bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of multiomics data for the identification of a cuproptosis-related gene signature predicting prognostic outcomes and drug responses in gastric cancer
Authors: Huang Hongxin , Zhu Chuming , Yan Mengpei , Wang Jihuan , Lv Jialun , Fang Lang , Xu Penghui , Chen Zetian , Wang Weizhi , Xu Zekuan 
Published: August 2023

Abstract
Background: Cuproptosis, a recently elucidated copper-dependent mechanism of cell death associated with the tricarboxylic acid cycle, lacks a comprehensive understanding of its relation to clinical prognosis and drug response in gastric cancer (GC). This study aims to discern potential prognostic signatures of cuproptosis-related genes (CRGs) and evaluate drug response.
Methods: Using publicly available datasets from TCGA and GEO, we initially obtained transcriptomic and clinical data of GC patients. We employed consensus clustering approach to delineate molecular subtypes based on the expression of CRGs. Utilizing least absolute shrinkage and selection operator (LASSO) regression analysis, we formulated a prognostic signature derived from the differentially expressed genes among these molecular subtypes. We constructed a nomogram that amalgamates both clinical characteristics and the prognostic model to provide a comprehensive prognosis prediction. Rigorous assessment of prognostic performance was carried out through Kaplan‒Meier curve analysis, the log-rank test, univariate and multivariate Cox regression, and time-dependent ROC curve analysis. Tumor Immune Dysfunction and Exclusion (TIDE) andthepRRophetic package in R were used to assess the potential response to chemotherapy and immunotherapy. Seurat was utilized to analyze the general characterization of the single-cell dataset. Additionally, the validation of hub gene expression in both cells and clinical samples was undertaken via qRT‒PCR.
Results: Upon conducting an exhaustive investigation into the distinct differential expression and prognostic implications of each CRG, we delineated two distinct cuproptosis-associated molecular subtypes. Following Lasso regression analyses, we formulated a prognostic model comprising six specific genes. Patients were effectively stratified into either high-risk or low-risk categories by utilizing this model. Patients classified as high-risk experienced poorer prognosis and were associated with higher TNM stages compared to those with low risk. Furthermore, patients belonging to the low-risk group exhibited enhanced benefits from chemotherapeutic drugs and demonstrated better susceptibility to immunotherapy. The validation of our prognostic model's efficacy was established through ROC analysis, affirming its commendable sensitivity and specificity.
Conclusions: Our study illuminates the significance of cuproptosis in drug response and clinical prognosis in Asian GC patients, underscoring its clinical significance and providing a reliable tool for predicting overall survival in this patient population.
Wolbachia and Mosquitoes: Exploring Transmission Modes and Coevolutionary Dynamics in Shandong Province, China
Authors: zang Chuanhui , Wang Xuejun , Liu Yan , Wang Haifang , Sun Qintong , Cheng Peng , Zhang Ye , Gong Maoqing , Liu Hongmei 
Published: August 2023

Abstract
Background
Mosquito-borne diseases, including outbreaks of novel mosquito-borne diseases, pose a serious threat to human health. Deployment of the intracellular symbiont Wolbachia has been proposed as a novel strategy to modify mosquitoes with increased resistance to pathogen infection. However, little is known about its interaction with mitochondria during maternal transmission.
Method
Here, we aimed to determine the genetic structures of 11 Culex pipiens pallens populations and the incidence of Wolbachia infections in Shandong Province, China, to gain a better understanding of the relationship between mosquitoes and Wolbachia. The genetic structure of the Cx. p. pallens population was investigated using the cytochrome oxidase subunit I (COI) gene. Wolbachia infection status assessment, molecular classification, and phylogenetic analysis were performed using molecular markers for the Wolbachia surface protein (WSP) gene. Mosquito–Wolbachia relationship was investigated using tanglegram and distance-based approaches.
Results
Sequence analysis of the COI gene revealed 26 different mitochondrial DNA haplotypes. The neutrality test and haplotype networks for Cx. p. pallens populations indicated that the species is undergoing demographic expansion in Shandong Province, with significant genetic differentiation between the populations from Qingdao and most other cities. The overall Wolbachia infection rate of Cx. p. pallens was 90.7%; 15 WSP haplotypes were detected.
Conclusion
Our study revealed the genetic structure of Cx. p. pallens and the prevalence of Wolbachia in Shandong Province, China, offering important scientific information required for developing Wolbachia-based vector control approaches in Shandong Province. These findings would advance current understanding of Wolbachia’s diversity and evolution, aiding in its application as a biocontrol agent.
The invasiveness of robot-assisted total hip replacement is similar to that of conventional surgery
Authors: Ma Mingyang , Cao Zheng , Yang Minzhi , Kong Xiangpeng , Chai Wei 
Published: August 2023

Abstract
Background: Robot-assisted total hip arthroplasty (R-THA) is increasingly being performed throughout the world. The invasiveness of this operation is unknown.
Methods: We retrospectively reviewed the cohort of consecutive osteonecrosis of the femoral head (ONFH) patients who received primary R-THA or manual THA (M-THA) from January 2020 to January 2022 in our institution. One experienced surgeon performed all procedures. We calculated the propensity score to match similar patients in different groups by multivariate logistic regression analysis for each patient. We included confounders consisting of age, sex, body mass index (BMI), and operation time. Preoperative serum markers and Harris hip scores (HHS), postoperative serum markers at first day and third day, complications rate, postoperative HHS and Forgotten Joint Score (FJS) at 6 months after surgery of different cohorts were compared.
Results: We analyzed 218 ONFH patients treated with THA (98 R-THA patients, and 120 M-THA patients). After propensity score matching, we generated cohorts of 95 patients in R-THA and M-THA groups. We found no significant difference in preoperative serum markers and HHS. In the R-THA cohort, the PLT count was significantly lower on the postoperative day 1 (192.36 ± 41.72*109/L Vs 210.47 ± 72.85*109/L, p < 0.05). The Hb level was significantly lower on the postoperative third day in the R-THA cohort (98.52 ± 12.99 g/L Vs 104.74 ± 13.15 g/L, p < 0.05). There was no significant difference in the other serum markers between the cohorts on postoperative day 1 and 3 (p > 0.05). The FJS was significantly higher in the R-THA than M-THA group (p = 0.01). There was no significant difference in the postoperative HHS or complication rate between the groups (p > 0.05).
Conclusion: The R-THA is not associated with a serious invasiveness compared to M-THA. Patients who underwent R-THA had a better early function compared to those who underwent M-THA.
Optimization of vision transformer-based detection of COVID-19 from chest X-ray images
Authors: Ko Jinsol , Park Soyeon , Woo Hyun Goo 
Published: August 2023

Abstract
Background: For diagnosing coronavirus disease 2019 (COVID-19), chest X-rays have emerged as a preferred modality because of their accessibility, affordability, and capability to identify various pathologies. Recent advances in deep learning algorithms have shown promise in distinguishing COVID-19 from other lung diseases. However, the use of different optimization methods can affect the performance of the deep learning models. We aimed to compare the effects of the different optimization methods, identifying the best-performing algorithms for the detection of COVID-19 using chest X-rays.
Methods: Chest X-ray images, including the seven classes of Normal, COVID-19, Viral Pneumonia, Bacterial Pneumonia, Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), and Tuberculosis, were obtained. We trained the Vision Transformer (ViT) model using different optimizers such as Adaptive Moment Estimation (Adam), AdamW, Nesterov accelerated Adam (NAdam), Rectified Adam (RAdam), Stochastic Gradient Descent with weight decay (SGDW), and Momentum, and compared their performances.
Results: We found that the RAdam optimizer at a learning rate of 10-5 achieved the highest accuracy, highest weighted average of F1-score, and lowest false negative rate of COVID-19 for both 4 Class and 7 Class Dataset. On the other hand, AdamW showed better performance for the samples with small sample sizes. The optimizers derived from Adam (i.e. Adam, AdamW, NAdam, and RAdam), showed robust results against different learning rates, while SGDW and Momentum showed less significant robustness.
Conclusions: We suggest that Adam-derived optimizers, particularly RAdam, showed best performance in training the ViT model for detecting COVID-19 using chest X-ray images. Our results may help in the efforts to improve the performance of the model and to make it clinically useful.
RETRACTED: Extraction of lipophilic components from rowanberry pomace with supercritical CO2 and their fractionation at subcritical conditions at low temperatures
Authors: Sarv Viive , Venskutonis Petras Rimantas , Jūrienė Laura , Baranauskienė Renata , Urbonavičienė Dalia , Viškelis Pranas , Bhat Rajeev 
Published: August 2023

Abstract

The authors have requested that this preprint be removed from Research Square.
Association between gut microbiota and venous thromboembolism: a two-sample Mendelian randomization study
Authors: Wang Chao , Wang Jia , Fei Bojian 
Published: August 2023

Abstract
Background: Recent studies have suggested an association between gut microbiota (GM) and venous thromboembolism (VTE). However, observational studies cannot indicate causality and population-level studies with a higher evidence level for causality are lacking. Therefore, our study aimed to explore the causal association of GM with VTE.
Methods: This study utilized the summary-level data of respective genome-wide association study for 196 gut microbial taxa and VTE. Two-sample Mendelian randomization (MR) design was deployed and comprehensively sensitive analyses were followed to validate the robustness of results. We used the inverse-variance weighted (IVW) method, the weighted median method, weighted mode method, simple mode method, MR-Egger regression, MR-Egger intercept test, Cochrane’s Q-test, outlier test, and leave-one-out analysis as the primary analysis.
Results: We identified suggestive associations between 17 bacterial traits and the risk of VTE. Porphyromonadaceae (IVW odds ratio (OR): 1.3729, p=0.0035) and Cyanobacteria (IVW OR: 1.2151, p=0.0048) were associated with increased risk of VTE. Three gut microbiota taxa (Eubacteriumrectalegroup (IVW OR: 1.0038, p=0.0278), Coprococcus2 (IVW OR: 1.0041, p = 0.0063), and LachnospiraceaeUCG001 (IVW OR: 1.0041, p=0.0009) were predicted to play a causal role in enhancing the risk of encompassing deep vein thrombosis. And three gut microbiota taxa (Christensenellaceae (IVW OR: 1.0023, p=0.0497), Streptococcaceae (IVW OR: 1.0031, p=0.0279), Victivallaceae (IVW OR: 1.0014, p=0.0493) were positively associated with pulmonary embolism.
Conclusions: This study suggested the role of the specific GM on the risk for VTE, which may provide new ideas and a theoretical basis for the prevention and treatment of VTE in the future.
Carriage rate and Antimicrobial resistance Profile of Staphylococcus aureus Among Healthcare Workers at Edna Adan University Hospital
Authors: Nour Hussein Mohamoud , Hashi Khadar Mohamed 
Published: August 2023

Abstract
Background: Staphylococcus aureus is a pathogen that causes a wide variety of clinical manifestations ranging from food poisoning, toxic shock syndrome, and infections that range from mild skin infections to serious and life threatening conditions such as, endocarditis, bacteremia and osteomyelitis (1). Ranking as the second most common cause of hospital acquired (nosocomial) bloodstream infections (2). About 20% of patients undergoing surgery acquire at least one nosocomial S. aureus infection, leading to increased morbidity, mortality, hospital stay, and costs (2).however, there is no any previous study conducted regarding this topic in Hargeisa, Somaliland.
Objectives:The main objective of this study was to determine the Carriage rate and Antimicrobial resistance Profile of Staphylococcus aureus Among Healthcare Workers at Edna Adan University Hospital
Methods: Hospital-based cross-sectional was conducted on a total of 80 healthcare workers from July to August 2023 at EAH. A simple random sampling technique was used and Samples were collected from HCWs at EAUH from July to August 2023. By using pre-moistened sterile cotton swabs and specimens were collected from the anterior nares and palms of the HCWs. The samples were collected by rotating the swabs gently two to three times on both nares of the study participants. Similarly, a second swab was used to collect specimen from both palms of the health care workers. Both swabs were cultured on blood agar and subculture onto Manitol Salt agar and incubated at 37 °C for 24 hrs.
Results: The overall prevalence of Staphylococcus aureus in this study was 20% (16/80) and methicillin-resistant Staphylococcus aureus was 7.5% (6/80). Carriage rate was highest among midwifes 7(29.2%) followed by nurses 5(26.3%) and doctors (3(17.6%) respectively. Similarly highest colonization rate of MRSA 3(60%) were observed among nurses and doctors 1(50%) followed by midwifes 2(28.6%). Length of healthcare service was significantly associated with MRSA colonization. Highest rate of resistance (100%) was found against Ampicillin, Cefoxitin (93.7%) Erythromycin (87.5% and Gentamycin (68.75%) respectively. S. aureus was found to be highly sensitive to Doxycycline (100%) Ciprofloxacin (100%) and Clindamycin (87.5%). Similarly, MRSA was completely showed (100%) resistance against Cefoxitin and ampicillin.
Conclusion: The prevalence of Staphylococcus aureus and Methicillin-resistant Staphylococcus aureus are high in this study. The present study encourages the need for regular screening and surveillance among hospital staff and the environment to prevent MRSA transmission among health-care personnel and Molecular detection of highly resistant strains of MRSA are suggested
Fixed-time synchronization of fractional-order chameleon hyperchaotic systems based on hyperbolic sliding mode
Authors: Li Shuaiwei , Zhao Xiaoshan , Yang Ruilong 
Published: August 2023

Abstract
This paper proposes a new control method for a four-dimensional hyperchaotic system using the terminal sliding mode control. It eliminates the need for the traditional activation function by replacing it with a hyperbolic tangent function. This method effectively deals with the effects of parameter uncertainties and external disturbances in the systems, also eliminates the chattering phenomenon in the synchronous process, enables the response system and the drive system to reach the synchronization state in a fixed time. Finally, numerical simulations with MATLAB software were applied to verify the effectiveness of this fixed time convergence technique.
Hippocampal volume and affect in response to fluctuating estrogens in menstrual cycle irregularity: A longitudinal single-subject study
Authors: Heller Carina , Güllmar Daniel , Koeppel Carina J. , Rojczyk Philine , Stein Heidemarie , Taylor Caitlin M. , Jacobs Emily G. , Derntl Birgit , Kikinis Zora , Walter Martin , Croy Ilona 
Published: August 2023

AbstractBackground The menstrual cycle is a critical indicator of women's reproductive, physical, and mental health, influenced by neuromodulatory sex steroid hormones, including estrogens like 17β-estradiol, and estrone. Irregular menstrual cycles can lead to various health conditions. Understanding the relationship between endogenous hormone fluctuations and brain function across the menstrual cycle is essential for comprehending mental health disorders prevalent in women. Here, we investigated the impact of hormonal variations on hippocampal morphology and affect in a participant with an irregular menstrual cycle. Methods In this dense-sampling longitudinal study, a healthy female with an irregular menstrual cycle underwent testing for five consecutive weeks, covering mostly the follicular phase and ovulation. Daily blood draws provided measurements of estradiol, estrone, and progesterone. T1-weighted MRI scans assessed bilateral hippocampal volumes. Psychological measures of positive and negative affect were collected each session. Statistical analyses included cubic regression curves, Spearman correlations, and mediation regression models to explore hormonal associations with hippocampal morphology and affect. Results Fluctuations were observed in hormonal concentrations, hippocampal volume, and affect across the 25 testing days. Estradiol and estrone correlated significantly with hippocampal volume, while progesterone did not show any significant association. Increased estrogen levels were linked to decreased positive affect, mediated by hippocampal volume fluctuations. Increased estrogen levels were further associated with increased negative affect, however, independently of hippocampal changes. Conclusion This study sheds light on the complex relationship between endogenous hormone fluctuations, hippocampal morphology, and affect in a participant with an irregular menstrual cycle. The findings suggest potential roles of estrogens and estrone in affect regulation, with implications for women's mental health and brain function. Further research is warranted to explore these associations in larger samples and various menstrual cycle patterns.
Esketamine prevents cognitive deficiency via intestinal flora/subdiaphragmatic vagus nerve/spleen axis after a secondary LPS exposure
Authors: Wu Yuming , Zhang Yujing , Xie Bing , Zhang Xinyu , Wang Guangzhi , Yuan Shiying 
Published: August 2023

Abstract
After resolution of primary infection, patients are susceptible to more severe secondary infection with unclear underlying mechanisms.To investigate whether esketamine treatment immediately after primary LPS exposure could alleviate second-infection-induced cognitive impairment. In this study, mice were injected intraperitoneally (i.p.) with lipopolysaccharides (LPS; 5 mg/kg) 10 days apart. Esketamine (10, 15 or 30 mg/kg) was i.p. injected immediately after the primary LPS injection. Splenectomy or subdiaphragmatic vagotomy (SDV) was performed 7 days before secondary LPS exposure or administration of antibiotics. Esketamine at 30 mg/kg mitigated splenomegaly at 3 and 10 days post primary LPS injection. It countered cognitive dysfunction and proinflammatory cytokine increases from secondary LPS exposure. Mice with splenectomy or SDV showed reduced proinflammatory cytokines, heightened hippocampal BDNF, and improved cognition after secondary infection, without added esketamine effect. FMT from esketamine-treated endotoxic mice to pseudo germ-free (PGF) mice attenuated hippocampal BDNF downregulation and cognitive dysfunction in PGF mice without splenectomy. FMT failed to reverse PGF mice's SDV-induced splenomegaly. Blocking BDNF signaling negated esketamine's ameliorating effects on secondary LPS-induced cognitive dysfunction. In conclusion, the intestinal flora/subdiaphragmatic vagus nerve/spleen axis-mediated downregulation of hippocampal BDNF had a profound effect on secondary LPS-induced inflammation and cognitive dysfunction.
Elevational and seasonal diversity of insect orders in the Shivapuri-Nagarjun National Park, Nepal
Authors: Saru Meena , Acharya Bhumika , Adhikari Asmita , Giri Susma 
Published: August 2023

Abstract
Insects fill many ecological niches and are crucial for sustaining ecosystems. Nevertheless, reported declines in insect diversity across the globe has raised grave concerns for these declines have significant ecological and economic ramifications. The current scenario of shifting environmental conditions, dwindling insect populations, and a dearth of information on these species in Nepal, one of the 36 biodiversity hotspots, necessitates immediate intervention. The essential first step in increasing our understanding of the species for appropriate conservation efforts is species inventory. Using three collecting techniques (cup trap, pitfall trap, and net swipe), we evaluated insect order diversity in the Shivapuri-Nagarjun National Park from February 2019 to February 2020 spanning three elevations (1660 m to 2700 m asl) and four seasons (Summer, Autumn, Winter, and Spring). Dipetra led the collection with a total of 632 individuals out of the 1467 insects belonging to 11 orders. The total count did not differ by elevation and was highest in the summer and lowest in the winter. While the ß-diversity was unaffected by elevation or season, the α-diversity varied according to both. We discuss the relationship between insect counts and air temperature as well as the relative abundance at various elevations and during various seasons. We also talk about the relationship between insect counts and air temperature and their relative abundance. For future reference, this study gathers the critical baseline data on the distribution of insect orders at SNNP.
Neck dissection of Level Ib for the treatment of cN0 HPV-negative oropharyngeal squamous cell carcinoma: Should it be safely omitted?
Authors: Sheng Surui , Ye Lulu , Ma Chunyue , Zhu Yun , He Yue 
Published: August 2023

Abstract
Background: Selective neck dissection (SND) of levels II-IV is traditionally recommended for the treatment of cN0 oropharyngeal squamous cell carcinoma (OPSCC). Whether to include level Ib in the dissection of cN0 neck tumors is debated because occult lymph node metastasis is frequently located at level II, which is closely posterior to level Ib. Moreover, neck dissection focusing on HPV-negative OPSCC is insufficient because the HPV-positive subtype accounts for most cases in many regions, especially in Western countries. The aim of this study was to clarify whether patients would potentially benefit from including level Ib in SND for cN0 HPV-negative OPSCC.
Methods: This retrospective cohort study included 198 cN0 HPV-negative OPSCC patients who underwent SND of levels II-IV (Group A) and levels Ib-IV (Group B). Neck recurrence (NR) was considered the primary endpoint. Overall survival (OS), disease-free survival (DFS), and disease-specific survival (DSS) were the secondary endpoints.
Results: In Group B, the rate of occult lymph node metastasis at level Ib of the ipsilateral neck was 6.1%. For the entire cohort, the rate of NR was 7.6% in Group A and 2.3% in Group B (p = 0.074). The 5-year OS and DFS rates were also not significantly different between Group A (50.0% and 43.2%) and Group B (57.6% and 51.6%), while Group B had higher 5-year DSS rate than Group A (60.7% vs. 47.9%, p = 0.018). For the tumor from the base of tongue, the rate of NR was obviously higher in Group A (12.2%) than in Group B (2.1%, p = 0.015). Patients in Group A had lower 5-year DFS (39.1% vs. 47.4%, p = 0.046) and DSS rates (46.5% vs. 56.3% p = 0.034). N2 stage was an independent predictive factor for both OPSCC (p= 0.017) and the primary tumor from the base of tongue (p = 0.007).
Conclusions: Even though the metastatic rate of cN0 OPSCC at level Ib was relatively low, including level Ib in SND should be considered for OPSCC originating from the base of tongue, especially in advanced stages, which would potentially lower the rate of NR and improve the survival benefit.