56,447 results match your criteria analyze biological


Artificial Intelligence and Cellular Segmentation in Tissue Microscopy Images.

Am J Pathol 2021 Jun 12. Epub 2021 Jun 12.

Department of Radiology and Committee on Medical Physics, University of Chicago, Chicago, IL, USA, 60637. Electronic address:

With applications in object detection, image feature extraction, image classification, and image segmentation, artificial intelligence is enabling high-throughput analysis of image data in a variety of biomedical imaging disciplines, ranging from radiology and pathology to cancer biology and immunology. Specifically, a growth in research surrounding deep learning has led to widespread application of computer vision techniques to analyze and mine data from biomedical images. The availability of open-source software packages and the development of novel, trainable deep neural network architectures has led to an increase in accuracy of cell detection and segmentation algorithms. Read More

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Multi-cohort profiling reveals elevated CSF levels of brain-enriched proteins in Alzheimer's disease.

Ann Clin Transl Neurol 2021 Jun 15. Epub 2021 Jun 15.

Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden.

Objective: Decreased amyloid beta (Aβ) 42 together with increased tau and phospho-tau in cerebrospinal fluid (CSF) is indicative of Alzheimer's disease (AD). However, the molecular pathophysiology underlying the slowly progressive cognitive decline observed in AD is not fully understood and it is not known what other CSF biomarkers may be altered in early disease stages.

Methods: We utilized an antibody-based suspension bead array to analyze levels of 216 proteins in CSF from AD patients, patients with mild cognitive impairment (MCI), and controls from two independent cohorts collected within the AETIONOMY consortium. Read More

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Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data.

Bioinformatics 2021 Jun 15. Epub 2021 Jun 15.

Division of Infection Medicine, Department of Clinical Sciences, Lund University, Sweden.

Summary: Protein-protein interactions (PPI) are central in many biological processes but difficult to characterize, especially in complex, unfractionated samples. Chemical cross-linking combined with mass spectrometry (MS) and computational modeling is gaining recognition as a viable tool in protein interaction studies. Here, we introduce Cheetah-MS, a web server for predicting the PPIs in a complex mixture of samples. Read More

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Comprehensive Cancer Survival by Neighborhood-Level Income in Ontario, Canada, 2006-2011.

J Registry Manag 2020 ;47(3):102-112

Background: Cancer survival statistics can provide a means to assess the effectiveness of the cancer care system, including early detection strategies, the quality of clinical care, and disease management. Disparities in cancer survival (for instance, by neighborhood-level income) persist in Ontario, Canada despite the existence of a universal health care system. Lower income has been associated with an increased incidence of cancer and worsened survival. Read More

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Fusion proteins of biologic agents in the treatment of rheumatoid arthritis (RA): A network meta-analysis.

Medicine (Baltimore) 2021 Jun;100(24):e26350

Department of Epidemiology and Biostatistics.

Background: To evaluate the efficacy of fusion proteins biologics (Etanercept (ETN), Anakinra (ANA), and Abatacept) combinations in the treatment of rheumatoid arthritis (RA) using network meta-analysis to rank those according to their performance medicines. The performance of these processes is ranked according to the results of the analysis and an explanatory study of the possible results is carried out.

Methods: Multiple databases including PubMed, EMBASE, and Cochrane Library were used to identify applicable articles and collect relevant data to analyze using STATA (14. Read More

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BAFF signaling drives interstitial transformation of mouse renal tubular epithelial cells in a Pin1-dependent manner.

In Vitro Cell Dev Biol Anim 2021 Jun 14. Epub 2021 Jun 14.

Urology Department, Third Affiliated Hospital of Soochow University, 185# Juqian Street, Changzhou, 213003, China.

Aberrant expression of B cell-activating factor belonging to TNF superfamily (BAFF) and its receptors results in abnormal biological activities in hematopoietic and non-hematopoietic cells and is closely associated with the occurrence and development of various diseases. However, the biological significance and potential mechanisms underlying BAFF signaling in renal tubular epithelial cells (RTECs) remain unknown. This study aimed to investigate the biological role of BAFF signaling in RTECs. Read More

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Structure of Tau filaments in Prion protein amyloidoses.

Acta Neuropathol 2021 Jun 14. Epub 2021 Jun 14.

Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.

In human neurodegenerative diseases associated with the intracellular aggregation of Tau protein, the ordered cores of Tau filaments adopt distinct folds. Here, we analyze Tau filaments isolated from the brain of individuals affected by Prion-Protein cerebral amyloid angiopathy (PrP-CAA) with a nonsense mutation in the PRNP gene that leads to early termination of translation of PrP (Q160Ter or Q160X), and Gerstmann-Sträussler-Scheinker (GSS) disease, with a missense mutation in the PRNP gene that leads to an amino acid substitution at residue 198 (F198S) of PrP. The clinical and neuropathologic phenotypes associated with these two mutations in PRNP are different; however, the neuropathologic analyses of these two genetic variants have consistently shown the presence of numerous neurofibrillary tangles (NFTs) made of filamentous Tau aggregates in neurons. Read More

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Nutritional targeting modification of silkworm pupae oil catalyzed by a smart hydrogel immobilized lipase.

Food Funct 2021 Jun 15. Epub 2021 Jun 15.

Jiangsu Key Laboratory Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China. and Attached Silkworm Medicine Factory, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, China and Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, China.

To prepare a nutritional supplement using silkworm pupae oil (SPO) as a feedstock, a microfluidic reactor with a smart hydrogel immobilized lipase was first constructed to reduce the relative content of palmitic acid at sn-1,3 and improve the nutritional function. The effects of flow rate, reaction temperature, and substrate molar ratio were investigated. In vitro digestion and pH-stat models were employed to analyze the digestion feature after the modification of SPO, while HPLC-ELSD, zeta potential, DSC, and TGA were used to evaluate the nutritional function. Read More

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MiR-3614-5p Is a Potential Novel Biomarker for Colorectal Cancer.

Front Genet 2021 28;12:666833. Epub 2021 May 28.

Department of General Surgery, The Armed Police Corps Hospital of Anhui, Hefei, China.

MiR-3614-5p has been found in a variety of cancers including colorectal cancer. However, the association of miR-3614-5p with colorectal cancer is still unclear. Based on the Cancer Genome Atlas (TCGA) database, the relationship between miR-3614-5p and colorectal cancer can be proved. Read More

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Increases in adipose tissue and muscle function are longitudinally associated with better quality of life in colorectal cancer survivors.

Sci Rep 2021 Jun 14;11(1):12440. Epub 2021 Jun 14.

Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. BOX 616, 6200 MD, Maastricht, The Netherlands.

Colorectal cancer (CRC) survivors need evidence-based guidelines pertaining to post-treatment body composition, which could benefit health-related quality of life (HRQoL). We aimed to describe the course of several body composition measures, and to assess longitudinal associations of these measures with HRQoL, fatigue and chemotherapy-induced peripheral neuropathy (CIPN). In a prospective cohort among stage I-III CRC survivors (n = 459), five repeated home visits from diagnosis up to 24 months post-treatment were executed. Read More

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Genome-wide detection and analysis of CRISPR-Cas off-targets.

Prog Mol Biol Transl Sci 2021 4;181:31-43. Epub 2021 Mar 4.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States; Department of Molecular, Cell and Cancer Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States. Electronic address:

The clustered, regularly interspersed, short palindromic repeats (CRISPR) technology is revolutionizing biological studies and holds tremendous promise for treating human diseases. However, a significant limitation of this technology is that modifications can occur on off-target sites lacking perfect complementarity to the single guide RNA (sgRNA) or canonical protospacer-adjacent motif (PAM) sequence. Several in vivo and in vitro genome-wide off-target profiling approaches have been developed to inform on the fidelity of gene editing. Read More

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Utilizing single-cell RNA sequencing for analyzing the characteristics of PBMC in patients with Kawasaki disease.

BMC Pediatr 2021 Jun 14;21(1):277. Epub 2021 Jun 14.

The Department of Pediatric Cardiology, Shenzhen Children's Hospital of China Medical University, Shenzhen, 518038, China.

Background: Kawasaki disease (KD) is the main cause of acquired heart disease in children and can lead to coronary artery lesions. This present study was designed to analyze the characteristics of KD peripheral blood mononuclear cells (PBMC) through single-cell RNA sequencing (scRNA-seq) and to explore the potential molecular mechanism of KD.

Methods: PBMC was collected from one healthy child and one KD patient, and was used to single-cell RNA sequencing for cell clusters identification and differently expressed gene (DEG) determination. Read More

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Simulated In Vitro Infant Gastrointestinal Digestion of Infant Formulas Containing Different Fat Sources and Human Milk: Differences in Lipid Profiling and Free Fatty Acid Release.

J Agric Food Chem 2021 Jun 14. Epub 2021 Jun 14.

Food College, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist, 150030 Harbin, China.

Simulated in vitro infant gastrointestinal digestion of human milk and four infant formulas containing different fat sources was analyzed and compared in this study. Although there are disadvantages brought about by its larger droplet size than infant formulas, human milk exhibited a higher lipolysis level due to the presence of MFGM interfacial layers. Higher hydrolysis efficiency of infant formulas (IFB, IFC, and IFM) was due to the presence of MFGM/phospholipid-enriched materials. Read More

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[Reoperation rate and related factors in patients with Crohn's disease].

Zhonghua Yi Xue Za Zhi 2021 Jun;101(22):1683-1689

Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China.

To analyze the cumulative reoperation rate of postoperative Crohn's disease (CD) patients and investigate the operation reasons and the effects of drugs on surgical recurrence. Patients with Crohn's disease who had undergone intestinal resection from January 2000 to March 2020 in Peking Union Medical College Hospital were enrolled. Patients were divided into reoperation and non-reoperation group according to whether they had a second operation. Read More

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Distinct Behavior of Traumatic versus Nontraumatic Intracerebral Hematomas: Different Biology or Impact of Age?

J Neurol Surg A Cent Eur Neurosurg 2021 Jun 14. Epub 2021 Jun 14.

Department of General and Trauma Surgery, BG Bergmannsheil University Hospital Bochum, Bochum, Germany.

Background And Study Aims:  Patients with large intracerebral hematomas (ICH) may demonstrate different demographics and underlying brain and systemic diseases, as well as different radiologic courses and distinct outcomes. It remains unclear whether their different behavior attributes to a different biology of the ICH or to the asymmetric characteristics of the two populations. To analyze and adjust for potential sources of selection and treatment bias, our study compared age-matched patients with traumatic and nontraumatic ICH in a single cohort diagnosed and treated in the same surgical department. Read More

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Proteomic analysis of pikeperch seminal plasma provides novel insight into the testicular development of domesticated fish stocks.

Animal 2021 Jun 11;15(7):100279. Epub 2021 Jun 11.

Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland.

Control of the reproduction of domesticated stocks is considered a prerequisite for aquaculture development of pikeperch. However, knowledge about the physiology of the captive pikeperch male reproductive system and the biology of semen is very limited, especially regarding protein characteristics. The aims of our study were to characterize pikeperch sperm quantity and quality parameters and to analyze changes in the proteome of the same males spawned for the first and second times. Read More

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Tailoring minimal synthetic receptors to reconstitute signaling properties through multiple tyrosine motifs.

Biochem Biophys Res Commun 2021 Jun 11;566:148-154. Epub 2021 Jun 11.

Laboratory of Cell Vaccine, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki-shi, Osaka, 567-0085, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan. Electronic address:

As intracellular signal transduction is important for determining cell fate, artificial control of signaling properties through engineered receptors is attractive in the fields of synthetic biology and cell therapy. In this study, we tailored minimal synthetic receptors to reconstitute signaling properties by incorporating multiple tyrosine motifs. The size of molecular parts including the linker between the tyrosine motifs was minimized as much as possible to create the minimal synthetic receptors. Read More

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Structural characterization, anticancer, hypoglycemia and immune activities of polysaccharides from Russula virescens.

Int J Biol Macromol 2021 Jun 11. Epub 2021 Jun 11.

School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510640, China; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), 381 Wushan Road, Guangzhou 510640, China. Electronic address:

Russula virescens is an edible wild mushroom that is widely distributed in south of China. This research aimed to analyze the structure characterization and evaluate the hypoglycemic, anticancer and immunological activities of two water soluble polysaccharides RVP-1 and RVP-2 from R. virescens. Read More

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In silico analysis of deleterious SNPs of human MTUS1 gene and their impacts on subsequent protein structure and function.

PLoS One 2021 14;16(6):e0252932. Epub 2021 Jun 14.

Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.

The mitochondrial tumor suppressor 1 (MTUS1) gene acts as a crucial tumor suppressor by inhibiting growth and proliferation of eukaryotic cells including tumor cell lines. Down regulation of MTUS1 gene has been implicated in a wide range of cancers as well as various human diseases. Alteration through nsSNPs can potentially damage the structure and/or function of the protein. Read More

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Network pharmacology and molecular docking study on the mechanism of colorectal cancer treatment using Xiao-Chai-Hu-Tang.

PLoS One 2021 14;16(6):e0252508. Epub 2021 Jun 14.

Shanghai University of Traditional Chinese Medicine, Shanghai, China.

Background And Objective: We aimed to predict the targets and signal pathways of Xiao-Chai-Hu-Tang (XCHT) in the treatment of colorectal cancer (CRC) based on network pharmacology, just as well as to further analyze its anti-CRC material basis and mechanism of action.

Methods: We adopted Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) and Traditional Chinese Medicine Integrated Database (TCMID) databases to screen the active ingredients and potential targets of XCHT. CRC-related targets were retrieved by analyzing published microarray data (accession number GSE110224) from the Gene Expression Omnibus (GEO) database. Read More

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Gas Chromatography-Mass Spectrometry Paired with Total Vaporization Solid-Phase Microextraction as a Forensic Tool.

J Vis Exp 2021 May 25(171). Epub 2021 May 25.

Department of Chemistry & Chemical Biology, Indiana University - Purdue University Indianapolis; Forensic & Investigative Sciences Program, Indiana University - Purdue University Indianapolis;

Gas Chromatography - Mass Spectrometry (GC-MS) is a frequently used technique for the analysis of numerous analytes of forensic interest, including controlled substances, ignitable liquids, and explosives. GC-MS can be coupled with Solid-Phase Microextraction (SPME), in which a fiber with a sorptive coating is placed into the headspace above a sample or immersed in a liquid sample. Analytes are sorbed onto the fiber which is then placed inside the heated GC inlet for desorption. Read More

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Characteristics of arterial catheter use and related complications in dogs and cats in an intensive care unit.

J Vet Emerg Crit Care (San Antonio) 2021 Jun 14. Epub 2021 Jun 14.

Department of Veterinary Surgical and Radiological Sciences|School of Veterinary Medicine, University of California, Davis, Davis, California, USA.

Objective: To identify characteristics of arterial catheter use, including indwelling times and reasons for removal, and analyze potential risk factors for complications based on patient- and catheter-related variables.

Design: Prospective clinical study from July 2012 to September 2016.

Setting: University teaching hospital. Read More

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Droplet microarrays for cell culture: effect of surface properties and nanoliter culture volume on global transcriptomic landscape.

Mater Today Bio 2021 Jun 30;11:100112. Epub 2021 Apr 30.

Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.

The development of novel chemically developed and physically defined surfaces and environments for cell culture and screening is important for various biological applications. The Droplet microarray (DMA) platform based on hydrophilic-superhydrophobic patterning enables high-throughput cellular screening in nanoliter volumes and on various biocompatible surfaces. Here we performed phenotypic and transcriptomic analysis of HeLa-CCL2 cells cultured on DMA, with a goal to analyze cellular response on different surfaces and culture volumes down to 3 nL, compared with conventional cell culture platforms. Read More

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Investigation on the Direct and Bystander Effects in HeLa Cells Exposed to Very Low α-Radiation Using Electrical Impedance Measurement.

ACS Omega 2021 Jun 26;6(22):13995-14003. Epub 2021 May 26.

Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong SAR, China.

The impact of radiation-induced bystander effect (RIBE) is still not well understood in radiotherapy. RIBEs are biological effects expressed by nonirradiated cells near or far from the irradiated cells. Most radiological studies on cancer cells have been based on biochemical characterization. Read More

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Computational Analysis and Phylogenetic Clustering of SARS-CoV-2 Genomes.

Bio Protoc 2021 Apr 20;11(8):e3999. Epub 2021 Apr 20.

CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India.

COVID-19, the disease caused by the novel SARS-CoV-2 coronavirus, originated as an isolated outbreak in the Hubei province of China but soon created a global pandemic and is now a major threat to healthcare systems worldwide. Following the rapid human-to-human transmission of the infection, institutes around the world have made efforts to generate genome sequence data for the virus. With thousands of genome sequences for SARS-CoV-2 now available in the public domain, it is possible to analyze the sequences and gain a deeper understanding of the disease, its origin, and its epidemiology. Read More

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Comprehensive Analysis of GLUT1 Immune Infiltrates and ceRNA Network in Human Esophageal Carcinoma.

Front Oncol 2021 28;11:665388. Epub 2021 May 28.

Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, China.

Background: Glucose transporter 1 (GLUT1) is encoded by the solute carrier family 2A1 (SLC2A1) gene and is one of the glucose transporters with the greatest affinity for glucose. Abnormal expression of GLUT1 is associated with a variety of cancers. However, the biological role of GLUT1 in esophageal carcinoma (ESCA) remains to be determined. Read More

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Proteomic Analysis Reveals That Placenta-Specific Protein 9 Inhibits Proliferation and Stimulates Motility of Human Bronchial Epithelial Cells.

Front Oncol 2021 28;11:628480. Epub 2021 May 28.

Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China.

Placenta-specific protein 9 (PLAC9) is a putative secretory protein that was initially identified in the placenta and is involved in cell proliferation and motility. Bioinformatics analyses revealed that PLAC9 is repressed in lung cancers (LCs), especially lung adenocarcinomas, compared to that in the paired adjacent normal tissues, indicating that PLAC9 might be involved in the pathogenesis of pulmonary diseases. To investigate the potential role of PLAC9 in the abnormal reprogramming of airway epithelial cells (AECs), a key cause of pulmonary diseases, we constructed a stable PLAC9-overexpressing human bronchial epithelial cell line (16HBE-GFP-). Read More

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venom and its components - an overview.

J Venom Res 2021 28;11:26-33. Epub 2021 May 28.

Laboratory of Genetics, Butantan Institute, São Paulo, SP, Brazil.

Belonging to the Viperidae family, are widely distributed in South America, tropical savanna ecoregion (Cerrado) of Argentina, Bolivia, Brazil, and Paraguay with medical importance in Brazil. Accidents caused by this species have a rapid local action with the development of tissue inflammation, causing erythema, pain, and increased clotting time, which can culminate in gangrene or tissue necrosis. venom has a rich composition that remains underexplored, which is of utmost importance, both for elucidating the envenoming process and the vast library of new bioactive molecules kind of venom can offer. Read More

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Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies.

Chem Sci 2021 Apr 13;12(20):6929-6948. Epub 2021 Apr 13.

Department of Mathematics, Michigan State University MI 48824 USA

Antibody therapeutics and vaccines are among our last resort to end the raging COVID-19 pandemic. They, however, are prone to over 5000 mutations on the spike (S) protein uncovered by a Mutation Tracker based on over 200 000 genome isolates. It is imperative to understand how mutations will impact vaccines and antibodies in development. Read More

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Zoantharian Endosymbiont Community Dynamics During a Stress Event.

Front Microbiol 2021 28;12:674026. Epub 2021 May 28.

Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Japan.

Coral reefs are complex ecosystems composed of many interacting species. One ecologically important group consists of zoantharians, which are closely related to reef-building corals. Like corals, zoantharians form mutualistic symbioses with dinoflagellate micro-algae (family Symbiodiniaceae), but their associations remain underexplored. Read More

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