bluuebunny/crossref_metadata_2025_split huggingface dataset:
H3AGWAS: a portable workflow for genome wide association studies
Authors: Brandenburg Jean-Tristan , Clark Lindsay , Botha Gerrit , Panji Sumir , Baichoo Shakuntala , Fields Christopher , Hazelhurst Scott 
Published: November 2022

Abstract
Background
Genome-wide association studies (GWAS) are a powerful method to detect associations between variants and phenotypes. A GWAS requires several complex computations with large data sets, and many steps may need to be repeated with varying parameters. Manual running of these analyses can be tedious, error-prone and hard to reproduce.

Results
The H3AGWAS workflow from the Pan-African Bioinformatics Network for H3Africa is a powerful, scalable and portable workflow implementing pre-association analysis, implementation of various association testing methods and post-association analysis of results.

Conclusions
The workflow is scalable—laptop to cluster to cloud (e.g., SLURM, AWS Batch, Azure). All required software is containerised and can run under Docker or Singularity.
Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing
Authors: Lin Shuting , Yi Soojin , Qiu Peng 
Published: November 2022

AbstractThe effect of DNA methylation on the regulation of gene expression has been extensively discussed in the literature. However, the potential association between DNA methylation and alternative splicing is not understood well. In this study, we integrated multiple omics data types from The Cancer Genome Atlas (TCGA) and systematically examined the relationship between DNA methylation and alternative splicing. Using the methylation data and exon expression data, we identified many CpG sites significantly associated with exon expression in various types of cancers. We further observed that the direction and strength of significant CpG-exon correlation tended to be consistent across different cancer contexts, indicating that some CpG-exon correlation patterns reflect fundamental biological mechanisms that transcend tissue- and cancer- types. We also discovered that CpG sites correlated with exon expressions were more likely to be associated with patient survival outcomes compared to CpG sites that did not correlate with exon expressions. Furthermore, we found that CpG sites were more strongly correlated with exon expression than expression of isoforms harboring the corresponding exons. This observation suggests that a major effect of CpG methylation on alternative splicing may be related to the inclusion or exclusion of exons, which subsequently impacts the relative usage of various isoforms. Overall, our study revealed correlation patterns between DNA methylation and alternative splicing, which provides new insights into the role of methylation in the transcriptional process.
Genome-wide association study and genetic mapping of BhWAX conferring mature fruit cuticular wax in wax gourd
Authors: Yan Jinqiang , Chen Feng , Sun Piaoyun , Liu Wenrui , Xie Dasen , Qian Yulei , Jiang Biao 
Published: November 2022

Abstract
Background
Wax gourd [Benincasa hispida (Thunb) Cogn. (2n = 2x = 24)] is an economically important vegetable crop of genus Benincasa in the Cucurbitaceae family. Fruit is the main consumption organ of wax gourd. The mature fruit cuticular wax (MFCW) is an important trait in breeding programs, which is also of evolutionary significance in wax gourd. However, the genetic architecture of this valuable trait remains unrevealed.

Results
In this study, genetic analysis revealed that the inheritance of MFCW was controlled by a single gene, with MFCW dominant over non-MFCW, and the gene was primarily named as BhWAX. Genome-wide association study (GWAS) highlighted a 1.1 Mb interval on chromosome 9 associated with MFCW in wax gourd germplasm resources. Traditional fine genetic mapping delimited BhWAX to a 0.5 Mb region containing 12 genes. Based on the gene annotation, expression analysis and co-segregation analysis, Bhi09G001428 that encodes a membrane bound O-acyltransferase (MBOAT) was proposed as the candidate gene for BhWAX. Moreover, it was demonstrated that the efficiency of a cleaved amplified polymorphic sequences (CAPS) marker in the determination of MFCW in wax gourd reached 80%.

Conclusions
In closing, the study identified the candidate gene controlling MFCW and provided an efficient molecular marker for the trait in wax gourd for the first time, which will not only be beneficial for functional validation of the gene and marker-assisted breeding of wax gourd, but also lay a foundation for analysis of its evolutionary meaning among cucurbits.
The association between dietary total antioxidant capacity and odds and severity of irritable bowel syndrome among Iranian adults: a cross-sectional study
Authors: Saneie Solaleh , Aminianfar Azadeh , Shidfar Farzad , Keshteli Ammar Hassanzadeh , Esmaillzadeh Ahmad , Adibi Peyman 
Published: November 2022

Abstract
Background
Little evidence is available in terms of the role of dietary antioxidants in the management of irritable bowel syndrome (IBS) disease. This study aimed to examine the association between dietary total antioxidant capacity (dTAC) and odds of IBS and its severity.

Methods
This cross-sectional study was conducted on 3,362 Iranian adults who were referred to health centers in Isfahan province, Iran. Participants' dietary intakes were collected using a semi-quantitative validated food frequency questionnaire (DS-FFQ). The dTAC was measured by the ferric-reducing antioxidant power (FRAP) method. Multivariable binary or ordinal logistic regression analyses were performed to estimate any associations between dTAC and odds of IBS, IBS severity, and IBS subtypes.

Results
The average age and BMI of the participants and dTAC score were 36.3 ± 7.87 year, 24.9 ± 3.82 kg/m2. The prevalence of IBS, IBS with constipation (IBS-C), IBS with diarrhoea (IBS-D), mixed IBS (IBS-M), and un-subtyped IBS (IBS-U) were 22.2, 7.5, 4.6, 3.8, and 6.2%, respectively. In crude and adjusted models, the results did not show any significant association between dTAC and odds of IBS among whole and gender-age stratified populations. Being in the third compared with the first tertile of dTAC was not also significantly associated with odds of IBS severity. Besides, there were no significant associations between dTAC and odds of IBS-C, IBS-D, IBS-M, and IBS-U.

Conclusion
This study indicates that dTAC may not be associated with the odds of IBS and its severity even after stratification for gender and body mass index.
Adverse outcomes after non-hepatic surgeries in patients with alcoholic liver diseases: a propensity-score matched study
Authors: Wu Hsin-Yun , Chang Chuen-Chau , Yeh Chun-Chieh , Chen Ming-Yao , Cherng Yih-Giun , Chen Ta-Liang , Liao Chien-Chang 
Published: November 2022

Abstract
Background
The influence of alcoholic liver disease (ALD) on the postoperative outcomes is not completely understood. Our purpose is to evaluate the complications and mortality after nonhepatic surgeries in patients with ALD.

Methods
We conducted a retrospective cohort study included adults aged 20 years and older who underwent nonhepatic elective surgeries using data of Taiwan’s National Health Insurance, 2008–2013. Using a propensity-score matching procedure, we selected surgical patients with ALD (n = 26,802); or surgical patients without ALD (n = 26,802) for comparison. Logistic regression was used to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) of postoperative complications and in-hospital mortality associated with ALD.

Results
Patients with ALD had higher risks of acute renal failure (OR 2.74, 95% CI 2.28–3.28), postoperative bleeding (OR 1.64, 95% CI 1.34–2.01), stroke (OR 1.51, 95% CI 1.34–1.70) septicemia (OR 1.47, 95% CI 1.36–1.58), pneumonia (OR 1.43, 95% CI 1.29–1.58), and in-hospital mortality (OR 2.64, 95% CI 2.24–3.11) than non-ALD patients. Patients with ALD also had longer hospital stays and higher medical expenditures after nonhepatic surgical procedures than the non-ALD patients. Compared with patients without ALD, patients with ALD who had jaundice (OR 4.82, 95% CI 3.68–6.32), ascites (OR 4.57, 95% CI 3.64–5.74), hepatic coma (OR 4.41, 95% CI 3.44–5.67), gastrointestinal hemorrhage (OR 3.84, 95% CI 3.09–4.79), and alcohol dependence syndrome (OR 3.07, 95% CI 2.39–3.94) were more likely to have increased postoperative mortality.

Conclusion
Surgical patients with ALD had more adverse events and a risk of in-hospital mortality after nonhepatic surgeries that was approximately 2.6-fold higher than that for non-ALD patients. These findings suggest the urgent need to revise the protocols for peri-operative care for this population.
Efficacy and safety of heparin plus dexamethasone after partial splenic embolization for liver cirrhosis with massive splenomegaly
Authors: Lu Haohao , Zheng Chuansheng , Xiong Bin , Xia Xiangwen 
Published: November 2022

Abstract
Purpose
The aim of this study was to investigate the efficacy and safety of the combination of low-molecular-weight heparin + dexamethasone after partial splenic embolization in cirrhotic patients with massive splenomegaly.

Methods
This study included 116 patients with liver cirrhosis complicated with massive splenomegaly who underwent PSE in Union Hospital from January 2016 to December 2019, and they met the criteria. They were divided into two groups: PSE + Hep + Dex group (N = 54) and PSE group (N = 62). We conducted a retrospective study to analyze the efficacy and safety of the two groups of patients.

Results
The volume of splenic embolization was 622.34 ± 157.06 cm3 in the PSE + Hep + DEX group and 587.62 ± 175.33 cm3 in the PSE group (P = 0.306). There was no statistically difference in the embolization rate of the spleen between the two groups (P = 0.573). WBC peaked 1 week after PSE and PLT peaked 1 month after PSE in both groups; it gradually decreased later, but was significantly higher than the preoperative level during the 12-month follow-up period. The incidences of abdominal pain (46.3% vs 66.1%, P = 0.039), fever (38.9% vs 75.8%, P < 0.001), PVT (1.9% vs 12.9%, P = 0.026), refractory ascites (5.6% vs 19.4%, P = 0.027) were lower in the PSE + Hep + DEX group than in the PSE group. The VAS score of abdominal pain in PSE group was higher than that in PSE + Hep + DEX group on postoperative days 2–8 (P < 0.05). Splenic abscess occurred in 1(1.6%) patient in the PSE group and none (0.0%) in the PSE + Hep + DEX group (P = 0.349).

Conclusions
The combined use of dexamethasone and low-molecular-weight heparin after PSE is a safe and effective treatment strategy that can significantly reduce the incidence of complications after PSE (such as post-embolization syndrome, PVT, refractory ascites).
Nurses’ competence in recognition and management of delirium in older patients: development and piloting of a self-assessment tool
Authors: Hoch Jonas , Bauer Jürgen M. , Bizer Martin , Arnold Christine , Benzinger Petra 
Published: November 2022

Abstract
Background
Delirium is a common condition in elderly inpatients. Health care professionals play a crucial role in recognizing delirium, initiating preventive measures and implementing a multicomponent treatment strategy. Yet, delirium often goes unrecognized in clinical routine. Nurses take an important role in preventing and managing delirium. This study assesses clinical reasoning of nurses using case vignettes to explore their competences in recognizing, preventing and managing delirium.

Methods
The study was conducted as an online survey. The questionnaire was based on five case vignettes presenting cases of acutely ill older patients with different subtypes of delirium or diseases with overlapping symptoms. In a first step, case vignettes were developed and validated through a multidisciplinary expert panel. Scoring of response options were summed up to a Geriatric Delirium Competence Questionnaire (GDCQ) score including recognition and management tasks The questionnaire was made available online. Descriptive analyses and group comparisons explores differences between nurses from different settings. Factors explaining variance in participants’ score were evaluated using correlations and linear regression models.

Results
The questionnaire demonstrated good content validity and high reliability (kappa = 0.79). The final sample consisted of 115 nurses. Five hundred seventy-five case vignettes with an accuracy of 0.71 for the correct recognition of delirium presence or absence were solved. Nurses recognized delirium best in cases describing hyperactive delirium (79%) while hypoactive delirium was recognized least (44%). Nurses from geriatric and internal medicine departments had significantly higher GDCQ-score than the other subgroups. Management tasks were correctly identified by most participants.

Conclusions
Overall, nurses’ competence regarding hypoactive delirium should be strengthened. The online questionnaire might facilitate targeting training opportunities to nurses’ competence.
Cross-cultural adaptation of the Taiwan Chinese version of the Falls Efficacy Scale-International for community-dwelling elderly individuals
Authors: Chang Kai-Chieh , Chen Hsin-Shui , Horng Yi-Shiung , Liou Horng-Hui , Liang Huey-Wen 
Published: November 2022

Abstract
Background
The Falls Efficacy Scale-International (FES-I) is a commonly used questionnaire to evaluate concerns about falling. We adapted a Taiwan Chinese version (FES-ITC) and evaluated its reliability and validity in community-dwelling elderly individuals. The discriminative validity was tested in relation to several known risk factors for fear of falling (FOF).

Methods
The questionnaire was adapted through translation, back-translation, and expert review processes. A convenience sample of 135 community-dwelling elderly individuals (at least 60 years old) completed the adapted questionnaire, and 31 of them had a retest within 7–10 days. Cronbach’s α and an intraclass correlation coefficient (ICC) were used to evaluate the internal consistency and test–retest reliability. Principal component factor analysis was performed to assess the factor-construct validity. The discriminative validity was tested in relation to demographic features, fall-related history and performances on three functional tests: timed up and go, four-stage balance and 30-s chair stand tests. Effect sizes were computed. Correlation coefficients between physical functional performance and FES-ITC scores were computed. Receiver operating characteristic curves were used to determine the cutoff point for the score to differentiate high and low concern of falling.

Results
The FES-ITC questionnaire had high internal consistency (Cronbach’s α = 0.94) and excellent test–retest reliability (ICC = 0.94). Principal component factor analysis yielded a two-factor model, with several items requiring high demand on postural control loading on factor 2. FES-ITC scores discriminated individuals with different ages, reporting FOF, reporting falls in the past year and using walking aids. However, FES-ITC scores did not differ between the participants who were at risk of falling and those who were not at risk based on functional test performance and there was no correlation found between them.

Conclusion
The FES-ITC was highly reliable and had adequate construct and discriminative validity. The lack of correlation between FES-ITC scores and functional test performance implied the presence of FOF even in individuals with good functional performance. Further follow up studies are warranted to verify the predictive validity of the FES-ITC.
Carotid artery corrected flow time and respiratory variations of peak blood flow velocity for prediction of hypotension after induction of general anesthesia in elderly patients
Authors: Wang Ji , Li Yulan , Su Hang , Zhao Juan , Tu Faping 
Published: November 2022

AbstractBackgroundPostinduction hypotension is closely related to postoperative complications. Elderly patients with compromised cardiovascular compensatory reserve are more susceptible to hypotension after induction of general anesthesia. This study investigated whether the carotid artery corrected flow time (FTc) and respiratory variation of peak blood flow velocity in the common carotid artery (ΔVpeak) could predict postinduction hypotension in elderly patients.MethodsThis prospective observational study included elderly patients aged 65 to 75 who were scheduled for elective surgery under general anesthesia with ASA physical status class of I-II, without cardiovascular disease, hypertension, diabetes, or obesity. Anesthesia was induced by midazolam, sufentanil, and etomidate and was maintained by sevoflurane. The carotid artery FTc and ΔVpeak were measured by ultrasound before induction of anesthesia. Hemodynamic data were recorded before induction and then during the first 10 min after induction.ResultsNinety-nine patients were included in the final analysis, of whom 63 developed postinduction hypotension. The area under the receiver operating characteristic curves was 0.87 (0.78 to 0.93) for carotid artery FTc and 0.67 (0.56 to 0.76) for ΔVpeak, respectively. The optimal cutoff value for predicting postinduction hypotension was 379.1 ms for carotid artery FTc, with sensitivity and specificity of 72.2 and 93.7%, respectively. The best cutoff value was 7.5% for ΔVpeak, with sensitivity and specificity of 55.6 and 75.0%, respectively.ConclusionsThe carotid artery FTc is a reliable predictor of postinduction hypotension in elderly patients with ASA status of I or II, without cardiovascular disease, hypertension, diabetes, or obesity. Elderly patients with a carotid artery FTc less than 379.1 ms before anesthesia have a higher risk of postinduction hypotension.Trial registrationClinical Trial Registry on August 2nd, 2020 (www.chictr.org.cn; ChiCTR2000035190).
The effect of calcineurin inhibitors on anthropometric measurements in kidney transplant recipients
Authors: Sayilar Emel Isiktas , Ersoy Alparslan , Ersoy Canan , Oruc Aysegul , Ayar Yavuz , Sigirli Deniz 
Published: November 2022

Abstract
Background
This study was designed to investigate the effect of calcineurin inhibitors (CNIs), cyclosporine (CsA), and tacrolimus (Tac) on anthropometrics in kidney transplant recipients.

Methods
111 of 128 adult kidney transplant recipients who received post-transplant CNIs were included in this retrospective study. Anthropometrics were recorded in the pre-transplant and post-transplant 4-year follow-up periods (1st, 3rd, 6th, 12th, 24th, 36th and 48th months).

Results
Compared to pre-transplant values, significant increases in body weight and body mass index (between 3rd and 48th months), waist and hip circumferences (between 1st and 48th months), waist-to-hip ratio (between 1st and 3rd or 6th months) and neck circumference (between 1st and 12th or 24th months) were observed in both CsA and Tac groups. A significant increase was noted in post-transplant body fat percentage values for the 3rd to 24th months in the CsA group, whereas for the 24th to 48th months in both CsA and Tac groups. Hip circumferences percentage changes from the pre-transplant period to the 1st, 12th and 24th months were significantly higher in CsA than in the Tac group. At each time point, there was no significant difference in percentage changes for other anthropometric parameters between the CsA and Tac groups. De novo diabetes mellitus developed in 8.3% of the CsA group and 19.1% of the Tac group.

Conclusions
After a successful kidney transplant, anthropometric measurements increase in most recipients. Although the effect of calcineurin inhibitor type on weight gain is unclear, a regression analysis showed that CNI type was not a risk factor for the development of obesity in the 48th month. However, it is helpful to be cautious about its dyslipidemic effect in patients using CsA and the potential hazards of using Tac in patients with a diabetic predisposition.
The effectiveness of skilled breathing and relaxation techniques during antenatal education on maternal and neonatal outcomes: a systematic review
Authors: Leutenegger Vanessa , Grylka-Baeschlin Susanne , Wieber Frank , Daly Deirdre , Pehlke-Milde Jessica 
Published: November 2022

Abstract
Background
Several studies have investigated the relationship between antenatal education classes and pregnancy outcomes. These studies have shown positive effects on mothers, such as a lower epidural rate in the intervention groups. However, until now, the impact on outcomes for mothers and newborns of antenatal education classes that focus on breathing and relaxation techniques has not been examined.

Aim
Investigate the effects of skilled breathing and relaxation techniques provided in antenatal education classes on maternal and neonatal birth outcomes.

Methods
The protocol for this study was registered with PROSPERO (ID: CRD42020192289). A systematic literature search was undertaken and completed in January 2022, using the databases MEDLINE, CINAHL, clinicalTrials.gov, Cochrane Library, Embase and MIDIRS according to a priori formulated PICO criteria: population (pregnant women), intervention (antenatal education classes with integrated breathing and relaxation techniques), comparison (antenatal education classes that do not include skilled breathing and relaxation techniques), and outcome (maternal and neonatal outcomes). The quality of the studies was assessed by two reviewers using the standardised instruments RoB 2 and ROBINS-I.

Results
Ten studies were included in this review, nine randomised controlled trials and one quasi-experimental study. The results indicate that skilled breathing and relaxation techniques may positively influence self-efficacy, the need for pharmacological support, specifically the use of epidural anaesthesia, and the memory of labour pain. No effects were found in relation to predefined neonatal outcomes. The quality of evidence on maternal and neonatal outcomes is inconsistent across studies, as different antenatal education classes with varying interventions, including breathing and relaxation techniques, were offered in the studies.

Conclusions
Women who attended an antenatal education class with breathing and relaxation techniques appear to benefit from the intervention. This applies to the practical implementation and use of breathing and relaxation techniques during labour, increased self-confidence and self-efficacy, and a increased feeling of being in control during labour. This demonstrates the importance of information provision and a focus on breathing and relaxation techniques in antenatal education.