bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular crosstalk of mesangial cells and tubular epithelial cells in diabetic kidney disease
Authors: Jiang Shan , Su Hua 
Published: October 2023

AbstractDiabetic kidney disease (DKD) is a major cause of end-stage renal disease and imposes a heavy global economic burden; however, little is known about its complicated pathophysiology. Investigating the cellular crosstalk involved in DKD is a promising avenue for gaining a better understanding of its pathogenesis. Nonetheless, the cellular crosstalk of podocytes and endothelial cells in DKD is better understood than that of mesangial cells (MCs) and renal tubular epithelial cells (TECs). As the significance of MCs and TECs in DKD pathophysiology has recently become more apparent, we reviewed the existing literature on the cellular crosstalk of MCs and TECs in the context of DKD to acquire a comprehensive understanding of their cellular communication. Insights into the complicated mechanisms underlying the pathophysiology of DKD would improve its early detection, care, and prognosis.
Harnessing large language models (LLMs) for candidate gene prioritization and selection
Authors: Toufiq Mohammed , Rinchai Darawan , Bettacchioli Eleonore , Kabeer Basirudeen Syed Ahamed , Khan Taushif , Subba Bishesh , White Olivia , Yurieva Marina , George Joshy , Jourde-Chiche Noemie , Chiche Laurent , Palucka Karolina , Chaussabel Damien 
Published: October 2023

AbstractBackgroundFeature selection is a critical step for translating advances afforded by systems-scale molecular profiling into actionable clinical insights. While data-driven methods are commonly utilized for selecting candidate genes, knowledge-driven methods must contend with the challenge of efficiently sifting through extensive volumes of biomedical information. This work aimed to assess the utility of large language models (LLMs) for knowledge-driven gene prioritization and selection.MethodsIn this proof of concept, we focused on 11 blood transcriptional modules associated with an Erythroid cells signature. We evaluated four leading LLMs across multiple tasks. Next, we established a workflow leveraging LLMs. The steps consisted of: (1) Selecting one of the 11 modules; (2) Identifying functional convergences among constituent genes using the LLMs; (3) Scoring candidate genes across six criteria capturing the gene’s biological and clinical relevance; (4) Prioritizing candidate genes and summarizing justifications; (5) Fact-checking justifications and identifying supporting references; (6) Selecting a top candidate gene based on validated scoring justifications; and (7) Factoring in transcriptome profiling data to finalize the selection of the top candidate gene.ResultsOf the four LLMs evaluated, OpenAI's GPT-4 and Anthropic's Claude demonstrated the best performance and were chosen for the implementation of the candidate gene prioritization and selection workflow. This workflow was run in parallel for each of the 11 erythroid cell modules by participants in a data mining workshop. Module M9.2 served as an illustrative use case. The 30 candidate genes forming this module were assessed, and the top five scoring genes were identified as BCL2L1, ALAS2, SLC4A1, CA1, and FECH. Researchers carefully fact-checked the summarized scoring justifications, after which the LLMs were prompted to select a top candidate based on this information. GPT-4 initially chose BCL2L1, while Claude selected ALAS2. When transcriptional profiling data from three reference datasets were provided for additional context, GPT-4 revised its initial choice to ALAS2, whereas Claude reaffirmed its original selection for this module.ConclusionsTaken together, our findings highlight the ability of LLMs to prioritize candidate genes with minimal human intervention. This suggests the potential of this technology to boost productivity, especially for tasks that require leveraging extensive biomedical knowledge.
Outcomes of viral coinfections in infants hospitalized for acute bronchiolitis
Authors: Bermúdez-Barrezueta Lorena , López-Casillas Pablo , Rojo-Rello Silvia , Sáez-García Laura , Marugán-Miguelsanz José Manuel , Pino-Vázquez María de la Asunción 
Published: October 2023

Abstract
Background and Objective
The clinical relevance of the detection of multiple respiratory viruses in acute bronchiolitis (AB) has not been established. Our goal was to evaluate the effect of viral coinfections on the progression and severity of AB.

Methods
A retrospective observational study was conducted in a tertiary hospital in Spain from September 2012 to March 2020. Infants admitted for AB with at least one respiratory virus identified by molecular diagnostic techniques were included. A comparison was made between single-virus infections and viral coinfections. The evolution and severity of AB were determined based on the days of hospitalization and admission to the pediatric intensive care unit (PICU).

Results
Four hundred forty-five patients were included (58.4% male). The median weight was 5.2 kg (IQR 4.2–6.5), and the median age was 2.5 months (IQR 1.4–4.6). A total of 105 patients (23.6%) were admitted to the PICU. Respiratory syncytial virus (RSV) was the most frequent etiological agent (77.1%). A single virus was detected in 270 patients (60.7%), and viral coinfections were detected in 175 (39.3%), of which 126 (28.3%) had two viruses and 49 (11%) had three or more viruses. Hospital length of stay (LOS) increased in proportion to the number of viruses detected, with a median of 6 days (IQR 4–8) for single infections, 7 days (IQR 4–9) for coinfections with two viruses and 8 days (IQR 5–11) for coinfections with ≥ 3 viruses (p = 0.003). The adjusted Cox regression model showed that the detection of ≥ 3 viruses was an independent risk factor for a longer hospital LOS (HR 0.568, 95% CI 0.410–0.785). No significant association was observed between viral coinfections and the need for PICU admission (OR 1.151; 95% CI 0.737–1.797).

Conclusions
Viral coinfections modified the natural history of AB, prolonging the hospital LOS in proportion to the number of viruses detected without increasing the need for admission to the PICU.
A massive immature mediastinal teratoma treated with chemotherapy and surgical resection: a case report
Authors: Mardani Parviz , Kamran Hooman , Ghaderpanah Rezvan , Geramizadeh Bita , Fouladi Damoun , Shahriarirad Reza , Amirian Armin 
Published: October 2023

Abstract
Background
Teratoma is a type of germ cell tumor consisting of one or multiple tissues derived from germinal layers. The location and size of the tumor can cause various presentations. Here we report one of the largest ever cases of immature cystic teratoma.

Case Presentation
In this report, we presented a 24-year-old patient with dyspnea, chest pain, nausea, and anorexia. A computed tomography scan revealed a giant, right-sided mass measuring about 190 × 150 × 140 mm. Chemotherapy was initiated for the patient, followed by thoracotomy. Histopathological evaluation revealed the nature of the mass to be an immature mediastinal teratoma.

Conclusion
the incidence of immature mediastinal teratoma is uncommon, and due to its rarity, the diagnosis needs more profound evaluation studies such as radiological and pathological assessments. Immature teratomas are optimally treated by a combination of chemotherapy and complete resection.
Maternal adverse childhood experiences (ACEs) and DNA methylation of newborns in cord blood
Authors: Collender Phillip , Bozack Anne K. , Veazie Stephanie , Nwanaji-Enwerem Jamaji C. , Van Der Laan Lars , Kogut Katherine , Riddell Corinne , Eskenazi Brenda , Holland Nina , Deardorff Julianna , Cardenas Andres 
Published: October 2023

AbstractBackgroundAdverse childhood experiences (ACEs) increase the risk of poor health outcomes later in life. Psychosocial stressors may also have intergenerational health effects by which parental ACEs are associated with mental and physical health of children. Epigenetic programming may be one mechanism linking parental ACEs to child health. This study aimed to investigate epigenome-wide associations of maternal preconception ACEs with DNA methylation patterns of children. In the Center for the Health Assessment of Mothers and Children of Salinas study, cord blood DNA methylation was measured using the Illumina HumanMethylation450 BeadChip. Preconception ACEs, which occurred during the mothers’ childhoods, were collected using a standard ACE questionnaire including 10 ACE indicators. Maternal ACE exposures were defined in this study as (1) the total number of ACEs; (2) the total number of ACEs categorized as 0, 1–3, and > 4; and (3) individual ACEs. Associations of ACE exposures with differential methylated positions, regions, and CpG modules determined using weighted gene co-expression network analysis were evaluated adjusting for covariates.ResultsData on maternal ACEs and cord blood DNA methylation were available for 196 mother/newborn pairs. One differential methylated position was associated with maternal experience of emotional abuse (cg05486260/FAM135Bgene;qvalue < 0.05). Five differential methylated regions were significantly associated with the total number of ACEs, and 36 unique differential methylated regions were associated with individual ACEs (Šidákpvalue < 0.05). Fifteen CpG modules were significantly correlated with the total number of ACEs or individual ACEs, of which 8 remained significant in fully adjusted models (pvalue < 0.05). Significant modules were enriched for pathways related to neurological and immune development and function.ConclusionsMaternal ACEs prior to conception were associated with cord blood DNA methylation of offspring at birth. Although there was limited overlap between differential methylated regions and CpGs in modules associated with ACE exposures, statistically significant regions and networks were related to genes involved in neurological and immune function. Findings may provide insights to pathways linking psychosocial stressors to health. Further research is needed to understand the relationship between changes in DNA methylation and child health.
Modelling in vitro gametogenesis using induced pluripotent stem cells: a review
Authors: Romualdez-Tan Maria Victoria 
Published: October 2023

AbstractIn vitro gametogenesis (IVG) has been a topic of great interest in recent years not only because it allows for further exploration of mechanisms of germ cell development, but also because of its prospect for innovative medical applications especially for the treatment of infertility. Elucidation of the mechanisms underlying gamete development in vivo has inspired scientists to attempt to recapitulate the entire process of gametogenesis in vitro. While earlier studies have established IVG methods largely using pluripotent stem cells of embryonic origin, the scarcity of sources for these cells and the ethical issues involved in their use are serious limitations to the progress of IVG research especially in humans. However, with the emergence of induced pluripotent stem cells (iPSCs) due to the revolutionary discovery of dedifferentiation and reprogramming factors, IVG research has progressed remarkably in the last decade. This paper extensively reviews developments in IVG using iPSCs. First, the paper presents key concepts from groundwork studies on IVG including earlier researches demonstrating that IVG methods using embryonic stem cells (ESCs) also apply when using iPSCs. Techniques for the derivation of iPSCs are briefly discussed, highlighting the importance of generating transgene-free iPSCs with a high capacity for germline transmission to improve efficacy when used for IVG. The main part of the paper discusses recent advances in IVG research using iPSCs in various stages of gametogenesis. In addition, current clinical applications of IVG are presented, and potential future applications are discussed. Although IVG is still faced with many challenges in terms of technical issues, as well as efficacy and safety, novel IVG methodologies are emerging, and IVG using iPSCs may usher in the next era of reproductive medicine sooner than expected. This raises both ethical and social concerns and calls for the scientific community to cautiously develop IVG technology to ensure it is not only efficacious but also safe and adheres to social and ethical norms.
Angiotensin(1-7) attenuates tooth movement and regulates alveolar bone response during orthodontic force application in experimental animal model
Authors: Abuohashish Hatem , Shahin Suliman , Alamri Abdulaziz , Salloot Zainah , Alhawaj Hussain , Omar Omar 
Published: October 2023

Abstract
Background
Renin–angiotensin system and its ACE2/Ang(1-7)/Mas receptor axis regulates skeletal response to multiple physiological and pathological conditions. Recent research suggested a vital role of Ang(1-7) in regulating alveolar bone metabolism and remodeling. In this context, this study evaluated the effects of the Ang(1-7)/Mas receptor axis on orthodontic tooth movement (OTM) and the alveolar bone response to mechanical load.

Methods
A coil spring was placed between the right maxillary first molar and the anterior tooth of Wistar rats to apply bidirectional mechanical force. Ang(1-7) with or without a specific Mas receptor antagonist (A779) was infused using subcutaneous osmotic pumps (200 and 400 ng/kg/min: respectively). Animals were killed after 5 and 14 days from the OTM procedure after the clinical evaluation of tooth movement and mobility. Morphometric analysis of alveolar bone structure was conducted using micro-CT and the histological picture was evaluated after H&E staining. Moreover, collagen fiber distribution was assessed using Picro-Sirius red stain. In addition, bone samples were collected from the pressure and tension sites around the anterior tooth for gene expression analysis.

Results
Ang(1-7) infusion suppressed the tooth movement and mobility after 14 days of the orthodontic force application. Additionally, Ang(1-7) infusion preserved the morphometric and histological structure of the alveolar bone at pressure and tension sides. These effects were abolished by adding A779 infusion. Collagen fiber distribution was dysregulated mainly by the A779 Mas receptor blockage. Ang(1-7) affected the bone formation, remodeling- and vascularity-related genes in the pressure and tension sides, suggesting a prominent suppression of osteoclastogenesis. Ang(1-7) also improved osteoblasts-related genes on the tension side, whereas the osteoclasts-related genes were augmented by A779 on the pressure side.

Conclusion
Collectively, the activation of Ang(1-7)/Mas receptor axis appears to hinder tooth movement and regulates alveolar bone remodeling in response to mechanical force.

Graphical abstract
Potential of algal-based products for the management of potato brown rot disease
Authors: Hamed Seham M. , Kamal Marwa , Messiha Nevein A. S. 
Published: October 2023

Abstract
Background
Ralstonia solanacearum causes potato brown rot disease, resulting in lower crop’s production and quality. A sustainable and eco-friendly method for controlling the disease is required. Algae’s bioactive chemicals have shown the potential to enhance plant defenses. For the first time, the efficacy of foliar application of Acanthophora spicifera and Spirulina platensis seaweed extracts, along with the utilization of dried algal biomasses (DABs) of Turbinaria ornata and a mixture of Caulerpa racemosa and Cystoseira myrica (1:1)on potato yield and brown rot suppression were investigated under field conditions. Field experiments were conducted in three locations: Location 1 (Kafr Shukr district, Kaliobeya governorate), Location 2 (Moneira district, Kaliobeya governorate), and Location 3 (Talia district, Minufyia governorate). Locations 1 and 2 were naturally infested with the pathogen, while location 3 was not. The study evaluated potato yield, plant nutritive status and antioxidants, soil available nitrogen-phosphorus-potassium (N-P-K), and organic matter percentage. Additionally, the shift in soil microbial diversity related to R. solanacearum suppression was examined for the most effective treatment.

Results
The results revealed that seaweed extracts significantly increased potato yield at all locations, which correlated with higher phosphorus absorption, while T. ornate DAB increased potato yield only at location 2, accompanied by noticeable increases in soil nitrogen and plant phosphorus. The mixed DABs of C. racemosa and C. myrica demonstrated greater disease suppression than foliar applications. The disease-suppressive effect of the mixed DABs was accompanied by significant increases in flavonoids and total antioxidant capacity (TAC). Moreover, the application of mixed DABs increased soil bacterial biodiversity, with a higher abundance of oligotrophic marine bacterial species such as Sphingopyxis alaskensis and growth-promoting species like Glutamicibacter arilaitensis, Promicromonospora sp., and Paenarthrobacter nitroguajacolicus in all three locations compared to the untreated control. Klebsiella sp., Pseudomonas putida, and P. brassicacearum abundances were increased by the mixed DABs in Location 1. These species were less abundant in locations 2 and 3, where Streptomyces sp., Bacillus sp., and Sphingobium vermicomposti were prevalent.

Conclusions
The results demonstrated that the used seaweed extracts improved potato yield and phosphorous absorption, while the mixed DABs potentially contributed in disease suppression and improved soil microbial diversity.
Dietary diversity, undernutrition and associated factors among pregnant women in Gindeberet district, Oromia, Ethiopia: a cross-sectional study
Authors: Tafasa Segni Mulugeta , Darega Jiregna , Dida Nagasa , Gemechu Feyisa Dudema 
Published: October 2023

AbstractBackgroundAppropriate levels of dietary diversity are essential for proper physiology of human being and it is crucial to consume healthy foods at every phase of life, especially during pregnancy. Inadequate dietary diversity and malnutrition are risk factors for low birth weight, intrauterine growth reduction and small for gestational age. This study was aimed to assess dietary diversity, undernutrition and associated factors among pregnant women in Gindeberet district, Oromia, Ethiopia, 2020.MethodA community based cross-sectional study was conducted among 627 pregnant women in Gindeberet district selected by systematic random sampling from October 10/2020– November 10/2020. Data were collected through interviewer administered questionnaires. The collected data were coded and entered to Epi-info version 7.2.2.6 and analyzed by SPSS version 23. Logistic regression analysis was carried out to identify factor associated with undernutrition and dietary diversity. Level of statistical significance was declared at p-value < 0.05.Resultsoverall prevalence of inadequate dietary diversity and undernutrition were 276 (44.4%) and 110 (17.7%) respectively. Pregnant women who did not receive antenatal care (AOR = 2.32, [95% CI: 1.38, 3.90]), family size ≥ 5 (AOR: 2.93; [95%CI: 1.10, 7.79]), unprotected sources of water (AOR: 4.14; [95% CI: 1.63, 10.52]) were significantly associated with undernutrition. Rural residence (AOR = 2.59, [95% CI: 1.66–4.04]), pregnant women who did not received ANC (AOR = 2.52, [95% CI: 1.58–4.03]) and nutrition information (AOR = 1.43; [95% CI: 1.10, 2.10]) were significantly associated with dietary diversity among pregnant women.Conclusionundernutrition and inadequate dietary diversity among pregnant women were high in study area. Source of drinking water, ANC visit and family size were significantly associated with pregnant women undernutrition. Place of residence, ANC visit and nutrition information were significantly associated with inadequate dietary diversity. Therefore, pregnant women, government, non-governmental organization and stakeholders should focus on importance of ANC visit, clean source of drinking water and adequate dietary diversity to improve nutritional status of pregnant women.
Fully automated radiosynthesis of [68Ga]Ga-FAPI-46 with cyclotron produced gallium
Authors: Rosenberg Adam J. , Cheung Yiu-Yin , Liu Fei , Sollert Carina , Peterson Todd E. , Kropski Jonathan A. 
Published: October 2023

Abstract
Background
Radiopharmaceuticals capable of targeting the fibroblast activation protein have become widely utilized in the research realm as well as show great promise to be commercialized; with [68Ga]Ga-FAPI-46 being one of the most widely utilized. Until now the synthesis has relied on generator-produced gallium-68. Here we present a developed method to utilize liquid-target cyclotron-produced gallium-68 to prepare [68Ga]Ga-FAPI-46.

Results
A fully-automated manufacturing process for [68Ga]Ga-FAPI-46 was developed starting with the 68Zn[p,n]68Ga cyclotron bombardment to provide [68Ga]GaCl3, automated purification of the [68Ga]GaCl3, chelation with the precursor, and final formulation/purification. The activity levels produced were sufficient for multiple clinical research doses, and the final product met all release criteria. Furthermore, the process consistently provides < 2% of Ga-66 and Ga-67 at the 4-h expiry, meeting the Ph. Eur. standards.

Conclusions
The automated radiosynthesis on the GE FASTlab 2 module purifies the cyclotron output into [68Ga]GaCl3, performs the labeling, formulates the product, and sterilizes the product while transferring to the final vial. Production of > 40 mCi (> 1480 MBq) of [68Ga]Ga-FAPI-46 in excellent radiochemical yield was achieved with all batches meeting release criteria.
Depression and health-related quality of life of patients with type 2 diabetes attending tertiary level hospitals in Dhaka, Bangladesh
Authors: Namdeo Manish K. , Verma Sarita , Das Gupta Rajat , Islam Rubana , Nazneen Shaila , Rawal Lal B. 
Published: October 2023

Abstract
Introduction
Type 2 diabetes mellitus (T2DM) and depression are closely linked. People with T2DM are at increased risk of developing depression and vice versa. T2DM and depression comorbid conditions adversely affect Health-Related Quality of Life (HRQOL) and management of T2DM. In this study, we assessed depression and HRQOL among patients with T2DM in Dhaka, Bangladesh.

Methods
A cross-sectional study was conducted in two tertiary-level hospitals in Dhaka, Bangladesh. Data were collected from 318 patients with T2DM. A set of standard tools, PHQ-9 (for assessing depression) and EuroQol-5D-5L (for assessing the HRQOL), were used. Statistical analyses, including Chi-square and Fisher's exact tests, Wilcoxon (Mann–Whitney), and Spearman's correlation coefficient tests, were performed using SPSS (v.20).

Results
The majority of the patients (58%) were females, with a mean age (standard deviation) of 52 ± 10 years, and 74% of patients lived in urban areas. The prevalence of depression was 62% (PHQ-9 score ≥ 5). Over three-quarters (76%) reported problems in the anxiety/ depression dimension of EQ-5D, followed by pain/discomfort (74%), mobility (40%), self-care (36%), and usual activities (33%). The depression and T2DM comorbid condition were associated with all the five dimensions of EQ-5D (χ2 statistics with df = 1 was 52.33, 51.13, 52.67, 21.61, 7.92 for mobility, self-care, usual activities, pain/discomfort, and anxiety/ depression dimensions respectively, p- < 0.01). The mean EQ-5D index (0.53 vs. 0.75) and the mean EQ-5D VAS (65 vs. 76) both showed lower values in T2DM patients with depression compared to T2DM patients without depression (Wilcoxon test, p- < 0.001).

Conclusions
We conclude that the majority of the patients with T2DM had comorbid conditions, and the HRQOL was negatively affected by comorbid depression in T2DM patients. This suggests the importance of timely screening, diagnosis, treatment, and follow-up of comorbid depression in T2DM patients to improve overall health and QOL.