bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multifrequency dielectric mapping of fixed mice colon tissues in cell culture media via scanning electrochemical microscopy
Authors: Vyas Varun , Kotla Niranjan G. , Rochev Yury , Poudel Anup , Biggs Manus 
Published: February 2023

Alternating current scanning electrochemical microscopy (AC-SECM) is a powerful tool for characterizing the electrochemical reactivity of surfaces. Here, perturbation in the sample is induced by the alternating current and altered local potential is measured by the SECM probe. This technique has been used to investigate many exotic a range of biological interfaces including live cells and tissues, as well as the corrosive degradation of various metallic surfaces, etc. In principle, AC-SECM imaging is derived from electrochemical impedance spectroscopy (EIS) which has been used for a century to describe interfacial and diffusive behaviour of molecules in solution or on a surface. Increasingly bioimpedance centric medical devices have become an important tool to detect evolution of tissue biochemistry. Predictive implications of measuring electrochemical changes within a tissue is one of the core concepts in developing minimally invasive and smart medical devices. In this study, cross sections of mice colon tissue were used for AC-SECM imaging. A 10 micron sized platinum probe was used for two-dimensional (2D) tan δ mapping of histological sections at a frequency of 10 kHz, Thereafter, multifrequency scans were performed at 100 Hz, 10 kHz, 300 kHz, and 900 kHz. Loss tangent (tan δ) mapping of mice colon revealed microscale regions within a tissue possessing a discrete tan δ signature. This tan δ map may be an immediate measure of physiological conditions in biological tissues. Multifrequency scans highlight subtle changes in protein or lipid composition as a function of frequency which was recorded as loss tangent maps. Impedance profile at different frequencies could also be used to identify optimal contrast for imaging and extracting the electrochemical signature specific for a tissue and its electrolyte.
Determinants of arterial elastic function in middle-aged and elderly people: A population-based cross-sectional study from a low-income population in China
Authors: Sun Jiayi , Zhang Zhen , Fei Yunhan , Gao Yannan , Li Zejian , Gao Shuai , Wang Yunfan , Liu Jie , Tu Jun , Wang Haiying , Wang Jinghua , Ning Xianjia , Zhao Wenjuan , Zhang Wenjuan 
Published: February 2023

BackgroundArterial stiffness is closely associated with the occurrence of many cardiovascular and cerebrovascular diseases. However, the risk factors and mechanisms related to arterial stiffness development have only been partially elucidated. We aimed to describe arterial elastic function and its influencing factors in middle-aged and elderly people in rural China.MethodsThis was a cross-sectional study conducted among residents, aged ≥45 years, of Tianjin, China, between April and July 2015. Data regarding participant demographics, medical history, lifestyle, and physical examination results were collected and assessed the association with arterial elastic function using linear regression.ResultsOf the 3,519 participants, 1,457 were male (41.4%). Brachial artery distensibility (BAD) decreased by 0.5%/mmHg with every 10-year increment in age. The mean BAD value was 0.864%/mmHg lower in women than in men. With each unit increase in mean arterial pressure, the BAD decreased by 0.042%/mmHg. In patients with hypertension or diabetes, the BAD decreased by 0.726 and 0.183%/mmHg, respectively, compared with those without hypertension or diabetes. For each unit increase in triglyceride (TG) level, the mean BAD increased by 0.043%/mmHg. With each increase in body mass index (BMI) category, the BAD increased by 0.113%/mmHg. Brachial artery compliance (BAC) decreased by 0.007 ml/mmHg with each 10-year increase in age, and brachial artery resistance (BAR) increased by 30.237 dyn s–1 cm–5. The mean BAC in women was 0.036 ml/mmHg lower and the mean BAR was 155.231 dyn s–1 cm–5 higher in women than in men. In individuals with hypertension, the mean BAC decreased by 0.009 ml/mmHg and the mean BAR increased by 26.169 dyn s–1 cm–5. With each increase in BMI category, the mean BAC increased by 0.005 ml/mmHg and the mean BAR decreased by 31.345 dyn s–1 cm–5. For each unit increase in TG level, the mean BAC increased by 0.001 ml/mmHg.ConclusionThese findings indicate that age, sex, mean arterial pressure, BMI, diabetes, hypertension, and TG level are independently associated with the components of peripheral arterial elasticity. Understanding the factors influencing arterial stiffness is important for developing interventions to minimize arterial aging and cardiovascular and cerebrovascular diseases caused by arterial aging.
Screening and mutation analysis of phenylalanine hydroxylase deficiency in newborns from Jiangxi province
Authors: Zeng Baitao , Lu Qing , Chen Shaohong , Guan Huizhen , Xu Xiaolan , Zou Yongyi , Wang Feng , Huang Shuhui , Liu Yanqiu , Yang Bicheng 
Published: February 2023

Background: Phenylalanine hydroxylase deficiency (PAHD) is an autosomal recessive disorder of amino acid metabolism and caused by mutations in the phenylalanine hydroxylase (PAH) gene. Without timely and appropriate dietary management, the disturbance of amino acid metabolism may impair cognitive development and neurophysiological function. Newborn screening (NBS) can aid the early diagnosis of PAHD, which can give accurate therapy to PAHD patients in time. In China, the PAHD incidence and PAH mutation spectrum vary enormously across the provinces. A total of 5,541,627 newborns from Jiangxi province were screened by NBS between 1997 and 2021.Method: One seventy one newborns from Jiangxi province were diagnosed with PAHD. By Sanger sequencing and the multiplex ligation-dependent probe amplification (MLPA) analysis, mutation analysis was performed in 123 PAHD patients. Using an arbitrary values (AV)-based model, we compared the observed phenotype with the predicted phenotype based on the genotype.Results: In this study, we speculated the PAHD incidence of Jiangxi province was about 30.9 per 1,000,000 live births (171/5,541,627). We summarized the PAH mutation spectrum in Jiangxi province for the first time. Two novel variants (c.433G &gt; C, c.706 + 2T &gt; A) were found. The most prevalent variant was c.728G &gt; A (14.1%). The overall prediction rate of the genotype-phenotype was 77.4%.Conclusion: This mutation spectrum is very meaningful to improve the diagnostic rate of PAHD and to increase the accuracy genetic counseling. This study offers data for the genotype-phenotype prediction suitable for Chinese population.
A composite score based on immune-related gene prognostic index and m6A risk score of head and neck squamous cell carcinoma
Authors: Yang Yizhou , Cai Zeman , Huang Kaichun , Li Mei , Wang Xiao , Lin Yinbing , Chen Sijie , Yang Zhining , Lin Zhixiong 
Published: February 2023

Background: Immunotherapy has been demonstrated favorable in head and neck squamous cell carcinoma (HNSCC). Studies indicated that immune-related gene prognostic index (IRGPI) was a robust signature, and N6-methyladenosine (m6A) methylation had a significant impact on the tumor immune microenvironment (TIME) and immunotherapy of head and neck squamous cell carcinoma. Thus, combining indicated that immune-related gene prognostic index with m6A status should offer a better predictive power for immune responses.Methods: Head and neck squamous cell carcinoma samples from the cancer genome atlas (TCGA, n = 498) and gene expression omnibus database (GSE65858, n = 270) were used in this study. Cox regression analysis was used to construct the indicated that immune-related gene prognostic index through immune-related hub genes which were identified by weighted gene co-expression network analysis (WGCNA). The m6A risk score was constructed by least absolute shrinkage and selection operator (LASSO) regression analysis. Principal component analysis was used to construct a composite score, and systematically correlate subgroups according to tumor immune microenvironment cell-infiltrating characteristics.Results: A composite score was determined based on indicated that immune-related gene prognostic index and m6A risk score. Head and neck squamous cell carcinoma patients in the cancer genome atlas were divided into four subgroups: A (IRGPI-High&amp;m6A-risk-High, n = 127), B (IRGPI-High&amp;m6A-risk-Low, n = 99), C (IRGPI-Low&amp;m6A-risk-High, n = 99), and D (IRGPI-Low&amp;m6A-risk-Low, n = 128), and overall survival (OS) was significantly different between subgroups (p &lt; 0.001). The characteristics of tumor immune microenvironment cell infiltration in the four subgroups were significantly different in subgroups (p &lt; 0.05). The receiver operating characteristic (ROC) curves show the predictive value of composite score for overall survival was superior to other scores.Conclusion: The composite score is a promising prognostic signature which might distinguish immune and molecular characteristics, predict prognosis, and guide more effective immunotherapeutic strategies for head and neck squamous cell carcinoma.
Predicting lncRNA-protein interactions with bipartite graph embedding and deep graph neural networks
Authors: Ma Yuzhou , Zhang Han , Jin Chen , Kang Chuanze 
Published: February 2023

Background: Long non-coding RNAs (lncRNAs) play crucial roles in numerous biological processes. Investigation of the lncRNA-protein interaction contributes to discovering the undetected molecular functions of lncRNAs. In recent years, increasingly computational approaches have substituted the traditional time-consuming experiments utilized to crack the possible unknown associations. However, significant explorations of the heterogeneity in association prediction between lncRNA and protein are inadequate. It remains challenging to integrate the heterogeneity of lncRNA-protein interactions with graph neural network algorithms.Methods: In this paper, we constructed a deep architecture based on GNN called BiHo-GNN, which is the first to integrate the properties of homogeneous with heterogeneous networks through bipartite graph embedding. Different from previous research, BiHo-GNN can capture the mechanism of molecular association by the data encoder of heterogeneous networks. Meanwhile, we design the process of mutual optimization between homogeneous and heterogeneous networks, which can promote the robustness of BiHo-GNN.Results: We collected four datasets for predicting lncRNA-protein interaction and compared the performance of current prediction models on benchmarking dataset. In comparison with the performance of other models, BiHo-GNN outperforms existing bipartite graph-based methods.Conclusion: Our BiHo-GNN integrates the bipartite graph with homogeneous graph networks. Based on this model structure, the lncRNA-protein interactions and potential associations can be predicted and discovered accurately.
Hypermethylation of Smad7 in CD4+ T cells is associated with the disease activity of rheumatoid arthritis
Authors: Hu Yiping , Xu Bihua , He Juan , Shan Hongying , Zhou Gengmin , Wang Deli , Bai Lu , Shang Hongxi , Nie Liping , Pan Fan , Lan Hui Yao , Wang Qingwen 
Published: February 2023

BackgroundSmad7 is protective in a mouse model of rheumatoid arthritis. Here we investigated whether Smad7-expressing CD4+ T cells and the methylation of Smad7 gene in CD4+ T cells contribute to the disease activity of RA in patients.MethodsPeripheral CD4+ T cells were collected from 35 healthy controls and 57 RA patients. Smad7 expression by CD4+ T cells were determined and correlated with the clinical parameters of RA including RA score and serum levels of IL-6, CRP, ESR, DAS28-CRP, DAS28-ESR, Swollen joints and Tender joints. Bisulfite sequencing (BSP-seq) was used to determine the DNA methylation in Smad7 promoter (-1000 to +2000) region in CD4+ T cells. In addition, a DNA methylation inhibitor, 5-Azacytidine (5-AzaC), was added to CD4+ T cells to examine the possible role of Smad7 methylation in CD4+ T cell differentiation and functional activity.ResultsCompared to the heath controls, Smad7 expression was significantly decreased in CD4+ T cells from RA patients and inversely correlated with the RA activity score and serum levels of IL-6 and CRP. Importantly, loss of Smad7 in CD4+ T cell was associated with the alteration of Th17/Treg balance by increasing Th17 over the Treg population. BSP-seq detected that DNA hypermethylation occurred in the Smad7 promoter region of CD4+ T cells obtained from RA patients. Mechanistically, we found that the DNA hypermethylation in the Smad7 promoter of CD4+ T cells was associated with decreased Smad7 expression in RA patients. This was associated with overreactive DNA methyltransferase (DMNT1) and downregulation of the methyl-CpG binding domain proteins (MBD4). Inhibition of DNA methylation by treating CD4+ T cells from RA patients with 5-AzaC significantly increased Smad7 mRNA expression along with the increased MBD4 but reduced DNMT1 expression, which was associated with the rebalance in the Th17/Treg response.ConclusionDNA hypermethylation at the Smad7 promoter regions may cause a loss of Smad7 in CD4+ T cells of RA patients, which may contribute to the RA activity by disrupting the Th17/Treg balance.
End-member characteristics of sediment grain size in modern Yellow River delta sediments and its environmental significance
Authors: Meng Liwei , Wang Longsheng , Zhao Jiawen , Zhan Chao , Liu Xianbin , Cui Buli , Zeng Lin , Wang Qing 
Published: February 2023

IntroductionThe sediments of the Yellow River delta record the environmental changes in the Yellow River basin on a long time scale and are sensitive to the river diversion and sedimentary environment evolution.MethodsIn this study, cores YDC and YDG in the delta near the estuary of the Yellow River since 1976 were taken as the research object, and the parameterized end-member analysis model was used to analyze the grain-size data of the cores.ResultsThe results show that: The main sediments were silty and sand (58% and 77.9%). The grain-size parameters showed opposite changes with wide grain-size ranges and mixed sizes obviously. End member 1 (EM1) and end member 2 (EM2) were composed of clay and fine silt with fine particle sizes of 0.04 mm and 9.8 mm, respectively, and were deposited under weak hydrodynamic conditions during long-distance transport along the Yellow River. End member 3 (EM3) and end member 4 (EM4) were coarse silt with mode particle sizes of 40.14 mm and 66.89 mm, respectively. These were deposited by waves and tidal currents under strong dynamic conditions.DiscussionAccording to the channel changes and the sedimentary facies data of the modern Yellow River delta, before the Yellow River was diverted in 1996, the cores YDC and YDG were both in the estuary-front bar sedimentary environment. In 1996, the Yellow River was diverted to the Qing 8 course. Subsequently, the core YDC changed to the delta-plain sedimentary facies, and the core YDG changed to the delta-front facies. The sediment sources of the two cores changed from the Yellow River sediments to coastal sediment erosion and resuspension. The sedimentary environment changed from siltation to erosion. The results of this study are of great practical significance for estuary management and coastal engineering construction in the modern Yellow River delta and can provide a scientific basis for ecological protection and high-quality development of the Yellow River basin.
Can circulating oxidative stress-related biomarkers be used as an early prognostic marker for COVID-19?
Authors: Uysal Pelin , Yüksel Arzu , Durmus Sinem , Cuhadaroglu Çaglar , Gelisgen Remise , Uzun Hafize 
Published: February 2023

BackgroundOxidative stress plays an important role in the pathogenesis of many diseases. This study aimed to investigate the relationship between nuclear factor kappa B (NF-κB) and oxidative stress and the severity of the disease in new COVID-19 patients, and, to compare the levels of NF-κB, oxidized LDL (oxLDL), and lectin-like oxidized-LDL receptor-1 (LOX-1) with oxygen saturation, which is an indicator of the severity parameters of the disease in COVID-19 patients.MethodsIn this prospective study, 100 COVID-19 patients and 100 healthy subjects were selected.ResultsLOX-1, NF-κB, and oxLDL were found to be higher in COVID-19 patients compared to the healthy subjects (p &lt; 0.001 for all). According to the results of correlation analysis, it was found that there was no significant relationship between oxygen saturation and LOX-1, NF-κB and oxLDL parameters. There was significant relationship between oxLDL with LOX-1 and NF-κB in patients with COVID-19 disease. ROC analysis results of the highest discrimination power were oxLDL (AUC: 0.955, CI: 0.904–1.000; sensitivity: 77%, and specificity: 100%, for cutoff: 127.944 ng/l) indicating COVID-19.ConclusionOxidative stress plays an essential role in COVID-19. NF-κB, oxLDL, and LOX-1 seem to represent good markers in COVID-19. Our study also showed that oxLDL has the highest power in distinguishing patients with COVID-19 from the healthy subjects.
In vitro digestion of ESC-resistant Escherichia coli from poultry meat and evaluation of human health risk
Authors: Buberg May Linn , Wasteson Yngvild , Lindstedt Bjørn Arne , Witsø Ingun Lund 
Published: February 2023

IntroductionThe spread of antimicrobial resistance (AMR) has become a threat against human and animal health. Third and fourth generation cephalosporins have been defined as critically important antimicrobials by The World Health Organization. Exposure to Extended spectrum cephalosporin-resistant E. coli may result in consumers becoming carriers if these bacteria colonize the human gut or their resistance genes spread to other bacteria in the gut microbiota. In the case that these resistant bacteria at later occasions cause disease, their resistance characteristics may lead to failure of treatment and increased mortality. We hypothesized that ESC-resistant E. coli from poultry can survive digestion and thereby cause infections and/or spread their respective resistance traits within the gastro-intestinal tract.MethodsIn this study, a selection of 31 ESC-resistant E. coli isolates from retail chicken meat was exposed to a static in vitro digestion model (INFOGEST). Their survival, alteration of colonizing characteristics in addition to conjugational abilities were investigated before and after digestion. Whole genome data from all isolates were screened through a custom-made virulence database of over 1100 genes for virulence- and colonizing factors.Results and discussionAll isolates were able to survive digestion. Most of the isolates (24/31) were able to transfer their blaCMY2-containing plasmid to E. coli DH5-á, with a general decline in conjugation frequency of digested isolates compared to non-digested. Overall, the isolates showed a higher degree of cell adhesion than cell invasion, with a slight increase after digestion compared non-digested, except for three isolates that displayed a major increase of invasion. These isolates also harbored genes facilitating invasion. In the virulence-associated gene analysis two isolates were categorized as UPEC, and one isolate was considered a hybrid pathogen. Altogether the pathogenic potential of these isolates is highly dependent on the individual isolate and its characteristics. Poultry meat may represent a reservoir and be a vehicle for dissemination of potential human pathogens and resistance determinants, and the ESC-resistance may complicate treatment in the case of an infection.
Retrospective analysis of Plasmodium vivax genomes from a pre-elimination China inland population in the 2010s
Authors: Liu Ying , Zhang Tao , Chen Shen-Bo , Cui Yan-Bing , Wang Shu-Qi , Zhang Hong-Wei , Shen Hai-Mo , Chen Jun-Hu 
Published: February 2023

IntroductionIn malaria-free countries, imported cases are challenging because interconnections with neighboring countries with higher transmission rates increase the risk of parasite reintroduction. Establishing a genetic database for rapidly identifying malaria importation or reintroduction is crucial in addressing these challenges. This study aimed to examine genomic epidemiology during the pre-elimination stage by retrospectively reporting whole-genome sequence variation of 10 Plasmodium vivax isolates from inland China.MethodsThe samples were collected during the last few inland outbreaks from 2011 to 2012 when China implemented a malaria control plan. After next-generation sequencing, we completed a genetic analysis of the population, explored the geographic specificity of the samples, and examined clustering of selection pressures. We also scanned genes for signals of positive selection.ResultsChina’s inland populations were highly structured compared to the surrounding area, with a single potential ancestor. Additionally, we identified genes under selection and evaluated the selection pressure on drug-resistance genes. In the inland population, positive selection was detected in some critical gene families, including sera, msp3, and vir. Meanwhile, we identified selection signatures in drug resistance, such as ugt, krs1, and crt, and noticed that the ratio of wild-type dhps and dhfr-ts increased after China banned sulfadoxine-pyrimethamine (SP) for decades.DiscussionOur data provides an opportunity to investigate the molecular epidemiology of pre-elimination inland malaria populations, which exhibited lower selection pressure on invasion and immune evasion genes than neighbouring areas, but increased drug resistance in low transmission settings. Our results revealed that the inland population was severely fragmented with low relatedness among infections, despite a higher incidence of multiclonal infections, suggesting that superinfection or co-transmission events are rare in low-endemic circumstances. We identified selective signatures of resistance and found that the proportion of susceptible isolates fluctuated in response to the prohibition of specific drugs. This finding is consistent with the alterations in medication strategies during the malaria elimination campaign in inland China. Such findings could provide a genetic basis for future population studies, assessing changes in other pre-elimination countries.