8,262 results match your criteria phenotyping methods


EYS-Associated Sector Retinitis Pigmentosa.

Graefes Arch Clin Exp Ophthalmol 2021 Sep 27. Epub 2021 Sep 27.

Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.

Purpose: Sector retinitis pigmentosa (RP) is a rare form of rod-cone degeneration typically associated with mutations in the RHO gene. We describe six unrelated patients presenting with this atypical phenotype in association with biallelic mutations in EYS gene.

Methods: Multinational, multicentre cross-sectional case series. Read More

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September 2021

The role of diffusion tensor imaging of the liver in children with autoimmune hepatitis.

Pol J Radiol 2021 2;86:e461-e467. Epub 2021 Aug 2.

Department of Diagnostic Radiology, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt.

Purpose: To evaluate the role of diffusion tensor imaging (DTI) of the liver in children with autoimmune hepatitis (AIH).

Material And Methods: A prospective study was done on 42 children with AIH (30 girls and 12 boys, with a mean age of 13 years) and 20 age- and sex-matched healthy control children. They underwent DTI of the liver and laboratory tests. Read More

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Immunomonitoring of Human Breast Milk Cells During HCMV-Reactivation.

Front Immunol 2021 9;12:723010. Epub 2021 Sep 9.

Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.

Background: Breast milk leukocytes may play a role in protecting the infant from pathogens. The dynamics and the role of lymphocytes in human cytomegalovirus (HCMV)-seropositive mothers shedding HCMV into breast milk during the first months postpartum (p.p. Read More

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September 2021

Mechanisms Underlying Motivational Dysfunction in Schizophrenia.

Front Behav Neurosci 2021 10;15:709753. Epub 2021 Sep 10.

Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom.

Negative symptoms are a debilitating feature of schizophrenia which are often resistant to pharmacological intervention. The mechanisms underlying them remain poorly understood, and diagnostic methods rely on phenotyping through validated questionnaires. Deeper endo-phenotyping is likely to be necessary in order to improve current understanding. Read More

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September 2021

Integrative analysis of metabolomic, genomic, and imaging-based phenotypes identify very-low-density lipoprotein as a potential risk factor for lumbar Modic changes.

Eur Spine J 2021 Sep 25. Epub 2021 Sep 25.

Department of Orthopaedics and Traumatology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.

Purpose: Modic changes (MC) on magnetic resonance imaging (MRI) have been associated with the development and severity of low back pain (LBP). The etiology of MC remains elusive, but it has been suggested that altered metabolism may be a risk factor. As such, this study aimed to identify metabolomic biomarkers for MC phenotypes of the lumbar spine via a combined metabolomic-genomic approach. Read More

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September 2021

Advancement in Detection Methods: From Conventional to Electrochemical-Based Sensing Detection.

Biosensors (Basel) 2021 Sep 18;11(9). Epub 2021 Sep 18.

Collaborative Microelectronic Design Excellence Centre (CEDEC), [email protected], Universiti Sains Malaysia, Level 1, Block C, No. 10 Persiaran Bukit Jambul, Bayan Lepas 11900, Malaysia.

Large-scale food-borne outbreaks caused by are rarely seen nowadays, thanks to the advanced nature of the medical system. However, small, localised outbreaks in certain regions still exist and could possess a huge threat to the public health if eradication measure is not initiated. This review discusses the progress of detection approaches covering their basic principles, characteristics, applications, and performances. Read More

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September 2021

A comprehensive digital phenotype for postpartum hemorrhage.

J Am Med Inform Assoc 2021 Sep 24. Epub 2021 Sep 24.

Sema4, Stamford, Connecticut, USA.

Objective: We aimed to establish a comprehensive digital phenotype for postpartum hemorrhage (PPH). Current guidelines rely primarily on estimates of blood loss, which can be inaccurate and biased and ignore complementary information readily available in electronic medical records (EMR). Inaccurate and incomplete phenotyping contributes to ongoing challenges in tracking PPH outcomes, developing more accurate risk assessments, and identifying novel interventions. Read More

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September 2021

Recurrent preterm birth risk assessment for two delivery subtypes: A multivariable analysis.

J Am Med Inform Assoc 2021 Sep 24. Epub 2021 Sep 24.

Institute for Computational Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

Objective: The study sought to develop and apply a framework that uses a clinical phenotyping tool to assess risk for recurrent preterm birth.

Materials And Methods: We extended an existing clinical phenotyping tool and applied a 4-step framework for our retrospective cohort study. The study was based on data collected in the Genomic and Proteomic Network for Preterm Birth Research Longitudinal Cohort Study (GPN-PBR LS). Read More

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September 2021

Sleep duration, sleep problems and perceived stress are associated with hippocampal subfield volumes in later life: Findings from The Irish Longitudinal Study on Ageing (TILDA).

Sleep 2021 Sep 24. Epub 2021 Sep 24.

The Irish Longitudinal Study on Ageing, Trinity College Dublin, Ireland.

Study Objectives: This study examines the cross-sectional and two-year follow-up relationships between sleep and stress and total hippocampal volume and hippocampal subfield volumes among older adults.

Methods: 417 adults (aged 68.8±7. Read More

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September 2021

Estimated Prevalence and Number of PiMZ Genotypes of Alpha-1 Antitrypsin in Seventy-Four Countries Worldwide.

Int J Chron Obstruct Pulmon Dis 2021 17;16:2617-2630. Epub 2021 Sep 17.

Pneumology Department, Hospital Universitari Vall d'Hebron/Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain.

Background: The α-1 antitrypsin (AAT) protease inhibitor PiMZ is a moderately deficient genotype, until recently considered of little or negligible risk. However, a growing number of studies show that MZ carriers have an increased risk of developing lung and liver diseases, if exposed to smoking or other airborne or industrial pollutants, and hepatotoxic substances.

Methods: We used the epidemiological studies performed to determine the frequencies of PiM and PiZ worldwide, based on the following criteria: 1) samples representative of the general population; 2) AAT phenotyping or genotyping characterized by adequate methods, including isoelectric focusing and polymerase chain reaction; and 3) studies with reliable results assessed with a coefficient of variation calculated from the sample size and 95% confidence intervals, to measure the precision of the results in terms of dispersion of the data around the mean. Read More

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September 2021

Understanding the burden of interstitial lung disease post-COVID-19: the UK Interstitial Lung Disease-Long COVID Study (UKILD-Long COVID).

BMJ Open Respir Res 2021 Sep;8(1)

Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK.

Introduction: The COVID-19 pandemic has led to over 100 million cases worldwide. The UK has had over 4 million cases, 400 000 hospital admissions and 100 000 deaths. Many patients with COVID-19 suffer long-term symptoms, predominantly breathlessness and fatigue whether hospitalised or not. Read More

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September 2021

Automation assisted anaerobic phenotyping for metabolic engineering.

Microb Cell Fact 2021 Sep 23;20(1):184. Epub 2021 Sep 23.

Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5, Canada.

Background: Microorganisms can be metabolically engineered to produce a wide range of commercially important chemicals. Advancements in computational strategies for strain design and synthetic biological techniques to construct the designed strains have facilitated the generation of large libraries of potential candidates for chemical production. Consequently, there is a need for high-throughput laboratory scale techniques to characterize and screen these candidates to select strains for further investigation in large scale fermentation processes. Read More

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September 2021

Integrated molecular and immune phenotype of HER2-positive breast cancer and response to neoadjuvant therapy: a NeoALTTO exploratory analysis.

Clin Cancer Res 2021 Sep 21. Epub 2021 Sep 21.

Departmen of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale Tumori

Background: Little is known about the efficacy of HER2-targeted therapy in patients with breast cancer showing different HER2-pathway dependence and immune phenotypes. Herein, we report a NeoALTTO exploratory analysis evaluating the clinical value of 22 types of tumor-infiltrating immune cells by CIBERSORT and 5 immune-related metagenes in the overall patient population, and in subgroups defined by the TRAR-classifier as HER2-addicted (TRAR-low) or not (TRAR-high).

Methods: Association of baseline TRAR, immune-related metagenes, and CIBERSORT data with pathological complete response (pCR) and event free survival (EFS) were assessed using logistic and Cox regression models. Read More

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September 2021

High-Throughput Oxygen Consumption Measurements in Leaf Tissue Using Oxygen Sensitive Fluorophores.

Methods Mol Biol 2022 ;2363:63-75

Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Perth, WA, Australia.

Respiratory rate measurements are crucial assays to understand mitochondrial biochemistry as well as metabolic regulation within tissues. Several technologies currently exist that can measure plant respiratory oxygen consumption or carbon dioxide evolution rates over short durations by either isolated mitochondria or plant tissues. Here we describe recently developed alternative methods for measuring tissue oxygen consumption rates (OCRs) using systems reliant on oxygen sensitive fluorophores. Read More

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January 2022

Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria.

Sci Rep 2021 Sep 20;11(1):18661. Epub 2021 Sep 20.

Institute of Infection and Global Health, University of Liverpool, Liverpool, L7 3EA, UK.

Detection and accurate quantitation of viable Mycobacterium tuberculosis is fundamental to understanding mycobacterial pathogenicity, tuberculosis (TB) disease progression and outcomes; TB transmission; drug action, efficacy and drug resistance. Despite this importance, methods for determining numbers of viable bacilli are limited in accuracy and precision owing to inherent characteristics of mycobacterial cell biology-including the tendency to clump, and "differential" culturability-and technical challenges consequent on handling an infectious pathogen under biosafe conditions. We developed an absolute counting method for mycobacteria in liquid cultures using a bench-top flow cytometer, and the low-cost fluorescent dyes Calcein-AM (CA) and SYBR-gold (SG). Read More

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September 2021

Insights into the expanding phenotypic spectrum of inherited disorders of biogenic amines.

Nat Commun 2021 Sep 20;12(1):5529. Epub 2021 Sep 20.

University Children's Hospital Heidelberg, Dietmar-Hopp Metabolic Center, Heidelberg, Germany.

Inherited disorders of neurotransmitter metabolism are rare neurodevelopmental diseases presenting with movement disorders and global developmental delay. This study presents the results of the first standardized deep phenotyping approach and describes the clinical and biochemical presentation at disease onset as well as diagnostic approaches of 275 patients from the registry of the International Working Group on Neurotransmitter related Disorders. The results reveal an increased rate of prematurity, a high risk for being small for gestational age and for congenital microcephaly in some disorders. Read More

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September 2021

Clinical application of fetal genome-wide sequencing during pregnancy: position statement of the Canadian College of Medical Geneticists.

J Med Genet 2021 Sep 20. Epub 2021 Sep 20.

Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.

Purpose And Scope: The aim of this position statement is to provide recommendations for Canadian healthcare professionals regarding the use of genome-wide sequencing (GWS) in the context of diagnostic testing of the fetus during pregnancy. This statement was developed to facilitate clinical translation of GWS as a prenatal diagnostic test and the development of best practices in Canada, but the applicability of this document is broader and aims to help professionals in other healthcare systems.

Methods Of Statement Development: A multidisciplinary group was assembled to review existing literature on fetal GWS for genetic diagnosis in the context of suspected monogenic diseases and to make recommendations relevant to the Canadian context. Read More

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September 2021

Latent Class Analysis Reveals COVID-19-related ARDS Subgroups with Differential Responses to Corticosteroids.

Am J Respir Crit Care Med 2021 Sep 20. Epub 2021 Sep 20.

Columbia University, Medicine/Pulmonary and Critical Care, New York City, New York, United States.

Rationale Two distinct subphenotypes have been identified in acute respiratory distress syndrome (ARDS), but the presence of subgroups in ARDS associated with COVID-19 is unknown. The objective of this study was to identify clinically relevant, novel subgroups in COVID-19-related ARDS, and compare them to previously described ARDS subphenotypes. Methods Eligible participants were adults with COVID-19 and ARDS at Columbia University Irving Medical Center. Read More

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September 2021

Paraspinal muscle imaging measurements for common spinal disorders: review and consensus-based recommendations from the ISSLS degenerative spinal phenotypes group.

Eur Spine J 2021 Sep 20. Epub 2021 Sep 20.

Faculty of Health Sciences and Western's Bone and Joint Institute, Western University, London, ON, Canada.

Purpose: Paraspinal muscle imaging is of growing interest related to improved phenotyping, prognosis, and treatment of common spinal disorders. We reviewed issues related to paraspinal muscle imaging measurement that contribute to inconsistent findings between studies and impede understanding.

Methods: Three key contributors to inconsistencies among studies of paraspinal muscle imaging measurements were reviewed: failure to consider possible mechanisms underlying changes in paraspinal muscles, lack of control of confounding factors, and variations in spinal muscle imaging modalities and measurement protocols. Read More

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September 2021

A Deep Learning-Based Method for Automatic Assessment of Stomatal Index in Wheat Microscopic Images of Leaf Epidermis.

Front Plant Sci 2021 3;12:716784. Epub 2021 Sep 3.

School of Computer and Artificial Intelligence, Wuhan University of Technology, Wuhan, China.

The stomatal index of the leaf is the ratio of the number of stomata to the total number of stomata and epidermal cells. Comparing with the stomatal density, the stomatal index is relatively constant in environmental conditions and the age of the leaf and, therefore, of diagnostic characteristics for a given genotype or species. Traditional assessment methods involve manual counting of the number of stomata and epidermal cells in microphotographs, which is labor-intensive and time-consuming. Read More

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September 2021

High-Throughput Phenotyping and Random Regression Models Reveal Temporal Genetic Control of Soybean Biomass Production.

Front Plant Sci 2021 3;12:715983. Epub 2021 Sep 3.

Department of Agronomy, Purdue University, West Lafayette, IN, United States.

Understanding temporal accumulation of soybean above-ground biomass (AGB) has the potential to contribute to yield gains and the development of stress-resilient cultivars. Our main objectives were to develop a high-throughput phenotyping method to predict soybean AGB over time and to reveal its temporal quantitative genomic properties. A subset of the SoyNAM population ( = 383) was grown in multi-environment trials and destructive AGB measurements were collected along with multispectral and RGB imaging from 27 to 83 days after planting (DAP). Read More

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September 2021

A Roadmap to Gene Discoveries and Novel Therapies in Monogenic Low and High Bone Mass Disorders.

Front Endocrinol (Lausanne) 2021 13;12:709711. Epub 2021 Aug 13.

Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.

Genetic disorders of the skeleton encompass a diverse group of bone diseases differing in clinical characteristics, severity, incidence and molecular etiology. Of particular interest are the monogenic rare bone mass disorders, with the underlying genetic defect contributing to either low or high bone mass phenotype. Extensive, deep phenotyping coupled with high-throughput, cost-effective genotyping is crucial in the characterization and diagnosis of affected individuals. Read More

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Inherited Ventricular Arrhythmia in Zebrafish: Genetic Models and Phenotyping Tools.

Rev Physiol Biochem Pharmacol 2021 Sep 18. Epub 2021 Sep 18.

Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.

In the last years, the field of inheritable ventricular arrhythmia disease modelling has changed significantly with a push towards the use of novel cellular cardiomyocyte based models. However, there is a growing need for new in vivo models to study the disease pathology at the tissue and organ level. Zebrafish provide an excellent opportunity for in vivo modelling of inheritable ventricular arrhythmia syndromes due to the remarkable similarity between their cardiac electrophysiology and that of humans. Read More

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September 2021

Mouse resources at the RIKEN BioResource Research Center and the National BioResource Project core facility in Japan.

Mamm Genome 2021 Sep 16. Epub 2021 Sep 16.

Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan.

The RIKEN BioResource Research Center (BRC) was established in 2001 as a comprehensive biological resource center in Japan. The Experimental Animal Division, one of the BRC infrastructure divisions, has been designated as the core facility for mouse resources within the National BioResource Project (NBRP) by the Japanese government since FY2002. Our activities regarding the collection, preservation, quality control, and distribution of mouse resources have been supported by the research community, including evaluations and guidance on advancing social and research needs, as well as the operations and future direction of the BRC. Read More

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September 2021

Retinal degeneration in mice and humans with neuronal ceroid lipofuscinosis type 8.

Ann Transl Med 2021 Aug;9(15):1274

Department of Ophthalmology & Vision Science, School of Medicine, University of California, Davis, Sacramento, California, USA.

Background: Ceroid lipofuscinosis type 8 belongs to a heterogenous group of vision and life-threatening neurodegenerative diseases, neuronal ceroid lipofuscinosis (NCL). Effective therapy is limited to a single drug for treatment of ceroid lipofuscinosis type 2, necessitating animal disease models to facilitate further therapeutic development. Murine models are advantageous for therapeutic development due to easy genetic manipulation and rapid breeding, however appropriate genetic models need to be identified and characterized before being used for therapy testing. Read More

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Neuroinflammatory gene expression in chronic prostatitis/chronic pelvic pain syndrome patients: insights into etiology and phenotype biology.

Transl Androl Urol 2021 Aug;10(8):3340-3347

Glickman Urological and Kidney Institute, The Cleveland Clinic, Cleveland, OH, USA.

Background: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) has diverse clinical phenotypes and its etiology is multifactorial. Studies to date of gene expression in humans have been limited to small numbers of target genes. NanoString can simultaneously measure hundreds of genes. Read More

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Open source 3D phenotyping of chickpea plant architecture across plant development.

Plant Methods 2021 Sep 16;17(1):95. Epub 2021 Sep 16.

School of Life and Environmental Sciences, Sydney Institute of Agriculture, The University of Sydney, NSW, 2570, Brownlow Hill, Australia.

Background: Being able to accurately assess the 3D architecture of plant canopies can allow us to better estimate plant productivity and improve our understanding of underlying plant processes. This is especially true if we can monitor these traits across plant development. Photogrammetry techniques, such as structure from motion, have been shown to provide accurate 3D reconstructions of monocot crop species such as wheat and rice, yet there has been little success reconstructing crop species with smaller leaves and more complex branching architectures, such as chickpea. Read More

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September 2021

Ex Vivo Expansion and CRISPR-Cas9 Genome Editing of Primary Human Natural Killer Cells.

Curr Protoc 2021 Sep;1(9):e246

Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Natural killer (NK) cells are potent innate immune cells that provide the surveillance and elimination of infected, stressed, and malignant cells. The unique immune recognition mechanisms and functions of NK cells make them an attractive cell type for immunology research and adoptive immunotherapy. However, primary NK cells are challenging to culture ex vivo and lack efficient genetic tools, hindering the research of NK cells and the development of NK cell therapeutics. Read More

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September 2021

and variants in neonatal-onset versus infantile-onset primary congenital glaucoma.

Br J Ophthalmol 2021 Sep 15. Epub 2021 Sep 15.

Advanced Eye Center, Post Graduate Institute of Medical Education and Research, Chandigarh, India.

Objective: To compare and variants in a cohort of neonatal-onset (NO) and infantile-onset (IO) primary congenital glaucoma (PCG).

Methods: This prospective observational study included 43 infants with PCG (14 NO and 29 IO) presenting between January 2017 and January 2019 with a minimum 1-year follow-up. and genes were screened using Sanger sequencing with in-silico analysis of the variants using Polymorphism Phenotyping v. Read More

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September 2021

Ablation of USP21 in skeletal muscle promotes oxidative fibre phenotype, inhibiting obesity and type 2 diabetes.

J Cachexia Sarcopenia Muscle 2021 Sep 15. Epub 2021 Sep 15.

College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyeonggi-Do, South Korea.

Background: Skeletal muscle as a metabolic consumer determines systemic energy homeostasis by regulating myofibre type conversion and muscle mass control. Perturbation of the skeletal muscle metabolism elevates the risk of a variety of diseases including metabolic disorders. However, the regulatory pathways and molecules are not completely understood. Read More

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September 2021