bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple genes deletion based on Cre-loxP marker-less gene deletion system for the strains from the genus of Pectobacterium
Authors: Che Shu , Zhuo Yuanxu , Yang Liping , Wang Huan , Cui Zhongli , Fan Jiaqin 
Published: April 2024

Abstract

Strains from the genus of Pectobacterium are significant bacterial phytopathogens causing substantial economic losses globally. To understanding molecular pathogenic mechanism of Pectobacterium, genetic manipulation is often the initial work as in many other pathogens. We previously obtained many single gene deletion mutants carrying some different special antibiotic markers using homologous recombination for Pectobacterium. However, many biological processes involve multiple functionally genes, so multiple-gene deletion mutants are needed, but the limitation in types of antibiotic markers have controlled us to do so, even though the antibiotic markers might result in some unexpected effects on our understanding about the pathogenicity. In this study, we firstly introduced Cre-loxP system to construct marker-less multiple-gene deletion mutants in Pectobacterium strains.
Single-nuclei transcriptome of brain-dead donor heart with long QT syndrome revealed neuronal modulation of cardiac immunity
Authors: Wen Zhi , Shuai Shao , Feng Yu , Wang Zheng , Wu Jianqiang , Wu Changxue , Tian Mingwu 
Published: April 2024

Abstract

Background: Brain dead (BD) donor hearts with long QT syndrome (LQTS) showed accelerated cardiac allograft vasculopathy (CAV). We determine the differences between non-arrhythmic and LQTS myocardium through single-nuclei RNA sequencing (snRNAseq) analysis.
Methods: 16 non-arrhythmic and 4 LQTS BD donors myocardial snRNAseq were retrieved. Propensity score matching of baseline characteristics were performed before downstream analyses. Multi-omics integration of differential plasma proteomes between BD and healthy individuals were performed. Myocardium of experimental traumatic brain injury (TBI) was analyzed using flow cytometry and western blot. Pathway enrichment score and immune cell compositions correlation analysis were performed on 166 BD myocardium gene expression microarrays.
Results: LQTS showed significant increased T and Mast cell while B lymphocytes had most differentially expression genes (DEG). Cellchat revealed increased neuronal signaling modulating immunity in LQTS. Integrated network of plasma differential proteome with neuronal DEG revealed activated integrin cell surface interaction. Following TBI, total immune cell counts increased at 6 and 24 hours compared with sham, but were not statistically significant. CD3+ T cells significantly increased at 6h and further infiltrated at 24h, B220+ B cells increased only at 24h. Western blot results showed expression of Itgb1 and CD44 significantly up-regulated 6h after TBI. Integrin pathway activation significantly correlates with CD4 T cell composition.
Conclusions: Increased CD3+ T lymphocyte infiltrates were implicated in LQTS heart through neuronal regulation of immunity and activated integrin cell surface interaction. This suggested host B cell priming through inverted recognition of donor T lymphocytes causing accelerated CAV through antibody-mediated rejection.
The association between peripheral sensitivity of thyroid hormones and contrast-induced acute kidney injury: a retrospective study on euthyroid patients underwent coronary angiography
Authors: Fang Yuan , Chen Hao , Wang Zijie , Lv Jingyi , Zhao Zhenni , Wang Danan , Li Duanbin , Fu Guosheng , Zhang Wenbin 
Published: April 2024

Abstract

Purpose: Peripheral sensitivity of thyroid hormones (PSTH) plays a vital role in many renal diseases, but the relationship between PSTH and contrast-induced acute kidney injury (CI-AKI) is still not clear. Our study aimed to identify the association between PSTH and CI-AKI in euthyroid patients with stable coronary heart disease (SCAD) underwent coronary angiography (CAG).
Methods: This is a retrospective cross-sectional study which enrolled 2482 euthyroid patients with SCAD underwent CAG. CI-AKI was defined by serum creatinine (Scr) elevation. The indicator of PSTH was serum free triiodothyronine / free thyroxine (FT3/FT4) ratio. Multivariable logistic regression analysis was performed with confounders being adjusted, while receiver operator characteristic (ROC) analysis was performed with area under ROC curve (AUC) being calculated. Besides, subgroup analysis was also conducted.
Results: Overall, 297 (12.0%) patients were diagnosed with CI-AKI. Patients with CI-AKI had lower FT3/FT4 (2.34±0.46 vs. 2.54±0.48, P<0.001). Higher FT3/FT4 was proven to be negatively associated with the incidence of CI-AKI (adjusted OR [95%CI] = 0.573 [0.421 to 0.779], P < 0.001). A similar negative association was also observed for FT3 (adjusted OR [95%CI] = 0.524 [0.367 to 0.748], P < 0.001), but not for FT4. Furthermore, we found FT3/FT4 performed well in predicting the incidence of CI-AKI (AUC: 0.613). These findings between FT3/FT4 and CI-AKI were consistent across subgroups.
Conclusion: PSTH was negatively associated with the incidence of CI-AKI in euthyroid patients with SCAD who underwent CAG.
Mesothelin- and nucleolin-specific T cells from combined short peptides effectively kill triple-negative breast cancer cells
Authors: Thongchot Suyanee , Aksonnam Krittaya , Prasopsiri Jaturawitt , Sa-nguanraksa Doonyapat , O-Charoenrat Pornchai , Thuwajit Peti , Yenchitsomanus Pa-thai , Thuwajit Chanitra 
Published: April 2024

Abstract

Background Triple-negative breast cancer (TNBC), known for its aggressiveness and limited treatment options, presents a significant challenge. Adoptive cell transfer, involving the ex vivo generation of antigen-specific T cells from peripheral blood mononuclear cells (PBMCs), emerges as a promising approach. The overexpression of mesothelin (MSLN) and nucleolin (NCL) in TNBC samples underscores their potential as targets for T-cell therapy. This study explored the efficacy of multi-peptide pulsing of PBMCs to generate MSLN/NCL-specific T cells targeting MSLN+/NCL+ TNBC cells.
Methods TNBC patient samples were confirmed for both MSLN and NCL expression via immunohistochemistry. Synthesized MSLN and NCL peptides were combined and administered to activate PBMCs from healthy donors. The cancer-killing ability of the resultant T cells was assessed using crystal violet staining, and their subtypes and cytotoxic cytokines were characterized through flow cytometry and cytokine bead array.
Results Findings showed that 85.3% (127/149) of TNBC cases were positive for either MSLN or NCL, or both; with single positivity rates for MSLN and NCL of 14.1% and 28.9%, respectively. MSLN and NCL peptides, with high binding affinity for HLA-A*02, were combined and introduced to activated PBMCs from healthy donors. The co-pulsed PBMCs significantly induced TEM and TEMRA CD3+/CD8+ T cells and IFN-γ production, compared to single-peptide pulsed or unpulsed conditions. Notably, MSLN/NCL-specific T cells successfully induced cell death in MSLN+/NCL+ MDA-MB-231 cells, releasing key cytotoxic factors such as perforin, granzymes A and B, Fas ligand, IFN-γ, and granulysin.
Conclusions These findings serve as a proof-of-concept for using multiple immunogenic peptides as a novel therapeutic approach in TNBC patients.
The Psychological Consequences of 6 February 2023 Kahramanmaraş Earthquakes
Authors: Kiymis Ibrahim , Fakioglu Merve 
Published: April 2024

Abstract

The Kahramanmaraş Earthquakes (2023) are the largest and most destructive earthquakes witnessed in the era of the Republic of Turkey. Earthquakes lead to serious mental health problems such as PTSD in individuals. Earthquakes that cause significant death and injury on a large scale, such as the Kahramanmaraş Earthquakes, can result in various mental health problems. Therefore, the aim of the study was to examine the effects of variables such as Post-Traumatic Stress Disorder (PTSD), event impact, psychological resilience, depression, and anxiety levels on adult earthquake survivors affected by the Kahramanmaraş Earthquakes, using a quantitative research approach with survey techniques. A total of 662 earthquake survivors were reached. The effect of variables on each other was analyzed using Structural Equation Modeling (SEM). According to the findings of the study, event impact had a significant and positive effect on PTSD (β = 0.780, p = 0.000). Unexpectedly, resilience did not have a significant effect on PTSD (β=-0.04, p > 0.05). PTSD had a significant and positive effect on anxiety (β = 0.936, p = 0.000) and depression (β = 0.643, p = 0.000). Consequently, event impact's severity increased PTSD, which in turn led to anxiety and depression. Surprisingly, psychological resilience did not serve as a protective factor against PTSD. For future research, it is recommended to examine psychological resilience with different event types, on different sample groups, and using more comprehensive and varied methods.
Genetic analysis of QTLs for lysine content in four maize DH populations
Authors: Zhang Xiaolei , Wen Hongtao , Wang Jing , Zhao Lin , Chen Lei , Li Jialei , Guan Haitao , Cui Zhenhai , Liu Baohai 
Published: April 2024

Abstract

Background
Low level of lysine in maize endosperm is considered to be a major problem for determining the nutritional quality of food and feed. Improving the lysine content is favorable to improve maize quality by optimizing feeding requirement. Understanding the genetic basis of lysine content benefits greatly improving maize yield and optimizing end-use quality.
Results
Four double haploid (DH) populations were generated and used to identify quantitative trait loci (QTL) associated with lysine content. The broad-sense heritability indicated the majority of lysine content variations were largely controlled by genetic factors. A total of 12 QTLs were identified in a range of 4.42–12.66% in term of phenotypic variation explained (PVE) which suggested that a large number of minor-effect QTLs mainly contributed to the genetic component of lysine content. Five well-known genes encoding key enzymes in maize lysine biosynthesis pathways locate within QTLs identified in this study.
Conclusions
The information presented will pave a path to explore candidate genes regulating lysine biosynthesis pathways and be useful for marker-assisted selection and gene pyramiding in high-lysine maize breeding programs.
Rifampin-resistant periprosthetic joint infections are associated with worse functional outcome in both acute and chronic infection types
Authors: Baumgärtner Tobias , Bdeir Mohamad , Dally Franz-Joseph , Gravius Sascha , Hai Asseel Abd El , Assaf Elio , Hetjens Svetlana , Miethke Thomas , Darwich Ali 
Published: April 2024

Abstract

Periprosthetic joint infections (PJI) pose a significant challenge in orthopaedic surgery, often requiring extensive surgical debridement and prolonged antibiotic treatment to eliminate the causative pathogens. Rifampin, known for its potent activity against biofilms, has been crucial in managing PJI by penetrating and disrupting these formations, thereby improving treatment efficacy. In this sense, antibiotic protocols lacking rifampin have shown increased failure rates. Consequently, the development of rifampin resistance could severely influence the prognosis of PJI. The aim of this clinical study was to assess how rifampin resistance affects the functional outcome in patients with PJI. In this single-centre comparative cohort study, we systematically documented all patients who presented with a PJI during the period spanning from 2018 to 2020. Two distinct groups were established for the study: Group 1 comprised 35 patients with a PJI caused by rifampin-susceptible pathogens and group 2 consisted of 28 patients with PJI caused by rifampin-resistant pathogens. A total of 63 patients (34 females) with a mean age of 68 years and a mean follow up of 37 months were included. The examination of patient-specific parameters did not reveal any identified risk factors as influential. Patients with a rifampin-resistant pathogen underwent a greater number of surgical revisions (6.9 ± 5.1 compared to 3.59 ± 3.39, p = 0.0011) and had extended durations of antibiotic treatment (p = 0.0052). The results of the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score revealed significant differences in clinical outcome between both groups in every domain, even when stratified by acute and chronic entities. In total the WOMAC increased significantly from 21.57 ± 14.9 points in group 1 to 71.47 ± 62.7 points in group 2 (p < 0.001). The higher failure rates observed in group 2 were not statistically significant (p = 0.44). The current study demonstrates that PJI caused by rifampin-resistant bacteria are associated with a significantly worse functional outcome in both acute and chronic infection types without significantly affecting total failure rates.
Evaluation of geographic variations in appendicectomy outcomes within Western Australia assessing the impact of surgical wait times and rate of negative appendicectomies in both urban and rural locations statewide
Authors: Scaddan Beau , Asedy Balsam Al , Lee Samantha , Lari Parsa Rastegar 
Published: April 2024

Abstract

Purpose: Surgery wait times after diagnosis of appendicitis are an important factor influencing the success of a patient’s treatment. The proposed study will be a quantitative multicentre retrospective cohort design with the primary aim of assessing the difference between appendicectomy wait times between rural and urban hospitals in Western Australia and the effect of this on operative outcomes. Selected outcome measures will be examined by time from initial presentation at an Emergency Department to the patient being diagnosed and then time of diagnosis to surgery being performed. The secondary aim is to compare rates of negative appendicectomies between hospitals.
Methods: Appendicectomy patients will be identified from Operating Room register by medical student data collectors, then each respective hospital’s Emergency Room data collection will subsequently be accessed to complete case report forms based on demographics and Clinical Findings, Pre-operative investigations and Management and follow up. Case report forms with >95% completeness will be accepted for pooled analysis. The expected duration of retrospective data collection will be 8 months. This includes the four two-week data collection periods and the subsequent one month follow up per collection period for possible postoperative complications. This study RGS6483 has received HREC approval by the Royal Perth Hospital HREC Ethics Committee, with a waiver of consent obtained.
Dissemination of results: Data will be collected and stored online through a secure server running the Research Electronic Data Capture (REDCap) web application. No patient-identifiable data will be entered into the system. Results will subsequently be shared via scientific journal publication and presentation at relevant meetings.
Isolated Congenital Tracheal Stenosis in a 2-Year-Old Female: A Case Report
Authors: Musabyemungu Jean Aime , Kebedi Jemima , Shah Mitali , Kirigha Edmond , Odoro Juma , Hussein Khalif , Hussein Fadhil , Kadernani Yakub , Mokaya Pravin , Ndiritu Simon , Oburu Gilbert , Omulo Tom 
Published: April 2024

Abstract

Background: Congenital tracheal stenosis (CTS) is a rare but potentially life-threatening pediatric condition characterized by narrowing of the trachea. This narrowing leads to significant breathing difficulties, often accompanied by recurrent respiratory infections. CTS frequently coexists with other congenital malformations, particularly those affecting the heart and pulmonary artery. However, isolated cases where CTS occurs without accompanying anomalies are exceptionally rare and pose unique diagnostic and treatment challenges. This report describes the case of a 2-year-old female who was initially misdiagnosed and treated for laryngomalacia and asthma. However, her symptoms were not alleviated due tounderlying, undiagnosed isolated CTS.
Case Presentation: This case involved a 2-year-old female with a history of breathing difficulties, productive cough, and recurrent pneumonia who was treated for laryngomalacia and asthma and who presented with persistent respiratory distress and dysmorphic features. Imaging, including laryngoscopy and chest CT scans, revealed distal tracheal narrowing. The diagnosis was tracheobronchitis secondary to distal congenital tracheal stenosis with no other associated cardiac or respiratory congenital malformations. Surgical intervention entailed resection of the stenotic segment and anastomosis, followed by intensive postoperative care in the ICU and a structured plan for bronchoscopy dilation procedures. Patient recovery requires successful surgical correction and emphasizes the critical role of multidisciplinary care.
Conclusion: This report underscores the crucial significance of promptly identifying and accurately managing isolated congenital stenosis in children. This highlights the risk of misdiagnosis due to nonspecific respiratory symptoms and showcases the effectiveness of a multidisciplinary treatment approach, resulting in a successful outcome.
Characterization of constant resistance large deformation cable forces in loess slopes
Authors: Yu Xin , Long Jian-hui , Tao Zhi-gang 
Published: April 2024

Abstract

The use of prestressing anchor cables is already mature in the monitoring and treatment of slopes, but constant resistance large deformation (NPR) cables’ theory and application technology for soil slope reinforcement is still under investigation. In order to explore the anchoring performance of NPR (Negative Poisson Ratio) cables in loess slope, the stress characteristics of NPR cables in loess medium were simulated and analysed by ABAQUS finite element software. First, STATIC and GENERAL quasi-static analysis methods are used to simulate the NPR cable under static tensile conditions. The consistency of its constant resistance deformation characteristics with experimental results found in the literature is verified. Second, the interaction model between the NPR cable coupled with the loess medium is established, and its constant resistance is calculated, about 24.08% larger than the original, while its plastic deformation is reduced by about 37.14%. The compressive stress on the contact surface between NPR cable and loess is concentrated near the free end of the sleeve, and the shear stress on the X-Y plane shows a conjugate symmetry trend. It is proven that the loess is prone to serious damage at the free end. The research results reveal the typical shear failure mechanism of NPR cable in loess medium, which provides an important theoretical basis for prevention of landslides and monitoring of loess slopes.
Deep multi-view graph clustering with incomplete views
Authors: Chang Kerou , Zhu Changming , Miao Duoqian 
Published: April 2024

Abstract

Deep multi-view graph clustering has made good progress in solving large-scale problems. However, existing deep multi-view graph clustering methods suffer from the following issues: (1) How to combine data processing with multi-view clustering in deep learning, (2) How to learn the local and global information of the graph in deep learning. To this end, a novel method, called deep multi-view graph clustering with the incomplete view (DMVGC-IV), is proposed in this paper, which successfully solves the above two difficulties. Specifically, deep metric learning networks are employed on multiple views to obtain the graph structure. It approximately maintains the semantic distance of data points in the subspace. Then, DMVGC-IV combines global and local structures with a graph-fusion layer. By integrating autoencoder’s reconstruction and multi-view graph learning into a unified framework, our model can jointly optimize the cluster label assignments and embeddings suitable for graph clustering. Experiments use five commonly used multi-view data sets and compare them with five advanced multi-view clustering methods to verify the effectiveness of the proposed method.
Using Mendelian randomization to unveil the truth: does COVID-19 impact QT interval prolongation?
Authors: Zheng Zequn , Song Yongfei , Tan Xuerui 
Published: April 2024

Abstract

Background
QT interval, a vital marker of ventricular electrical activity during depolarization and repolarization, garnered significant attention during the COVID-19 pandemic. However, it remains unclear whether COVID-19 directly affects QT interval prolongation. This study leverages Mendelian randomization (MR) to investigate the genetic causation between COVID-19 and QT interval alterations.
Methods
In over 1000,000 individuals of European ancestry, genetic proxies representing three COVID-19 phenotypes (COVID-19, hospitalized COVID-19, and severe COVID-19), were identified under the primary MR assumption, and serve as instrumental variables (IVs). Genetic causal effects of COVID-19 on QT intervals from 84,630 UK Biobank participants were inferred using univariate two-sample MR (TSMR) and multi-exposure-adjusted multivariate MR (MVMR). MR-RAPS method and radial MR frame were used to provide robustness and outlier variant detection for effect assessment, and sensitivity analysis was further applied to detect the presence of horizontal pleiotropy.
Results
Independent 15, 33, and 29 IVs were used in COVID-19, hospitalized COVID-19, and severe COVID-19, respectively. Univariate TSMR analyses showed non-significant causal effect estimates between COVID-19 and the QT interval across all COVID-19 phenotypes. MR-RAPS and outlier-corrected radial MR analyses further supported this null causal estimation. In confounder-adjusted MVMR analysis, this nonsignificant causality was independent of BMI, smoking, and alcohol consumption. Sensitivity analyses failed to reveal any evidence of bias arising from horizontal pleiotropy, abnormal data distribution, or weak instruments.
Conclusions
Genetically, COVID-19 is not causally associated with QT interval prolongation. Inconsistent findings in observational research may be attributed to residual confounding.