bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle
Authors: Ribeiro Gabriela , Baldi Fernando , Cesar Aline S. M. , Alexandre Pâmela A. , Peripolli Elisa , Ferraz José B. S. , Fukumasu Heidge 
Published: November 2022

AbstractBackgroundPotential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs.ResultsThe systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10).ConclusionHere we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.
Profiling the transcriptomic signatures and identifying the patterns of zygotic genome activation – a comparative analysis between early porcine embryos and their counterparts in other three mammalian species
Authors: Zhai Yanhui , Yu Hao , An Xinglan , Zhang Zhiren , Zhang Meng , Zhang Sheng , Li Qi , Li Ziyi 
Published: November 2022

Abstract
Background
The transcriptional changes around zygotic genome activation (ZGA) in preimplantation embryos are critical for studying mechanisms of embryonic developmental arrest and searching for key transcription factors. However, studies on the transcription profile of porcine ZGA are limited.

Results
In this study, we performed RNA sequencing in porcine in vivo developed (IVV) and somatic cell nuclear transfer (SCNT) embryo at different stages and compared the transcriptional activity of porcine embryos with mouse, bovine and human embryos. The results showed that the transcriptome map of the early porcine embryos was significantly changed at the 4-cell stage, and 5821 differentially expressed genes (DEGs) in SCNT embryos failed to be reprogrammed or activated during ZGA, which mainly enrichment to metabolic pathways. c-MYC was identified as the highest expressed transcription factor during ZGA. By treating with 10,058-F4, an inhibitor of c-MYC, the cleavage rate (38.33 ± 3.4%) and blastocyst rate (23.33 ± 4.3%) of porcine embryos were significantly lower than those of the control group (50.82 ± 2.7% and 34.43 ± 1.9%). Cross-species analysis of transcriptome during ZGA showed that pigs and bovines had the highest similarity coefficient in biological processes. KEGG pathway analysis indicated that there were 10 co-shared pathways in the four species.

Conclusions
Our results reveal that embryos with impaired developmental competence may be arrested at an early stage of development. c-MYC helps promote ZGA and preimplantation embryonic development in pigs. Pigs and bovines have the highest coefficient of similarity in biological processes during ZGA. This study provides an important reference for further studying the reprogramming regulatory mechanism of porcine embryos during ZGA.
Quality appraisal for systematic literature reviews of health state utility values: a descriptive analysis
Authors: Muchadeyi Muchandifunga Trust , Hernandez-Villafuerte Karla , Schlander Michael 
Published: November 2022

Abstract
Background
Health state utility values (HSUVs) are an essential input parameter to cost-utility analysis (CUA). Systematic literature reviews (SLRs) provide summarized information for selecting utility values from an increasing number of primary studies eliciting HSUVs. Quality appraisal (QA) of such SLRs is an important process towards the credibility of HSUVs estimates; yet, authors often overlook this crucial process. A scientifically developed and widely accepted QA tool for this purpose is lacking and warranted.

Objectives
To comprehensively describe the nature of QA in published SRLs of studies eliciting HSUVs and generate a list of commonly used items.

Methods
A comprehensive literature search was conducted in PubMed and Embase from 01.01.2015 to 15.05.2021. SLRs of empirical studies eliciting HSUVs that were published in English were included. We extracted descriptive data, which included QA tools checklists or good practice recommendations used or cited, items used, and the methods of incorporating QA results into study findings. Descriptive statistics (frequencies of use and occurrences of items, acceptance and counterfactual acceptance rates) were computed and a comprehensive list of QA items was generated.

Results
A total of 73 SLRs were included, comprising 93 items and 35 QA tools and good recommendation practices. The prevalence of QA was 55% (40/73). Recommendations by NICE and ISPOR guidelines appeared in 42% (16/40) of the SLRs that appraised quality. The most commonly used QA items in SLRs were response rates (27/40), statistical analysis (22/40), sample size (21/40) and loss of follow up (21/40). Yet, the most commonly featured items in QA tools and GPRs were statistical analysis (23/35), confounding or baseline equivalency (20/35), and blinding (14/35). Only 5% of the SLRS used QA to inform the data analysis, with acceptance rates of 100% (in two studies) 67%, 53% and 33%. The mean counterfactual acceptance rate was 55% (median 53% and IQR 56%).

Conclusions
There is a considerably low prevalence of QA in the SLRs of HSUVs. Also, there is a wide variation in the QA dimensions and items included in both SLRs and extracted tools. This underscores the need for a scientifically developed QA tool for multi-variable primary studies of HSUVs.
Risk factors for refractory enterocutaneous fistula following button jejunostomy removal and its treatment using a novel extraperitoneal approach in patients with oesophageal cancer: a retrospective cohort study
Authors: Kamada Teppei , Ohdaira Hironori , Nakashima Keigo , Nishide Ryo , Takahashi Junji , Ito Eisaku , Nakaseko Yuichi , Suzuki Norihiko , Yoshida Masashi , Eto Ken , Suzuki Yutaka 
Published: November 2022

Abstract
Background
Enterocutaneous fistula after removal of the jejunostomy tube leads to multiple problems, such as cosmetic problems, decreased quality of life, electrolyte imbalances, infectious complications, and increased medical costs. However, the risk factors for refractory enterocutaneous fistula (REF) after button jejunostomy removal remain unclear. Therefore, in this study, we assessed the risk factors for REF after button jejunostomy removal in patients with oesophageal cancer and reported the surgical outcomes of the novel extraperitoneal approach (EPA) for REF closure.

Methods
This retrospective cohort study included 47 patients who underwent button jejunostomy removal after oesophagectomy for oesophageal cancer. We assessed the risk factors for REF in these patients and reported the surgical outcomes of the novel EPA for REF closure at the International University of Health and Welfare Hospital between March 2013 and October 2021. The primary endpoint was defined as the occurrence of REF after removal of the button jejunostomy, which was assessed using a maintained database. The risk factors and outcomes of the EPA for REF closure were retrospectively analysed.

Results
REFs occurred in 15 (31.9%) patients. In the univariate analysis, REF was significantly more common in patients with albumin level < 4.0 g/dL (p = 0.026), duration > 12 months for button jejunostomy removal (p = 0.003), and with a fistula < 15.0 mm (p = 0.002). The multivariate analysis revealed that a duration > 12 months for button jejunostomy removal (odds ratio [OR]: 7.15; 95% confidence interval [CI]: 1.38–36.8; p = 0.019) and fistula < 15.0 mm (OR: 8.08; 95% CI: 1.50–43.6; p = 0.002) were independent risk factors for REF. EPA for REF closure was performed in 15 patients. The technical success rate of EPA was 88.2%. Of the 15 EPA procedures, fistula closure was achieved in 12 (80.0%). The complications of EPA (11.7%) were major leakages (n = 3) and for two of them, EPA procedure was re-performed, and closure of the fistula was finally achieved.

Conclusion
This study suggested that duration > 12 months for button jejunostomy removal and fistula < 15.0 mm are the independent risk factors for REF after button jejunostomy removal. EPA for REF closure is a novel, simple, and useful surgical option for patients with REF after oesophagectomy.
Dementia is (not) a natural part of ageing: a cross-sectional study on dementia knowledge and misconceptions in Swiss and Italian young adults, adults, and older adults
Authors: Pacifico Deborah , Fiordelli Maddalena , Fadda Marta , Serena Sabatini , Piumatti Giovanni , Carlevaro Fabio , Magno Francesca , Franscella Giovanni , Albanese Emiliano 
Published: November 2022

AbstractBackgroundIncreasing public awareness and understanding of dementia is the second key action area of the 2017 WHO Global action plan on a public health response to dementia. To achieve this aim, the first indispensable step is to understand the average level of dementia knowledge and to identify areas of low dementia knowledge. We aimed to quantify dementia knowledge in the general population, and to explore the extent to which it differs by age, sex, education, and indirect experience with dementia.MethodsWe conducted an online cross-sectional survey in two Italian-speaking sites, south Switzerland (Ticino) and northern Italy (Piedmont). The survey was distributed between September and December 2019. We registered socio-demographic characteristics including whether the participant had contact with a person living with dementia, and measured dementia knowledge with the Dementia Knowledge Assessment Survey (DKAS).ResultsMisconceptions about dementia were common among respondents, and lack of knowledge has been identified in dementia causes, characteristics, risk factors, and health promotion. Our results point out the lack of knowledge about how to communicate and relate with, and take care of a person living with dementia. The overall DKAS score was significantly and positively associated with female sex (β = 0.21;p < 0.001), educational level (β = 0.15;p < 0.001) and contact with a person living with dementia (β = 0.17;p < 0.001), but not with age (β = -0.01;p = 0.57).ConclusionOur results confirmed that general population’s knowledge of dementia is thin. Interventional studies that rely on participatory action research methods are warranted to co-design interventions aimed at improving dementia knowledge and understanding in the public.
Investigating pathways for predisposing, enabling and need factors in predicting the use of STI/HIV-testing services among Syrian and Iraqi migrants in Scania, Sweden – a cross-sectional study with directed acyclic graphs for modelling pathways to testing
Authors: Svensson Pia , Agardh Anette , Zdravkovic Slobodan , Asamoah Benedict Oppong 
Published: November 2022

Abstract
Background
Some groups of migrants have increased vulnerability to Sexually Transmitted Infections (STI) and Human Immunodeficiency Virus (HIV) transmission partly due to a lower uptake of disease preventive activities targeting the general population in receiving country. Limited access to economic and social resources and poor language skills may exacerbate exposure to sexual risks and utilization of health services.

Aim
To explore general and migrant specific predictors for STI/HIV-testing among Syrian and Iraqi migrants in Sweden and to investigate potential pathways that link predisposing, enabling and need- factors to STI/HIV-testing.

Method
Cross-sectional study design based on a migration specific framework for health care utilization. Directed acyclic graphs (DAGs) were used to model assumptions about factors associated with the uptake of STI/HIV-testing services. Bi-variable and multivariable logistic regression analyses assessed individual predictors while adjusting for covariates. The magnitude of the indirect effect of mediating variables were estimated with bootstrap analyses and a method for decomposing the total effect.

Result
The pathways between younger age, unmarried, and self-identifying as bi- or homosexual and testing were mainly indirect, mediated by experiences of sexual coercion and other risk behaviours. One third of the indirect mediating effect of the pathway between higher education and testing could be attributed to Swedish language skills.

Conclusion
Utilization of STI/HIV-testing services among Syrian and Iraqi migrants seemed to be motivated by sexual risk exposure and risk awareness. Interventions should focus on language-adapted information about available screening services and where to go for advice on sexual wellbeing and sexual rights. Such activities should be implemented within an integration promoting framework, addressing structures that increase STI/HIV risk exposure, specifically targeting vulnerable subgroups of migrants.
Comparison of ARIMA model, DNN model and LSTM model in predicting disease burden of occupational pneumoconiosis in Tianjin, China
Authors: Lou He-Ren , Wang Xin , Gao Ya , Zeng Qiang 
Published: November 2022

Abstract
Background
This study aims to explore appropriate model for predicting the disease burden of pneumoconiosis in Tianjin by comparing the prediction effects of Autoregressive Integrated Moving Average (ARIMA) model, Deep Neural Networks (DNN) model and multivariate Long Short-Term Memory Neural Network (LSTM) models.

Methods
Disability adjusted life year (DALY) was used to evaluate the disease burden of occupational pneumoconiosis. ARIMA model, DNN model and multivariate LSTM model were used to establish prediction model. Three performance evaluation metrics including Root Mean Squared Error (RMSE), Mean Absolute Error (MAE) and Mean Absolute Percentage Error (MAPE) were used to compare the prediction effects of the three models.

Results
From 1990 to 2021, there were 10,694 cases of pneumoconiosis patients in Tianjin, resulting in a total of 112,725.52 person-years of DALY. During this period, the annual DALY showed a fluctuating trend, but it had a strong correlation with the number of pneumoconiosis patients, the average age of onset, the average age of receiving dust and the gross industrial product, and had a significant nonlinear relationship with them. The comparison of prediction results showed that the performance of multivariate LSTM model and DNN model is much better than that of traditional ARIMA model. Compared with the DNN model, the multivariate LSTM model performed better in the training set, showing lower RMES (42.30 vs. 380.96), MAE (29.53 vs. 231.20) and MAPE (1.63% vs. 2.93%), but performed less stable than the DNN on the test set, showing slightly higher RMSE (1309.14 vs. 656.44), MAE (886.98 vs. 594.47) and MAPE (36.86% vs. 22.43%).

Conclusion
The machine learning techniques of DNN and LSTM are an innovative method to accurately and efficiently predict the burden of pneumoconiosis with the simplest data. It has great application prospects in the monitoring and early warning system of occupational disease burden.
Promotion effect of apical tooth germ cell-conditioned medium on osteoblastic differentiation of periodontal ligament stem cells through regulating miR-146a-5p
Authors: Xie Yueqiang , Zheng Yaxin , Chen Liangjiao , Lan Zedong 
Published: November 2022

Abstract
Background
MicroRNAs (miRNAs) play an important role in gene regulation that controls stem cells differentiation.
Periodontal ligament stem cells (PDLSCs) could differentiate into osteo-/cementoblast-like cells that secretes cementum-like matrix both in vitro and in vivo. Whether miRNAs play key roles in osteoblastic differentiation of PDLSCs triggered by a special microenviroment remains elusive. In this study, we aimed to investigate potential miRNA expression changes in osteoblastic differentiation of PDLSCs by the induction of apical tooth germ cell-conditioned medium (APTG-CM).

Methods and results
First, we analyzed the ability of APTG-CM to osteogenically differentiate PDLSCs. The results exhibited an enhanced mineralization ability, higher ALP activity and increased expression of osteogenic genes in APTG-CM-induced PDLSCs. Second, we used miRNA sequencing to analyze the miRNA expression profile of PDLSCs derived from three donors under 21-day induction or non-induction of APTG-CM. MiR-146a-5p was found to be up-regulated miRNA in induced PDLSCs and validated by RT-qPCR. Third, we used lentivirus-up/down system to verify the role of miR-146a-5p in the regulation of osteoblastic differentiation of PDLSCs.

Conclusions
In conclusion, our results demonstrated that miR-146a-5p was involved in the promotion effect of APTG-CM on osteoblastic differentiation of PDLSCs, and suggested that miR-146a-5p might be a novel way in deciding the direction of PDLSCs differentiation.
Was EU’s COVID-19 vaccine procurement strategy irrational? A re-analysis based on cost-effectiveness considerations
Authors: Gandjour Afschin 
Published: November 2022

Abstract
Aim
The European Union (EU) has received criticism for being slow to secure coronavirus disease (COVID-19) vaccine contracts in 2020 before the approval of the first COVID-19 vaccine. This study aimed to retrospectively analyze the EU’s COVID-19 vaccine procurement strategy. To this end, the study retrospectively determined the minimum vaccine efficacy that made vaccination cost-effective from a societal perspective in Germany before clinical trial announcements in late 2020. The results were compared with the expected vaccine efficacy before the announcements.

Methods
Two strategies were analyzed: vaccination followed by the complete lifting of mitigation measures and a long-term mitigation strategy. A decision model was constructed using, for example, information on age-specific fatality rates, intensive care unit costs and outcomes, and herd protection thresholds. The base-case time horizon was 5 years. Cost-effectiveness of vaccination was determined in terms of the costs per life-year gained. The value of an additional life-year was borrowed from new, innovative oncological drugs, as cancer is a condition with a perceived threat similar to that of COVID-19.

Results
A vaccine with 50% efficacy against death due to COVID-19 was not clearly cost-effective compared with a long-term mitigation strategy if mitigation measures were planned to be lifted after vaccine rollout. The minimum vaccine efficacy required to achieve cost-effectiveness was 40% in the base case. The sensitivity analysis showed considerable variation around the minimum vaccine efficacy, extending above 50% for some of the input variables.

Conclusions
This study showed that vaccine efficacy levels expected before clinical trial announcements did not clearly justify lifting mitigation measures from a cost-effectiveness standpoint. Hence, the EU’s sluggish procurement strategy still appeared to be rational at the time of decision making.
Zero-profile implant versus conventional cage–plate construct in anterior cervical discectomy and fusion for the treatment of single-level degenerative cervical spondylosis: a systematic review and meta-analysis
Authors: Kahaer Alafate , Chen Ruilin , Maitusong Muzaipaer , Mijiti Peierdun , Rexiti Paerhati 
Published: November 2022

Abstract
Background
The clinical outcomes of single-level anterior cervical discectomy and fusion (ACDF) with the Zero-profile (Zero-p) were evaluated in comparison with the anterior cervical cage–plate construct (CPC).

Methods
We performed a systematic search covering PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science, Medline, China National Knowledge Infrastructure (NCKI), Wan Fang Database, and Wei Pu Database. Articles focused on single-level ACDF or data of the single - level that can be extracted were included, and articles that did not directly compare Zero-p and CPC were excluded. Twenty-seven studies were included with a total of 1866 patients, 931 in the Zero-p group and 935 in the CPC group. All outcomes were analyzed using Review Manager 5.4.

Results
The meta-analysis outcomes indicated that operative time (WMD = − 12.47, 95% CI (− 16.89, − 8.05), P < 0.00001), intraoperative blood loss (WMD = − 13.30, 95% CI (− 18.83, − 7.78), P < 0.00001), risk of adjacent segment degeneration (ASD) (OR 0.31, 95% CI (0.20, 0.48), P < 0.0001), risk of dysphagia of short-term (OR 0.40, 95% CI (0.30, 0.54), P < 0.0001), medium-term (OR 0.31, 95% CI (0.20, 0.49), P < 0.0001), and long-term (OR 0.29, 95% CI (0.17, 0.51), P < 0.0001) of Zero-p group were significantly lower. The JOA score of Zero-p group at the final follow-up was significantly higher (WMD = − 0.17, 95% CI (− 0.32, − 0.03), P = 0.02). There were no significant differences in length of stay (LOS), Neck Disability Index (NDI), Visual Analogue Score (VAS), fusion rate, segmental Cobb angle, cervical Cobb angle, prevertebral soft tissue thickness (PSTT), SF-36, subsidence, implant failure, and hoarseness between the two groups. This study was registered with PROSPERO, CRD42022347146.

Conclusion
Zero-p group reduced operative time, intraoperative blood loss, JOA score at follow-up and reduced the incidence of dysphagia and postoperative ASD, but the two devices had the same efficacy in restoring the cervical curvature, preventing the cage subsidence, and in postoperative VAS, NDI, LOS, PSTT, SF-36, fusion rate, implant failure, and hoarseness in single-level ACDF. The use of Zero-p in single-level ACDF was recommended.