bluuebunny/crossref_metadata_2025_split huggingface dataset:
KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations
Authors: Wu Jinyang , Ning Zhiwei , Ding Yidong , Wang Ying , Peng Qinke , Fu Laiyi 
Published: August 2023

Abstract
Recent studies have demonstrated the significant role that circRNA plays in the progression of human diseases. Identifying circRNA-disease associations (CDA) in an efficient manner can offer crucial insights into disease diagnosis. While traditional biological experiments can be time-consuming and labor-intensive, computational methods have emerged as a viable alternative in recent years. However, these methods are often limited by data sparsity and their inability to explore high-order information. In this paper, we introduce a novel method named Knowledge Graph Encoder from Transformer for predicting CDA (KGETCDA). Specifically, KGETCDA first integrates more than 10 databases to construct a large heterogeneous non-coding RNA dataset, which contains multiple relationships between circRNA, miRNA, lncRNA and disease. Then, a biological knowledge graph is created based on this dataset and Transformer-based knowledge representation learning and attentive propagation layers are applied to obtain high-quality embeddings with accurately captured high-order interaction information. Finally, multilayer perceptron is utilized to predict the matching scores of CDA based on their embeddings. Our empirical results demonstrate that KGETCDA significantly outperforms other state-of-the-art models. To enhance user experience, we have developed an interactive web-based platform named HNRBase that allows users to visualize, download data and make predictions using KGETCDA with ease. The code and datasets are publicly available at https://github.com/jinyangwu/KGETCDA.
NCAE: data-driven representations using a deep network-coherent DNA methylation autoencoder identify robust disease and risk factor signatures
Authors: Martínez-Enguita David , Dwivedi Sanjiv K , Jörnsten Rebecka , Gustafsson Mika 
Published: August 2023

Abstract
Precision medicine relies on the identification of robust disease and risk factor signatures from omics data. However, current knowledge-driven approaches may overlook novel or unexpected phenomena due to the inherent biases in biological knowledge. In this study, we present a data-driven signature discovery workflow for DNA methylation analysis utilizing network-coherent autoencoders (NCAEs) with biologically relevant latent embeddings. First, we explored the architecture space of autoencoders trained on a large-scale pan-tissue compendium (n = 75 272) of human epigenome-wide association studies. We observed the emergence of co-localized patterns in the deep autoencoder latent space representations that corresponded to biological network modules. We determined the NCAE configuration with the strongest co-localization and centrality signals in the human protein interactome. Leveraging the NCAE embeddings, we then trained interpretable deep neural networks for risk factor (aging, smoking) and disease (systemic lupus erythematosus) prediction and classification tasks. Remarkably, our NCAE embedding-based models outperformed existing predictors, revealing novel DNA methylation signatures enriched in gene sets and pathways associated with the studied condition in each case. Our data-driven biomarker discovery workflow provides a generally applicable pipeline to capture relevant risk factor and disease information. By surpassing the limitations of knowledge-driven methods, our approach enhances the understanding of complex epigenetic processes, facilitating the development of more effective diagnostic and therapeutic strategies.
Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches
Authors: Yi Dohun , Nam Jin-Wu , Jeong Hyobin 
Published: August 2023

Abstract
Structural variants (SVs) are genomic rearrangements that can take many different forms such as copy number alterations, inversions and translocations. During cell development and aging, somatic SVs accumulate in the genome with potentially neutral, deleterious or pathological effects. Generation of somatic SVs is a key mutational process in cancer development and progression. Despite their importance, the detection of somatic SVs is challenging, making them less studied than somatic single-nucleotide variants. In this review, we summarize recent advances in whole-genome sequencing (WGS)-based approaches for detecting somatic SVs at the tissue and single-cell levels and discuss their advantages and limitations. First, we describe the state-of-the-art computational algorithms for somatic SV calling using bulk WGS data and compare the performance of somatic SV detectors in the presence or absence of a matched-normal control. We then discuss the unique features of cutting-edge single-cell-based techniques for analyzing somatic SVs. The advantages and disadvantages of bulk and single-cell approaches are highlighted, along with a discussion of their sensitivity to copy-neutral SVs, usefulness for functional inferences and experimental and computational costs. Finally, computational approaches for linking somatic SVs to their functional readouts, such as those obtained from single-cell transcriptome and epigenome analyses, are illustrated, with a discussion of the promise of these approaches in health and diseases.
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation
Authors: Davidson Russell B , Coletti Mark , Gao Mu , Piatkowski Bryan , Sreedasyam Avinash , Quadir Farhan , Weston David J , Schmutz Jeremy , Cheng Jianlin , Skolnick Jeffrey , Parks Jerry M , Sedova Ada 
Published: August 2023

Abstract

Motivation
Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction.

Results
We present the predicted structural proteome (25 134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.

Availability and implementation
All data and code are available in public repositories, detailed at https://github.com/BSDExabio/SAFA. The structural models of the S. divinum proteome have been deposited in the ModelArchive repository at https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv.
Predicting insect body masses based on linear measurements: a phylogenetic case study on geometrid moths
Authors: Araújo Foerster Stênio Ítalo , Javoiš Juhan , Holm Sille , Tammaru Toomas 
Published: August 2023

Abstract
Dry body mass (DBM) is perhaps the most biologically informative variable describing body size in invertebrates. Unfortunately, obtaining species-specific indices of DBM is problematic because body mass inevitably changes during the course of the life of an individual. Here, we present a phylogenetically informed analysis of allometric relationships between body size and various linear measurements in the moth family Geometridae, which relies on DBM recorded at a fixed time point of adult life. We demonstrate that all measurements of wing size predict DBM with reasonable accuracy, with the distance between the most distal ends of the two forewings in traditionally mounted moths showing the best performance. Abdomen width provides independent morphometric information and can be used as a proxy of body plan, i.e. a measurement of shape that is not dependent on size. Incorporating abdomen width into the regression models considerably increases their predictive ability. We also show that the allometric relationships are reasonably consistent between the two sexes, between monophyletic clades of Geometridae and between the two geographical regions involved in the study (northern Europe and equatorial Africa). The derived equations thus appear to be general enough to be applied in various studies, from comparative phylogenetic analyses to applied projects monitoring insect biomass.
Dual roles of cellular communication network factor 6 (CCN6) in the invasion and metastasis of oral cancer cells to bone via binding to BMP2 and RANKL
Authors: Hochi Hiroaki , Kubota Satoshi , Takigawa Masaharu , Nishida Takashi 
Published: August 2023

Abstract
The acquisition of motility via epithelial–mesenchymal transition (EMT) and osteoclast induction are essential for the invasion and metastasis of oral squamous cell carcinoma (OSCC) to bone. However, the molecule suppressing both EMT and osteoclastogenesis is still unknown. In this study, we found that cellular communication network factor 6 (CCN6) was less produced in a human OSCC cell line, HSC-3 with mesenchymal phenotype, than in HSC-2 cells without it. Notably, CCN6 interacted with bone morphogenetic protein 2 (BMP2) and suppressed the cell migration of HSC-3 cells stimulated by BMP2. Moreover, knockdown of CCN6 in HSC-2 cells led to the promotion of EMT and enhanced the effect of transforming growth factor-β (TGF-β) on the promotion of EMT. Furthermore, CCN6 combined with BMP2 suppressed EMT. These results suggest that CCN6 strongly suppresses EMT in cooperation with BMP2 and TGF-β. Interestingly, CCN6 combined with BMP2 increased the gene expression of receptor activator of nuclear factor-κB ligand (RANKL) in HSC-2 and HSC-3 cells. Additionally, CCN6 interacted with RANKL, and CCN6 combined with RANKL suppressed RANKL-induced osteoclast formation. In metastatic lesions, increasing BMP2 due to the bone destruction led to interference with binding of CCN6 to RANKL, which results in the promotion of bone metastasis of OSCC cells due to continuous osteoclastogenesis. These findings suggest that CCN6 plays dual roles in the suppression of EMT and in the promotion of bone destruction of OSCC in primary and metastatic lesions, respectively, through cooperation with BMP2 and interference with RANKL.
IL-38 alleviates airway remodeling in chronic asthma via blocking the profibrotic effect of IL-36γ
Authors: Zhang Min , Zhou Jian-Xia , Huang Chu-Qin , Feng Kang-Ni , Zou Xiao-Ling , Cen Jie-Mei , Meng Ping , Li Hong-Tao , Zhang Tian-Tuo 
Published: August 2023

Abstract
Airway remodeling is a major feature of asthma. Interleukin (IL)-36γ is significantly upregulated and promotes airway hyper-responsiveness (AHR) in asthma, but its role in airway remodeling is unknown. Here, we aimed to investigate the role of IL-36γ in airway remodeling, and whether IL-38 can alleviate airway remodeling in chronic asthma by blocking the effects of IL-36γ. IL-36γ was quantified in mice inhaled with house dust mite (HDM). Extracellular matrix (ECM) deposition in lung tissues and AHR were assessed following IL-36γ administration to mice. Airway inflammation, AHR, and remodeling were evaluated after IL-38 or blocking IL-36 receptor (IL-36R) treatment in asthmatic mice. The effects of lung fibroblasts stimulated with IL-36γ and IL-38 were quantified in vitro. Increased expression of IL-36γ was detected in lung tissues of HDM-induced asthmatic mice. The intratracheal instillation of IL-36γ to mice significantly enhanced the ECM deposition, AHR, and the number of activated lung fibroblasts around the airways. IL-38 or blocking IL-36R treated asthmatic mice showed a significant alleviation in the airway inflammation, AHR, airway remodeling, and number of activated fibroblasts around airways as compared with the HDM group. In vitro, IL-36γ promoted the activation and migration of human lung fibroblasts (HFL-1). The administration of IL-38 can counteract these biological processes induced by IL-36γ in HFL-1cells. The results indicated that IL-38 can mitigate airway remodeling by blocking the profibrotic effects of IL-36γ in chronic asthma. IL-36γ may be a new therapeutic target, and IL-38 is a potential candidate agent for inhibiting airway remodeling in asthma.
Low CD4 Count or Being Out of Care Increases the Risk for Mpox Hospitalization Among People With Human Immunodeficiency Virus and Mpox
Authors: Philpott David C , Bonacci Robert A , Weidle Paul J , Curran Kathryn G , Brooks John T , Khalil George , Feldpausch Amanda , Pavlick Jessica , Wortley Pascale , O’Shea Jesse G 
Published: August 2023

Abstract
Human immunodeficiency virus (HIV)–associated immunosuppression may increase the risk of hospitalization with mpox. Among persons diagnosed with mpox in the state of Georgia, we characterized the association between hospitalization with mpox and HIV status. People with HIV and a CD4 count &lt;350 cells/mm3 or who were not engaged in HIV care had an increased risk of hospitalization.
Time series DNA barcoding provides insight into factors influencing wood-boring and bark-feeding insect communities in Scots pine, Sitka spruce, and Noble fir stands
Authors: de Becquevort Sophie , Mckeown Niall J , Blake Max , Shaw Paul W 
Published: August 2023

Abstract
Bark-feeding and wood-boring insect pests can have significant negative impacts on conifers and wood production. The damage they cause is expected to increase in the future due to climate change and the growth of international trade. This study employed DNA barcoding of beetle juveniles (Coleoptera) sampled from standing trap trees and cut log piles at regular intervals over a 2-yr period to monitor the beetle community dynamics and associated environmental factors. Tree species was found to have a major influence on beetle communities, most strikingly at the start of early decay stages. Lower species diversity was reported from standing trap tree samples compared to log pile samples, likely due to higher residual defences in dying and recently dead trees. While the species identified from standing trap trees are more likely to be a threat to the forestry sector, the species found in the log piles are more likely to be beneficial due to their high abundance and their ability to compete with pests for breeding substrate. The analysis of beetles collected inside trees revealed additional information on ontogenetic niches and host preferences beyond that acquired solely from flight interception trap data. Our results offer insights on community composition and dynamics of bark-feeding and wood-boring insect species in Welsh conifer forests and provide resources for monitoring and management of potential pest species.
Inflammation in acute myocardial infarction: the good, the bad and the ugly
Authors: Matter Michael A , Paneni Francesco , Libby Peter , Frantz Stefan , Stähli Barbara E , Templin Christian , Mengozzi Alessandro , Wang Yu-Jen , Kündig Thomas M , Räber Lorenz , Ruschitzka Frank , Matter Christian M 
Published: August 2023

Abstract
Convergent experimental and clinical evidence have established the pathophysiological importance of pro-inflammatory pathways in coronary artery disease. Notably, the interest in treating inflammation in patients suffering acute myocardial infarction (AMI) is now expanding from its chronic aspects to the acute setting. Few large outcome trials have proven the benefits of anti-inflammatory therapies on cardiovascular outcomes by targeting the residual inflammatory risk (RIR), i.e. the smouldering ember of low-grade inflammation persisting in the late phase after AMI. However, these studies have also taught us about potential risks of anti-inflammatory therapy after AMI, particularly related to impaired host defence. Recently, numerous smaller-scale trials have addressed the concept of targeting a deleterious flare of excessive inflammation in the early phase after AMI. Targeting different pathways and implementing various treatment regimens, those trials have met with varied degrees of success. Promising results have come from those studies intervening early on the interleukin-1 and -6 pathways. Taking lessons from such past research may inform an optimized approach to target post-AMI inflammation, tailored to spare ‘The Good’ (repair and defence) while treating ‘The Bad’ (smouldering RIR) and capturing ‘The Ugly’ (flaming early burst of excess inflammation in the acute phase). Key constituents of such a strategy may read as follows: select patients with large pro-inflammatory burden (i.e. large AMI); initiate treatment early (e.g. ≤12 h post-AMI); implement a precisely targeted anti-inflammatory agent; follow through with a tapering treatment regimen. This approach warrants testing in rigorous clinical trials.
The patient experience of in-hospital telemetry monitoring: a qualitative analysis
Authors: Holm Marianne Sætrang , Fålun Nina , Bendz Bjørn , Fridlund Bengt , Langørgen Jørund , Pettersen Trond R , Sandau Kristin E , Norekvål Tone M 
Published: August 2023

Abstract

Aims
In-hospital telemetry monitoring has been an integrated part of arrhythmia monitoring for decades. A substantial proportion of patients require arrhythmia monitoring during stays in non-intensive care units. However, studies exploring patients’ experiences of telemetry monitoring are scarce. Therefore, the aim was to explore and describe patients’ experiences of in-hospital telemetry monitoring in a non-intensive care setting.

Methods and results
Twenty face-to-face, semi-structured interviews were conducted. Interviews were conducted before discharge at two university hospitals in Norway. The patients were purposively sampled, resulting in a well-balanced population comprising 11 men and nine women, mean age 62 years (range 25–83). Average monitoring time was 9 days (range 3–14). Data were audiotaped, transcribed verbatim, and coded using NVivo software. Qualitative content analysis using an inductive approach was performed. Patients expressed a need for individualized information during telemetry monitoring. Their feelings of safety were related to responses from nurses from the central monitoring station when alarms from the telemetry were triggered. Despite perceived physical restrictions and psychological limitations associated with telemetry monitoring, they found monitoring to be beneficial because it facilitated the diagnosis of arrhythmia. Moreover, they expressed a need for improvements in wearable monitoring equipment. Patients expressed ambivalent feelings about discontinuing the telemetry and their readiness for discharge.

Conclusion
Patients need individualized information about the results of their telemetry monitoring in order to better understand the arrhythmia management and to increase their experience of safety after discharge. The limitations patients experienced should be taken into consideration in further upgrades of telemetry monitoring equipment.
Definitive aetiology of unexplained syncope after cardiovascular autonomic tests in a tertiary syncope unit
Authors: Torabi Parisa , Hamrefors Viktor , Sutton Richard , Brignole Michele , Fedorowski Artur 
Published: August 2023

Abstract

Aims
Syncope is a common condition with many possible causes, ranging from benign to life-threatening aetiologies. Establishing a diagnosis can be difficult, and specialized syncope units, using cardiovascular autonomic tests (CATs), including a head-up tilt test, can increase the diagnostic yield. However, up to one-fifth of examined patients have inconclusive CAT results. The aim of the present study was to investigate the predictive value of history, and clinical findings for unexplained syncope after CAT and characterize the group with negative results.

Methods and results
Consecutive syncope patients [n = 2663, 61% women, median age 52 (32–69) years] were evaluated and CAT explained aetiology of syncope in 79% of cases, whereas 21% remained unexplained. Predictors of negative CAT were older age at first syncope (+8% higher odds per 10-year increment, P = 0.042), higher supine heart rate (HR; +12% per 10 b.p.m.; P = 0.003), absence of prodromes (+48%; P &lt; 0.001), hypertension (+45%; P = 0.003), diabetes (+82%; P &lt; 0.001), heart failure (+98%; P = 0.014), and coronary artery disease (+51%; P = 0.027). Compared with vasovagal syncope, patients with negative CAT were older, reported more often the absence of prodromes, and had a higher burden of cardiovascular comorbidities.

Conclusion
A cardiovascular autonomic test established the cause of syncope in 79% of patients evaluated in a syncope unit. Syncope without prodromes and cardiovascular comorbidities were significant predictors of failure to reveal an aetiology from assessment by CAT. These are known risk factors for cardiac syncope and patients with inconclusive CAT warrant further investigation.
Legionella relative abundance in shower hose biofilms is associated with specific microbiome members
Authors: Cavallaro Alessio , Rhoads William J , Sylvestre Émile , Marti Thierry , Walser Jean-Claude , Hammes Frederik 
Published: August 2023

Abstract
Legionella are natural inhabitants of building plumbing biofilms, where interactions with other microorganisms influence their survival, proliferation, and death. Here, we investigated the associations of Legionella with bacterial and eukaryotic microbiomes in biofilm samples extracted from 85 shower hoses of a multiunit residential building. Legionella spp. relative abundance in the biofilms ranged between 0–7.8%, of which only 0–0.46% was L. pneumophila. Our data suggest that some microbiome members were associated with high (e.g. Chthonomonas, Vrihiamoeba) or low (e.g. Aquabacterium, Vannella) Legionella relative abundance. The correlations of the different Legionella variants (30 Zero-Radius OTUs detected) showed distinct patterns, suggesting separate ecological niches occupied by different Legionella species. This study provides insights into the ecology of Legionella with respect to: (i) the colonization of a high number of real shower hoses biofilm samples; (ii) the ecological meaning of associations between Legionella and co-occurring bacterial/eukaryotic organisms; (iii) critical points and future directions of microbial-interaction-based-ecological-investigations.