bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiovascular disease incidence prediction by machine learning and statistical techniques: a 16-year cohort study from eastern Mediterranean region
Authors: Mehrabani-Zeinabad Kamran , Feizi Awat , Sadeghi Masoumeh , Roohafza Hamidreza , Talaei Mohammad , Sarrafzadegan Nizal 
Published: April 2023

Abstract
Background
Cardiovascular diseases (CVD) are the predominant cause of early death worldwide. Identification of people with a high risk of being affected by CVD is consequential in CVD prevention. This study adopts Machine Learning (ML) and statistical techniques to develop classification models for predicting the future occurrence of CVD events in a large sample of Iranians.

Methods
We used multiple prediction models and ML techniques with different abilities to analyze the large dataset of 5432 healthy people at the beginning of entrance into the Isfahan Cohort Study (ICS) (1990–2017). Bayesian additive regression trees enhanced with “missingness incorporated in attributes” (BARTm) was run on the dataset with 515 variables (336 variables without and the remaining with up to 90% missing values). In the other used classification algorithms, variables with more than 10% missing values were excluded, and MissForest imputes the missing values of the remaining 49 variables. We used Recursive Feature Elimination (RFE) to select the most contributing variables. Random oversampling technique, recommended cut-point by precision-recall curve, and relevant evaluation metrics were used for handling unbalancing in the binary response variable.

Results
This study revealed that age, systolic blood pressure, fasting blood sugar, two-hour postprandial glucose, diabetes mellitus, history of heart disease, history of high blood pressure, and history of diabetes are the most contributing factors for predicting CVD incidence in the future. The main differences between the results of classification algorithms are due to the trade-off between sensitivity and specificity. Quadratic Discriminant Analysis (QDA) algorithm presents the highest accuracy (75.50 ± 0.08) but the minimum sensitivity (49.84 ± 0.25); In contrast, decision trees provide the lowest accuracy (51.95 ± 0.69) but the top sensitivity (82.52 ± 1.22). BARTm.90% resulted in 69.48 ± 0.28 accuracy and 54.00 ± 1.66 sensitivity without any preprocessing step.

Conclusions
This study confirmed that building a prediction model for CVD in each region is valuable for screening and primary prevention strategies in that specific region. Also, results showed that using conventional statistical models alongside ML algorithms makes it possible to take advantage of both techniques. Generally, QDA can accurately predict the future occurrence of CVD events with a fast (inference speed) and stable (confidence values) procedure. The combined ML and statistical algorithm of BARTm provide a flexible approach without any need for technical knowledge about assumptions and preprocessing steps of the prediction procedure.
N-terminal region of Drosophila melanogaster Argonaute2 forms amyloid-like aggregates
Authors: Narita Haruka , Shima Tomohiro , Iizuka Ryo , Uemura Sotaro 
Published: April 2023

Abstract
Background
Argonaute proteins play a central role in RNA silencing by forming protein-small RNA complexes responsible for the silencing process. While most Argonaute proteins have a short N-terminal region, Argonaute2 in Drosophila melanogaster (DmAgo2) harbors a long and unique N-terminal region. Previous in vitro biochemical studies have shown that the loss of this region does not impair the RNA silencing activity of the complex. However, an N-terminal mutant of Drosophila melanogaster has demonstrated abnormal RNA silencing activity. To explore the causes of this discrepancy between in vitro and in vivo studies, we investigated the biophysical properties of the region. The N-terminal region is highly rich in glutamine and glycine residues, which is a well-known property for prion-like domains, a subclass of amyloid-forming peptides. Therefore, the possibility of the N-terminal region functioning as an amyloid was tested.

Results
Our in silico and biochemical assays demonstrated that the N-terminal region exhibits amyloid-specific properties. The region indeed formed aggregates that were not dissociated even in the presence of sodium dodecyl sulfate. Also, the aggregates enhanced the fluorescence intensity of thioflavin-T, an amyloid detection reagent. The kinetics of the aggregation followed that of typical amyloid formation exhibiting self-propagating activity. Furthermore, we directly visualized the aggregation process of the N-terminal region under fluorescence microscopy and found that the aggregations took fractal or fibril shapes. Together, the results indicate that the N-terminal region can form amyloid-like aggregates.

Conclusions
Many other amyloid-forming peptides have been reported to modulate the function of proteins through their aggregation. Therefore, our findings raise the possibility that aggregation of the N-terminal region regulates the RNA silencing activity of DmAgo2.
Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size
Authors: Mahto Arunima , Yadav Antima , P. V. Aswathi , Parida Swarup K. , Tyagi Akhilesh K. , Agarwal Pinky 
Published: April 2023

Abstract
Background
Rice grain size (GS) is an essential agronomic trait. Though several genes and miRNA modules influencing GS are known and seed development transcriptomes analyzed, a comprehensive compendium connecting all possible players is lacking. This study utilizes two contrasting GS indica rice genotypes (small-grained SN and large-grained LGR). Rice seed development involves five stages (S1–S5). Comparative transcriptome and miRNome atlases, substantiated with morphological and cytological studies, from S1–S5 stages and flag leaf have been analyzed to identify GS proponents.

Results
Histology shows prolonged endosperm development and cell enlargement in LGR. Stand-alone and comparative RNAseq analyses manifest S3 (5–10 days after pollination) stage as crucial for GS enhancement, coherently with cell cycle, endoreduplication, and programmed cell death participating genes. Seed storage protein and carbohydrate accumulation, cytologically and by RNAseq, is shown to be delayed in LGR. Fourteen transcription factor families influence GS. Pathway genes for four phytohormones display opposite patterns of higher expression. A total of 186 genes generated from the transcriptome analyses are located within GS trait-related QTLs deciphered by a cross between SN and LGR. Fourteen miRNA families express specifically in SN or LGR seeds. Eight miRNA-target modules display contrasting expressions amongst SN and LGR, while 26 (SN) and 43 (LGR) modules are differentially expressed in all stages.

Conclusions
Integration of all analyses concludes in a “Domino effect” model for GS regulation highlighting chronology and fruition of each event. This study delineates the essence of GS regulation, providing scope for future exploits. The rice grain development database (RGDD) (
www.nipgr.ac.in/RGDD/index.php; https://doi.org/10.5281/zenodo.7762870) has been developed for easy access of data generated in this paper.
Triglyceride-glucose index, symptomatic intracranial artery stenosis and recurrence risk in minor stroke patients with hypertension
Authors: Wang Yongle , Liu Tingting , Li Yanan , Zhang Kaili , Fan Haimei , Ren Jing , Li Juan , Li Yali , Li Xinyi , Wu Xuemei , Wang Junhui , Xue Lixi , Gao Xiaolei , Yan Yuping , Li Gaimei , Liu Qingping , Niu Wenhua , Du Wenxian , Liu Yuting , Niu Xiaoyuan 
Published: April 2023

Abstract
Background
The triglyceride-glucose (TyG) index, a simple measure of insulin resistance, is associated with intracranial atherosclerosis (ICAS) and stroke. In hypertensive populations, this association may be pronounced. The aim was to investigate the relationship between TyG and symptomatic intracranial atherosclerosis (sICAS) and recurrence risk in ischemic stroke patients with hypertension.

Methods
This prospective, multicenter cohort study included patients with acute minor ischemic stroke with a preadmission diagnosis of hypertension from September 2019 to November 2021 with a 3-month follow-up. The presence of sICAS was determined by a combination of clinical manifestations, the location of the infarction, and the corresponding artery with moderate-to-severe stenosis. ICAS burden was determined by the degree and number of ICAS occurrences. Fasting blood glucose (FBG) and triglyceride (TG) were measured to calculate TyG. The main outcome was ischemic stroke recurrence during the 90-day follow-up. Multivariate regression models were used to explore the association of TyG, sICAS, and ICAS burden with stroke recurrence.

Results
There were 1281 patients with a mean age of 61.6 ± 11.6 years; 70.1% were male, and 26.4% were diagnosed with sICAS. There were 117 patients who experienced stroke recurrence during follow-up. Patients were categorized according to quartiles of TyG. After adjusting for confounders, the risk of sICAS was greater (OR 1.59, 95% CI 1.04–2.43, p = 0.033) and the risk of stroke recurrence was significantly higher (HR 2.02, 95% CI 1.07–3.84, p = 0.025) in the fourth TyG quartile than in the first quartile. The restricted cubic spline (RCS) plot revealed a linear relationship between TyG and sICAS, and the threshold value for TyG was 8.4. Patients were then dichotomized into low and high TyG groups by the threshold. Patients with high TyG combined with sICAS had a higher risk of recurrence (HR 2.54, 95% CI 1.39–4.65) than patients with low TyG without sICAS. An interaction effect on stroke recurrence between TyG and sICAS was found (p = 0.043).

Conclusion
TyG is a significant risk factor for sICAS in hypertensive patients, and there is a synergistic effect of sICAS and higher TyG on ischemic stroke recurrence.
Trial registration number: The study was registered on 16 August 2019 at https://www.chictr.org.cn/showprojen.aspx?proj=41160 (No. ChiCTR1900025214).
Long non-coding RNA crnde promotes deep vein thrombosis by sequestering miR-181a-5p away from thrombogenic Pcyox1l
Authors: He Xin , Liu Yu , Li Yaozhen , Wu Kemin 
Published: April 2023

Abstract
Background
Deep vein thrombosis (DVT) is an interplay of genetic and acquired risk factors, where functional interactions in lncRNA-miRNA-mRNA ceRNA networks contribute to disease pathogenesis. Based on the high-throughput transcriptome sequencing prediction, we have assessed the contribution of lncRNA Crnde/miR-181a-5p/Pcyox1l axis to thrombus formation.

Methods
DVT was modeled in mice by inferior vena cava stenosis, and inferior vena cava tissues were harvested for high-throughput transcriptome sequencing to screen differentially expressed lncRNAs and mRNAs. The key miRNA binding to Crnde and Pcyox1l was obtained through searching the RNAInter and mirWalk databases. The binding affinity between Crnde, miR-181a-5p, and Pcyox1l was examined by FISH, dual luciferase reporter gene, RNA pull-down, and RIP assays. Functional experiments were conducted in DVT mouse models to assess thrombus formation and inflammatory injury in inferior vena cava.

Results
It was noted that Crnde and Pcyox1l were upregulated in the blood of DVT mice. Crnde competitively bound to miR-181a-5p and inhibited miR-181a-5p expression, and Pcyox1l was the downstream target gene of miR-181a-5p. Silencing of Crnde or restoration of miR-181a-5p reduced inflammatory injury in the inferior vena cava, thus curtailing thrombus formation in mice. Ectopic expression of Pcyox1l counterweighed the inhibitory effect of Crnde silencing.

Conclusions
Therefore, Crnde sequesters miR-181a-5p to release Pcyox1l expression via ceRNA mechanism, thus aggravating thrombus formation in DVT.
Mesenchymal–epithelial transition in lymph node metastases of oral squamous cell carcinoma is accompanied by ZEB1 expression
Authors: Horny Kai , Sproll Christoph , Peiffer Lukas , Furtmann Frauke , Gerhardt Patricia , Gravemeyer Jan , Stoecklein Nikolas H. , Spassova Ivelina , Becker Jürgen C. 
Published: April 2023

Abstract
Background
Oral squamous cell carcinoma (OSCC), an HPV-negative head and neck cancer, frequently metastasizes to the regional lymph nodes but only occasionally beyond. Initial phases of metastasis are associated with an epithelial–mesenchymal transition (EMT), while the consolidation phase is associated with mesenchymal–epithelial transition (MET). This dynamic is referred to as epithelial–mesenchymal plasticity (EMP). While it is known that EMP is essential for cancer cell invasion and metastatic spread, less is known about the heterogeneity of EMP states and even less about the heterogeneity between primary and metastatic lesions.

Methods
To assess both the heterogeneity of EMP states in OSCC cells and their effects on stromal cells, we performed single-cell RNA sequencing (scRNAseq) of 5 primary tumors, 9 matching metastatic and 5 tumor-free lymph nodes and re-analyzed publicly available scRNAseq data of 9 additional primary tumors. For examining the cell type composition, we performed bulk transcriptome sequencing. Protein expression of selected genes were confirmed by immunohistochemistry.

Results
From the 23 OSCC lesions, the single cell transcriptomes of a total of 7263 carcinoma cells were available for in-depth analyses. We initially focused on one lesion to avoid confounding inter-patient heterogeneity and identified OSCC cells expressing genes characteristic of different epithelial and partial EMT stages. RNA velocity and the increase in inferred copy number variations indicated a progressive trajectory towards epithelial differentiation in this metastatic lesion, i.e., cells likely underwent MET. Extension to all samples revealed a less stringent but essentially similar pattern. Interestingly, MET cells show increased activity of the EMT-activator ZEB1. Immunohistochemistry confirmed that ZEB1 was co-expressed with the epithelial marker cornifin B in individual tumor cells. The lack of E-cadherin mRNA expression suggests this is a partial MET. Within the tumor microenvironment we found immunomodulating fibroblasts that were maintained in primary and metastatic OSCC.

Conclusions
This study reveals that EMP enables different partial EMT and epithelial phenotypes of OSCC cells, which are endowed with capabilities essential for the different stages of the metastatic process, including maintenance of cellular integrity. During MET, ZEB1 appears to be functionally active, indicating a more complex role of ZEB1 than mere induction of EMT.
Can carotid artery Doppler variations induced by the end-expiratory occlusion maneuver predict fluid responsiveness in septic shock patients?
Authors: D’Arrigo Sonia , Dell’Anna Antonio Maria , Sandroni Claudio , Messina Antonio , Cacciola Sofia , Pacini Chiara , Antonelli Massimo 
Published: April 2023

Abstract
Background
An increase in cardiac index (CI) during an end-expiratory occlusion test (EEOt) predicts fluid responsiveness in ventilated patients. However, if CI monitoring is unavailable or the echocardiographic window is difficult, using the carotid Doppler (CD) could be a feasible alternative to track CI changes. This study investigates whether changes in CD peak velocity (CDPV) and corrected flow time (cFT) during an EEOt were correlated with CI changes and if CDPV and cFT changes predicted fluid responsiveness in patients with septic shock.

Methods
Prospective, single-center study in adults with hemodynamic instability. The CDPV and cFT on carotid artery Doppler and hemodynamic variables from the pulse contour analysis EV1000™ were recorded at baseline, during a 20-s EEOt, and after fluid challenge (500 mL). We defined responders as those who increased CI ≥ 15% after a fluid challenge.

Results
We performed 44 measurements in 18 mechanically ventilated patients with septic shock and without arrhythmias. The fluid responsiveness rate was 43.2%. The changes in CDPV were significantly correlated with changes in CI during EEOt (r = 0.51 [0.26–0.71]). A significant, albeit lower correlation, was found for cFT (r = 0.35 [0.1–0.58]). An increase in CI ≥ 5.35% during EEOt predicted fluid responsiveness with 78.9% sensitivity and 91.7% specificity, with an area under the ROC curve (AUROC) of 0.85. An increase in CDPV ≥ 10.5% during an EEOt predicted fluid responsiveness with 96.2% specificity and 53.0% sensitivity with an AUROC of 0.74. Sixty-one percent of CDPV measurements (from − 13.5 to 9.5 cm/s) fell within the gray zone. The cFT changes during EEOt did not accurately predict fluid responsiveness.

Conclusions
In septic shock patients without arrhythmias, an increase in CDPV greater than 10.5% during a 20-s EEOt predicted fluid responsiveness with > 95% specificity. Carotid Doppler combined with EEOt may help optimize preload when invasive hemodynamic monitoring is unavailable. However, the 61% gray zone is a major limitation (retrospectively registered on Clinicaltrials.gov NCT04470856 on July 14, 2020).
Effect of vitamin D supplementation on type 2 diabetes biomarkers: an umbrella of interventional meta-analyses
Authors: Musazadeh Vali , Kavyani Zeynab , Mirhosseini Naghmeh , Dehghan Parvin , Vajdi Mahdi 
Published: April 2023

Abstract
Background
Vitamin D supplementation exerts several supporting effects on improving glycemic status, however, results are inconclusive. Thus, in the present study, we aimed to conduct an umbrella of meta-analysis regarding the impact of vitamin D on type 2 diabetes (T2DM) biomarkers.

Methods
The Scopus, PubMed, Web of Science, Embase, and Google Scholar online databases were searched up to March 2022. All meta-analyses evaluating the impact of vitamin D supplementation on T2DM biomarkers were considered eligible. Overall, 37 meta-analyses were included in this umbrella meta-analysis.

Results
Our findings indicated that vitamin D supplementation significantly decreased fasting blood sugar (FBS) (WMD =  − 3.08; 95% CI: − 3.97, − 2.19, p < 0.001, and SMD =  − 0.26; 95% CI: − 0.38, − 0.14, p < 0.001), hemoglobin A1c (HbA1c) (WMD =  − 0.05; 95% CI: − 0.10, − 0.01, p = 0.016, and SMD =  − 0.16; 95% CI: − 0.27, − 0.05, p = 0.004), insulin concentrations (WMD =  − 2.62; 95% CI: − 4.11, − 1.13; p < 0.001, and SMD =  − 0.33; 95% CI: − 0.56, − 0.11, p = 0.004), and homeostatic model assessment for insulin resistance (HOMA-IR) (WMD =  − 0.67; 95% CI: − 1.01, − 0.32, p < 0.001, and SMD =  − 0.31; 95% CI: − 0.46, − 0.16, p < 0.001).

Conclusion
This umbrella meta-analysis proposed that vitamin D supplementation may improve T2DM biomarkers.
An innovative inpatient protocol for alcohol withdrawal prevention in a 16-year-old adolescent: a case report
Authors: Moubayed Dina , Chadi Nicholas 
Published: April 2023

Abstract
Background
Alcohol cessation in youth with daily drinking poses a risk of severe and life-threatening alcohol withdrawal. If unsupervised, alcohol withdrawal in heavy users can cause severe complications, such as seizures, delirium tremens, and death. We present the case of a teenager admitted at our pediatric center for the prevention of alcohol withdrawal using an innovative protocol, including a fixed-dosage benzodiazepine regimen.

Case description
A 16-year-old Caucasian male, known to have anxiety and an attention deficit disorder, was electively admitted for medical stabilization and surveillance of alcohol withdrawal. He had been previously diagnosed with alcohol use disorder and had a past history of withdrawal symptoms. He was prescribed a course of thiamine, folic acid, as well as a fixed-dosage benzodiazepine taper over 5 days. His withdrawal symptoms were evaluated using a standardized Clinical Institute Withdrawal Assessment for Alcohol scale. During his stay, he reported minimal symptoms, as well as a score on the Clinical Institute Withdrawal Assessment for Alcohol scale consistently lower than 5. His mood, motivation, eating habits and sleeping patterns significantly improved during his stay. He developed no medical complications and demonstrated pride in his successes. He was successfully transferred to a long-term rehabilitation center.

Conclusions
A withdrawal prevention protocol was developed on the basis of existing literature. It included a soothing environment, basic laboratory work evaluating the medical complications of alcohol use, as well as medication aiming to prevent and reduce potential withdrawal symptoms. The patient responded well to the fixed-dosage taper with minimal symptoms and discomfort. Although alcohol use in adolescents is frequent, alcohol withdrawal in this population is rarely seen in a pediatric hospital setting. Nonetheless, given the lack of existing guidelines regarding alcohol withdrawal in adolescents, standardized protocols could be greatly beneficial for the prevention of this condition in this population.
Targeting G-quadruplex motifs interferes with differentiation of adipose-derived mesenchymal stem cells
Authors: Ambrosio Maria Rosaria , Migliaccio Teresa , Napolitano Fabiana , Di Somma Sarah , Maneli Giovanni , Amato Jussara , Pagano Bruno , Randazzo Antonio , Portella Giuseppe , Formisano Pietro , Malfitano Anna Maria 
Published: April 2023

Abstract
Background
G-quadruplex (G4) motifs are nucleic acid secondary structures observed in mammalian genomes and transcriptomes able to regulate various cellular processes. Several small molecules have been developed so far to modulate G4 stability, frequently associated with anticancer activity. However, how G4 structures are regulated over homeostatic conditions is mostly unexplored. Here, we used human adipose-derived mesenchymal stem cells (ASCs) to address the role of G4 motifs during adipogenic differentiation.

Methods
Adipocyte differentiation of ASCs was investigated in the presence or absence of a well-known G4 ligand, Braco-19. Cell viability was determined by sulforhodamine B assay. Cell dimension and granularity, DNA G4 motifs and cell cycle were detected by flow cytometry. Lipid droplet accumulation was assessed by Oil Red O staining. Cell senescence was evaluated by β-galactosidase staining. Gene expression was measured by qPCR. Protein release in the extracellular medium was quantified by ELISA.

Results
Braco-19 used at non-cytotoxic concentrations induced morphological changes in mature adipocytes partially restoring an undifferentiated-like status. Braco-19 reduced lipid vacuolization and PPARG, AP2, LEP and TNFA mRNA levels in terminally differentiated cells. No effect was observed in cell senescence, fibrotic markers, IL-6 and IL-8 production, while the secretion of VEGF was dose-dependently reduced. Interestingly, G4 structures were increased in differentiated adipocytes compared to their precursors. Braco-19 treatment reduced G4 content in mature adipocytes.

Conclusions
Our data highlight a new role of G4 motifs as genomic structural elements related to human ASC differentiation into mature adipocytes, with potential implications in physio-pathological processes.