration, poor prognosis, and even death. The HALP score (hemoglobin, albumin, lymphocyte, and platelet) is a novel indicator developed to reflect both systemic inflammation and the nutritional status of patients. The goal of this study was to reveal the relationship between the HALP score and the risk of HT after IVT in people with acute ischemic stroke (AIS).MethodsA total of 753 patients with AIS were included in this study. Patients were divided into quartiles according to baseline HALP score. The HALP score was calculated as follows: hemoglobin (g/L) × albumin (g/L) × lymphocytes (/L)/platelets (/L). Binary logistic regression was used to reveal the connection between HALP score and HT.ResultsThe baseline HALP score were significantly lower in the HT than non-HT patients (p &lt; 0.001). The HALP score were divided into four quartiles: Q1 (&lt;27.4), Q2 (27.4–37.6), Q3 (37.7–49.6), Q4 (&gt;49.6), respectively. Moreover, the severity of HT increased with decreasing HALP level (p &lt; 0.001). In multivariable logistic regression, taking the Q4 as the reference, the association between Q1 and HT remained, after adjusting for confounding variables [odds ratio (OR) = 3.197, 95% confidence interval (CI) = 1.634–6.635, p = 0.003].ConclusionThe HALP value can predict the HT risk after IVT in patients with AIS. A lower HALP level was associated with an increased severity of HT post-IVT.