bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combinatorial interactions among natural structural variants of Brassica SOC1 promoters and SVP depict conservation of binding affinity despite molecular diversity
Authors: Kaur Simran , Sisodia Rinki , Gupta Bharat , Madhurantakam Chaithanya , Singh Anandita 
Published: March 2023

Abstract
Genes constituting floral regulatory network can be targeted to generate climate resilient, early flowering crops. SOC1, a central integrator of flowering, is downregulated by SVP. In highly duplicated, amphidiploid genome of Brassica juncea, flowering is plausibly mediated by combinatorial interactions among natural variants of multiple SOC1 promoters and SVP. Although fluctuating temperatures can influence energetics of molecular interactions, a mechanistic view on how these impact phenotypes remains unexplored. Analysis of binding patterns of biomolecules thus underpin new paradigms for precision trait engineering. Herein, we characterize 9 natural variants (homeologs and isoforms) of B. juncea SVP differing in MIKC domains. Generation and characterization of refined models of 15 SVP proteins (natural and hypothetical) and 3 SOC1 promoter fragments revealed extensive structural diversity. Despite this, binding affinity of 48 docked complexes were comparable except in cases where truncated proteins were involved. Investigation of 27 docked complexes for distribution and type of molecular contacts (π-π stacking, hydrophobic interactions, Van-der-Waals forces, Hydrogen bonds); shared or unique interacting patterns, revealed substantial variation suggesting involvement of compensatory mutations for preserving binding. Yeast one-hybrid assays validated binding potential predicted in docked complexes. Conserved amino-acid residues and nucleotides involved in non-covalent interactions were identified. Computational alanine substitution, established the cruciality of amino-acid hotspots conferring stability to docked complexes. Our study is relevant from an application standpoint. Identification of conserved amino-acid hotspots is essential for rational protein design since targeted mutagenesis of these can modify natural binding spectrum of regulatory proteins, and is a way forward for trait engineering.
Determination of pesticide residues in fruits: a systematic review and meta-analyses
Authors: Rahimi Alireza , Khazaei Salman , Ahmadi Sarina , Mehri Fereshteh 
Published: March 2023

Abstract
The present study assessed different pesticide residues (insecticide, fungicide, herbicide, acaricide, ovacide, nematicide, miticide, and veterinary substance) in various fruits based on the type of fruits and the mainland. The studies conducted on concentrations of pesticides in various fruits were collected from reliable databases such as Web of Science, PubMed, and Scopus from November 17, 1995, to October 26, 2021. Based on the findings, the average level of pesticides in various fruits was 0.44 mg/kg and 95% CI (0.39-0.49 mg/kg). The ranking of pesticides in different fruits was in the order of fungicide> nematicide > insecticide > herbicide > acaricide > ovacide > veterinary substance. The highest and the lowest mean and 95% CI of pesticides were related to raspberries 6.03 mg/kg (1.4, 8.5 mg/kg) and nectarine 0.015mg/kg (0.012, 0.019 mg/kg). Furthermore, according to the mainland the pesticide concentration in different fruits was in the order of fungicide> veterinary substance > nematicide > insecticide > herbicide > acaricide > ovacide > miticide. The highest concentration of pesticides in Europe and North America was related to veterinary substance and herbicide while fungicide was reported in Africa, Asia, and South America. The value of this meta-analysis lies in risk models and that it can be used by health strategists and monitoring programs aiming to lower the concentration of different pesticide residues in various fruits.
A novel defined basement membrane-related genes signature for predicting the prognosis of Hepatocellular carcinoma
Authors: Luo Yijiang , Zhang Xueyong , Yang Hao 
Published: March 2023

Abstract

Background.Hepatocellular carcinoma (HCC) is a highly heterogeneous disease with poor prognosis, making the prediction of the prognosis much challenges. Basement membrane-related genes (BMRGs) play an important role in the progression of cancer. Thus, they are often used as targets to inhibit tumor progression. However, the value of BMRGs in predicting prognosis of HCC still remains to be further elucidated. This study aimed to find the relationship between BMRGs and HCC and the value of BMRGs in predicting the prognosis of HCC.Methods.We acquired transcriptome and clinical data of HCC from The Cancer Genome Atlas (TCGA) and randomly divided the data into training and test sets in order to develop a reliable prognostic signature of BMRGs for HCC. The BMRGs model was built using multivariate Cox regression, least absolute shrinkage and selection operator (LASSO), and univariate Cox regression. The risk signature was further validated and assessed using the principal component analysis (PCA), Kaplan-Meier analysis, and time-dependent receiver operating characteristics (ROC). To forecast the overall survival, a nomogram and calibration curves were created (OS). Functional enrichment analysis was used to evaluate the potential biological pathways. We also conducted immunological research and a pharmacological comparison between the high- and low-risk groups in this study.Results.We identified 16 differentially expressed genes and constructed a risk model of four BMRGs, including COL2A1, CTSA, LAMB1,P3H1. The PCA analysis showed that the signature could distinguish the high- and low-risk groups well. Patients in the low-risk group showed significantly better outcome compared with patients in the high-risk group. Receiver operating characteristic (ROC) curve analysis show predictive capacity. Moreover, the nomogram showed good predictability. Univariate and multivariate Cox regression analysis validated that the model results supported the hypothesis that BMRGs were independent risk factors for HCC. Furthermore, analysis of clinical characteristics and tumor microenvironment (TME) between risk groups showed significant difference. Functional analysis revealed different immune-related pathways were enriched, and immune status were different between two risk groups. Mediation analysis with IC50 revealed that the two risk group were significantly different, which could be a guidance of systemic treatment. Finally, we further verified in clinical samples that the mRNA and protein expression levels of the four genes in this model are significantly higher in liver cancer tissues than in adjacent tissues.Conclusion.A novel BMRGs signature can be used for prognostic prediction in HCC. This provide us with a potential progression trajectory as well as predictions of therapeutic response.
Cyclic Betaines act as feeding deterrents in Nereis diversicolor
Authors: Fletcher Nichola , Ohnstad Hannah , Hardege Joerg D. 
Published: March 2023

Abstract
Nereis diversicolor is a widely distributed bioturbating ragworm that inhabits the coastal and estuarine regions of Northwestern Europe and is prey to numerous fish and crustacean species. In order for survival, this like many other invertebrate species, needs to develop strategies to detect and/or escape the numerous predators. The worms utilise chemical cues within the environment to aid predator detection and avoidance. Trigonelline and Homarine are cyclic betaines both present in a variety of animals within the marine environment including crustaceans and fish that are established predators of the worms and have been shown to inhibit feeding behaviours in other prey species (Poulin et al, 2018). We explored potential impacts that these chemicals have on the foraging behaviour of Nereis diversicolor populations from the Humber Estuary, UK. In lab experiments both Trigonelline and Homarine at specific concentrations (10− 3 M and 10− 4 M) significantly reduce foraging behaviour confirming that predator associated odour compounds can impact prey feeding behaviours.
Indications and Outcome of Flexible Bronchoscopy at Muhimbili National Hospital in Dar es Salaam: Tanzania
Authors: Lyimo Tito , Kyaruzi Victor Meza , Byomuganyizi Moses , Khamisi Ramadhani Hassan 
Published: March 2023

Abstract
Background:A flexible bronchoscopy is an essential tool that is globally used for the diagnosis and treatment of Broncho-pulmonary diseases. However the indication and outcome of flexible bronchoscopy has not been widely documented in majority of low resource settings.
Objective:To determine the indications and outcome of flexible bronchoscopy (FB) at Muhimbili National Hospital (MNH).
Methodology: A cross sectional analytical study was conducted for a period of 12months. Details involving indications and outcome of flexible bronchoscopy includes; bronchoscopy findings, therapeutic value, diagnostic yield, and early procedural related complications together with their demographic data were documented after each procedure followed by analysis using SPSS version 25.
Results:Among 151 patients underwent flexible bronchoscopy 76(50.3%) were male and 75(49.7%) were female. The median age of 58 years with IQR (43, 65). Among the indications of flexible bronchoscopy, Cough and hemoptysis were the leading by 82.1% and 25.2% respectively. On the other hand hyperemic mucosa (31.1%) and endobronchial mass (21.2%) constituted the majority of the bronchoscopy findings. The overall diagnostic yield was 34.3% and procedural related complications was 18.54%. Among the indications for flexible bronchoscopy, the hemoptysis was associated with procedure related complications by 31.6% (p-value<0.020, OR 2.779). Among sampling technique of flexible bronchoscopy, the endobronchial biopsy and BAL sampling technique were associated with procedure related complications by 39.5 %( p-value<0.001, OR 4.393) and 14.7 %( p-value<0.005, OR 1.870) respectively
Conclusion: We have demonstrated that flexible bronchoscopy is a safe and reliable procedure in diagnosis of respiratory maladies including MTB at Muhimbili National Hospital.
Long-term monitoring of COVID 19 prevalence in raw and treated wastewater in Salvador, a largest capital of Brazilian Northeast
Authors: Rolo Carolina Araújo , Machado Bruna Aparecida Souza , Carmo Matheus , Fernandes Rosângela , Fonseca Maísa Santos , Hodel Saraiva , Silva Jéssica Rebouças , Nunes Danielle Devequi Gomes , Almeida Santos , de Andrade Jailson 
Published: March 2023

Abstract
Wastewater-based epidemiology (WBE) becomes an interesting epidemiological approach to monitoring the prevalence of SARS-CoV-2 broadly and non-invasively. Herein, we employing for the first time WBE, associated or not with the PEG 8000 precipitation method, for detection of SARS-CoV-2 in samples of raw or treated wastewater from 22 municipal wastewater treatment stations (WWTPs) located in Salvador, the fourth most populous city in Brazil. Our results demonstrate the success of the application of WBE for detecting SARS-CoV-2 in both types of evaluated samples, regardless the usage of PEG 8000 concentration procedure. Further, an increase in SARS-CoV-2 positivity rate was observed in samples collected in months that presented the highest number of confirmed COVID-19 cases (May/2021, June/2021 and January/2022). While PEG 8000 concentration step was found to significantly increase the positivity rate in treated wastewater samples (p < 0.005), a strong positive correlation (r: 0.84; p < 0.002) between non-concentrated raw wastewater samples with the number of new cases of COVID-19 (April/2021 – February/2022) was observed. In general, the present results reinforce the efficiency of WBE approach to monitor the presence of SARS-CoV-2 in either low- and high-capacity WWTPs. The successful usage of WBE even in raw wastewater samples makes it an interesting low-cost tool for epidemiological surveillance.
Evaluation of rs10811661 polymorphism in CDKN2A / B in colon and gastric cancer
Authors: Beihaghi Maria , Sahebi Reza , Beihaghi Mohammad Reza , nessiani Raheleh khosravi , Yarasmi Majedeh Ramian , Gholamalizadeh Sajad , Shahabnavaie Fatemeh 
Published: March 2023

Abstract
One of the causes of colon and gastric cancer is the regulation of carcinogenic genes, tumor inhibitors, and micro-RNA. The purpose of this study is to apply rs10811661 polymorphism in CDKN2A /B gene as an effective biomarker of colon cancer and early detection of gastric cancer. As a result,400 blood samples, inclusive of 200 samples from healthy individuals and 200 samples (100 samples from intestinal cancer,100 samples from stomach cancer) from the blood of someone with these cancers, to determine the genotype of genes in healthful and ill people through PCR-RFLP approach and Allelic and genotypic tests of SPSS software. An observe the connection between gastric cancer and bowel cancer risk and genotypes, the t-student test for quantitative variables and Pearson distribution for qualitative variables have been tested and the results have been evaluated using the Chi-square test. The effects confirmed that the highest frequency of TT genotypes is in infected individuals and CC genotype is in healthful individuals. In addition, it confirmed that women were more inclined than men to T3 tumor invasion and most grade II and III colon cancers, and in older sufferers with gastric cancer, the tumor grade tended to be grade I. Among genetic variety and rs10811661, with invasiveness, there is a tumor size and degree in the affected person. In summary, our findings suggest that the rs10811661 polymorphism of the CDKN2A / B gene is strongly associated with the occurrence of intestinal cancer and Stomach is linked to its potential role as a prognostic biomarker for the management of bowel cancer and stomach.
Altered local RAS in the liver increased the risk of NAFLD in male mouse offspring produced by in vitro fertilization
Authors: Bo Le , Wei Lun , Shi Linling , Luo Chao , Gao Shasha , Zhou Anwen , Mao Caiping 
Published: March 2023

Abstract
Background: Assisted reproductive technology (ART) is associated with an increased risk of adverse metabolic health in offspring, and these findings have been demonstrated in animal models without parental infertility issues. However, it is unclear what changes lead to abnormal metabolism. The activation of the renin-angiotensin system (RAS) has been related to various aspects of metabolic syndrome. Thus, we focused on the local RAS of the liver, which is the central organ for glucose and lipid metabolism in offspring conceived by in vitro fertilization (IVF), and studied the role of local liver RAS in metabolic diseases.
Methods: Male C57BL/6 mouse offspring obtained by natural pregnancy and IVF were fed a standard chow diet or a high-fat diet (HFD) from 4 weeks of age through 16 weeks of age. We assessed glucose and lipid metabolism, hepatic histopathology, and the gene and protein expression of key RAS components. In addition, the blocker losartan was used from 4 weeks of age through 16 weeks of age to investigate the regulatory mechanisms of abnormal local RAS on metabolic activity in the IVF offspring liver.
Results: The growth trajectories of IVF offspring body and liver weights were different from those of naturally pregnant offspring. Impaired glucose tolerance (IGT) and insulin resistance (IR) occurred in IVF-conceived male offspring. After continuous HFD feeding, male offspring in the IVF group underwent earlier and more severe IR. Furthermore, there was a trend of lipid accumulation in the livers of chow-fed IVF offspring. Hepatic steatosis was also more serious in the IVF offspring after HFD treatment. Type 1 receptor (AT1R), which is the primary receptor mediating the action of angiotensin (Ang) II, has been confirmed to be upregulated in IVF offspring livers. Losartan reduced or even eliminated most of the significant differences between the IVF and NC groups after HFD consumption.
Conclusions: The upregulation of AT1R expression in the liver increased the activity of the local RAS, resulting in abnormal glucose and lipid metabolism and lipid accumulation in the liver, significantly increasing the risk of nonalcoholic fatty liver disease (NAFLD) in IVF offspring.
MiR-128-3p inhibits vascular smooth muscle cell proliferation of spontaneously hypertensive rats via targeting KLF4
Authors: Xie Liang , Weng Qing , Zhu Ying , Li Shanshan , Liu Niannian 
Published: March 2023

Abstract
Background Hypertension as a refractory disease has always been a major clinical problem. The proliferation of vascular smooth muscle cells (VSMCs) plays core roles in vascular remodeling of hypertension. MicroRNAs are a type of small noncoding RNA that modulate gene expression via binding different target genes.
Methods and results In this study, we investigated that miR-128-3p inhibited the proliferation of SHR-VSMCs via targeting KLF4. Firstly, we found that the expression levels of miR-128-3p were significantly reduced in SHR aorta and VSMCs compared with WKY. Overexpression of miR-128-3p arrested the function of proliferation in VSMCs. Furthermore, we confirmed that KLF4 was a direct target gene of miR-128-3p, and knockdown of KLF4 suppressed the proliferation.
Conclusions Our findings indicated that overexpression of miR-128-3p in SHR attenuates vascular remodeling and hypertension.
An analysis of racial inequities in emergency department triage among patients with stroke symptoms in the United States.
Authors: Neves Gabriel , DeToledo John , Morris James , Xu K. Tom 
Published: March 2023

Abstract
Background
Racial inequities exist in treatment and outcomes in patients with acute stroke.
Objectives
Our objective was to determine if racial inequities exist in time-lapse between patient presentation and provider assessment in patients with stroke symptoms in Emergency Departments (ED) across the U.S.
Methods
This was a retrospective, observational study of the National Hospital Ambulatory Medical Care Survey (NHAMCS) 2014–2018. We identified visits with stroke symptoms and stratified the proportion of door-to-provider (DTP) times by racial groups. We used broad and narrow definitions of stroke symptoms. We performed bivariate and multivariate analyses using race, DTP times, and clinical and demographic characteristics as covariates.
Results
Between 2014–2018, there were an average of 138.58 million total annual ED visits. Of the total ED visits, 0.36–7.39% of the ED visits presented with stroke symptoms, the average DTP time ranged from 39 to 49 minutes, and the proportion of the visits with a triage level of 1 (immediate) or 2 (emergent) ranged from 16.03–23.27% for stroke symptoms. No statistically significant racial disparities were found in DTP or ED triage level, except that when compared to non-Hispanic whites with atypical stroke symptoms, significantly longer DTP times were found in blacks (by 15.88 minutes, 95% CI: 4.29–27.48) and Hispanics (by 14.77 minutes, 95% CI: 3.37–26.16). Non-Hispanic whites were significantly more frequently diagnosed with a stroke/TIA than racial minority groups (p = 0.045) for atypical stroke symptoms.
Conclusion
In our population-based analysis, we did not identify consistently significant racial disparities in the DTP times or ED triage level at ED triage for stroke symptoms.
Growth differentiation factor-15 as predictor of periodontal treatment effects in patients with periodontitis: a randomized-controlled clinical trial
Authors: Isola Gaetano , Tartaglia Gianluca Martino , Santonocito Simona , Chaurasia Akhilanand , Marya Anand , Giudice Antonino La 
Published: March 2023

Abstract
Background: It has been shown that periodontal treatment could potentially decrease the risk of developing cardiovascular disease (CVD) and that growth differentiation factor 15 (GDF-15) is a valuable biomarker of early CVD risk. This study evaluated the efficacy of periodontal treatment on growth differentiation factor 15 (GDF-15) and related circulating systemic risk biomarkers such as glutathione peroxidase 1 (GPx-1), c-reactive protein (hs-CRP), and surfactant protein D (SP-D) and explored whether patients with high GDF-15 at baseline showed increased clinical benefits with two non-surgical treatments protocols at 6-months follow-up.
Methods: Patients with periodontitis were randomized to receive quadrant (Q-SRP, n=23) or full-mouth disinfection (FMD, n=23) protocols. Clinical and periodontal parameters were recorded in all enrolled patients. Serum concentrations of GDF-15, GPx-1, hs-CRP, and SP-D concentrations were assessed at baseline and 30, 90, and 180-days follow-up through enzyme-linked immunosorbent assay (ELISA) and nephelometric assay techniques.
Results: Q-SRP was more effective than FMD in lowering periodontal parameters, and the mean proportions of GDF-15 (p=0.005), GPx-1 (p=0.025), hs-CRP (p<0.001), and SP-D (p=0.042) after 6 months of treatment. Periodontal parameters were significantly associated with concentrations of GDF-15, GPx-1, hs-CRP, and SP-D at 6-months follow-up. Furthermore, the ANOVA analysis revealed that Q-SRP significantly influenced the upregulation of GPx-1 and on downregulation of GDF-15, and SP-D and substantially impacted the effectiveness of periodontal therapy at 6 months follow-up.
Conclusion: The results evidenced that, in comparison with FMD, Q-SRP was more effective at reducing periodontal variables and positively impacting GDF-15, GPx-1, hs-CRP, and SP-D concentrations, although patients who exhibited higher GDF-15 and SP-D and lowered GPx-1 at baseline, more benefited the effects of periodontal treatment at 6-month follow-up.
Could a risk prediction model based on patient record data improve our understanding of carotid stenosis?
Authors: Hervik Kjersti , Wilsgaard Tom , Myrmel Truls , Kjørstad Knut Eivind 
Published: March 2023

Abstract
Digitalised patient records represent a large potential source of real-world data. Nevertheless, confidentiality and data protection has made big data extraction from patient records impossible in the past. Future options for artificial intelligence in free text reading might enable data extraction while maintaining confidentiality. In turn this could enable improvement in risk prediction for several disease groups. Still, it is not known if free text record data provides an appropriate data source for this purpose. In this project we have analysed a pilot dataset of patients with carotid stenosis in order to estimate the stroke risk in relation to treatment, and by that to assess the individual risk profile. The pilot dataset is applied to design a statistical model suitable for patient record data analysis. In this article a detailed description of the data set, and the methods behind our model choice will be presented.