bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urinary equol levels are positively associated with urinary estradiol excretion in women
Authors: Fujitani Tomoko , Fujii Yukiko , Lyu Zhaoqing , Harada Sassa Mariko , Harada Kouji H. 
Published: September 2021

AbstractIsoflavones found in soy products are a promising class of nutrients that may have a positive effect on human health. In particular, the phytoestrogen metabolite equol is associated with a reduced risk of developing female hormone-related diseases. However, the effect of equol on estrogen remains unclear. Equol can modify blood and urinary estradiol (E2) levels. The aim of this cross-sectional study was to examine the associations between urinary estrogen levels, equol levels, and equol production status in Japanese women. We analyzed urine samples from 520 women by gas chromatography-mass spectrometry. Urinary E2 and 4-hydroxylated E2 levels were higher in equol producers (EQP) than in non-EQPs (P < 0.0001 and P=0.00112, respectively). After adjusting for age and tobacco use by analysis of covariance, the association remained significant (β = 0.299, P < 0.0001). Analysis of covariance demonstrated that equol levels in urine were also positively associated with urinary E2 (β = 0.597, P < 0.0001). The log equol concentration showed a significant, but moderate, negative association with the serum E2 concentration (β = − 0.0225, P = 0.0462). Our findings suggest that equol may promote urinary E2 excretion and modify blood E2 levels in women.
Paraoxonase 1 gene variants concerning cardiovascular mortality in conventional cigarette smokers and non-smokers treated with hemodialysis
Authors: Grzegorzewska Alicja E. , Ostromecka Kamila , Świderska Monika K. , Adamska Paulina , Mostowska Adrianna , Jagodziński Paweł P. 
Published: September 2021

AbstractCigarette smoking effects might correspond with paraoxonase 1 gene (PON1) single nucleotide variants (SNVs). We investigated the association of PON1 rs705379, rs854560, and rs662 with cardiovascular mortality in hemodialysis (HD) patients concerning conventional cigarette smoking. Cardiovascular, cardiac, coronary heart disease (CHD)- and non-CHD-related deaths were analyzed in 206 HD cigarette smokers and 659 HD non-smokers. P-values were adjusted for sex, age, and high-density lipoprotein cholesterol. Among all smokers, the rs705379 TT genotype was associated with cardiovascular (P = 0.028), cardiac (P = 0.046), and cardiac non-CHD-related (P = 0.001) mortality. Non-diabetic smokers showed similar qualitative significance to all smokers concerning mentioned death rates (P-values 0.011, 0.044, and 0.009, respectively). In diabetic non-smokers, the rs705379 T allele correlated with CHD-related deaths (P = 0.020). The rs854560 T allele was associated with lower cardiovascular mortality in non-diabetic smokers (P = 0.008). The rs854560 TT genotype showed a negative non-significant correlation with non-CHD-related cardiac death in all non-smokers (P = 0.079). In diabetic smokers, the rs662 G allele was associated with higher cardiac mortality (P = 0.005). In all non-smokers and non-diabetic non-smokers, the rs662 G correlated with cardiovascular deaths (P = 0.020 and P = 0.018, respectively). Genotyping PON1 SNVs may help argue HD smokers harboring the rs705379 TT genotype or T allele and non-smokers possessing the rs662 G allele for prevention against cardiovascular diseases. These groups are more burdened genetically for cardiovascular mortality.
Network pharmacology-based investigation of potential targets of astragalus membranaceous-angelica sinensis compound acting on diabetic nephropathy
Authors: Dong Youzi , Zhao Quanlin , Wang Yuguo 
Published: September 2021

AbstractTo explore the mechanism of the Astragalus membranaceous (AM)-Angelica sinensis (AS) compound in the treatment of diabetic nephropathy (DN) we used network pharmacology and molecular docking. Screen the components and targets of the AM-AS compound in the TCMSP and the BATMAN-TCM, and establish a component-target interaction network by Cytoscape 3.7.2. After searching relevant targets of DN in related databases, the common targets of the AM-AS compound and DN were obtained by comparison. Gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis were performed through David database. Molecular docking was performed by PyMoL2.3.0 and AutoDock Vina software. After screening, 142 main targets of the AM-AS compound in the treatment of DN have been identified. Target network was established and the topology of PPI network was analyzed. KEGG pathway enrichment analysis shows that these targets are related to apoptosis, oxidative stress, inflammation, insulin resistance, etc. Molecular docking shows that the target proteins have good combinations with the main active components of the AM-AS compound. AM-AS compound may treat DN by acting on VEGFA, TP53, IL-6, TNF, MARK1, etc., and regulate apoptosis, oxidative stress, inflammation, glucose, and lipid metabolism processes. The in vivo study results suggest that AM-AS compound can significantly reduce the FBG level of diabetic rats, increase the level of INS, improve renal functions, reduce urinary proteins, inhibit glycogen deposition, granulocyte infiltration and collagen fiber proliferation in renal tissue, and restrain the progress of DN. In vivo study combined with network pharmacology and molecular docking methods provides new ideas for the pathogenesis and treatments of DN.
Genomic background selection to reduce the mutation load after random mutagenesis
Authors: Karunarathna Nirosha L. , Patiranage Dilan S. R. , Harloff Hans-Joachim , Sashidhar Niharika , Jung Christian 
Published: September 2021

AbstractRandom mutagenesis is a standard procedure to increase allelic variation in a crop species, especially in countries where the use of genetically modified crops is limited due to legal constraints. The chemical mutagen EMS is used in many species to induce random mutations throughout the genome with high mutation density. The major drawback for functional analysis is a high background mutation load in a single plant that must be eliminated by subsequent backcrossing, a time and resource-intensive activity. Here, we demonstrate that genomic background selection combined with marker-assisted selection is an efficient way to select individuals with reduced background mutations within a short period. We identified BC1 plants with a significantly higher share of the recurrent parent genome, thus saving one backcross generation. Furthermore, spring rapeseed as the recurrent parent in a backcrossing program could accelerate breeding by reducing the generation cycle. Our study depicts the potential for reducing the background mutation load while accelerating the generation cycle in EMS-induced winter oilseed rape populations by integrating genomic background selection.
Prediction of hospitalization using artificial intelligence for urgent patients in the emergency department
Authors: Lee Jung-Ting , Hsieh Chih-Chia , Lin Chih-Hao , Lin Yu-Jen , Kao Chung-Yao 
Published: September 2021

AbstractTimely assessment to accurately prioritize patients is crucial for emergency department (ED) management. Urgent (i.e., level-3, on a 5-level emergency severity index system) patients have become a challenge since under-triage and over-triage often occur. This study was aimed to develop a computational model by artificial intelligence (AI) methodologies to accurately predict urgent patient outcomes using data that are readily available in most ED triage systems. We retrospectively collected data from the ED of a tertiary teaching hospital between January 1, 2015 and December 31, 2019. Eleven variables were used for data analysis and prediction model building, including 1 response, 2 demographic, and 8 clinical variables. A model to predict hospital admission was developed using neural networks and machine learning methodologies. A total of 282,971 samples of urgent (level-3) visits were included in the analysis. Our model achieved a validation area under the curve (AUC) of 0.8004 (95% CI 0.7963–0.8045). The optimal cutoff value identified by Youden's index for determining hospital admission was 0.5517. Using this cutoff value, the sensitivity was 0.6721 (95% CI 0.6624–0.6818), and the specificity was 0.7814 (95% CI 0.7777–0.7851), with a positive predictive value of 0.3660 (95% CI 0.3586–0.3733) and a negative predictive value of 0.9270 (95% CI 0.9244–0.9295). Subgroup analysis revealed that this model performed better in the nontraumatic adult subgroup and achieved a validation AUC of 0.8166 (95% CI 0.8199–0.8212). Our AI model accurately assessed the need for hospitalization for urgent patients, which constituted nearly 70% of ED visits. This model demonstrates the potential for streamlining ED operations using a very limited number of variables that are readily available in most ED triage systems. Subgroup analysis is an important topic for future investigation.
Identification of immune-related subtypes of colorectal cancer to improve antitumor immunotherapy
Authors: Zheng Xiaobo , Gao Yong , Yu Chune , Fan Guiquan , Li Pengwu , Zhang Ming , Yu Jing , Xu Mingqing 
Published: September 2021

AbstractImmunotherapy involving immune checkpoint inhibitors (ICIs) for enhancing immune system activation is promising for tumor management. However, the patients’ responses to ICIs are different. Here, we applied a non-negative matrix factorization algorithm to establish a robust immune molecular classification system for colorectal cancer (CRC). We obtained data of 1503 CRC patients (training cohort: 488 from The Cancer Genome Atlas; validation cohort: 1015 from the Gene Expression Omnibus). In the training cohort, 42.8% of patients who exhibited significantly higher immunocyte infiltration and enrichment of immune response-associated signatures were subdivided into immune classes. Within the immune class, 53.1% of patients were associated with a worse overall prognosis and belonged to the immune-suppressed subclass, characterized by the activation of stroma-related signatures, genes, immune-suppressive cells, and signaling. The remaining immune class patients belonged to the immune-activated subclass, which was associated with a better prognosis and response to anti-PD-1 therapy. Immune-related subtypes were associated with different copy number alterations, tumor-infiltrating lymphocyte enrichment, PD-1/PD-L1 expression, mutation landscape, and cancer stemness. These results were validated in patients with microsatellite instable CRC. We described a novel immune-related class of CRC, which may be used for selecting candidate patients with CRC for immunotherapy and tailoring optimal immunotherapeutic treatment.
Biodiversity and biocatalyst activity of culturable hydrocarbonoclastic fungi isolated from Marac–Moruga mud volcano in South Trinidad
Authors: Ramdass Amanda C. , Rampersad Sephra N. 
Published: September 2021

AbstractMud volcanoes (MVs) are visible signs of oil and gas reserves present deep beneath land and sea. The Marac MV in Trinidad is the only MV associated with natural hydrocarbon seeps. Petrogenic polyaromatic hydrocarbons (PAHs) in its sediments must undergo biogeochemical cycles of detoxification as they can enter the water table and aquifers threatening ecosystems and biota. Recurrent hydrocarbon seep activity of MVs consolidates the growth of hydrocarbonoclastic fungal communities. Fungi possess advantageous metabolic and ecophysiological features for remediation but are underexplored compared to bacteria. Additionally, indigenous fungi are more efficient at PAH detoxification than commercial/foreign counterparts and remediation strategies remain site-specific. Few studies have focused on hydrocarbonoclastic fungal incidence and potential in MVs, an aspect that has not been explored in Trinidad. This study determined the unique biodiversity of culturable fungi from the Marac MV capable of metabolizing PAHs in vitro and investigated their extracellular peroxidase activity to utilize different substrates ergo their extracellular oxidoreductase activity (> 50% of the strains decolourized of methylene blue dye). Dothideomycetes and Eurotiomycetes (89% combined incidence) were predominantly isolated. ITS rDNA sequence cluster analysis confirmed strain identities. 18 indigenous hydrocarbonoclastic strains not previously reported in the literature and some of which were biosurfactant-producing, were identified. Intra-strain variability was apparent for PAH utilization, oil-tolerance and hydroxylase substrate specificity. Comparatively high levels of extracellular protein were detected for strains that demonstrated low substrate specificity. Halotolerant strains were also recovered which indicated marine-mixed substrata of the MV as a result of deep sea conduits. This work highlighted novel MV fungal strains as potential bioremediators and biocatalysts with a broad industrial applications.
A Hopf physical reservoir computer
Authors: Shougat Md Raf E Ul , Li XiaoFu , Mollik Tushar , Perkins Edmon 
Published: September 2021

AbstractPhysical reservoir computing utilizes a physical system as a computational resource. This nontraditional computing technique can be computationally powerful, without the need of costly training. Here, a Hopf oscillator is implemented as a reservoir computer by using a node-based architecture; however, this implementation does not use delayed feedback lines. This reservoir computer is still powerful, but it is considerably simpler and cheaper to implement as a physical Hopf oscillator. A non-periodic stochastic masking procedure is applied for this reservoir computer following the time multiplexing method. Due to the presence of noise, the Euler–Maruyama method is used to simulate the resulting stochastic differential equations that represent this reservoir computer. An analog electrical circuit is built to implement this Hopf oscillator reservoir computer experimentally. The information processing capability was tested numerically and experimentally by performing logical tasks, emulation tasks, and time series prediction tasks. This reservoir computer has several attractive features, including a simple design that is easy to implement, noise robustness, and a high computational ability for many different benchmark tasks. Since limit cycle oscillators model many physical systems, this architecture could be relatively easily applied in many contexts.
Improving the thermal structure predictions in the Yellow Sea by conducting targeted observations in the CNOP-identified sensitive areas
Authors: Liu Kun , Guo Wuhong , Da Lianglong , Liu Jingyi , Hu Huiqin , Cui Baolong 
Published: September 2021

AbstractTargeted observation is an appealing procedure for improving model predictions. However, studies on oceanic targeted observations have been largely based on modeling efforts, and there is a need for field validating operations. Here, we report the results of a field targeted observation that is designed based on the sensitive areas identified by the Conditional Nonlinear Optimal Perturbation approach to improve the 7th day thermal structure prediction in the Yellow Sea. By introducing the technique of cycle data assimilation and the new concept of time-varying sensitive areas, an observing strategy is designed and validated by a set of Observing System Simulation Experiments. Then, the impact of targeted observations was investigated by a choreographed field campaign in the summer of 2019. The results of the in-field Observing System Experiments show that, compared to conventional local data assimilation, conducting targeted observations in the sensitive areas can yield more benefit at the verification time. Furthermore, dynamic analysis demonstrates that the refinement of vertical thermal structures is mainly caused by the changes in the upstream horizontal temperature advection driven by the Yellow Sea Cold Water Mass circulation. This study highlights the effectiveness of targeted observations on reducing the forecast uncertainty in the ocean.
VCAM1 expression in the myocardium is associated with the risk of heart failure and immune cell infiltration in myocardium
Authors: Wang Tongyu , Tian Jiahu , Jin Yuanzhe 
Published: September 2021

AbstractIschemic heart disease (IHD) and dilated cardiomyopathy (DCM) are the two most common etiologies of heart failure (HF). Both forms share common characteristics including ventricle dilation in the final stage. Immune mechanisms in HF are increasingly highlighted and have been implicated in the pathogeneses of IHD and DCM. A better understanding of adhesion molecule expression and correlated immune cell infiltration could enhance disease detection and improve therapeutic targets. This study was performed to explore the common mechanisms underlying IHD and DCM. After searching the Gene Expression Omnibus database, we selected the GSE42955, GSE76701, GSE5406, GSE133054 and GSE57338 datasets for different expressed gene (DEGs) selection and new cohort establishment. We use xcell to calculate immune infiltration degree, ssGSEA and GSEA to calculate the pathway and biological enrichment score, consensus cluster to identify the m6A modification pattern, and LASSO regression to make risk predicting model and use new combined cohort to validate the results. The screening stage revealed that vascular cell adhesion molecule 1 (VCAM1) play pivotal roles in regulating DEGs. Subsequent analyses revealed that VCAM1 was differentially expressed in the myocardium and involved in regulating immune cell infiltration. We also found that dysregulated VCAM1 expression was associated with a higher risk of HF by constructing a clinical risk-predicting model. Besides, we also find a connection among the m6A RNA modification ,expression of VCAM1 and immune regulation. Those connection can be linked by the Wnt pathway enrichment alternation. Collectively, our results suggest that VCAM-1 have the potential to be used as a biomarker or therapy target for HF and the m6A modification pattern is associated with the VCAM1 expression and immune regulation.
Evolution of the ε and γ phases in biodegradable Fe–Mn alloys produced using laser powder-bed fusion
Authors: Donik Črtomir , Kraner Jakob , Kocijan Aleksandra , Paulin Irena , Godec Matjaž 
Published: September 2021

AbstractThe key feature of Fe–Mn alloys is gradual degradability and non-magneticity, with laser power bed fusion (LPBF) parameters influencing the microstructure and chemical composition. Our study focuses on biodegradable Fe–Mn alloys produced by mechanically mixing pure metal feedstock powders as part of the LPBF process. The Mn content and, consequently, the γ-ε phase formation in LPBF samples are directly correlated with an adapted energy–density (E) equation by combining the five primary LPBF parameters. We varied laser power (P) in a range of 200–350 W and scanning speed at 400 and 800 mm/s, and a comprehensive study was performed on samples with similar E. The study also showed an almost linear correlation between the LPBF's laser power and the material's hardness and porosity. The corrosion resistance was significantly reduced (from 13 to 400 μm/year) for the LPBF samples compared to a conventionally produced sample due to the dual-phase microstructure, increased porosity and other defects. The static immersion test showed that the process parameters greatly influence the quantity of oxides and the distribution of their diameters in the LPBF samples and, therefore, their corrosion stability. The most challenging part of the study was reducing the amount of ε phase relative to γ phase to increase the non-magnetic properties of the LPBF samples.
Contour features predict valence and threat judgements in scenes
Authors: Damiano Claudia , Walther Dirk B. , Cunningham William A. 
Published: September 2021

AbstractQuickly scanning an environment to determine relative threat is an essential part of survival. Scene gist extracted rapidly from the environment may help people detect threats. Here, we probed this link between emotional judgements and features of visual scenes. We first extracted curvature, length, and orientation statistics of all images in the International Affective Picture System image set and related them to emotional valence scores. Images containing angular contours were rated as negative, and images containing long contours as positive. We then composed new abstract line drawings with specific combinations of length, angularity, and orientation values and asked participants to rate them as positive or negative, and as safe or threatening. Smooth, long, horizontal contour scenes were rated as positive/safe, while short angular contour scenes were rated as negative/threatening. Our work shows that particular combinations of image features help people make judgements about potential threat in the environment.
Associations of vascular and bone status in arthritis patients
Authors: Pusztai Anita , Hamar Attila , Czókolyová Monika , Gulyás Katalin , Horváth Ágnes , Végh Edit , Pethő Zsófia , Szamosi Szilvia , Balogh Emese , Bodnár Nóra , Bodoki Levente , Szentpétery Ágnes , Bhattoa Harjit Pal , Kerekes György , Juhász Balázs , Szekanecz Éva , Hodosi Katalin , Domján Andrea , Szántó Sándor , Raterman Hennie G. , Lems Willem F. , Szekanecz Zoltán , Szűcs Gabriella 
Published: September 2021

AbstractCardiovascular (CV) disease and osteoporosis (OP) have been associated with rheumatoid arthritis (RA) and ankylosing spondylitis (AS). Bone and vascular biomarkers and parameters along with the effect of 1-year anti-TNF therapy on these markers were assessed in order to determine correlations between vascular pathophysiology and bone metabolism in RA and AS. Thirty-six patients treated with etanercept or certolizumab pegol and 17 AS patients treated with ETN were included in a 12-month follow-up study. Bone and vascular markers were previously assessed by ELISA. Bone density was measured by DXA and quantitative CT (QCT). Flow-mediated vasodilation (FMD), common carotid intima-media thickness (IMT) and pulse-wave velocity (PWV) were assessed by ultrasound. Multiple correlation analyses indicated associations between bone and vascular markers. Osteoprotegerin, sclerostin and cathepsin K were significantly associated with FMD, IMT and PWV, respectively (p < 0.05). Moreover, total and trabecular BMD determined by QCT inversely correlated with IMT (p < 0.05). On the other hand, among vascular parameters, platelet-derived growth factor BB and IMT correlated with DXA femoral and QCT total BMD, respectively (p < 0.05). In the RM-ANOVA analysis, anti-TNF treatment together with baseline osteocalcin, procollagen 1 N-terminal propeptide (P1NP) or vitamin D3 levels determined one-year changes in IMT (p < 0.05). In the MANOVA analysis, baseline disease activity indices (DAS28, BASDAI), the one-year changes in these indices, as well as CRP exerted effects on multiple correlations between bone and vascular markers (p < 0.05). As the pattern of interactions between bone and vascular biomarkers differed between baseline and after 12 months, anti-TNF therapy influenced these associations. We found a great number of correlations in our RA and AS patients undergoing anti-TNF therapy. Some of the bone markers have been associated with vascular pathophysiology, while some vascular markers correlated with bone status. In arthritis, systemic inflammation and disease activity may drive both vascular and bone disease.