bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Friction Resistance Between Different Bracket Systems: An In Vitro Study
Authors: Bhanderi Vrushika , Digumarthi Uday Kumar 
Published: October 2024

Introduction The efficiency of tooth movement associated with orthodontic sliding mechanics can be compromised by friction between archwire and tube or bracket slot. Orthodontic brackets and archwires are important constituents of an orthodontic appliance system. Friction is an uncontrolled variable of particular interest when continuous arch techniques are used to align and move teeth by way of sliding a tube or bracket along an arch. Aim and Objectives Comparison of frictional resistance between different bracket systems of 3M and MO brands in combination with different wires of 3M, MO, and G&H brands. Evaluation of frictional resistance between two different types of bracket systems and different types of wire combinations. Materials and Methods Two types of bracket systems were used: metal bracket system and ceramic bracket system (3M and MO brands). Four different orthodontic wire alloys were used: stainless steel (SS), TMA, NiTi, and CuNiTi (3M, MO, and G&H brands). A rectangular block made up of self-cure acrylic resin was designed to hold the bracket during the mechanical test. Each bracket base was glued to an acrylic block with cyanoacrylate glue. The wire segment was inserted into the bracket and was ligated passively with SS ligature wire. The bracket–wire combination was submitted to mechanical tests with a universal testing machine. One end of the acrylic block was mounted to the lower grip of the universal testing machine. The free end of the archwire was fixed to the upper grip of the universal testing machine. The friction which was generated between the wire and bracket was measured under dry conditions and at room temperature. The test wire was pulled through the bracket at a speed of 0.5 cm/min. The load cell registered a maximum force level. This data was stored in the computer and was submitted to statistical analysis, and parameter tests were applied. Results The highest mean friction resistance of 5.998 N was generated by group B2-E2 (ceramic bracket – MO + TMA archwire – MO). The lowest mean friction resistance of 2.552 N was generated by group A1-C1 (metal bracket – 3M + SS wire – 3M). There was a statistically significant difference between the friction generated by the metal bracket on SS archwire and the ceramic bracket on TMA archwire regardless of 3M or MO brand material ( p value < .0001) and metal bracket ( p = .0004).
Routine Use of Indwelling Urinary Catheters During Endovascular Abdominal Aortic Aneurysm Repair is Not Necessary
Authors: Simone Avital , Carmon Lauren , Rao Priya , Cichocki Meghan , Yuan Karen , Blecha Matthew , Bechara Carlos F. , Soult Michael C. 
Published: October 2024

Objective Endovascular infra-renal abdominal aortic aneurysm repair (EVAR) has proven to be an effective, less invasive alternative to open aortic aneurysm repair with decreased 30-day mortality. Historically, urinary drainage catheters were routinely placed preoperatively before EVAR in our institution. A shift to reduced catheter placement has occurred in conjunction with percutaneous EVARs becoming more routine. Urethral catheterization carries risk of infection (UTI), urinary retention and prostatic trauma inducing hematuria. The purpose of this study was to evaluate whether avoidance of urinary catheter placement during EVAR is an effective practice to reduce cost and morbidity. Methods This was a single-institution, retrospective review of 177 consecutive patients who underwent elective infrarenal EVAR. Ruptured aneurysms and emergent EVAR were excluded. The study end points were postoperative UTI, urinary retention, length of stay, and readmission within 30 days. Univariable analysis was performed for these four outcomes in patients with (N = 92 and without (N = 65) preoperative urinary catheter placement. A more expansive multivariable investigation for risk of urinary retention following EVAR was conducted with binary logistic regression with co-variates including age, sex, femoral cutdown, estimated blood loss (EBL), urinary catheter, congestive heart failure, diabetes, and postoperative urinary retention as co-variates. Results Patients who had a Urinary catheter placed had an over two fold higher event rate of urinary retention (10.9% vs 4.6%) This urinary retention trend lacked power to reach significance (OR 2.52 (.665-9.55). Placement of urinary catheter also had a strong trend towards increased rate of UTI but lacking power for significance (7.6% vs 3.10%, OR 1.96 (.556-6.57). There was no difference with or without urinary catheter placement regarding 30-day readmission (yes catheter 7.6% vs no catheter 6.2%, P = .725), or length of stay (yes catheter 2.13 days vs no catheter 1.74 days, P = .723). Urinary retention was significantly associated with the development of a UTI with 23% of patients who had retention developing UTI compared with 4.2% of patients without retention developing UTI (adjusted odds ratio = 17.98, P = .019). Increased blood loss ( P = .027) was also associated with increased rate of UTI on multivariable analysis. Conclusions Avoidance of preoperative urinary catheter placement displays a trend towards avoiding urinary retention and UTI. Patients who develop post EVAR urinary retention experience a significantly increased rate of UTI. Selective urinary catheter placement should be used to help reduce urinary-related complications following elective EVAR.
Factors affecting the outcomes of in vitro fertilization in women with endometriosis: Preliminary data from Vietnam
Authors: Le Minh Tam , Tran Giang Ngoc Ha , Nguyen Quoc Huy Vu 
Published: October 2024

Objectives: This study aimed to assess the efficacy of in vitro fertilization (IVF) in patients with endometriosis and identify related factors that may influence treatment outcomes. Methods: This retrospective descriptive study was conducted between November 2018 and November 2022. The study group comprised individuals who were diagnosed with endometriosis (endometrioma and/or adenomyosis) indicated for in vitro fertilization. The control group (129 patients with 249 cycles), which included patients without endometriosis and had an equivalent mean age as the study group patients. Results: In the endometriosis group, the quantities of retrieved oocytes and Anti-Müllerian Hormone (AMH) were reduced compared to the control group. The overall dose of gonadotropin and the duration of ovarian stimulation were significantly higher than the control group. The endometriosis group exhibited a Metaphase II (MII) oocyte rate of 82.3% and an oocyte fertilization rate of 82.2%. However, in patients with endometriosis, the rates of implantation, clinical pregnancy, and ongoing pregnancy were significantly lower than in patients without endometriosis. Besides, the clinical pregnancy rate of women with endometriosis was remarkably higher in the groups with maternal age ⩽35 years, a ratio of Follicle-stimulating Hormone to Luteinizing Hormone (FSH/LH) ⩽1.5, and over 10 retrieved oocytes. Conclusion: Endometriosis was associated with a decreased rate of implantation, clinical pregnancy, and ongoing pregnancy after in vitro fertilization treatment compared with patients without endometriosis. In vitro fertilization outcomes in patients with endometriosis were influenced by maternal age ⩽35 years, FSH/LH ratio ⩽1.5, and number of retrieved oocytes over 10.
Resolution of tuberculosis blood RNA signatures fails to discriminate persistent sputum culture positivity after 8 weeks of anti-tuberculous treatment
Authors: Calderwood Claire J. , Sanchez Martinez Alvaro , Greenan-Barrett James , Turner Carolin T. , Oguti Blanché , Roe Jennifer K. , Gupta Rishi , Martineau Adrian R. , Noursadeghi Mahdad 
Published: October 2024

BackgroundConcerted efforts aim to reduce the burden of 6 months of anti-tuberculous treatment for tuberculosis (TB). Treatment cessation at 8 weeks is effective for most but incurs increased risk of disease relapse. We tested the hypothesis that blood RNA signatures or C-reactive protein (CRP) measurements discriminate 8-week sputum culture status, as a prerequisite for a biomarker to stratify risk of relapse following treatment cessation at this time-point.MethodsWe identified blood RNA signatures of TB disease or cure by systematic review. We evaluated these signatures and CRP measurements in a pulmonary TB cohort, pre-treatment, at 2 and 8 weeks of treatment, and sustained cure after treatment completion. We tested biomarker discrimination of 8-week sputum culture status using area under the receiver operating characteristic curve (AUROC) analysis and, secondarily, assessed correlation of biomarker scores with time to culture positivity at 8 weeks of treatment.Results12 blood RNA signatures were reproduced in the dataset from 44 individuals with sputum culture-positive pulmonary TB. These normalised over time from TB treatment initiation. 11 out of 44 cases with blood RNA, CRP and sputum culture results were sputum culture-positive at 8 weeks of treatment. None of the contemporary blood RNA signatures discriminated sputum culture status at this time-point or correlated with bacterial load. CRP achieved modest discrimination with AUROC 0.69 (95% CI 0.52–0.87).ConclusionsSelected TB blood RNA signatures and CRP do not provide biomarkers of microbiological clearance to support TB treatment cessation at 8 weeks. Resolution of blood transcriptional host responses in sputum culture-positive individuals suggestsMycobacterium tuberculosismay colonise the respiratory tract without triggering a detectable immune response.
Predicting stroke occurrences: a stacked machine learning approach with feature selection and data preprocessing
Authors: Chakraborty Pritam , Bandyopadhyay Anjan , Sahu Preeti Padma , Burman Aniket , Mallik Saurav , Alsubaie Najah , Abbas Mohamed , Alqahtani Mohammed S. , Soufiene Ben Othman 
Published: October 2024

AbstractStroke prediction remains a critical area of research in healthcare, aiming to enhance early intervention and patient care strategies. This study investigates the efficacy of machine learning techniques, particularly principal component analysis (PCA) and a stacking ensemble method, for predicting stroke occurrences based on demographic, clinical, and lifestyle factors. We systematically varied PCA components and implemented a stacking model comprising random forest, decision tree, and K-nearest neighbors (KNN).Our findings demonstrate that setting PCA components to 16 optimally enhanced predictive accuracy, achieving a remarkable 98.6% accuracy in stroke prediction. Evaluation metrics underscored the robustness of our approach in handling class imbalance and improving model performance, also comparative analyses against traditional machine learning algorithms such as SVM, logistic regression, and Naive Bayes highlighted the superiority of our proposed method.
Be-dataHIVE: a base editing database
Authors: Schneider Lucas , Minary Peter 
Published: October 2024

AbstractBase editing is an enhanced gene editing approach that enables the precise transformation of single nucleotides and has the potential to cure rare diseases. The design process of base editors is labour-intensive and outcomes are not easily predictable. For any clinical use, base editing has to be accurate and efficient. Thus, any bystander mutations have to be minimized. In recent years, computational models to predict base editing outcomes have been developed. However, the overall robustness and performance of those models is limited. One way to improve the performance is to train models on a diverse, feature-rich, and large dataset, which does not exist for the base editing field. Hence, we develop BE-dataHIVE, a mySQL database that covers over 460,000 gRNA target combinations. The current version of BE-dataHIVE consists of data from five studies and is enriched with melting temperatures and energy terms. Furthermore, multiple different data structures for machine learning were computed and are directly available. The database can be accessed via our website https://be-datahive.com/ or API and is therefore suitable for practitioners and machine learning researchers.
repDilPCR: a tool for automated analysis of qPCR assays by the dilution-replicate method
Authors: Yosifov Deyan Yordanov , Reichenzeller Michaela , Stilgenbauer Stephan , Mertens Daniel 
Published: October 2024

Abstract
Background
The dilution-replicate experimental design for qPCR assays is especially efficient. It is based on multiple linear regression of multiple 3-point standard curves that are derived from the experimental samples themselves and thus obviates the need for a separate standard curve produced by serial dilution of a standard. The method minimizes the total number of reactions and guarantees that Cq values are within the linear dynamic range of the dilution-replicate standard curves. However, the lack of specialized software has so far precluded the widespread use of the dilution-replicate approach.

Results
Here we present repDilPCR, the first tool that utilizes the dilution-replicate method and extends it by adding the possibility to use multiple reference genes. repDilPCR offers extensive statistical and graphical functions that can also be used with preprocessed data (relative expression values) obtained by usual assay designs and evaluation methods. repDilPCR has been designed with the philosophy to automate and speed up data analysis (typically less than a minute from Cq values to publication-ready plots), and features automatic selection and performance of appropriate statistical tests, at least in the case of one-factor experimental designs. Nevertheless, the program also allows users to export intermediate data and perform more sophisticated analyses with external statistical software, e.g. if two-way ANOVA is necessary.

Conclusions
repDilPCR is a user-friendly tool that can contribute to more efficient planning of qPCR experiments and their robust analysis. A public web server is freely accessible at https://repdilpcr.eu without registration. The program can also be used as an R script or as a locally installed Shiny app, which can be downloaded from https://github.com/deyanyosifov/repDilPCR where also the source code is available.
Characterization and genomic analysis of the lytic bacteriophage vB_EclM_HK6 as a potential approach to biocontrol the spread of Enterobacter cloacae contaminating food
Authors: Temsaah Hasnaa R. , Azmy Ahmed F. , Ahmed Amr E. , Elshebrawy Hend Ali , Kasem Nahed Gomaa , El-Gohary Fatma A. , Lood Cédric , Lavigne Rob , Abdelkader Karim 
Published: October 2024

Abstract
Background
Increased prevalence of Enterobacter cloacae within food products underscores food as an underexplored reservoir for antibiotic resistance, thus requiring particular intervention. Bacteriophages have been explored as a promising approach for controlling bacterial growth in different matrices. Moreover, their specific interaction and self-replication, put them apart from traditional methods for controlling bacteria in different matrices.

Methods
Sixteen Enterobacter cloacae strains were recovered from raw chicken. These strains were used to isolate bacteriophages using enrichment protocol. The broad-spectrum bacteriophage was evaluated in terms of thermal, pH, shearing stress and storge. Moreover, its infection kinetics, in vitro antibacterial activity, cytotoxicity were also assessed. Genomic sequencing was performed to exclude any potential virulence or resistance genes. Finally, the capability of the isolated phages to control bacterial growth in different chicken samples was assessed alone and in combination with sodium nitrite.

Results
The lytic bacteriophage vB_EclM_HK6 was isolated and showed the broadest spectrum being able to infect 8/16 E. cloacae strains with a lytic activity against its host strain, E. cloacae EC21, as low as MOI of 10–6. The phage displays a latent period of 10 min and burst size of 115 ± 44 and resistance frequency of 5.7 × 10–4 ± 3.0 × 10–4. Stability assessment revealed a thermal tolerance up to 60 ˚C, wide range pH stability (3–10) and the ability to withstand shearing stress up to 250 rpm. HK6 shows no cytotoxicity against oral epithelial cells up to 1012 PFU/ml. Genomic analysis revealed a Strabovirus with total size of 177,845 bp that is free from known resistance and virulence genes. Finally, HK6 pretreatment of raw chicken, chicken nuggets and ready-made cheese salad shows a reduced bacterial count up to 4.6, 2.96 and 2.81 log-units, respectively. Moreover, combing HK6 with sodium nitrite further improved the antibacterial activity in both raw chicken and chicken nuggets without significant enhancement in case of cheese salad.

Conclusion
Enterobacter bacteriophage vB_EclM_HK6 presents a safe and effective approach for controlling E. cloacae contaminating stored chicken food samples. Moreover, they could be combined with a reduced concentrations of sodium nitrite to improve the killing capacity.
Potential protective association of the AA genotype and a allele of CXCR4 rs2228014 polymorphism with COVID-19 severity in adult egyptians
Authors: Korayem Osama H. , Ahmed Amr E. , Meabed Mohamed H. , Magdy Doaa M. , Abdelghany Wafaa M. 
Published: October 2024

Abstract
Background
By the end of December 2019, a new coronavirus, termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged, and the cause of the disease was named coronavirus disease 2019 (COVID-19). Several genetic factors have been implicated in diverse responses to SARS-CoV-2 infection, such as the C-X-C chemokine receptor 4 (CXCR4) rs2228014 polymorphism, which has been previously studied in various diseases but has not been explored in the context of COVID-19 severity. The current study aimed to assess the association between the rs2228014 polymorphism in the CXCR4 gene and the severity of COVID-19, which has not been previously reported.

Method
This cross-sectional study analyzed 300 adult Egyptian COVID-19 patients (156 with mild or moderate and 144 with severe or critical symptoms) admitted to Assiut University Quarantine Hospital from June to September 2022 during the omicron variant. The rs2228014 polymorphism in the CXCR4 gene was detected using real-time PCR with a TaqMan assay probe. Receiver operating characteristic (ROC) curve analysis was used to determine the best cutoff values for C-reactive protein (CRP) that can be used to estimate the severity of COVID-19. P values less than 0.05 were considered to indicate statistical significance.

Results
No significant differences in the allelic or genotypic frequencies of CXCR4 rs2228014 were detected between the severity groups. However, the exclusive presence of the AA genotype in mild or moderate cases suggests its potential protective role. Additionally, significant differences in myalgia presentation, leukocyte counts and antibiotic use, were observed among different genotypes. Statistical data showed that the severity of COVID-19 could be predicted at a cutoff value of CRP > 30 mg/L, with a sensitivity of 74.3% and a specificity of 42.9%.

Conclusion
The present findings suggest a potential protective role of the AA genotype and A allele of CXCR4 rs2228014 against severe COVID-19. Additionally, factors such as lack of vaccination and comorbidities such as hypertension, renal disease, and diabetes mellitus were associated with increased disease severity.
Comparison of proximal gastrectomy and total gastrectomy in proximal gastric cancer: a meta-analysis of postoperative health condition using the PGSAS-45
Authors: Yang Xiangyu , Zeng Zhili , Liao Ziyue , Zhu Caiyu , Wang Hongyang , Wu Haijuan , Cao Shu , Liang Weizheng , Li Xiushen 
Published: October 2024

Abstract
Purpose
Proximal gastrectomy (PG) offers advantages over total gastrectomy (TG) in enhancing the postoperative nutritional status of patients with proximal gastric cancer (PGC), yet its effect on long-term quality of life is still debated. This study aims to thoroughly compare postoperative health condition outcomes between PG and TG.

Methods
We conducted a systematic search of English-language articles from the PubMed, Web of Science, and Cochrane Library databases, covering studies published up to February 2023. Key evaluation endpoints included surgical outcomes and postoperative health condition, assessed using the Post-Gastrectomy Syndrome Assessment Scale-45 (PGSAS-45).

Results
Six retrospective cohort studies were included in the analysis. The PG group demonstrated no significant negative impact on surgical outcomes compared to the TG group. Notably, patients who underwent PG experienced a superior postoperative health condition, characterized by fewer gastroesophageal reflux symptoms (WMD = -0.106, 95% CI -0.183 to -0.029, P < 0.01), less weight loss (WMD = 4.440, 95% CI 3.900 to 4.979, P < 0.01), and reduced dietary dissatisfaction (WMD = -0.205, 95% CI -0.385 to -0.025, P = 0.03).

Conclusion
This study provides compelling evidence that PG is superior to TG in enhancing postoperative health condition for patients with proximal gastric cancer, without compromising surgical outcomes. However, further rigorous randomized controlled trials are necessary to inform surgical decision-making more effectively.
Successful corneal endothelium preservation in the management of epithelial downgrowth with 5-fluorouracil injections and membranectomy
Authors: Kam Ka Wai , Ma Andre , Ng Joanna , Choi Paul , Yip Wilson Wai Kuen , Young Alvin L. 
Published: October 2024

AbstractA 74-year-old Chinese man underwent extracapsular cataract extraction in his right eye and developed a translucent iris membrane 4 months later. He was treated with two intracameral 5-FU injections and membranectomy at 2 weeks apart. At one year following the second membranectomy, the patient maintained a clear cornea without residual or recurrent membrane, an endothelial cell density of 1072 cell/mm2, a visual acuity of 20/50 and a normal intraocular pressure. Our technique of using dispersive and cohesive viscoelastics in protecting the corneal endothelium from intracameral 5-FU, helped preserve corneal endothelial cells and maintain corneal clarity at one year after surgery.
Eggplant latent viroid is located in the chloroplasts and nuclei of eggplant infected cells
Authors: Eiras Marcelo , Aragonés Verónica , Marqués Jorge , Gómez María Dolores , Daròs José-Antonio 
Published: October 2024

AbstractViroids that belong to genera Avsunviroid and Pelamovirod (family Avsunviroidae) replicate and accumulate in the chloroplasts of infected cells. In this report, we confirmed by RNA in situ hybridization using digoxigenin-UTP-labelled riboprobes that the positive strands of eggplant latent viroid (ELVd), the only member of genus Elaviroid within the family Avsunviroidae, also accumulate in the chloroplasts of infected cells. However, comparison of ELVd in situ hybridization signals with those from bona fide chloroplastic and nuclear non-coding RNAs, such as chloroplast 5S rRNA and U1 small nuclear RNA, supports the notion that this viroid is also present in the nuclei of infected cells. These results suggest that the subcellular localization of viroids within the family Avsunviroidae may be more complex than previously assumed with dynamic presence in several compartments during the infectious cycle.