bluuebunny/crossref_metadata_2025_split huggingface 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractBackgroundRecent 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.MethodsPregnant 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.Result336 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).ConclusionsPregnant 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

Abstract
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

Abstract
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.