bluuebunny/crossref_metadata_2025 huggingface dataset:
Joint analysis of scATAC-seq datasets using epiConv
Authors: Lin Li , Zhang Liye
Published: July 2022

Background

Technical improvement in ATAC-seq makes it possible for high throughput profiling the chromatin states of single cells. However, data from multiple sources frequently show strong technical variations, which is referred to as batch effects. In order to perform joint analysis across multiple datasets, specialized method is required to remove technical variations between datasets while keep biological information.

Results

Here we present an algorithm named epiConv to perform joint analyses on scATAC-seq datasets. We first show that epiConv better corrects batch effects and is less prone to over-fitting problem than existing methods on a collection of PBMC datasets. In a collection of mouse brain data, we show that epiConv is capable of aligning low-depth scATAC-Seq from co-assay data (simultaneous profiling of transcriptome and chromatin) onto high-quality ATAC-seq reference and increasing the resolution of chromatin profiles of co-assay data. Finally, we show that epiConv can be used to integrate cells from different biological conditions (T cells in normal vs. germ-free mouse; normal vs. malignant hematopoiesis), which reveals hidden cell populations that would otherwise be undetectable.

Conclusions

In this study, we introduce epiConv to integrate multiple scATAC-seq datasets and perform joint analysis on them. Through several case studies, we show that epiConv removes the batch effects and retains the biological signal. Moreover, joint analysis across multiple datasets improves the performance of clustering and differentially accessible peak calling, especially when the biological signal is weak in single dataset.
Complete genome sequencing and investigation on the fiber-degrading potential of Bacillus amyloliquefaciens strain TL106 from the tibetan pig
Authors: Shang Zhenda , Liu Suozhu , Duan Yanzhen , Bao Chengling , Wang Jian , Dong Bing , Cao Yunhe
Published: July 2022

Background

Cellulolytic microorganisms are considered a key player in the degradation of feed fiber. These microorganisms can be isolated from various resources, such as animal gut, plant surfaces, soil and oceans. A new strain of Bacillus amyloliquefaciens, TL106, was isolated from faeces of a healthy Tibetan pigs. This strain can produce cellulase and shows strong antimicrobial activity in mice. Thus, in this study, to better understand the strain of B. amyloliquefaciens TL106 on degradation of cellulose, the genome of the strain TL106 was completely sequenced and analyzed. In addition, we also explored the cellulose degradation ability of strain TL106 in vitro.

Results

TL106 was completely sequenced with the third generation high-throughput DNA sequencing. In vitro analysis with enzymatic hydrolysis identified the activity of cellulose degradation. TL106 consisted of one circular chromosome with 3,980,960 bp and one plasmid with 16,916 bp, the genome total length was 3.99 Mb and total of 4,130 genes were predicted. Several genes of cellulases and hemicellulase were blasted in Genbank, including β-glucosidase, endoglucanase, ß-glucanase and xylanase genes. Additionally, the activities of amylase (20.25 U/mL), cellulase (20.86 U/mL), xylanase (39.71 U/mL) and β-glucanase (36.13 U/mL) in the fermentation supernatant of strain TL106 were higher. In the study of degradation characteristics, we found that strain TL106 had a better degradation effect on crude fiber, neutral detergent fiber, acid detergent fiber, starch, arabinoxylan and β-glucan of wheat and highland barley .

Conclusions

The genome of B. amyloliquefaciens TL106 contained several genes of cellulases and hemicellulases, can produce carbohydrate-active enzymes, amylase, cellulase, xylanase and β-glucanase. The supernatant of fermented had activities of strain TL106. It could degrade the fiber fraction and non-starch polysaccharides (arabinoxylans and β-glucan) of wheat and highland barley. The present study demonstrated that the degradation activity of TL106 to crude fiber which can potentially be applied as a feed additive to potentiate the digestion of plant feed by monogastric animals.
Role of ferroptosis-related genes in coronary atherosclerosis and identification of key genes: integration of bioinformatics analysis and experimental validation
Authors: Meng Qingwen , Xu Yiqian , ling Xuebin , Liu Huajiang , Ding Shun , Wu Haolin , Yan Dongming , Fang Xingyue , Li Tianfa , Liu Qibing
Published: July 2022

Background

Coronary atherosclerosis (CA) is the most common type of atherosclerosis. However, the inherent pathogenesis and mechanisms of CA are unclear, and the relationship with ferroptosis-related genes (FRGs) has not been reported. The purpose of this study was to use bioinformatics techniques to evaluate potential therapeutic targets for CA.Please provide the given name for author “Dingshun”.Please provide the given name for author “Dingshun”.

Methods

First, the GSE132651 dataset was acquired from the Gene Expression Omnibus database. Gene Ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and Protein–Protein interaction network were successively conducted. Next, overlapping genes between hub genes and CA genes were found. FRGs were found when comparing the CA group with the normal group. The correlation between overlapping genes and FRGs was further analyzed. At last, we performed Elisa to validate the expression of these genes in human blood specimens. Mice aortic tissues were used for western blot to detect the expression of proteins.

Results

Based on the GSE132651 dataset, 102 differentially expressed genes were identified. Five overlapping genes between hub genes and CA genes were found (CCNA2, RRM2, PBK, PCNA, CDK1). TFRC and GPX4 were found to be FRGs. TFRC was positively correlated with CCNA2, PBK, PCNA, CDK1, RRM2, with CDK1 being the strongest correlation. GPX4 was negatively correlated with these genes, among which CCNA2 was the strongest correlation. The ELISA results showed that CCNA2, CDK1, and TFRC expression were markedly increased in serum of the CA samples compared with controls, while GPX4 expression was markedly decreased in the CA samples. The western blot results show that GPX4 expression was lower in the model group, TFRC, CDK1, and CCNA2 protein expression were high in the model group.

Conclusions

Ferroptosis-related genes GPX4 and TFRC were closely correlated with the identified overlapping genes CCNA2 and CDK1, which may serve as targeted therapies for the treatment of CA.
Assessing the effectiveness of empirical calibration under different bias scenarios
Authors: Hwang Hon , Quiroz Juan C. , Gallego Blanca
Published: July 2022

Background

Estimations of causal effects from observational data are subject to various sources of bias. One method for adjusting for the residual biases in the estimation of treatment effects is through the use of negative control outcomes, which are outcomes not believed to be affected by the treatment of interest. The empirical calibration procedure is a technique that uses negative control outcomes to calibrate p-values. An extension of this technique calibrates the coverage of the 95% confidence interval of a treatment effect estimate by using negative control outcomes as well as positive control outcomes, which are outcomes for which the treatment of interest has known effects. Although empirical calibration has been used in several large observational studies, there is no systematic examination of its effect under different bias scenarios.

Methods

The effect of empirical calibration of confidence intervals was analyzed using simulated datasets with known treatment effects. The simulations consisted of binary treatment and binary outcome, with biases resulting from unmeasured confounder, model misspecification, measurement error, and lack of positivity. The performance of the empirical calibration was evaluated by determining the change in the coverage of the confidence interval and the bias in the treatment effect estimate.

Results

Empirical calibration increased coverage of the 95% confidence interval of the treatment effect estimate under most bias scenarios but was inconsistent in adjusting the bias in the treatment effect estimate. Empirical calibration of confidence intervals was most effective when adjusting for the unmeasured confounding bias. Suitable negative controls had a large impact on the adjustment made by empirical calibration, but small improvements in the coverage of the outcome of interest were also observable when using unsuitable negative controls.

Conclusions

This work adds evidence to the efficacy of empirical calibration of the confidence intervals in observational studies. Calibration of confidence intervals is most effective where there are biases due to unmeasured confounding. Further research is needed on the selection of suitable negative controls.
Association of serum creatinine with hepatic steatosis and fibrosis: a cross-sectional study
Authors: Ma Juan , Wei Zhongcao , Wang Qian , Lu Xiaolan , Zhou Zhihua , Li Ruohan , Shu Qiuai , Liu Yixin , Wang Jinhai , Liu Na , Shi Haitao
Published: July 2022

Background

Recent studies have shown that chronic kidney disease (CKD) prevalence is significantly higher in patients with hepatic steatosis (HS); however, it remains unclear whether HS is associated with serum creatinine (SCr). We aimed to explore the association between SCr levels and HS in a Chinese population.

Methods

We performed a cross-sectional study among 56,569 Chinese individuals. SCr level, other clinical and laboratory parameters, abdominal ultrasound and noninvasive fibrosis scores were extracted, and the fibrosis 4 score (FIB-4) was calculated.

Results

A total of 27.1% of the subjects had HS. After 1:1 propensity score matching (PSM) according to sex and age, we included 13,301 subjects with HS and 13,301 subjects without HS. SCr levels were significantly higher in the HS group than in the non-HS group [73.19 ± 15.14(μmoI/L) vs. 71.75 ± 17.49(μmoI/L), p < 0.001]. Univariate and multivariate regression analyses showed a positive association between SCr and the prevalence of HS. Stepwise regression analysis showed that the association between SCr and HS was independent of other metabolic syndrome components. The prevalence of HS increased significantly with increasing SCr levels. Metabolism-related indicators and liver enzymes were significantly higher in the HS group than in the non-HS group; furthermore, these parameters increased with increasing SCr levels. FIB-4 was significantly higher in the HS group than in the non-HS group but did not show an increasing trend with increasing SCr levels.

Conclusions

Our results showed an independent association between SCr level and HS risk in a Chinese population.
Impact of age, sex, race, and regionality on major clinical outcomes of COVID-19 in hospitalized patients in the United States
Authors: Sundaram Suneha S. , Melquist Stephanie , Kalgotra Pankush , Srinivasan Sachin , Parasa Sravanthi , Desai Madhav , Sharma Prateek
Published: July 2022

Background

The COVID-19 pandemic has affected all people across the globe. Regional and community differences in timing and severity of surges throughout the pandemic can provide insight into risk factors for worse outcomes in those hospitalized with COVID-19.

Methods

The study cohort was derived from the Cerner Real World Data (CRWD) COVID-19 Database made up of hospitalized patients with proven infection from December 1, 2019 through November 30, 2020. Baseline demographic information, comorbidities, and hospital characteristics were obtained. We performed multivariate analysis to determine if age, race, comorbidity and regionality were predictors for mortality, ARDS, mechanical ventilation or sepsis hospitalized patients with COVID-19.

Results

Of 100,902 hospitalized COVID-19 patients included in the analysis (median age 52 years, IQR 36–67; 50.7% female), COVID-19 case fatality rate was 8.5% with majority of deaths in those ≥ 65 years (70.8%). In multivariate analysis, age ≥ 65 years, male gender and higher Charlson Comorbidity Index (CCI) were independent risk factors for mortality and ARDS. Those identifying as non-Black or non-White race have a marginally higher risk for mortality (OR 1.101, CI 1.032–1.174) and greater risk of ARDS (OR 1.44, CI 1.334–1.554) when compared to those who identify as White. The risk of mortality or ARDS was similar for Blacks as Whites. Multivariate analysis found higher mortality risk in the Northeast (OR 1.299, CI 1.22–1.29) and West (OR 1.26, CI 1.18–1.34). Larger hospitals also had an increased risk of mortality, greatest in hospitals with 500–999 beds (OR 1.67, CI 1.43–1.95).

Conclusion

Advanced age, male sex and a higher CCI predicted worse outcomes in hospitalized COVID-19 patients. In multivariate analysis, worse outcomes were identified in small minority populations, however there was no difference in study outcomes between those who identify as Black or White.
A triple-classification for the evaluation of lung nodules manifesting as pure ground-glass sign: a CT-based radiomic analysis
Authors: Yu Ziyang , Xu Chenxi , Zhang Ying , Ji Fengying
Published: July 2022

Objectives

To construct a noninvasive radiomics model for evaluating the pathological degree and an individualized treatment strategy for patients with the manifestation of ground glass nodules (GGNs) on CT images.

Methods

The retrospective primary cohort investigation included patients with GGNs on CT images who underwent resection between June 2015 and June 2020. The intratumoral regions of interest were segmented semiautomatically, and radiomics features were extracted from the intratumoral and peritumoral regions. After feature selection by ANOVA, Max-Relevance and Min-Redundancy (mRMR) and Least Absolute Shrinkage and Selection Operator (Lasso) regression, a random forest (RF) model was generated. Receiver operating characteristic (ROC) analysis was calculated to evaluate each classification. Shapley additive explanations (SHAP) was applied to interpret the radiomics features.

Results

In this study, 241 patients including atypical adenomatous hyperplasia (AAH) or adenocarcinoma in situ (AIS) (n = 72), minimally invasive adenocarcinoma (MIA) (n = 83) and invasive adenocarcinoma (IAC) (n = 86) were selected for radiomics analysis. Three intratumoral radiomics features and one peritumoral feature were finally identified by the triple RF classifier with an average area under the curve (AUC) of 0.960 (0.963 for AAH/AIS, 0.940 for MIA, 0.978 for IAC) in the training set and 0.944 (0.955 for AAH/AIS, 0.952 for MIA, 0.926 for IAC) in the testing set for evaluation of the GGNs.

Conclusion

The triple classification based on intra- and peritumoral radiomics features derived from the noncontrast CT images had satisfactory performance and may be used as a noninvasive tool for preoperative evaluation of the pure ground-glass nodules and developing of individualized treatment strategies.
The preventive effect of low-dose aspirin in a PPAR-γ antagonist treated mouse model of preeclampsia
Authors: Guo Yongbing , Zhu Yuchun , Sun Yu , Yang Huixia
Published: July 2022

Background

Preeclampsia (PE) is one of the leading causes of maternal and perinatal mortality and morbidity. Low-dose aspirin (LDA) is the most widely used drug to prevent PE, but the recommended dose of LDA varies according to different guidelines. Peroxisome proliferator-activated receptor (PPAR)-γ is involved in the formation of the placenta during pregnancy and is expressed in women with severe PE. In the present study, Our purpose was to investigate whether aspirin intervention in preeclampsia was related to PPAR-γ.

Methods

We administered pregnant mice with PPAR-γ-specific antagonist(T0070907) 2 mg/kg/d at 8.5–12.5 days of pregnancy. Mice treated with T0070907 developed key features of preeclampsia. Two doses of LDA (10 mg/kg/d and 20 mg/kg/d) were administered to the mice with a PE phenotype for intervention.

Results

LDA effectively decreased the increase in blood pressure in mice caused by T0070907 and decreased urinary protein levels and the urinary protein/creatinine ratio. LDA also inhibited the overexpression of endoglin and IL-β treated by T0070907. In addition, LDA evidently increased the placental weight and alleviates the degree of placental lesions of placenta and kidney. LDA alleviated the inhibition of PPAR-γ mRNA expression. The beneficial effect of 20 mg LDA was significantly better than that of 10 mg.

Conclusions

(1) LDA has a preventive effect against PE treated by PPAR-γ antagonist. (2) The preventive effect of LDA against PE is dose-dependent.
Experience of a telehealth and education program with maternal and perinatal outcomes in a low-resource region in Colombia
Authors: Escobar María Fernanda , Echavarria María Paula , Vasquez Hilda , Nasner Daniela , Ramos Isabella , Hincapié María Antonia , Pabon Stephanie , Kusanovic Juan Pedro , Martínez-Ruíz Diana Marcela , Carvajal Javier Andrés
Published: July 2022

Introduction

Maternal morbidity and mortality rates associated with perinatal care remain a significant public health concern. Rural populations from low and middle-income countries have multiple barriers to access that contribute to a lack of adherence to prenatal care, and high rates of maternal mortality and morbidity. An intervention model based on telehealth and education was implemented between a tertiary high complex care hospital and a second-level hospital from a limited source region.

Objectives

We sought to identify an association in maternal and perinatal care quality indicators after implementing a model based on telehealth and education for patients with obstetric emergencies between two hospitals in a southwestern region of Colombia.

Methods

We conducted an ecological study between 2017 and 2019 to compare before and after obstetric emergency care through telemedicine from a secondary care center (Hospital Francisco de Paula Santander-HFPS) to the referral center (Fundación Valle del Lili-FVL). The intervention included verification visits to determine the installed capacity of care, a concerted improvement plan, and on-site educational training modules in obstetric and perinatal care.

Results

There were 102 and 148 patients treated before and after telemedicine implementation respectively. Clinical indicators after model implementation showed a reduction in perinatal mortality of 29%. In addition, a reduction in the need for transfusion of blood products due to postpartum hemorrhage was observed as well as the rate of eclampsia.

Conclusions

Implementing a model based on telehealth and education between secondary and tertiary care centers allowed the strengthening of the security of care in obstetric emergencies and had a positive effect on perinatal mortality.
Exploring weight bias internalization in pregnancy
Authors: Nagpal Taniya S. , Salas Ximena Ramos , Vallis Michael , Piccinini-Vallis Helena , Alberga Angela S , Bell Rhonda C , da Silva Danilo F , Davenport Margie H , Gaudet Laura , Rodriguez Angela C Incollingo , Liu Rebecca H , Myre Maxine , Nerenberg Kara , Nutter Sarah , Russell-Mayhew Shelly , Souza Sara C S , Vilhan Candace , Adamo Kristi B
Published: July 2022

Background

Recent research has shown that pregnant individuals experience weight stigma throughout gestation, including negative comments and judgement associated with gestational weight gain (GWG). Weight bias internalization (WBI) is often a result of exposure to weight stigma and is detrimental to biopsychological health outcomes. The purpose of this study was to explore WBI in pregnancy and compare scores based on maternal weight-related factors including pre-pregnancy body mass index (BMI), obesity diagnosis and excessive GWG.

Methods

Pregnant individuals in Canada and USA completed a modified version of the Adult Weight Bias Internalization Scale. Self-reported pre-pregnancy height and weight were collected to calculate and classify pre-pregnancy BMI. Current weight was also reported to calculate GWG, which was then classified as excessive or not based on Institute of Medicine (2009) guidelines. Participants indicated if they were diagnosed with obesity by a healthcare provider. Inferential analyses were performed comparing WBI scores according to pre-pregnancy BMI, excessive GWG, and obesity diagnosis. Significance was accepted asp < 0.05 and effect sizes accompanied all analyses.

Result

336 pregnant individuals completed the survey, with an average WBI score of 3.9 ± 1.2. WBI was higher among those who had a pre-pregnancy BMI of obese than normal weight (p = 0.04, η2 = 0.03), diagnosed with obesity than not diagnosed (p < 0.001, Cohen’s d = 1.3), and gained excessively versus not (p < 0.001, Cohen’s d = 1.2).

Conclusions

Pregnant individuals who have a higher BMI, obesity and gain excessively may experience WBI. Given that weight stigma frequently occurs in pregnancy, effective person-oriented strategies are needed to mitigate stigma and prevent and care for WBI.
Pacific Islands Cohort on Cardiometabolic Health Study: rationale and design
Authors: Guerrero Rachael T. Leon , Hattori-Uchima Margaret P. , Badowski Grazyna , Aflague Tanisha F. , Wood Kathryn , Hammond Kristi , Perez Remedios
Published: July 2022

Background

Pacific Islanders, including those residing in the US Affiliated Pacific Islands (USAPI), experience some of the highest mortality rates resulting from non-communicable diseases (NCDs) worldwide. The Pacific Island Health Officers’ Association declared a Regional State of Health Emergency in 2010 due to the epidemic of NCDs in the USAPI. Obesity, a known risk factor for NCDs, has become an epidemic among both children and adults in Micronesia and other parts of the USAPI. There is some recent information about overweight and obesity (OWOB) among young children in the USAPI, but there is no data looking at the relationship between children and their biological parents. The Pacific Islands Cohort on Cardiometabolic Health (PICCAH) Study aims to collect data on NCD lifestyle factors from two generations of families (n = 600 child-parent dyads or 1,200 participants) living in Guam, Pohnpei, and Palau.

Methods

The PICCAH Study is an epidemiological study using community-based convenience sampling to recruit participants in USAPI of Guam, Palau, and Pohnpei. The goal is to recruit participant dyads consisting of 1 child plus their biological parent in Guam (500 dyads or 1,000 participants), Pohnpei (50 dyads or 100 participants), and Palau (50 dyads or 100 participants). All participants are having the following information collected: demographic, health, and lifestyle information; anthropometry; diet; physical activity; sleep; acanthosis nigricans; blood pressure; and serum levels of fasting plasma glucose, fasting insulin, glycated hemoglobin, total cholesterol, triglycerides, LDL, and HDL.

Discussion

The PICCAH Study is designed to establish the baseline of a generational epidemiologic cohort with an emphasis on cardiometabolic risk, and to better understand the extent of DM and CVD conditions and related risk factors of those living in the USAPI jurisdictions of Guam, Pohnpei, and Palau. This study also serves to further build research capacity in the underserved USAPI Region.
ARIMA and ARIMA-ERNN models for prediction of pertussis incidence in mainland China from 2004 to 2021
Authors: Wang Meng , Pan Jinhua , Li Xinghui , Li Mengying , Liu Zhixi , Zhao Qi , Luo Linyun , Chen Haiping , Chen Sirui , Jiang Feng , Zhang Liping , Wang Weibing , Wang Ying
Published: July 2022

Objective

To compare an autoregressive integrated moving average (ARIMA) model with a model that combines ARIMA with the Elman recurrent neural network (ARIMA-ERNN) in predicting the incidence of pertussis in mainland China.

Background

The incidence of pertussis has increased rapidly in mainland China since 2016, making the disease an increasing public health threat. There is a pressing need for models capable of accurately predicting the incidence of pertussis in order to guide prevention and control measures. We developed and compared two models for predicting pertussis incidence in mainland China.

Methods

Data on the incidence of pertussis in mainland China from 2004 to 2019 were obtained from the official website of the Chinese Center for Disease Control and Prevention. An ARIMA model was established using SAS (ver. 9.4) software and an ARIMA-ERNN model was established using MATLAB (ver. R2019a) software. The performances of these models were compared.

Results

From 2004 to 2019, there were 104,837 reported cases of pertussis in mainland China, with an increasing incidence over time. The incidence of pertussis showed obvious seasonal characteristics, with the peak lasting from March to September every year. Compared with the mean squared error (MSE), mean absolute error (MAE), and mean absolute percentage error (MAPE) of the ARIMA model, those of the ARIMA-ERNN model were 81.43%, 95.97% and 80.86% lower, respectively, in fitting performance. In terms of prediction performance, the MAE, MSE and MAPE were 37.75%, 56.88% and 43.75% lower, respectively.

Conclusion

The fitting and prediction performances of the ARIMA-ERNN model were better than those of the ARIMA model. This provides theoretical support for the prediction of infectious diseases and should be beneficial to public health decision making.
Management of arthrofibrosis in neuromuscular disorders: a review
Authors: Martinez-Lozano Edith , Beeram Indeevar , Yeritsyan Diana , Grinstaff Mark W. , Snyder Brian D. , Nazarian Ara , Rodriguez Edward K.
Published: July 2022

Arthrofibrosis, or rigid contracture of major articular joints, is a significant morbidity of many neurodegenerative disorders. The pathogenesis depends on the mechanism and severity of the precipitating neuromuscular disorder. Most neuromuscular disorders, whether spastic or hypotonic, culminate in decreased joint range of motion. Limited range of motion precipitates a cascade of pathophysiological changes in the muscle-tendon unit, the joint capsule, and the articular cartilage. Resulting joint contractures limit functional mobility, posing both physical and psychosocial burdens to patients, economic burdens on the healthcare system, and lost productivity to society. This article reviews the pathophysiology of arthrofibrosis in the setting of neuromuscular disorders. We describe current non-surgical and surgical interventions for treating arthrofibrosis of commonly affected joints. In addition, we preview several promising modalities under development to ameliorate arthrofibrosis non-surgically and discuss limitations in the field of arthrofibrosis secondary to neuromuscular disorders.
Delay discounting, probability discounting, and interdental cleaning frequency
Authors: DeFulio Anthony , Rzeszutek Mark
Published: July 2022

Background

Interdental cleaning is recommended by dentists but many people do not floss regularly. The health benefits of interdental cleaning are delayed, and sensitivity to delay is an important factor in many health behaviors. Thus, the present studies explore the relationship between frequency of flossing, and sensitivity to delayed and probabilistic outcomes.

Method

Crowd-sourced subjects were recruited in two studies (n = 584 and n = 321, respectively). In both studies, subjects reported their frequency of flossing and completed delay discounting and probability discounting tasks. Discounting was measured with area under the curve, and linear regression was used to analyze the results.

Results

Findings show that higher levels of delay discounting were associated with less frequent flossing (p < 0.001, both studies). In contrast, probability discounting was not significantly associated with flossing frequency (ns, both studies).

Conclusion

The findings are consistent with prior studies involving other health behaviors such as attendance at primary care and medication adherence. Results suggest that interventions that reduce delay discounting may help promote regular interdental cleaning, and that delay discounting is a more robust predictor of health behaviors than probability discounting. In addition, interdental cleaning appears to be a reasonable target behavior for evaluating potentially generalizable behavioral health interventions. Thus, interventions that are successful in promoting oral health behaviors should be considered as candidates for evaluation in other health behavior domains.
Low LINC02147 expression promotes the malignant progression of oral submucous fibrosis
Authors: Chen Jun , Li Wenjie , Liu Binjie , Xie Xiaoli
Published: July 2022

Background

Key lncRNAs associated with the malignant progression of oral submucous fibrosis (OSF) to oral squamous cell carcinoma (OSCC) were identified.

Methods

Key lncRNAs with sequential changes from normal oral mucosa (NOM) to OSF to OSCC were identified based on the GEO database. Kaplan–Meier analysis was used to screen lncRNAs related to OSCC prognosis. Cox regression analysis was used to validate the independent prognostic value. qPCR was used to confirm the expression of the candidate lncRNAs. Gene set enrichment analysis (GSEA), nucleocytoplasmic separation assay, fluorescence in situ hybridization, RNA knockdown, western blot, and cell viability assay were performed to investigate the biological functions of the candidate lncRNA. A nomogram was constructed to quantitatively predict OSCC prognosis based on TCGA.

Results

Bioinformatics methods indicated that LINC02147 was sequentially downregulated from NOM to OSF to OSCC, as confirmed by clinical tissues and cells. Meanwhile, low LINC02147 expression, as an independent prognostic factor, predicted a poor prognosis for OSCC. GSEA and in vitro studies suggested that low LINC02147 expression promoted OSF malignant progression by promoting cell proliferation and differentiation. A LINC02147 signature-based nomogram successfully quantified each indicator’s contribution to the overall survival of OSCC.

Conclusions

Low LINC02147 expression promoted OSF malignant progression and predicted poor OSCC prognosis.
Virtual training and technical assistance: a shift in behavioral health workforce access and perceptions of services during emergency restrictions
Authors: Powell Kristen G. , Chaple Michael J. , Henry Maxine , Morton Cory , Becker Sara J. , Gotham Heather J. , Hagle Holly N. , Helle Ashley C. , Krom Laurie J. , Martin Rosemarie , Molfenter Todd D. , Roget Nancy , Rutkowski Beth A. , Velez-Echevarria Isa I. , Yanez Ruth ,   Cross-Technology Transfer Center (TTC) Workgroup on Virtual Learning, Powell Kristen G. , Chaple Michael J. , Henry Maxine , Morton Cory , Becker Sara J. , Gotham Heather J. , Hagle Holly N. , Helle Ashley C. , Krom Laurie J. , Martin Rosemarie , Molfenter Todd D. , Roget Nancy , Rutkowski Beth A. , Velez-Echevarria Isa I. , Yanez Ruth
Published: July 2022

Background

To respond to the COVID-19 pandemic, the Substance Abuse and Mental Health Services Administration-funded Technology Transfer Centers had to rapidly adapt to ensure that the behavioral health workforce had continuous access to remote training and technical assistance (TTA). Although the Technology Transfer Centers have historically relied partially upon virtual methods for delivering TTA, the shift to a strictly virtual approach necessitated by COVID-19 restrictions has raised new questions for how to best proceed with services when social distancing guidelines are relaxed. The objective of this exploratory paper was to compare TTA provision in the six-month period prior to (9/1/19 thru 2/28/20) and during (4/1/20 thru 9/30/20) early COVID-19 restrictions to determine the extent to which the shift to virtual service provision impacted the behavioral health and medical workforce. Specifically, we examined participants’ access to TTA, geographic reach of TTA, and workforce perceptions of satisfaction and utility with TTA provision.

Method

Participant and event-level data were analyzed to compare the following metrics before and during the COVID pandemic: number of events and attendees; participant demographics; zip codes reached; coverage of rural, suburban, and urban areas; and perceptions of satisfaction with and utility of training.

Results

Findings showed a 40% increase in the number of events delivered (p < .001) and a 270% increase in the number of attendees (p < .001) during the COVID period when TTCs relied exclusively on virtual delivery. Geospatial analyses linking zip codes to a schematic of rural, suburban, and urban classifications throughout the United States revealed significant increases in the number of zip codes reached during the COVID time period. Satisfaction levels were comparable before and during the pandemic.

Conclusions

Findings show that expanded access to TTA services via virtual formats resulted in reach to more diverse attendees and regions, and did not come at the expense of satisfaction. Results suggest that virtual TTA should continue to be an important component of TTA offerings post-pandemic.
Shared understanding of resilient practices in the context of inpatient suicide prevention: a narrative synthesis
Authors: Berg Siv Hilde , Rørtveit Kristine , Walby Fredrik A. , Aase Karina
Published: July 2022

Background

The prevailing patient safety strategies in suicide prevention are suicide risk assessments and retrospective reviews, with emphasis on minimising risk and preventing adverse events. Resilient healthcare focuses on how everyday clinical practice succeeds and emphasises learning from practice, not from adverse events. Yet, little is known about resilient practices for suicidal inpatients. The aim of the study is to draw upon the perspectives of patients and healthcare professionals to inform the conceptual development of resilient practices in inpatient suicide prevention.

Methods

A narrative synthesis was conducted of findings across patients and healthcare professionals derived from a qualitative case study based on interviews with patients and healthcare professionals in addition to a systematic literature review.

Results

Three sub-themes categorise resilient practices for healthcare professionals and for patients hospitalised with suicidal behaviour: 1) interactions capturing non-verbal cues; 2) protection through dignity and watchfulness; and 3) personalised approaches to alleviate emotional pressure. The main theme, the establishment of relationships of trust in resilient practices for patients in suicidal crisis, is the foundation of their communication and caring.

Conclusion

Clinical practice for patients hospitalised with suicidal behaviour has characteristics of complex adaptive systems in terms of dynamic interactions, decision-making under uncertainty, tensions between goals solved through trade-offs, and adaptations to patient variability and interpersonal needs. To improve the safety of patients hospitalised with suicidal behaviour, variability in clinical practice should be embraced.

Trial registration

https://doi.org/10.1136/bmjopen-2016-012874
The relationship between community public health, behavioral health service accessibility, and mass incarceration
Authors: Ramezani Niloofar , Breno Alex J. , Mackey Benjamin J. , Viglione Jill , Cuellar Alison Evans , Johnson Jennifer E. , Taxman Faye S.
Published: July 2022

Background

The relationship between healthcare service accessibility in the community and incarceration is an important, yet not widely understood, phenomenon. Community behavioral health and the criminal legal systems are treated separately, which creates a competing demand to confront mass incarceration and expand available services. As a result, the relationship between behavioral health services, demographics and community factors, and incarceration rate has not been well addressed. Understanding potential drivers of incarceration, including access to community-based services, is necessary to reduce entry into the legal system and decrease recidivism. This study identifies county-level demographic, socioeconomic, healthcare services availability/accessibility, and criminal legal characteristics that predict per capita jail population across the U.S. More than 10 million individuals pass through U.S. jails each year, increasing the urgency of addressing this challenge.

Methods

The selection of variables for our model proceeded in stages. The study commenced by identifying potential descriptors and then using machine learning techniques to select non-collinear variables to predict county jail population per capita. Beta regression was then applied to nationally available data from all 3,141 U.S. counties to identify factors predicting county jail population size. Data sources include the Vera Institute’s incarceration database, Robert Wood Johnson Foundation’s County Health Rankings and Roadmaps, Uniform Crime Report, and the U.S. Census.

Results

Fewer per capita psychiatrists (z-score = -2.16;p = .031), lower percent of drug treatment paid by Medicaid (-3.66;p < .001), higher per capita healthcare costs (5.71;p < .001), higher number of physically unhealthy days in a month (8.6;p < .001), lower high school graduation rate (-4.05;p < .001), smaller county size (-2.66,p = .008; -2.71,p = .007; medium and large versus small counties, respectively), and more police officers per capita (8.74;p < .001) were associated with higher per capita jail population. Controlling for other factors, violent crime rate did not predict incarceration rate.

Conclusions

Counties with smaller populations, larger percentages of individuals that did not graduate high school, that have more health-related issues, and provide fewer community treatment services are more likely to have higher jail population per capita. Increasing access to services, including mental health providers, and improving the affordability of drug treatment and healthcare may help reduce incarceration rates.
Achieving universal reproductive health coverage for deaf women in Ghana: an explanatory study of knowledge of contraceptive methods, pregnancy and safe abortion practices
Authors: Nketsia William , Mprah Wisdom Kwadwo , Opoku Maxwell Peprah , Juventus Duorinaah , Amponteng Michael
Published: July 2022

Background

The first world conference on sexual and reproductive health (SRH) in 1994 helped create the awareness that reproductive health is a human right. Over the years, attempts have been made to extend services to all persons; however, lapses persist in service provision for all in need. Recently, countries have been encouraged to target minority groups in their reproductive health service provision. However, studies have rarely attempted to develop deeper insights into the experiences of deaf men and women regarding their knowledge of SRH. The purpose of this study was to develop an in-depth understanding of the knowledge of deaf persons regarding services such as knowledge of contraceptive methods, pregnancy and safe abortion practices.

Methods

A sequential explanatory mixed-methods approach was adopted for this study. In the first quantitative phase, 288 deaf persons recruited from three out of the 16 regions in Ghana participated in this study. They completed a 31-item questionnaire on the main issues (knowledge of contraceptive methods, pregnancy and safe abortion practices) addressed in this study. In the second phase, a semi-structured interview guide was used to collect data from 60 participants who took part in the first phase. The key trend emerging in the first phase underpinned the interview guide used for the data collection. While the quantitative data were subjected to the computation of means, t-tests, analyses of variance, correlations and linear regressions to understand the predictors, the in-depth interviews were analysed using the thematic method of analysis.

Results

The results showed a convergence between the quantitative and qualitative data. For instance, the interview material supported the initial findings that deaf women had little knowledge of contraceptive methods. The participants offered reasons explaining their inability to access services and the role of religion in their understanding of SRH.

Conclusion

The study concludes by calling on policymakers to consider the needs of deaf persons in future SRH policies. The study limitations and other implications for future policymaking are discussed.
Healthcare utilization for somatic conditions among Swedish patients in opioid substitution treatment, with and without on-site primary healthcare
Authors: Vikbladh Teodor , Troberg Katja , Håkansson Anders , Dahlman Disa
Published: July 2022

Background

Opioid substitution treatment (OST) populations are aging and have increased mortality and somatic morbidity compared to general populations internationally. While OST patients have poor self-rated physical health and unmet healthcare needs, documented healthcare utilization has been sparsely investigated. The aim of this study was to assess registered healthcare utilization for somatic conditions in a sample of Swedish OST patients, and compare healthcare utilization among OST patients with and without use of on-site primary healthcare (PHC).

Methods

Patients in OST in Malmö, Sweden, were recruited for a survey study conducted in 2017–2018. Survey data were compared with comprehensive patient records from specialized and primary care during one year prior to study inclusion (totaln = 190). All patient records were examined for healthcare utilization, source of healthcare (PHC, emergency care and secondary care), and documented diagnoses and symptoms. Factors associated with healthcare utilization were analyzed by using logistic regression analysis. Patients with and without on-site PHC were compared by using descriptive statistics and Chi-2 test.

Results

A total of 88% of the sample had been in direct or indirect contact with somatic healthcare during one year (PHC 66%; emergency care 28%; secondary care 67%). The most prevalent somatic diagnoses were infectious diseases (39%) and symptom diagnoses (37%). Respiratory, dermatological and musculoskeletal diagnoses, and trauma/intoxication were documented in 21–26% of the sample, respectively. PHC utilization was associated with older age and being born in Sweden. Among patients with on-site PHC (n = 25), the number utilizing secondary care was 84%, and certain diagnostic codes were more frequent in this group.

Conclusion

OST patients are seemingly underserved as regards their physical health. Since increased OST access decreases opioid overdose fatalities, the life expectancy among OST patients is likely to increase and thereby also increases the risk of age-related conditions. Thus, easily accessible physical healthcare is of great importance in this group. On-site PHC might be a way to establish healthcare contact with OST patients, especially for non-acute conditions, although further research is needed.
Molecular characterization of a novel subgenotype of lumpy skin disease virus strain isolated in Inner Mongolia of China
Authors: Zan Xiaohui , Huang Haibi , Guo Yu , Di Dongdong , Fu Cun , Wang Shirong , Wu Youzhi , Wang Jialei , Wang Yan , Ma Yanhua , Chai Chunxia , Su Rui , Song Qingqing , Wang Wei
Published: July 2022

Background

The outbreak of Lumpy skin disease (LSD) in cattle caused by LSD virus (LSDV) was first reported in August 2019 in China. Since then, several LSD outbreaks have been reported in seven different provinces of China. Until now, several Lumpy skin disease virus (LSDV) strains from China have been reported and sequenced including LSDV/Xinjiang/2019 (MN598005.1), China/GD01/2020 (MW355944.1), and LSDV/Hongkong/2021 (MW732649.1). In October 2020, more than 1,700 cattle imported from Chile arrived in Xilingol, Inner Mongolia, and were diagnosed with LSD. Currently, limited data on the origin of the virus is available.

Methods

Nucleotide sequences of the ORF11, ORF36, ORF74, ORF117, ORF126 genes and the complete genome of LSDV strains and isolates were downloaded from NCBI database. MEGA7.0 was used to perform phylogenetic analysis with Neighbor-Joining (NJ). DNASTAR software is used to analyze homologous comparison analysis with related genes of reference strains included in Genbank.

Results

Compared with other strains isolated from China, the results of full genome sequence analysis showed the LSDV/NMG/2020 strain belonged to the recombinant strains. The LSDV/NMG/2020 strain is different from the current LSDV field isolates in Africa, the Middle East, Europe, and the newly emerged LSDV Russia variants. Based on the identities of P32, RPO30, EEV, GPCR and LSDV117 genes (99.8%, 99%, 99.8%, 99% and 98.7%), the sub-cluster recombinant containing LSDV/NMG/2020 strain is phylogenetically closer to the Russia strain (Saratov/2017).

Conclusions

In this study, we reported a new isolated LSDV strain named LSDV/NMG/2020. The results of genomic characterization and phylogenetic analysis demonstrated that the LSDV/NMG/2020 isolate was a vaccine-like recombinant strain.
Prevalence, antimicrobial susceptibilities and risk factors of Methicillin resistant Staphylococcus aureus (MRSA) in dairy bovines
Authors: Selim Abdelfattah , Kelis Khalid , AlKahtani Muneera D. F. , Albohairy Fatima M. , Attia Kotb A.
Published: July 2022

Staphylococcus aureus is a common mastitis pathogen in dairy cows, and methicillin-resistant S. aureus (MRSA) has been found in dairy farms all over the world. The study carried out on bovines from three governorates in Egypt, with the goal of determining the prevalence of MRSA in positive milk samples of subclinical mastitis, performing an antibiotic susceptibility test against MRSA isolates and determining the risk factors associated with MRSA. A total of 350 quarter milk samples (n = 200 mixed breed cow; n = 150 water buffalo) were collected and examined for subclinical mastitis using the California mastitis test (CMT) before being exposed to standard microbiological procedures for S. aureus isolation. The disc diffusion method was used to phenotypically analyse the positive S. aureus isolates for MRSA, which was verified by a PCR assay targeting the mecA gene. According to the findings of the study, 41.4% (145/350) milk samples were positive based on CMT, while 35.7% (125/350) of positive samples identified as MRSA based on PCR assay. However, the obtained results revealed non-significant disparity between cattle and buffalo and all predicted risk factors were strongly associated with prevalence of subclinical mastitis. The in-vitro antibiotic susceptibility test revealed that cefoxitin was completely resistant, whereas linezolid, ciprofloxacin, and trimethoprim + sulphamethoxazole were sensitive against the MRSA isolates. The relevance of S. aureus to public health, as well as the development of resistance to antibiotics like methicillin, needs ongoing testing of antimicrobial medications against MRSA isolates.