bluuebunny/crossref_metadata_2025_split huggingface dataset:
m5U-SVM: identification of RNA 5-methyluridine modification sites based on multi-view features of physicochemical features and distributed representation
Authors: Ao Chunyan , Ye Xiucai , Sakurai Tetsuya , Zou Quan , Yu Liang 
Published: April 2023

Abstract
Background
RNA 5-methyluridine (m5U) modifications are obtained by methylation at the C5 position of uridine catalyzed by pyrimidine methylation transferase, which is related to the development of human diseases. Accurate identification of m5U modification sites from RNA sequences can contribute to the understanding of their biological functions and the pathogenesis of related diseases. Compared to traditional experimental methods, computational methods developed based on machine learning with ease of use can identify modification sites from RNA sequences in an efficient and time-saving manner. Despite the good performance of these computational methods, there are some drawbacks and limitations.

Results
In this study, we have developed a novel predictor, m5U-SVM, based on multi-view features and machine learning algorithms to construct predictive models for identifying m5U modification sites from RNA sequences. In this method, we used four traditional physicochemical features and distributed representation features. The optimized multi-view features were obtained from the four fused traditional physicochemical features by using the two-step LightGBM and IFS methods, and then the distributed representation features were fused with the optimized physicochemical features to obtain the new multi-view features. The best performing classifier, support vector machine, was identified by screening different machine learning algorithms. Compared with the results, the performance of the proposed model is better than that of the existing state-of-the-art tool.

Conclusions
m5U-SVM provides an effective tool that successfully captures sequence-related attributes of modifications and can accurately predict m5U modification sites from RNA sequences. The identification of m5U modification sites helps to understand and delve into the related biological processes and functions.
The right ventricular dysfunction and ventricular interdependence in patients with DM: assessment using cardiac MR feature tracking
Authors: Shi Rui , Yang Zhi-Gang , Guo Ying-Kun , Qian Wen-Lei , Gao Yue , Li Xue-Ming , Jiang Li , Xu Hua-Yan , Li Yuan 
Published: April 2023

Abstract
Background
To investigate the difference of right ventricular (RV) structural and functional alteration in patients with diabetes mellitus (DM) with preserved left ventricular ejection fraction (LVEF), and the ventricular interdependence in these patients, using cardiac MR (CMR) feature tracking.

Methods
From December 2016 to February 2022, 148 clinically diagnosed patients with DM who underwent cardiac MR (CMR) in our hospital were consecutively recruited. Fifty-four healthy individuals were included as normal controls. Biventricular strains, including left/right ventricular global longitudinal strain (LV-/RVGLS), left/right ventricular global circumferential strain (LV-/RVGCS), left/right ventricular global radial strain (LV-/RVGRS) were evaluated, and compared between patients with DM and healthy controls. Multiple linear regression and mediation analyses were used to evaluate DM's direct and indirect effects on RV strains.

Results
No differences were found in age (56.98 ± 10.98 vs. 57.37 ± 8.41, p = 0.985), sex (53.4% vs. 48.1%, p = 0.715), and body surface area (BSA) (1.70 ± 0.21 vs. 1.69 ± 0.17, p = 0.472) between DM and normal controls. Patients with DM had decreased RVGLS (− 21.86 ± 4.14 vs. − 24.49 ± 4.47, p = 0.001), RVGCS (− 13.16 ± 3.86 vs. − 14.92 ± 3.08, p = 0.011), and no decrease was found in RVGRS (22.62 ± 8.11 vs. 23.15 ± 9.05, p = 0.743) in patients with DM compared with normal controls. The difference in RVGLS between normal controls and patients with DM was totally mediated by LVGLS (indirect effecting: 0.655, bootstrapped 95%CI 0.138–0.265). The difference in RVGCS between normal controls and DM was partly mediated by the LVGLS (indirect effecting: 0.336, bootstrapped 95%CI 0.002–0.820) and LVGCS (indirect effecting: 0.368, bootstrapped 95%CI 0.028–0.855).

Conclusions
In the patients with DM and preserved LVEF, the difference in RVGLS between DM and normal controls was totally mediated by LVGLS. Although there were partly mediating effects of LVGLS and LVGCS, the decrease in RVGCS might be directly affected by the DM.
Effect of dual residual risk of cholesterol and inflammation on all-cause mortality in patients with cardiovascular disease
Authors: Yang Ling , Yue Qing , Fang Fang , Zhang Yinggen , Liu Peipei , Zhang Zihao , Wang Guodong , Chen Shuohua , Wu Shouling , Yang Xiuhong 
Published: April 2023

Abstract
Background
Randomized controlled trials confirm that risks of residual cholesterol and residual inflammation remains in patients with cardiovascular disease (CVD) even after lipid-lowering therapy. This study aims to investigate the association between dual residual risk of cholesterol and inflammation and all-cause mortality in a real-world population with CVD.

Methods
Patients with a CVD history who first took statins between 1 January 2010 and 31 December 2017 in the Kailuan Study were selected as study participants. According to low-density lipoprotein cholesterol (LDL-C) and hypersensitive C-reactive protein levels, patients were divided into those with no residual risk, residual inflammatory risk (RIR), residual cholesterol risk (RCR), and residual cholesterol and inflammatory risk (RCIR). Cox proportional hazard model was conducted to determine hazard ratio (HR) of all-cause mortality for RIR, RCR, and RCIR. Stratified analysis was conducted according to good medication adherence and 75% of the percentage LDL-C decline, high SMART 2 risk score, and blood pressure and blood glucose at standard levels.

Results
After 6.10 years of follow-up, 377 all-cause deaths occurred in 3509 participants (mean age 63.69 ± 8.41 years, 86.78% men). After adjusting for related risk factors, the HR and (95% confidence interval [CI]) of all-cause mortality in the RIR, RCR, and RCIR was 1.63 (1.05, 2.52), 1.37 (0.98, 1.90), and 1.75 (1.25, 2.46), compared with no residual risk. Similar associations were observed in participants with moderate or low statin compliance, a lower percentage of LDL-C decline, high SMART 2 risk score, uncontrolled blood pressure, and uncontrolled blood glucose, in the RCIR had a 1.66-fold, 2.08-fold, 1.69-fold, 2.04-fold, and 2.05-fold higher risk of all-cause mortality, respectively, than the reference.

Conclusion
Risks of residual cholesterol and residual inflammation remain in patients with CVD after receiving statins, and their combined effect significantly increases the risk of all-cause mortality. Here, this increased risk was dependent on statin compliance, LDL-C reduction, SMART 2 risk score, and blood pressure and blood glucose control.
Acalculous cholecystitis is a common extrahepatic manifestation of hepatitis E and suggests a more serious condition
Authors: Cao Xuemei , Jiang Wei , Shi Lingfeng , Wang Yanping , Chen Jie , Huang Wenxiang , Zhang Shujun 
Published: April 2023

Abstract
Background
This study aimed to understand the incidence and clinical significance of acalculous cholecystitis in patients with acute hepatitis E (HE).

Patients and methods
A single center enrolled 114 patients with acute HE. All patients underwent imaging of the gallbladder, and patients with gallstones and cholecystectomy were excluded.

Results
Acalculous cholecystitis was found in 66 patients (57.89%) with acute HE. The incidence in males was 63.95%, which was significantly higher than in females (39.29%) (P = 0.022). The mean length of hospital stay and the incidence of spontaneous peritonitis in patients with cholecystitis (20.12 ± 9.43 days and 9.09%, respectively) were significantly higher than those in patients without cholecystitis (12.98 ± 7.26 days and 0%, respectively) (P < 0.001 and P = 0.032). Albumin, total bile acid, bilirubin, cholinesterase, and prothrombin activity in patients with cholecystitis were significantly inferior to those in patients without cholecystitis (P < 0.001, P < 0.001, P < 0.001, P < 0.001 and P = 0.003, respectively). After correction by multivariate analysis, albumin and total bile acid were found to be closely related to acalculous cholecystitis in HE.

Conclusion
Acalculous cholecystitis is very common in patients with acute HE, and may serve as a predictor of increased peritonitis, synthetic decompensation, and longer hospital stay.
Application of 3D-printed osteotomy guide plates in proximal femoral osteotomy for DDH in children: a retrospective study
Authors: Sun Jian , Mu Yulei , Cui Yong , Qu Jing , Lian Feng 
Published: April 2023

Abstract
Background
Patients with developmental dysplasia of the hip (DDH) have complex proximal femoral deformities, and orthopedic surgery lacks objectivity. Expectations for surgical outcomes are often not achieved, and postoperative problems are common. Using 3D-printed technology in orthopedics offers a novel approach to precise and individualized treatment in modern orthopedics. The aim of this study was to investigate the value of the application of 3D-printed osteotomy guide plates in femoral osteotomy. The clinical indices of femoral osteotomy in children with DDH using 3D-printed osteotomy guide plates were compared with those of traditional osteotomy.

Methods
The clinical data of children with DDH who underwent open reduction and Salter pelvic osteotomy combined with femoral osteotomy from September 2010 to September 2020 were retrospectively collected and analyzed. Based on the inclusion and exclusion criteria, a total of 36 patients were included in the study: 16 in the guide plate group and 20 in the conventional group. Operation time (total), operation time (femoral side), X-ray fluoroscopy times (total), X-ray fluoroscopy times (femoral side) and intraoperative blood loss were analyzed and compared between the two groups. Comparison of treatment-related indicators such as postoperative neck-shaft angle, postoperative anteversion angle, hospitalization time, and hospitalization expenses is made between the two groups. The two groups of patients were evaluated at the last follow-up using the McKay clinical evaluation criteria.

Results
Between the two groups, there were significant differences in operation time (total), operation time (femoral side), X-ray fluoroscopy times (total), X-ray fluoroscopy times (femoral side) and intraoperative blood loss (P < 0.05). The postoperative neck-shaft angle, postoperative anteversion angle, hospitalization time and hospitalization expenses did not differ significantly (P > 0.05). The MacKay clinical evaluation did not significantly differ at the most recent follow-up (P > 0.05).

Conclusions
Children with DDH undergoing proximal femoral osteotomy using 3D-printed osteotomy guide plates benefit from a simpler surgical procedure, shorter operative time, less bleeding and less radiation exposure during surgery. This technique is of great clinical value.
Concordance of adenosine deaminase with immunoglobulins and lymphocyte subsets in EBV-related diseases
Authors: Shi Ting , Ding Qi , Liu Xinglou , Ai Guo , Zhou Hua , Huang Linlin 
Published: April 2023

Abstract
Background
Clinical manifestations of Epstein–Barr virus (EBV) infection are diverse. This study aimed to explore the immune response in EBV-related diseases and the correlation between immune cells and adenosine deaminase (ADA) levels.

Methods
This study was conducted at the Children’s Hospital of Soochow University. In total, 104 patients with EBV-associated respiratory tract infection (EBV-RTI), 32 patients with atypical EBV infection, 54 patients with EBV-associated infectious mononucleosis (IM1, with normal alanine aminotransferase [ALT] levels), 50 patients with EBV-IM2 (with elevated ALT levels), 50 patients with acute respiratory infection (AURI, with other pathogens), and 30 healthy controls were enrolled in this study. Indicators of ADA, immunoglobulins (Igs), and lymphocyte subsets were analyzed for EBV-related diseases.

Results
Differences in the white blood cell, lymphocyte counts, ADA levels, IgA, IgG and IgM titers, percentage of CD3+, CD3+CD4+, CD3+CD8+, CD16+CD56+, CD3−CD19+, and CD19+CD23+ lymphocytes, and CD4+/CD8+ ratio between EBV-related disease groups were all statistically significant (P < 0.01). ADA levels in the EBV-related disease groups were significantly higher than those in the control group (P < 0.01). The lymphocyte count, ADA levels, IgA and IgG titers, and percentage of CD3+ and CD3+CD8 + lymphocytes in the atypical EBV infection, EBV-IM1, and EBV-IM2 groups were significantly higher than those in the EBV-RTI, AUTI, and control groups (P < 0.01), whereas the percentage of CD3+CD4+, CD3−CD19+, and CD19+CD23+ lymphocytes and CD4+/CD8+ ratio showed the opposite trend. ADA levels were consistent with and closely related to the viral load and cellular and humoral immunity in EBV-related diseases.

Conclusions
ADA levels, humoral immunity, and cellular immunity were diverse in EBV-related diseases, and ADA was closely related to Igs and lymphocyte subsets.
A graph neural network-based interpretable framework reveals a novel DNA fragility–associated chromatin structural unit
Authors: Sun Yu , Xu Xiang , Lin Lin , Xu Kang , Zheng Yang , Ren Chao , Tao Huan , Wang Xu , Zhao Huan , Tu Weiwei , Bai Xuemei , Wang Junting , Huang Qiya , Li Yaru , Chen Hebing , Li Hao , Bo Xiaochen 
Published: April 2023

AbstractBackgroundDNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation.ResultsHere, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility–associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation.ConclusionsOur study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome.
Factors related to mortality in critically ill histoplasmosis: a multicenter retrospective study in Guadeloupe and French Guyana
Authors: Camous Laurent , Surel Arthur , Kallel Hatem , Nicolas Muriel , Martino Frederic , Valette Marc , Demoule Alexandre , Pommier Jean-David 
Published: April 2023

Abstract
Purpose
To describe clinical and biological features and the outcomes of patients admitted for histoplasmosis in two intensive care units (ICU) in French Guyana and in the French West Indies (Guadeloupe).

Methods
All patients admitted to these two ICUs for culture-proven histoplasmosis between January 2014 to August 2022 were included in the study. Using univariate and multivariate analysis, we assessed risk factors at ICU admission that were associated with death.

Results
Forty patients were included (65% men). Median age was 56 years and simplified acute physiologic score (SAPS) II was 65. HIV was found in 58%, another immunodeficiency was identified in 28%, and no underlying immunodeficiency could be identified in 14% of patients. Within the first 24 h of ICU admission, 85% of patients had acute respiratory failure, 78% had shock, 30% had coma, and 48% had hemophagocytic lymphohistiocytosis. Mechanical ventilation was instituted in 78% of patients and renal replacement therapy in 55%. The 30-day mortality was 53%. By multivariate analysis, factors independently associated with 30-day mortality were SOFA score (odds ratio [OR] 1.5, 95% confidence interval [CI] [1.1–2.1]), time between symptom onset and treatment per day (OR 1.1, 95% CI 1.0–1.1), and hemophagocytic lymphohistiocytosis (OR 6.4, 95% CI 1.1–47.5).

Conclusion
Histoplasmosis requiring ICU admission is a protean disease with multiple and severe organ involvement. Immunodeficiency is found in most patients. The prognosis remains severe despite appropriate treatment and is worsened by late treatment initiation.
ReactiveFnJ: A choreographed model for Fork-Join Workflow in Serverless Computing
Authors: Bharti Urmil , Goel Anita , Gupta S. C. 
Published: April 2023

AbstractFunction-as-a-Service (FaaS) is an event-based reactive programming model where functions run in ephemeral stateless containers for short duration. For building complex serverless applications, function composition is crucial to coordinate and synchronize the workflow of an application. Some serverless orchestration systems exist, but they are in their primitive state and do not provide inherent support for non-trivial workflows like, Fork-Join. To address this gap, we propose a fully serverless and scalable design model ReactiveFnJ for Fork-Join workflow. The intent of this work is to illustrate a design which is completely choreographed, reactive, asynchronous, and represents a dynamic composition model for serverless applications based on Fork-Join workflow. Our design uses two innovative patterns, namely, Relay Composition and Master-Worker Composition to solve execution time-out challenges. As a Proof-of-Concept (PoC), the prototypical implementation of Split-Sort-Merge use case, based on Fork-Join workflow is discussed and evaluated. The ReactiveFnJ handles embarrassingly parallel computations, and its design does not depend on any external orchestration services, messaging services, and queue services. ReactiveFnJ facilitates in designing fully automated pipelines for distributed data processing systems, satisfying the Serverless Trilemma in true essence. A file of any size can be processed using our effective and extensible design without facing execution time-out challenges. The proposed model is generic and can be applied to a wide range of serverless applications that are based on the Fork-Join workflow pattern. It fosters the choreographed serverless composition for complex workflows. The proposed design model is useful for software engineers and developers in industry and commercial organizations, total solution vendors and academic researchers.
Tau in cerebrospinal fluid induces neuronal hyperexcitability and alters hippocampal theta oscillations
Authors: Brown Jessica , Camporesi Elena , Lantero-Rodriguez Juan , Olsson Maria , Wang Alice , Medem Blanca , Zetterberg Henrik , Blennow Kaj , Karikari Thomas K. , Wall Mark , Hill Emily 
Published: April 2023

AbstractAlzheimer’s disease (AD) and other tauopathies are characterized by the aggregation of tau into soluble and insoluble forms (including tangles and neuropil threads). In humans, a fraction of both phosphorylated and non-phosphorylated N-terminal to mid-domain tau species, are secreted into cerebrospinal fluid (CSF). Some of these CSF tau species can be measured as diagnostic and prognostic biomarkers, starting from early stages of disease. While in animal models of AD pathology, soluble tau aggregates have been shown to disrupt neuronal function, it is unclear whether the tau species present in CSF will modulate neural activity. Here, we have developed and applied a novel approach to examine the electrophysiological effects of CSF from patients with a tau-positive biomarker profile. The method involves incubation of acutely-isolated wild-type mouse hippocampal brain slices with small volumes of diluted human CSF, followed by a suite of electrophysiological recording methods to evaluate their effects on neuronal function, from single cells through to the network level. Comparison of the toxicity profiles of the same CSF samples, with and without immuno-depletion for tau, has enabled a pioneering demonstration that CSF-tau potently modulates neuronal function. We demonstrate that CSF-tau mediates an increase in neuronal excitability in single cells. We then observed, at the network level, increased input–output responses and enhanced paired-pulse facilitation as well as an increase in long-term potentiation. Finally, we show that CSF-tau modifies the generation and maintenance of hippocampal theta oscillations, which have important roles in learning and memory and are known to be altered in AD patients. Together, we describe a novel method for screening human CSF-tau to understand functional effects on neuron and network activity, which could have far-reaching benefits in understanding tau pathology, thus allowing for the development of better targeted treatments for tauopathies in the future.
Graphical Abstract
Light ion dynamics in the topside ionosphere and plasmasphere during geomagnetic storms
Authors: Pakhotin I. P. , Burchill J. K. , Förster M. , Lomidze L. 
Published: April 2023

AbstractStorm-time topside ionosphere plasma composition, especially the light ion fraction, is an important parameter which controls magnetosphere–ionosphere coupling, plays a part in the growth of local instabilities, and provides information about the ring current, ion upflow, movement of ionization and other important physical processes and parameters. Ion composition is difficult to estimate on fine scales as empirical models tend to be parametrized by fixed inputs, ignoring the role of memory in plasma, and to preferentially capture large scales, while ground radars have limited coverage. In particular, ionospheric composition measurements at mid-latitude are lacking. Here we show, using the new Swarm SLIDEM effective ion mass measurement, a superposed epoch analysis of storm-time dayside and nightside effective ion mass changes, demonstrating the extent and timescales of motion of the [O+]/[H+] transition height with the main phase of geomagnetic storms, as well as directly observing evidence for the latitude dependence of these dynamics.
Graphical Abstract