bluuebunny/crossref_metadata_2025_split huggingface dataset:
CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs
Authors: Nguyen Thi-Hau , Nguyen Ha-Nam , Vu Trung Nghia 
Published: January 2024

AbstractAnalyzing the interactions of circular RNAs (circRNAs) is a crucial step in understanding their functional impacts. While there are numerous visualization tools available for investigating circRNA interaction networks, these tools are typically limited to known circRNAs from specific databases. Moreover, these existing tools usually require complex installation procedures which can be time-consuming and challenging for users. There is a lack of a user-friendly web application that facilitates interactive exploration and visualization of circRNA interaction networks. CircNetVis is an interactive online web application to enhance the analysis of human/mouse circRNA interactions. The tool allows three different input formats of circRNAs including circRNA IDs from CircBase, circRNA coordinates (chromosome, start position, end position), and circRNA sequences in the FASTA format. It integrates multiple interaction networks for visualization and investigation of the interplay between circRNA, microRNAs, mRNAs and RNA binding proteins. CircNetVis also enables users to interactively explore the interactions of unknown circRNAs which are not reported from previous databases. The tool can generate interactive plots and allows users to save results as output files for offline usage. CircNetVis is implemented as a web application using R-shiny and freely available for academic use at https://www.meb.ki.se/shiny/truvu/CircNetVis/.
MSCAN: multi-scale self- and cross-attention network for RNA methylation site prediction
Authors: Wang Honglei , Huang Tao , Wang Dong , Zeng Wenliang , Sun Yanjing , Zhang Lin 
Published: January 2024

Abstract
Background
Epi-transcriptome regulation through post-transcriptional RNA modifications is essential for all RNA types. Precise recognition of RNA modifications is critical for understanding their functions and regulatory mechanisms. However, wet experimental methods are often costly and time-consuming, limiting their wide range of applications. Therefore, recent research has focused on developing computational methods, particularly deep learning (DL). Bidirectional long short-term memory (BiLSTM), convolutional neural network (CNN), and the transformer have demonstrated achievements in modification site prediction. However, BiLSTM cannot achieve parallel computation, leading to a long training time, CNN cannot learn the dependencies of the long distance of the sequence, and the Transformer lacks information interaction with sequences at different scales. This insight underscores the necessity for continued research and development in natural language processing (NLP) and DL to devise an enhanced prediction framework that can effectively address the challenges presented.

Results
This study presents a multi-scale self- and cross-attention network (MSCAN) to identify the RNA methylation site using an NLP and DL way. Experiment results on twelve RNA modification sites (m6A, m1A, m5C, m5U, m6Am, m7G, Ψ, I, Am, Cm, Gm, and Um) reveal that the area under the receiver operating characteristic of MSCAN obtains respectively 98.34%, 85.41%, 97.29%, 96.74%, 99.04%, 79.94%, 76.22%, 65.69%, 92.92%, 92.03%, 95.77%, 89.66%, which is better than the state-of-the-art prediction model. This indicates that the model has strong generalization capabilities. Furthermore, MSCAN reveals a strong association among different types of RNA modifications from an experimental perspective. A user-friendly web server for predicting twelve widely occurring human RNA modification sites (m6A, m1A, m5C, m5U, m6Am, m7G, Ψ, I, Am, Cm, Gm, and Um) is available at http://47.242.23.141/MSCAN/index.php.

Conclusions
A predictor framework has been developed through binary classification to predict RNA methylation sites.
Basic helix-loop-helix (bHLH) gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses
Authors: Chen Xingyu , Yao Caimei , Liu Jiahao , Liu Jintao , Fang Jingmei , Deng Hong , Yao Qian , Kang Tairan , Guo Xiaoqiang 
Published: January 2024

Abstract
Background
Rye (Secale cereale), one of the drought and cold-tolerant crops, is an important component of the Triticae Dumortier family of Gramineae plants. Basic helix-loop-helix (bHLH), an important family of transcription factors, has played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, no systemic analysis of the bHLH transcription factor family has yet been reported in rye.

Results
In this study, 220 bHLH genes in S. cereale (ScbHLHs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these ScbHLH genes are systematically analyzed. These 220 ScbHLH members are divided into 21 subfamilies and one unclassified gene. Throughout evolution, the subfamilies 5, 9, and 18 may have experienced stronger expansion. The segmental duplications may have contributed significantly to the expansion of the bHLH family. To systematically analyze the evolutionary relationships of the bHLH family in different plants, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression response characteristics of 22 ScbHLH genes in various biological processes and stress responses were analyzed. Some candidate genes, such as ScbHLH11, ScbHLH48, and ScbHLH172, related to tissue developments and environmental stresses were screened.

Conclusions
The results indicate that these ScbHLH genes exhibit characteristic expression in different tissues, grain development stages, and stress treatments. These findings provided a basis for a comprehensive understanding of the bHLH family in rye.
Glutamine metabolism-related genes and immunotherapy in nonspecific orbital inflammation were validated using bioinformatics and machine learning
Authors: Wu Zixuan , Li Na , Gao Yuan , Cao Liyuan , Yao Xiaolei , Peng Qinghua 
Published: January 2024

Abstract
Background
Nonspecific orbital inflammation (NSOI) is an idiopathic, persistent, and proliferative inflammatory condition affecting the orbit, characterized by polymorphous lymphoid infiltration. Its pathogenesis and progression have been linked to imbalances in tumor metabolic pathways, with glutamine (Gln) metabolism emerging as a critical aspect in cancer. Metabolic reprogramming is known to influence clinical outcomes in various malignancies. However, comprehensive research on glutamine metabolism's significance in NSOI is lacking.

Methods
This study conducted a bioinformatics analysis to identify and validate potential glutamine-related molecules (GlnMgs) associated with NSOI. The discovery of GlnMgs involved the intersection of differential expression analysis with a set of 42 candidate GlnMgs. The biological functions and pathways of the identified GlnMgs were analyzed using GSEA and GSVA. Lasso regression and SVM-RFE methods identified hub genes and assessed the diagnostic efficacy of fourteen GlnMgs in NSOI. The correlation between hub GlnMgs and clinical characteristics was also examined. The expression levels of the fourteen GlnMgs were validated using datasets GSE58331 and GSE105149.

Results
Fourteen GlnMgs related to NSOI were identified, including FTCD, CPS1, CTPS1, NAGS, DDAH2, PHGDH, GGT1, GCLM, GLUD1, ART4, AADAT, ASNSD1, SLC38A1, and GFPT2. Biological function analysis indicated their involvement in responses to extracellular stimulus, mitochondrial matrix, and lipid transport. The diagnostic performance of these GlnMgs in distinguishing NSOI showed promising results.

Conclusions
This study successfully identified fourteen GlnMgs associated with NSOI, providing insights into potential novel biomarkers for NSOI and avenues for monitoring disease progression.
Effects of paclobutrazol seed priming on seedling quality, photosynthesis, and physiological characteristics of fragrant rice
Authors: Zhang Yingying , He Zhenzhen , Xing Pipeng , Luo Haowen , Yan Zhuosheng , Tang Xiangru 
Published: January 2024

Abstract
Background
Paclobutrazol is widely used in the agricultural field. This study investigated the effects of seed priming with different concentrations of paclobutrazol on seedling quality, 2-acetyl-1-pyrroline (2-AP, a key aroma component of fragrant rice) biosynthesis, and related physiological and biochemical indicators in fragrant rice seedlings.

Results
The experiment is being conducted at the College of Agriculture, South China Agricultural University. In the experiment, three concentrations of paclobutrazol (Pac 1: 20 mg·L−1; Pac 2: 40 mg·L−1; Pac 3: 80 mg·L−1) were used to initiate the treatment of fragrant rice seeds, while water treatment was used as a control (CK). The results showed that compared with CK, paclobutrazol treatment reduced plant height, increased stem diameter, and increased fresh and dry weight of aromatic rice seedlings. Moreover, paclobutrazol treatment also increased the seedlings’ photosynthetic pigment content and net photosynthetic rate.

Conclusions
This study demonstrates that paclobutrazol primarily increases the content of proline by reducing the content of glutamate and down-regulating the expression of P5CS2, thereby promoting the conversion of proline to the aromatic substance 2-AP. Under the appropriate concentration of paclobutrazol (40 mg·L−1~80 mg·L−1), the seedling quality, stress resistance, and aroma of fragrant rice can be improved.
Clinical prognostic impact of C-NLR in heart failure patients with different ejection fractions: a retrospective study
Authors: Yang Fazhi , Zhang Lihua , Huang Wei , Liu Dajin , Yang Yunhong , Gu Wenyi , Shi Tao , Yang Sirui , Chen Lixing 
Published: January 2024

Abstract
Objection
Inflammatory conditions and immune disorders may worsen the prognosis of chronic heart failure (CHF) patients. The aim of this study was to evaluate the prognostic value of a new indicator, C-NLR, composed of C-reactive protein (CRP) and neutrophil-to-lymphocyte ratio (NLR), for the risk of all-cause mortality in HF patients with different ejection fractions.

Methods
A total of 1221 CHF patients admitted to the First Affiliated Hospital of Kunming Medical University from January 2017 to October 2021 were enrolled in this study. All patients were divided into 2 groups according to the median C-NLR. Kaplan–Meier survival curves were used to compare the all-cause mortality among CHF patients with different ejection fractions. Cox proportional hazards analysis was used to evaluate the relationships between variables and mortality. The predictive value of the C-NLR was assessed by using receiver operating characteristic (ROC) analyses.

Results
We collected data from 1192 patients with CHF. Kaplan–Meier survival analysis revealed that patients with low LCR levels had better overall survival (OS). After multivariate adjustment Cox proportional hazards analysis, the level of C-NLR was still independently related to mortality.

Conclusions
C-NLR was a competent independent predictor in HF with different ejection fractions, and routine measurement of C-NLR would help clinical doctors identify patients with a poor prognosis.
Potential Added Value of 18F-FDG PET Metabolic Parameters in Predicting Disease Relapse in Type 1 Autoimmune Pancreatitis
Authors: Chen Shengxin , Wang Guanyun , Wu Lang , Chen Dexin , Fang Kaixuan , Liu Wenjing , Xu Baixuan , Zhai Ya-qi , Li Mingyang 
Published: January 2024

Abstract
Background
The predictive value of 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) metabolic parameters for predicting AIP relapse is currently unknown. This study firstly explored the value of 18F-FDG PET/CT parameters as predictors of type 1 AIP relapse.

Methods
This multicenter retrospective cohort study analyzed 51 patients who received 18F-FDG PET/CT prior to treatment and did not receive maintenance therapy after remission. The study collected baseline characteristics and clinical data and conducted qualitative and semi-quantitative analysis of pancreatic lesions and extrapancreatic organs. The study used three thresholds to select the boundaries of pancreatic lesions to evaluate metabolic parameters, including the maximum standard uptake value (SUVmax), mean standard uptake value (SUVmean), total lesion glycolysis (TLG), metabolic tumor volume (MTV), and tumor-to-normal liver standard uptake value ratio (SUVR). Univariate and multivariate analyses were performed to identify independent predictors and build a recurrence prediction model. The model was internally validated using the bootstrap method and a nomogram was created for clinical application.

Results
In the univariable analysis, the relapsed group showed higher levels of SUVmax (6.0 ± 1.6 vs. 5.2 ± 1.1; P = 0.047), SUVR (2.3 [2.0–3.0] vs. 2.0 [1.6–2.4]; P = 0.026), and TLG2.5 (234.5 ± 149.1 vs. 139.6 ± 102.5; P = 0.020) among the 18F-FDG PET metabolic parameters compared to the non-relapsed group. In the multivariable analysis, serum IgG4 (OR, 1.001; 95% CI, 1.000–1.002; P = 0.014) and TLG2.5 (OR, 1.007; 95% CI, 1.002–1.013; P = 0.012) were independent predictors associated with relapse of type 1 AIP. A receiver-operating characteristic curve of the predictive model with these two predictors demonstrated an area under the curve of 0.806.

Conclusion
18F-FDG PET/CT metabolic parameters, particularly TLG2.5, are potential predictors for relapse in patients with type 1 AIP. A multiparameter model that includes IgG4 and TLG2.5 can enhance the ability to predict AIP relapse.
Multimodal home-based rehabilitation intervention after discharge from inpatient geriatric rehabilitation (GeRas): study protocol for a multicenter randomized controlled trial
Authors: Abel Bastian , Bongartz Martin , Rapp Kilian , Roigk Patrick , Peiter Janine , Metz Brigitte , Finger Benjamin , Büchele Gisela , Wensing Michel , Roth Catharina , Schmidberger Oliver , König Hans-Helmut , Gottschalk Sophie , Dams Judith , Deuster Oliver , Immel Désirée , Micol William , Bauer Jürgen M. , Benzinger Petra 
Published: January 2024

Abstract
Background
Geriatric rehabilitation aims to maintain the functional reserves of older adults in order to optimize social participation and prevent disability. After discharge from inpatient geriatric rehabilitation, patients are at high risk for decreased physical capacity, increased vulnerability, and limitations in mobility. As a result, ageing in place becomes uncertain for a plethora of patients after discharge from geriatric rehabilitation and effective strategies to prevent physical decline are required. Collaboration between different health-care providers is essential to improve continuity of care after discharge from inpatient geriatric rehabilitation. The aim of this study is to evaluate the effectiveness of a multi-professional home-based intervention program (GeRas) to improve functional capacity and social participation in older persons after discharge from inpatient geriatric rehabilitation.

Methods
The study is a multicenter, three-arm, randomized controlled trial with a three-month intervention period. Two hundred and seventy community-dwelling older people receiving inpatient geriatric rehabilitation will be randomized with a 1:1:1 ratio to one of the parallel intervention groups (conventional IG or tablet IG) or the control group (CG). The participants of both IGs will receive a home-based physical exercise program supervised by physical therapists, a nutritional recommendation by a physician, and social counseling by social workers of the health insurance company. The collaboration between the health-care providers and management of participants will be realized within a cloud environment based on a telemedicine platform and supported by multi-professional case conferences. The CG will receive usual care, two short handouts on general health-related topics, and facultative lifestyle counseling with general recommendations for a healthy diet and active ageing. The primary outcomes will be the physical capacity measured by the Short Physical Performance Battery and social participation assessed by the modified Reintegration to Normal Living Index, three months after discharge.

Discussion
The GeRas program is designed to improve the collaboration between health-care providers in the transition from inpatient geriatric rehabilitation to outpatient settings. Compared to usual care, it is expected to improve physical capacity and participation in geriatric patients after discharge from inpatient geriatric rehabilitation.

Trial registration
German Clinical Trials Register (DRKS00029559). Registered on October 05, 2022.
Finger nodules with a papulovesicular hands and feet eruption: a complicated human Orf virus infection
Authors: Salvi Martina , Tiecco Giorgio , Rossi Luca , Venturini Marina , Battocchio Simonetta , Castelli Francesco , Quiros-Roldan Eugenia 
Published: January 2024

Abstract
Background
Orf virus (ORFV) is the pathogen responsible for Orf, a zoonotic viral infection that can be spread to humans from sheep and goats. Here, we present a case of human Orf complicated by an immune-related reaction, to raise awareness of this under-recognized disease avoiding unnecessary investigations and overtreatment.

Case report
A 51-year-old woman with no previous medical history presented with a one-week history of three asymptomatic swelling nodules with a grey necrotic center and red outer halo on her index finger. At physical examination there was also a pruritic papulovesicular eruption on her hands and feet. She reported a recent contact with a goat which had a similar nodular lesion in its mouth. A biopsy of the lesions was performed and a diagnosis of Orf complicated by widespread erythema multiforme was made based on the clinical and histopathological features. The lesions spontaneously resolved within the next 2 weeks.

Conclusions
Orf is not very prevalent in our region, so we performed a biopsy of the lesion to guide us toward a diagnosis. However, we should remember that the diagnosis of ecthyma relies on clinical evaluation and epidemiological criteria.
Expanding the genotype-phenotype spectrum in SCN8A-related disorders
Authors: Hebbar Malavika , Al-Taweel Nawaf , Gill Inderpal , Boelman Cyrus , Dean Richard A. , Goodchild Samuel J. , Mezeyova Janette , Shuart Noah Gregory , Johnson J. P. , Lee James , Michoulas Aspasia , Huh Linda L. , Armstrong Linlea , Connolly Mary B. , Demos Michelle K. 
Published: January 2024

Abstract
Background
SCN8A-related disorders are a group of variable conditions caused by pathogenic variations in SCN8A. Online Mendelian Inheritance in Man (OMIM) terms them as developmental and epileptic encephalopathy 13, benign familial infantile seizures 5 or cognitive impairment with or without cerebellar ataxia.

Methods
In this study, we describe clinical and genetic results on eight individuals from six families with SCN8A pathogenic variants identified via exome sequencing.

Results
Clinical findings ranged from normal development with well-controlled epilepsy to significant developmental delay with treatment-resistant epilepsy. Three novel and three reported variants were observed in SCN8A. Electrophysiological analysis in transfected cells revealed a loss-of-function variant in Patient 4.

Conclusions
This work expands the clinical and genotypic spectrum of SCN8A-related disorders and provides electrophysiological results on a novel loss-of-function SCN8A variant.
Predictive value of cytokines combined with human neutrophil lipocalinin acute ischemic stroke-associated pneumonia
Authors: Zhang Mingming , Shi Xiaoqian , Zhang Bin , Zhang Yingqi , Chen Ying , You Daofeng , Zhao Hongmin , Lu Qianqian , Ma Yanrong 
Published: January 2024

Abstract
Objective
To explore the predictive value of interleukin-6 (IL-6) combined with human neutrophil lipocalin (HNL) of stroke-associated pneumonia (SAP) in patients who were diagnosed with acute ischemic stroke (AIS).

Methods
108patients were divided into two groups: pneumonia group (52 cases) and non-pneumonia group (56 cases), according to whether the patients developed SAP within 7 days of admission. General information was compared between the two groups, like age, gender, history of hypertension, diabetes mellitus, cardiovascular disease, dysphagia, smoking and alcoholhistory. Clinical data were recorded and compared, including lipid profile, interleukin-6 (IL-6), homocysteine (Hcy), National Institutes of Health Stroke Scale (NIHSS) score, and HNL. Multivariate Logistic regression analysis was used to screen the risk factors of AIS-AP, and the predictive value of IL-6 and HNL alone and in combination was evaluated by receiver operating characteristic curve (ROC curve).

Results
Logistic regression analysis showed that dysphagia (OR,0.018; 95% CI, 0.001 ~ 0.427; P = 0.013), increased NIHSS scores(OR,0.012; 95% CI, 0.000 ~ 0.434; P = 0.016), and high levels of IL-6 (OR,0.014; 95% CI, 0.000 ~ 0.695; P = 0.032)and HNL (OR,0.006; 95% CI, 0.000 ~ 0.280; P = 0.009) were independent risk factors for SAP with significant difference (all P < 0.05). According to the ROC curve analysis of IL-6, the area under the curve (AUC) was 0.881 (95% CI: 0.820 ~ 0.942), and the optimal cutoff value was 6.89 pg/mL with the sensitivity of 73.1% and specificity of 85.7%. As for the ROC curve analysis of HNL, the AUC was 0.896 (95% CI: 0.839 ~ 0.954), and the best cutoff value was 99.66ng/mL with the sensitivity of 76.9% and specificity of 89.3%. The AUC of the combination of IL-6 and HNL increased to 0.952 (95% CI: 0.914 ~ 0.989), and the sensitivity and specificity increased to 80.8% and 92.9%, respectively.

Conclusion
In this research, the levels of IL-6 ≥ 6.89 pg/mL and HNL ≥ 99.66ng/mL were considered as risk factors for AIS patients complicated with SAP. The combined detection had higher predictive value for patients with SAP, which may help to identify who were in highrisk.
Low-molecular-weight heparin for the prevention of preeclampsia in high-risk pregnancies without thrombophilia: a systematic review and meta-analysis
Authors: Chen Jiahui , Huai Jing , Yang Huixia 
Published: January 2024

Abstract
Objectives
To systematically evaluate the efficacy of low molecular weight heparin (LMWH) to prevent preeclampsia in high risk pregnant women without thrombophilia.

Search strategy
PubMed, Embase and the Cochrane library were searched for articles published before 1st August 2022 using the combination keywords “preeclampsia”, “Low Molecular Weight Heparin”, “LMWH”, “Heparin, Low Molecular Weight”, “Dalteparin”, “Nadroparin”, and “Tinzaparin”. Selection criteria: Randomized controlled trials evaluating the use of LMWH in pregnant women at high risk of preeclampsia without thrombophilia.

Data collection and analysis
Ten studies were included in the meta-analysis (1758 patients in total). Outcomes were expressed as relative risk (RR) with 95% confidence intervals (CI).

Results
LMWH reduced the incidence of PE (RR = 0.67; 95% CI = 0.50–0.90; P = 0.009) in high risk pregnant women without thrombophilia. Subgroup analysis found that the prophylactic effect of LMWH was only significant in studies using low-dose aspirin (LDA) as the primary intervention. The combination of LMWH and LDA was also effective for the prevention of preterm birth and fetal growth restriction, but had no effect on the incidence of placenta abruption.

Conclusion
For women at high risk of developing preeclampsia without thrombophilia, the combination of LMWH and low-dose aspirin is effective for the prevention of preeclampsia, preterm birth and fetal growth restriction and is superior to LDA alone.