4,669 results match your criteria enabling quantitative

MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional Analysis.

J Proteome Res 2021 Apr 13. Epub 2021 Apr 13.

Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, United States.

Metaproteomics by mass spectrometry (MS) is a powerful approach to profile a large number of proteins expressed by all organisms in a highly complex biological or ecological sample, which is able to provide a direct and quantitative assessment of the functional makeup of a microbiota. The human gastrointestinal microbiota has been found playing important roles in human physiology and health, and metaproteomics has been shown to shed light on multiple novel associations between microbiota and diseases. MS-powered proteomics generally relies on genome data to define search space. Read More

View Article and Full-Text PDF

Comparative Metabolic Modeling of Multiple Sulfate-reducing Prokaryotes Reveals Versatile Energy Conservation Mechanisms.

Biotechnol Bioeng 2021 Apr 12. Epub 2021 Apr 12.

Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.

Sulfate-reducing prokaryotes (SRPs) are crucial participants in the cycling of sulfur, carbon, and various metals in the natural environment and in engineered systems. Despite recent advances in genetics and molecular biology bringing a huge amount of information about the energy metabolism of SRPs, little effort has been made to link this important information with their biotechnological studies. This study aims to construct multiple metabolic models of SRPs that systematically compile genomic, genetic, biochemical, and molecular information about SRPs to study their energy metabolism. Read More

View Article and Full-Text PDF

Coupled mathematical modeling of cisplatin electroporation.

Bioelectrochemistry 2021 Feb 24;140:107788. Epub 2021 Feb 24.

Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Instituto de Fısica del Plasma (INFIP), Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina. Electronic address:

The use of electrochemotherapy (ECT) is a well-established technique to increase the cellular uptake of cytotoxic agents within certain cancer treatment strategies. The study of the mechanisms that take part in this complex process is of high interest to gain a deeper knowledge of it, enabling the improvement of these strategies. In this work, we present a coupled multi-physics electroporation model based on a related previous one, to describe the effect of a set of electric pulses on cisplatin transport across the plasma membrane. Read More

View Article and Full-Text PDF
February 2021

Accelerated 3D whole-brain T1, T2, and proton density mapping: feasibility for clinical glioma MR imaging.

Neuroradiology 2021 Apr 9. Epub 2021 Apr 9.

Radiology & Nuclear Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands.

Purpose: Advanced MRI-based biomarkers offer comprehensive and quantitative information for the evaluation and characterization of brain tumors. In this study, we report initial clinical experience in routine glioma imaging with a novel, fully 3D multiparametric quantitative transient-state imaging (QTI) method for tissue characterization based on T1 and T2 values.

Methods: To demonstrate the viability of the proposed 3D QTI technique, nine glioma patients (grade II-IV), with a variety of disease states and treatment histories, were included in this study. Read More

View Article and Full-Text PDF

eQTLHap: a tool for comprehensive eQTL analysis considering haplotypic and genotypic effects.

Brief Bioinform 2021 Apr 8. Epub 2021 Apr 8.

School of Computing and Information Systems, The University of Melbourne, Parkville, 3010, Australia.

Motivation: The high accuracy of recent haplotype phasing tools is enabling the integration of haplotype (or phase) information more widely in genetic investigations. One such possibility is phase-aware expression quantitative trait loci (eQTL) analysis, where haplotype-based analysis has the potential to detect associations that may otherwise be missed by standard SNP-based approaches.

Results: We present eQTLHap, a novel method to investigate associations between gene expression and genetic variants, considering their haplotypic and genotypic effect. Read More

View Article and Full-Text PDF

Action Levels for the Prevention of Work-Related Musculoskeletal Disorders in the Neck and Upper Extremities: A Proposal.

Ann Work Expo Health 2021 Apr 8. Epub 2021 Apr 8.

Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Medicon Village, SE-223 81, Lund, Sweden.

There are several well-known risk factors for work-related musculoskeletal disorders (MSDs). Despite this knowledge, too many people still work in harmful conditions. The absence of occupational exposure limits (OELs) for physical workload impedes both supervision and preventive work. Read More

View Article and Full-Text PDF

Toward more robust and reproducible diffusion kurtosis imaging.

Magn Reson Med 2021 Apr 8. Epub 2021 Apr 8.

Center for Biomedical Imaging, New York University Grossman School of Medicine, New York, NY, USA.

Purpose: The general utility of diffusion kurtosis imaging (DKI) is challenged by its poor robustness to imaging artifacts and thermal noise that often lead to implausible kurtosis values.

Theory And Methods: A robust scalar kurtosis index can be estimated from powder-averaged diffusion-weighted data. We introduce a novel DKI estimator that uses this scalar kurtosis index as a proxy for the mean kurtosis to regularize the fit. Read More

View Article and Full-Text PDF

EzMAP: Easy Microbiome Analysis Platform.

BMC Bioinformatics 2021 Apr 7;22(1):179. Epub 2021 Apr 7.

Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Gyeongbuk, Korea.

Background: The rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past decade, several computational pipelines have been developed to efficiently process and annotate these microbiome data. However, most of these pipelines require an implementation of additional tools for downstream analyses as well as advanced programming skills. Read More

View Article and Full-Text PDF

Use of nucleic acids amplification methods in Marek's disease diagnosis and pathogenesis studies.

Acta Virol 2021 ;65(1):27-32

Marek's disease (MD) is a lymphoproliferative disease of chickens with strong economic impact on poultry industry. Although successful vaccination has enabled control of the disease, outbreaks occur in commercial flocks, resulting in substantial economic losses. Together with vaccination, accurate and fast diagnosis of MD remain the most important tools for its efficient control. Read More

View Article and Full-Text PDF
January 2021

Respiratory motion correction for enhanced quantification of hepatic lesions in simultaneous PET and DCE-MR imaging.

Phys Med Biol 2021 Apr 6. Epub 2021 Apr 6.

Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, Berlin, 10587, GERMANY.

Simultaneous PET-MR imaging is a hybrid technique in oncological hepatic imaging combining soft-tissue and functional contrast of dynamic contrast enhanced MR (DCE-MR) with metabolic information from PET. In this context, respiratory motion represents a major challenge by introducing blurring, artifacts and misregistration in the liver. In this work, we propose a free-breathing 3D non-rigid respiratory motion correction framework for simultaneously acquired DCE-MR and PET data, which makes use of higher spatial resolution MR data to derive motion information used directly during image reconstruction to minimize image blurring and motion artifacts. Read More

View Article and Full-Text PDF

Deep learning classification of lipid droplets in quantitative phase images.

PLoS One 2021 5;16(4):e0249196. Epub 2021 Apr 5.

Department of Physics, University of Idaho, Moscow, Idaho, United States of America.

We report the application of supervised machine learning to the automated classification of lipid droplets in label-free, quantitative-phase images. By comparing various machine learning methods commonly used in biomedical imaging and remote sensing, we found convolutional neural networks to outperform others, both quantitatively and qualitatively. We describe our imaging approach, all implemented machine learning methods, and their performance with respect to computational efficiency, required training resources, and relative method performance measured across multiple metrics. Read More

View Article and Full-Text PDF

Older adults' experiences with and perceptions of the use of socially assistive robots in aged care: A systematic review of quantitative evidence.

Arch Gerontol Geriatr 2021 Mar 19;95:104399. Epub 2021 Mar 19.

KU Leuven - University of Leuven, Centre for Biomedical Ethics and Law, Faculty of Medicine, Kapucijnenvoer 35 box 7001, B-3000 Leuven, Belgium. Electronic address:

Background: Socially assistive robots (SARs) are created to meet challenges of the global increase of older adults. SARs are autonomous embodied technologies, equipped with auditory and visual faculties, enabling them to interact with users while performing assistive roles. Despite studies focusing on older adults' experiences with and perceptions of SARs, it remains unclear what these encompass. Read More

View Article and Full-Text PDF

Fully automated counting of DNA damage foci in tumor cell culture: A matter of cell separation.

DNA Repair (Amst) 2021 Mar 16;102:103100. Epub 2021 Mar 16.

Department of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Tumor Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt; Mildred-Scheel Cancer Career Center HATRICs4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.

Analysis and quantification of residual, unrepaired DNA double-strand breaks by detecting damage-associated γH2AX or 53BP1 foci is a promising approach to evaluate radiosensitivity or radiosensitization in tumor cells. Manual foci quantification by eye is well-established but unsatisfactory due to inconsistent foci numbers between different observers, lack of information about foci size and intensity and the time-consuming scoring process. Therefore, automated foci counting is an important goal. Read More

View Article and Full-Text PDF

Bone Density Micro-CT Assessment during Embedding of the Innovative Multi-Spiked Connecting Scaffold in Periarticular Bone to Elaborate a Validated Numerical Model for Designing Biomimetic Fixation of Resurfacing Endoprostheses.

Materials (Basel) 2021 Mar 12;14(6). Epub 2021 Mar 12.

Laboratory of Bone Implants Research and Design, Department of Technology Design, Institute of Mechanical Technology, Poznan University of Technology, 60-965 Poznan, Poland.

Our team has been working for some time on designing a new kind of biomimetic fixation of resurfacing endoprostheses, in which the innovative multi-spiked connecting scaffold (MSC-Scaffold) that mimics the natural interface between articular cartilage and periarticular trabecular bone in human joints is the crucial element. This work aimed to develop a numerical model enabling the design of the considered joint replacement implant that would reflect the mechanics of interacting biomaterials. Thus, quantitative micro-CT analysis of density distribution in bone material during the embedding of MSC-Scaffold in periarticular bone was applied. Read More

View Article and Full-Text PDF

Reduced Expression Impairs Mitotic Removal of H2B Monoubiquitination, Alters Chromatin Compaction and Induces Chromosome Instability That May Promote Oncogenesis.

Cancers (Basel) 2021 Mar 2;13(5). Epub 2021 Mar 2.

Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E0V9, Canada.

Chromosome instability (CIN) is an enabling feature of oncogenesis associated with poor patient outcomes, whose genetic determinants remain largely unknown. As mitotic chromatin compaction defects can compromise the accuracy of chromosome segregation into daughter cells and drive CIN, characterizing the molecular mechanisms ensuring accurate chromatin compaction may identify novel CIN genes. In vitro, histone H2B monoubiquitination at lysine 120 (H2Bub1) impairs chromatin compaction, while in vivo H2Bub1 is rapidly depleted from chromatin upon entry into mitosis, suggesting that H2Bub1 removal may be a pre-requisite for mitotic fidelity. Read More

View Article and Full-Text PDF

Smartphone-enabled field monitoring tool for rapid hexavalent chromium detection in water.

Anal Bioanal Chem 2021 Apr 2. Epub 2021 Apr 2.

Department of Civil Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India.

Chromium contamination of soil and water is a serious environmental and public health concern as the hexavalent form of chromium [Cr(VI)] is readily soluble in water and is a confirmed carcinogen. There is an imminent need for a robust, low-cost, and simple analytical technique to facilitate in situ monitoring of Cr(VI) in water. Current quantitative methods of Cr(VI) detection are largely laboratory-based, time-consuming, expensive, and require training for implementation. Read More

View Article and Full-Text PDF

Penn Access Summer Scholars program: a mixed method analysis of a virtual offering of a premedical diversity summer enrichment program.

Med Educ Online 2021 Dec;26(1):1905918

Program for Diversity and Inclusion, Academic Programs Office, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

In the USA, numerous summer programs are available for undergraduate students that seek to increase the number of individuals from groups underrepresented in medicine (URM) that matriculate to medical school. These programs have typically been conducted at research-focused institutions, involving hands-on-research and various enrichment experiences. For 2020, the COVID-19 pandemic resulted in the suspension of on-campus student activities at American universities, necessitating a switch to a virtual format for these URM-focused programs. Read More

View Article and Full-Text PDF
December 2021

Cross-sectional analysis of women in neurosurgery: a Canadian perspective.

Neurosurg Focus 2021 Mar;50(3):E13

4Department of Surgery (Neurosurgery), Université Laval, Québec City, Québec, Canada.

Objective: Although the past decades have seen a steady increase of women in medicine in general, women continue to represent a minority of the physician-training staff and workforce in neurosurgery in Canada and worldwide. As such, the aim of this study was to analyze the experiences of women faculty practicing neurosurgery across Canada to better understand and address the factors contributing to this disparity.

Methods: A historical, cross-sectional, and mixed-method analysis of survey responses was performed using survey results obtained from women attending neurosurgeons across Canada. Read More

View Article and Full-Text PDF

Small extracellular vesicles derived from interferon-γ pre-conditioned mesenchymal stromal cells effectively treat liver fibrosis.

NPJ Regen Med 2021 Mar 30;6(1):19. Epub 2021 Mar 30.

Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan.

Mesenchymal stromal cells (MSCs) are used for ameliorating liver fibrosis and aiding liver regeneration after cirrhosis; Here, we analyzed the therapeutic potential of small extracellular vesicles (sEVs) derived from interferon-γ (IFN-γ) pre-conditioned MSCs (γ-sEVs). γ-sEVs effectively induced anti-inflammatory macrophages with high motility and phagocytic abilities in vitro, while not preventing hepatic stellate cell (HSC; the major source of collagen fiber) activation in vitro. The proteome analysis of MSC-derived sEVs revealed anti-inflammatory macrophage inducible proteins (e. Read More

View Article and Full-Text PDF

Field Application of NIR Spectroscopy for the Discrimination of the Species That Are Intermediate Hosts of in Brazil.

Front Public Health 2021 12;9:636206. Epub 2021 Mar 12.

Environmental Health Monitoring and Prevention Laboratory, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil.

Near Infrared Spectroscopy (NIRS) is a spectroscopic technique that evaluates the vibrational energy levels of the chemical bonds of molecules within a wavelength range of 750-2,500 nm. This simple method acquires spectra that provide qualitative and quantitative data on the chemical components of the biomass of living organisms through the interaction between the electromagnetic waves and the sample. NIRS is an innovative, rapid, and non-destructive technique that can contribute to the differentiation of species based on their chemical phenotypes. Read More

View Article and Full-Text PDF

Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family.

Plant Physiol 2021 Mar 26. Epub 2021 Mar 26.

Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick NJ 08901-8520, USA.

Dietary flavonoids play an important role in human nutrition and health. Flavonoid biosynthesis genes have recently been identified in lettuce (Lactuca sativa); however, few mutants have been characterized. We now report the causative mutations in Green Super Lettuce (GSL), a natural light green mutant derived from the red line NAR; and GSL-Dark Green (GSL-DG), an olive-green natural derivative of GSL. Read More

View Article and Full-Text PDF

Machine learning for proton path tracking in proton computed tomography.

Phys Med Biol 2021 Mar 25. Epub 2021 Mar 25.


A Machine Learning approach to the problem of calculating the proton paths inside a scanned object in proton Computed Tomography is presented. The method is developed in order to mitigate the loss in both spatial resolution and quantitative integrity of the reconstructed images caused by multiple Coulomb scattering of protons traversing the matter. Two Machine Learning models were used: a forward neural network and the XGBoost method. Read More

View Article and Full-Text PDF

A multi-inversion multi-echo spin and gradient echo echo planar imaging sequence with low image distortion for rapid quantitative parameter mapping and synthetic image contrasts.

Magn Reson Med 2021 Mar 25. Epub 2021 Mar 25.

Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.

Purpose: Brain imaging exams typically take 10-20 min and involve multiple sequential acquisitions. A low-distortion whole-brain echo planar imaging (EPI)-based approach was developed to efficiently encode multiple contrasts in one acquisition, allowing for calculation of quantitative parameter maps and synthetic contrast-weighted images.

Methods: Inversion prepared spin- and gradient-echo EPI was developed with slice-order shuffling across measurements for efficient acquisition with T , T , and weighting. Read More

View Article and Full-Text PDF

Multiparametric Quantitative MRI in Neurological Diseases.

Front Neurol 2021 8;12:640239. Epub 2021 Mar 8.

Department of Neurology, Goethe University, Frankfurt, Germany.

Magnetic resonance imaging (MRI) is the gold standard imaging technique for diagnosis and monitoring of many neurological diseases. However, the application of conventional MRI in clinical routine is mainly limited to the visual detection of macroscopic tissue pathology since mixed tissue contrasts depending on hardware and protocol parameters hamper its application for the assessment of subtle or diffuse impairment of the structural tissue integrity. Multiparametric quantitative (q)MRI determines tissue parameters quantitatively, enabling the detection of microstructural processes related to tissue remodeling in aging and neurological diseases. Read More

View Article and Full-Text PDF

All-systolic first-pass myocardial rest perfusion at a long saturation time using simultaneous multi-slice imaging and compressed sensing acceleration.

Magn Reson Med 2021 Mar 10. Epub 2021 Mar 10.

School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.

Purpose: To enable all-systolic first-pass rest myocardial perfusion with long saturation times. To investigate the change in perfusion contrast and dark rim artefacts through simulations and surrogate measurements.

Methods: Simulations were employed to investigate optimal saturation time for myocardium-perfusion defect contrast and blood-to-myocardium signal ratios. Read More

View Article and Full-Text PDF

Approaches to patient satisfaction measurement of the healthcare food services: A systematic review.

Clin Nutr ESPEN 2021 Apr 19;42:61-72. Epub 2021 Jan 19.

Nutrition & Dietetics Department, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia. Electronic address:

Background & Aims: Monitoring consumer's satisfaction is important in ensuring effective foodservice improvements and to provide a patient-centred foodservice experience. The aim of this study is to systematically review available patient foodservice satisfaction survey instruments developed and validated within the acute and long-term care settings.

Methods: A literature search of four scientific databases was performed to identify relevant studies with 50 participants or greater. Read More

View Article and Full-Text PDF

Importance of suberin biopolymer in plant function, contributions to soil organic carbon and in the production of bio-derived energy and materials.

Biotechnol Biofuels 2021 Mar 20;14(1):75. Epub 2021 Mar 20.

Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.

Suberin is a hydrophobic biopolymer of significance in the production of biomass-derived materials and in biogeochemical cycling in terrestrial ecosystems. Here, we describe suberin structure and biosynthesis, and its importance in biological (i.e. Read More

View Article and Full-Text PDF