bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrence of Escherichia Coli O157:H7 in lactating cows and dairy farm environment and the antimicrobial susceptibility pattern at Adami Tulu Jido Kombolcha District, Ethiopia
Authors: Mesele Frehiwot , Leta Samson , Amenu Kebede , Abunna Fufa 
Published: January 2023

Abstract
Background
Food-borne pathogens are the foremost causes of food-borne human illness in the world. Escherichia coli O157:H7 (E. coli O157:H7) is one of the major food-borne pathogenic bacteria around the world. Though evidence is lacking; especially in developing countries like Ethiopia, the potential health impact of E. coli O157:H7 can be high where food production, handling and consumption is often taking place under unhygienic conditions. In Ethiopia, studies reported E. coli and E. coli O157: H7 from food of animal origin, mainly meat and milk, and also animal surfaces and feces. The objective of the present study was to investigate the occurrence of E. coli O157:H7 in raw milk and the dairy production farm environment and further assess the antimicrobial resistance pattern of the bacterium.

Methods
Samples of milk from individual lactating cows’ and dairy farm environmental samples (feces, water and manure) were collected at Adami Tulu Jido Kombolcha district (ATJKD) and analyzed for the presence of E. coli O157:H7. Standard microbiological techniques including culture, biochemical testing and serological test were performed to isolate and identify the bacterium. The bacterial isolates were evaluated for antimicrobial susceptibility patterns using disk diffusion method. A questionnaire was used to collect possible factors affecting E. coli O157:H7 occurrence.

Results
The overall prevalence of E. coli O157:H7 was 4.7% (19/408) (95% CI: 2.6; 6.7). Out of 19 E. coli O157:H7 isolates, 4/50, 7/154, 2/50, and 6/154 were from water, milk, manure, and feces samples, respectively. From potential risk factors considered in this study area, floor type, cleaning of pens, milking location and hand washing during the time of milking were significantly associated with the occurrence of E. coli O157:H7. The antimicrobial susceptibility pattern indicated varying degrees of resistance. All of the isolates were found to be resistant ampicillin, cephalothin, and rifampin, and 100% susceptibility was observed against the drugs: chloramphenicol, ciprofloxacin, gentamicin, nalidixic acid, kanamycin, and tetracycline. Concerning streptomycin, 63.15% of the isolates were susceptible and 36.8% showed intermediate susceptibility.

Conclusions
The occurrence of multi-drug resistance E. coli O157:H7 observed both in lactating cows and in dairy farm environments can sustain a continuous transmission of the bacteria. The occurrence of multidrug-resistant E. coli o157:H7could hamper the control and prevention efforts.
Gut microbiota composition can reflect immune responses of latent tuberculosis infection in patients with poorly controlled diabetes
Authors: Huang Hung-Ling , Luo Yong-Chun , Lu Po-Liang , Huang Cheng-Hsieh , Lin Kun-Der , Lee Meng-Rui , Cheng Meng-Hsuan , Yeh Yao-Tsung , Kao Cheng-Yuan , Wang Jann-Yuan , Yang Jinn-Moon , Chong Inn-Wen 
Published: January 2023

Abstract
Background
Diabetes mellitus (DM) is a major risk factor for tuberculosis (TB). Evidence has linked the DM-related dysbiosis of gut microbiota to modifiable host immunity to Mycobacterium tuberculosis infection. However, the crosslinks between gut microbiota composition and immunological effects on the development of latent TB infection (LTBI) in DM patients remain uncertain.

Methods
We prospectively obtained stool, blood samples, and medical records from 130 patients with poorly-controlled DM (pDM), defined as ever having an HbA1c > 9.0% within previous 1 year. Among them, 43 had LTBI, as determined by QuantiFERON-TB Gold in-Tube assay. The differences in the taxonomic diversity of gut microbiota between LTBI and non-LTBI groups were investigated using 16S ribosomal RNA sequencing, and a predictive algorithm was established using a random forest model. Serum cytokine levels were measured to determine their correlations with gut microbiota.

Results
Compared with non-LTBI group, the microbiota in LTBI group displayed a similar alpha-diversity but different beta-diversity, featuring decrease of Prevotella_9, Streptococcus, and Actinomyces and increase of Bacteroides, Alistipes, and Blautia at the genus level. The accuracy was 0.872 for the LTBI prediction model using the aforementioned 6 microbiome-based biomarkers. Compared with the non-LTBI group, the LTBI group had a significantly lower serum levels of IL-17F (p = 0.025) and TNF-α (p = 0.038), which were correlated with the abundance of the aforementioned 6 taxa.

Conclusions
The study results suggest that gut microbiome composition maybe associated with host immunity relevant to TB status, and gut microbial signature might be helpful for the diagnosis of LTBI.
Impaired cell–cell communication and axon guidance because of pulmonary hypoperfusion during postnatal alveolar development
Authors: Li Debao , Wang Jing , Fang Yuan , Hu Yuqing , Xiao Yingying , Cui Qing , Jiang Chuan , Sun Sijuan , Chen Hao , Ye Lincai , Sun Qi 
Published: January 2023

Abstract
Background
Pulmonary hypoperfusion is common in children with congenital heart diseases (CHDs) or pulmonary hypertension (PH) and causes adult pulmonary dysplasia. Systematic reviews have shown that some children with CHDs or PH have mitigated clinical outcomes with COVID-19. Understanding the effects of pulmonary hypoperfusion on postnatal alveolar development may aid in the development of methods to improve the pulmonary function of children with CHDs or PH and improve their care during the COVID-19 pandemic, which is characterized by cytokine storm and persistent inflammation.

Methods and results
We created a neonatal pulmonary hypoperfusion model through pulmonary artery banding (PAB) surgery at postnatal day 1 (P1). Alveolar dysplasia was confirmed by gross and histological examination at P21. Transcriptomic analysis of pulmonary tissues at P7(alveolar stage 2) and P14(alveolar stage 4) revealed that the postnatal alveolar development track had been changed due to pulmonary hypoperfusion. Under the condition of pulmonary hypoperfusion, the cell–cell communication and axon guidance, which both determine the final number of alveoli, were lost; instead, there was hyperactive cell cycle activity. The transcriptomic results were further confirmed by the examination of axon guidance and cell cycle markers. Because axon guidance controls inflammation and immune cell activation, the loss of axon guidance may explain the lack of severe COVID-19 cases among children with CHDs or PH accompanied by pulmonary hypoperfusion.

Conclusions
This study suggested that promoting cell–cell communication or supplementation with guidance molecules may treat pulmonary hypoperfusion–induced alveolar dysplasia, and that COVID-19 is less likely to cause a cytokine storm in children with CHD or PH accompanied by pulmonary hypoperfusion.

Graphical Abstract
Relationship between early-onset stroke and triglyceride-glucose index among young Chinese adults
Authors: Xu Wenqi , Zhao Haiyan , Han Xu , Liu Jianrong , Li Haixia , Sun Junyan , Xing Aijun , Chen Shuohua , Wu Shouling , Wu Yuntao 
Published: January 2023

Abstract
Background
The triglyceride–glucose index (TyG index), an alternative indicator of peripheral insulin resistance (IR), is associated with cardiovascular disease (CVD) in the general population. The aim of this research was to determine the correlation between early-onset stroke and the TyG index among young Chinese adults.

Methods
Participants (age ≤ 40 years) who attended their first physical examination in Kailuan General Hospital or its 11 subsidiary hospitals between 2006 and 2012 were enrolled. The subjects were divided into four equal points according to the quartile of the TyG index, with the lowest quartile (Q1) as the reference group. A Cox proportional hazard model was employed to assess the correlation between early-onset stroke incidence and the TyG index. Restricted cubic spline analysis was further conducted to examine nonlinear associations. The TyG index was calculated as Ln [Triglyceride (TG, mg/dL) × Fasting Blood Glucose (FBG, mg/dL)/2].

Results
Overall, 35,999 subjects met the inclusion criteria. Their mean age was 30.8 ±  5.7 years, and 77.1% of subjects were males. During a median observation period of 11 years, 281 stroke events occurred (62 hemorrhagic strokes and 219 ischemic strokes). Compared to the Q1 group (as the lowest group), subjects in groups Q2-Q4 had significantly higher risks of early-onset stroke (P < 0.05) after adjustment for relevant confounders in the Cox proportional hazards model. Similar results were consistent with ischemic stroke. However, no significant associations were observed between the risk of hemorrhage and the baseline TyG index. The restricted cubic splines revealed that the risk of stroke progressively increased with a high TyG index ≥ 8.41.

Conclusions
The TyG index may be a major risk factor for early-onset stroke among young Chinese adults. A TyG index ≥ 8.41 can be used as an indicator for screening high-risk stroke groups.
Long-term efficacy and safety of anticoagulant for cavernous transformation of the portal vein cirrhotic patient with extrahepatic portal vein obstruction
Authors: Zhou Yongjie , Zhuang Zhiquan , Yu Tianzhu , Zhang Wen , Ma Jingqin , Yu Jiaze , Yan Zhiping , Luo Jianjun 
Published: January 2023

Abstract
Background/aims
Cavernous transformation of the portal vein (CTPV) in cirrhotic patients with extrahepatic portal vein obstruction (EHPVO) was a relatively rare disease and had no consensus on the treatment. Our study aimed to explore the value of anticoagulation with warfarin treatment for CTPV cirrhotic patients with EHPVO.
Methods: From January 2015 to December 2019, the clinical characteristics of cirrhotic patients who were diagnosed as CTPV with EHPVO were retrospectively analyzed. Eligible patients were distributed into the anticoagulation group (n = 46) and control group (n = 38). The change of portal vein thrombosis, hepatic decompensation, survival and adverse events were evaluated between the two groups.

Results
The median follow-up of our patients was 51 months in the anticoagulation group and 44 months in the control group. The progress rate of the portal vein was higher in patients from the control groups (n = 12) than in patients from the anticoagulation group (n = 4, p = 0.008). There was no significant difference between the partial recanalization rate and stable rate between the two groups. Patients in anticoagulation group developed less hepatic decompensation than those in control group (13.0% vs 34.2%, p = 0.021). The Kaplan-Meier curve showed that patients in the anticoagulation group had a better prognosis than patients in the control group (P < 0.022). There were no serious complications due to warfarin treatment.

Conclusion
For CTPV cirrhotic patients with EHPVO, anticoagulation with warfarin treatment was effective and safe. Anticoagulants could prevent portal vein thrombosis progression, hepatic decompensation and death. In addition, our results showed little benefit of anticoagulants on thrombosis recanalization.
AFAP1L1 promotes gastric cancer progression by interacting with VAV2 to facilitate CDC42-mediated activation of ITGA5 signaling pathway
Authors: Sun Bo , Ding Bai , Chen Yu , Peng Chuang , Chen Xu 
Published: January 2023

Abstract
Background
The actin filament-associated protein (AFAP) family genes include AFAP1/AFAP-110, AFAP1L1 and AFAP1L2/XB130. Increasing evidence indicates these three AFAP family members participate in tumor progression, but their clinical significance and molecular mechanisms in gastric cancer (GC) remain unclear.

Methods
We first analyzed expression of AFAP family genes using public datasets and verified the results. The clinical significance of AFAP family genes in GC patients was also analyzed. In vitro and in vivo experiments were applied to explore the function of AFAP1L1. Enrichment analysis was used to explore potential molecular mechanisms. We then performed additional experiments, such as cell adhesion assay, co-immunoprecipitation and so on to confirm the downstream molecular mechanisms of AFAP1L1.

Results
Public data analyses and our verification both showed AFAP1L1 was the only AFAP family members that was significantly upregulated in GC compared with normal gastric tissues. Besides, only AFAP1L1 could predict poor prognosis and act as an independent risk factor for GC patients. In addition, AFAP1L1 promotes GC cells proliferation, migration, invasion in vitro and tumor growth, metastasis in vivo by inducing epithelial-to-mesenchymal transition (EMT). In terms of mechanism, AFAP1L1 interacts with VAV guanine nucleotide exchange factor 2 (VAV2) to activate Rho family GTPases CDC42, which finally promotes expression of integrin subunit alpha 5 (ITGA5) and activation of integrin signaling pathway.

Conclusion
AFAP1L1 promotes GC progression by inducing EMT through VAV2-mediated activation of CDC42 and ITGA5 signaling pathway, indicating AFAP1L1 may be a promising prognostic biomarker and therapeutic target for GC patients.
The efficacy of intravenous iron for treatment of anemia before cardiac surgery: An updated systematic review and meta-analysis with trial sequential analysis
Authors: Liu Hong-Mei , Tang Xi-sha , Yu Hong , Yu Hai 
Published: January 2023

Abstract
Background
Preoperative anemia is common in patients undergoing cardiac surgery with various etiologies, among which iron deficiency is the leading cause. However, the benefit of intravenous (IV) iron for the treatment of anemia before cardiac surgery is uncertain. This updated meta-analysis aimed to evaluate the efficacy of IV iron in adult cardiac surgery patients with preoperative anemia.

Methods
This review was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We searched Embase, PubMed and the Cochrane Central Register of Controlled Trials to identify eligible randomized controlled trials (RCTs) and observational studies. Quality was assessed using the Cochrane Collaboration risk of bias tool and Newcastle–Ottawa scale, and the strength of evidence was assessed using the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) criteria. Trial sequential analysis was performed on the primary outcome (transfusion rate) to confirm whether firm evidence was reached.

Results
Six RCTs (936 patients) and 5 observational studies (1350 patients) were included in this meta-analysis. The IV iron group and the control group were comparable in terms of transfusion rate [55.1% vs 60.9%, risk ratio (RR) = 0.91, 95% confidence interval (CI) 0.81–1.03, P = 0.13, low quality]. There were no significant differences in units transfused per patient, ICU stay and hospital length of stay between the two groups. And pooled data showed a benefit of IV iron compared to the control group on mortality (2.76% vs 3.75%, RR = 0.58, 95% CI 0.36–0.95, P = 0.03, moderate quality) and no mortality reduction existed when including only RCTs.

Conclusions
This meta-analysis suggested that IV iron treatment for patients with anemia before cardiac surgery did not reduce the transfusion requirement (low quality), but it was associated with decreased mortality (moderate quality). More large-scale, high-quality randomized clinical trials are warranted to confirm or refute our findings.
PROSPERO registry reference: CRD42022331875.
Insulin resistance in polycystic ovary syndrome across various tissues: an updated review of pathogenesis, evaluation, and treatment
Authors: Zhao Han , Zhang Jiaqi , Cheng Xiangyi , Nie Xiaozhao , He Bing 
Published: January 2023

AbstractPolycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by chronic ovulation dysfunction and overabundance of androgens; it affects 6–20% of women of reproductive age. PCOS involves various pathophysiological factors, and affected women usually have significant insulin resistance (IR), which is a major cause of PCOS. IR and compensatory hyperinsulinaemia have differing pathogeneses in various tissues, and IR varies among different PCOS phenotypes. Genetic and epigenetic changes, hyperandrogenaemia, and obesity aggravate IR. Insulin sensitization drugs are a new treatment modality for PCOS. We searched PubMed, Google Scholar, Elsevier, and UpToDate databases in this review, and focused on the pathogenesis of IR in women with PCOS and the pathophysiology of IR in various tissues. In addition, the review provides a comprehensive overview of the current progress in the efficacy of insulin sensitization therapy in the management of PCOS, providing the latest evidence for the clinical treatment of women with PCOS and IR.
Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing
Authors: Smajlović Haris , Shajii Ariya , Berger Bonnie , Cho Hyunghoon , Numanagić Ibrahim 
Published: January 2023

AbstractSecure multiparty computation (MPC) is a cryptographic tool that allows computation on top of sensitive biomedical data without revealing private information to the involved entities. Here, we introduce Sequre, an easy-to-use, high-performance framework for developing performant MPC applications. Sequre offers a set of automatic compile-time optimizations that significantly improve the performance of MPC applications and incorporates the syntax of Python programming language to facilitate rapid application development. We demonstrate its usability and performance on various bioinformatics tasks showing up to 3–4 times increased speed over the existing pipelines with 7-fold reductions in codebase sizes.
The effects of a moderate physical activity intervention on physical fitness and cognition in healthy elderly with low levels of physical activity: a randomized controlled trial
Authors: Galle Sara A. , Deijen Jan Berend , Milders Maarten V. , De Greef Mathieu H. G. , Scherder Erik J. A. , van Duijn Cornelia M. , Drent Madeleine L. 
Published: January 2023

Abstract
Background
Increasing physical activity is one of the most promising and challenging interventions to delay or prevent cognitive decline and dementia.

Methods
We conducted a randomized controlled trial to assess the effects of a physical activity intervention, aimed at increasing step count, in elderly with low levels of physical activity on measures of strength, balance, aerobic capacity, and cognition. Participants were assigned to 9 months of exercise counseling or active control.

Results
The intention-to-treat analyses show that the intervention, compared to control, increases the level of physical activity, but has no significant effect on physical fitness and cognition. Those who increased their physical activity with 35% or more show significant improvements in aerobic capacity, gait speed, verbal memory, executive functioning, and global cognition, compared to those who did not achieve a 35% increase.

Limitations
The number of participants that achieved the intended improvement was lower than expected.

Conclusion
Responder analyses suggest an improvement of physical fitness and cognition in those who achieved an increase in physical activity of at least 35%.

Trial registration
The trial protocol is registered at the Dutch Trial Register NL5675, August 1, 2016.
Deep learning and radiomic feature-based blending ensemble classifier for malignancy risk prediction in cystic renal lesions
Authors: He Quan-Hao , Feng Jia-Jun , Lv Fa-Jin , Jiang Qing , Xiao Ming-Zhao 
Published: January 2023

Abstract
Background
The rising prevalence of cystic renal lesions (CRLs) detected by computed tomography necessitates better identification of the malignant cystic renal neoplasms since a significant majority of CRLs are benign renal cysts. Using arterial phase CT scans combined with pathology diagnosis results, a fusion feature-based blending ensemble machine learning model was created to identify malignant renal neoplasms from cystic renal lesions (CRLs). Histopathology results were adopted as diagnosis standard. Pretrained 3D-ResNet50 network was selected for non-handcrafted features extraction and pyradiomics toolbox was selected for handcrafted features extraction. Tenfold cross validated least absolute shrinkage and selection operator regression methods were selected to identify the most discriminative candidate features in the development cohort. Feature’s reproducibility was evaluated by intra-class correlation coefficients and inter-class correlation coefficients. Pearson correlation coefficients for normal distribution and Spearman's rank correlation coefficients for non-normal distribution were utilized to remove redundant features. After that, a blending ensemble machine learning model were developed in training cohort. Area under the receiver operator characteristic curve (AUC), accuracy score (ACC), and decision curve analysis (DCA) were employed to evaluate the performance of the final model in testing cohort.

Results
The fusion feature-based machine learning algorithm demonstrated excellent diagnostic performance in external validation dataset (AUC = 0.934, ACC = 0.905). Net benefits presented by DCA are higher than Bosniak-2019 version classification for stratifying patients with CRL to the appropriate surgery procedure.

Conclusions
Fusion feature-based classifier accurately distinguished malignant and benign CRLs which outperformed the Bosniak-2019 version classification and illustrated improved clinical decision-making utility.
Harnessing electromagnetic fields to assist bone tissue engineering
Authors: Zhao Hongqi , Liu Chaoxu , Liu Yang , Ding Qing , Wang Tianqi , Li Hao , Wu Hua , Ma Tian 
Published: January 2023

AbstractBone tissue engineering (BTE) emerged as one of the exceptional means for bone defects owing to it providing mechanical supports to guide bone tissue regeneration. Great advances have been made to facilitate the success of BTE in regenerating bone within defects. The use of externally applied fields has been regarded as an alternative strategy for BTE. Electromagnetic fields (EMFs), known as a simple and non-invasive therapy, can remotely provide electric and magnetic stimulation to cells and biomaterials, thus applying EMFs to assist BTE would be a promising strategy for bone regeneration. When combined with BTE, EMFs improve cell adhesion to the material surface by promoting protein adsorption. Additionally, EMFs have positive effects on mesenchymal stem cells and show capabilities of pro-angiogenesis and macrophage polarization manipulation. These advantages of EMFs indicate that it is perfectly suitable for representing the adjuvant treatment of BTE. We also summarize studies concerning combinations of EMFs and diverse biomaterial types. The strategy of combining EMFs and BTE receives encouraging outcomes and holds a promising future for effectively treating bone defects.