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https://www.readbyqxmd.com/read/27914366/rapid-and-low-cost-biosensor-for-the-detection-of-staphylococcus-aureus
#1
Ghadeer A R Y Suaifan, Sahar Alhogail, Mohammed Zourob
Staphylococcus aureus (S. aureus) is one of the most common etiological agents in hospital-acquired infections and food-borne illness. S. aureus toxins and virulence proteases often circulate in host blood vessels leading to life-threatening diseases. Standard identification approaches include bacterial culturing method, which takes several days. Other nucleic acid-based methods were expensive and required trained personnel. To surmount these limitations, a paper-based biosensor was developed. The sensing mechanism was based on the proteolytic activity of S...
November 21, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27911396/automated-quantification-and-analysis-of-cell-counting-procedures-using-imagej-plugins
#2
Jacob O'Brien, Heyam Hayder, Chun Peng
The National Institute of Health's ImageJ is a powerful, freely available image processing software suite. ImageJ has comprehensive particle analysis algorithms which can be used effectively to count various biological particles. When counting large numbers of cell samples, the hemocytometer presents a bottleneck with regards to time. Likewise, counting membranes from migration/invasion assays with the ImageJ plugin Cell Counter, although accurate, is exceptionally labor intensive, subjective, and infamous for causing wrist pain...
November 17, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911038/quantitating-the-cell-turning-images-into-numbers-with-imagej
#3
REVIEW
Ellen T Arena, Curtis T Rueden, Mark C Hiner, Shulei Wang, Ming Yuan, Kevin W Eliceiri
Modern biological research particularly in the fields of developmental and cell biology has been transformed by the rapid evolution of the light microscope. The light microscope, long a mainstay of the experimental biologist, is now used for a wide array of biological experimental scenarios and sample types. Much of the great developments in advanced biological imaging have been driven by the digital imaging revolution with powerful processors and algorithms. In particular, this combination of advanced imaging and computational analysis has resulted in the drive of the modern biologist to not only visually inspect dynamic phenomena, but to quantify the involved processes...
December 2, 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/27910021/quantitative-fluorescence-in-situ-hybridization-qfish
#4
Ivan Y Iourov
Fluorescence in situ hybridization (FISH) has a wide spectrum of applications in current molecular cytogenetic and cancer research. This is a unique technique that can be used for chromosomal DNA analysis in all cell types, at all stages of the cell cycle, and at molecular resolution. Recent developments in microscopy and imaging systems have allowed quantification of digital FISH images (quantitative FISH or QFISH) and have provided a new way for molecular cytogenetic analysis at single-cell level. QFISH can be applied for studying chromosome imbalances in interphase nuclei or metaphase spreads, measuring relative DNA content at chromosomal loci and identifying parental origin of homologous chromosomes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27907228/measurement-of-postmortem-pupil-size-a-new-method-with-excellent-reliability-and-its-application-to-pupil-changes-in-the-early-postmortem-period
#5
Luise Fleischer, Susanne Sehner, Axel Gehl, Martin Riemer, Tobias Raupach, Sven Anders
Measurement of postmortem pupil width is a potential component of death time estimation. However, no standardized measurement method has been described. We analyzed a total of 71 digital images for pupil-iris ratio using the software ImageJ. Images were analyzed three times by four different examiners. In addition, serial images from 10 cases were taken between 2 and 50 h postmortem to detect spontaneous pupil changes. Intra- and inter-rater reliability of the method was excellent (ICC > 0.95). The method is observer independent and yields consistent results, and images can be digitally stored and re-evaluated...
December 1, 2016: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/27897414/a-comparative-study-of-software-programmes-for-cross-sectional-skeletal-muscle-and-adipose-tissue-measurements-on-abdominal-computed-tomography-scans-of-rectal-cancer-patients
#6
Jeroen L A van Vugt, Stef Levolger, Arvind Gharbharan, Marcel Koek, Wiro J Niessen, Jacobus W A Burger, Sten P Willemsen, Ron W F de Bruin, Jan N M IJzermans
BACKGROUND: The association between body composition (e.g. sarcopenia or visceral obesity) and treatment outcomes, such as survival, using single-slice computed tomography (CT)-based measurements has recently been studied in various patient groups. These studies have been conducted with different software programmes, each with their specific characteristics, of which the inter-observer, intra-observer, and inter-software correlation are unknown. Therefore, a comparative study was performed...
November 22, 2016: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/27893108/choroidal-thickness-influences-near-infrared-reflectance-intensity-in-eyes-with-geographic-atrophy-due-to-age-related-macular-degeneration
#7
Rosa Dolz-Marco, Orly Gal-Or, K Bailey Freund
Purpose: To evaluate the effects of retinal and choroidal thickness on near-infrared reflectance (NIR) scanning laser ophthalmoscopy in eyes with geographic atrophy (GA) secondary to non-neovascular age-related macular degeneration (AMD). Methods: This was a cross-sectional review of the clinical records and multimodal imaging data of eyes diagnosed with GA secondary to non-neovascular AMD. Imaging modalities included color fundus photography, fundus autofluorescence, NIR, and structural spectral-domain optical coherence tomography (SD-OCT)...
November 1, 2016: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/27891745/cardiac-extracellular-matrix-is-associated-with-adverse-outcome-in-patients-with-chronic-heart-failure
#8
Franz Duca, Caroline Zotter-Tufaro, Andreas A Kammerlander, Adelheid Panzenböck, Stefan Aschauer, Daniel Dalos, Benedikt Köll, Benedikt Börries, Hermine Agis, Renate Kain, Klaus Aumayr, Florian Klinglmüller, Julia Mascherbauer, Diana Bonderman
AIMS: Accumulation of extracellular matrix (ECM) is known to play a crucial role in the pathophysiology of heart failure (HF). However, its prognostic relevance is poorly investigated. METHODS AND RESULTS: A total of 73 HF patients who underwent LV endomyocardial biopsy were enrolled in our study. ECM area was quantified by TissueFAXS and ImageJ software. Patients were followed-up at 6-month intervals. The study endpoint was defined as hospitalization for a cardiac reason and/or cardiac death...
November 27, 2016: European Journal of Heart Failure
https://www.readbyqxmd.com/read/27891327/analysis-of-fetal-palate-to-assist-pre-natal-ultrasound
#9
Anjali Shastry, Yogitha Ravindranath, Roopa Ravindranath
INTRODUCTION: Cleft palate is one of the major facial congenital malformation in newborns. Pre-natal detection of this malformation is limited to detection of clefting of hard palate but isolated soft palate clefting still remains challenge for sonologists. As Indian literature is limited present study was attempted to provide dimensions and position of fetal palate by digitized images. AIM: To study dimensions, position and differences in parameters between second and third trimester fetuses...
October 2016: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/27890650/diana-an-imagej-tool-for-object-based-3d-co-localization-and-distance-analysis
#10
Jean-François Gilles, Marc Dos Santos, Thomas Boudier, Susanne Bolte, Nicolas Heck
We present a new plugin for ImageJ called DiAna, for Distance Analysis, which comes with a user-friendly interface. DiAna proposes robust and accurate 3D segmentation for object extraction. The plugin performs automated object-based co-localization and distance analysis. DiAna offers an in-depth analysis of co-localization between objects and retrieves 3D measurements including co-localizing volumes and surfaces of contact. It also computes the distribution of distances between objects in 3D. With DiAna, we furthermore introduce an original method, which allows for estimating the statistical significance of object co-localization...
November 24, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27887759/implementing-an-open-access-casa-software-for-the-assessment-of-stallion-sperm-motility-relationship-with-other-sperm-quality-parameters
#11
Elisa Giaretta, Mauro Munerato, Marc Yeste, Giovanna Galeati, Marcella Spinaci, Carlo Tamanini, Gaetano Mari, Diego Bucci
Setting an open-access computer assisted sperm analysis (CASA) may benefit the evaluation of motility in mammalian sperm, especially when economic constraints do not allow the use of a commercial system. There have been successful attempts to develop such a device in Zebra fish sperm and the system has been used in very few studies on mammalian spermatozoa. Against this background, the present study aimed at developing an open-access CASA system for mammalian sperm using the horse as a model and based upon the Image J software previously established for Zebra fish sperm...
November 13, 2016: Animal Reproduction Science
https://www.readbyqxmd.com/read/27884532/morphometric-analysis-of-the-folliculostellate-cells-and-luteinizing-hormone-gonadotropic-cells-of-the-anterior-pituitary-of-the-men-during-the-aging-process
#12
Jovana Čukuranović Kokoris, Ivan Jovanović, Vukica Pantović, Miljan Krstić, Milica Stanojković, Verica Milošević, Slađana Ugrenović, Vesna Stojanović
The aim of this research was to quantify the changes in the morphology and density of the anterior pituitary folliculostellate (FS) and luteinizing hormone (LH) cells. Material was tissue of the pituitary gland of the 14 male cadavers. Tissue slices were immunohistochemically stained with monoclonal anti-LH antibody and polyclonal anti-S100 antibody for the detection of LH and FS cells, respectively. Digital images of the stained slices were afterwards morphometrically analyzed by ImageJ. Results of the morphometric analysis showed significant increase of the FS cells volume density in cases older than 70 years...
November 17, 2016: Tissue & Cell
https://www.readbyqxmd.com/read/27881701/externally-visible-thrombus-partially-predicts-internal-thrombus-deposition-in-extracorporeal-membrane-oxygenators
#13
Charles F Evans, Tieluo Li, Vikas Mishra, Diana L Pratt, Isa S K Mohammed, Zachary N Kon, Bartley P Griffith
AIM: We sought to quantify the location and volume of thrombus in used hollow-fiber membrane oxygenators and correlate the volume of thrombus with patient demographics, flow characteristics and anticoagulation parameters. METHODS: Hollow-fiber membrane oxygenators (Quadrox D, Maquet, Rastatt, Germany) were collected after clinical use in ECMO circuits and divided into sections. Each section was digitally imaged and analyzed using ImageJ software. The location and total volume (cm(3)) of thrombus was calculated for different sections...
November 22, 2016: Perfusion
https://www.readbyqxmd.com/read/27867942/quantification-of-calcified-particles-in-human-valve-tissue-reveals-asymmetry-of-calcific-aortic-valve-disease-development
#14
Katsumi Yabusaki, Joshua D Hutcheson, Payal Vyas, Sergio Bertazzo, Simon C Body, Masanori Aikawa, Elena Aikawa
Recent studies indicated that small calcified particles observable by scanning electron microscopy (SEM) may initiate calcification in cardiovascular tissues. We hypothesized that if the calcified particles precede gross calcification observed in calcific aortic valve disease (CAVD), they would exhibit a regional asymmetric distribution associated with CAVD development, which always initiates at the base of aortic valve leaflets adjacent to the aortic outflow in a region known as the fibrosa. Testing this hypothesis required counting the calcified particles in histological sections of aortic valve leaflets...
2016: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/27864948/using-frons-width-to-differentiate-blow-fly-species-diptera-calliphoridae-phormia-regina-meigen-and-protophormia-terraenovae-robineau-desvoidy
#15
Sarah V Langer, Christopher J Kyle, David V Beresford
Protophormia terraenovae (Robineau-Desvoidy) (Diptera: Calliphoridae) and Phormia regina (Meigen) (Diptera: Calliphoridae) are morphologically similar blow fly species commonly used for estimating postmortem intervals. Field collection and storage of adults can result in color changes, in particular on calypters and palps; often collected specimens show damage such as wing fray or fungal growth. We measured the frons width: total head width ratio using photographs (ImageJ version 1.49) to differentiate these two species...
November 16, 2016: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/27864759/histochemical-staining-of-%C3%AE-glucuronidase-and-its-spatial-quantification
#16
Chloé Béziat, Jürgen Kleine-Vehn, Elena Feraru
Microscope images of plant specimens showing expression of GUS markers, besides being very beautiful, provide useful information regarding various biological processes. However, the information extracted from these images is often purely qualitative, and in many publications is not subjected to quantification. Here, we describe a very simple quantification method for GUS histochemical staining that enables detection of subtle differences in gene expression at cellular, tissue, or organ level. The quantification method described is based on the freely available image analysis software ImageJ that is widely used by the scientific community...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27864757/genome-wide-association-mapping-of-root-traits-in-the-context-of-plant-hormone-research
#17
Daniela Ristova, Wolfgang Busch
Genome-wide association (GWA) mapping is a powerful method for the identification of alleles that underlie quantitative traits. It enables one to understand how genetic variation translates into phenotypic variation. In particular, plant hormone signaling pathways play a key role in shaping phenotypes. This chapter presents a protocol for genome-wide association mapping of root traits of Arabidopsis thaliana in the context of hormone research. We describe a specific protocol for acquiring primary and lateral root trait data that is appropriate for GWA studies using FIJI (ImageJ), and subsequent GWA mapping using a user-friendly Internet application...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27861404/the-latino-eyelid-anthropometric-analysis-of-a-spectrum-of-findings
#18
Constance L Fry, Thomas C Naugle, Shelley A Cole, Jonathan Gelfond, Geetha Chittoor, Angeline F Mariani, Martin W Goros, Barrett G Haik, Venkata Saroja Voruganti
PURPOSE: Published anthropometric measurements of the Latino eyelid are limited. This study describes features spanning the morphologic range from non-Latino whites to East Asians in the spectrum of the Latino eyelid. METHODS: A cross-sectional study of 68 people (32 Latinos, 18 non-Latino whites, and 18 East Asians, ages 18-39), approved by the Institutional Review Board and HIPAA-compliant, was performed. Saliva samples determined genetic components. Indirect anthropometric measurements were performed with ImageJ software...
November 15, 2016: Ophthalmic Plastic and Reconstructive Surgery
https://www.readbyqxmd.com/read/27860441/effects-of-human-chorionic-gonadotropin-on-testicular-interstitial-tissues-in-men-with-non-obstructive-azoospermia
#19
S Oka, K Shiraishi, H Matsuyama
Non-obstructive azoospermia is a severe condition because spermatogenesis per se is disrupted. Although microdissection testicular sperm extraction is the standard therapy for non-obstructive azoospermia, sperm retrieval is unsuccessful in approximately 50% of patients. For these patients, we conducted human chorionic gonadotropin-based salvage hormonal therapy, and sperm retrieval was possible in 10-20% of patients. The objectives of this study were to assess the changes in interstitial lesions in patients with non-obstructive azoospermia and to evaluate the effects of human chorionic gonadotropin on these tissues...
November 16, 2016: Andrology
https://www.readbyqxmd.com/read/27853188/lineage-mapper-a-versatile-cell-and-particle-tracker
#20
Joe Chalfoun, Michael Majurski, Alden Dima, Michael Halter, Kiran Bhadriraju, Mary Brady
The ability to accurately track cells and particles from images is critical to many biomedical problems. To address this, we developed Lineage Mapper, an open-source tracker for time-lapse images of biological cells, colonies, and particles. Lineage Mapper tracks objects independently of the segmentation method, detects mitosis in confluence, separates cell clumps mistakenly segmented as a single cell, provides accuracy and scalability even on terabyte-sized datasets, and creates division and/or fusion lineages...
November 17, 2016: Scientific Reports
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