bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulmonary lymphangiomatosis: insights into an ultra-rare disease
Authors: Polke M. , Polke N. , Piel S. , Brunnemer E. , Wälscher J. , Buschulte K. , Warth A. , Heussel C. P. , Eichinger M. , Frankenstein L. , Eichhorn M. , Miliauskas S. , Herth F. J. F. , Kreuter M. 
Published: November 2024

Abstract
Background
Pulmonary lymphangiomatosis (PL) is an ultrarare disease characterized by diffuse infiltration of the lung, pleura and/or mediastinum by abnormal lymphatic proliferation. Consented diagnostic or treatment approaches are not established. We therefore aimed to collect data on diagnostics and treatments in a cohort of patients with PL from a tertiary center for rare lung diseases.

Methods
Clinical, radiological and outcome data from PL patients were collected retrospectively.

Results
12 patients were diagnosed between 1996 and 2022 in our center. PL was diagnosed more commonly in female (58%), never smokers (75%) and younger patients (mean age 42 years). Main clinical symptoms comprised haem- and chyloptysis (58%) and dyspnea on exertion (83%). Pulmonary function was mostly restrictive (mean VC 59%) with impaired DLCO (mean 65%). Radiological assessment mainly showed mediastinal involvement (83%), and pleural effusion (67%), pleural thickening (67%) and bronchial wall thickening (67%) while interstitial changes were rare. Diagnosis was confirmed by surgical or transbronchial cryobiopsy. 8 patients were treated with sirolimus, 3 of these combined with a surgical intervention and in one case surgical intervention was necessary 9 months after initiation of sirolimus. Clinical and radiological improvement was demonstrated for all patients treated with sirolimus. 1 patient received a lung transplant due disease progression. Survival rates were 90% after a mean follow up of at least 3 months.

Conclusion
This case series illustrates the variability of the clinical presentation of PL. Among our patients, those treated with sirolimus showed significant clinical, functional and radiological improvement. However, further investigation is needed to understand the pathogenesis of lymphangiomatosis in order to establish therapeutic approaches.
Urinary DNA-methylation and protein biomarkers identify urothelial carcinoma among other genitourinary diseases and cancer-free individuals
Authors: Lang Kerstin , Köhler Christina U. , Wichert Katharina , Deix Thomas , Bartsch Georg , Sommer Gudrun , Lübke Christiane , Roghmann Florian , Reike Moritz J. , Krentel Harald , Engellandt Katja , Schiermeier Sven , Menke Valentin , Noldus Joachim , Behrens Thomas , Brüning Thomas , Käfferlein Heiko U. 
Published: November 2024

Abstract
Background
For more than 80 years, cystoscopy has been the gold standard for identification of urothelial carcinoma (UCa). Because of many factors, such as pain of the patients during this procedure or the costs involved, non-invasive detection of UCa remains a challenge. Herein, we verify our previously identified urinary biomarkers C-X-C Motif Chemokine Ligand 16 (CXCL16) and transforming growth-factor beta induced protein (TGFBI) on the protein level as well as the CpG sites ALOX5, TRPS1 and an intergenic region on Chromosome 16 on DNA methylation level in an independent cross-sectional study.

Methods
We collected N = 1119 urines from individuals coming to urological and gynecological check-ups, follow-up care or patients suspicious for UCa or already diagnosed for different urologic or gynecologic cancer entities. We performed methylation analysis of various CpG sites with DNA isolated from urine sediment and quantified the concentration of the protein markers CXCL16 and TGFBI in the corresponding urine supernatant using ELISA. We tested for patient-group differences with two-sided Wilcoxon rank sum tests and examined the performance with receiver operating characteristic curves. For verification, we analyzed the marker performance with previously set cutoff-values and marker combinations with established and experimental algorithms (with logical OR-conjunction, iterative threshold-based biomarker and score combining algorithm “PanelomiX”).

Results
Evaluation confirmed that our previously identified protein and DNA methylation biomarkers can distinguish UCa from frequent urological and gynecological cancers. CXCL16 and TGFBI discriminated UCa cases with a sensitivity of 31% and 56% and a specificity of 94% and 85%, respectively. Combining methylation markers resulted in UCa detection in men with a sensitivity of 54% and a specificity of 94%. Extending analysis by combining all methylation and protein markers (up to five markers in total) yielded a convincingly high specificity of 97% at a sensitivity of 72% for the identification of UCa patients within a heterogeneous collective of cancer-free individuals and patients suffering from urological or gynecological cancers.

Conclusion
Combining various biomarkers at protein and DNA level demonstrates a new option of non-invasive UCa diagnosis in urine, and thus might help to reduce the number of unnecessary cystoscopies, especially in patients without a history of UCa.
Strategies and interventions for achieving cardiovascular disease risk factor control in low- and middle-income countries: a review of the literature
Authors: Asamoah Kofi Tekyi , Dei-Asamoa Richard , Akumiah Florence Koryo , Ekpata Legbel Armor 
Published: November 2024

AbstractCardiovascular diseases (CVDs) are the leading cause of morbidity and mortality globally, with increasing rates in low- and low-middle-income countries (LMICs), particularly sub-Saharan Africa (SSA). These occur due to exposure to various risk factors, such as tobacco smoking, physical inactivity, hypertension, and diabetes. There are unique features in LMICs that contribute to the risk factor profile and quality of care offered in these countries. These include cultural influences on diet (carbohydrate-dense diet, use of salt-based spices and preservatives), the lack of dedicated spaces for physical activity, and perceptions of desirable body sizes. The attendant complications affect individuals, families and the community at large. Furthermore, there is a dearth of research to inform change at both the individual and policy level in LMICs. Lifestyle modification is the cornerstone of risk factor control and requires engaging relevant stakeholders in healthcare to enforce sustainable behaviour change among individuals. This includes measures from the individual level to national leadership and requires multisectoral collaboration to ensure sustainability. Such methods include building health worker capacity through a task shifting approach, strengthening the health worker-patient relationship, employing digital/technological applications, and engaging families and communities to serve as accountability partners in the management of CVD and related risk factors. There is a need for increased contextually relevant research output to inform contemporary methods to improve CVD and risk factor control in LMICs.
α-mannosidosis diagnosis in Brazilian patients with MPS-like symptoms
Authors: Marins Maryana , Curiati Marco Antonio , Gomes Caio Perez , Martin Renan Paulo , Nicolicht-Amorim Priscila , Yamamoto Joyce Umbelino da Silva , D’Almeida Vânia , Martins Ana Maria , Pesquero João Bosco 
Published: November 2024

Abstract
Background
α-mannosidosis is an inborn error of metabolism caused by the deficiency of the lysosomal enzyme α-mannosidase, which is encoded by the MAN2B1 gene and inherited in an autosomal recessive manner. The impairment of affected individuals is multisystemic and very similar to the observed in some mucopolysaccharidosis (MPS) patients. The aim of this study was to search for α-mannosidosis cases in individuals with clinical suspicion of MPS without a confirmed diagnosis. Biochemical and molecular analysis were standardized by our group for this study. Two hundred and fifty samples from patients with clinical suspicion of MPS, but with inconclusive MPS biochemical and/or molecular analysis, were screened for α-mannosidase activity. Subsequently the MAN2B1 gene was sequenced in samples from 53 patients by the Sanger method.

Results
The measurement of enzymatic activity detected fifty-three samples with abnormal results, suggesting α-mannosidosis. Molecular analysis confirmed three affected families, which presented the nonsense variant p.Ser899Ter. This variant generates a premature stop codon in exon 22, resulting in a truncated protein with no residual enzymatic activity.

Conclusion
In conclusion, this work brings data for the beginning of a genetic characterization of α-mannosidosis in the Brazilian population. It also shows that α-mannosidosis cases may be underdiagnosed due to the clinical similarity to MPS and the lack of information about this ultra-rare disease. Based on our data, we strongly recommend to all screening centers to consider α-mannosidosis testing together with screening for MPS as a tool for diagnosis to MPS-like phenotype individuals, since the phenotype similarity between these diseases poses a significant challenge for clinicians worldwide and often leads to the failure of the correct clinical diagnosis and treatment.
Conjoint analysis of methylation, transcriptomic, and proteomic profiles in pemphigus vulgaris
Authors: Luo Xiaojia , Ouyang Jianting , Jiang Fuqiong , Zhang Yaozhong , Wang Yuan , Wu Yongzhuo , Hu Lingyu 
Published: November 2024

Abstract
Background
The underlying pathogenesis of pemphigus vulgaris, an autoimmune skin disorder, remains incompletely understood. An integrative analysis comprising DNA methylation, mRNA expression, and proteomic data in patients with pemphigus vulgaris was conducted to identify potential pathogenic contributors and explore the molecular mechanisms involved in its pathogenesis.

Results
The analysis revealed differentially methylated regions (DMRs) in the promoter, exon, intron, and downstream regions in the peripheral blood DNA of patients with pemphigus vulgaris. Associations between methylation levels and both transcriptomic and proteomic profiles revealed that differentially expressed genes between patients with pemphigus vulgaris and healthy controls were primarily linked to biological functions such as platelet activation and coagulation, cellular adhesion, and immunoglobulin binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis highlighted notable pathway abnormalities, including those related to platelet activation, focal adhesions, tight junctions, and infectious inflammatory responses. Notably, genes such as FGA (fibrinogen alpha chain), VWF (von Willebrand factor), and ACTG1 (actin gamma 1) were dysregulated, with a prominent role in platelet activation.

Conclusion
The dysregulation of genes such as FGA, VWF, and ACTG1 suggests that alterations in their transcription and expression may contribute to the pathogenesis of pemphigus vulgaris.
Human VCP mutant ALS/FTD microglia display immune and lysosomal phenotypes independently of GPNMB
Authors: Clarke Benjamin E. , Ziff Oliver J. , Tyzack Giulia , Petrić Howe Marija , Wang Yiran , Klein Pierre , Smith Claudia A. , Hall Cameron A. , Helmy Adel , Howell Michael , Kelly Gavin , Patani Rickie 
Published: November 2024

Abstract
Background
Microglia play crucial roles in maintaining neuronal homeostasis but have been implicated in contributing to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, the role of microglia in ALS/FTD remains incompletely understood.

Methods
Here, we generated highly enriched cultures of VCP mutant microglia derived from human induced pluripotent stem cells (hiPSCs) to investigate their cell autonomous and non-cell autonomous roles in ALS pathogenesis. We used RNA-sequencing, proteomics and functional assays to study hiPSC derived VCP mutant microglia and their effects on hiPSC derived motor neurons and astrocytes.

Results
Transcriptomic, proteomic and functional analyses revealed immune and lysosomal dysfunction in VCP mutant microglia. Stimulating healthy microglia with the inflammatory inducer lipopolysaccharide (LPS) showed partial overlap with VCP mutant microglia in their reactive transformation. LPS-stimulated VCP mutant microglia displayed differential activation of inflammatory pathways compared with LPS-stimulated healthy microglia. Conserved gene expression changes were identified between VCP mutant microglia, SOD1 mutant mice microglia, and postmortem ALS spinal cord microglial signatures, including increased expression of the transmembrane glycoprotein GPNMB. While knockdown of GPNMB affected inflammatory and phagocytosis processes in microglia, this was not sufficient to ameliorate cell autonomous phenotypes in VCP mutant microglia. Secreted factors from VCP mutant microglia were sufficient to activate the JAK-STAT pathway in hiPSC derived motor neurons and astrocytes.

Conclusions
VCP mutant microglia undergo cell autonomous reactive transformation involving immune and lysosomal dysfunction that partially recapitulate key phenotypes of microglia from other ALS models and post mortem tissue. These phenotypes occur independently of GPNMB. Additionally, VCP mutant microglia elicit non cell autonomous responses in motor neurons and astrocytes involving the JAK-STAT pathway.
Selective metabolic regulations by p53 mutant variants in pancreatic cancer
Authors: Caporali Sabrina , Butera Alessio , Ruzza Alessia , Zampieri Carlotta , Bantula’ Marina , Scharsich Sandra , Ückert Anna-Katerina , Celardo Ivana , Kouzel Ian U. , Leanza Luigi , Gruber Andreas , Montero Joan , D’Alessandro Angelo , Brunner Thomas , Leist Marcel , Amelio Ivano 
Published: November 2024

Abstract
Background
Approximately half of all human cancers harbour mutations in the p53 gene, leading to the generation of neomorphic p53 mutant proteins. These mutants can exert gain-of-function (GOF) effects, potentially promoting tumour progression. However, the clinical significance of p53 GOF mutations, as well as the selectivity of individual variants, remains controversial and unclear.

Methods
To elucidate the metabolic regulations and molecular underpinnings associated with the specific p53R270H and p53R172H mutant variants (the mouse equivalents of human p53R273H and p53R175H, respectively), we employed a comprehensive approach. This included integrating global metabolomic analysis with epigenomic and transcriptomic profiling in mouse pancreatic cancer cells. Additionally, we assessed metabolic parameters such as oxygen consumption rate and conducted analyses of proliferation and cell–cell competition to validate the biological impact of metabolic changes on pancreatic ductal adenocarcinoma (PDAC) phenotype. Our findings were further corroborated through analysis of clinical datasets from human cancer cohorts.

Results
Our investigation revealed that the p53R270H variant, but not p53R172H, sustains mitochondrial function and energy production while also influencing cellular antioxidant capacity. Conversely, p53R172H, while not affecting mitochondrial metabolism, attenuates the activation of pro-tumorigenic metabolic pathways such as the urea cycle. Thus, the two variants selectively control different metabolic pathways in pancreatic cancer cells. Mechanistically, p53R270H induces alterations in the expression of genes associated with oxidative stress and reduction in mitochondrial respiration. In contrast, p53R172H specifically impacts the expression levels of enzymes involved in the urea metabolism. However, our analysis of cell proliferation and cell competition suggested that the expression of either p53R270H or p53R172H does not influence confer any selective advantage to this cellular model in vitro. Furthermore, assessment of mitochondrial priming indicated that the p53R270H-driven mitochondrial effect does not alter cytochrome c release or the apoptotic propensity of pancreatic cancer cells.

Conclusions
Our study elucidates the mutant-specific impact of p53R270H and p53R172H on metabolism of PDAC cancer cells, highlighting the need to shift from viewing p53 mutant variants as a homogeneous group of entities to a systematic assessment of each specific p53 mutant protein. Moreover, our finding underscores the importance of further exploring the significance of p53 mutant proteins using models that more accurately reflect tumor ecology.
Effects of prebiotics on microbial diversity and abundance in young children with acute malnutrition: study protocol for a multi-centered, double-blinded randomized controlled trial
Authors: Saleem Javeria , Zakar Rubeena , Iqbal Sanaullah , Arshad Muhammad , Shahzad Ruhma , Batool Munazza , Nawaz Muhammad , Butt Muhammad Salman , Fischer Florian 
Published: November 2024

Abstract
Background
The anti-inflammatory and antimicrobial benefits of prebiotics may present an affordable and cost-effective strategy for not only the prevention but also treatment of malnutrition. Therefore, the present trial has been designed with the aim to evaluate the role of prebiotics on the gut microbiome of severe acute malnourished (SAM) children.

Methods
The study is designed as a prospective, double-blinded, triple-armed, multi-centered randomized controlled trial, with 6–59 months old uncomplicated SAM children recruited to the experimental group receiving ready-to-use therapeutic food (RUTF) plus prebiotics and the active comparator group receiving RUTF plus starch for 2 months duration (8 weeks). Healthy children with matching age and gender will be recruited to placebo comparator group and will receive starch as a placebo during the study period. A total of 58 participants will be recruited to each arm with 1:1:1 allocation ratio following a pre-defined inclusion and exclusion criteria. The results of the gut microbiome diversity will serve as the primary outcome, while weight-for-height/length z-score, mid-upper-arm circumference, neurodevelopment assessment, and body mass accumulation will serve as the secondary outcome. Data collection and evaluations will be conducted at baseline and at the end of the trial (week 8), while the safety monitoring will be conducted at every second week. For analysis, the principles of intention-to-treat will be followed.

Conclusions
Conclusively, the results of the present trial would provide useful insights and high-quality data for the treatment and management of SAM children by evaluating the effect of RUTF plus prebiotic on the gut microbiome diversity of children, leading to medical evidence for designing the large-scale studies.

Trial registration
The present trial is registered at ClinicalTrials.gov with identifier No: NCT06155474 and registration date 4 December 2023.
Pharmacophore-based virtual screening, molecular docking, and molecular dynamics investigation for the identification of novel, marine aromatase inhibitors
Authors: Kotb Mohamed A. , Abdelmawgood Islam Ahmed , Ibrahim Ibrahim M. 
Published: November 2024

AbstractBreast cancer remains a leading cause of mortality among women worldwide. Our current research focuses on identifying effective therapeutic agents by targeting the human aromatase enzyme. Aromatase inhibitors (AIs) have been effective in treating postmenopausal breast cancer but face challenges such as drug resistance and long-term side effects like cognitive decline and osteoporosis. Natural products, especially from marine organisms, are emerging as potential sources for new drug candidates due to their structural diversity and pharmacological properties. This study aims to discover marine natural products capable of inhibiting human aromatase by combining ligand-based and structure-based pharmacophore models for virtual screening against the Comprehensive Marine Natural Products Database. From the initial virtual screening of more than 31,000 compounds, 1,385 marine natural products were identified as possible candidates. Following initial molecular docking analysis, only four compounds managed to pass the criteria this research has introduced to confirm strong binding affinity to aromatase. All four compounds yielded acceptable binding affinities, with CMPND 27987 having the highest −10.1 kcal/mol. All four hits were subjected to molecular dynamics, and CMPND 27987 was further confirmed to be the most stable at the protein’s active site, with an MM-GBSA free binding energy of −27.75 kcal/mol. Our in silico studies indicate that CMPND 27987 interacts effectively within the binding site of the human aromatase, maintaining high affinity and stability. Based on these findings, we propose that CMPND 27987 could hold significant potential for further lead optimization and drug development.
In silico prediction of the action of bromelain on PI3K/Akt signalling pathway to arrest nasopharyngeal cancer oncogenesis by targeting phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha protein
Authors: Shamsuri Alyaa Syafiqah , Sim Edmund Ui -Hang 
Published: November 2024

Abstract
Objective
This research investigates the potential anti-tumour effects of bromelain, an aqueous extract from pineapple stems and fruits, on nasopharyngeal cancer (NPC). While bromelain is known for its medicinal properties in various cancers, its impact on NPC remains unexplored.

Results
Using in silico methods, we studied the predicted interactions between bromelain and key proteins involved in NPC oncogenesis, specifically β-catenin, PIK3CA, mTOR, EGFR, and BCL2. Molecular docking strategies were performed using a myriad of computational tools. A 3D model of bromelain was constructed using SWISS-MODEL, followed by molecular docking simulations performed with ClusPro. The binding affinities of the docked complexes were evaluated using HawkDock, and the interactions were analysed with LigPlot+. The docking scores indicated potential spontaneous interactions, with binding affinities based on being − 103.89 kcal/mol (PIK3CA), -73.16 kcal/mol (EGFR), -71.18 kcal/mol (mTOR), -65.22 kcal/mol (β-catenin), and − 57.48 kcal/mol (BCL2). LigPlot + analysis revealed the presence of hydrogen bonds, hydrophobic interactions, and salt bridges, indicating stable predicted interactions.

Conclusion
Our findings suggest that bromelain can target key proteins involved in NPC oncogenesis, with the strongest affinity towards PIK3CA. This suggests a hypothetical insight into bromelain’s anticancer effects on NPC through the modulation of the PI3K/Akt signaling pathway.