Tag: cytoscape

LncRNA/circRNA-mRNA networks in CARAS | JIR

Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…

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Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle

Almeida OAC, Moreira GCM, Rezende FM et al (2019) Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics 20:1–20. doi.org/10.1186/s12864-019-5811-1 Article  Google Scholar  Alshawi A, Essa A, Al-Bayatti S, Hanotte O (2019) Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and…

Continue Reading Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle

Fatty Acid Metabolism-Related lncRNAs as Biomarkers for SKCM

Introduction Skin cutaneous melanoma (SKCM), as one of the most aggressive types of cancer due to its elevated degree of heterogeneity, has gained increasing attention during the past few decades.1 Also known as “the cancer that rises with the sun”,2 melanoma originates from cancerous melanocytes due to molecular or genetic…

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Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles

Rignot, E., Jacobs, S., Mouginot, J. & Scheuchl, B. Ice-shelf melting around antarctica. Science (80-) 341, 266–270 (2013). Article  ADS  CAS  Google Scholar  Wadham, J. L. et al. Ice sheets matter for the global carbon cycle. Nat. Commun. 10, 1–17 (2019). Google Scholar  Adusumilli, S., Fricker, H. A., Medley, B.,…

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How to run Aracne cytoscape plugin ?

How to run Aracne cytoscape plugin ? 0 I’m intended to infer Gene Regulatory Network (GRN) using ARACNE algorithm and using gene expression matrix. I already have a gene expression matrix file and a list of TFs. But i’m not able to understand how to import in Cytoscape and draw…

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Identification and validation of key miRNAs for colon cancer

Introduction With nearly 2 million new cases and 1 million deaths worldwide in 2020, colorectal cancer is the third-most common cancer and the second leading cause of cancer-related deaths.1 According to data from the US Surveillance, Epidemiology and End Results program and the National Program of Cancer Registries program, the…

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Key Genes for Pyroptosis-induced Salivary Gland Inflammation

Kaiyuan Zhang,1,* Ziyue Luo,1,* Xinchao Zhu,1 Xinyi Yao,1 Dingqi Lu,2 Liying Chen,1 Tao Hong,1 Yating Ren,1 Xinchang Wang3 1Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China; 2First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China;…

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Genetic risk converges on regulatory networks mediating early type 2 diabetes

Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006). Article  ADS  PubMed  Google Scholar  Halban, P. A. et al. β-cell failure in type 2 diabetes: postulated mechanisms and prospects for prevention and treatment. Diabetes Care…

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140releng-powerpc64le-quarterly][biology/cytoscape] Failed for cytoscape-3.6.1 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/140releng-powerpc64le-quarterly/84b4661ec108/logs/cytoscape-3.6.1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=140releng-powerpc64le-quarterly&build=84b4661ec108 Log: =>> Building biology/cytoscape build started at Sat Dec 2…

Continue Reading 140releng-powerpc64le-quarterly][biology/cytoscape] Failed for cytoscape-3.6.1 in build

The Role of circRNA-miRNA-mRNA Regulatory Network and its Potential Biomarker Function in Colorectal Cancer

Background: Revealing the process and mechanism of colorectal cancer will facilitate the discovery of new biomarkers and contribute to the development of targeted drugs. Objective: This study aimed to explore the potentially functional circRNA-miRNA-mRNA network in colorectal cancer (CRC), and further explore its mechanism. Methods: Bioinformatics analysis was used to…

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String App in Cytoscape

String App in Cytoscape 1 I am performing network analysis using string app plug-in cytoscape. But the results are not what I want since there are no any edges. why it happen? App String cytoscape • 136 views Greetings, It’s not clear to me what happened here. I added the…

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Bioinformatics Jobs and Scope in India – Top 10 Jobs in Bioinformatics

Bioinformatics develops as a region of limitless possibility in the  science and technology, where biology converges with computing capability. Consider a future in which every strand of DNA contains the key to revolutionary discoveries and individualized therapy. Welcome to the dynamic world of Bioinformatics, a discipline that bridges conventional divides…

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Genome editing approaches with CRISPR/Cas9: the association of NOX4 expression in breast cancer patients and effectiveness evaluation of different strategies of CRISPR/Cas9 to knockout Nox4 in cancer cells | BMC Cancer

A. Bioinformatics analyzes Search strategy and study selection From April to June 2021, we read relevant and related publications in Medline, EMBASE, Web of Science, and Wanfang. The search term “NOX4” have been used. The articles that fit specified criteria were all added at once: (1) Participants were split into…

Continue Reading Genome editing approaches with CRISPR/Cas9: the association of NOX4 expression in breast cancer patients and effectiveness evaluation of different strategies of CRISPR/Cas9 to knockout Nox4 in cancer cells | BMC Cancer

Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification

Introduction The development of multicellular organisms requires the activation of different gene batteries which specify the identity of each individual cell type. Such shifts in cellular identity are driven by shifts in the gene regulatory network (GRN) consisting of transcription factors (TFs) binding to the enhancers and promoters of their…

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Knockdown of GNL3L alleviates the progression of COPD

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic bronchitis disease characterized by persistent airflow limitation, which can be prevented and treated. COPD is the third leading cause of death in the world reported in 2020.1 With the progression of the disease, COPD will lead to respiratory failure, pulmonary…

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GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21

Experimental model and subject details Mice Male ICR mice (Laboratory Animal Center of Zhejiang Academy of Medical Sciences) at age of 3 months (M), 9 M and 36 M, male C57BL/B6 wild‐type (WT) mice (Shanghai Slac Laboratory) at age of 3 M and 10 M, male GDF11-flox mice (GDF11f/f, mice carrying the “floxed” GDF11…

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Gene Ontology enrichment with BINGO and ClueGO

Gene Ontology enrichment with BINGO and ClueGO 0 Hi, I would like to run some GO BP enrichment analysis in Cytoscape (not GSEA based on expression or rankings, just hypergeometric tests on shortlist vs. reference). There are two conditions I would like to fulfill when carrying it out: 1-To be…

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Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer

Mice The research conducted in this study complied with all of the relevant ethical regulations. The animal protocols were approved by and performed in accordance with the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. C57BL/6, OT-I50, pmel51 and Rosa26-Cas9 knock-in52 mice were purchased from The…

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Inhibition of providencia vermicola FabD

Introduction Microbial resistance has become a problem in the contemporary medical environment due to the inadequate development of new antibiotics and the asinine prescription of antibiotics in both developed and developing nations. Antimicrobial resistance (AMR), which affects wealthy and developing nations, is a global concern.1 AMR is a problem for…

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RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome | Briefings in Bioinformatics

Abstract Bacterial infections often involve virulence factors that play a crucial role in the pathogenicity of bacteria. Accurate detection of virulence factor genes (VFGs) is essential for precise treatment and prognostic management of hypervirulent bacterial infections. However, there is a lack of rapid and accurate methods for VFG identification from…

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Expression profiles of circRNAs and biomarkers for COPD

Introduction Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease featured by airflow obstruction with high prevalence, morbidity, and mortality. It is reported that COPD is the third leading cause of death globally at present, and the incidence of COPD in adults over 40 years is more than…

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Bioinformatics analysis and experimental validation of tumorigenic role of PPIA in gastric cancer

Expression of PPIA in pan-cancer and prognostic value of PPIA in GC To assess the effects of PPIA on the genesis of human tumor, TCGA database was utilized to detect the mRNA levels of PPIA in 33 types of cancer. The findings demonstrated that the levels of PPIA were upregulated…

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How I add new organism “Beauveria bassiana (strain ARSEF 2860)” in ClueGo plug-in of cytoscape?

How I add new organism “Beauveria bassiana (strain ARSEF 2860)” in ClueGo plug-in of cytoscape? 0 How I add the new organism “Beauveria bassiana (strain ARSEF 2860)” in ClueGo plug-in of Cytoscape? I try several times, but it does not work. Could you please help me to add it or…

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Identification of circRNA-miRNA-mRNA network as biomarkers for interstitial cystitis/bladder pain syndrome

Research Paper Advance Articles Shi-Qin Yang1, *, , Liao Peng1, *, , Le-De Lin1, , Yuan-Zhuo Chen1, , Meng-Zhu Liu1, , Chi Zhang1, , Jia-Wei Chen1, , De-Yi Luo1, , 1 Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China * Equal contribution…

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Single-cell transcriptomics reveals the brain evolution of web-building spiders

Animals for single-cell sequencing Adult samples of the aerial web-building spider (Hylyphantes graminicola) were collected from Anci district, Langfang, Hebei, China (39° 31.90’ N, 116° 38.15’ E) between September and October 2020. Collected spiders used for brain dissection were housed individually in a glass tube (Φ12 mm × 80 mm) at temperature- and humidity-controlled condition (24–26 °C and 50–60%…

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Identification of hub genes associated with gastric cancer

Introduction GC is a common malignant tumor of digestive system. According to the International Agency for Research on Cancer (IARC) of the World Health Organization, there were 19.29 million new cancer cases and 9.96 million deaths worldwide in 2020, of which the number of new cases of GC was 1089,103…

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Bioinformatic Analysis of circRNAs in Human ASO

Introduction Arteriosclerosis obliterans (ASO) is a chronic disorder with atherosclerosis involving lower extremity arteries leading to arterial stenosis or occlusion. The incidence continues to increase with age, affecting about 202 million people worldwide to varying degree.1–3 Despite the proposed theories of lipid infiltration, arterial intimal injury, and chronic inflammation, the…

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NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection

        NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…

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A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

A computational protocol, CaseOLAP LIFT, and a use case are presented for investigating mitochondrial proteins and their associations with cardiovascular disease as described in biomedical reports. This protocol can be easily adapted to study user-selected cellular components and diseases. This computational protocol is significant because it allows a work to…

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Combining GO and KEGG enrichments

Combining GO and KEGG enrichments 0 Hi, I have a set of DEGs for which I have carried out GO and Kegg enrichment analysis. Thus, I have twos sets of enriched terms for those genes, one with GOs and another one with KEGGs. I would like to produce a network…

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A Primer in Biological Data Analysis and Visualization

With the development of next-generation sequencing (NGS) technologies and new sequencers, the exponential growth of biological information generated by the scientific community has brought benefits as well as new challenges to researchers. In the era of big data, the field of bioinformatics has made significant progress in the analysis and…

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Identification of a lncRNA/circRNA-miRNA-mRNA ceRNA Network in Alzheimer’s Disease

Background: Alzheimer’s disease (AD) occurs in the elderly and pre-elderly, characterized by decline of memory, cognitive dysfunction, impairment of learning capacity, and motor dysfunction. Recently a competitive endogenous RNA (ceRNA) network has been found to be related to AD progression, but there is still little understanding of the ceRNA regulatory…

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A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders

Dear community members, We are pleased to present myBrain-Seq, an open source tool for miRNA-seq data analysis of neuropsychiatric data. The source code and complete manual is available in GitHub. MyBrain-Seq enables simple and highly reproducible analysis of miRNA data. It incorporates commonly used processes and statistical corrections to adapt…

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Crohn’s Disease treatment after failure of anti-TNF therapy

Introduction Crohn’s Disease (CD) is a typical group of inflammatory bowel disease, a chronic intestinal disease with an unclear cause that fluctuates between clinical remission and relapse. The disease may affect the entirety of the gastrointestinal tract, frequently manifesting as segmental, asymmetric, and transmural lesions. 21–47% of patients present with…

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Bioinformatics Analyst/Developer (REMOTE ROLE) at The Fountain Group

Max Pay $49.95/hour W2. W2 Candidates only, C2C not possible. Our company offers our consultants a suite of benefits after a qualification period including health, vision, dental, life and disability insurance. 100% remote role, no expectation of onsite work. Description Seeking a Strong scientific understanding and experience in bioinformatics Will…

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SPECTRAFORCE hiring Bioinformatics Scientist III (Remote) in Ridgefield, Connecticut, United States

Job Title: Bioinformatics Scientist III (Remote) Duration: 12 Months Note: Looking for a remote or local candidate for this role. Local to Ridgefield, CT 06877. Pay Rate starts from $50/hr on W2 Duties And Responsibilities Strong scientific understanding and experience in bioinformatics Design, implement and/or deploy data analysis workflows for…

Continue Reading SPECTRAFORCE hiring Bioinformatics Scientist III (Remote) in Ridgefield, Connecticut, United States

Bioinformatics Analyst/Developer (REMOTE ROLE) – The Fountain Group

Max Pay $49.95/hour W2. W2 Candidates only, C2C not possible. Our company offers our consultants a suite of benefits after a qualification period including health, vision, dental, life and disability insurance. 100% remote role, no expectation of onsite work. Description Seeking a Strong scientific understanding and experience in bioinformatics Will…

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Signatures of necroptosis-related genes as diagnostic markers of endometriosis and their correlation with immune infiltration | BMC Women’s Health

Technical roadmap Figure 1. Fig. 1 Analysis of endometriosis-related differentially expressed genes Using the limma package, we first normalized the expression profile data of the endometriosis datasets, GSE7305 and GSE11691. The data distribution before and after standardized treatment is revealed in a box plot (Figs. 2A–D). We found that the data after…

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G. lucidum triterpenes restores intestinal flora balance in non-hepatitis B virus-related hepatocellular carcinoma: evidence of 16S rRNA sequencing and network pharmacology analysis

. 2023 Sep 18:14:1197418. doi: 10.3389/fphar.2023.1197418. eCollection 2023. Affiliations Expand Affiliation 1 Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, China. Free PMC article Item in Clipboard Wei Xiong et al. Front Pharmacol. 2023. Free PMC article…

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Functional analysis of differentially expressed circular RNAs in sheep subcutaneous fat | BMC Genomics

Chikwanha, O. C., P. Vahmani, V. Muchenje, M. E. R. Dugan and C. Mapiye (2018). Nutritional enhancement of sheep meat fatty acid profile for human health and wellbeing. Food research international (Ottawa, Ont.) 104: 25–38. doi.org/10.1016/j.foodres.2017.05.005. Khan R, Raza SHA, Schreurs N, Xiaoyu W, Hongbao W, Ullah I, et al….

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Virulence Characteristics of Salmonella Enteritidis

Introduction As an important zoonosis pathogen, Salmonella is widely distributed in nature and one of the four major pathogens causing global diarrhea diseases.1 Salmonella has six subspecies and 2659 serotypes, among which Salmonella Enteritidis (S. Enteritidis) are the most common serotypes causing Salmonella outbreaks.1 S. Enteritidis has a wide variety…

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Protistan predation selects for antibiotic resistance in soil bacterial communities

Courtenay M, Castro-Sanchez E, Fitzpatrick M, Gallagher R, Lim R, Morris G. Tackling antimicrobial resistance 2019-2024–the UK’s five-year national action plan. J Hosp Infect. 2019;101:426–7. Article  CAS  PubMed  Google Scholar  D’Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, et al. Antibiotic resistance is ancient. Nature. 2011;477:457–61….

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Transcriptomic landscape of the interaction between the entomopathogenic fungus Beauveria bassiana and its tolerant host Tribolium castaneum revealed by dual RNA-seq

Fungal infection To test a natural way of interaction between adult T. castaneum with B. bassiana conidia, insects were maintained feeding on conidia-covered corn kernels during different short time periods (i.e., 3, 6, 12, and 24h), and then separated and maintained in rearing conditions. At all time periods assayed, T….

Continue Reading Transcriptomic landscape of the interaction between the entomopathogenic fungus Beauveria bassiana and its tolerant host Tribolium castaneum revealed by dual RNA-seq

Whole transcriptome analysis in offspring whose fathers were exposed to a developmental insult: a novel avian model

Werboff, J. & Gottlier, J. S. Drug in pregnancy: Behavioral teratology. Obstet. Gynecol. Surv. 18, 420–423 (1963). Article  Google Scholar  Yanai, J. G. The effect of alcohol consumed by parent mice on the susceptibility to audiogenic seizure and the open-field behavior of their offspring. Behav. Genet. 3, 418 (1973). Google…

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Network analysis with cytoscape

Network analysis with cytoscape 0 Hi Biostars, I try to use cytoscape on my RNA-seq data. After converting about 1000 DEGs into ENTREZID, I put the list into cytoscape and it makes a very complicated network. Could we use this tool to identify which gene/transcription factor is important from our…

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Elucidating the molecular mechanisms underlying anti-inflammatory effects of Morchella esculenta in the arachidonic acid metabolic pathway by network pharmacology and molecular docking

Identification of the anti-inflammatory target of active ingredients in Morchella esculenta The active ingredient of “Morchella esculenta” according to the NPASS database was (E)-Octadec-11-En-9-Yinoic Acid (EOYA) (Fig. 1), numbered NPC179764, with a chemical formula of C18H30O2, and ‘SMILE’ value, CCCCCC/C=C/C#CCCCCCCCC(=O)O. The targets obtained by searching the “EOYA Smile Value” in the…

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Study on potential differentially expressed genes in idiopathic pulmonary fibrosis by bioinformatics and next generation sequencing data analysis

Abstract Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the…

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Total Flavonoids of Rhizoma Drynariae Treat Osteoarthritis

Introduction Osteoarthritis (OA) is a common degenerative joint disease characterized by chronic pain and ambulation limitation, affecting about 250 million people worldwide.1 With increased aging population, the OA incidence rapidly increases and OA has become a major cause of disability.2,3 The morbidity of OA is closely related to articular cartilage,…

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Revealing mechanism of Methazolamide for treatment of ankylosing spondylitis based on network pharmacology and GSEA

Braun, J. & Sieper, J. Ankylosing spondylitis. Lancet 369, 1379–1390. doi.org/10.1016/S0140-6736(07)60635-7 (2007). Article  PubMed  Google Scholar  Lai, S. W., Kuo, Y. H. & Liao, K. F. Incidence of inflammatory bowel disease in patients with ankylosing spondylitis. Ann. Rheum. Dis. 80, e144. doi.org/10.1136/annrheumdis-2019-216362 (2021). Article  PubMed  Google Scholar  Bukowski, B. R….

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Ferroptosis-related factors in the substantia nigra are associated with Parkinson’s disease

Cell types and their proportion in the SN of PD patients Based on the cell annotation results on the Single Cell Portal uploaded by Prof. Macosko’s group, cells were extracted and classified into different types from human SN samples (Fig. 1A). After 135,344 cells were extracted from 34 PD samples and…

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RNA-sequencing and bioinformatics analysis | COPD

Introduction COPD, a common preventable and treatable disease characterized by persistent airflow limitation and respiratory symptoms, is associated with exposure to harmful environments. COPD is currently the third leading cause of death globally. The high incidence and mortality of COPD, which seriously threaten human health, represent a public health problem…

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Integrated unbiased multiomics defines disease-independent placental clusters in common obstetrical syndromes | BMC Medicine

Barker DJ. The origins of the developmental origins theory. J Intern Med. 2007;261:412–7. Article  CAS  PubMed  Google Scholar  Barker DJ, Gluckman PD, Godfrey KM, Harding JE, Owens JA, Robinson JS. Fetal nutrition and cardiovascular disease in adult life. Lancet. 1993;341:938–41. Article  CAS  PubMed  Google Scholar  Cain MA, Salemi JL, Tanner…

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Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation

Location and sample collection Samples were taken from 10 composting piles (between May and August 2020) at a food waste (FW) composting facility (Zhejiang, China; 30°52′51.50″N; 119°46′12.87″E). A consistent pre-treatment method was used for each pile. Specifically, about 8 tons of FW was collected every 3 days and subsequently crushed into…

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Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties | CABI Agriculture and Bioscience

Anon. Human Development Report 1997. 1997. Bailey TL, Johnson J, Grant CE, Noble WS. The MEME suite. Nucleic Acids Res. 2015;43(W1):W39-49. doi.org/10.1093/NAR/GKV416. Article  CAS  PubMed  PubMed Central  Google Scholar  Balchin D, Hayer-Hartl M, Hartl FU. In vivo aspects of protein folding and quality control. Science. 2016;353(6294):aac4354. doi.org/10.1126/science.aac4354. Article  CAS  PubMed …

Continue Reading Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties | CABI Agriculture and Bioscience

Identification and Analysis of NET- related genes in OA

Introduction OA is a degenerative joint disease that primarily affects the elderly population. It is a multifactorial disorder with a complex pathogenesis, involving a variety of joint tissues. In addition to the well-established degradation of articular cartilage, OA encompasses a comprehensive joint pathology, encompassing the synovial membrane, subchondral bone, menisci,…

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Gut microbial carbohydrate metabolism contributes to insulin resistance

Study participants and data collection The study participants were recruited from 2014 to 2016 during their annual health check-ups at the University of Tokyo Hospital. The individuals included both male and female Japanese individuals aged from 20 to 75 years. The exclusion criteria were as follows: established diagnosis of diabetes,…

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Programs To Open .GMT Files

What is a GMT File? A GMT file, also known as Gene Matrix Transposed, is a specific type of file that is extensively used in the field of genomics and bioinformatics. Derived from the title, when a file carries a .gmt extension, it signifies that the file contains a matrix…

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Selective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesicles

Clinical samples and plasma preparation Blood samples from control individuals and patients with multiple myeloma, liver cancer, and lung cancer were obtained from Oregon Health and Science University (OHSU) by Knight Cancer Institute Biolibrary and Oregon Clinical and Translational Research Institute (OCTRI). All samples were collected under OHSU institutional review…

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Interrogating the viral dark matter of the rumen ecosystem with a global virome database

Gregory, A. C. et al. Marine DNA viral macro-and microdiversity from pole to pole. Cell 177, 1109–1123.e1114 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016). Article  CAS  PubMed  Google Scholar  Camarillo-Guerrero, L….

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Analysis of endoplasmic reticulum stress-related gene signature for the prognosis and pattern in diffuse large B cell lymphoma

Swerdlow, S. H. et al. The 2016 revision of the World Health Organization classification of lymphoid neoplasms. Blood 127, 2375–2390 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Sehn, L. H. & Salles, G. Diffuse large B-cell lymphoma. N. Engl. J. Med. 384, 842–858 (2021). Article  CAS  PubMed  PubMed Central …

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DyNet on metabolic network

DyNet on metabolic network 0 Hi, everyone, Have you ever tried to introduce DyNet to create an overlay of two metabolite networks? I worked on metabolism data and was trying to figure out the metabolite in net1 whose edges changed the most in net2. The EDGEs here were filtered by…

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The question about the Cytohubba

The question about the Cytohubba 1 Hello everyone! I used the Cytohubba to analysis the interaction of hub genes,but i got gene IDs instead of gene symbols,how can i convert it back to gene symbols? Thank you! cytoscape cytohubba gene network • 914 views let me add an answer for…

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WGCNA Analysis – blockwiseModules data processing

WGCNA Analysis – blockwiseModules data processing 0 Good evening, I am currently running a WGCNA analysis. As suggested by a colleague, I switched from regular single-block WGCNA calculation to blockwiseModules, due to large (42,000 genes) dataset size. By setting the max block dimension to 40,000 , I obtain two separate…

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Dithiotreitol and Next Generation Sequencing of Bacterial 16S rRNA Shows Similar Diagnostic Security as Periprosthetic Tissue Cultures to Diagnose PJI

Introduction The need for a revision of a total joint replacement can be caused by various complications. The most common reasons for revision surgery are aseptic loosening, malpositioning of the implant and Periprosthetic Joint Infections (PJI) [1]. The incidence of PJI is lower than the incidence of aseptic loosening [2],…

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Bioconductor – gaggle

DOI: 10.18129/B9.bioc.gaggle     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see gaggle. Broadcast data between R and Gaggle Bioconductor version: 3.14 This package contains functions enabling data exchange between R and Gaggle enabled bioinformatics software, including Cytoscape, Firegoose and Gaggle Genome Browser….

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Bioinformatics analysis of hedgehog interacting protein in colorectal cancer: a study based on GEO data and TCGA data | BMC Gastroenterology

HHIP was lowly expressed in CRC tissues and HHIP expression was associated with cancer patient prognosis We acquired the RNA-sequencing data of CRC from TCGA public database. To pursue possible roles of HHIP in carcinostasis, we first analyzed HHIP expression in 33 types of human cancers. As shown in Fig. 1A,…

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Bioconductor – RCX

DOI: 10.18129/B9.bioc.RCX   R package implementing the Cytoscape Exchange (CX) format Bioconductor version: Release (3.17) Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format…

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Identification of immuno-inflammation-related biomarkers | JIR

Introduction Acute myocardial infarction (AMI) is the sudden irreversible necrosis of heart muscle, which commonly results from atherosclerotic plaque disruption and subsequent interruption of blood flow.1 It is one of the heart diseases with the highest prevalence and incidence and brings enormous health and financial burdens.2 Despite the rapid development…

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A multi-database based ceRNA regulatory network for gastric cancer prognosis

Abstract Abstract   Objective: Circular RNA(circRNA) is a kind of endogenous non-coding RNA, which may be related to the occurrence and development of cancer. Based on the GEO database, this paper constructs a circRNA as a competitive endogenous RNAs(ceRNAs) that binds with microRNAs (miRNAs) to affect and regulate the expression…

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A predicted CRISPR-mediated symbiosis between uncultivated archaea

Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67 (2010). Article  CAS  PubMed  Google Scholar  Andersson, A. F. & Banfield, J. F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320, 1047–1050 (2008). Article  CAS  PubMed  Google…

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Immune Cell Infiltration and Novel Biomarkers of CAD

Introduction Coronary artery disease (CAD) is a major cause of death and disability worldwide,1 and has been proved to be triggered by the interaction of environmental and genetic risk factors. It is considered to be a systemic, progressive inflammatory disease. The atherosclerotic plaque formed in CAD accumulates chronically in the…

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CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data | Bioinformatics | Oxford Academic | A travel guide to Cytoscape plugins

Synopsis Summary: The CluePedia Cytoscape plugin is a search toolbar for new markers potentially associated to pathways. CluePedia calculates linear furthermore non-linear statistical dependencies from experimenta data. Genes, proteinaceous and miRNAs can be connected founded on within silico and/or experimentally information and integrated into a ClueGO network of terms/pathways. Interrelations…

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Research software engineer supporting open-source bioinformatics software and services (0.6 fte) – Maastricht University – job portal

Sign in Sign up EN All jobs Research software engineer supporting open-source bioinformatics software and services (0.6 fte) Published Deadline Location today 8 Sep Maastricht Do you want to play a role in creating the connection between ICT and Biology? Maastricht University is looking for a research software engineer to…

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GPX4 is a key ferroptosis biomarker and correlated with immune cell populations and immune checkpoints in childhood sepsis

Identification of DE-FRGs in sepsis After the debatch normalization treatment of GSE26378 and GSE26440 (Fig. 2A, Supplementary Figure 1), the differential expression analysis was performed, including 20,021 significantly differentially expressed genes, including 12,758 upregulated genes and 7,263 downregulated genes. log2FC ≥ 1, adjusted P < 0.05 (Fig. 2B). To explore differentially expressed FRG in sepsis, we extracted…

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Systems biology approaches to identify potential targets and inhibitors of the intestinal microbiota to treat depression

Dean, J. & Keshavan, M. The neurobiology of depression: An integrated view. Asian J. Psychiatry 27, 101–111 (2017). Article  Google Scholar  Ng, M. et al. Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: A systematic analysis for the Global Burden of Disease Study…

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Query regarding cytoscape installation and uninstallation in ubuntu

Query regarding cytoscape installation and uninstallation in ubuntu 0 I installed Cytoscape in my Ubuntu system but I can not run it now it will be okay if I can install it or uninstall it perfectly for your kind information I have Java installed in my system. In my scenario,…

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Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

Rantanen M, Karpechko AY, Lipponen A, Nordling K, Hyvärinen O, Ruosteenoja K, et al. The Arctic has warmed nearly four times faster than the globe since 1979. Commun Earth Environ. 2022;3:1–10. Article  Google Scholar  Kwok R. Arctic sea ice thickness, volume, and multiyear ice coverage: losses and coupled variability (1958–2018)….

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Bioinformatics Data Manager at University of Surrey

We invite applications for the position of Biomedical Data Manager, to work full-time in support of new initiatives in Health and Biomedical Informatics and the new informatics-based MSc programme in the Faculty of Health and Medical Sciences.  Reporting to the Professor of Health and Biomedical Informatics, the Biomedical Data Manager…

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Integration of bulk RNA sequencing data and single-cell RNA sequencing analysis on the heterogeneity in patients with colorectal cancer

Bao X, Shi R, Zhao T, Wang Y, Anastasov N, Rosemann M et al (2021) Integrated analysis of single-cell RNA-seq and bulk RNA-seq unravels tumour heterogeneity plus M2-like tumour-associated macrophage infiltration and aggressiveness in TNBC. Cancer Immunol Immunother 70(1):189–202 Article  CAS  PubMed  Google Scholar  Becht E, McInnes L, Healy J,…

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Identification of molecular mechanisms causing skin lesions of cutaneous leishmaniasis using weighted gene coexpression network analysis (WGCNA)

Data information We downloaded all the data used in this research from National Center for Biotechnology Information Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo/). We used the data set GSE1278317 to construct a co-expression network by Differential Gene Expression analysis (DGEs) and Weighted Gene Co-expression Network Analysis (WGCNA). The Data was obtained from…

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Establishment of risk model, analysis of immunoinfiltration

Introduction Atrial fibrillation (AF) is a tachyarrhythmia whose incidence and prevalence are steadily increasing with better chronic disease management in the aging global population. As of 2020, 37.5 million patients worldwide were affected by AF, accounting for 0.51% of the global population.1 As a common arrhythmia, AF greatly increases the…

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IJMS | Free Full-Text | Analysis of CircRNA Expression in Peripheral Blood of Holstein Cows in Response to Heat Stress

1. Introduction With the global temperature rise, the dairy industry is confronted with a significant challenge brought about by severely damaging impacts of heat stress. Heat stress increases mortality rates and threatens the health of livestock, especially in highly productive and intolerant species. The increase in ambient temperature–humidity index (THI)…

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Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage

Wyatt, G. R. & Cohen, S. S. A new pyrimidine base from bacteriophage nucleic acids. Nature 170, 1072–1073 (1952). Article  CAS  PubMed  Google Scholar  Kallen, R. G., Simon, M. & Marmur, J. The new occurrence of a new pyrimidine base replacing thymine in a bacteriophage DNA:5-hydroxymethyl uracil. J. Mol. Biol….

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How to successfully upload gene expression data in DyNetViewer

How to successfully upload gene expression data in DyNetViewer 0 I need to construct a dynamic PPI interaction analysis using gene expression data from three time points. I have this cytoscape app called DyNetViewer which requires me to put the data in a txt file before uploading it. I have…

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DyNetViewer

DyNetViewer 0 I need to construct a dynamic PPI interaction analysis using gene expression data from three time points. I have this cytoscape app called DyNetViewer which requires me to put the data in a txt file before uploading it. I have my data in txt file but it gives…

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Comprehensive analysis of the coding and non-coding RNA transcriptome expression profiles of hippocampus tissue in tx-J animal model of Wilson’s disease

Behavioral testing After undergoing a four-day training program, the mice were subjected to a positioning cruise experiment on the fifth day. The experiment involved comparing the escape latency and swimming distance in the quadrant opposite to the platform between the WD group and the control group. The findings indicated that…

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Analysis of tRNA-derived small RNAs

Introduction Sarcoidosis is a multisystem inflammatory disease of unknown aetiology that is characterised by non-caseating epithelioid granulomatous lesions (aggregates of lymphocytes, macrophages, epithelioid cells, and giant cells).1 Typical clinical features include bilateral hilar lymph node lesions, pulmonary infiltration, and eye and skin lesions. Some patients may also have neurological and…

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Integrated analysis of circRNA-associated ceRNA in ischemic stroke

1 Introduction Stroke is the leading cause of permanent disability (Diener and Hankey, 2020). The latest global burden of disease (GBD) study (GBD 2019 Diseases and Injuries Collaborators, 2020) indicated that stroke is the leading cause of death in the Chinese population. The overall lifetime risk of stroke in China…

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Three genes expressed in relation to lipid metabolism considered as potential biomarkers for the diagnosis and treatment of diabetic peripheral neuropathy

Screening for pivotal genes in diabetic peripheral neuropathy In screening the DEGs, a total of 6 DPN samples and 6 control samples were included in the GEO dataset GSE95849, and this dataset was normalised. A principal component analysis (PCA) of GSE95849 was conducted to demonstrate clustering using scatter plots. Each…

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Deep exome sequencing identifies enrichment of deleterious mosaic variants in neurodevelopmental disorder genes and mitochondrial tRNA regions in bipolar disorder

GBD 2016 Disease Injury Incidence Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet. 2017;390:1211–59. Article  Google Scholar  Kato T. Current understanding of bipolar disorder:…

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Human microglia show unique transcriptional changes in Alzheimer’s disease

Podlesny-Drabiniok, A., Marcora, E. & Goate, A. M. Microglial phagocytosis: a disease-associated process emerging from Alzheimer’s disease genetics. Trends Neurosci. 43, 965–979 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Calsolaro, V. & Edison, P. Neuroinflammation in Alzheimer’s disease: current evidence and future directions. Alzheimers Dement. 12, 719–732 (2016). Article …

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Human bone marrow-derived mesenchymal stem overexpressing microRNA-124-3p inhibit DLBCL progression by downregulating the NFATc1/cMYC pathway | Stem Cell Research & Therapy

Microarray-based expression analysis and GEO database analysis The DLBCL-related miRNA expression profiles of GSE29493 and GSE40239 were retrieved from the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/). MiR-124’s pan cancer analysis is conducted through online websites (www.picb.ac.cn/dbDEMC/). Bioinformatics predicted NFATc1 as the target of miR-124-3p The miRbase (www.mirbase.org/), miRDB (mirdb.org), and…

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Epigenetic regulation of human-specific gene expression in the prefrontal cortex | BMC Biology

Preuss TM. The human brain: rewired and running hot. Ann N Y Acad Sci. 2011;1225 Suppl 1(Suppl 1):E182-191. Article  PubMed  Google Scholar  Roth G, Dicke U. Evolution of the brain and intelligence in primates. Prog Brain Res. 2012;195:413–30. Article  PubMed  Google Scholar  Laland K, Seed A. Understanding human cognitive uniqueness….

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Screening and verification of key ubiquitination genes

Introduction Liver cancer is the third most common cause of cancer death globally with hepatocellular carcinoma (HCC) accounting for the majority of liver cancer.1,2 Early HCC (stage I/II) treatment mainly includes radical surgical resection, radiofrequency ablation and liver transplantation.3,4 However, there is a lack of typical clinical symptoms with early-stage…

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Pinostrobin, a fingerroot compound, regulates miR-181b-5p and induces acute leukemic cell apoptosis

Leukemia cell culture The human acute promyelocytic leukemia cell line (NB4) and the human acute lymphocytic leukemia cell line (MOLT-4) were purchased from Cell Lines Service (Eppelheim, Germany). Leukemia cells were cultured in RPMI-1640 medium supplemented with 10% (v/v) FBS and 1% (v/v) penicillin–streptomycin (Gibco Life Technologies, Waltham, MA, USA)….

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An integrated tumor, immune and microbiome atlas of colon cancer

Samples used in this observational cohort study (tumor tissue and matched healthy colon tissue, AC-ICAM cohort) are from patients with colon cancer diagnosed at Leiden University Medical Center, the Netherlands, from 2001 to 2015 that did not object for future use of human tissues for scientific research and that were…

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Bioinformatics-Based Identification of CircRNA-MicroRNA-mRNA Network for Calcific Aortic Valve Disease

Background. Calcific aortic valve disease (CAVD) is the most common native valve disease. Valvular interstitial cell (VIC) osteogenic differentiation and valvular endothelial cell (VEC) dysfunction are key steps in CAVD progression. Circular RNA (circRNAs) is involved in regulating osteogenic differentiation with mesenchymal cells and is associated with multiple disease progression,…

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Predictive network analysis identifies JMJD6 and other potential key drivers in Alzheimer’s disease

Cerejeira, J., Lagarto, L. & Mukaetova-Ladinska, E. B. Behavioral and psychological symptoms of dementia. Front. Neurol. 3, 73 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Murphy, M. P. & LeVine, H. III Alzheimer’s disease and the amyloid-beta peptide. J. Alzheimers Dis. 19, 311–323 (2010). Article  PubMed  PubMed Central  Google…

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Toxic mechanisms of MWCNTs for ocular cells.

Introduction Carbon nanotubes (CNTs) are nano-sized one-dimensional tubular structures rolled by single (single-walled CNTs, SWCNTs) or multiple layers (multi-walled CNTs, MWCNTs) of graphene with unique electrochemical, mechanical and thermal properties, which render them as attracted engineered nanomaterials for various commercial applications.1–4 An increase in the production and utilization of CNTs…

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Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution

Manrique, P., Dills, M. & Young, M. J. The human gut phage community and its implications for health and disease. Viruses 9, 141 (2017). Article  PubMed  PubMed Central  Google Scholar  Li, Z. et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J….

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