bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated bioinformatics to identify potential key biomarkers for COVID-19-related chronic urticaria
Authors: Zhang Teng , Feng Hao , Zou Xiaoyan , Peng Shixiong 
Published: December 2022

BackgroundA lot of studies have revealed that chronic urticaria (CU) is closely linked with COVID-19. However, there is a lack of further study at the gene level. This research is aimed to investigate the molecular mechanism of COVID-19-related CU via bioinformatic ways.MethodsThe RNA expression profile datasets of CU (GSE72540) and COVID-19 (GSE164805) were used for the training data and GSE57178 for the verification data. After recognizing the shared differently expressed genes (DEGs) of COVID-19 and CU, genes enrichment, WGCNA, PPI network, and immune infiltration analyses were performed. In addition, machine learning LASSO regression was employed to identify key genes from hub genes. Finally, the networks, gene-TF-miRNA-lncRNA, and drug-gene, of key genes were constructed, and RNA expression analysis was utilized for verification.ResultsWe recognized 322 shared DEGs, and the functional analyses displayed that they mainly participated in immunomodulation of COVID-19-related CU. 9 hub genes (CD86, FCGR3A, AIF1, CD163, CCL4, TNF, CYBB, MMP9, and CCL3) were explored through the WGCNA and PPI network. Moreover, FCGR3A, TNF, and CCL3 were further identified as key genes via LASSO regression analysis, and the ROC curves confirmed the dependability of their diagnostic value. Furthermore, our results showed that the key genes were significantly associated with the primary infiltration cells of CU and COVID-19, such as mast cells and macrophages M0. In addition, the key gene-TF-miRNA-lncRNA network was constructed, which contained 46 regulation axes. And most lncRNAs of the network were proved to be a significant expression in CU. Finally, the key gene-drug interaction network, including 84 possible therapeutical medicines, was developed, and their protein-protein docking might make this prediction more feasible.ConclusionsTo sum up, FCGR3A, TNF, and CCL3 might be potential biomarkers for COVID-19-related CU, and the common pathways and related molecules we explored in this study might provide new ideas for further mechanistic research.
Applying behavioral studies to the ecotoxicology of corals: A case study on Acropora millepora
Authors: Roepke Lisa K. , Brefeld David , Soltmann Ulrich , Randall Carly J. , Negri Andrew P. , Kunzmann Andreas 
Published: December 2022

Behavioral responses are considered sensitive and effective indicators of organism stress. As the demand for standardized coral toxicity tests grows, innovative tools that allow for automatic and quantitative measurements of these behaviors may complement ecotoxicological studies. The rapid growth of competitive marine algae in aquaculture systems is a major issue for generating coral spat for reef restoration, and the application of non-toxic antifouling (AF) coatings might effectively mitigate this issue. While these coatings do not appear to be toxic to sensitive coral larvae, their potential to affect larval mobility has not been tested. In this context, we tested the effect of three recently-developed and potentially non-toxic AF coatings: (i) antiadhesive, (ii) cerium dioxide (CeO2-x) nanoparticle, and (iii) encapsulated biocide dichlorooctylisothiazolinone (DCOIT) on the swimming velocity and activity of Acropora millepora coral larvae for potential use in reef-restoration activities. The behavior of 32 coral larvae per AF treatment were recorded, each for 25 min, in a self-constructed dark box with two camera recording sets in parallel. The tracking analysis was performed with the software Noldus EthoVision XT. The mean larval swimming velocity on control tiles of 93.1 ± 5.6 mm min-1 (and activity of 62.8 ± 5.2%) was nearly 2-fold faster (higher) than on the antiadhesive, (CeO2-x) nanoparticle and DCOIT coatings, respectively. Larvae exposed to the DCOIT-coated tiles remained almost stationary. Although the underlying cause and consequence of these results require further investigation, tracking of coral larval swimming behavior was identified as a reliable and feasible method for assessing potential non-lethal responses to AF coatings. As changes in behavior could have significant consequences for larval survival and settlement, they are important endpoints to consider, and the quantification of behavioral responses may be a meaningful and sensitive tool. Therefore, we recommend the use of behavioral studies for coral larval assessments in ecotoxicology as a valuable endpoint. For methodological standardization and implementation, our study also features a detailed guide for video-processing and track analysis of A. millepora coral larvae in EthoVision.
Nitrogen-loss and associated microbial communities in sediments from the Yangtze Estuary and adjacent sea
Authors: Teng Zhenzhen , Zhen Yu , Yu Zhigang , Mi Tiezhu , Cai Tao 
Published: December 2022

IntroductionDenitrification and anammox play the crucial role for N removal processes in coastal ecosystems, but the ecological distribution of denitrifying and anammox microorganisms and their N removal rates in the Yangtze Estuary and its adjacent sea are required in-depth analysis.MethodsHere, we utilized high-throughput sequencing, qPCR, and 15N isotope to reveal the community structure and function of denitrifying and anammox microorganisms in the surface sediments from Yangtze Estuary and adjacent sea.ResultsThe results suggested that the gene abundances of nirS and nirK for denitrifiers were higher than AMX 16S rRNA for anammox bacteria. The genera composition of nirS- and nirK-encoding denitrifiers communities showed different distribution patterns. Furthermore, Candidatus Anammoximicrobium dominated the anammox community, implying the anammox oxidation capacity of the other genera should be noted in marine sediments.DiscussionCompared to anammox, denitrification was the dominant contributor of nitrogen removal process and contributed 73.5% on average. The sediment Chla was the key factor to regulate denitrification and anammox rates, indicating the fresh organic matter was more labile and easier to be utilized by NOx− removal processes.
Study of friction and wear behaviors of Fe-based amorphous coatings by MD simulations
Authors: Chu Zhenhua , Zhou Yuyun , Xu Fa , Xu Jingxiang , Zheng Xingwei , Luo Xiaotao , Shu Yan , Zhang Zheng , Hu Qingsong 
Published: December 2022

In this study, molecular dynamics simulation is adopted to investigate the friction and wear mechanism of Fe-based amorphous composited coatings. It was found that the ceramic phase can improve plasticity of the composite coatings to reduce wear. In addition, when the Al2O3 content is 15 wt%, due to the stress concentration between ceramic phase and amorphous phase, the viscosity flow in the amorphous phase results in plastic deformation. Through this, the best wear resistance has been obtained. In addition, with the increase of compression depth, the number of atoms accumulated constantly increases, and the degree of plastic deformation becomes higher in the composite coatings. Finally, a high sliding speed results in the reduction of the wear resistance of coatings.
Efficacy of acupoint stimulation as a treatment for uremic pruritus: A systematic review and meta-analysis
Authors: Lu Ping-Hsun , Chung Chia-Hsiang , Chuo Hui-En , Lin I-Hsin , Lu Po-Hsuan 
Published: December 2022

BackgroundUremic pruritus causes sleep disturbances, poor quality of life, and increased morbidity in patients with chronic kidney disease. Acupuncture has been shown to improve uremic pruritus. There is limited evidence of the efficacy of traditional Chinese therapies. We conducted a systematic review and meta-analysis to evaluate the efficacy of acupoint stimulation therapy in patients with uremic pruritus.MethodsA systematic search of seven databases (up to Sep 2022) was conducted for randomized controlled trials that evaluated the clinical efficacy of acupuncture, acupressure, auricular acupressure, acupoint injection, acupoint thermal therapy, acupoint sticking therapy, or transcutaneous electrical acupoint stimulation in the treatment of patients with uremic pruritus. Two reviewers selected eligible articles for inclusion in the meta-analysis and evaluated the risk of bias via Cochrane Collaboration. The results of pruritus assessments and uremic pruritus-related laboratory parameters were analyzed.ResultsForty trials published between 2002 and 2022, including a total of 2,735 participants, were identified for inclusion in the meta-analysis. The effective rates for acupuncture, auricular acupressure, and the combination of acupoint injection and acupoint massage were significantly greater in patients with uremic pruritus compared to the control group. The levels of serum BUN, PTH, and histamine levels were significantly lower vs. control group.ConclusionsAcupuncture, auricular acupressure, and the combination of acupoint injection and acupoint massage seem to be effective in improving uremic pruritus in patients with chronic kidney disease. However, further investigation of these potential treatments is now warranted in larger patient populations and over a longer time frame.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022354585, identifier: PROSPERO CRD42022354585.
TissueGrinder, a novel technology for rapid generation of patient-derived single cell suspensions from solid tumors by mechanical tissue dissociation
Authors: Scheuermann Stefan , Lehmann Jonas M. , Ramani Mohan Ramkumar , Reißfelder Christoph , Rückert Felix , Langejürgen Jens , Pallavi Prama 
Published: December 2022

IntroductionRecent advances hold promise of making personalized medicine a step closer to implementation in clinical settings. However, traditional sample preparation methods are not robust and reproducible. In this study, the TissueGrinder, a novel mechanical semi-automated benchtop device, which can isolate cells from tissue in a very fast and enzyme-free way is tested for cell isolation from surgically resected tumor tissues.MethodsThirty-three surgically resected tumor tissues from various but mainly pancreatic, liver or colorectal origins were processed by both novel TissueGrinder and explant method. An optimized processing program for tumors from pancreatic, liver or colorectal cancer was developed. The viability and morphological characteristics of the isolated cells were evaluated microscopically. Expression of pancreatic cancer markers was evaluated in cells isolated from pancreatic tumors. Finally, the effect of mechanical stress on the cells was evaluated by assessing apoptosis markers via western blotting.ResultsTissueGinder was more efficient in isolating cells from tumor tissue with a success rate of 75% when compared to explant method 45% in terms of cell outgrowth six weeks after processing. Cells isolated with TissueGinder had a higher abundance and were more heterogeneous in composition as compared to explant method. Mechanical processing of the cells with TissueGrinder does not lead to apoptosis but causes slight stress to the cells.DiscussionOur results show that TissueGrinder can process solid tumor tissues more rapidly and efficiently and with higher success rate compared to the conventionally used explant method. The results of the study suggest that the TissueGrinder might be a suitable method for obtaining cells, which is important for its application in individualized therapy. Due to the great variance in different tumor entities and the associated individual tissue characteristics, a further development of the dissociation protocol for other types of tumors and normal tissue will be targeted.
Frequent exacerbators of chronic obstructive pulmonary disease have distinguishable sputum microbiome signatures during clinical stability
Authors: Dang Xiaomin , Kang Yongyong , Wang Xiaojian , Cao Wen , Li Minhui , He Ying , Pan Xinjie , Ye Kai , Xu Dan 
Published: December 2022

IntroductionFrequent exacerbation phenotype of chronic obstructive pulmonary disease (COPD) represents a more concerning disease subgroup requiring better prevention and intervention, of which airway microbiome provides new perspective for further exploration.MethodsTo investigate whether frequent exacerbators of COPD have distinguishable sputum microbiome during clinical stability, COPD patients at high disease grades with or without frequent exacerbation were recruited for sputum microbiome analysis. Sputum samples were collected during clinical stability and underwent 16S rRNA sequencing, which was then subjected for amplicon sequence variants (ASVs)-based microbiome analysis.ResultsOur results revealed that compared with healthy controls and infrequent exacerbators, frequent COPD exacerbators have distinguishably dysbiotic sputum microbiome, as featured by fewer ASVs features, lower alpha diversity, distinct beta diversity patterns. Further taxonomic compositional analysis illustrated the structural distinctions between frequent COPD exacerbators and infrequent exacerbators at differential taxa levels and highlighted Stenotrephomonas due to its prominent elevation in frequent COPD exacerbators, providing a promising candidate for further exploration of microbiome biomarker. Moreover, we also demonstrated that frequent exacerbation phenotype is distinguishable from infrequent exacerbation phenotype with respect of functional implications.ConclusionOur study demonstrated the first positive correlation between the frequent exacerbation phenotype of COPD and the sputum microbiome during clinical stability in a single-center Chinese COPD cohort and provide potential diagnostic and therapeutic targets for further investigation.
Probiotic supplementation during pregnancy alters gut microbial networks of pregnant women and infants
Authors: Huang Ting , Li Zhe , Tye Kian Deng , Chan Sze Ngai , Tang Xiaomei , Luo Huijuan , Wang Dongju , Zhou Juan , Duan Xia , Xiao Xiaomin 
Published: December 2022

BackgroundProbiotic supplementation has been popular and widespread, yet we still lack a comprehensive understanding of how probiotic supplementation during pregnancy affects the gut microbial networks of pregnant women and infants. In this study, we firstly used network analysis to compare the gut microbiota of pregnant women with and without probiotic supplementation, as well as their infants.MethodsThirty-one pairs of healthy pregnant women and infants were recruited and randomly divided into the probiotic group (15 mother-infant pairs) and the control group (16 mother-infant pairs). Pregnant women in the probiotic group consumed combined probiotics from 32 weeks to delivery. Fecal samples were collected from pregnant women and infants at several time points. Gut microbiota was evaluated using 16S rRNA gene sequencing. Intestinal microbial network and topological properties were performed using the molecular ecological network analysis.ResultsNo significant difference was found between the probiotic and control groups on the microbial alpha and beta diversity. As the gestational age increased, the total links, average degree, average clustering coefficient, robustness, and the proportion of positive correlations were increased in pregnant women with probiotics administration. In contrast, these indices were decreased in infants in the probiotic group.ConclusionProbiotic supplement does not change the microbial diversity of pregnant women and infants, but significantly alters the intestinal microbial network structure and properties. Although pregnant women have more complicated and stable networks after probiotic administration, their infants have less stable networks.
Horizontal gene transfer via OMVs co-carrying virulence and antimicrobial-resistant genes is a novel way for the dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae
Authors: Li Ping , Luo Wanying , Xiang Tian-Xin , Jiang Yuhuan , Liu Peng , Wei Dan-Dan , Fan Linping , Huang Shanshan , Liao Wenjian , Liu Yang , Zhang Wei 
Published: December 2022

IntroductionThe rapidly increased isolation rate of CR-HvKP worldwide has brought great difficulties in controlling clinical infection. Moreover, it has been demonstrated that the transmission of drug-resistant genes among bacteria can be mediated by outer membrane vesicles (OMVs), which is a new way of horizontal gene transfer (HGT). The transmission of virulence genes among bacteria has also been well studied; however, it remains unclear whether virulence and drug-resistant genes can be co-transmitted simultaneously. Co-transmission of virulence and drug-resistant genes is essential for the formation and prevalence of CR-HvKP.MethodsFirst, we isolated OMVs from CR-HvKP by cushioned-density gradient ultracentrifugation (C-DGUC). TEM and DLS were used to examine the morphology and size of bacterial OMVs. OMV-mediated gene transfer in liquid cultures and the acquisition of the carbapenem gene and virulence gene was confirmed using colony-PCR. Antimicrobial susceptibility testing, mCIM and eCIM were conducted for the resistance of transformant. Serum killing assay, assessment of the anti-biofilm effect and galleria mellonella infection model, mucoviscosity assay, extraction and quantification of capsules were verified the virulence of transformant. Pulsed-field gel electrophoresis (PFGE), S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting hybridization confirmed the plasmid of transformant.ResultsFirstly, OMVs were isolated from CR-HvKP NUHL30457 (K2, ST86). TEM and DLS analyses revealed the spherical morphology of the vesicles. Secondly, our study demonstrated that CR-HvKP delivered genetic material, incorporated DNA within the OMVs, and protected it from degradation by extracellular exonucleases. Thirdly, the vesicular lumen DNA was delivered to the recipient cells after determining the presence of virulence and carbapenem-resistant genes in the CR-HvKP OMVs. Importantly, S1-PFGE and Southern hybridization analysis of the 700603 transformant strain showed that the transformant contained both drug-resistant and virulence plasmids.DiscussionIn the present study, we aimed to clarify the role of CRHvKP-OMVs in transmitting CR-HvKP among K. pneumoniae. Collectively, our findings provided valuable insights into the evolution of CR-HvKP.
Physical-model guided self-distillation network for single image dehazing
Authors: Lan Yunwei , Cui Zhigao , Su Yanzhao , Wang Nian , Li Aihua , Han Deshuai 
Published: December 2022

MotivationImage dehazing, as a key prerequisite of high-level computer vision tasks, has gained extensive attention in recent years. Traditional model-based methods acquire dehazed images via the atmospheric scattering model, which dehazed favorably but often causes artifacts due to the error of parameter estimation. By contrast, recent model-free methods directly restore dehazed images by building an end-to-end network, which achieves better color fidelity. To improve the dehazing effect, we combine the complementary merits of these two categories and propose a physical-model guided self-distillation network for single image dehazing named PMGSDN.Proposed methodFirst, we propose a novel attention guided feature extraction block (AGFEB) and build a deep feature extraction network by it. Second, we propose three early-exit branches and embed the dark channel prior information to the network to merge the merits of model-based methods and model-free methods, and then we adopt self-distillation to transfer the features from the deeper layers (perform as teacher) to shallow early-exit branches (perform as student) to improve the dehazing effect.ResultsFor I-HAZE and O-HAZE datasets, better than the other methods, the proposed method achieves the best values of PSNR and SSIM being 17.41dB, 0.813, 18.48dB, and 0.802. Moreover, for real-world images, the proposed method also obtains high quality dehazed results.ConclusionExperimental results on both synthetic and real-world images demonstrate that the proposed PMGSDN can effectively dehaze images, resulting in dehazed results with clear textures and good color fidelity.
Elderly onset of MELAS in a male: A case report
Authors: Diao Sheng-Peng , Chen Song-Fa , Liu Ai-Qun , Zhou Zhi-Hua , Peng Zhong-Xing , Hong Ming-Fan 
Published: December 2022

BackgroundMitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) is one of the most common maternally inherited mitochondrial diseases which rarely affects elderly people.Case presentationWe reported the case of a 61-year-old male patient with MELAS. He was experiencing acute migraine-like headaches as the first symptoms. Laboratory data showed elevated lactate and creatine kinase levels. Brain magnetic resonance imaging (MRI) found a high signal intensity lesion in the left occipital-temporal-parietal lobe on diffusion-weighted imaging (DWI). Magnetic resonance angiography (MRA) revealed reversible vasoconstriction of the middle cerebral arteries and superficial temporal arteries. A muscle biopsy suggested minor muscle damage. A genetic study revealed a mitochondrial DNA A3243G mutation.ConclusionElderly onset of MELAS is rare and easily misdiagnosed as an ischemic stroke. MELAS with the onset of stroke-like episodes should be considered in adult or elderly patients with imaging findings that are atypical for cerebral infarction. The use of multimodal MRI in the clinical diagnosis of MELAS could be extremely beneficial.