bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a TRP channel-related risk model for predicting prognosis and therapeutic effects of patients with hepatocellular carcinoma
Authors: Pang Chong , Xu Zhe , Han Jilong , Li Fujun , Zhu Hongyan , Zhang Jiaqi , Wang Dong , Xu Xundi 
Published: September 2023

Abstract
Purpose
TRP channels have been implicated in cancer progression. Our study seeks to establish a prognostic model for hepatocellular carcinoma (HCC) by utilizing genes related to TRP channels.

Methods
We used the TCGA and ICGC databases as training and validation cohorts, respectively. We calculated the risk scores using Lasso–Cox regression analysis based on the expression levels of prognostic genes and performed survival analysis to compare overall survival between high- and low-risk groups. Then we compared the clinicopathologic characteristics and conducted biological functional analysis. We also explored immune cell infiltration and compared the drug sensitivity.

Results
Using bioinformatics algorithms, we identified 11 TRP-related genes and calculated the risk scores. Patients in the high-risk group demonstrated worse overall survival, as well as more advanced T stage and pathologic stage. The risk score showed a significant association with the cell cycle. The high-risk group had more ICI and RTK targets with elevated expression and showed better therapeutic effect to chemotherapy including 5-fluorouracil, camptothecin, docetaxel, doxorubicin, gemcitabine, and paclitaxel. Overall, an individualized nomogram was constructed by integrating the risk score and requisite clinicopathologic parameters to predict the overall survival of HCC patients.

Conclusions
We successfully established a highly accurate prognostic model for predicting overall survival and therapeutic effects using TRP channel-related genes.
Integrated analysis of tumor microenvironment features to establish a diagnostic model for papillary thyroid cancer using bulk and single-cell RNA sequencing technology
Authors: Wang Yizeng , Song Wenbin , Li Yingxi , Liu Zhaoyi , Zhao Ke , Jia Lanning , Wang Xiaoning , Jiang Ruoyu , Tian Yao , He Xianghui 
Published: September 2023

Abstract
Background
Characterizing tumor microenvironment using single-cell RNA sequencing has been a promising strategy for cancer diagnosis and treatment. However, a few studies have focused on diagnosing papillary thyroid cancer (PTC) through this technology. Therefore, our study explored tumor microenvironment (TME) features and identified potential biomarkers to establish a diagnostic model for papillary thyroid cancer.

Methods
The cell types were identified using the markers from the CellMarker database and published research. The CellChat package was conducted to analyze the cell–cell interaction. The SCEVAN package was used to identify malignant thyroid cells. The SCP package was used to perform multiple single-cell downstream analyses, such as GSEA analysis, enrichment analysis, pseudotime trajectory analysis, and differential expression analysis. The diagnostic model of PTC was estimated using the calibration curves, receiver operating characteristic curves, and decision curve analysis. RT-qPCR was performed to validate the expression of candidate genes in human papillary thyroid samples.

Results
Eight cell types were identified in the scRNA-seq dataset by published cell markers. Extensive cell–cell interactions like FN1/ITGB1 existed in PTC tissues. We identified 26 critical genes related to PTC progression. Further, eight subgroups of PTC tumor cells were identified and exhibited high heterogeneity. The MDK/LRP1, MDK/ALK, GAS6/MERTK, and GAS6/AXL were identified as potential ligand-receptor pairs involved in the interactions between fibroblasts/endothelial cells and tumor cells. Eventually, the diagnostic model constructed by TRPC5, TENM1, NELL2, DMD, SLC35F3, and AUTS2 showed a good efficiency for distinguishing the PTC and normal tissues.

Conclusions
Our study comprehensively characterized the tumor microenvironment in papillary thyroid cancer. Through combined analysis with bulk RNA-seq, six potential diagnostic biomarkers were identified and validated. The diagnostic model we constructed was a promising tool for PTC diagnosis. Our findings provide new insights into the heterogeneity of thyroid cancer and the theoretical basis for diagnosing thyroid cancer.
Identification of single nucleotide polymorphisms (SNPs) associated with chronic graft-versus-host disease in patients undergoing allogeneic hematopoietic cell transplantation
Authors: Mougeot Jean-Luc C. , Beckman Micaela F. , Hovan Allan J. , Hasséus Bengt , Legert Karin Garming , Johansson Jan-Erik , von Bültzingslöwen Inger , Brennan Michael T. , Bahrani Mougeot Farah 
Published: September 2023

Abstract
Introduction
Chronic graft-versus-host disease (cGVHD) is a debilitating side effect of allogeneic hematopoietic cell transplantation (HCT), affecting the quality of life of patients. We used whole exome sequencing to identify candidate SNPs and complete a multi-marker gene-level analysis using a cohort of cGVHD( +) (N = 16) and cGVHD( −) (N = 66) HCT patients.

Methods
Saliva samples were collected from HCT patients (N = 82) pre-conditioning in a multi-center study from March 2011 to May 2018. Exome sequencing was performed and FASTQ files were processed for sequence alignments. Significant SNPs were identified by logistic regression using PLINK2v3.7 and Fisher’s exact test. One cGVHD( −) patient sample was excluded from further analysis since no SNP was present in at least 10% of the sample population. The FUMA platform’s SNP2GENE was utilized to annotate SNPs and generate a MAGMA output. Chromatin state visualization of lead SNPs was completed using Epilogos tool. FUMA’s GENE2FUNC was used to obtain gene function and tissue expression from lead genomic loci.

Results
Logistic regression classified 986 SNPs associated with cGVHD( +). SNP2GENE returned three genomic risk loci, four lead SNPs, 48 candidate SNPs, seven candidate GWAS tagged SNPs, and four mapped genes. Fisher’s exact test identified significant homozygous genotypes of four lead SNPs (p < 0.05). GENE2FUNC analysis of multi-marker SNP sets identified one positional gene set including lead SNPs for KANK1 and KDM4C and two curated gene sets including lead SNPs for PTPRD, KDM4C, and/or KANK1.

Conclusions
Our data suggest that SNPs in three genes located on chromosome 9 confer genetic susceptibility to cGVHD in HCT patients. These genes modulate STAT3 expression and phosphorylation in cancer pathogenesis. The findings may have implications in the modulation of pathways currently targeted by JAK inhibitors in cGVHD clinical trials.
Reliability of intraoperative visual evoked potentials (iVEPs) in monitoring visual function during endoscopic transsphenoidal surgery
Authors: Mattogno Pier Paolo , D’Alessandris Quintino Giorgio , Rigante Mario , Granata Giuseppe , Di Domenico Michele , Perotti Valerio , Montano Nicola , Giordano Martina , Chiloiro Sabrina , Doglietto Francesco , Olivi Alessandro , Lauretti Liverana 
Published: September 2023

Abstract
Objective
To refine a reliable and reproducible intraoperative visual evoked potentials (iVEPs) monitoring protocol during endoscopic transsphenoidal surgery. To assess the reliability of baseline iVEPs in predicting preoperative visual status and perioperative iVEP variation in predicting postoperative visual outcome.

Methods
Sixty-four patients harboring tumors of the pituitary region were included. All patients underwent endoscopic endonasal approach (EEA) with iVEPs monitoring, using a totally intravenous anesthetic protocol. Ophthalmological evaluation included visual acuity and visual field studies.

Results
Preoperatively, visual acuity was reduced in 86% and visual field in 76.5% of cases. Baseline iVEPs amplitude was significantly correlated with preoperative visual acuity and visual field (p = 0.001 and p = 0.0004, respectively), confirming the reliability of the neurophysiological/anesthetic protocol implemented.
Importantly, perioperatively the variation in iVEPs amplitude was significantly correlated with the changes in visual acuity (p < 0.0001) and visual field (p = 0.0013). ROC analysis confirmed that iVEPs are an accurate predictor of perioperiative visual acuity improvement, with a 100% positive predictive value in patients with preoperative vision loss.

Conclusions
iVEPs during EEA is highly reliable in describing preoperative visual function and can accurately predict postoperative vision improvement.

Significance
iVEPs represent a promising resource for carrying out a more effective and safe endoscopic transsphenoidal surgery.
On understanding and predicting issue links
Authors: Lüders Clara Marie , Pietz Tim , Maalej Walid 
Published: September 2023

AbstractStakeholders in software projects use issue trackers like JIRA or Bugzilla to capture and manage issues, including requirements, feature requests, and bugs. To ease issue navigation and structure project knowledge, stakeholders manually connect issues via links of certain types that reflect different dependencies, such as Epic-, Block-, Duplicate-, or Relate- links. Based on a large dataset of 16 JIRA repositories, we study the commonalities and differences in linking practices and link types across the repositories. We then investigate how state-of-the-art machine learning models can predict common link types. We observed significant differences across the repositories and link types, depending on how they are used and by whom. Additionally, we observed several inconsistencies, e.g., in how Duplicate links are used. We found that a transformer model trained on titles and descriptions of linked issues significantly outperforms other optimized models, achieving an encouraging average macro F1-score of 0.64 for predicting nine popular link types across all repositories (weighted F1-score of 0.73). For the specific Subtask- and Epic- links, the model achieves top F1-scores of 0.89 and 0.97, respectively. If we restrict the task to predict the mere existence of links, the average macro F1-score goes up to 0.95. In general, the shorter issue text, possibly indicating precise issues, seems to improve the prediction accuracy with a strong negative correlation of $$-$$
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0.73. We found that Relate-links often get confused with the other links, which suggests that they are likely used as default links in unclear cases. Our findings particularly on the quality and heterogeinity of issue link data have implications for researching and applying issue link prediction in practice.
Stand der Weiterbildung aus Sicht der Ärzt*innen in Weiterbildung
Authors: Doukas Panagiotis , Marchiori Elena , Adili Farzin , Meisenbacher Katrin , Mulorz Joscha 
Published: September 2023

Zusammenfassung
Fragestellung
Die umfassende Weiterbildung des gefäßchirurgischen Nachwuchses bleibt auch im Jahr 2023 ein relevantes Thema für angehende Gefäßchirurg*innen und Weiterbildende. Dabei bewegt sich die Weiterbildung der modernen Gefäßchirurg*in im Spannungsfeld zwischen praktischer, theoretischer und akademischer Ausbildung. Hier stellt sich die Frage, inwieweit die verschiedenen Anforderungen der Weiterbildung im klinischen Alltag der Assistenzärzt*innen abgedeckt und strukturierte Lehrcurricula überhaupt vorhanden und umgesetzt werden.

Material und Methoden
Um den aktuellen Weiterbildungsstatus der Assistenzärzt*innen in Deutschland zu eruieren, führte das Junge Forum der Deutschen Gesellschaft für Gefäßchirurgie und Gefäßmedizin (DGG) vom 22. Mai 2023 bis zum 9. Juni 2023 eine Umfrage unter allen ihren Mitgliedern in Weiterbildung durch. Die Umfrage umfasste dabei verschiedene Aspekte der Weiterbildung von der Lehre praktischer Fertigkeiten bis zu strukturellen Aspekten.

Ergebnisse
Insgesamt nahmen 81 Mitglieder der DGG teil. Das Durchschnittsalter lag bei 35 Jahren, der Frauenanteil bei 38,3 %. 48 % der Befragten arbeiteten in Krankenhäusern der Maximalversorgung. Insgesamt waren 39,5 % mit ihrer Weiterbildung zufrieden oder sehr zufrieden, während 30,7 % nur mäßig zufrieden waren. Strukturierte Weiterbildungskonzepte existierten in 53 % der Kliniken. 55 % der Teilnehmenden würden ihre Weiterbildungseinrichtung weiterempfehlen.

Schlussfolgerung
Die Umfrage zeigt ein deutliches Verbesserungspotenzial bei der Umsetzung der gefäßchirurgischen Weiterbildung in fast allen Bereichen. Zudem gibt es ein großes Bedürfnis nach alternativen Arbeitszeitkonzepten, um Freiräume für akademisches Arbeiten und Privatleben zu schaffen. Diese Aspekte gilt es in Zukunft zu adressieren, um eine größere Zufriedenheit und Qualität der gefäßchirurgischen Weiterbildung herzustellen.
The Challenges and Opportunities for Mental Health Twin Research in Nigeria
Authors: Oginni Olakunle Ayokunmi , Ayorinde Ayoyinka , Ayodele Kehinde Dorcas , Opara Onyedikachi Joseph , Mapayi Boladale , Mosaku Kolawole 
Published: September 2023

AbstractThe recent interest in increasing diversity in genetic research can be useful in uncovering novel insights into the genetic architecture of mental health disorders – globally and in previously unexplored settings such as low- and middle-income settings like Nigeria. Genetic research into mental health is potentially promising in Nigeria and we reflect on the challenges and opportunities for twin research which may be particularly suited to Nigeria. The higher rates of twinning in Africa and Nigeria specifically, make the twin design an affordable and readily maintainable approach for genetic research in the country. Despite potential challenges with recruitment, data collection, data analysis and dissemination; the success of current efforts suggest that the twin design can tapped even further for greater impact in the country. We highlight some ways in which the scope of twin research can be increased and suggest some ways in which existing challenges can be overcome including recent Patient Participant Involve and Engagement activities.
Investigation into the Influence of Socio-Cultural Factors on Attitudes toward Artificial Intelligence
Authors: Kim Seong-Won , Lee Youngjun 
Published: September 2023

AbstractIn this study, the influence of socio-cultural factors on attitudes toward artificial intelligence (AI) was investigated. In total, 1,677 Korean middle school students were selected to participate, and a test tool was used to measure the attitude toward AI. As a result, according to socio-cultural factors, middle school students’ attitudes toward AI were affected differently by gender- or AI-related experiences. In particular, students experiencing difficulties because of socio-cultural factors showed a more positive attitude toward AI if they had an AI education. On the other hand, interest toward AI and programming experience had a significant effect on attitudes toward AI and was not affected by socio-cultural factors. In particular, students with high interest toward AI or experience with block- and text-based programming languages showed significantly positive attitudes toward AI. Hence, the disparity in middle school students’ attitude toward AI according to socio-cultural factors was found.
The impact of environmental factors on traits of Hedera helix L. vegetative shoots
Authors: Blinkova Olena , Rawlik Katarzyna , Jagodziński Andrzej M. 
Published: September 2023

AbstractHedera helix L. is an evergreen vine native to Europe. Nowadays, it is commonly recognized as an expansive species, posing danger to biodiversity of natural ecosystems. Obtaining the relationships between morphological variability, productive parameters of vegetative individuals, and variations in environmental factors (on the example of the Kórnik Arboretum) is important for understanding the successful adaptation and dispersion of H. helix. Thus, the issue of our studies was to discover the link between environmental factors and morphometric measurements of H. helix. We collected data on leaf length, leaf width, leaf petiole length, plant stem length, and the number of leaves per stem. We assessed values of ecological plasticity and correlation between the studied parameters. The results indicated the tolerance of ivy to wide variation in edaphic conditions. The limiting environmental factors for growth of the studied subpopulations were soil moisture and light intensity. We found large variability of leaf morphometric parameters and shoot length. Close correlation links were detected between leaf length/leaf width, leaf length/leaf petiole length, and leaf width/leaf petiole length. The length of the average leaf and the length of leaf petiole were the most variable parameters under different values of light intensity. Weak relationships were found between light intensity at the soil surface and plant stem length/the number of leaves per shoot. A high level of index of morphological integration of H. helix individuals and a close relationship between the quality index/subpopulation compositions were established in this study. A direct relationship between light intensity and specific leaf area values was established. The value of specific leaf area decreased linearly with increasing light intensity at the soil surface.
Special issue dedicated to the 8th International Conference on Variable Neighborhood Search (ICVNS 2021)
Authors: Mladenović Nenad , Sifaleras Angelo , Sleptchenko Andrei 
Published: September 2023

AbstractThis special issue contains 15 papers submitted by the participants of the 8th International Conference on Variable Neighborhood Search (ICVNS 2021), which was held in Abu Dhabi, U.A.E., online due to COVID-19 restrictions, on March 22–24, 2021.
In Situ Spatially Resolved Coating Thickness Measurements in Thermal Spraying
Authors: Hudomalj Uroš , Fallahi Sichani Ehsan , Weiss Lukas , Nabavi Majid , Wegener Konrad 
Published: September 2023

AbstractAchieving target coating thickness is one of the main objectives in thermal spraying. Despite this, there is a lack of measurement methods that could evaluate in situ the coating thickness with a sufficient accuracy that could be used as a robust feedback signal for online, closed-loop process control. This paper presents a novel approach for in situ spatially resolved coating thickness measurements. The measurement technique is based on a high-resolution 3D camera to capture the surface topography and include it in the thickness measurement. The technique provides results of total coating thickness with excellent accuracy when compared to the reference microscopical method. It also gives a 3D view of the coating thicknesses around the observed area as well as information about the thickness of individual coating layers. Moreover, the approach enables in situ evaluation of surface roughness, and a nondestructive estimation of coating porosity.
Fibroblast Growth Factor Receptor 2 (FGFR2), a New Gene Involved in the Genesis of Autism Spectrum Disorder
Authors: Nicotera Antonio Gennaro , Amore Greta , Saia Maria Concetta , Vinci Mirella , Musumeci Antonino , Chiavetta Valeria , Federico Concetta , Spoto Giulia , Saccone Salvatore , Di Rosa Gabriella , Calì Francesco 
Published: September 2023

AbstractAutism spectrum disorder (ASD) is a long-known complex neurodevelopmental disorder, and over the past decades, with the enhancement of the research genomic techniques, has been the object of intensive research activity, and many genes involved in the development and functioning of the central nervous system have been related to ASD genesis. Herein, we report a patient with severe ASD carrying a G > A de novo variant in the FGFR2 gene, determining a missense mutation. FGFR2 encodes for the ubiquitous fibroblast growth factor receptor (FGFR) type 2, a tyrosine kinase receptor implicated in several biological processes. The mutated version of this protein is known to be responsible for several variable overlapping syndromes. Even if there still is only sparse and anecdotal data, recent research highlighted a potential role of FGFR2 on neurodevelopment. Our findings provide new insights into the potential causative role of FGFR2 gene in complex neurodevelopmental disorders.
Diverse functions of myeloid-derived suppressor cells in autoimmune diseases
Authors: Xiong Xin , Zhang Yang , Wen Yu 
Published: September 2023

AbstractSince myeloid-derived suppressor cells (MDSCs) were found suppressing immune responses in cancer and other pathological conditions, subsequent researchers have pinned their hopes on the suppressive function against immune damage in autoimmune diseases. However, recent studies have found key distinctions of MDSC immune effects in cancer and autoimmunity. These include not only suppression and immune tolerance, but MDSCs also possess pro-inflammatory effects and exacerbate immune disorders during autoimmunity, while promoting T cell proliferation, inducing Th17 cell differentiation, releasing pro-inflammatory cytokines, and causing direct tissue damage. Additionally, MDSCs could interact with surrounding cells to directly cause tissue damage or repair, sometimes even as an inflammatory indicator in line with disease severity. These diverse manifestations could be partially attributed to the heterogeneity of MDSCs, but not all. The different disease types, disease states, and cytokine profiles alter the diverse phenotypes and functions of MDSCs, thus leading to the impairment or obversion of MDSC suppression. In this review, we summarize the functions of MDSCs in several autoimmune diseases and attempt to elucidate the mechanisms behind their actions.
Space–time heterogeneity of drought characteristics in Sabah and Sarawak, East Malaysia: implications for developing effective drought monitoring and mitigation strategies
Authors: Huang Yuk Feng , Ng Jing Lin , Fung Kit Fai , Weng Tan Kok , AlDahoul Nouar , Ahmed Ali Najah , Sherif Mohsen , Chaplot Barkha , Chong Kai Lun , Elshafie Ahmed 
Published: September 2023

AbstractNatural calamities like droughts have harmed not just humanity throughout history but also the economy, food, agricultural production, flora, animal habitat, etc. A drought monitoring system must incorporate a study of the geographical and temporal fluctuation of the drought characteristics to function effectively. This study investigated the space–time heterogeneity of drought features across Sabah and Sarawak, East Malaysia. The Standardized Precipitation Index (SPIs) at timescales of 1-month, 3-months, and 6-months was selected to determine the spatial distribution of drought characteristics. Rainfall hydrographs for the area for 30 years between 1988 and 2017 have been used in this study. A total of six five-year sub-periods were studied, with an emphasis on the lowest and highest drought occurrence. The sub-periods were a division of the 30 years over an arbitrary continual division for convenience. The results showed that the sub-periods 1993–1997 and 2008–2012 had the highest and lowest comparative drought events. The drought conditions were particularly severe in Central and Eastern parts of East Malaysia, owing to El Nino events and the country's hilly terrain. Understanding how and when drought occurs can aid in establishing and developing drought mitigation strategies for the region.