bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic relatedness, virulence, and drug susceptibility of Campylobacter isolated from water and wild birds
Authors: Andrzejewska Małgorzata , Grudlewska-Buda Katarzyna , Śpica Dorota , Skowron Krzysztof , Ćwiklińska-Jurkowska Małgorzata , Szady-Grad Małgorzata , Indykiewicz Piotr , Wiktorczyk-Kapischke Natalia , Klawe Jacek J. 
Published: November 2022

IntroductionThis study aimed to identify the characteristics of Campylobacter isolated from wild birds (Black-headed gulls Chroicocephalus ridibundus and Great tits Parus major) and collect surface water samples (from rivers, ponds, ornamental lakes, freshwater beaches). Research material included 33 Campylobacter isolates. All the strains were isolated by different monitoring and surveillance plans.MethodsThe prevalence of selected genes (flaA, cadF, iam, cdtB, wlaN, sodB, tet0) encoding virulence factors and resistance among Campylobacter spp. was assessed by the PCR method. The genetic similarities of isolates were determined by Pulsed-Field Gel Electrophoresis (PFGE). The susceptibility of Campylobacter isolates to clinically important antimicrobials: erythromycin, tetracycline, and ciprofloxacin, previously assessed by E-test, was presented in the form of drug susceptibility profiles depending on the origin of the isolates.ResultsThe cadF, flaA, cdtB, and sodB genes exhibited the highest detection rate. Statistically significant differences between the presence of wlaN virulence genes were noted among different species of the isolates. No genetically identical isolates were found. The most numerous antibiotic susceptibility profile included strains susceptible to all antibiotics studied (profile A-33.3%). The second most common were the tetracycline - and ciprofloxacin-resistant (profile B-27.2%), and tetracycline-resistant profile (C-24.2%) respectively.DiscussionThe study revealed the virulent properties of Campylobacter isolated from water samples, and wild birds, and high resistance rates to tetracycline, and fluoroquinolones. The lack of genetic relatedness among strains isolated from water, and birds may indicate other sources of surface water contamination with Campylobacter bacteria than birds. The presence of Campylobacter spp. in wild birds could also have other environmental origins.
Advancing fence datasets: Comparing approaches to map fence locations and specifications in southwest Montana
Authors: Buzzard Simon A. , Jakes Andrew F. , Pearson Amy J. , Broberg Len 
Published: November 2022

Fencing is a major anthropogenic feature affecting wildlife distributions and movements, but its impacts are difficult to quantify due to a widespread lack of spatial data. We created a fence model and compared outputs to a fence mapping approach using satellite imagery in two counties in southwest Montana, USA to advance fence data development for use in research and management. The model incorporated road, land cover, ownership, and grazing boundary spatial layers to predict fence locations. We validated the model using data collected on randomized road transects (n = 330). The model predicted ~34,700 km of fences with a mean fence density of 0.93 km/km2 and a maximum density of 14.9 km/km2. We also digitized fences using Google Earth Pro in a random subset of our study area in survey townships (n = 50). The Google Earth approach showed greater agreement (K = 0.76) with known samples than the fence model (K = 0.56) yet was unable to map fences in forests and was significantly more time intensive. We also compared fence attributes by land ownership and land cover variables to assess factors that may influence fence specifications (e.g., wire heights) and types (e.g., number of barbed wires). Private land fences had bottom wires that were closer to the ground and top wires higher from the ground when compared to fences on public lands, with sample means at ~22 cm and ~26 cm, and ~115 cm and ~111 cm, respectively. Both bottom wire means were well below recommended heights for ungulates navigating underneath fencing (≥ 46 cm), while top wire means were closer to the 107 cm maximum fence height recommendation. We found that both fence type and land ownership were correlated (χ2 = 45.52, df = 5, p = 0.001) as well as fence type and land cover type (χ2 = 140.73, df = 15, p = 0.001). We provide tools for estimating fence locations, and our novel fence type assessment demonstrates an opportunity for updated policy to encourage the adoption of “wildlife-friendlier” fencing standards to facilitate wildlife movement in the western U.S. while supporting rural livelihoods.
Validity of regional network systems on reperfusion therapy in diabetes mellitus and non-diabetes mellitus patients with ST-segment elevation myocardial infarction
Authors: Li Xicong , Lu Lifei , Yuan Qi , Yang Lixia , Du Liping , Guo Ruiwei 
Published: November 2022

BackgroundPatients with ST-segment elevation myocardial infarction (STEMI) with diabetes mellitus (DM) had higher mortality and poorer prognosis than those without DM. Previous studies had demonstrated the effectiveness of regional network systems (RNS) for reperfusion therapy in patients with STEMI. However, the differences in nursing care with RNS in subgroups of patients with DM with STEMI were unclear. Our study aimed to evaluate the validity of RNS in reperfusion therapy in patients with STEMI with or without DM.MethodsWe retrospectively enrolled patients with STEMI who received reperfusion therapy at the chest pain center of the 920th Hospital in Kunming City, Yunnan Province from 2019 to 2021. Personal information and hospitalization information for patients with STEMI were collected through the chest pain center registration system. Univariate and multivariate logistic regression were used to analyze factors associated with outcomes in patients with STEMI who received RNS. Wilcoxon rank-sum test and chi-squared test were used to analyze the differences in reperfusion therapy times and clinical outcomes between RNS and non-RNS in patients with STEMI with or without DM.ResultsThis study enrolled 1,054 patients with STEMI, including 148 patients with DM and 906 patients without DM. Logistic regression analysis indicated that DM was associated with patients with STEMI who received RNS [OR 1.590 95% CI (1.034–2.446), P = 0.035]. RNS may decrease the reperfusion therapy time in patients with STEMI and patients without DM with STEMI, including the first medical contact (FMC) to door, FMC to wire and FMC to catheterization laboratory activity (all P &lt; 0.05). However, we found no significant difference in reperfusion therapy times with and without RNS in patients with DM (all P &gt; 0.05).ConclusionRegional network systems may decrease the reperfusion therapy time in patients without DM with STEMI, but no decrease was found in patients with DM with STEMI.
The dynamic change of propagation from meteorological drought to hydrological drought at the basin scale: A case study from the Weihe River Basin, China
Authors: Zhao Panpan , Xie Bingbo , Huang Xudong , Qu Bo 
Published: November 2022

Current climate change has led to frequent drought events in the Weihe River Basin, and the risks and impacts of drought are becoming increasingly severe. In order to study meteorological drought and hydrological drought at different scales and the propagation of drought between them, in this study, meteorological and hydrological drought conditions were calculated for 3-, 6-, 9-, and 12-month timescales based on 56 years of monthly precipitation and monthly runoff data of the Weihe River Basin using the Standardized Precipitation Index (SPI) and the Streamflow Drought Index (SDI), respectively. We explore analyzing the differences between them and their relationship and establishing regression equations based on the relationship and the dynamic propagation time of meteorological and hydrological droughts at different timescales. The results demonstrate that 1) the frequencies of both meteorological and hydrological droughts have shown an increasing trend in the last 56 years; 2) the relationship between meteorological drought and hydrological drought varied over time; 3) according to dynamic change analysis, propagation time tends to be shorter on the 3-month timescale and longer on the 6-month, 9-month, and 12-month timescales; and 4) the accelerated propagation time between meteorological drought and hydrological drought may be related to the increase in precipitation and temperature. The findings not only provide scientific support for the formulation of drought prevention and disaster reduction strategies in this basin but also have important scientific and practical application value.
Isotopic (δ2H and δ13C) tracing the provenance and fate of individual fatty acids fueling migrating animals: A case study of the monarch butterfly (Danaus plexippus)
Authors: Pilecky Matthias , Wassenaar Leonard I. , Kainz Martin J. , Anparasan Libesha , Ramirez M. Isabel , McNeil Jeremy N. , Hobson Keith A. 
Published: November 2022

IntroductionAmong long-distance migratory insects, the monarch butterfly (Danaus plexippus) is one of the most iconic, whose journey is fueled by nectar from flowering plants along the migratory route which may involve up to 3,500 km. Understanding how and where monarchs obtain their dietary resources to fuel migratory flight and ensure overwintering stores would provide new insights into the migratory strategy of this species and subsequently help focus conservation efforts.MethodsThis pilot study was designed as a first attempt to assess the composition, dynamics, and isotopic (δ2H, δ13C) composition of essential and non-essential fatty acids (FA) acquired or manufactured de novo from larval host milkweed (Asclepias spp.) by monarch butterflies and from adult emergence to overwintering.ResultsData from controlled laboratory isotopic tracer tests suggested that adult monarchs convert their dietary energy mainly into 16:0 and 18:1 fatty acids and store them as neutral lipids in their abdomen. FA isotopic composition reflects not only dietary sources but also subsequent isotopic fractionation from metabolism. On the other hand, δ2H values of essential omega-3 fatty acid alpha-linolenic acid (ALA) correlated with δ2HWing, as markers of an individual’s geographic origin and indicated the importance of larval diet. Additionally, in wild-type females, high isotopic fractionation in δ13CALA between neutral and polar lipids might indicate increased bioconversion activity during gravidity. Finally, δ2HLIN showed positive H isotope fractionation from larval dietary sources, indicating that catabolic processes were involved in their manufacture. Furthermore, δ2HLIN showed a negative correlation with δ2HWing values, which could potentially be useful when investigating individual life-history traits, such as migratory catabolic efforts or periods of fasting.DiscussionThis interpretation was supported by significant larger variations in δ2HLIN and δ2HLIN overwintering monarchs compared to other FA. Altogether, our results provide the first evidence that the H isotopic analysis of individual fatty acids in migrating and overwintering monarchs can be used to infer the nutritional history of individuals including the provenance of nectaring sites used to fuel key life history events.
Heat wave induces oxidative damage in the Chinese pond turtle (Mauremys reevesii) from low latitudes
Authors: Tao Weijie , Ou Junwei , Wu Danyang , Zhang Qiong , Han Xingzhi , Xie Lei , Li Shuran , Zhang Yongpu 
Published: November 2022

IntroductionGlobal warming has led to frequent heat waves, causing global organisms to face severe survival challenges. However, the way in which heat waves threaten the fitness and survival of animals remains largely unclear. Oxidative damage and immunity are widely considered the link between heat waves and threats to animals.MethodsTo evaluate the oxidative damage caused by heat waves and to reveal the physiological resistance to heat waves by the antioxidant defense of animals from different latitudes, we exposed both high-latitude (Zhejiang) and low-latitude (Hainan) populations of Chinese pond turtle (Mauremys reevesii) to simulate heat waves and a moderate thermal environment for 1 week, respectively. Next, we compared the oxidative damage by malondialdehyde (MDA) and antioxidant capacity by superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), and total antioxidant capacity (T-AOC) in the liver tissues and evaluated the innate immunity by serum complement protein levels (C3, C4) and lysozyme activity in plasma of turtles.Results and discussionWe found that heat waves significantly increased the content of MDA and the activity of CAT, whereas it decreased the activity of SOD, T-AOC, and GSH/GSSG in turtles from low latitudes. Furthermore, heat waves increased CAT activity but decreased GSH/GSSG in turtles from high latitudes. Although the turtles from high latitudes had higher levels of innate immunity, the heat waves did not affect the innate immunity of C3, C4, or lysozyme in either population. These results indicate that the low-latitude population suffered higher oxidative damage with lower antioxidant capacities. Therefore, we predict that Chinese pond turtles from low latitudes may be more vulnerable to heat waves caused by climate warming. This study reveals the physiological and biochemical resistance to heat waves in Chinese pond turtles from different latitudes and highlights the importance of integrative determination of fitness-related responses in evaluating the vulnerability of ectotherms from different latitudes to climate warming.
Comprehensive bioinformatics analysis reveals biomarkers of DNA methylation-related genes in varicose veins
Authors: Li Shengyu , Liu Yuehan , Liu Mingming , Wang Lizhao , Li Xiaofeng 
Published: November 2022

Background: Patients with Varicose veins (VV) show no obvious symptoms in the early stages, and it is a common and frequent clinical condition. DNA methylation plays a key role in VV by regulating gene expression. However, the molecular mechanism underlying methylation regulation in VV remains unclear.Methods: The mRNA and methylation data of VV and normal samples were obtained from the Gene Expression Omnibus (GEO) database. Methylation-Regulated Genes (MRGs) between VV and normal samples were crossed with VV-associated genes (VVGs) obtained by weighted gene co-expression network analysis (WGCNA) to obtain VV-associated MRGs (VV-MRGs). Their ability to predict disease was assessed using receiver operating characteristic (ROC) curves. Biomarkers were then screened using a random forest model (RF), support vector machine model (SVM), and generalized linear model (GLM). Next, gene set enrichment analysis (GSEA) was performed to explore the functions of biomarkers. Furthermore, we also predicted their drug targets, and constructed a competing endogenous RNAs (ceRNA) network and a drug target network. Finally, we verified their mRNA expression using quantitative real-time polymerase chain reaction (qRT-PCR).Results: Total three VV-MRGs, namely Wnt1-inducible signaling pathway protein 2 (WISP2), Cysteine-rich intestinal protein 1 (CRIP1), and Odd-skipped related 1 (OSR1) were identified by VVGs and MRGs overlapping. The area under the curves (AUCs) of the ROC curves for these three VV-MRGs were greater than 0.8. RF was confirmed as the optimal diagnostic model, and WISP2, CRIP1, and OSR1 were regarded as biomarkers. GSEA showed that WISP2, CRIP1, and OSR1 were associated with oxidative phosphorylation, extracellular matrix (ECM), and respiratory system functions. Furthermore, we found that lncRNA MIR17HG can regulate OSR1 by binding to hsa-miR-21-5p and that PAX2 might treat VV by targeting OSR1. Finally, qRT-PCR results showed that the mRNA expression of the three genes was consistent with the results of the datasets.Conclusion: This study identified WISP2, CRIP1, and OSR1 as biomarkers of VV through comprehensive bioinformatics analysis, and preliminary explored the DNA methylation-related molecular mechanism in VV, which might be important for VV diagnosis and exploration of potential molecular mechanisms.
Network pharmacology- and molecular docking-based approaches to unveil the pharmacological mechanisms of dihydroartemisinin against esophageal carcinoma
Authors: Wang Haixia 
Published: November 2022

Objective: Dihydroartemisinin (DHA) is an active metabolite of artemisinin and its derivatives, which is a potent drug extensively applied in clinical treatment of malaria. The antitumor properties of DHA have received increasing attention. However, there is no systematic summary on the pharmacological mechanisms of DHA against esophageal carcinoma (ESCA). The present study implemented network pharmacology- and molecular docking-based approaches to unveil the pharmacological mechanisms of DHA against ESCA.Methods: DHA targets were accessed through integrating the SwissTargetPrediction, HERB, as well as BATMAN-TCM platforms. In TCGA-ESCA dataset, genes with differential expression were screened between 161 ESCA and 11 normal tissue specimens. DHA targets against ESCA were obtained through intersection. Their biological significance was evaluated with functional enrichment analysis. A prognostic signature was established via uni- and multivariate cox regression analyses. DHA-target interactions were predicted via molecular docking. Molecular dynamics simulation was implemented to examine the stability of DHA binding to potential targets. Results: The study predicted 160 DHA targets as well as 821 genes with differential expression in ESCA. Afterwards, 16 DHA targets against ESCA were obtained, which remarkably correlated to cell cycle progression. The ADORA2B- and AURKA-based prognostic signature exhibited the reliability and independency in survival prediction. The stable docking of DHA-ADORA2B and DHA-AURKA was confirmed.Conclusion: Collectively, this study systematically revealed the basis and mechanism of DHA against ESCA through targeting multi-target and multi-pathway mechanisms, and thus offered theoretical and scientific basis for the clinical application of DHA.
Identification of two robust subclasses of sepsis with both prognostic and therapeutic values based on machine learning analysis
Authors: Zhou Wei , Zhang Chunyu , Zhuang Zhongwei , Zhang Jing , Zhong Chunlong 
Published: November 2022

BackgroundSepsis is a heterogeneous syndrome with high morbidity and mortality. Optimal and effective classifications are in urgent need and to be developed.Methods and resultsA total of 1,936 patients (sepsis samples, n=1,692; normal samples, n=244) in 7 discovery datasets were included to conduct weighted gene co-expression network analysis (WGCNA) to filter out candidate genes related to sepsis. Then, two subtypes of sepsis were classified in the training sepsis set (n=1,692), the Adaptive and Inflammatory, using K-means clustering analysis on 90 sepsis-related features. We validated these subtypes using 617 samples in 5 independent datasets and the merged 5 sets. Cibersort method revealed the Adaptive subtype was related to high infiltration levels of T cells and natural killer (NK) cells and a better clinical outcome. Immune features were validated by single-cell RNA sequencing (scRNA-seq) analysis. The Inflammatory subtype was associated with high infiltration of macrophages and a disadvantageous prognosis. Based on functional analysis, upregulation of the Toll-like receptor signaling pathway was obtained in Inflammatory subtype and NK cell-mediated cytotoxicity and T cell receptor signaling pathway were upregulated in Adaptive group. To quantify the cluster findings, a scoring system, called, risk score, was established using four datasets (n=980) in the discovery cohorts based on least absolute shrinkage and selection operator (LASSO) and logistic regression and validated in external sets (n=760). Multivariate logistic regression analysis revealed the risk score was an independent predictor of outcomes of sepsis patients (OR [odds ratio], 2.752, 95% confidence interval [CI], 2.234-3.389, P&lt;0.001), when adjusted by age and gender. In addition, the validation sets confirmed the performance (OR, 1.638, 95% CI, 1.309-2.048, P&lt;0.001). Finally, nomograms demonstrated great discriminatory potential than that of risk score, age and gender (training set: AUC=0.682, 95% CI, 0.643-0.719; validation set: AUC=0.624, 95% CI, 0.576-0.664). Decision curve analysis (DCA) demonstrated that the nomograms were clinically useful and had better discriminative performance to recognize patients at high risk than the age, gender and risk score, respectively.ConclusionsIn-depth analysis of a comprehensive landscape of the transcriptome characteristics of sepsis might contribute to personalized treatments and prediction of clinical outcomes.
Low high-density lipoprotein cholesterol levels predicting poor outcomes in patients with hepatitis B virus-related acute-on-chronic liver failure
Authors: Zhang Yue , Chen Peng , Zhang Yun , Nie Yuan , Zhu Xuan 
Published: November 2022

BackgroundLipid profile disorders frequently occur in patients with advanced liver diseases. High-density lipoprotein cholesterol (HDL-C) levels decrease rapidly during acute conditions of some diseases, and HDL-C levels may be related to mortality in patients with hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF).Materials and methodsA retrospective cohort study was conducted on 200 subjects with HBV-ACLF. The patients were separated into non-survivors and survivors according to their 28-day outcome. Univariate and multivariate Cox regression analyses were performed to identify predictors of mortality, and the performance of these predictors was evaluated by receiver operating characteristic (ROC) curve analysis. Kaplan–Meier analysis was performed to draw survival curves of HDL-C.ResultsThe 28-day mortality in the cohort was 27.0%. HDL-C levels differed markedly between non-survivors and survivors. In the multivariate analysis, HDL-C, the Child-Turcotte-Pugh (CTP), model for end-stage liver disease (MELD), and Chinese Group on the Study of Severe Hepatitis B-ACLF II (COSSH-ACLF II) scores were identified as independent predictors for mortality (HR = 0.806, 95% CI: 0.724–0.898; HR = 1.424, 95% CI: 1.143–1.775; HR = 1.006, 95% CI: 1.002–1.007; and HR = 1.609, 95% CI: 1.005–2.575, respectively). Patients with lower HDL-C levels had a worse prognosis than those with higher HDL-C levels. In ROC analysis, the prognostic accuracy for mortality was similar between HDL-C (AUROC: 0.733) and the CTP, MELD, and COSSH-ACLF II scores (AUROC: 0.753; 0.674 and 0.770, respectively).ConclusionThe HDL-C level may serve as a potential indicator for the prognosis of HBV-ACLF and can be used as a simple marker for risk assessment and selection of therapeutic options.
PCW-A1001, AI-assisted de novo design approach to design a selective inhibitor for FLT-3(D835Y) in acute myeloid leukemia
Authors: Jang Seong Hun , Sivakumar Dakshinamurthy , Mudedla Sathish Kumar , Choi Jaehan , Lee Sungmin , Jeon Minjun , Bvs Suneel Kumar , Hwang Jinha , Kang Minsung , Shin Eun Gyeong , Lee Kyu Myung , Jung Kwan-Young , Kim Jae-Sung , Wu Sangwook 
Published: November 2022

Treating acute myeloid leukemia (AML) by targeting FMS-like tyrosine kinase 3 (FLT-3) is considered an effective treatment strategy. By using AI-assisted hit optimization, we discovered a novel and highly selective compound with desired drug-like properties with which to target the FLT-3 (D835Y) mutant. In the current study, we applied an AI-assisted de novo design approach to identify a novel inhibitor of FLT-3 (D835Y). A recurrent neural network containing long short-term memory cells (LSTM) was implemented to generate potential candidates related to our in-house hit compound (PCW-1001). Approximately 10,416 hits were generated from 20 epochs, and the generated hits were further filtered using various toxicity and synthetic feasibility filters. Based on the docking and free energy ranking, the top compound was selected for synthesis and screening. Of these three compounds, PCW-A1001 proved to be highly selective for the FLT-3 (D835Y) mutant, with an IC50 of 764 nM, whereas the IC50 of FLT-3 WT was 2.54 μM.