bluuebunny/crossref_metadata_2025_split huggingface dataset:
scMultiSim: simulation of single cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions
Authors: Zhang Xiuwei , Li Hechen , Zhang Ziqi , Squires Michael , Chen Xi 
Published: September 2023

Abstract
Simulated single-cell data is essential for designing and evaluating computational methods in the absence of experimental ground truth. Existing simulators typically focus on modeling one or two specific biological factors or mechanisms that affect the output data, which limits their capacity to simulate the complexity and multi-modality in real data. Here, we present scMultiSim, an in silico simulator that generates multi-modal single-cell data, including gene expression, chromatin accessibility, RNA velocity, and spatial cell locations while accounting for the relationships between modalities. scMultiSim jointly models various biological factors that affect the output data, including cell identity, within-cell gene regulatory networks (GRNs), cell-cell interactions (CCIs), and chromatin accessibility, while also incorporating technical noises. Moreover, it allows users to adjust each factor's effect easily. We validated scMultiSim’s simulated biological effects and demonstrated its applications by benchmarking a wide range of computational tasks, including multi-modal and multi-batch data integration, RNA velocity estimation, GRN inference and CCI inference using spatially resolved gene expression data, many of them were not benchmarked before due to the lack of proper tools. Compared to existing simulators, scMultiSim can benchmark a much broader range of existing computational problems and even new potential tasks.
Unraveling groundwater-stream connections at the continental scale
Authors: Yang Chen , Condon Laura , Maxwell Reed 
Published: September 2023

Abstract
Groundwater is a critical component of the terrestrial water cycle, yet the extent and depth of its connections with other hydrologic components, such as streamflow, remain unquantified. Here, we conducted a backward particle tracking simulation based on high-resolution integrated hydrologic modeling across the contiguous United States (CONUS). We quantified the lateral length and vertical depth of groundwater flow discharged to streams as baseflow. Our simulation results suggest that water may travel underground almost 240km to emerge in a stream and that lateral groundwater flow lengths longer than 50 km are common across North America. Confined groundwater, aquifers typically 10–100m below the ground surface, significantly contributes to baseflow. Boundaries of surface water and groundwater watersheds rarely match and only align at continental divides. Our results suggest that about one-quarter of the baseflow over CONUS is inter-basin groundwater flow and that water-balance approaches underestimate these quantities due to concurrent groundwater exportation and importation of a watershed. This nested nature of groundwater flow is an important characteristic that determines how far and how deep water flows to supply streamflow. Our findings have fundamental significance for understanding the movement of groundwater and its interactions with other hydrologic components in the terrestrial water cycle.
The Impact of psychological factors, depression, and anxiety on tobacco abuse in Primary Health Care adults: A Secondary Data Analysis
Authors: Méndez-López Fátima , Oliván-Blázquez Bárbara , Domínguez-García Marta , López-Del-Hoyo Yolanda , Rabanaque Isabel , Casado-Vicente Verónica , Martí-Lluch Ruth , Magallón-Botaya Rosa 
Published: September 2023

Abstract

Smoking is a growing public health issue that has a negative influence on social and psychological well-being. The presence of certain personal factors on health-promoting behavior influences mental well-being and less dependence on tobacco in the population. We aimed to explore the relationship between tobacco dependency, the degree of severity of anxious and depressive symptoms, and certain related personal characteristics and adult health behavior. This study includes 391 participants of 35– 74 years old from the lists of the primary health care centers located in Aragón (Spain). Data were analyzed using descriptive, bivariate, multivariate and mediation analysis. The primary variable was tobacco consumption, evaluated qualitatively (presence or absence) and quantitatively, as consumption measured through the number of cigarettes. High patient activation and health literacy were predictors of having a lower risk of being a smoker and lower daily cigarette consumption. However, being single and having more severe depressive symptoms were significantly higher predictors of smoking and higher daily cigarette consumption. The associations between the presence of tobacco dependence and the constructs of health literacy and patient activation, mediated by depression, were significant. The severity of depressive and anxious symptoms and personal factors are related to tobacco dependence. These correlations must be considered while developing particular preventative efforts to reduce population smoking rates.
Unravelling the Genetic Link: An Umbrella Review on HLA-B∗15:02 and Anti-Epileptic Drug-induced Stevens–Johnson Syndrome / Toxic Epidermal Necrolysis
Authors: Liu Wei Yang Christopher , tham Kar Mun , Yek Jia Lin Jacklyn 
Published: September 2023

Abstract
Purpose
This umbrella review was conducted to summarize the evidence between association between HLA*1502 allele with various antiepileptic induced Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN).
Methods
Pubmed, Scopus and EMBASE were searched for eligible reviews in May 2023. Study was registered in PROSPERO. Two authors independently screened titles and abstracts and assessed full-text reviews for eligibility. The quality of meta-analyses was appraised with AMSTAR-2 and the quality of case control studies were appraised with Newcastle- Ottawa Scale (NOS). Narrative summaries of each anti-epileptic drug were analysed. Pre-established protocol was registered on the International Prospective Register of Systematic Reviews database (ID: CRD42023403957).
Results
Included studies are meta-analyses and case control studies evaluating the association of HLA-B*1502 allele with the following antiepileptics: 7 meta-analyses for Carbamazepine (CBZ), 3 meta-analyses for Lamotrigine (LTG), 3 case-control studies for Oxcarbazepine (OXC), 9 case-control studies Phenytoin (PHT) and 4 case-control studies study for Phenobarbitone.
The findings of this umbrella review suggest that there is strong association between HLA B-1502 with SJS/TEN for Carbamazepine and Oxcarbazepine and a milder association for Lamotrigine and Phenytoin.
Conclusions
In summary, although HLA-B*1502 is less likely to be associated with Phenytoin or Lamotrigine -induced SJS/TEN compared to Carbamazepine-induced SJS/TEN, it is a significant risk factor which if carefully screened could potentially reduce development of SJS/TEN. In view of potential morbidity and mortality, HLA-B*1502 testing may be beneficial in patients who are initiating Lamotrigine / Phenytoin therapy. However, further studies are required to examine the association of other alleles with development of SJS/TEN and to explore the possibility of genome-wide association studies prior to initiation of treatment.
Development of a CT-based scoring system to predict progression after intraoperative radiotherapy in locally advanced pancreatic cancer with initial stable disease
Authors: Cai Wei , Zhu Yongjian , Teng Ze , Li Dengfeng , Cong Rong , Chen Zhaowei , Ma Xiaohong , Zhao Xinming 
Published: September 2023

Abstract
Objectives
We aimed to develop a risk scoring system integrating CT imaging features and serum carbohydrate antigen 19 − 9 (CA19-9) for stratifying the short-term outcomes in locally advanced pancreatic cancer (LAPC) patients receiving intraoperative radiotherapy (IORT) with initial stable disease (SD).
Materials and Methods
We retrospectively recruited 103 consecutive patients with LAPC who received IORT as first-line treatment. All patients underwent CT examinations and serum CA19-9 test baseline and post-IORT. Clinical and CT imaging features were analyzed. The risk scoring system was constructed using the coefficient of the independent risk factors for progression-free survival (PFS) from cox regression model. Time-dependent receiver operating characteristic (ROC) curve was used to evaluate the predictive performance of the scoring system.
Results
All patients developed disease progression after IORT and the median PFS time was 6.40 (95% confidence interval [CI]:4.95–7.86) months. Multivariable analysis revealed that CA19-9 non-response (hazard ratio [HR] = 1.672, P = 0.018), the percentage change of relative enhanced ratio (HR = 2.318, P = 0.030), rim-enhancement (HR = 1.784, P = 0.007), and peripancreatic fat infiltration (HR, 1.799, P = 0.006) were significant correlated with poor PFS. Time-dependent ROC showed a satisfactory predictive performance for disease progress with area under the curve (AUC) all above 0.70. Low-risk patients (risk score < 5) progress significantly slower than high-risk patients (risk score ≥ 5) (P < 0.001).
Conclusion
The scoring system integrating CT imaging features and CA19-9 can be used as a convenient and practical method for prognosis prediction in LAPC patients showing SD receiving IORT.
Unsupervised machinery prognostics approach based on wavelet packet decomposition and variational autoencoder
Authors: de Godói Leonardo Franco , Nóbrega Eurípedes Guilherme de Oliveira 
Published: September 2023

Abstract
The prognosis of rotating machinery has been very prominent in recent years thanks to the advances in digital signal processing and intelligent systems. Unsupervised machine learning methods have been adopted along with signal processing techniques in both time and frequency domain to build indicators that describe the degradation of mechanical systems. This paper proposes a novel method for generating a degradation indicator for estimating the remaining useful life of rotating machinery critical components, based on a beta variational autoencoder neural network that processes statistical distributions in a feature hyperspace whose coordinates mix time-domain analysis and wavelet packet decomposition of vibration signals. Indicators are calculated using bearing vibration signals from a publicly available dataset, aiming to enhance the visibility of monotonic trends, and are used to assess different hyperparameter configurations of the proposed methodology. Based on the comparison with recently published results on the same dataset, the proposed method produced robust indicators capable of detecting early changes in degradation models, generating more accurate RUL estimates.
MHESMMR: A multilevel model for Predicting the Regulation of miRNAs Expression by Small Molecules
Authors: Guan Yong-jian , Yu Chang-Qing , Li Li-Ping , You Zhu-Hong , Wei Meng-meng , Wang Xin-Fei , Guo Lu-Xiang , Yang Chen 
Published: September 2023

Abstract
According to the expression of miRNA in pathological processes, miRNAs can be divided into oncogenes or tumor suppressors. Prediction of the regulation relations between miRNAs and small molecules (SMs) becomes a vital goal for miRNA-target therapy. But traditional biological approaches are laborious and expensive. Thus, there is an urgent need to develop a computational model. In this study, we proposed a computational model to predict whether the regulatory relationship between miRNAs and SMs is up-regulated or down-regulated. Specifically, we first use the Large-scale Information Network Embedding (LINE) algorithm to construct the node features from the self-similarity networks, then use the General Attributed Multiplex Heterogeneous Network Embedding (GATNE) algorithm to extract the topological information from the attribute network, and finally utilize the LightGBM algorithm to predict the regulatory relationship between miRNAs and SMs. In the 5-fold cross-validation experiment, the average accuracies of the proposed model on the SM2miR dataset reached 79.59% and 80.37% for up-regulation pairs and down-regulation pairs, respectively. In addition, we compared our model with another published model. Moreover, in the case study for 5-FU, 7 of 10 candidate miRNAs are confirmed by related literature. Therefore, we believe that our model can promote the research of miRNA-targeted therapy.
Identification of volatile metabolites produced from gut microbial levodopa metabolism using an untargeted metabolomics approach
Authors: Pennington Taylor R. , Eshima Jarrett , Smith Barbara S. 
Published: September 2023

Abstract

Interspecies pathways in the gut microbiome have been shown to metabolize levodopa, the primary treatment for Parkinson’s disease, and reduce its bioavailability. While the enzymatic reactions have been identified, the ability to establish the resulting macromolecules as biomarkers of microbial metabolism remains technically challenging. In this study, we leveraged an untargeted mass spectrometry-based approach to investigate volatile organic compounds (VOCs) produced during levodopa metabolism byEnterococcus faecalis,Clostridium sporogenes, andEggerthella lenta. We cultured these organisms with and without their respective bioactive metabolites and detected levodopa-induced shifts in VOC profiles. We then utilized bioinformatics to identify significant differences in 2,6-dimethylpyrazine, 4,6-dimethylpyrimidine, and 4,5-dimethylpyrimidine associated with its biotransformation. Supplementing cultures with inhibitors of levodopa-metabolizing enzymes revealed specific modulation of levodopa-associated diazines, verifying their relationship to its metabolism. Furthermore, functional group analysis depicts strain-specific VOC profiles that reflect interspecies differences in metabolic activity that can be leveraged to assess microbiome functionality in individual patients. Collectively, this work identifies previously uncharacterized metabolites of microbiome-mediated levodopa metabolism with applications for point-of-care testing and offers an alternative approach to evaluate interindividual differences in treatment response.
Comparative efficacy and safety of almonertinib and osimertinib for advanced non-cellular lung cancer: a real-world non-inferiority study
Authors: Qi Rongbin , Fu Xinyu , Liang Jiawei , Yu Yingying , Xu Hailing , Shen Mo , He Susu , Lv Dongqing 
Published: September 2023

Abstract
Background Almonertinib is an oral third-generation tyrosine kinase inhibitor (TKI) targeting the epidermal growth factor receptor (EGFR). It has exhibited substantial antitumor efficacy and well-tolerated toxicity in prior clinical investigations. This study investigated the non-inferiority of almonertinib compared to osimertinib in patients with advanced EGFR-positive non-small cell lung cancer (NSCLC).
Method In this retrospective analysis, patients with EGFR-positive NSCLC, experiencing progression after treatment with first- or second-generation EGFR-TKIs were administered either almonertinib or osimertinib, with or without concomitant treatment with anti-angiogenic agents and chemotherapy, until disease progression or the occurrence of unacceptable drug toxicity.
Result One hundred eighty-two patients were enrolled in the study and categorized into two groups based on the method of administration: almonertinib (n=79) and osimertinib (n=103). Thirty-nine percent of these patients had central nervous system metastases. Almonertinib exhibited efficacy comparable to that of osimertinib considering progression-free survival (PFS) (HR 0.92, 95% CI 0.65-1.31; median PFS 9.63 months vs. 11.4 months; p=0.65). EGFR-T790M mutations were observed in 75% and 87% of the almonertinib and osimertinib groups, with a median PFS of 15.37 and 12.0 months, respectively, of the two groups (p=0.39). Overall, both groups had manageable safety profile, with the majority being grade 2 and below adverse event. Compared to patients taking osimertinib, those taking almonertinib had fewer drug-related adverse reactions, mainly in terms of subjective patient perception, including onychomycosis, diarrhea, mouth ulcers, and skin rash.
Conclusion Almonertinib may be a potentially superior treatment option for patients with advanced NSCLC harboring EGFR mutations, as it demonstrates comparable efficacy to osimertinib while significantly reducing adverse reactions.
Spatiotemporal variability of droughts over the Arabian Peninsula and associated mechanisms
Authors: Saharwardi Md Saquib , Dasari Hari Prasad , Gandham Harikishan , Ashok Karumuri , Hoteit Ibrahim 
Published: September 2023

Abstract

This study examines the spatiotemporal variability of drought and associated physical processes over the Arabian Peninsula (AP). For this purpose, we computed the standardized precipitation evapotranspiration index (SPEI) for the period 1951–2020 using the Climate Research Unit and ERA5 Reanalysis datasets. By applying rotated empirical orthogonal function analysis on the SPEI data, we identified four homogeneous and coherent drought regions. In comparison with the southern region, the droughts in the northern homogeneous regions were more significantly correlated. All four sub-regions of the AP exhibit a significant drying trend (p < 0.01) with an abrupt acceleration in drought frequency and intensity over the last two decades. The increase in droughts is associated with the reduction of synoptic activity and an increase in the high pressure over the AP. Seasonally, potential evapotranspiration is the dominant driver of summer droughts in the AP, whereas both precipitation and temperature are important for driving winter droughts. The summer droughts, mainly over the northern AP, are due to the occurrence of an anomalous equivalent barotropic high associated with anomalous dry and hot conditions. However, anomalous dry conditions in winter are a result of an anomalous paucity of winter storms caused by the weakening of the sub-tropical jets.
Factors influencing vitamin B6 status in domestic cats: age, body condition score, and inflammation
Authors: Chu Vy , Fascetti Andrea J. , Larsen Jennifer A. , Montano Maria , Giulivi Cecilia 
Published: September 2023

Abstract
Limited studies are available on the vitamin B6 status in domestic cats. To this end, we evaluated glutamate-oxaloacetate transaminase activity in hemolysates with and without pyridoxal 5’-phosphate supplementation in two feline populations: a cohort of 60 domestic (sexually intact and specific pathogen-free) cats maintained under strictly controlled conditions with optimal diets (Feline Nutrition and Pet Care Center) and a cohort of 57 cats randomly selected between December 2022 to January 2023 that visited the Veterinary Medicine Teaching Hospital to seek care under different circumstances. We analyzed the data based on the animal's age, sex, body condition score, and diagnosis to elucidate the main factors driving vitamin B6 deficiencies in domestic cats. Based on the age and body condition scores, most cats with vitamin B6 deficiency had a low body condition score (41.7%), suggesting low food intake and/or malassimilation, as most were of advanced age (≥7 y old; 66.7%). This result is consistent with the increased energy requirements and compromised digestibility in older cats linked to a higher proportion of underweight elderly cats. When the data of vitamin B6-deficient cats were analyzed in terms of medical diagnosis, most (58.4%) had a condition associated with an increased inflammatory response, whether through an infection (feline coronavirus; 25%) or via diseases associated directly or indirectly with an inflammatory response (33.4%). Thus, our study supports that vitamin B6 supplementation may be indicated in older animals, especially those undergoing an active inflammation process.
Evaluation of the Uroanalysis Values of Canines Supplemented With Porcine Peptides and Ascorbic Acid
Authors: Acero Kelvin Roberto Pinto , Cárdenas Diego Mauricio Buitrago , Molano Carlos Eduardo Rodríguez , Romero Melisa Daniela Munevar 
Published: September 2023

Abstract
Bioactive peptides have considerable animal health promoting properties. The effects of supplementation with collagen peptides and vitamin C (PolyPet®) on urinalysis were evaluated in a total of 24 Labrador retrievers with similar feeding and handling characteristics randomly selected into three groups (control group, group 1, and group 1). 2). The treatments consisted of supplementing a group with 6.6 gr daily with PolyPet®, group 2 with 3.3 gr and the last group (control group) without any supplementation. Urine samples were taken at days 0, 30 and 60 from the 24 canines in the study. The urinalysis parameters evaluated were protein, ascorbic acid, urinary protein/urinary creatinine ratio (UP/UC), nitrites, specific gravity, crystalluria, pH, calciuria, odor, creatinuria, and body weight. It was determined that there was no significant difference between the values ​​of urinary protein presence, in group 1 the UP/UC ratio increased slightly. In the presence of crystals, there was no significant difference compared to the three groups. For amorphous urate and uric acid crystals, there was an increase with porcine collagen peptide supplementation and the variables triple phosphate, struvite crystals and weight loss were positively affected by supplementation. The use of collagen peptides and vitamin C (PolyPet®) demonstrated positive effects on the health of canines, being considered as a safe food for healthy individuals.
Comparing Gut Microbiota Discrepancies between Primary Sjogren's Syndrome and Healthy Controls: A Systematic Review
Authors: Zhao Qian , Han Minghua , Du Yage , Zheng Jie , Cao Zhaoming , Lu Yao , Lu Yanhui 
Published: September 2023

Abstract

Background: The importance of the gut microbiota in primary Sjogren’s syndrome is gaining significant recognition. This systematic review summarized the previous findings on the discrepancies in gut microbiota between patients with primary Sjogren’s syndrome and healthy controls.
Methods: From the establishment of the database until September 1, 2023, we conducted searches using electronic databases. We were interested in identifying specific bacterial changes between primary Sjogren’s syndrome and healthy controls as our primary outcomes. Secondary outcomes included exploring the relationship between gut microbiota and clinical parameters. To assess the quality of the included studies, we used the Newcastle-Ottawa scale.
Results: A total of 9 articles were included in the analysis, comprising 504 case groups and 1313 control groups. According to two or more of the included studies, it was found that the gut microbiota of primary Sjogren’s syndrome patients was characterized by decreased butyrate-producing bacteria and increased pro-inflammatory microorganisms, as well as significantly lower levels of Actinobacteria, Firmicutes, Fusobacteria, and Proteobacteria. Furthermore, the Firmicutes/Bacteroidetes ratio was lower in patients with primary Sjogren’s syndrome than in controls. Finally, it was found that Roseburia has been shown to have a negative correlation with disease activity, as well as a negative correlation with IL-12 and IL-6.
Conclusions: Patients with primary Sjogren’s syndrome exhibited reduced diversity in their gut microbiota and decreased abundance of short-chain fatty acid producers, which may offer potential therapeutic targets for future interventions.
Trial registration: CRD42023421915.