bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics analysis of miRNA and its associated genes to identify potential biomarkers of oral submucous fibrosis and oral malignancy
Authors: Mohanan Ezhuthachan Mithu , Jhala Dhwani , More Chandramani B. , Patel Amrutlal K. , Joshi Chaitanya 
Published: January 2023

AbstractBackgroundMicroRNAs are a group of non‐coding RNA that controls the gene expression. The interaction between miRNA and mRNA is thought to be dynamic. Oral cancer “The cancer of mouth” is quite prevailing in developing countries. miRNA has been found associated with oral cancer targeting tumor growth, cell proliferation, metastasis, invasion. The significant association of miRNA with genes could be used as a remarkable tool for diagnosis as well as prognostic analysis of oral cancer.AimThe aim of the present study is to evaluate common upregulated and downregulated miRNAs in oral submucous fibrosis (OSMF) and oral malignancy (OM) patients that can be used as diagnostic biomarkers, and to find out their interactions with target genes to establish associated networks in cancer pathways.Methods and ResultsUsing miRDeep2 and DESeq analysis, the upregulated and downregulated miRNA in OSMF (Oral Submucous Fibrosis) and OM (Oral Malignancies) samples were compared to GEO (Gene Expression Omnibus) control dataset. There were 50 common downregulated miRNAs and 13 common upregulated miRNAs in OSMF and OM samples. miRNet analysis of common upregulated miRNA and common downregulated miRNA identified 1295 and 5954 genes, respectively connected with cancer pathways. From analysis of Hub genes, HRAS, STAT3, TP53, MYC, PTEN, CTNNB1, CCND1, JUN, VEGFA, KRAS were found associated with downregulated miRNA and VEGFA, TP53, MDM2, PTEN, MYC, ERBB2, CDKN1A, HSP90AA1, CCND1, AKTI were found associated with upregulated miRNA. The gene enrichment analysis of these hub genes were associated with cell communication, metabolic process, cell proliferation, and cellular component organization. Hub Genes linked with upregulated miRNA had an enrichment ratio of 11.828, whereas hub genes linked with downregulated miRNA had an enrichment ratio of 45.912.ConclusionWe identified common deregulated miRNAs between OSMF and OM patients, which were further analyzed to find out associations with the genes correlated to cancer pathways. The hub genes identified in this study were found to have a significant impact on tumor growth and carcinogenesis. Also, the enrichment of these genes has revealed that the genes are associated with cellular communication, metabolic processes and various biological regulation. These deregulated miRNAs can be used to make a panel of biomarkers to diagnose oral cancer from blood even before its onset.
Analyzing the performance of long short‐term memory architectures for malware detection models
Authors: Avci Cigdem , Tekinerdogan Bedir , Catal Cagatay 
Published: January 2023

SummaryMalicious software forms a threat to many software‐intensive systems and as such several malware detection approaches have been introduced, often based on sequential data analysis. Long short‐term memory (LSTM) is an artificial recurrent neural network (RNN) architecture that is effective for sequential data analysis, however, no study has yet analyzed the performance of different LSTM architectures for the application of malware detection. In this article, we aim to evaluate and benchmark the performance of LSTM‐based malware detection approaches on specific LSTM architectures to provide insight into malware detection. Our method builds LSTM‐based malware prediction models and performs experiments using different LSTM architectures including Vanilla LSTM, stacked LSTM, bi‐directional LSTM, and CNN‐LSTM. We evaluated the performance of each of these architectures and different configurations. Our study, as a contribution, shows that Bidirectional LSTM with hyperparameter optimization is found to be overperforming other selected LSTM architectures. This study shows that different LSTM approaches and architectures are applicable to the malware detection problem. Quality attributes such as efficiency and accuracy, and the software system architecture adopted for the implementation impact the selection of the LSTM approach.
Genome‐wide Association Study of Methotrexate‐Induced Liver Injury in Rheumatoid Arthritis Patients
Authors: Eektimmerman Frank , Swen Jesse J. , den Broeder Alfons A. , Hazes Johanna M. W. , Kurreeman Fina S. , Verstappen Suzanne M. M. , Nair Nisha , Pawlik Andrzej , Nurmohamed Mike T. , Dolžan Vita , Böhringer Stefan , Allaart Cornelia F. , Guchelaar Henk‐Jan 
Published: January 2023

Hepatotoxicity is a serious adverse drug reaction related to methotrexate (MTX). However, the cause of drug‐induced liver injury (DILI) is still unclear and unpredictable. Genetic risk factors may predispose for MTX‐DILI. Therefore, we conducted a nested case‐control genome‐wide association study to explore genetic risk factors associated with MTX‐DILI. Seven international groups contributed blood samples and data of patients with rheumatoid arthritis who used MTX. MTX‐DILI was defined as an alanine aminotransferase (ALT) level of at least three times the upper limit of normal (ULN), to increase contrast controls ALT levels did not raise above two times the ULN. Per study site, control subjects and patients with MTX‐DILI (ratio 3:1) were matched for age, gender, and duration of MTX use. Patients were genotyped using Illumina GSA MD‐24v1‐0 and data were imputed using the 1000 Genomes reference panel. Single‐nucleotide polymorphisms (SNPs) were analyzed using an additive genetic model, corrected for sex, country, and age. A P‐value of ≤ 5 × 10−8 was considered significant, whereas a P‐value of ≤ 5 × 10−6 was considered suggestive. A total of 108 MTX‐DILI cases and 311 controls were included for association analysis. None of the SNPs were significantly associated with MTX‐DILI. However, we found seven suggestive genetic variants associated with MTX‐DILI (P‐values 7.43 × 10−8 to 4.86 × 10−6). Of those, five SNPs were in the intronic protein‐coding regions of FTCDNL1, BCOR, FGF14, RBMS3, and PFDN4/DOK5. Investigation of candidates SPATA9 (rs72783407), PLCG2 (rs60427389), RAVER2 (rs72675408), JAK1 (rs72675451), PTPN2 (rs2476601), MTHFR C677T (rs1801133), and into the HLA region did not show significant findings. No genetic variants associated with MTX‐DILI were found, whereas suggestive SNPs need further investigation.
Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment
Authors: Simons Ariel Levi , Theroux Susanna , Osborne Melisa , Nuzhdin Sergey , Mazor Raphael , Steele Joshua 
Published: January 2023

AbstractAssessments of the ecological health of algal assemblages in streams typically focus on measures of their local diversity and classify individuals by morphotaxonomy. Such assemblages are often connected through various ecological processes, such as dispersal, and may be more accurately assessed as components of regional‐, rather than local‐scale assemblages. With recent declines in the costs of sequencing and computation, it has also become increasingly feasible to use metabarcoding to more accurately classify algal species and perform regional‐scale bioassessments. Recently, zeta diversity has been explored as a novel method of constructing regional bioassessments for groups of streams. Here, we model the use of zeta diversity to investigate whether stream health can be determined by the landscape diversity of algal assemblages. We also compare the use of DNA metabarcoding and morphotaxonomy classifications in these zeta diversity‐based bioassessments of regional stream health. From 96 stream samples in California, we used various orders of zeta diversity to construct models of biotic integrity for multiple assemblages of diatoms, as well as hybrid assemblages of diatoms in combination with soft‐bodied algae, using taxonomy data generated with both DNA sequencing as well as traditional morphotaxonomic approaches. We compared our ability to evaluate the ecological health of streams with the performance of multiple algal indices of biological condition. Our zeta diversity‐based models of regional biotic integrity were more strongly correlated with existing indices for algal assemblages classified using metabarcoding compared to morphotaxonomy. Metabarcoding for diatoms and hybrid algal assemblages involved rbcL and 18S V9 primers, respectively. Importantly, we also found that these algal assemblages, independent of the classification method, are more likely to be assembled under a process of niche differentiation rather than stochastically. Taken together, these results suggest the potential for zeta diversity patterns of algal assemblages classified using metabarcoding to inform stream bioassessments.
Emissions trading in China: New political economy dynamics
Authors: Wang Zexiang , Paavola Jouni 
Published: January 2023

AbstractChina has pledged to peak carbon emissions by 2030 and to become carbon neutral by 2060. Achieving the targets would need great improvement of its emissions trading scheme (ETS) that covers half of the country's emissions. Lessons from the European Union have shown that the ETS is not only a product of the changing circumstances, but its implementation and revisions are also continuously affected by the evolving context. Using a political economy perspective, we examine whether the changing environment is also affecting China's ETS. Our analysis centres on two recent contextual dynamics with relevance to the ETS: (1) the change in the ETS authority in 2018; and (2) the impacts of the deteriorating economic environment on the climate‐energy policy complex. We find that China's ETS and its broad climate ambitions are still constrained by the tensions between the long‐term socio‐economic benefits of low‐carbon policies and the short‐term economic interests behind the government's policy motives, which led to conflicting interests and priorities among regulatory agencies and local governments. The analysis contributes to the political economy debates on emissions trading and China's environmental governance. It also provides practical insights to the policymakers with an in‐depth inquiry into the structural barriers to China's net‐zero targets.
Heterogeneity in cardiovascular death or hospitalization for heart failure benefits with flozins is linked to weight
Authors: Ghosal Samit , Sinha Binayak , Mukherjee Rik 
Published: January 2023

AbstractAimsCardiovascular outcome trials with sodium–glucose cotransporter 2 inhibitors (SGLT‐2is) have documented a positive impact on micro‐ and macrovascular complications of type 2 diabetes (T2D). Most analyses suggest that these benefits are independent of achieving metabolic control. This meta‐regression analysis was undertaken to explore the relationship between metabolic components positively influenced by SGLT‐2is and a reduction in cardiovascular death (CV death) or hospitalization due to heart failure (hHF).Methods and resultsA database search was conducted using the Cochrane Library to identify relevant studies. Analysis was conducted using CMA and RStudio (2022.07.1) software. The hazard ratios of the individual studies were used to compute the random effects model mean effect size for CV death or hHF, and the prediction interval was used to identify the uncertainty in the summary treatment effect. Heterogeneity was quantified using Q statistics. A pooled population of 46 969 patients from five studies was included for analysis. The Cochrane risk of bias tool was used to assess the quality of the studies. There was a significant 23% reduction in CV deaths or hHFs in the SGLT‐2i arm compared with the placebo arm [hazard ratio (HR): 0.77, 95% confidence interval (CI) 0.70–0.85]. However, the prediction interval (0.57–1.05) and the Q statistics [8.06 > degrees of freedom (df) of 4] were indicative of uncertainty in the true effect or heterogeneity. Nearly 50% of the variance of the observed effects were related to the true effects (I2 = 50%). Among the moderators selected, a significant correlation of the outcomes was found with the weight variable (P < 0.01). Weight differential could explain the entire variance in true effect size (R2 = 1.00) ruling out any sampling error.ConclusionsThe results of this meta‐regression analysis suggest that the beneficial effects of SGLT‐2is in reducing CV deaths and hHFs are related to the weight variable.
Conductive coating, cation‐intercalation, and oxygen vacancies co‐modified vanadium oxides as high‐rate and stable cathodes for aqueous zinc‐ion batteries
Authors: Tan Shandong , Sang Zhiyuan , Yi Zhehan , Guo Jingdong , Zhang Xueqi , Li Pinxiang , Si WenPing , Liang Ji , Hou Feng 
Published: January 2023

AbstractLayered vanadium oxides are promising cathode materials for zinc‐ion batteries (ZIBs) owing to their high capacity, but the sluggish electron/ion migration kinetics and structural collapse/dissolution severely limit their Zn2+‐storage performance. Herein, poly(3,4‐ethylenedioxythiophene) coated and Mn2+‐intercalated vanadium oxides with rich oxygen vacancies (MnVOH@PEDOT) are prepared as the cathodes for ZIBs. The PEDOT coating, synergistic with oxygen vacancies, tailors the electron conductivity, and the Mn2+‐intercalation enlarges the interlayer spacing for rapid Zn2+‐ions diffusion. In addition, the pre‐intercalated Mn2+‐ions act as “pillars” to stabilize the structure, and the PEDOT coating prevents the direct contact of vanadium oxides with electrolyte to inhibit its dissolution during cycling. Thus, the MnVOH@PEDOT cathode exhibits superior discharge capacity, favorable rate capability (336.0 mAh g−1 at 8 A g−1), and satisfying cyclic durability (84.8% capacity retention over 2000 cycles). This work offers a facile and synergistic design strategy for achieving favorable cathodes for ZIBs.image
Adaptive geometric multigrid for the mixed finite cell formulation of Stokes and Navier–Stokes equations
Authors: Saberi S. , Meschke G. , Vogel A. 
Published: January 2023

AbstractThe unfitted finite element methods have emerged as a popular alternative to classical finite element methods for the solution of partial differential equations and allow modeling arbitrary geometries without the need for a boundary‐conforming mesh. On the other hand, the efficient solution of the resultant system is a challenging task because of the numerical ill‐conditioning that typically entails from the formulation of such methods. We use an adaptive geometric multigrid solver for the solution of the mixed finite cell formulation of saddle‐point problems and investigate its convergence in the context of the Stokes and Navier–Stokes equations. We present two smoothers for the treatment of cutcells in the finite cell method and analyze their effectiveness for the model problems using a numerical benchmark. Results indicate that the presented multigrid method is capable of solving the model problems independently of the problem size and is robust with respect to the depth of the grid hierarchy.
Analysis of changing United States Practice Advisory guidelines on COVID‐19 vaccine uptake in pregnancy
Authors: Rodriguez Gabriella F. , Vilariño Valerie , Agasse Eva , Galli Johnny , Potter JoNell 
Published: January 2023

SynopsisThe rate of COVID‐19 vaccine uptake in pregnant individuals approximately doubled following the release of a US Practice Advisory recommending COVID‐19 immunization in pregnancy.
Type and timing of antiretroviral therapy during pregnancy: Impact on risk of preterm delivery and small‐for‐gestational age births in Canada, a retrospective cohort study
Authors: Schneidman Jillian , Lee Terry , Sauve Laura , Brophy Jason , Bitnun Ari , Singer Joel , Money Deborah , Kakkar Fatima , Boucoiran Isabelle ,   for the Canadian Perinatal HIV Surveillance Program (CPHSP)
Published: January 2023

AbstractObjectiveTo evaluate the impact of type and timing of antiretroviral therapy (ART) on the risk of preterm delivery (PTD) and small‐for‐gestational age (SGA) birth among pregnant women and people living with HIV in Canada.MethodsData for this retrospective cohort study were analyzed from the Canadian Perinatal HIV Surveillance Program from 1990 to 2020. The association between ART and risk of PTD (<37 weeks) and SGA birth (<10th percentile) was explored using mixed effects logistic regression and time‐dependent Cox proportional hazards models.ResultsOverall, there were 14.9% (654 of 4379) PTD and 18.5% (732 of 3947) SGA cases. A higher risk of PTD was observed with nonnucleoside reverse transcriptase inhibitor–(adjusted hazard ratio [aHR], 1.73; P = 0.019) and boosted protease inhibitor– (aHR, 186; P = 0.007) based regimens compared with integrase strand transfer inhibitor (INSTI)–based regimens. ART initiation prior to conception was associated with a lower risk of SGA birth compared with ART initiation after conception at 1 to 14 weeks (adjusted odds ratio [aOR], 0.69; P = 0.024) and > 14 weeks (aOR, 0.70; P = 0.005).ConclusionINSTI‐based ART regimens were associated with lower risk of PTD compared with other regimens, and ART initiation before conception was associated with a lower risk of SGA birth. These findings, with overall safety data, should be considered when providing pregnancy counseling to people living with HIV.
Development of the crop coefficient for vertically trained cucumber vines grown in soilless media under naturally ventilated greenhouse conditions
Authors: Goyal Pooja , Sharda Rakesh , Siag Mukesh , Biwalkar Nilesh 
Published: January 2023

AbstractIn the wake of climate change and water scarcity issues, protected cultivation combined with precise irrigation management allows effective water resource utilization. This research was intended to find the actual crop evapotranspiration (ETc) of vertically trained cucumber vines in a soilless medium and develop crop coefficients (Kc) under greenhouse conditions. Experiments were performed in three micro‐lysimeters (volume 0.015 m3) placed inside a naturally ventilated greenhouse from April to June 2018 (season I) and September to December 2019 (season II) with a planting density of 0.32 m2/plant. The FAO‐56 Penman–Monteith equation was used to calculate reference evapotranspiration (ETo), and lysimeters were used to calculate the actual ETc. The average actual ETc of cucumber vines in season II (147.81 mm) was almost half of the ETc in season I (275.24 mm). The higher ETc in season I was due to a higher ETo of 493 mm during season I compared to 150 mm in season II inside the greenhouse. Kc values for season I were 0.3, 0.74, 1.11 and 0.68 compared to 0.3, 0.77, 1.38 and 0.79 in season II during the initial development, mid and end stages of cucumber vines, respectively, under greenhouse conditions.
Rapid and accurate screening of cystic echinococcosis in sheep based on serum Fourier‐transform infrared spectroscopy combined with machine learning algorithms
Authors: Dawuti Wubulitalifu , Dou Jingrui , Zheng Xiangxiang , Lü Xiaoyi , Zhao Hui , Yang Lingfei , Lin Renyong , Lü Guodong 
Published: January 2023

AbstractCystic echinococcosis (CE) in sheep is a serious zoonotic parasitic disease caused by Echinococcus granulosus sensu stricto (s.s.). Presently, the screening technology for CE in sheep is time‐consuming and inaccurate, and novel screening technology is urgently needed. In this work, we combined machine‐learning algorithms with Fourier transform infrared (FT‐IR) spectroscopy of serum to establish a quick and accurate screening approach for CE in sheep. Serum samples from 77 E. granulosus s.s.‐infected sheep to 121 healthy control sheep were measured by FT‐IR spectrometer. To optimize the classification accuracy of the serum FI‐TR method for the E. granulosus s.s.‐infected sheep and healthy control sheep, principal component analysis (PCA), linear discriminant analysis, and support vector machine (SVM) algorithms were used to analyze the data. Among all the bands, 1500–1700 cm−1 band has the best classification effect; its diagnostic sensitivity, specificity, and accuracy of PCA‐SVM were 100%, 95.74%, and 96.66%, respectively. The study showed that serum FT‐IR spectroscopy combined with machine learning algorithms has great potential for rapid and accurate screening methods for the CE in sheep.
Scaffolds containing GAG‐mimetic cellulose sulfate promote TGF‐β interaction and MSC Chondrogenesis over native GAGs
Authors: Menezes Roseline , Sherman Lauren , Rameshwar Pranela , Arinzeh Treena Livingston 
Published: January 2023

AbstractCartilage tissue engineering strategies seek to repair damaged tissue using approaches that include scaffolds containing components of the native extracellular matrix (ECM). Articular cartilage consists of glycosaminoglycans (GAGs) which are known to sequester growth factors. In order to more closely mimic the native ECM, this study evaluated the chondrogenic differentiation of mesenchymal stem cells (MSCs), a promising cell source for cartilage regeneration, on fibrous scaffolds that contained the GAG‐mimetic cellulose sulfate. The degree of sulfation was evaluated, examining partially sulfated cellulose (pSC) and fully sulfated cellulose (NaCS). Comparisons were made with scaffolds containing native GAGs (chondroitin sulfate A, chondroitin sulfate C and heparin). Transforming growth factor‐beta3 (TGF‐β3) sequestration, as measured by rate of association, was higher for sulfated cellulose‐containing scaffolds as compared to native GAGs. In addition, TGF‐β3 sequestration and retention over time was highest for NaCS‐containing scaffolds. Sulfated cellulose‐containing scaffolds loaded with TGF‐β3 showed enhanced chondrogenesis as indicated by a higher Collagen Type II:I ratio over native GAGs. NaCS‐containing scaffolds loaded with TGF‐β3 had the highest expression of chondrogenic markers and a reduction of hypertrophic markers in dynamic loading conditions, which more closely mimic in vivo conditions. Studies also demonstrated that TGF‐β3 mediated its effect through the Smad2/3 signaling pathway where the specificity of TGF‐β receptor (TGF‐ βRI)‐phosphorylated SMAD2/3 was verified with a receptor inhibitor. Therefore, studies demonstrate that scaffolds containing cellulose sulfate enhance TGF‐β3‐induced MSC chondrogenic differentiation and show promise for promoting cartilage tissue regeneration.