bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproducible and Opposing Microbiome Signatures Distinguish Autoimmune Diseases and Cancers: A Systematic Review and Meta-Analysis
Authors: Islam Md Zohorul , Tran Melissa , Xu Tao , Tierney Braden T. , Patel Chirag , Kostic Aleksandar David 
Published: December 2021

Abstract
Background: The gut microbiome promotes specific immune responses, and in turn the immune system has a hand in shaping the microbiome. Cancer and autoimmune diseases are two major disease families that result from the contrasting manifestations of immune dysfunction. We hypothesized that the opposing immunological profiles between cancer and autoimmunity yield analogously inverted gut microbiome signatures. To test this, we conducted a systematic review and meta-analysis on gut microbiome signatures and their directionality in cancers and autoimmune conditionsMethodology: We searched PubMed, Web of Science, and EMBAS to identify relevant articles to be included in this study. The study was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statements and PRISMA 2009 checklist. Study estimates were pooled by a generic inverse variance random-effects meta-analysis model. The relative abundance of microbiome features was converted to log fold-change and the standard error was calculated from the p-values, sample size and fold-change. Results: We screened 3,874 potentially relevant publications. A total of 82 eligible studies comprising 37 autoimmune and 45 cancer studies with 4,208 healthy human controls and 5,957 disease cases from 27 countries were included in this study. We identified a set of microbiome features that show consistent, opposite directionality between cancers and autoimmune diseases in multiple studies. Fusobacterium and Peptostreptococcus were the most consistently increased genera among the cancer cases which were found to be associated in a remarkable 13 (+0.54 log fold-change in 5 studies) and 11 studies (+3.75 log fold-change in 5 studies), respectively. Conversely, Bacteroides was the most prominent genus, which was found to be increased in 12 autoimmune studies (+0.24 log fold-change in 6 studies) and decreased in six cancer studies (-0.32 log fold-change in 4 studies). Sulfur-metabolism pathways were found to be the most frequent pathways among the member of cancer-increased genus and species.Conclusions: The surprising reproducibility of these associations across studies and geographies suggests a shared underlying mechanism shaping the microbiome across cancers and autoimmune diseases.
Preparation and Methylene Blue Adsorption Capacity of HDPE/PVA Foaming Composites
Authors: Li Fenghong , Wang Zhe , Li Pengzhen , Da Wei , Lv Weisi , Guo Keyun , Huang Feihong 
Published: December 2021

Abstract
High density polyethylene (HDPE) and polyvinyl alcohol (PVA) are blended with maleic anhydride grafted amorphous-alpha olefin copolymer as the compatibilizer. The effects of different raw material ratio and the content of compatibilizer and foaming agent on the mechanical properties of the material are studied. It is found that the increasing content of PVA added to HDPE has a negative effect on the properties of the composites. The compatibility and mechanical properties are improved after adding MAH-g-APAO and the most appropriate addition amount is 4%. Foaming agent can make the material lightweight but will decrease the mechanical properties of the material. The composites have a good effect on the removal of methylene blue (MB). Through the experiment, it is found that the initial concentration of MB and adsorption time will also influence the adsorption. The experiment to explore the influence of pH value and temperature of solution on the removal efficiency shows that alkaline environment and high temperature can promote the removal of MB. At 343.15 K, the adsorption capacity (qe) reaches 2.08 mg·g-1. Using the composites to remove dye has the advantages of environmental protection, simple operation and easy recycling. It has broad application prospects in the field of dye wastewater treatment.
Top of Basilar Artery Infarction: A Case Series from Sudan
Authors: Daoud Mahmoud Hussien Salih , Ahmed.E.Abushama Ejlal , Mahmmoud Abdallah.H , Eljack Moh.Mah.Fadelallah , Hussein Khabab Abbashar , Haroun Mazin S. , Elsheikh Duaa Baderaldeen Ibraheem , Abdelkareim.G.Mohammed Sulieman , Eltayeb.O.Eltayeb Ahmed , Allah Yusif Abduelmagid.M.Naiem , Ahmed Al ameen Ahmed Alameen , Yusif Mohamed Yusif Mohamed , Mokhtar Asmaa Esam Abbas , Awadalbari Sarra Nasreldeen Ibrahim , Eltayeb Rowda Babikir Osman 
Published: December 2021

Abstract
The posterior circulation represents 20% of blood supply of the brain and its occlusion commonly by embolism cause brainstem, cerebellar and lower cerebral infarction. The clinical presentation varies from mild innocent symptoms leading to sever neurological deficit or death. Time of intervention is vital commonly with antithrombatic drugs or through intervention. Here, we report two Sudanese patients who had a complicated medical sequence over months ended as top of basilar artery occlusion received anticoagulants and supportive therapy according to their condition showed a variable recovery over weeks.
Motherhood Modulates Cognitive Biases Toward Family Members: the Maternal Self-concept Re-examined Through Categorization Tasks
Authors: Jiang Mengyin , Sui Jie 
Published: December 2021

Abstract
The self-bias is a robust effect where self-related information is processed with greater priority than other-related information. Interestingly, the advantages of self-bias can be extended to close others – faster and more accurate responses for one’s mother and best friend have been observed compared to strangers – suggesting that significant others play an important role in the formation of one’s self-concept. Moreover, important life experiences such as childbirth can also impact the self-concept. Motherhood is a major transformation for women as one prepares to become a mother while maintaining the integrity of the pre-pregnant self-concept to achieve an ideal maternal self. The current study explored how the transition into motherhood changes the self-concept and subsequently impact the categorization of information for family members in postpartum mothers. In two experiments, results consistently revealed biases towards the self and close kin (one’s baby and mother) regardless of stimulus type (names in Experiment 1, faces in Experiment 2) and response category (self/other, family/non-family, familiar/non-familiar). A family bias (for baby and mother) over friend was observed in the family/non-family but not in the familiar/non-familiar categorization task, suggesting that motherhood may enhance the boundary between family and non-family to facilitate the processing of family-related information.
The extensive intergenerational molecular effects of ocean acidification on the olfactory epithelium transcriptome of a marine fish are associated with a better viral resistance
Authors: Cohen-Rengifo Mishal , Danion Morgane , Gonzalez Anne-Alicia , Bégout Marie-Laure , Madec Lauriane , Cormier Alexandre , Noël Cyril , Cabon Joëlle , Vitré Thomas , Mark Felix C. , Mazurais David 
Published: December 2021

Abstract
Background

Progressive climate-induced ocean acidification (OA) impacts marine life in ways that are difficult to predict but are likely to become exacerbated over generations. Although marine fishes can balance internal acid-base homeostasis efficiently, indirect ionic regulation effects that alter neurosensory systems can result in behavioural abnormalities. In marine invertebrates, OA can also affect immune system function, but whether this is the case in marine fishes of ecological and commercial importance is not yet understood. Farmed fish are highly susceptible to disease outbreak yet strategies for overcoming such threats in the wake of OA are wanting. Here, we exposed two generations of the European sea bass (Dicentrarchus labrax) to end-of-century predicted CO2 levels (IPCC RCP8.5), with parents being exposed for four years and their offspring for two years. Our design included a transcriptomic analysis of the olfactory rosette (collected from the F1 offspring) and a viral challenge (exposing F1 offspring to betanodavirus) where we assessed survival rates.
Results

We discovered long-term intergenerational molecular trade-offs in both sensory and immune systems. Specifically, RNA-Seq analysis of the olfactory rosette, the peripheral olfactory organ, from two-year-old F1 offspring revealed extensive regulation in genes involved in ion transport and neuronal signalling, including GABAergic signalling. We also detected extensive OA-induced intergenerational up-regulation of genes associated with odour transduction, synaptic plasticity, neuron excitability and wiring and down-regulation of genes involved in energy metabolism. In addition, intergenerational exposure to OA induced up-regulation of genes involved in innate antiviral immunity (pathogen recognition receptors and interferon-stimulated genes) in combination with down-regulation of the protein biosynthetic machinery. Consistently, OA-exposed F1 fish challenged with betanodavirus, which causes damage to the nervous system of marine fish, had acquired improved resistance.
Conclusion

F1 exposed to OA-intergenerational acclimation showed superior viral resistance, though as their metabolic and odour transduction programs were altered, odour-mediated behaviours might be consequently altered. Our results reveal that trade-offs in adaptive plastic responses is a core feature of the olfactory epithelium transcriptome in OA-exposed fish, suggesting that intergenerational plasticity propagate with progressive exposure to OA and will have important consequences for how cultured and wild fish interacts with its environment.
Knowledge, Attitude and Acceptance of a COVID-19 Vaccine in Indian Population : a Cross Sectional Study
Authors: Soni Aditya , Tripathi Devanshi , Bhaskar Manju , Modi Rujul 
Published: December 2021

Abstract
INTRODUCTION: The COVID-19 pandemic keeping on to devastate the world. A vaccine provides the best hope to control the pandemic. Understanding vaccine acceptance is important, because there is relatively high vaccine hesitancy for existing vaccines and relatively low vaccination coverage. MATERIALS AND METHODS: Participants included are adults between the age group of 18-29 years (n=100). This is a cross-sectional, web based observational study conducted over a period of 1 month. An online survey is carried out through distribution of questionnaire via social network with snow ball effect. RESULTS: A total 100 participants were included in the study. Almost more than half (55%) of the young adults aged between 18 and 29 years were oblivious about the COVID-19 vaccine availability, followed by 22% person aged between 30-39 years and 22% of the persons aged between 40- 59 years and around 1% of more than 60 years were oblivious about the vaccine availability. Among the study participants, nearly 40% were willing to take COVID-19 vaccine when it is available for use and only 30% did not want the vaccination. CONCLUSION: The most dominant factor for vaccine hesitancy is because of adverse effects following immunization. Vaccine acceptability may be increased once additional information about vaccine safety and efficacy is available in the public domain, preferably from a trusted, centralized source of information.
Prediction modeling of isoscapes for stable isotopes in China’s rice based on environmental similarity
Authors: Sheng Meiling , Zhang Weixing , Nie Jing , Li Chunlin , Zhu A-Xing , Hu Hao , Lou Weidong , Deng Xunfei , Lyu Xiaonan , Ren Zhouqiao , Rogers Karyne M. , Zhang Yongzhi , YUAN Yuwei 
Published: December 2021

Abstract
Rice quality is directly related to human health, so it is important to have traceability systems that can trace inferior or contaminated rice back to its geographical origin. This ensures farming practices in substandard regions become better regulated to improve rice quality, origin labelling and consumer trust. However, tracing the origin of rice on the marketplace requires an accurate database benchmarking the isotope distribution over areas of rice production. Large stable isotope data sets can be used to determine the geographical origin of rice through predictive isoscape models. This study presents the first rice isoscape based on environmental similarity to predict the geospatial distribution of δ13C, δ2H and δ18O values of Chinese rice and provides uncertainty at every location such prediction is made. For this study, 794 rice samples were collected in 2017 from primary rice production regions of China. An independent verification shows that the predicted isotope distribution from this new approach is of high accuracy, with a root mean squared error (RMSE) of 0.51‰, 7.09‰ and 2.06‰ for δ13C, δ2H and δ18O values respectively. In addition, uncertainty in the spatial distribution of isotopes can be used to indicate the prediction accuracy and to guide future sampling. Our results indicate that an isoscape prediction method based on environmental similarity is effective to predict the spatial distribution of stable isotope in rice, and is an effective tool for building isotope distribution in rice over large areas with complex environment. This method could also be used to predict potential isotopic variations in future years due to climate change.
Comparative efficacy of tocilizumab and baricitinib in COVID-19 treatment: a retrospective cohort study
Authors: Kojima Yuichi , Nakakubo Sho , Takei Nozomu , Kamada Keisuke , Yamashita Yu , Nakamura Junichi , Matsumoto Munehiro , Horii Hiroshi , Sato Kazuki , Shima Hideki , Suzuki Masaru , Konno Satoshi 
Published: December 2021

Abstract
Background

Although the biological agents tocilizumab and baricitinib have been shown to improve the outcomes of patients with COVID-19, a comparative evaluation has not been performed. The aim of our study was to evaluate the comparative effect of the use of tocilizumab and baricitinib on patient outcomes in COVID-19.
Methods

A retrospective, single-center study was conducted using the data of patients with COVID-19 admitted to Hokkaido University hospital between April 2020 and September 2021 and were treated with tocilizumab or baricitinib. The clinical characteristics of the patients who received each drug were compared. Univariate and multivariate logistic regression analyses were performed against the outcomes of all-cause mortality and the improvement in respiratory status. The development of secondary infection events was analyzed using the Kaplan–Meier method and the log-rank test.
Results

Among the 459 patients hospitalized with COVID-19 during the study, 64 received tocilizumab and 34 received baricitinib, and they were included in the study. Most patients were treated with concomitant steroids, and the severity of the disease at the time of initiation of biological agents was similar. The use of tocilizumab or baricitinib was not associated with all-cause mortality or the improvement in respiratory status within 28 days of drug administration. Age, chronic renal disease, and comorbid respiratory disease were independent prognostic factors for all-cause mortality, whereas anti-viral drug use and severity of COVID-19 at baseline were associated with the improvement in respiratory status. There was no significant difference in the infection-free survival rate between patients treated with tocilizumab and those with baricitinib.
Conclusion

There were no differences in efficacy and safety between tocilizumab and baricitinib in the treatment of COVID-19. Both these biological agents are expected to be equally safe and clinically effective.
Combinatorial Assembly and Optimisation of Designer Cellulosomes - A Galactomannan Case Study
Authors: Vanderstraeten Julie , Fonseca Maria João Maurício da , De Groote Philippe , Grimon Dennis , Gerstmans Hans , Kahn Amaranta , Moraïs Sarah , Bayer Edward A. , Briers Yves 
Published: December 2021

Abstract
Background: Designer cellulosomes are self-assembled chimeric enzyme complexes that can be used to improve lignocellulosic biomass degradation. They are composed of a synthetic multimodular backbone protein, termed the scaffoldin, and a range of different chimeric docking enzymes that degrade polysaccharides. Over the years, several functional designer cellulosomes have been constructed. Since many parameters influence the efficiency of these multi-enzyme complexes, there is a need to optimise designer cellulosome architecture by testing combinatorial arrangements of docking enzyme and scaffoldin variants. However, the modular cloning procedures are tedious and cumbersome. Results: VersaTile is a combinatorial DNA assembly method, allowing the rapid construction and thus comparison of a range of modular proteins. Here, we present the extension of the VersaTile platform to facilitate the construction of designer cellulosomes. We have constructed a tile repository, composed of dockerins, cohesins, linkers, tags and enzymatically active modules. The developed toolbox allows us to efficiently create and optimise designer cellulosomes at an unprecedented speed. As a proof of concept, a trivalent designer cellulosome able to degrade the specific hemicellulose substrate, galactomannan, was constructed and optimised. The main factors influencing cellulosome efficiency were found to be the selected dockerins and linkers and the docking enzyme ratio on the scaffoldin. The optimised designer cellulosome was able to hydrolyse the galactomannan polysaccharide and release mannose and galactose monomers. Conclusion: We have eliminated one of the main technical hurdles in the designer cellulosome field and anticipate the VersaTile platform to be a starting point in the development of more elaborate multi-enzyme complexes.
NLRP3 is Highly Expressed in Stomach Adenocarcinoma and May Serve as a Novel Prognostic Biomarker
Authors: Yuan Chenxi , Wang Qingwei , Song Yipeng , Yu Jinming 
Published: December 2021

Abstract
Background: Stomach adenocarcinoma (STAD) is a common cancer type around the world. The prognosis in advanced patients is poor. Since NLRP3 was not extensively studied in the field of tumor, so we aimed to identify the impact of NLRP3 on STAD by bioinformatics analyses and in vitro experiments. Methods: TCGA , kaplan-Meier Plotter and TIMER database were utilized in this study. We compared the expression of NLRP3 in different cancers and evaluated its influence on survival of gastric carcinoma patients. The correlations between clinical information and NLRP3 expression were analyzed using logistic regression. Clinicopathologic characteristics associated with overall survival in were analyzed by Cox regression. In addition, we explored the correlation between NLRP3 and immune infiltrates. GSEA and co-expressed gene with NLRP3 were also done in this study. Finally, we verified the NLRP3 expression in paired gastric cancer tissues and adjacent normal tissues by western blot and q-PCR. We also constructed NLRP3 overexpression model in gastric cancer cell line and observed cell proliferation ability.Results: NLRP3 expressed disparately in gastric tumor tissues and normal tissues. Cox regression analysis indicated that up-regulated NLRP3 was an independent prognostic factor for bad prognosis in STAD. Logistic regression analysis showed increased NLRP3 expression was significantly correlated with unfavorable clinicopathologic parameters such as higher T stage, higher histologic grade and worse survival outcome. Specifically, a positive correlation between increased NLRP3 expression and immune infiltrating level of various immune cells was observed. Conclusion: Together with all these findings, increased NLRP3 expression correlates with poor prognosis, unfavorable clinicopathologic parameters and increased proportion of immune cells in STAD. In vitro analysis revealed that cell proliferation ability was enhanced in gastric cancer cells trasnfected with NLRP3 overexpression. These conclusions indicate that NLRP3 has great potential to serve as a biomarker for evaluating prognosis in patients diagnosed with gastric carcinoma.
A Novel Prognostic Signature Based on Cell-In-Cell-Related Genes for Predicting Survival and Tumor Microenvironment in Pancreatic Cancer
Authors: Song Jianlu , Ruze Rexiati , Chen Yuan , Xu Ruiyuan , Yin Xinpeng , Wang Chengcheng , Zhao Yupei 
Published: December 2021

Abstract
Background: Pancreatic cancer (PC) is a highly malignant tumor featured with high intra-tumoral heterogeneity and poor prognosis. Cell-in-cell (CIC) structures have been reported in multiple tumor types, and their presence is thought to promote clonal selection and tumor evolution. Here, we aimed to establish a CIC-related gene signature for predicting the prognosis and evaluating immune microenvironment in PC. Methods: In this study, the gene expression data, as well as corresponding clinicopathological data of PC and normal pancreatic tissues were collected from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) databases. Differential gene expression analysis, random forest screening, least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analysis were performed on 101 CIC-related genes to construct a prognostic gene signature. The effectiveness and robustness of the prognostic gene signature were evaluated by receiver operating characteristic (ROC) curves, Kaplan-Meier survival analysis and establishing the nomogram model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to annotate the biological functions of the differentially expressed genes (DEGs). Quantitative real-time PCR (qRT-PCR), western blotting and immunohistochemistry (IHC) staining were validated the core gene expression in both mRNA and protein levels. Results: A 4-gene signature was constructed to stratify patients into the low-risk and high-risk groups with distinct survival outcomes, somatic mutation profiles and immune features. The high-risk group had poorer prognosis than did the low-risk group. This signature was found to be an independent prognostic factor for PC patients with favorable predictive efficiency. Functional enrichment analyses showed that numerous terms and pathways associated with invasion and metastasis were enriched in the high-risk group. Moreover, the high-risk group had a higher tumor mutation burdens and lower immune cell infiltrations. KRT7, as the most important risk gene, was significantly associated with the worse prognosis of PC. CIC formation assay performing in PC cell lines indicated that KRT7 expression was correlated with CIC frequency. Conclusions: The signature based on four CIC-related genes could be applicable for predicting the prognosis of PC, and targeting CIC processes may be a potential therapeutic option. Further studies are needed to reveal the underlying molecular mechanisms and biological implications of CIC in PC progression.