bluuebunny/crossref_metadata_2025 huggingface dataset:
Deregulation in adult IgA vasculitis skin as the basis for the discovery of novel serum biomarkers
Authors: Bajželj Matija , Hladnik Matjaž , Blagus Rok , Jurčić Vesna , Markež Ana , Toluay Tanya Deniz , Sodin-Šemrl Snežna , Hočevar Alojzija , Lakota Katja
Published: December 2023

Introduction
Immunoglobulin A vasculitis (IgAV) in adults has a variable disease course, with patients often developing gastrointestinal and renal involvement and thus contributing to higher mortality. Due to understudied molecular mechanisms in IgAV currently used biomarkers for IgAV visceral involvement are largely lacking. Our aim was to search for potential serum biomarkers based on the skin transcriptomic signature.
Methods
RNA sequencing analysis was conducted on skin biopsies collected from 6 treatment-naïve patients (3 skin only and 3 renal involvement) and 3 healthy controls (HC) to get insight into deregulated processes at the transcriptomic level. 15 analytes were selected and measured based on the transcriptome analysis (adiponectin, lipopolysaccharide binding protein (LBP), matrix metalloproteinase-1 (MMP1), C-C motif chemokine ligand (CCL) 19, kallikrein-5, CCL3, leptin, C-X-C motif chemokine ligand (CXCL) 5, osteopontin, interleukin (IL)-15, CXCL10, angiopoietin-like 4 (ANGPTL4), SERPIN A12/vaspin, IL-18 and fatty acid-binding protein 4 (FABP4)) in sera of 59 IgAV and 22 HC. Machine learning was used to assess the ability of the analytes to predict IgAV and its organ involvement.
Results
Based on the gene expression levels in the skin, we were able to differentiate between IgAV patients and HC using principal component analysis (PCA) and a sample-to-sample distance matrix. Differential expression analysis revealed 49 differentially expressed genes (DEGs) in all IgAV patient’s vs HC. Patients with renal involvement had more DEGs than patients with skin involvement only (507 vs 46 DEGs) as compared to HC, suggesting different skin signatures. Major dysregulated processes in patients with renal involvement were lipid metabolism, acute inflammatory response, and extracellular matrix (ECM)-related processes. 11 of 15 analytes selected based on affected processes in IgAV skin (osteopontin, LBP, ANGPTL4, IL-15, FABP4, CCL19, kallikrein-5, CCL3, leptin, IL-18 and MMP1) were significantly higher (p-adj < 0.05) in IgAV serum as compared to HC. Prediction models utilizing measured analytes showed high potential for predicting adult IgAV.
Conclusion
Skin transcriptomic data revealed deregulations in lipid metabolism and acute inflammatory response, reflected also in serum analyte measurements. LBP, among others, could serve as a potential biomarker of renal complications, while adiponectin and CXCL10 could indicate gastrointestinal involvement.
Urban Hybrid DEM Modeling Methodology Based on Multi-source Data
Authors: ZHANG Longqi , He Wenwen , Luo Yabo , Liu Xinliang
Published: December 2023

Building a high-resolution Digital Elevation Model (DEM) in urban areas has been a challenging task so far because of the complicated and trivial topographic character caused by dense buildings, dense artificial vegetation, such as deep manual intervention. The paper presents a heterogeneous urban DEM and modeling method based on a large-scale digital topographic map, Digital Surface Model (DSM) generated by popular UAV photogrammetry or laser radar point cloud data. The method is first to extract elevation points, contour lines, road edges, steep slopes, building outlines, retaining walls, steps, and such topographic linear elements as possible from a large-scale topographic map; then to merge elevation information from DEM, DSM, point clouds data to generate a series of 3d-lines or polygons with elevation; even to struct some necessary 3D auxiliary lines according to geometric features to some abrupt terrain features; finally to create a Triangulated Irregular Network (TIN), which is able to accurately represents the terrain, using constrained TIN create function of ArcGIS. And evaluation precision was not uniform in the data bound because of multi-source data with different precision, so it was called Heterogeneous DEM(HDEM). The experiment showed that the HDEM has high consistency with the topographic map and is more suitable for flood analysis, urban fine management, real three-dimensional construction, etc.
An augmented transformer model trained on family specific variant data leads to improved prediction of variants of uncertain significance
Authors: Joshi Dinesh , Pradhan Swatantra , Sajeed Rakshanda , Sriniva Rajgopal , Rana Sadhna
Published: December 2023

Variants of uncertain significance (VUS) represent variants that lack sufficient evidence to be confidently associated to a disease, thus posing a challenge in the interpretation of genetic testing results. In this work, we present an improved gene specific approach to variant prediction that leverages a pre-trained protein language model for predicting VUS. Our deep learning model combines zero-shot log odd scores from evolutionary scale model (ESM-2) as a feature along with embeddings from ESM-2 as features for training a supervised model on variants associated with the gene. Our training set creation approach uses variant data from a gene family if the gene of interest has low or no functional data for training a gene specific predictor. We demonstrated the accuracy of our method by testing it on VUS of an enzyme Alpha-N-acetylglucosaminidase (NAGLU) whose deficiency due to mutations is known to cause a rare genetic disorder, Mucopolysaccharidosis IIIB or Sanfillipo B disease. Our model augmented with contextual information from the gene family improved prediction of VUS in the NAGLUgene and outperformed state-of-the-art pathogenicity predictors. Our results also indicate that for genes with sparse or no experimental variant impact data, the family variant data can serve as proxy training data for making accurate predictions.
Discovery and Engineering of a Novel Peptide, Temporin-WY2, from Frog Skin Secretion, With Enhanced In Vitro and In Vivo Antimicrobial Efficacy against Multi-drug Resistant Bacteria
Authors: Zhou Xiaowei , Liao Fengting , Ye Zhuming , Cheng Jinsheng , Zhu Jianhua , Chen Xiaoling , Wang Tao , Jiang Yangyang , Ma Chengbang , Zhou Mei , Chen Tianbao , Shaw Chris , Wang Lei
Published: December 2023

Infections by drug-resistant microorganisms are a threat to global health and antimicrobial peptides are considered to be a new hope for their treatment. Temporin-WY2 was identified from the cutaneous secretion of the Ranidae frog, Amolops wuyiensis. It presented with a potent anti-Gram-positive bacterial efficacy, but its activity against Gram-negative bacteria and cancer cell lines was unremarkable. Also, it produced a relatively high lytic effect on horse erythrocytes. For further improvement of its functions, a perfect amphipathic analogue, QUB-1426, and two lysine-clustered analogues, 6K-WY2 and 6K-1426, were synthesised and investigated. The modified peptides were found to be between 8- to 64-fold more potent against Gram-negative bacteria than the original peptide. Additionally, the 6K analogues showed a rapid killing rate. Also, their antiproliferation activities were more than 100-fold more potent than the parent peptide. All of the peptides that were examined demonstrated considerable biofilm inhibition activity. Moreover, QUB-1426, 6K-WY2 and 6K-1426, demonstrated in vivo antimicrobial activity against MRSA and E. coli in an insect larvae model. Overall, QUB-1426, 6K-WY2 and 6K-1426, with dual antimicrobial and anticancer functions, are proposed as putative drug candidates for the future.
Total Knee Arthroplasty in Two Female Patients with Type 1 Diabetes- Associated Charcot Neuroarthropathy: Case Reports and a Review of the Literature Series
Authors: Lei Chao , Huang Wen-zhou , Mei Lin , Sun Kuo , Mao Xin-zhan
Published: December 2023

Charcot neuroarthropathy, a rare musculoskeletal disorder resulting from peripheral neuropathy.This systemic disease primarily affects the forefoot and ankle joints in diabetic patients, with type 1 diabetes cases being less frequent than type 2. The condition often leads to high disability and mortality rates due to delayed diagnosis and the absence of distinctive pathophysiological features. Knee joint Charcot neuroarthropathy, particularly in type 1 diabetes, is uncommonly reported due to the lack of standardized diagnostic and treatment protocols, notably in knee arthroplasty, which exhibits significant outcome variability. This article discusses two female type 1 diabetes patients with knee joint Charcot neuroarthropathy, characterized by poor blood sugar control, high blood glucose levels (over 20mmol/L), and elevated glycated hemoglobin. Both underwent total knee arthroplasty; one also received autologous bone grafting with titanium mesh screw fixation. The paper also reviews relevant literature.
Evaluating the influence of sarcopenia and myosteatosis on clinical outcomes in gastric cancer patients undergoing immune checkpoint inhibitor therapy
Authors: Deng Guiming , Song Haibin , Du Zhongze , Xue Yingwei , Li Yuanzhou , Song Hongjiang
Published: December 2023

Objective:The primary objective of this retrospective study was to assess the influence of sarcopenia and myosteatosis on clinical outcomes in patients with gastric cancer (GC) who underwent treatment with Immune Checkpoint Inhibitors (ICIs).
Methods:In this retrospective analysis, the study cohort comprised patients who had received immunotherapy for gastric cancer. Sarcopenia, evaluated at the L3 vertebral level, was determined based on pre-treatment CT scans using the Receiver Operating Characteristic (ROC) analysis to establish the optimal skeletal muscle index cut-off value. Myosteatosis was defined using the mean Skeletal Muscle Density (SMD), with a threshold value of <41 Hounsfield Units (HU) for patients with a Body Mass Index (BMI) < 25 kg/m² and <33 HU for patients with a BMI ≥ 25 kg/m². Statistical analyses, including the log-rank test and the Cox proportional hazard model, were employed to compare both Progression-Free Survival (PFS) and Overall Survival (OS). Nomograms predicting PFS and OS were developed based on the results of multivariate analyses.
Results: The study encompassed a total of 124 patients who had undergone ICIs for GC, among which 27.4% exhibited sarcopenia, and 29.8% displayed myosteatosis. Patients with sarcopenia or myosteatosis exhibited significantly reduced PFS and OS compared to those without these conditions. Furthermore, both sarcopenia and myosteatosis emerged as independent prognostic factors for PFS and OS in GC patients receiving ICIs. The prediction models for PFS and OS demonstrated C-indexes of 0.757 and 0.777, respectively.
Conclusion: The findings of this study affirm the utility of sarcopenia and myosteatosis as reliable biomarkers for forecasting clinical outcomes in patients with gastric cancer who are undergoing treatment with ICIs.
Dual strategy of La3+ doping and carbon coating enhancing the rate performance of NaTi2(PO4)3 anode materials
Authors: Liu Xiaojuan , Li Zhifeng , Zhong Xiaohui , Wang Chunxiang , Dmytro Sydorov
Published: December 2023

NaTi2(PO4)3 (NTP) is considered a promising anode material for sodium-ion batteries due to its open and stable framework structure. However, its poor conductivity prevents its direct application as an anode material. In this paper, a dual strategy of La3+ doping and carbon coating is proposed to improve the conductivity of NTP. The results show that the NTP-La0.06@C electrode doped with 6% La has excellent electrochemical performance, and the coulombic efficiency is up to 95.31% in the first cycle. The initial specific capacity is 103.05 mAh·g− 1 with a capacity retention of 97.30% after 1000 cycles at 10C rate. Even after 2000 cycles, there is still a specific capacity of 98.62 mAh·g− 1 with a capacity retention of 92.71%, and as well as the NTP-La0.06@C has a higher Na+-insert diffusion coefficient of 3.19×10− 11 cm2·s− 1 than the pristine NTP@C of 2.35×10− 11 cm2·s− 1 during charging. Therefore, the La3+ doping and carbon coating strategy shows great potential in improving the performance of NaTi2(PO4)3 anode materials.
Exploring the role of HOXB13, a regulator gene, in fatty acid metabolism and gastric epithelial cell intestinalization during Helicobacter pylori Infection: insights from single- cell RNA sequencing analysis
Authors: Chen Si-Hai , Qiu Jia-Yu , Peng Jian-Xiang , Hu Yi , Zhao Ru-Lin , Gong Xiao-Ling , Xie Jun , Li Nian-Shuang , Xie Yong
Published: December 2023

Background
To systematically identify the changes in epithelial cell types during the gastrointestinal epithelial transformation, further explore the dynamic changes of key transcription factors and metabolic pathways during the gastrointestinal metaplasia process, and investigate the specific role of Helicobacter pylori (H. pylori) in this process.
Methods
Based on an in-depth analysis of single cell sequencing data, we identified specific transcription factors involved in the gastric epithelial intestinalization process using SCENIC analysis and validated them through immunohistochemistry. Based on these findings, we further investigated the differentiation trajectory of gastric epithelial cells during metaplasia and examined changes in metabolic pathways throughout this process. Finally, we studied the impact of H. pylori infection on these specific transcription factors using PCR analysis and Western blotting.
Results:
During the process of intestinal metaplasia, we have confirmed that the proportion of pit mucous cells gradually decreases while the number of intestinal metaplasia cells increases. Through SCENIC analysis, we have identified HOXB13, HOXA10, and ONECUT2 as potential characteristic transcription factors in intestinal metaplasia cells. Additionally, immunohistochemistry validation has shown a significant increase in HOXB13 expression in intestinal metaplasia tissues compared to non-atrophic gastritis tissues. In the non-atrophic gastritis group, the expression of gastric tissue infected with H. pylori was higher than that of the non-infected group. Trajectory analysis has revealed that pathways related to lipid metabolism play important roles during the process of intestinal metaplasia. Furthermore, cell experiments have confirmed a significant upregulation of HOXB13 after H. pylori infection.
Conclusion
This single cell RNA sequencing analysis establishes a solid foundation for investigating the cellular types, key transcription factors, and metabolic pathways associated with gastrointestinal epithelial cell differentiation. Our findings indicate that HOXB13 plays a critical role as a transcription factor in gastrointestinal epithelial metaplasia. Additionally, we have observed that H. pylori infection enhances the expression of HOXB13, which subsequently impacts fatty acid metabolism in normal gastric mucosa through downstream target genes CEL and GPD1. As a result, HOXB13 emerges as a promising therapeutic target to address H. pylori-induced intestinal metaplasia and offers potential insights into the development of treatment strategies for this condition.
Mechanisms for carbon stock driving and scenario modeling in typical mountainous watersheds of northeastern China
Authors: zhang Jin , zhang wenguang , Zhang Xinyan , Li Yuhong , Feng Mingming , Qi Peng , Huang Yiqiang , Li Rui , Jiang Ming , Zou Yuanchun , Wu Yi
Published: December 2023

Watershed ecosystems play a pivotal role in maintaining the global carbon cycle and reducing global warming by serving as vital carbon reservoirs for sustainable ecosystem management. In this study, we based on the "quantity-mechanism-scenario" frameworks to evaluate carbon stocks in mid to high latitudes alpine watersheds in China and explored the mechanisms of climate change and land use influence on the ability of watershed ecosystems to store carbon. The results showed that the carbon stock of the watershed increased by about 15.9 Tg from 1980 to 2020. Vegetation, precipitation, land-use change, and economic production have the strongest explanatory power for carbon stocks. Under different climate scenarios, it was found that the SSP2-4.5 scenario had a significant rise in carbon stock from 2020 to 2050, roughly 24.1 Tg. This increase was primarily observed in the southeastern region of the basin, with forest and grassland effectively protected. Conversely, according to the SSP5-8.5 scenario, the carbon stock would decrease by about 50.53 Tg with the expansion of cultivated and construction land in the basin's southwest part. Therefore, given the vulnerability of mid to high latitudes mountain watersheds, global warming trends continue to pose a greater threat to carbon sequestration in watersheds. Our findings carry important implications for tackling potential ecological threats in mid to high latitudes watersheds in the Northern Hemisphere and assisting policymakers in creating carbon sequestration plans, as well as for reducing climate change.
Sentinel – 5P derived Tropospheric NO 2 Concentration during the COVID-19 Pandemic Lockdown: Impacts of Urbanisation and Industrialisation in South Tamil Nadu, India
Authors: Rose R. S. Suja , Ponnukalai Bhavya
Published: December 2023

In emerging nations, rising urbanisation exacerbates existing issues like pollution. The biophysical and social conditions of cities are negatively impacted by unplanned urbanisation and the increase in industrialisation. Power plants, industries and vehicles are the substantial birthplaces of air pollution. The first instance of COVID-19 was discovered in China, the government implemented a curfew from March 26, 2020, to May 31, 2020, as part of a national COVID-19 pandemic prevention strategy. In the state of Tamil Nadu, in particular urban areas like Madurai, Virudhunagar, Tirunelveli, especially Thoothukudi, is experiencing a problem with air pollution as a result of booming industrial activity as well as urbanization. The impact of the recent environmental contamination is evaluated by a comprehensive regional and temporal study and it is considered vital. The confinement and isolation measures implemented during the COVID-19 pandemic impacted NO2 concentrations in 11 cities of southern Tamil Nadu is analysed. The impact of urbanization and industrialization on local air quality was assessed during the period of lockdown. Using remote sensing techniques, the study quantified the changes in atmospheric pollutant NO2 concentrations and represented them spatiotemporally which was observed during these 4 periods. In the study area, a general decline in NO2 content is seen. A significant number of places in the eastern region exhibit an increase in NO2 concentration as a result of lockdown relaxations. Therefore, NO2 pollution can be controlled if enough effort is put into it.
Giant Kerr nonlinearity of terahertz waves mediated by stimulated phonon polaritons in a microcavity chip
Authors: Wu Qiang , Huang Yibo , Lu Yao , Li Wei , Xu Xitan , Jiang Xinda , Ma Ruobin , Chen Lu , Ruan Ningjuan , Xu Jingjun
Published: December 2023

Optical Kerr effect, in which input light intensity linearly alters the refractive index, has enabled the generation of optical solitons, supercontinuum spectra, and frequency combs, playing vital roles in the on-chip devices, fiber communications, and quantum manipulations. Especially, terahertz Kerr effect, featuring fascinating prospects in future high-rate computing, artificial intelligence, and cloud-based technologies, encounters a great challenge due to the rather low power density and feeble Kerr response. Here, we demonstrate a giant terahertz frequency Kerr nonlinearity mediated by stimulated phonon polaritons. Under the influences of the giant Kerr nonlinearity, the power-dependent refractive index change would result in a frequency shift in the microcavity, which was experimentally demonstrated via the measurement of the resonant mode of a chip-scale lithium niobate Fabry-Pérot microcavity. Attributed to the existence of stimulated phonon polaritons, the nonlinear coefficient extracted from the frequency shifts are orders of magnitude larger than that of visible and infrared light, which is also theoretically demonstrated by nonlinear Huang equations. This work opens an avenue for many rich and fruitful terahertz Kerr effect based physical, chemical, and biological systems that have terahertz fingerprints.
Study on risk factors of diabetic peripheral neuropathy and development of a prediction model based on machine learning
Authors: Cui Qiyuan , Wang Li , Wang Xiaoyan , Zheng Yun , Lin Jiaxi , Liu Lu , Zhu Jinzhou , He Mingqing
Published: December 2023

(1) Background: Diabetic peripheral neuropathy (DPN) stands as a prevalent complication in individuals with diabetes. This study aims to develop and validate a machine learning-based model to predict the probability of DPN in patients diagnosed with type 2 diabetes mellitus.
(2) Methods: We conducted a retrospective analysis of data pertaining to 628 patients with type 2 diabetes mellitus who received treatment at the First Affiliated Hospital of Soochow University between 2022 and 2023. This dataset encompassed medical histories, physical examinations, and results from biochemical index tests. The cohort was divided into training and validation datasets at an 8:2 ratio randomly. Feature selection, parameter optimization, and model construction were carried out within the training set, while the validation set was employed to assess the predictive performance of the models. We utilized machine learning algorithms such as Gradient Boosting Machines (GBM), Random Forest (RF), Support Vector Machines (SVM), Naïve Bayes, Decision Trees (DT) and traditional logistic regression (LR). The performance of these models was evaluated through the receiver operating characteristic (ROC) curve, calibration curve, and decision curve analysis (DCA). To interpret the best-performing model, we employed Shapley Additive exPlanation (SHAP) Plots and Local Interpretable Model Agnostic Explanations (LIME).
(3) Results: The dataset, comprising 628 individuals from the First Affiliated Hospital of Soochow University, yielded significant variables following selection by the Boruta algorithm and logistic multivariate regression analysis. These significant variables included Age, HOMA-IR, Duration of diabetes, and (blood urea nitrogen) BUN. The GBM model outperformed the other models, demonstrating an accuracy of 0.9316, an F1-score of 0.9385, and an AUC of 0.9294. The validation set cohorts was further subdivided within the study, indicating that the GBM model remained an effective classifier in different subgroups.
(4) Conclusions: The GBM model was composed of age, HOMA-IR, duration of diabetes and BUN may assist doctors with the early identification of DPN in patients with type 2 diabetes mellitus.
Augmentation of Anaerobic Pentose Phosphate Pathway Dysregulates Tetrahydrobiopterin Metabolism in Myalgic Encephalomyelitis/ Chronic Fatigue Syndrome (ME/CFS) Patients with Orthostatic Intolerance: A Pilot Study
Authors: Bulbule Sarojini , Gottschalk Carl Gunnar , Drosen Molly E , Peterson Daniel , Arnold Leggy A , Roy Avik
Published: December 2023

Tetrahydrobiopterin (BH4), an essential cofactor of amino acid metabolism, was found to be strongly elevated in ME/CFS patients with Orthostatic intolerance (ME + OI). However, the molecular mechanism of BH4 upregulation is poorly understood in ME + OI patients. Here, we report that the activation of the non-oxidative pentose phosphate pathway (PPP) plays a critical role in the biosynthesis of BH4 in ME + OI patients. Microarray-based gene screening followed by real-time PCR-based validation, ELISA assay, and finally enzyme kinetic studies of glucose-6-phosphate dehydrogenase (G6PDH), transaldolase (TALDO1), and transketolase (TK) enzymes revealed that the augmentation of anaerobic PPP is critical in the pathogenesis of ME + OI. Along with the upregulated anaerobic PPP enzymes, we observed that biopterin metabolites such as BH4 and dihydrobiopterin (BH2) are strongly upregulated suggesting the disruption of biopterin homeostasis in ME + OI patients. To explore the molecular role of anaerobic PPP in biopterin metabolism, we devised a novel cell culture strategy to induce non-oxidative PPP by treating human microglial cells with ribose-5-phosphate (R5P) under a hypoxic condition of 85%N2/10%CO2/5%O2 followed by the analysis of BH4 and BH2 upregulation via ELISA, immunoblot and dual immunocytochemical analyses. These results confirmed that the activation of non-oxidative PPP is indeed required for the upregulation of both BH4 and BH2. Moreover, the siRNA knocking down of the taldo1 gene strongly inhibited the expression of GTP cyclohydrolase 1 (GTPCH1) and subsequent production of BH4 and its metabolic conversion to BH2 in R5P-treated and hypoxia-induced C20 human microglia cells. To test the functional role of ME + OI plasma-derived biopterins, exogenously added plasma samples of ME + OI plasma with high BH4 upregulated inducible nitric oxide synthase (iNOS) and nitric oxide (NO) in human microglial cells indicating that the non-oxidative PPP-induced-biopterins could stimulate inflammatory response in ME + OI patients.
Optimization of in situ exopolysaccharides production by Lactobacillus helveticus MB2-1 in yogurt and its vitro functional characteristics
Authors: Ge Zhiwen , Wang Dan , Zhao Wenting , Wang Pan , Dong Mingsheng , Wang Junjuan , Zhao Yuanyuan , Zhao Xiaoyan
Published: December 2023

In order to improve the in situ exopolysaccharides (EPS) production of Lactobacillus helveticus MB2-1 in Sayram ketteki yogurt and explore its functional characteristics, the production optimization, rheology and microstructure of fermented yogurt, and emulsifying properties, antioxidant, antibiofilm activities of the in situ EPS were investigated. Based on the results of response surface methodology (RSM), the fermentation temperature 37℃, fermentation time 8.0 h and incubation amount 7.0% (w/w) was the optimum condition for L. helveticus MB2-1 growth and yogurt formation, and the obtained production of in situ EPS could be up to 340 mg/L. Under the optimized fermentation conditions, the rheology analysis illustrated that the Sayram ketteki yogurt fermented by L. helveticus MB2-1 formed better gel structure than the control yogurt. Besides, the in situ EPS presented fine emulsifying properties, which could be comparable to other biological emulsifiers. The in situ EPS exhibited potent antioxidant activities as well. Moreover, the antibiofilm activities of the in situ EPS on foodborne pathogens biofilm formation were obvious. Taken together, the results illustrated that the EPS produced in situ by L. helveticus MB2-1 in Sayram ketteki yogurt has the potentiality to be considered as a beneficial substitute for functional food products.
L. plantarum surface-displayed VP6 (PoRV) protein can prevent PoRV infection in piglets
Authors: Wang Junhong , Wang Haixu , Zhang Dongliang , Liu Fangyuan , Li Xiaoxu , Gao Ming , Cheng Mingyang , Bao Hongyu , Zhan Jiaxing , Zeng Yan , Wang Chunfeng , Cao Xin
Published: December 2023

Porcine rotavirus (PoRV) poses a threat to the development of animal husbandry and human health, leading to substantial economic losses. Among its components, VP6 protein constitutes a major portion of the viral particles and serves as the core structural protein of the virus. In this study, we first developed an antibiotics free and environmentally friendly vector called asd-araC-PBAD-alr (AAPA). Subsequently, we constructed recombinant Lactobacillus plantarum (L. plantarum) strains induced by arabinose to express VP6 and VP6-pFc fusion proteins. Our findings revealed that NC8/Δalr-pCXa-VP6-S and NC8/Δalr-pCXa-VP6-pFc-S strains were capable of enhancing body immunity and protecting suckling mice and piglets from rotavirus infection. The novel recombinant L. plantarum strains developed in this study hold promising potential as oral vaccines to enhance body immunity and present a new strategy for preventing PoRV infection.
T2DM/CKD genetic risk scores and the progression of diabetic kidney disease in T2DM subjects
Authors: Galuška David , Pácal Lukáš , Chalásová Katarína , Divácká Petra , Řehořová Jitka , Svojanovský Jan , Hubáček Jaroslav A. , Lánská Věra , Kaňková Kateřina
Published: December 2023

This study explored the predictive value of genetic risk scores (GRS) for diabetic kidney disease (DKD) progression, Major Cardiovascular Events (MCVE), and All-Cause Mortality (ACM) in type 2 diabetes mellitus (T2DM) patients. We assessed 30 T2DM and CKD GWAS-derived single nucleotide polymorphisms (SNPs) in 400 Central European patients. Our analysis showed significant correlations between age, diabetes duration, diastolic blood pressure, total cholesterol, and eGFR with DKD progression (P < 0.05). No individual SNP strongly correlated with DKD progression, although CERS2 and SHROOM3 were near significance. WSF1 was associated with MCVE (P = 0.029), and CANCAS1, CERS2, and C9 were linked to ACM (P < 0.02). GRS did not surpass traditional clinical factors in predicting DKD, MCVE, or ACM. The model combining genetic and clinical factors only slightly improved the area under the curve (AUC) compared to the clinical model alone of 0.582 (95% CI 0.487–0.676) and 0.645 (95% CI 0.556–0.735), respectively, but this was not statistically significant (P = 0.06). Our findings underscore the complexity of genetic predictors in DKD progression and their interaction with clinical factors. Despite the potential of personalized medicine using genetic markers, our results suggest that conventional clinical factors are still crucial in predicting DKD in the Czech T2DM population. GWAS-derived GRSs did not show enhanced predictive capacity over standard clinical factors in this group.
Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are robust to differential shedding
Authors: Beerenwinkel Niko , Dreifuss David , Huisman Jana , Rusch Johannes , Caduff Lea , Ganesanandamoorthy Pravin , Devaux Alexander , Gan Charles , Stadler Tanja , Kohn Tamar , Ort Christoph , Julian Timothy
Published: December 2023

The COVID-19 pandemic has accelerated the development and adoption of wastewater-based epidemiology. Wastewater samples can provide genomic information for detecting and assessing the spread of SARS-CoV-2 variants in communities and for estimating important epidemiological parameters such as the growth advantage of the variant. However, despite demonstrated successes, epidemiological data derived from wastewater suffers from potential biases. Of particular concern are differential shedding profiles that different variants of concern exhibit, because they can shift the relationship between viral loads in wastewater and prevalence estimates derived from clinical cases. Using mathematical modeling, simulations, and Swiss surveillance data, we demonstrate that this bias does not affect estimation of the growth advantage of the variant and has only a limited and transient impact on estimates of the effective reproduction number. Thus, population-level epidemiological parameters derived from wastewater maintain their advantages over traditional clinical-derived estimates, even in the presence of differential shedding among variants.
Relationships between prognosis and nutritional intake of Mycobacterium avium complex lung disease
Authors: Wakamatsu Kentaro , Nagata Nobuhiko , Honjo Satoshi , Kumazoe Hiroyuki , Hayashi Yuri , Katsuki Kouta , Hara Makiko , Nagaoka Aiko , Noda Naotaka , Kiyotani Ruriko , Fukui Izumi , Ose Mizuko , Ikematsu Yuki , Tatsuta Miyoko , Katahira Katsuyuki , Akasaki Takashi , Otsuka Junji , Maki Sanae , Izumi Miiru , Kawasaki Masayuki , Harada Yasuko
Published: December 2023

Objective Previous studies on prognostic factors in Mycobacterium avium complex (MAC) lung disease have consistently shown that nutritional status, specifically, low BMI, is a poor prognostic factor. However, there has been no study focusing on nutritional intake, and while several studies on prognosis have been published, none are prospective in design. This study aimed to prospectively examine relationships between prognosis and nutritional status and nutritional intake in patients with MAC lung disease.Patients and methods : This study included 174 outpatients and inpatients with MAC lung disease who were registered in our hospital between May 2010 and June 2016. At registration, sex, age, comorbidities, disease duration, bacterial strains, number of segments involved, disease type, treatment (with or without), nutritional status (body mass index [BMI]), waist circumference, lymphocyte count, serum albumin, serum cholinesterase, serum transferrin, total cholesterol, visceral fat area as assessed by abdominal CT, and nutritional intake were investigated, and their associations with all-cause mortality and disease-specific mortality risks were prospectively analyzed using Cox proportional hazard models.Results Older age, comorbidities, a large number of segments involved, fibrocavitary disease, low BMI, and low energy intake at registration were associated with all-cause mortality risk, whereas older age, a large number of segments involved, and low energy intake at registration were associated with disease-specific mortality risk.Conclusion Patients with MAC lung disease are characterized by low nutrient intake. It was suggested that low energy intake may be a risk factor for both all-cause and disease-specific deaths.Trial registration: This study was approved by the Ethics Committee of the National Hospital Organization Omuta Hospital (IRB approval number: 29 − 13). This study can be accessed via https://omuta.hosp.go.jp/profession/ethics_29.html
Analysis and Predictive Modeling of Perioperative Fever in Elderly Patients Undergoing Total Hip Arthroplasty for Femoral Neck Fractures
Authors: Yin Junxiang , Chen Xiangyu , Xu Kuixin , Qin Luyue , Yan Lianqi
Published: December 2023

Objective: To investigate the risk factors for perioperative fever in elderly patients undergoing primary total hip arthroplasty (THA) due to femoral neck fractures and establish a predictive model, providing insights for clinical practice.Methods: A retrospective study was conducted, collecting data from elderly patients (>60 years) who underwent unilateral primary hip arthroplasty for femoral neck fractures at the Northern People's Hospital of Jiangsu Province from January 2016 to January 2022. A total of 286 femoral neck fracture patients were selected after screening, including 190 without fever and 96 with fever. General information, including age, gender, body mass index (BMI), preoperative comorbidities (hypertension, diabetes, coronary heart disease), hospitalization duration, preoperative use of non-steroidal anti-inflammatory drugs, preoperative levels of white blood cells, neutrophils, hemoglobin, procalcitonin (PCT), erythrocyte sedimentation rate, albumin, and D-dimer, anesthesia method, operation duration, intraoperative blood loss, postoperative transfusion, and postoperative levels of white blood cells, neutrophils, hemoglobin, PCT, erythrocyte sedimentation rate, Alb, and D-dimer were collected for both groups. Multiple logistic regression analysis was performed to identify risk factors for postoperative fever after total hip arthroplasty, and the clinical predictive model's value was evaluated using the ROC curve.Results: The multiple logistic regression analysis revealed that anesthesia method, operation duration, intraoperative blood loss, postoperative PCT, and transfusion were risk factors for postoperative fever after total hip arthroplasty, while postoperative albumin level acted as a protective factor. A predictive model was constructed, and the ROC curve was plotted, with an AUC of 0.855 (sensitivity 0.847, specificity 0.708).Conclusion: The clinical predictive model based on postoperative albumin, anesthesia method, operation duration, intraoperative blood loss, postoperative PCT, and transfusion demonstrates excellent predictive value for the occurrence of postoperative fever after total hip arthroplasty.
Exploring the usefulness of the INLA model in predicting levels of crimes in the City of Johannesburg, South Africa
Authors: Coleman Toshka , Mokilane Paul , Holloway Jenny , Botha Nicolene , Koen Renee , Rangata Mapitsi , Dudeni-Tlhone Nontembeko
Published: December 2023

Crime prediction serves as a valuable tool for deriving insightful information that can inform policy decisions at both operational and strategic tiers. This information can be used to optimize resource allocation and personnel management for crime prevention. Traditionally, the Poisson model has been the widely used model for crime prediction. However, recent statistical advancements introduce Integrated Nested Laplace Approximations (INLA) as a promising alternative for spatial and temporal data analysis. This study focusses on crime prediction using the INLA model. Specifically, the first-order autoregressive model under the INLA modelling framework is employed on longitudinal data for crime predictions in different regions of the City of Johannesburg, South Africa. The model parameters and hyperparameters considering space and time are estimated through the INLA model. In this work, the suitability and performance of the INLA model for crime prediction is assessed, which effectively captures spatial and temporal patterns. This study contributes to research by first introducing a novel approach for South African crime prediction, secondly developing a model using no demographic information other than clustering attributes as an exogenous variable, thirdly quantifying prediction uncertainty, and finally addressing data scarcity through demonstrating how INLA can provide reliable crime predictions, where conventional methods are limited. Based on our findings, the INLA model accurately ranked areas by crime levels, achieving a 29% Mean Absolute Percentage Error (MAPE) and 0.8 R-Squared value for crime predictions.
Design and Failure Stress Analysis of Crane Hook by Using Mesh Sensitivity Analysis Approach on Finite Element Method
Authors: Zeleke Zablon , Tamiru Tesfaye , Ashuro Belachew , Bogale Dilnesaw
Published: December 2023

In realistic applications, crane hooks are used mostly under high loading conditions and subjected to high-stress concentrations which cause failure of these material handling equipment. Failure mainly occurs due to high-stress concentration on the hook at a specific point. Determining these maximum stress concentrations that cause failure and the point where they occur is vital in reducing the failure of hooks. Therefore, FEM analyses are useful for obtaining an understanding of stress concentration on hooks that lead to failure. In this study, both analytical and numerical analyses were performed on the hook which is subjected to a vertical load of 50ton (490.5kN) for specifically selected hook material. The maximum stress resulting from analytical calculations is 1410.1MPa, which is safe as compared to the yield strength of hook material. The maximum Von Mises stress, maximum principal strain, and total deformation of hook were determined by numerical method. To produce more reliable results numerically on ANSYS Workbench 19.2 mesh sensitivity analysis (MSA) was performed. The meshing size dependence of maximum stress was studied by refinement of meshes. From the convergence study, the maximum failure stress determined is 1412.4MPa, which is also safe as compared to the yield strength of the material. Even if there are some variations in the results of analytical and numerical approaches, both results are safe for the loading condition of the crane hook.
Risk, predictive factors and Nomogram of liver metastatic gastroesophageal junction cancer: A new study based on SEER Database
Authors: Tian chenrui , Li yang , Li Min
Published: December 2023

Purpose of the study:
Liver metastases were common in gastroesophageal junction cancer (GEJ) patients with poor prognosis. Using the Surveillance, Epidemiology, and End Results (SEER) database, the present study investigated the incidence, risk, and prognostic factors of liver metastases in GEJ patients diagnosed between 2010 and 2019 from the SEER database.
Study design:
The univariable and multivariable logistic and Cox regression models were used to investigate the risk factors for liver metastase development and prognosis, respectively. The liver metastases predicting nomograms were constructed, evaluated. The overall survival (OS) of patients with liver metastases was analyzed by the Kaplan–Meier method.
Results
Finally, a total of 8,197 eligible GEJ cancer patients were included and 1,558 of them were diagnosed with liver metastases. The median survival of the liver metastatic GEJ cancer patients was about 5 months. Age, TN stage, surgery, radiation, and regional lymph node dissection were significantly associated with liver metastases occurrence. The calibration curve and C-index exhibited good performance of the nomograms for predicting GEJ cancer patients.
Conclusions
The nomograms were expected to be effective tools for predicting the risk of liver metastases for GEJ cancer patients which may benefit clinical decision-making.
Word Count:
Liver metastases in GEJ tumors may remain asymptomatic in the early stages. Timely recognition of these symptoms is vital for early intervention. The three-year prognosis for gastroesophageal junction cancer with liver metastasis is unfavorable, and the associated risks warrant further investigation. In this study, our risk and prognosis model for predicting GEJ tumors with liver metastasis is anticipated to serve as an effective tool.
Hierarchical Chitosan/Carbon Composites for Enhancing Electricity Generation Performance of Geobacter sulfurreducens
Authors: Gao Sheng-Chao , Zhou Wen , Mai Ting-fang , Zhang Yue , Li Yuxuan , Gao Tian-peng , Liu Ying
Published: December 2023

Two types of chitosan/carbon composites including chitosan/carbon nanotubes (CS/CNTs) and chitosan/carbon black (CS/CB) were utilized to modify graphite electrode for the electrochemically active biofilm (EAB) growth of Geobacter sulfurreducens. The hierarchically novel carbon composites modified electrodes have been obtained via facile vacuum freeze-drying. CS/CNTs (5 h) showed porous structure and CS/CB (5 h) exhibited the lamellar structure. Compared with the control, the maximum current densities of EAB growth on the CS/CNTs (5 h) increased by 135%, CS/CNTs (10 h) with longer time only increased by 56%. Unexpectedly, the EAB growth on CS/CB (5 h) modified electrode showed relatively better performance than that of CS/CNTs (5 h) increasing by 16.7%. In addition, CS/CB (10 h) modified electrode increased by 48.9% comparing with CS/CNTs (10 h). It can be seen that the CS/CB with 5 h freeze-drying possessed a better characteristic structure for promoting EAB growth and enhancing performance.
Design for Assembly & Armoring (DfA2) Methodology for Passenger Vehicle Protection Operations – Case Study Applied to a Front Door Assembled
Authors: Candido Guido Muzio , Kaminski Paulo Carlos
Published: December 2023

The personnel protection market of civilian armored vehicles (CAVs) continually grows in emerging countries. Therefore, this article proposes a Design for Assembly and Armoring, DfA2 methodology for the lightweight ballistic protection operations of CAVs based on real practical situations showing the main difficulties and best practices of current armoring operating conditions. A bibliographic review focused on Design for Excellence (DfX) and automotive and ballistic protection design criteria were performed to introduce the base of the DfA2 proposal and apply it to a front door assembly case study, including CAD/CAE interface analysis. The authors presented the detailed armoring flow of the front door system using the DfA2 method. In addition, strategical cross sections showed critical areas of the referred assembly. The opaque and transparent armor parts installed comply with the NIJ-IIIA ballistic protection level. The DfA2 method provided meaningful automotive and ballistic considerations to integrate protection parts in the front door system. In addition, it proposed to conduct and spread the best practices for operation guidelines and procedure standards related to CAVs on shop floors. Furthermore, the DfA2 methodology intends to preserve the original functionalities and guarantees automobiles for consumers. The article integrates the practical operations of armoring companies with DfX tools and automotive and ballistic guidelines, all of which are incorporated in the DfA2.
An Adaptive Ensemble YOLOX Model with Roulette-based Re-sampling Strategy for Traffic Sign Detection and Recognition
Authors: Hu Rong , Zhang Ming , Chen Dequ , Xu Yong
Published: December 2023

As one of the key technologies for autonomous driving, traffic sign detection and recognition (TSDR) remains a challenging task due to the difficulty and complexity of traffic signs. Moreover, real-world traffic signs exhibit a long-tailed distribution (i.e., data for most categories are scarce while others are abundant), which has negative impact on the detection model. In this paper, we propose a novel model to tackle these challenging problems. Two adaptive copy-paste methods are proposed for the long-tailed data problem to expand the tail categories efficiently. To detect difficult traffic signs, we propose roulette-based re-sampling to emphasis on data of difficult categories. Furthermore, an adaptive ensemble YOLOX model with double-level head is proposed which adaptively assembles hierarchical head that emphasizes features at different levels by learning the feature representation of level-aware traffic signs. An adaptive class box fusion module is utilized to further improve the ensemble efficiency. Extensive experiments on TT100K and Comprehensive TT100K datasets show that the method proposed in this paper achieves significant improvements in both difficult traffic signs and alleviates long-tailed data problems. It can effectively improve the miss-detection problem of difficult traffic signs and meet the TSDR requirements of real-time and high accuracy.