bluuebunny/crossref_metadata_2025 huggingface dataset:
BCOOT-Based Binary Optimization for Microarray-Based Cancer Gene Selection and Classification: A Comparative Study
Authors: Yaqoob Abrar , Verma Navneet Kumar , Aziz Rabia Musheer
Published: November 2023

In this research, we introduce an innovative approach, for selecting genes in microarray-based cancer classification. Analysing gene expression using microarrays is crucial for disease and cancer detection. However, identifying the relevant gene markers is challenging due to the nature and high dimensional aspects of the data. We introduce the BCOOT (Binary COOT) optimization algorithm, which shows potential for gene selection tasks. We propose three variations; BCOOT, BCOOT-C and BCOOT-CGA. In our approach we transform the COOT algorithm into binary form using a hyperbolic tangent transfer function. The second strategy enhances exploration by incorporating a crossover operator (C) into BCOOT. For our method BCOOT-CGA we combine BCOOT C with a Genetic Algorithm to strengthen exploitation and identify robust and informative genes. To improve the gene selection process further we include a prefiltering step called redundancy relevance (mRMR) technique to eliminate redundant genes. To evaluate our proposed algorithms performance we conduct assessments, on six established microarray datasets comparing them with other robust optimization techniques and state of the art gene selection methodologies. In the classification step of our study, we utilize a Random Forest classifier. The experimental findings showcase that the BCOOT-CGA approach outperforms both BCOOT and BCOOT-C, surpassing alternative methods regarding the accuracy of predictions and the quantity of chosen genes in the majority of instances. This underscores the effectiveness of our proposed approach in enhancing microarray-based cancer classification, highlighting its potential to advance disease diagnosis and prognosis.
Climatic warming strengthening water constraint on seasonal peak photosynthesis in northern ecosystems
Authors: Zhang Shuo , Chen Xingan , Huang Yuefei , Yang Yuting , Tan Shen , Nie Chong , Wang Guang-Qian , Chen Zhichao
Published: November 2023

The seasonal peak of vegetation photosynthesis is a key indicator of terrestrial ecosystem productivity, bearing significant impacts on atmospheric CO2 concentrations. Recent remote sensing observations have indicated an escalating trend in peak photosynthesis, yet the sustained trajectory of this increase under warming remains uncertain. Notably, water availability and temperature emerge as paramount limiting factors governing vegetation photosynthesis. To probe these constraints, here we employ solar-induced chlorophyll fluorescence as a surrogate for photosynthesis, focusing on the examination of temperature and water-related restrictions on peak photosynthesis for northern ecosystems. Our findings unveil a discernible expansion of water-constrained zones in northern ecosystems over the past two decades. A general relationship is identified between mean annual temperature and precipitation that effectively distinguishes temperature-constrained and water-constrained ecosystems, which can be used to predict future changes in the constraint status in various climate change scenarios. Our results show that water-constrained regions will further expand by 4.51% and 11.13% by 2100 under the SSP245 and SSP585 scenarios.
The impact of the length of proximal margin on the prognosis of adenocarcinoma of gastroesophageal junction and strategies : A real-world study
Authors: Pang Tao , Nie Mingming , Fan lei , Wang Jia yang , Liu Zhao rui , Qin Ying yi , Yin Kai
Published: November 2023

Background: The optimal proximal margin (PM) length for SiewertII/III adenocarcinoma of the esophagogastric junction (AEJ) remains unclear. This study aimed to determine the optimal PM length using an abdominal approach to guide surgical decision-making.
Methods: A prospective study analyzed 304 consecutive patients diagnosed with SiewertII/III AEJ between January 2019 and December 2021. Total gastrectomy was performed via the abdominal approach, and PM length was measured on fixed gross specimens. X-Tile software determined the optimal PM cut-point based on progression-free survival (PFS). Univariate analyses compared baseline characteristics across PM groups, while survival analyses utilized Kaplan-Meier estimation and Cox proportional hazards regression for assessing the impact of margin length on survival. Multivariable analyses were conducted to adjust for confounding variables.
Results: The study included 264 AEJ cases classified as Siewert II (71.97%) or III (28.03%). The median gross PM length was 1.0 cm (IQR: 0.5 cm-1.5 cm, range: 0 cm-6 cm). PM length ≥1.2 cm was associated with a lower risk of disease progression compared to PM length 0.4 cm on PFS (HR = 0.41, 95% CI 0.20-0.84, P = 0.015). Moreover, PM ≥1.2 cm improved prognosis in subgroups of T4 or N3, tumor size <4 cm, Siewert II, and Lauren classification.
Conclusions: For Siewert type II/III AEJ, a proximal margin length ≥1.2 cm (1.65 cm in situ) is associated with improved outcomes. These findings offer valuable insights into the association between PM length and outcomes in SiewertII/III AEJ, providing guidance for surgical approaches and aiding clinical decision-making to enhance patient outcomes.
Causal relationship between gut microbiota and brain microbleeds: a comprehensive Mendelian randomization study
Authors: Gao Tianxiang , Liu Hanchen , Wu Congyan , Zhang Xiaoxi , Liu Jianmin
Published: November 2023

Background
Considerable evidence has been reported that alterations in gut microbiota composition could cause cerebrovascular diseases. The microbiota-gut-brain axis also hinted at a possible contribution of the gut microbiota to cerebrovascular diseases. However, the causal association between the gut microbiome and the risk of brain microbleeds (BMB) is unclear.
Methods
We performed two-sample bidirectional Mendelian randomization (MR) utilizing the summary-level data of respective genome-wide association study (GWAS) for 211 gut microbial taxa and two BMB phenotypes to reveal the causal association between gut microbiota and BMB.
Results
We identified 7 causal relationships between genetic liability in the gut microbiome and any BMB, including those involving the genus Lachnospiraceae. We found 13 associations between genetic liability in the gut microbiome and lobar BMB. Moreover, we found 6 associations between genetic liability in the gut microbiome and deep infratentorial BMB. The bidirectional, heterogeneity, and pleiotropy analyses confirmed the robustness of MR results.
Conclusion
Our MR analysis revealed that the gut microbiota was causally associated with BMB and may be helpful in providing new insights for further mechanistic and clinical studies of microbiota-mediated cerebrovascular diseases.
Rituximab added to conditioning regimen significantly improves erythroid engraftment in major incompatible ABO-group hematopoietic stem cell transplantation
Authors: Finazzi Maria Chiara , Weber Alessandra , Pavoni Chiara , Grassi Anna , Micò Maria Caterina , Algarotti Alessandra , Lussana Federico , Rambaldi Alessandro
Published: November 2023

ABO-group major incompatibility hematopoietic stem cell transplantation (HSCT) increases the risk of delayed red cell engraftment and other immunological complications. In this study, we evaluated the efficacy of pre-transplant infusion of rituximab in patients with ABO-incompatibility in improving red blood cell engraftment after HSCT, measured by time to reach transfusion independence. We performed a retrospective, single-center study including 131 consecutive patients transplanted with major or bidirectional ABO-incompatible grafts between 1st January 2013 and 31st December 2019. Fifty-one patients received infusion of rituximab during the conditioning regimen, while 80 patients did not receive any additional preventive treatment. Time to transfusion independence was significantly reduced for patients treated with rituximab (1 month, 95% CI, 0.5-2) compared with the control group (3.2 months, 95% CI 1.5–3.2, p = 0.02). By multivariable analysis, factors associated with a faster red blood cell engraftment were rituximab use (RR 1.86, 95% CI 1.18–2.91, p = 0.007) and having received a stem cell graft with a number of CD34 + cells ≥ 3.7 x10^6/kg (RR 2.19, 95% CI 1.34–3.57, p = 0.002). Although limited by the retrospective nature of the study, the results of this analysis show that rituximab added to conditioning regimens is feasible, safe, and able to improve post-transplant red blood cell engraftment.
Development and assessment of an efficient predictive nomogram for bloodstream infection in gallstone patients
Authors: Shen Xiuqing , Wu Changsheng , Zhong Rongxin , Chen Falin , Wang Sijie , Cao Pengju , Chen Shaoting
Published: November 2023

Objective The objective of this study was to create and authenticate a user-friendly nomogram for assessing the risk of bloodstream infections (BSI) in patients with gallstones.
Methods Data on 261 patients without BSI and 96 patients with BSI who had gallstones were gathered between January 2019 and April 2023. The ten variables—age, sex, white blood cell (WBC), neutrophil (NE%), calcitonin (PCT), γ-glutamyltransferase (GGT), total bilirubin (TBIL), direct bilirubin (DBIL), alkaline phosphatase (ALP), and glutamic oxaloacetic transaminase (AST)—were first screened using the single-factor regression analysis. Multiple regression analyses were used to optimize the risk model's predictive features. The prediction model's discrimination, calibration, and clinical application performance were evaluated using the consistency index (c-index), calibration curve, and clinical decision curve (DCA).
Results Nine variables show no multicollinearity, with the exception of gender, according to collinearity analysis. Multiple logistic regression analysis was included to select age, PCT, and AST predictors. Among them, age [OR = 0.562 (0.366–0.939), P = 0.028] is a protective factor for gallstone patients with blood flow infection (P < 0.05), whereas PCT [OR = 2.115 (1.244–3.597), P = 0.006], and AST [OR = 3.469 (1.942–6.198), P = 0.000] are risk factors for concurrent BSI in gallstone patients with gallstones (P < 0.05). On the basis of the anticipated variables, a prediction model was created. With a bootstrap validation of 0.7 and a C-index of 0.71, the prediction model's validation shows sufficient discrimination. The calibration curve showed how well the model can be corrected and how accurate its predictions are. The DCA results demonstrated that the predictive model was clinically effective when the threshold probability was between 17–77%, as the net return was more significant than the two extreme models.
Conclusion As an additional technique for predicting individuals with gallstones complicated by blood flow infection, the nomogram has some predictive power.
Genetic diversity of enteroviral meningitis, herpangina and hand, foot, and mouth disease in Kazakhstan
Authors: Dinara Kamalova , Assel Akhmetova , Asylulan Amirgazin , Igor Sytnik , Alexander Shevtsov
Published: November 2023

Enteroviral infection is a common cause of aseptic meningitis, herpangina, and hand, foot, and mouth disease in children. Limited data are available on the enteroviral subtypes associated with hospitalization for these conditions in Kazakhstan. We collected cerebrospinal fluid (CSF) and nasopharyngeal swabs (NSW) from children (N=152, median age=8 years) hospitalized with symptoms of aseptic meningitis (AM, N=139) or herpangina (HA, N=13) disease. We then genotyped enteroviral subtypes associated with AM (n=50) and HA (n=9) using next-generation sequencing (NGS) on the viral protein 1 (VP1), followed up by whole-genome sequencing of the isolated viral species. All identified EVs were species B EV, consisting of five echovirus (E6, E9, E11, E21 and E25) and three coxsackievirus (CVA9, CVB3 and CVB5) serotypes within the cohort. The most abundant EVs were CVA9 (38.5%), CVB5 (21.5%) and E6 (13.8%). Most HA samples (6/9) were genotyped with coxsackievirus CVA9, while AM was associated with a variety of both echovirus and coxsackievirus serotypes.
The results suggest that coxsackievirus CVA9 may be the dominant serotype circulating in the HA population, while AM is more diverse in terms of circulating echovirus and coxsackievirus serotypes. Further studies are needed to determine the clinical implications of these findings and to investigate potential differences in disease severity or outcomes associated with different EV serotypes.
Customized Passive-Dynamic Ankle-Foot Orthoses Can Improve Walking Economy and Speed for Many Individuals Post-Stroke
Authors: Skigen Jacob T. , Koller Corey A. , Nigro Luke , Reisman Darcy S. , McKee Zahra , Pinhey Shay R. , Henderson Adrienne , Wilken Jason M. , Arch Elisa S.
Published: November 2023

Background
Passive-dynamic ankle-foot orthoses (PD-AFOs) are often prescribed to address plantar flexor weakness during gait, which is commonly observed after stroke. However, limited evidence is available to inform the prescription guidelines of PD-AFO bending stiffness. This study assessed the extent to which PD-AFOs customized to match an individual’s level of plantar flexor weakness influence walking function, as compared to No AFO and their standard of care (SOC) AFO.
Methods
Mechanical cost-of-transport, self-selected walking speed, and key biomechanical variables were measured while individuals greater than six months post-stroke walked with No AFO, with their SOC AFO, and with a stiffness-customized PD-AFO. Outcomes were compared across these conditions using a repeated measures ANOVA or Friedman test (depending on normality) for group-level analysis and simulation modeling analysis for individual-level analysis.
Results
Twenty participants completed study activities. Mechanical cost-of-transport and self-selected walking speed improved with the stiffness-customized PD-AFOs. However, this did not result in a consistent improvement in other biomechanical variables. In line with the heterogeneous nature of the post-stroke population, the response to the PD-AFO was highly variable.
Conclusions
Stiffness-customized PD-AFOs can improve the mechanical cost-of-transport and self-selected walking speed in many individuals post-stroke, as compared to No AFO and participants’ standard of care AFO. This work provides initial efficacy data for stiffness-customized PD-AFOs in individuals post-stroke and lays the foundation for future studies to enable consistently effective prescription of PD-AFOs for patients post-stroke in clinical practice.
Trial Registration
Trial Number: NCT04619043
The circadian clock gene, BMAL1, promotes radiosensitization in nasopharyngeal carcinoma by inhibiting the epithelial-to-mesenchymal transition via the TGF-β1/Smads/Snail1 axis
Authors: Li Yuxin , Zhou Yu , Zhao Chaofen , Liu Lina , He Qianyong , Shang Kai , Xu Xinyu , Luo Xunyan , Zhou Dingan , Jin Feng
Published: November 2023

Acquired radio-resistance is thought to be one of the main causes of recurrent metastasis after failure of nasopharyngeal carcinoma (NPC) radiotherapy, which may be related to X-ray-induced epithelial–mesenchymal transition (EMT) activation. The circadian clock gene, BMAL1, has been shown to correlate with the sensitivity of NPCs to radiotherapy, but the specific mechanism has not been reported. NPC cells were irradiated by conventional fractionation to generate radiotherapy-resistant cells. NPC cells with BMAL1 gene stabilization/overexpression and interference were obtained by lentiviral transfection. Western blotting, colony formation analysis, cell counting kit-8 assays, wound-healing tests, Transwell assays, flow cytometry, the EDU method, nuclear plasma separation experiments, HE staining, immunohistochemical staining and TUNEL staining were performed to explore the influence and molecular mechanism of the circadian clock gene, BMAL1, on NPC-acquired radio-resistance and EMT through in vitro and in vivo experiments. The results indicated that there was a gradual downregulation of BMAL1 gene protein expression during the routine dose induction of radio-resistance in NPC cells. EMT activation was present in the radiation-resistant cell line 5-8FR, and was accompanied by the significant enhancement of proliferation, migration and invasion. The BMAL1 gene significantly increased the radiosensitivity of the radiation-resistant cell line 5-8FR and reversed the acquired radio-resistance of NPCs, which was accomplished by inhibiting the TGF-β1/Smads/Snail1 axis-mediated EMT.
EIF4A3 induced CircCHD7 promote osteosarcoma progression by sponge miR-608 and regulated FZD4/MMP2 expression through Wnt/β-catenin pathway
Authors: Yao Teng , Jun Gao , Zhang Deguang , Feng Zhenhua , Xu Yining , Zhang Zhenlei , Qiao Di , Wang Jiying , Shen Shuying , Ma Jianjun
Published: November 2023

Background
Osteosarcoma is a malignant tumor that tends to occur in adolescents. In recent years, surgical treatment has reduced mortality rates in patients with osteosarcoma. However, many patients still die of osteosarcoma, and further studies are needed to elucidate the complicated pathogenesis of this disease.
Methods
The function of circCHD7 was detected by transwell, clone formation, Cell Counting Kit 8, and apoptosis assays after knockdown of circCHD7 in 143B and HOS cells. Bioinformatics analysis was used to identify binding between miR-608 and circCHD7, and the results were further validated using luciferase, pull-down, and RNA immunoprecipitation assays. Bioinformatics and quantitative real-time polymerase chain reaction were used to identify downstream target genes of miR-608. The expression and effects of circCHD7 inhibitor were evaluated in stable sh-circCHD7 143B cell lines and a subcutaneous tumor model.
Results
CircCHD7, regulated by eIF4A3, was found to promote tumor proliferation and migration. Knockdown of circCHD7 and overexpression of miR-608 enhanced apoptosis and inhibited migration ability in osteosarcoma cells. The inhibitory effects of circCDH7 knockdown in 143B and HOS cells could be rescued by miR-608 inhibitor. Bioinformatics and western blotting results showed that miR-608 could regulate the expression of downstream matrix metalloproteinase 2 (MMP2) and Frizzled-4 (FZD4) and further modulate the Wnt/β-catenin pathway, thereby exerting inhibitory effects on osteosarcoma.
Conclusion
In this study, we discovered a new circRNA, circCHD7, that was regulated by eIF4A3 and modulated tumor growth through the miR-608/FZD4/MMP2 pathway. These findings provide insights into the potential application of circRNAs in the treatment of osteosarcoma.
Genetic determinants of Selenium availability, Selenium-response and risk of Polycystic Ovary Syndrome
Authors: Sharma Priya , Khetarpal Preeti
Published: November 2023

Selenium is a trace element and its deficiency has been associated with the risk of PCOS, a multifactorial syndrome that affects a large number of women worldwide. Several databases and literature were searched to find out genetic variants of the genes involved in selenium uptake, metabolism and regulation which may be significantly associated with risk of PCOS through Se related pathways. Genes whish require selenium for their biological actions to perform were also shortlisted. A total of eighteen significantly associated genes were identified which were shortlisted among forty-four variants that could play potential role in the PCOS risk among the study population. The genetic variant distribution data was available in-house and was obtained through GWAS study of the North India population. In silico tools were applied to understand the functional impact of these variants. Three variants namely LDLR(rs2228671), TNF (rs1041981), and SAA2 (rs2468844) are strongly associated with PCOS risk and have a functional impact on encoded protein. Certain variants of Se uptake genes such as DIO1, GPX2, TXNRD1, DIO2 GPX3 genes significantly increase or decrease risk of PCOS development. Se transporter gene SELENOP polymorphism rs9686343 with C allele significantly increased PCOS risk. Other potential genes that require selenium for their biological actions are involved in the inflammatory, antioxidant response, and energy homeostasis signaling pathways. Thus genetic variants of the population may affect the Se availability or Se deficiency may modulate the effect of Se-associated genes due to genetic polymorphism. This information may be helpful in dosage adjustment of Se supplementation for a population in order to have maximum benefits.
Risk of Erectile Dysfunction after Primary Obsessive-Compulsive Disorder: A Nationwide Population-Based Study
Authors: Shi Ming der , Chung Mei Hua , Ma Mi Chia , Chao Jian-Kang
Published: November 2023

Objective: Erectile dysfunction (ED) in patients with OCD (obsessive-compulsive disorder) has been investigated in very few limited studies. This study aimed to investigate the association between OCD and subsequent ED.
Methods: In this population-based retrospective cohort study, we used Taiwan’s National Health Insurance Research Database to analyze patients who were newly diagnosed with OCD between 2000 and 2016, We included 21,656 patients with OCD aged over 18 years old, with a 1:1 ratio by age and index year matched with patients in a non-OCD comparison group, for the risk of ED. Cox proportional hazards analysis was used to estimate the association between OCD and subsequent psychogenic ED. Results :After a 7-year follow-up, the incidence rate of psychogenic ED was higher in the OCD patients when compared with the non-OCD control group (3.39 vs.1.49 per 100,000 per person-year). Patients with OCD had a higher risk of developing psychogenic ED than the non-OCD cohort after the adjustment of the confounding factors (adjusted HR = 4.05, 95% confidence interval (CI) [2.06, 7.99], p < .001). This is the first study using a comprehensive nationwide database to analyze the association between psychogenic ED and OCD in Taiwan. After adjusting for the confounding factors, patients with OCD have a significantly higher risk of developing psychogenic ED.
Conclusions: Patients with OCD should be encouraged to take sexual history as part of their routine clinical assessment and appropriate preventive mental measures to maintain mental and sexual health.
A closer Look to the Factors Affecting the Switching Transient Times of Optocouplers
Authors: Hassan Warda H.A. , Kamh Sanaa A. , Soliman Fouad A. S. , El-Basit Wafaa Abd
Published: November 2023

The significant parameters for high-speed optoelectronic switch were the transient times. In the time domain, there is a time elapsed in the order of microseconds between applying a current pulse and seeing an output. So, the present work aimed to give a closer look on the factors affecting the transient times of the optocoupler switching action, namely; delay (td)-, rise (tr)-, in addition to storage (ts)- and fall (tf)-times. The switching transient times of the optocoupler (type 4N25) were investigated and plotted under the influence of different operating conditions such as: load resistance (RL), forward LED drive current (IF), bias collector voltage (VCC), emitter-base resistance (RBE) and temperature. Experimental results showed that, the value of the turn-on time (Ton=td+tr) was decreased with increasing the following; IF and RBE, while it increased with increasing VCC and temperature as well, while it unaffected by increasing RL. On the other hand, the turn-off time value (Toff=ts+tf) was shown to be decreased with increasing VCC and RBE while its value increased with increasing the following; RL, IF and temperature.
Proteomics-based Model for Predicting the Risk of Brain Metastasis in Patients with Resected Lung Adenocarcinoma carrying the EGFR Mutation
Authors: Deng Qiuhua , Wang Fengnan , Song Lei , Chen Liangyu , Huang Ying , Guo Zhihua , Yang Haihong
Published: November 2023

Purpose
By establishing a predictive model based on protein biomarkers, it is used to identify the high-risk population of The epidermal growth factor receptor(EGFR) mutated lung cancer patients who may experience brain metastasis after surgery, thereby reducing or delaying the occurrence of brain metastasis.
Methods
We conducted a retrospective study of BMs in the postoperative recurrent LUAD with EGFR mutation in the First Affiliated Hospital of Guangzhou Medical University. Tissue proteomic analysis was applied in the primary tumors of the resected LUAD in this study using liquid chromatography-mass spectrometry (LC-MS/MS). To identify potential markers to predict LUAD-BM, comparative analyses were processed on different groups to evaluate proteins associated with high-risk of BMs.
Results
A combination of three potential marker proteins were found to well distinguish distal metastasis (DM) and local recurrence (LR) of postoperative LUAD with EGFR mutation. GO analysis of significant changed proteins between BM and non-BM (NBM) indicates that lipid metabolism and cell cycle related pathways were involved in BMs of LUAD. And the enriched pathways correlated with BMs were found quite different in the comparison groups of postoperative adjuvant therapy, tyrosine kinase inhibitor (TKI) and chemotherapy groups. Finally, we developed a random forest algorithm model with eight proteins (RRS1, CPT1A, DNM1, SRCAP, MLYCD, PCID2, IMPAD1 and FILIP1), which showed excellent predictive value (AUC: 0.9401) of BM in patients with LUAD harboring EGFR mutation.
Conclusions
A predictive model, based on protein markers, was developed to precisely predict postoperative BM in operable LUAD carrying EGFR mutation.
A Reduced Proteomic Signature in Critically Ill Covid-19 Patients Determined With Plasma Antibody Micro-array and Machine Learning
Authors: Patel Maitray A. , Daley Mark , Nynatten Logan R. , Slessarev Marat , Cepinskas Gediminas , Fraser Douglas D.
Published: November 2023

Background: COVID-19 is a complex, multi-system disease with varying severity and symptoms. Identifying changes in critically ill COVID-19 patients’ proteomes enables a better understanding of markers associated with susceptibility, symptoms, and treatment. We performed plasma antibody microarray and machine learning analyses to identify novel biomarkers of COVID-19.
Methods: A case-control study comparing the concentration of 2000 plasma proteins in age- and sex-matched COVID-19 inpatients, non-COVID-19 sepsis controls, and healthy control subjects. Machine learning was used to identify a unique proteome signature in COVID-19 patients. Protein expression was correlated with clinically relevant variables and analyzed for temporal changes over hospitalization days 1, 3, 7, and 10. Expert-curated protein expression information was analyzed with Natural language processing (NLP) to determine organ- and cell-specific expression.
Results: Machine learning identified a 28-protein model that accurately differentiated COVID-19 patients from the other cohorts (balanced accuracy=0.95, AUC=1.00, F1=0.93), as well as an optimal nine-protein model (PF4V1, NUCB1, CrkL, SerpinD1, Fen1, GATA-4, ProSAAS, PARK7, and NET1) that maintained high classification ability (balanced accuracy=0.92, AUC=0.98, F1=0.93). Specific proteins correlated with hemoglobin, coagulation factors, hypertension, and high-flow nasal cannula intervention (P<0.01). Time-course analysis of the 28 leading proteins demonstrated no significant temporal changes within the COVID-19 cohort. NLP analysis identified multi-system expression of the key proteins, with the digestive and nervous systems being the leading systems.
Conclusions: The plasma proteome of critically ill COVID-19 patients was distinguishable from that of non-COVID-19 sepsis controls and healthy control subjects. The leading 28 proteins and their subset of 9 proteins yielded accurate classification models and are expressed in multiple organ systems. The identified COVID-19 proteomic signature helps elucidate COVID-19 pathophysiology and may guide future COVID-19 treatment development.
Vibrio Species and Cyanobacteria: Understanding their Association in Local Shrimp Farm using Canonical Correspondence Analysis (CCA)
Authors: Baki Dayang Najwa Binti Awg , Nillian Elexson , Lesen Dalene , Tung Teng Sing
Published: November 2023

In aquatic environments, Vibrio and cyanobacteria establish varying relationships influenced by environmental factors. To investigate their association, this study spanned 5 months at a local shrimp farm, covering the shrimp larvae stocking cycle until harvesting. A total of 32 samples were collected from Pond A (n = 6), Pond B (n = 6), effluent (n = 10), and influent (n = 10). Vibrio species and cyanobacteria density were observed, and canonical correspondence analysis (CCA) assessed their correlation. CCA revealed a minor correlation (p = 0.847, 0.255, 0.288, and 0.304) between Vibrio and cyanobacteria in Pond A, Pond B, effluent, and influent water, respectively. Notably, Vibrio showed a stronger correlation with pH (6.14–7.64), while cyanobacteria correlated with pH, salinity (17.4–24 ppt), and temperature (30.8–31.5 ℃), with salinity as the most influential factor. This suggests factors beyond cyanobacteria influence Vibrio survival. Future research could explore species-specific relationships, regional dynamics, and multidimensional landscapes to better understand Vibrio-cyanobacteria connections. Managing water parameters may prove more efficient in controlling vibriosis in shrimp farms than targeting cyanobacterial populations.
The Survival Effect of Neoadjuvant Therapy and Neoadjuvant Plus Adjuvant Therapy on Different AJCC 8th TNM Stages: A Propensity Score Matching Analysis Based on SEER Database
Authors: Hu Hao , Xu Yang , Zhang Qiang , Gao Yuan , Wu Zhenyu
Published: November 2023

Background: Currently, adjuvant therapy (AT) is the standard treatment for resectable pancreatic ductal adenocarcinoma (PDAC), and so is neoadjuvant therapy (NAT) for borderline resectable and locally advanced stages. However, it remains unclear whether AT improves survival after NAT and radical resection in all TNM stages.
Methods: The studied population was comprised of patients diagnosed with PDAC who underwent radical surgery, and was drawn from the Surveillance, Epidemiology, and End Results (SEER) database, spanning from 2010 to 2019. we employed Pearson’s chi-square test, univariate and multivariate Cox regression analysis, Kaplan-Meier (K-M) analysis, Log-rank test, and emphasis on propensity score matching (PSM) analysis.
Results: 13,868 PDAC patients were finally enlisted. After PSM, significant differences in survival were identified between AT and neoadjuvant therapy in combination with adjuvant therapy (NATAT) (p=0.023) as well as between NAT and NATAT (p<0.001). Upon stratified by AJCC 8th TNM stage, the survival advantage associated with AT was exclusively observed in stage III and stage IV, barring the subgroup T4N0M0. We also discovered that patients with potentially resectable diseases in stage III (T1-3N2M0) might have better survival upon receiving NATAT than AT alone, and some patients with NATAT in stage IV exhibited comparable survival to their counterparts without metastasis.
Conclusion: In this retrospective cohort study, we demonstrated that patients harboring tumors in late TNM stages might benefit from supplementary AT in terms of survival, the NAT may be beneficial for resectable PDAC with more than 3 lymph nodes metastasis, and certain patients with M1 disease might still benefit from comprehensive systemic therapy and radical resection.
Bootstrap methods for bias correcting probability distribution parameters characterizing extreme snow accumulations
Authors: Pomeyie Kenneth , Bean Brennan
Published: November 2023

Accurately quantifying the threat of collapse due to the weight of settled snow on the roof of a structure is crucial for ensuring structural safety. This quantification relies upon direct measurements of the snow water equivalent (SWE) of settled snow, though most weather stations in the United States only measure snow depth. The absence of direct load measurements necessitates the use of modeled estimates of SWE, which often results in the underestimation of the scale/variance ($\sigma$) parameter of the distribution of annual maximum SWE. This paper introduces a novel bias correction method that employs a bootstrap technique with regression-based models to calibrate the variance parameter of the distribution. The efficacy of this approach is demonstrated on real and simulated datasets. The findings reveal varied levels of success, with the efficacy of the proposed approach being inherently dependent on the quality of the selected regression-based model. These findings demonstrate that integrating our approach with a suitable regression-based model is able to produce unbiased or nearly unbiased annual maximum SWE distribution parameters in the absence of direct SWE measurements.
Prevalence and Associated factors of common mental disorders among pregnant women in Northwest, Ethiopia: a cross- sectional study
Authors: Kurbi Helina Abebe , Abebe Solomon Mekonnen , Mengistu Netsanet Worku , Ayele Tadesse Awoke , Toni Alemayehu Teklu
Published: November 2023

Maternal mental health is a neglected but major global public health challenge, making a substantial contribution to maternal and infant morbidity and mortality. The purpose of this study was to assess the prevalence of common mental disorders and their determinants among pregnant women in the Northwest of Ethiopia. Data were collected from 872 pregnant women residing at the Dabat Demographic and Surveillance Site via an interviewer-administered, standardized questionnaire using an online data kit (ODK) during June–August 2022. A multivariate logistic regression analysis was conducted, and the odds ratio and 95% confidence interval were calculated. Common mental disorders among pregnant women were found to be 13.1% (95% CI: 10.9–15.6). Factors significantly associated with antenatal common mental disorders were marital status (being married, AOR = 2.01 95% CI: 110–3.69), residence (rural, AOR = 2.94 95% CI: 1.72–5.04), family history of common mental disorders (yes, AOR = 4.66 95% CI: 2.09–10.70), unplanned pregnancy (yes, AOR = 1.70 95% CI: 1.02–2.81), and intimate partner violence (yes, AOR = 2.43 95% CI: 1.59–3.73). Common mental disorders are common among pregnant women in the study area, and designing high-quality evidence and interventions that would address the aforementioned factors is vital for the mothers as well as the growth and development of the children.
Reliable detection of genetic alterations in cyst fluid DNA for the diagnosis of brain tumors
Authors: On Jotaro , Natsumeda Manabu , Takahashi Haruhiko , Koyama Akihide , Shibuma Satoshi , Watanabe Jun , Saito Shoji , Kanemaru Yu , Tsukamoto Yoshihiro , Okada Masayasu , Ogura Ryosuke , Eda Takeyoshi , Tada Mari , Shimizu Hiroshi , Adachi Jun-ichi , Mishima Kazuhiko , Nishikawa Ryo , Kakita Akiyoshi , Oishi Makoto
Published: November 2023

Purpose Liquid biopsy of cyst fluid in brain tumors has not been extensively studied to date. The present study was performed to see whether diagnostic genetic alterations found in brain tumor tissue DNA could also be detected in cell-free DNA (cfDNA) of cyst fluid in cystic brain tumors.Methods Cyst fluid was obtained from 17 patients undergoing surgery for a cystic brain tumor with confirmed genetic alterations in tumor DNA. Pathological diagnoses based on WHO 2021 classification and diagnostic alterations in the tumor DNA, such as IDH1 R132H and TERT promoter mutation for oligodendrogliomas, were detected by Sanger sequencing. The same alterations were analyzed by both droplet digital PCR (ddPCR) and Sanger sequencing in cyst fluid cfDNA.Results Twenty genetic alterations were found in 17 tumor samples. All (100%) alterations were detected in cyst fluid cfDNA by ddPCR. Sixteen of the 20 (80%) alterations were also detected by Sanger sequencing of cyst fluid cfDNA. Variant allele frequency (VAF) in cyst fluid cfDNA was comparable to that of tumor DNA (R = 0.67, Pearson’s correlation).Conclusion Cell-free DNA obtained from cyst fluid in cystic brain tumors is a reliable alternative to tumor DNA when diagnosing brain tumors.
WITHDRAWN: Ultrafast Picosecond Laser Spectroscopy and ICP-OES Assisted Calibration-free of Toxic Metal Concentrations in Contaminated Agricultural Soils
Authors: El-Saeed Mohamed , Tawfik Walid , Khalil Ahmed A. I. , Mubarak Manal , Fikry Mohamed
Published: November 2023

Excess fertilizer and chemical use have contaminated soil with harmful heavy metals near the Abu-Zaabal facility in Egypt. This study pioneers an approach using picosecond laser-induced plasma spectroscopy (Ps-LIPS) and inductively coupled plasma optical emission spectrometry (ICP-OES) to quantify toxic metal levels without calibration constraints. A 100 mJ Nd: YAG laser with 170 picosecond pulses has been employed for the Ps-LIPS. Systematic soil sampling at six sites near the facility enabled Ps-LIPS to formulate unrestricted calibration-free curves for lead, cadmium, cobalt, zinc, iron, and nickel. Applying the Boltzmann distribution and plot methods anchored to calcium spectral lines determined plasma electron density and temperature under local thermodynamic equilibrium. Models were validated against ICP-OES, affirming Ps-LIPS with under 8% average relative error. Results revealed notable concentration variations contingent on the metal, sampling site, and orientation to the facility. This pioneering Ps-LIPS study demonstrates precise quantification of toxic metals in soils without prior calibration. It provides a pragmatic tool for contamination assessment, representing a seminal advance in environmental analytical methodology.
Development of Reverse Transcription Loop Mediated Isothermal Amplification (RT-LAMP) for rapid detection of viruses infecting patchouli (Pogostemon cablin)
Authors: Bano Humaira , Khan Jawaid A.
Published: November 2023

Patchouli (Pogostemon cablin) a highly valued medicinal plant, suffers significant economic losses following infection with Broad bean wilt virus 2 (BBWV2) and Peanut stripe virus (PStV). In this study, a field-based isothermal technique called reverse transcription loop-mediated isothermal amplification (RT-LAMP) was established for an early and specific identification of BBWV2 and PStV. The oligo primers for RT-LAMP assay were designed from the conserved domains of the coat protein genes of PStV and BBWV2. The reaction temperature and time duration were optimised to 65 0C for 60 min, followed by incubation at 85 0C for 10 min in a water bath. The LAMP amplicons positive for PStV and BBWV2 revealed characteristic ladder-type bands when analysed through gel electrophoresis. Further, a colorimetric assay using a metal ion-based indicator (Hydroxy-napthol Blue, HNB) was conducted to visualize the amplified products with the naked eye, thus facilitating accessibility to field practices. The assays developed in this study were virus-specific as no cross-amplification occurred with other viruses, and were 100 times more sensitive than RT-PCR. Thus, the RT-LAMP assays established in this study are quick, reliable, and cost-effective for the accurate identification of BBWV2 and PStV. It will facilitate screening of patchouli planting materials. Thus, may reduce the risk of virus spread and could be helpful in phytosanitary programs.
Structural Aspects and Characterization of Synthesized Novel Schiff Base of 4- Hydroxybenzaldehyde with Anilines for Optoelectronic Properties
Authors: Prasanti M. , Jha Anjali , Kumar B. Rajesh , Ch RaviShankar Kumar
Published: November 2023

Optical materials and organic and nonlinear molecules are the leading materials that exhibit semiconducting properties that are useful for industrial purposes in terms of their optical and electronic properties. These active organic materials developed into films are of vital importance in terms of their molecular structure, molecular properties, and electronic and optical properties compared to inorganic materials. The present article focuses on the development of thin films with the synthesis of Schiff base of 4-hydroxy benzaldehydes and substituted anilines to obtain target compounds using the green synthesis method. The formation of the Schiff base compounds was confirmed by spectral methods, infrared spectroscopy, ultraviolet spectroscopy, and proton NMR. Powdered XRD provide useful information of structure, composition and crystalline proximity of the synthesized Schiff base compounds. The optical properties of the refractive index and dielectric constant were confirmed by spectroscopic ellipsometry studies. Computational studies were performed using the Gaussian 16 package with the B3LYP method basis set 6-311++** for all molecular compounds to confirm the molecular structures, optimized geometry, and electronic and optical properties.The insights of these properties are best visualized in terms of quantum mechanical descriptors that occur due to changes in electron density. Studies of these Schiff base compounds with nitro groups proved to exhibit optical properties and behave as excellent organic semiconducting materials with an energy gap of 3.08 eV ; refractive index of 2.074, and dielectric constant of 4.303.
Impact of research activity on performance of general practices: a qualitative study.
Authors: Kenning Cassandra , Usher-Smith Juliet A , Jamison James , Jones Jennifer , Boaz Annette , Little Paul , Mallen Christian , Bower Peter , Park Sophie
Published: November 2023

Background
There is evidence that engaging in research is directly associated with better performance. If this relationship is to be strengthened, it is necessary to understand the mechanisms which might underlie that relationship.
Aim
To explore the perspectives of staff and wider stakeholders about mechanisms by which research activity might impact on the performance of general practices.
Design & Setting
Qualitative study using semi-structured interviews with general practice professionals and wider stakeholders in England.
Method
Individual interviews with purposively sampled staff in ‘research ready’ or ‘research active’ general practices and other stakeholders. Interviews were analysed using a Framework approach.
Results
Participants described potential ‘direct’ and ‘indirect’ impacts on their work. ‘Direct’ impacts included research changing practice work (e.g. additional records searches for particular conditions), bringing in additional resources (e.g. access to investigations or staff) and improving relationships with patients. ‘Indirect’ impacts included job satisfaction (e.g. perception of practice as a centre of excellence and innovation, and the variety afforded by research activity reducing burnout) and staff recruitment (increasing the attractiveness of the practice as a place to work). Respondents identified few negative impacts.
Conclusions
Staff and stakeholders identified a range of potential impacts of research activity on practice performance, with impacts on their working lives most salient. Negative impacts were not generally raised. Nevertheless, respondents generally discussed potential impacts rather than providing specific examples of those impacts. This may reflect the type of research activity conducted in general practice, often led by external collaborators.
Inhibition of Bacterial Biofilm Formation on Ureteral Stent Surface by Jelleine-1 Hydrogel Coating Doped with Copper Nanoparticles
Authors: Hu ZhiXiong , Wang Xun , Shi Hong Lei
Published: November 2023

Aims: Ureteral stent is commonly used after urological surgeries. But, pathogenic bacteria can colonize the surface of the stent and gradually build a biofilm. Biofilms can not only promote the growth and reproduction of pathogenic bacteria, but alsoprotect them from adverse factors (e.g., physical or chemical factors), increasing the risk of urinary tract infections.
Material and methods: In this study, the natural antibacterial peptide Jelleine-1 was made into a hydrogel loaded with copper nanoparticles, which was coated with a dip-coating machine to obtain a novel type of antibacterial ureteral-coated stent.
Key Findings: Verified the feasibility of coating antibacterial peptides on in vivo stent, endowing them with specific biological activity.In vitro antibacterial experiments showed that the coated stent has good antibacterial activity and can inhibit the formation of biofilms. Furthermore, in vivo antibacterial experiments were performed in female rabbits. The results showed that the bacterial count was reduced by 83% compared to that in the uncoated group.
Significance: Our antibacterial ureteral coated stent significantly reduced the risk of stent-related urinary tract infections.
A Novel Image Restoration Solution for Cross-Resolution Person Re-Identification
Authors: Peng Houfu , Lu Xing , Xia Daoxun , Xie Xiaoyao
Published: November 2023

Cross-resolution person re-identification (CR-ReID) is a highly practical task that primarily addresses the image misalignment issue due to image resolution variations, which are caused by differences in the distances between cameras and camera performance variations. The existing cutting-edge approaches attempted to use super-resolution (SR) techniques to recover lost details in low-resolution (LR) images. However, the existing SR techniques focus on improving low-level semantic information metrics. Evaluation techniques for high-level semantic recognition tasks are not well suited for low-level image quality metrics. We propose a new framework called image feature restoration using a Swin transformer (IFRSW), which uses the feature difference between LR and high-resolution (HR) images as the supervisory signal to constrain the SR module. We further improved the Swin Transformer by introducing a new multiresolution feature fusion strategy, enhancing its ability to extract features from multiresolution images. Additionally, we introduce a pooling technique called "softpooling" to preserve more information during the feature downsampling process. Our method exhibits a noteworthy 4.2\% in rank-1 accuracy improvement on a challenging real LR dataset CAVIR, surpassing the current optimal approach. Our method achieves superior performance to the existing state-of-the-art(SOTA) methods.
Utilizing Tumor-Derived Extracellular Microvesicles for Kidney Regeneration
Authors: Seledtsova Galina V. , Seledtsov Victor I. , Dorzhieva Ayana B , Ivanova Irina P , Khabalova Tatiana S. , Blinova Elena A. , Darinskas Adas , Delwig Alexei A.
Published: November 2023

Background
A comparative study was conducted to assess the potential of extracellular microvesicles (MVs) derived from mesenchymal stem cells (MSCs) and tumor cells in kidney regeneration using an experimental murine model of chronic kidney injury (CKI).
Methods
MVs were obtained from MSCs, L929 sarcoma, LLC carcinoma, or B16 melanoma cells. These MVs were then administered intravenously to CBA mice with CKI. Renal excretory function was evaluated based on serum concentrations of creatinine and fatty acid binding protein-1. Morphological changes in the kidneys were assessed histologically. Flow cytometry analysis was utilized to characterize T cells in spleens and renal cell infiltrates.
Results
The study revealed that both MSCs and MSC-derived MVs (MSC-MVs), as well as tumor-derived MVs (T-MVs), regardless of their origin, exhibited a comparable ability to improve both excretory function and the histological structure of the damaged kidney. Both MSC-MVs and T-MVs reduced the proportion of pro-inflammatory CD4 + CD44 + T cells in renal cell infiltrates and spleens of CKI mice. Furthermore, the MVs studied increased the numbers of natural CD4 + CD25 + FoxP3 + regulatory T cells in the spleen but not in renal cell infiltrates.
Conclusions
These findings suggest that T-MVs, similar to MSC-MVs, possess a universal capacity to stimulate kidney tissue restoration and provide anti-inflammatory immunomodulation of the kidney milieu.