bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of TraDIS to define the core essential genome of Campylobacter jejuni and Campylobacter coli
Authors: Stoakes Emily , Turner Keith , Baker Dave J. , Suau Sans Maria , Yasir Muhammad , Kalmar Lajos , Costigan Ruby , Lott Martin , Grant Andrew J. 
Published: April 2023

AbstractCampylobacter species are the major cause of bacterial gastroenteritis. As there is no effective vaccine, combined with the rapid increase in antimicrobial resistant strains, there is a need to identify new targets for intervention. Essential genes are those that are necessary for growth and/or survival, making these attractive targets. In this study, comprehensive transposon mutant libraries were created in six C. jejuni strains, four C. coli strains and one C. lari and C. hyointestinalis strain, allowing for those genes that cannot tolerate a transposon insertion being called as essential. Comparison of essential gene lists using core genome analysis can highlight those genes which are common across multiple strains and/or species. Comparison of C. jejuni and C. coli, the two species that cause the most disease, identified 316 essential genes. Genes of interest highlighted members of the purine pathway being essential for C. jejuni whilst also finding that a functional potassium uptake system is essential. Protein–protein interaction networks using these essential gene lists also highlighted proteins in the purine pathway being major ‘hub’ proteins which have a large number of interactors across the network. When adding in two more species (C. lari and C. hyointestinalis) the essential gene list reduces to 261. Within these 261 essential genes, there are many genes that have been found to be essential in other bacteria. These include htrB and PEB4, which have previously been found as core virulence genes across Campylobacter species in other studies. There were 21 genes which have no known function with eight of these being associated with the membrane. These surface-associated essential genes may provide attractive targets. The essential gene lists presented will help to prioritise targets for the development of novel therapeutic and preventative interventions.
Association between intraoperative pulmonary artery pressure and cardiovascular complications after off-pump coronary artery bypass surgery: a single-center observational study
Authors: Matsuo Mitsuhiro , Doi Toshio , Katsuki Masahito , Yoshimura Yuichiro , Ito Hisakatsu , Fukahara Kazuaki , Yoshimura Naoki , Yamazaki Mitsuaki 
Published: April 2023

Abstract

Background
The impact of intraoperative pulmonary hemodynamics on prognosis after off-pump coronary artery bypass (OPCAB) surgery remains unknown. In this study, we examined the association between intraoperative vital signs and the development of major adverse cardiovascular events (MACE) during hospitalization or within 30 days postoperatively.

Methods
This retrospective study analyzed data from a university hospital. The study cohort comprised consecutive patients who underwent isolated OPCAB surgery between November 2013 and July 2021. We calculated the mean and coefficient of variation of vital signs obtained from the intra-arterial catheter, pulmonary artery catheter, and pulse oximeter. The optimal cut-off was defined as the receiver operating characteristic curve (ROC) with the largest Youden index (Youden index = sensitivity + specificity – 1). Multivariate logistic regression analysis ROC curves were used to adjust all baseline characteristics that yielded P values of < 0.05.

Results
In total, 508 patients who underwent OPCAB surgery were analyzed. The mean patient age was 70.0 ± 9.7 years, and 399 (79%) were male. There were no patients with confirmed or suspected preoperative pulmonary hypertension. Postoperative MACE occurred in 32 patients (heart failure in 16, ischemic stroke in 16). The mean pulmonary artery pressure (PAP) was significantly higher in patients with than without MACE (19.3 ± 3.0 vs. 16.7 ± 3.4 mmHg, respectively; absolute difference, 2.6 mmHg; 95% confidence interval, 1.5 to 3.8). The area under the ROC curve of PAP for the prediction of MACE was 0.726 (95% confidence interval, 0.645 to 0.808). The optimal mean PAP cut-off was 18.8 mmHg, with a specificity of 75.8% and sensitivity of 62.5% for predicting MACE. After multivariate adjustments, high PAP remained an independent risk factor for MACE.

Conclusions
Our findings provide the first evidence that intraoperative borderline pulmonary hypertension may affect the prognosis of patients undergoing OPCAB surgery. Future large-scale prospective studies are needed to verify the present findings.
Impact of vitamin D receptor gene polymorphisms (TaqI and BsmI) on the incidence and severity of coronary artery disease: a report from southern Iran
Authors: Akhlaghi Boshra , Firouzabadi Negar , Foroughinia Farzaneh , Nikparvar Marzieh , Dehghani Pouyan 
Published: April 2023

Abstract
Background
The association of vitamin D level and vitamin D receptor (VDR) gene polymorphisms with the prevalence of coronary artery disease (CAD) has been evaluated in various studies; however, the reported results were inconsistent. Hence, we aimed to investigate the impact of two VDR gene polymorphisms, TaqI (rs731236) and BsmI (rs1544410), on the incidence and severity of CAD in Iranian population.

Methods
Blood samples were collected from 118 CAD patients underwent elective percutaneous coronary intervention (PCI) and 52 control subjects. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed for genotyping. SYTNAX score (SS) was calculated as a grading tool for complexity of CAD by an interventional cardiologist.

Results
TaqI polymorphism of VDR was not associated with the incidence of CAD. A significant difference was observed between CAD patients and controls regarding BsmI polymorphism of VDR (p < 0.001). GA and AA genotypes was significantly associated with a decreased risk of CAD (p = 0.01, p-adjusted = 0.01 and p < 0.001, p-adjusted = 0.001 respectively). A allele of BsmI polymorphism was shown to have a protective effect against CAD (p < 0.001, p-adjusted = 0.002). No association was found between TaqI and BsmI polymorphisms of VDR and SS as a measure of CAD severity.

Conclusion
Association of BsmI genotypes with the incidence of CAD revealed that the genetic variation of VDR might play a role in the pathogenesis of CAD.
Accounting for expected attrition in the planning of cluster randomized trials for assessing treatment effect heterogeneity
Authors: Tong Jiaqi , Li Fan , Harhay Michael O. , Tong Guangyu 
Published: April 2023

Abstract
Background
Detecting treatment effect heterogeneity is an important objective in cluster randomized trials and implementation research. While sample size procedures for testing the average treatment effect accounting for participant attrition assuming missing completely at random or missing at random have been previously developed, the impact of attrition on the power for detecting heterogeneous treatment effects in cluster randomized trials remains unknown.

Methods
We provide a sample size formula for testing for a heterogeneous treatment effect assuming the outcome is missing completely at random. We also propose an efficient Monte Carlo sample size procedure for assessing heterogeneous treatment effect assuming covariate-dependent outcome missingness (missing at random). We compare our sample size methods with the direct inflation method that divides the estimated sample size by the mean follow-up rate. We also evaluate our methods through simulation studies and illustrate them with a real-world example.

Results
Simulation results show that our proposed sample size methods under both missing completely at random and missing at random provide sufficient power for assessing heterogeneous treatment effect. The proposed sample size methods lead to more accurate sample size estimates than the direct inflation method when the missingness rate is high (e.g., ≥ 30%). Moreover, sample size estimation under both missing completely at random and missing at random is sensitive to the missingness rate, but not sensitive to the intracluster correlation coefficient among the missingness indicators.

Conclusion
Our new sample size methods can assist in planning cluster randomized trials that plan to assess a heterogeneous treatment effect and participant attrition is expected to occur.
A novel immune checkpoint score system for prognostic evaluation in pancreatic adenocarcinoma
Authors: Chen Yusheng , Lin Xuan , Zou Xuan , Qian Yunzhen , Liu Yu , Wang Ruijie , Wang Xu , Yu Xianjun , Liu Chen , Cheng He 
Published: April 2023

Abstract
Background
Pancreatic adenocarcinoma (PAAD) remains a lethal malignancy making the detection of novel prognostic biomarkers urgent. Limited studies have investigated the predictive capability of immune checkpoints in PAAD.

Method
Gene expression data and correlative clinical information of PAAD cohort were obtained from public databases, including TCGA, ICGC, GTEX and GEO databases. Risk factors were screened and used to establish a risk score model through LASSO and Cox regression analyses. The prognostic ability of the risk score model was demonstrated. The association between risk score with immune cells infiltration, immune checkpoint genes expression, immunogenic cell death, somatic mutations and signaling pathways enrichment were analysed. scRNA-seq data were collected to confirmed the immune checkpoints expression in PAAD samples. The prognosis prediction ability of OX40/TNFRSF4 was identified. The mRNA and protein expression of OX40 in our clinical specimens were examined by RT-PCR and IHC method and its prognosis ability was verified.

Results
First of all, the difference of immune microenvironment between pancreatic cancer and adjacent tissues was shown. A risk score system based on three immune checkpoints (OX40, TNFSF14 and KIR3DL1) was established. The risk score model was an independent prognostic factor and performed well regarding overall survival (OS) predictions among PAAD patients. A nomogram was established to facilitate the risk model application in clinical prognosis. Immune cells including naive B cells, CD8+ T cells and Tregs were negatively correlated with the risk score. The risk score was associated with expression of immune checkpoint genes, immunogenic cell death related genes and somatic mutations. Glycolysis processes, IL-2-STAT5, IL-6-STAT3, and mTORC1 signaling pathways were enriched in the high-risk score group. Furthermore, scRNA-seq data confirmed that TNFRSF4, TNFSF14 and KIR3DL1 were expressed on immune cells in PAAD samples. We then identified OX40 as an independent prognosis-related gene, and a higher OX40 expression was associated with increased survival rate and immune environment change. In 84 PAAD clinical specimens collected from our center, we confirmed that higher OX40 mRNA expression levels were related to a good prognosis. The protein expression of OX40 on tumor-infiltrating immune cells (TIICs), endothelial cells and tumor cells was verified in PAAD tissues by immunohistochemistry (IHC) method.

Conclusions
Overall, our findings strongly suggested that the three-immune checkpoints score system might be useful in the prognosis and design of personalized treatments for PAAD patients. Finally, we identified OX40 as an independent potential biomarker for PAAD prognosis prediction.
Diagnostic performance of the IMMY cryptococcal antigen lateral flow assay on serum and cerebrospinal fluid for diagnosis of cryptococcosis in HIV-negative patients: a systematic review
Authors: Macrae Catriona , Ellis Jayne , Keddie Suzanne H. , Falconer Jane , Bradley John , Keogh Ruth , Baerenbold Oliver , Hopkins Heidi , Jarvis Joseph N. 
Published: April 2023

Abstract
Background
The incidence of cryptococcosis amongst HIV-negative persons is increasing. Whilst the excellent performance of the CrAg testing in people living with HIV is well described, the diagnostic performance of the CrAg LFA has not been systematically evaluated in HIV-negative cohorts on serum or cerebrospinal fluid.

Methods
We performed a systematic review to characterise the diagnostic performance of IMMY CrAg® LFA in HIV-negative populations on serum and cerebrospinal fluid. A systematic electronic search was performed using Medline, Embase, Global Health, CENTRAL, WoS Science Citation Index, SCOPUS, Africa-Wide Information, LILACS and WHO Global Health Library. Studies were screened and data extracted from eligible studies by two independent reviewers. A fixed effect meta-analysis was used to estimate the diagnostic sensitivity and specificity.

Results
Of 447 records assessed for eligibility, nine studies met our inclusion criteria, including 528 participants overall. Amongst eight studies that evaluated the diagnostic performance of the IMMY CrAg® LFA on serum, the pooled median sensitivity was 96% (95% Credible Interval (CrI) 68–100%) with a pooled specificity estimate of 96% (95%CrI 84–100%). Amongst six studies which evaluated the diagnostic performance of IMMY CrAg® LFA on CSF, the pooled median sensitivity was 99% (95%CrI 95–100%) with a pooled specificity median of 99% (95%CrI 95–100%).

Conclusions
This review demonstrates a high pooled sensitivity and specificity for the IMMY CrAg® LFA in HIV-negative populations, in keeping with findings in HIV-positive individuals. The review was limited by the small number of studies. Further studies using IMMY CrAg® LFA in HIV-negative populations would help to better determine the diagnostic value of this test.
Multiple rib and vertebral fractures associated with Bordetella pertussis infection: a case report
Authors: Wang Jingqiao , Gao Junxiang , Fan Hongwei , Guo Haonan , Yin Zundong , Dong Mei , Huang Xiaoming 
Published: April 2023

Abstract
Background
Pertussis is a highly contagious respiratory disease caused by the bacterium Bordetella pertussis, characterized by paroxysms of severe coughing, and predominantly affects children. We report the first case of multiple fractures in the ribs, lumbar spine, and sacrum associated with severe coughing caused by Bordetella pertussis infection in an adult.

Case presentation
A 49-year-old female presented with acute-onset chest wall pain for 3 weeks. Imaging results revealed multiple fractures in the ribs and vertebrae, as well as bilateral pleural effusion, pericardial effusion, right pneumothorax, and enlargement of the left parapharyngeal and subclavian lymph nodes. The patient’s bone density scan, autoimmune antibodies, bone marrow biopsy, and sacral bone biopsy all came back normal. Imaging test results found no evidence of solid tumors or active TB infection. The patient later recalled having violent coughing prior to the onset of chest pain and several family members having similar symptoms. Her blood sample was sent to the CDC, revealing Bordetella pertussis toxin (PT) IgG titer of 110.68 IU/mL. The patient was diagnosed with pertussis and multiple stress fractures from violent coughing. Symptomatic treatments were administered, and the patient’s symptoms improved. The patient was followed up 8 weeks later, she reported no more coughing or chest pain.

Conclusions
Pertussis is not just a pediatric disease, but diagnosis in adults is challenging as patients may present with a myriad of confusing symptoms, such as multiple stress fractures due to violent coughing. Medical and epidemiological histories are key to reaching the correct diagnosis, which is essential for appropriate treatments to avoid further complications. Adult immunization should be suggested both for the protection of the adult population and to prevent transmission to children.
Does design change in total knee arthroplasty implants affect patient-reported outcomes?
Authors: Toossi Nader , Bucklen Brandon , Meding Lindsey K. , Meding John B. 
Published: April 2023

Abstract
Purpose
The purpose of this study is to compare the early results of patient-reported outcomes between two generations of a total knee system.

Methods
Between June 2018 and April 2020, 121 first-generation, cemented TKAs (89 patients) and 123 s-generation, cemented TKAs (98 patients) were performed by a single surgeon. Demographic and surgical data were collected from all patients. Starting at the 6-month follow-up, patient-reported outcome measures Knee Injury and Osteoarthritis Outcome Score, Joint Reconstruction (KOOS-JR) and Knee Society (KS) clinical and radiographic scores were prospectively recorded. This study represents a retrospective review of these prospectively collected data.

Results
There were no statistically significant differences between the two groups in terms of demographic variables such as age, body mass index, gender and race. KOOS-JR and Knee Society (KS) scores improved significantly (p < 0.001) from their preoperative values in both device generations. There were no differences, pre-operatively, between the two groups in terms of KOOS-JR, KS functional, KS objective, patient satisfaction, and expectation scores; however, there were statistically significant (p < 0.001) lower values of KOOS-JR and KS functional scores for first versus second generation at 6 months (81 vs. 89 and 69 vs. 74, respectively).

Conclusion
While significant improvement in KS objective, subjective, and patient satisfaction scores were noted with both knee systems, KOOS-JR and KS function scores were significantly higher at the early (6-month) follow-up in the second-generation group. Patients responded acutely to the design change as evidenced by significantly improved patient-reported outcome scores for the second generation.
Exploring the microbiome of oral epithelial dysplasia as a predictor of malignant progression
Authors: Wright Robyn J. , Pewarchuk Michelle E. , Marshall Erin A. , Murrary Benjamin , Rosin Miriam P. , Laronde Denise M. , Zhang Lewei , Lam Wan L. , Langille Morgan G. I. , Rock Leigha D. 
Published: April 2023

AbstractA growing body of research associates the oral microbiome and oral cancer. Well-characterized clinical samples with outcome data are required to establish relevant associations between the microbiota and disease. The objective of this study was to characterize the community variations and the functional implications of the microbiome in low-grade oral epithelial dysplasia (OED) using 16S rRNA gene sequencing from annotated archival swabs in progressing (P) and non-progressing (NP) OED. We characterised the microbial community in 90 OED samples — 30 swabs from low-grade OED that progressed to cancer (cases) and 60 swabs from low-grade OED that did not progress after a minimum of 5 years of follow up (matched control subjects). There were small but significant differences between P and NP samples in terms of alpha diversity as well as beta diversity in conjunction with other clinical factors such as age and smoking status for both taxa and functional predictions. Across all samples, the most abundant genus was Streptococcus, followed by Haemophilus, Rothia, and Neisseria. Taxa and predicted functions were identified that were significantly differentially abundant with progression status (all Ps and NPs), when samples were grouped broadly by the number of years between sampling and progression or in specific time to progression for Ps only. However, these differentially abundant features were typically present only at low abundances. For example, Campylobacter was present in slightly higher abundance in Ps (1.72%) than NPs (1.41%) and this difference was significant when Ps were grouped by time to progression. Furthermore, several of the significantly differentially abundant functions were linked to the Campylobacteraceae family in Ps and may justify further investigation. Larger cohort studies to further explore the microbiome as a potential biomarker of risk in OED are warranted.
Women in a safe and healthy urban environment: environmental top priorities for the women’s presence in urban public spaces
Authors: Sadeghi Ali Reza , Baghi Elahe Sadat Mousavi Sarvine , Shams Fatemeh , Jangjoo Sina 
Published: April 2023

AbstractToday, in developing countries, women's need to be present in urban public spaces and the establishment of everyday social interactions seem to be ignored more than other groups. Therefore, the present study aims to achieve the environmental components related to women’s presence in urban spaces and prioritize them. In this study, by scrutinizing the criteria obtained from the interviews, a questionnaire was prepared and randomly distributed among 256 women in the population. IBM SPSS has been used to analyze the data and explain the priorities. The results of the T-test show that security (T-value = 6.508 in T1 test), compatibility with behavioral patterns (T-value = 4.975 in T2 test), eventuality (T-value = 11.064 in T3 test), permeability (T-value = 10.220 in T4 test), attention to climate (T-value = 5.692 in T5 test), liberty (T-value = 11.184 in T6 test), collective memory (T-value = 7.367 in T7 test), variety (T-value = 1.816 in T8 test), complexity (T-value = 13.228 in T9 test), and identity (T-value of 18.905 in T10 test) are the most important criteria in motivating presence in urban public spaces, respectively. According to the results, among the individual characteristics of the respondents, the components of collective memory (r = 0.805), identity (r = 0.784), liberty (r = 0.703), and safety and security (r = 0.644) have had a positive correlation with the age of the respondents. The results of this study indicated that improving security (individual, social, and psychological) is the main environmental priority for women over 18 to be present in urban public spaces.
Gender-based violence and its associated factors among internally displaced women in Northwest Ethiopia: a cross-sectional study
Authors: Workie Keralem , Tinsae Techilo , Salelew Endalamaw , Asrat Biksegn 
Published: April 2023

AbstractBackgroundGender-based violence (GBV) is a common human right violence in conflict-affected communities. Women with GBV are prone to experience mental health problems such as post-traumatic stress disorder, depression, and anxiety. However, there is a paucity of evidence as to what extent the problem is affecting internally displaced women (IDW) in Ethiopia. This study aimed to assess the prevalence of GBV and its associated factors among IDW in Northwest Ethiopia.MethodsA cross-sectional study was conducted among IDW residing at three humanitarian sites from May to June 2022 in Northwest Ethiopia. Study participants were selected using a stratified simple random sampling technique from the three sites. GBV was assessed using a 6-item Assessment Screen to Identify Survivors Toolkit questionnaire for Gender-based violence (ASIST-GBV). Data were analyzed using binary logistic regression. All variables with ap-value of ≤ 0.05 in the multivariable analysis were defined to have a statistically significant association with GBV at a 95% confidence interval (CI).ResultsOf 424 approached candidates, 412 (97.2%) of them participated in the study. A one-year prevalence of GBV was 37.9% (95%CI = 33.2–42.6) among IDW in Northwest Ethiopia. The mean age of the participants was 31.3 (± 7.6) years. Young women, 18–24 years old (AOR = 3.52, 95%CI = 2.15–5.34,p ≤ 0.001) and 25–29 years old (AOR = 2.41, 95%CI = 1.57–3.24,p ≤ 0.001) had a statistically significant association with GBV. Moreover, having no social protection (AOR = 3.18, 95%CI = 2.65–6.22,p ≤ 0.001), being current alcohol user (AOR = 2.54, 95%CI = 1.22–4.78,p ≤ 0.001) and being single in marital status (AOR = 1.69, 95%CI = 1.18–2.87,p < 0.01) showed a statistical association with GBV.ConclusionWe found a high prevalence of GBV among IDW in Northwest Ethiopia which indicates that IDW are prone to GBV. We call for immediate action and special attention to young women in conflict-affected parts of Ethiopia. It is crucial to establish a system that ensures the safety, security, and well-being of women in humanitarian settings.