bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the Impact of Taurine on the Biochemical Properties of Urate Oxidase: Response Surface Methodology and Molecular Dynamics Simulation
Authors: Shahmoradi Parisa , Zaboli Maryam , Torkzadeh-Mahani Masoud 
Published: October 2023

Abstract
This paper investigates the impact of taurine as an additive on the structural and functional stability of urate oxidase. First, the effect of the processing parameters for the stabilization of Urate Oxidase (UOX) using taurine was examined using the response surface methodology (RSM) and the central composite design (CCD) model. The maximum stabilization of UOX with taurine was examined under various experimental conditions, including taurine concentration, temperature, and incubation time. Also, the study examines thermodynamic and kinetic parameters as well as structural changes, including intrinsic and ANS fluorescence, of urate oxidase with and without taurine. The results indicate that taurine treatment enhances the thermostability of uricase, with a longer half-life (135.91 min) compared to untreated urate oxidase (38.08 min) at 40°C. Thermo-inactivation experiments conducted at 40, 55, and 60°C demonstrate that the taurine-treated uricase has lower inactivation rate constants (Kinact) than untreated uricase. The examination of the inactivation process reveals that the increased thermostability of UOX-Taurine can be attributed to elevated activation energy (Ea) as well as greater values of ΔG# and ΔH# at a specific temperature. Furthermore, molecular dynamics simulation is conducted in order to get insights into the alterations in the structure of urate oxidase in the absence and presence of taurine under optimal conditions.
Using camera traps to estimate habitat preferences and occupancy patterns of vertebrates in boreal wetlands
Authors: Feldman Mariano , Mazerolle Marc , Imbeau Louis , Fenton Nicole 
Published: October 2023

Abstract
Wetlands are a critical habitat for boreal mammals and birds that rely on them for breeding, foraging, and resting. However, wetlands in boreal regions are under increasing natural and human pressure, leading to a reduction in habitat availability for these species. To inform management and conservation of wildlife, camera traps can help investigate habitat preferences. We aimed to evaluate the effect of habitat features on the occupancy of mammals and birds in boreal wetlands, namely beaver ponds and peatland ponds. We used a multispecies occupancy model to estimate the habitat associations of 11 mammals and 45 avian species detected at 50 ponds during the summers of 2018 and 2019 in Northern Quebec. The patterns of habitat response do not lend support to the hypothesis that beaver ponds host higher levels of occupancy of birds and mammals than peatland ponds. Our results suggest that certain mammals, such as Red Fox (Vulpes vulpes) and River Otters (Lontra canadensis), and birds including the American Pipit (Anthus rubescens), Common Raven (Corvus corax), Hooded Merganser (Lophodytes cucullatus), and Greater Yellowlegs (Tringa melanoleuca) preferred peatland ponds, whereas the Common Grackle (Quiscalus quiscula) preferred beaver ponds. We found a few effects of distance to roads, but no effect of amount of forest cover on species occupancy. The occupancy of 27% of mammals and 24% of birds decreased with increasing latitude. These findings offer valuable insights for the preservation of different wetland types and their associated wildlife communities.
A comparison of different dosing regimen of intravenous paracetamol for hemodynamically significant patent ductus arteriosus closure in premature neonates &lt; 32 weeks: a prospective observational study
Authors: Goyal Nikita , Haribalakrishna Anitha , Krishnamurthy Bhaskar 
Published: October 2023

Abstract
Objectives
To compare the efficacy of low vs conventional dose intravenous paracetamol in closure of hemodynamically significant patent ductus arteriosus.
Study design:
Preterm infants (< 32 weeks gestation) having echocardiographic evidence of hsPDA were given intravenous paracetamol at low dose (15mg/kg followed by 7.5 mg/kg 6 hourly) vs conventional dose (15 mg/kg 6 hourly) for five days.
Results
56 infants (28 in each group) were enrolled. Ductal closure was achieved in 96% infants in the low dose group and 100% infants in the conventional group (p = 1.00). Secondary outcomes including ductal reopening, need for second course of medical treatment, duration of hospital stay, cumulative oxygen requirement, mortality and other morbidities were comparable in both the groups. Mean paracetamol levels in both the groups were comparable (P = 0.67).
Conclusion
Low dose paracetamol was found to be equally effective compared to conventional dose paracetamol in closure of hsPDA.
Ultrastructural localization and characterization of P. gingivalis gingipain virulence factors in the substantia nigra of brains with and without Parkinson’s disease
Authors: Ermini Florian , Low Victoria F. , Song Jennifer J. , Tan Adelie Y.S. , Faull Richard L.M. , Dragunow Mike , Curtis Maurice A. , Dominy Stephen S. 
Published: October 2023

Abstract

Gingipains are protease virulence factors produced by Porphyromonas gingivalis, a Gram-negative bacterium best known for its role in chronic periodontitis. Gingipains were recently identified in the middle temporal gyrus of postmortem Alzheimer’s disease (AD) brains, where gingipain load correlated with AD diagnosis and tau and ubiquitin pathology. Since AD and Parkinson’s disease (PD) share some overlapping pathologic features, including nigral pathology and Lewy bodies, the current study explored whether gingipains are present in the substantia nigra pars compacta of PD brains. In immunohistochemical techniques and multi-channel fluorescence studies, gingipain antigens were abundant in dopaminergic neurons in the substantia nigra of both PD and neurologically normal control brains. 3-dimensional reconstructions of Lewy body containing neurons revealed that gingipains associated with the periphery of alpha-synuclein aggregates but were occasionally observed inside aggregates. In vitro proteomic analysis demonstrated that recombinant alpha-synuclein is cleaved by lysine-gingipain, generating multiple alpha-synuclein fragments including the non-amyloid component fragments. Immunogold electron microscopy with co-labeling of gingipains and alpha-synuclein confirmed the occasional colocalization of gingipains with phosphorylated (pSER129) alpha-synuclein. In dopaminergic neurons, gingipains localized to the perinuclear cytoplasm, neuromelanin, mitochondria, and nucleus. These data suggest that gingipains may accumulate in dopaminergic neurons in the substantia nigra and interact with alpha-synuclein.
Dietary E. coli promotes age-dependent chemotaxis decline in C. elegans
Authors: Noma Kentaro , Suryawinata Nadia , Yokosawa Rikuou , Tan Ke Hui Cassandra , Lai Alison Lok , Mori Ikue , Sone Ryusei 
Published: October 2023

Abstract
An animal’s ability to sense odors declines during aging, and its olfactory drive is tuned by internal states such as satiety. However, whether internal states modulate an age-dependent decline in odor sensation is unknown. To address this issue, we utilized the nematode Caenorhabditis elegans and compared their chemotaxis abilities toward attractive odorants when aged under different dietary conditions. Feeding with the standard laboratory diet, Escherichia coli attenuated the chemotaxis ability toward diacetyl, isoamyl alcohol, and benzaldehyde when aged. On the other hand, feeding with either the lactic acid bacteria Lactobacillus reuteri or food deprivation selectively maintained the chemotaxis ability toward diacetyl. Our results suggest that ingestion of E. coli causes age-dependent chemotaxis decline. The changes in chemotaxis behavior are attributed to the different expression of diacetyl receptor odr-10, and chemotaxis behavior of aged animals under food deprivation is shown to be dependent on daf-16. Our study demonstrates the molecular mechanism of how diet shapes the trajectory of age-dependent decline in chemosensory behaviors.
Seepage Characteristics and Stability Analysis of Bedding Slope Under Rainfall
Authors: Xu Fan , Liu Baohua , Liu Hongwei , Hu Huihua , Lin Hang 
Published: October 2023

Abstract
The soft interlayer and rock structure play a significant role in controlling the deformation of the bedding slope, while previous studies seldom consider the phenomenon of sudden change of local response in these key parts under rainfall conditions, and it is not clear about the mechanism of rainfall infiltration and damage mechanism of such slopes. In this paper, a large red-layered flat-dipping bedding landslide was selected as the research object, and numerical calculations based on the van Genuchten model for saturated-unsaturated flow were performed. The hydrological response and distribution patterns of pore water pressure and water content within the slope during rainfall were studied, stability analysis was performed based on the seepage field results, and the landslide evolution process was simulated and reproduced. The results showed that rainfall infiltration produces local saturated areas and forms stagnant layers on the rock layers in the slope, and the thickness and range gradually extend to the vicinity of the weak interlayer. Moreover, slope stability is affected by rainfall infiltration, and the transient safety factor gradually decreases with rainfall. According to the macroscopic deformation process of the slope model, three stages of instability and failure of rainfall-induced red-layered bedding slopes are generalized: slight uplift stage, strong uplift stage, and sliding-bending failure stage. The results of the study can provide a theoretical basis for the study of seepage, destabilization mechanism and stability evaluation of bedding slopes.
Risk factors for antimicrobial use in pig farms: a cross-sectional study in the Netherlands
Authors: Mallioris Panagiotis , Luiken Roosmarijn E.C. , Tobias Tijs , Vonk John , Wagenaar Jaap A. , Stegeman Arjan , Mughini-Gras Lapo 
Published: October 2023

Abstract

Background
Antimicrobial use (AMU) has decreased by 63% in Dutch pig farms since 2009. However, this decrease has stagnated in recent years. The problem mainly pertains to weaners, which have a six-fold higher AMU compared to sows/suckling piglets and fatteners. The aim of this study was to identify farm-level characteristics associated with i) total AMU among weaners, sows/sucklings and fatteners and ii) use of specific antimicrobial classes in the former two age groups.
Methods
In 2020, data from 154 Dutch pig farms were collected and analyzed in a cross-sectional study. These data included information on AMU and farm characteristics, focusing on weaners. A mixed-effects conditional Random Forest analysis was applied to select the subset of farm characteristics that was best associated with AMU.
Results
Overall, the main risk factors for total AMU in weaners were vaccination for PRRS vaccination in sucklings, being a conventional (vs organic or “The Better Life label”) farm, high within-farm pig density and early weaning. The largest protective effects for total AMU for sows/sucklings were E. coli vaccination of sows and having a search boar from own production. Regarding the other outcomes of those two age groups several risk factors overlapped such as farmer’s non-tertiary education, not having free-sow systems during lactation and conventional farming while another risk factor of interest for weaners were having fully slatted floors. In fatteners, the highest risk for their AMU was PRRS vaccination of sucklings.
Conclusions
Several on-farm characteristics associated with AMU in Dutch pig farms were identified. Some have been found elsewhere too, but others were novel, such as farmer’s education, lower pig aggression and free-sow systems, which were associated with decreased AMU. Certain farm practices can reduce structurally the need for AMU, as their effect is mediated through improvement of environmental conditions, biosecurity and animal welfare mitigating as such the risks of disease and stress in animals.
Natural and hybrid immunity after SARS-CoV-2 infection in children and adolescents
Authors: Rothoeft Tobias , Maier Christoph , Talarico Adriana , Hoffmann Anna , Schlegtendal Anne , Lange Berit , Petersmann Astrid , Denz Robin , Timmesfeld Nina , Toepfner Nicole , Vidal-Blanco Elena , Pfaender Stephanie , Lücke Thomas , Brinkmann Folke 
Published: October 2023

Abstract
Purpose The immune protection in children and adolescents with natural or hybrid immunity (vaccination & infection) against SARS-CoV-2 remains an understudied field. Aim of this study was to analyze different immune compartments in different age groups and whether humoral immune reactions correlate with a cellular immune response.Methods 72 children and adolescents with a preceding SARS-CoV-2 infection were recruited. 37 were vaccinated with an RNA-vaccine (BNT162b2). Humoral immunity was analyzed 3 to 26 months (median 10 months) after infection by measuring Spike protein (S), nucleocapsid (NCP) and neutralizing antibodies (nAB). Cellular immunity was analyzed using a SARS-CoV-2 specific interferon-γ release assay (IGRA).Results All children and adolescents had S antibodies; titers were higher in those with hybrid immunity (14900 BAU/ml vs. 2118 BAU/ml). NCP antibodies were detectable in > 90%. Neutralizing antibodies (nAB) were more frequently detected (90%) with higher titers (1914 RLU) in adolescents with hybrid immunity than in children with natural immunity (62,5%, 476 RLU). Children with natural immunity were less likely to have reactive IGRAs (43,8%) than adolescents with hybrid immunity (85%). The amount of interferon-γ released by T cells was comparable in natural and hybrid immunity.Conclusion Spike antibodies are the most reliable markers to monitor an immune reaction against SARS-CoV-2. High antibody titers of Spike antibodies and nAB correlated with cellular immunity, a phenomenon found only in adolescents with hybrid immunity. Hybrid immunity is associated with markedly higher antibody titers (S and nAB) and a higher probability of a cellular immune response than a natural immunity.
Evaluation of Neuromuscular Morphometry of the Vaginal Wall Using Protein Gene Product 9.5 (Pgp 9.5) and Smooth Muscle α-Actin (Sma) in Patients with Posterior Vaginal Wall Prolapse
Authors: ÇETİN MUSTAFA , birge özer , güney güven , arslan emine 
Published: October 2023

Abstract
Objective: This study aims to compare the neuromuscular structure of the vagina in women with posterior vaginal wall prolapse with women without prolapse, to determine any differences, and to show the role of neuromuscular structure in the physiopathology of prolapse.
Materials and Methods: In this prospective study, women aged between 40 and 75 years without any vaginal surgery history and without any abdominal prolapse surgery history were included. The study group included 31 women diagnosed with rectocele on examination, and the control group included 31women who underwent vaginal intervention and hysterectomy for conditions other than rectocele (colposcopy, conization, etc.) without anterior or posterior wall prolapse. Biopsy material was obtained from the epithelium of the posterior wall of the vagina, including the fascia that fits the Ap point. Immunohistochemical staining with Protein Gene Product 9.5 and smooth muscle α-actin was performed in the pathology laboratory. The epithelial thickness measurement and smooth muscle density parameters obtained with these immunohistochemical staining were compared between the two groups. The collected data were analyzed using SPSS 23 package program. P values less than 0.05 were considered statistically significant.
Findings: In the control group, muscle thickness and the number of nerves per mm2 of fascia were statistically significantly higher than in the study group (P<0.05).
Conclusion: We found that smooth muscle tissue and the number of nerves per mm2 of fascia were lower in posterior vaginal wall prolapse compared to the general population. Based on the correlation coefficients, age was the parameter that most affected the degree of prolapse, followed by the parity, the number of live births, and the number of vaginal deliveries.
Bioinformatics analyses of NET-related hub genes in chronic obstructive pulmonary disease and their association with immune infiltration
Authors: Xu Yanxin , Qiang Lixia , Wu Feiyan , Liu Yuanyuan , Jin Shoude 
Published: October 2023

Abstract
The early diagnosis of chronic obstructive pulmonary disease (COPD), a chronic inflammatory disease, remains challenging. Immune metabolism plays a crucial role in COPD pathogenesis, with neutrophils playing a key role. Although neutrophil extracellular traps (NETs) play a crucial function in preventing infection, irregular and excessive NETs creation can cause COPD to appear and progress. There is still confusion over the precise mechanism, thus more research is required. Herein, we aimed to determine the correlation and diagnostic markers of neutrophil extracellular trap (NET) genes that contribute to immunoinfiltration in COPD. The comprehensive gene expression dataset GSE76925 in the Gene Expression Omnibus database was subjected to differential gene expression analysis. In total, 558 differentially expressed genes were identified, which were then subjected to gene set enrichment analysis. Additionally, the correlation between their expression and immune infiltration was analyzed, and then validated by cluster analysis. Furthermore, 30 differentially expressed NET-related genes were identified and used to construct diagnostic and risk prediction models by random forest and Least absolute shrinkage and selection operator regression analysis. Seven key genes, namely CLEC6A, CTSG, ENTPD4, IRAK4, MAPK1, PIK3CA, and SELPLG, were identified The diagnostic model was validated by generating a receiver operating characteristic curve (ROC) using the GSE38974 dataset. The results revealed that the model exhibited high discrimination ability. Additionally, the models exhibited high diagnostic and risk prediction abilities for COPD. Analysis of single-cell sequencing data from the GSE128033 and GSE163295 datasets revealed that the seven key genes are highly expressed in COPD. Notably, SELPLG and MAPK1 are primarily expressed in monocytes and T cells. Additionally, the genes TLR4, CTSG, IRAK4, SELP, ELPLG, and MAPK1 were revealed to be involved in the pathogenesis of COPD through immune infiltration that leads to NETs. The purpose of this study is to determine the hub genes related to NETs and their association with immune cell infiltration in COPD lung tissue, and provides potential targets for the treatment of COPD.
Accumulation mechanism of metabolites markers identified by machine learning between Qingyuan and Xiushui counties in Polygonatum cyrtonema Hua
Authors: Gong Qiqi , Yu Jianfeng , Guo Zhicheng , Fu Ke , Xu Yi , Zou Hui , Li Cong , Si Jinping , Cai Shengguan , Chen Donghong , Han Zhigang 
Published: October 2023

Abstract
Polygonatum cyrtonema Hua (P. cyrtonema) is well known for its high medicinal value due to a wide variety of secondary metabolites. Nonetheless, the unclearness persists regarding the distribution and buildup processes of these metabolites across various regions. Using UPLC-ESI-MS/MS, a grand total of 482 metabolites were detected and identified in this research. Cluster analysis showed distinct metabolite profiles between Qingyuan County and Xiushui County. The identification of secondary metabolites, such as flavonoids, phenolic acids, and lignans, between the two regions was performed using support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF) machine learning techniques. Subsequently, the process of comparative transcriptomics and weighted gene co-expression analysis (WGCNA) uncovered genes associated with flavonoids such as CHI, UGT1, UGT2, ERF, as well as phenylpropane-related genes UGT3 and NAC. In addition, by comparing transcriptomes, four genes (PcOMT10/11/12/13) were selected as differentially expressed. Their impact on metabolic fluxes of the phenolpropane pathway was confirmed using a transient expression system in tobacco. The findings enhanced our comprehension of the variation in accumulation of secondary metabolites mediated by phenylpropanoids across various locations, and offered valuable genetic assets for the synthesis of bioactive compounds.
Tumor-to-Stroma CD8 + T Cells Ratio combined with Cancer-Associated Fibroblasts: An Innovative Approach to Predicting Lymph Node Metastases of Cervical Cancer
Authors: Guo Shuangshuang , Chen Peiyu , Yang Yang , Wei Wenfei , Pan YuHua , Zen Fanke , Fan Liangsheng , Wang Wei 
Published: October 2023

Abstract
Purpose
Precise identification of lymph node metastases is vital for the management of cervical cancer. However, the existing diagnostic methods for lymph node metastases have certain drawbacks. In this study, we aim to explore the expression of cancer-associated fibroblasts (CAFs) and tumor-to-stroma CD8+ T cells ratio (CD8+ T cells T:S ratio) and its association with lymph node metastases of cervical cancer.
Methods
110 cervical cancer tissues and 39 biopsy tissues from patients were investigated immunocytochemically for the expression of CAFs and CD8+ T cells. The statistical correlation analysis was carried out using the SPSS system.
Results
A strong and statistically significant negative correlation (r=-0.690; P<0.001) was observed between CAF density and CD8+ T cells T:S ratio. Not only were CAFs density and CD8+ T cells T:S ratio correlated with lymph node metastases respectively (P < 0.001), but the combination of them also significantly correlated with lymph node metastases (P < 0.001). Then, we constructed the combined diagnosis model ( Logit (P) =-4.446 + 0.300×CAFs + 0.752×CD8+ T cells T:S Ratio) of cervical cancer lymph node metastases. ROC curves analysis showed that the ROC curves areas for CAFs, CD8+ T cells T:S ratio, and a combination of both are 0.879, 0.747, and 0.951. Then, the prediction model was verified by biopsy specimens and consistent results were obtained.
Conclusions
The combination of CAF density and CD8+ T cells T:S ratio has a significant predictive value for lymph node metastases in patients with cervical cancer.