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Three dimensional reconstruction to visualize atrial fibrillation activation patterns on curved atrial geometry.

PLoS One 2021 9;16(4):e0249873. Epub 2021 Apr 9.

Department of Physics, UC San Diego, La Jolla, California, United States of America.

Background: The rotational activation created by spiral waves may be a mechanism for atrial fibrillation (AF), yet it is unclear how activation patterns obtained from endocardial baskets are influenced by the 3D geometric curvature of the atrium or 'unfolding' into 2D maps. We develop algorithms that can visualize spiral waves and their tip locations on curved atrial geometries. We use these algorithms to quantify differences in AF maps and spiral tip locations between 3D basket reconstructions, projection onto 3D anatomical shells and unfolded 2D surfaces. Read More

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Digital image processing to detect subtle motion in stony coral.

Sci Rep 2021 Apr 8;11(1):7722. Epub 2021 Apr 8.

Department of Aeronautics and Astronautics, University of Washington, Seattle, WA, 98195-2400, USA.

Coral reef ecosystems support significant biological activities and harbor huge diversity, but they are facing a severe crisis driven by anthropogenic activities and climate change. An important behavioral trait of the coral holobiont is coral motion, which may play an essential role in feeding, competition, reproduction, and thus survival and fitness. Therefore, characterizing coral behavior through motion analysis will aid our understanding of basic biological and physical coral functions. Read More

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Reduced spatial resolution MRI suffices to image and quantify drought induced embolism formation in trees.

Plant Methods 2021 Apr 6;17(1):38. Epub 2021 Apr 6.

IBG-2: Plant Sciences, Forschungszentrum Jülich, Jülich, Germany.

Background: Magnetic resonance imaging (MRI) is uniquely suited to non-invasively and continuously monitor embolism formation in trees. Depending on the MRI method used, quantitative parameter maps of water content and MRI signal relaxation behavior can be generated. The ability to measure dynamic differences in water content and relaxation behavior can be used to detect xylem embolism formation, even if xylem conduits are too small to be spatially resolved. Read More

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Urethral support in female urinary continence part 1: dynamic measurements of urethral shape and motion.

Int Urogynecol J 2021 Apr 6. Epub 2021 Apr 6.

Female Pelvic Medicine and Reconstructive Surgery (FPMRS), Division of Urogynecology, University of Chicago Pritzker School of Medicine, NorthShore University HealthSystem, 9650 Gross Point Road, Suite 3900, Skokie, IL, 60076, USA.

Introduction And Hypothesis: Urethral closure mechanism dysfunction in female stress urinary incontinence (SUI) is poorly understood. We aimed to quantify these mechanisms through changes in urethral shape and position during squeeze (voluntary closure) and Valsalva (passive closure) via endovaginal ultrasound in women with varying SUI severity.

Methods: In this prospective cohort study, 76 women who presented to our tertiary center for urodynamic testing as preoperative assessment were recruited. Read More

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DNA Tension Probes to Map the Transient Piconewton Receptor Forces by Immune Cells.

J Vis Exp 2021 Mar 20(169). Epub 2021 Mar 20.

Department of Chemistry, Emory University; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University;

Mechanical forces transmitted at the junction between two neighboring cells and at the junction between cells and the extracellular matrix are critical for regulating many processes ranging from development to immunology. Therefore, developing the tools to study these forces at the molecular scale is critical. Our group developed a suite of molecular tension sensors to quantify and visualize the forces generated by cells and transmitted to specific ligands. Read More

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Visualizing Lung Cellular Adaptations during Combined Ozone and LPS Induced Murine Acute Lung Injury.

J Vis Exp 2021 Mar 21(169). Epub 2021 Mar 21.

Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan;

Lungs are continually faced with direct and indirect insults in the form of sterile (particles or reactive toxins) and infectious (bacterial, viral or fungal) inflammatory conditions. An overwhelming host response may result in compromised respiration and acute lung injury, which is characterized by lung neutrophil recruitment as a result of the patho-logical host immune, coagulative and tissue remodeling response. Sensitive microscopic methods to visualize and quantify murine lung cellular adaptations, in response to low-dose (0. Read More

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Seasonal dynamics of natural Ostreococcus viral infection at the single cell level using VirusFISH.

Environ Microbiol 2021 Apr 5. Epub 2021 Apr 5.

Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.

Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free-living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral-host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral-host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Read More

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Multifunctional peptide-conjugated nanocarriers for pulp regeneration in a full-length human tooth root.

Acta Biomater 2021 Apr 1. Epub 2021 Apr 1.

Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX 75246, USA. Electronic address:

Dental pulp is a highly vascularized tissue, situated in an inextensible environment surrounded by rigid dentinal walls. The pulp receives its blood supply solely from the small apical foramen of a tooth root. Due to the unique anatomy that controls nutrition supply, regeneration of pulp tissue in a full-length tooth root has long been a challenge in regenerative endodontics. Read More

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'Statistical Irreproducibility' Does Not Improve with Larger Sample Size: How to Quantify and Address Disease Data Multimodality in Human and Animal Research.

J Pers Med 2021 Mar 23;11(3). Epub 2021 Mar 23.

Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.

Poor study reproducibility is a concern in translational research. As a solution, it is recommended to increase sample size (N), i.e. Read More

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Fluorine-19 Magnetic Resonance Imaging for Detection of Amyloid β Oligomers Using a Keto Form of Curcumin Derivative in a Mouse Model of Alzheimer's Disease.

Molecules 2021 Mar 4;26(5). Epub 2021 Mar 4.

Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan.

Recent evidence suggests that the formation of soluble amyloid β (Aβ) aggregates with high toxicity, such as oligomers and protofibrils, is a key event that causes Alzheimer's disease (AD). However, understanding the pathophysiological role of such soluble Aβ aggregates in the brain in vivo could be difficult due to the lack of a clinically available method to detect, visualize, and quantify soluble Aβ aggregates in the brain. We had synthesized a novel fluorinated curcumin derivative with a fixed keto form, named as Shiga-Y51, which exhibited high selectivity to Aβ oligomers in vitro. Read More

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New Techniques of Structure Elucidation for Sesquiterpenes.

Prog Chem Org Nat Prod 2021 ;114:253-311

Department of Chemistry, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Avenida Instituto Politécnico Nacional 2508, Mexico City, 07360, Mexico.

The most significant new techniques that have been used in the twenty-first century for the structure elucidation of sesquiterpenes and some derivatives are reviewed in this chapter. A distinctive feature of these methodologies is the combination of accurate experimental measurements with theoretical data obtained by molecular modeling calculations that allow to visualize, understand, and quantify many structural characteristics. This has been the case for NMR spectroscopy, which has expanded its potential for solving complex structural problems by means of comparison with quantum mechanical molecular models. Read More

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January 2021

Live imaging and quantitation of nascent transcription using the MS2/MCP system in the embryo.

STAR Protoc 2021 Mar 18;2(1):100379. Epub 2021 Mar 18.

Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.

Visualizing transcription live in is providing important new insights into the spatiotemporal regulation of transcription. Here, we describe a protocol to visualize and quantitate transcription from gene loci that are tagged with MS2 stem-loop sequences in the embryo. MS2 stem-loop sequences are recognized by a coat protein fused to a fluorescent protein and visualized with microscopy. Read More

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Development and Validation of a Nomogram for Preoperative Prediction of Central Compartment Lymph Node Metastasis in Patients with Papillary Thyroid Carcinoma and Type 2 Diabetes Mellitus.

Cancer Manag Res 2021 17;13:2499-2513. Epub 2021 Mar 17.

Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China.

Purpose: To develop and validate a nomogram to predict central compartment lymph node metastasis in PTC patients with Type 2 Diabetes.

Patients And Methods: The total number of enrolled patients was 456. The optimal cut-off values of continuous variables were obtained by ROC curve analysis. Read More

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Computing infection distributions and longitudinal evolution patterns in lung CT images.

BMC Med Imaging 2021 03 23;21(1):57. Epub 2021 Mar 23.

Shanghai United Imaging Intelligence Co., Ltd, Shanghai, China.

Background: Spatial and temporal lung infection distributions of coronavirus disease 2019 (COVID-19) and their changes could reveal important patterns to better understand the disease and its time course. This paper presents a pipeline to analyze statistically these patterns by automatically segmenting the infection regions and registering them onto a common template.

Methods: A VB-Net is designed to automatically segment infection regions in CT images. Read More

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Micro-positron emission tomography imaging of angiogenesis based on F-RGD for assessing liver metastasis of colorectal cancer.

Hepatobiliary Pancreat Dis Int 2021 Mar 9. Epub 2021 Mar 9.

Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China. Electronic address:

Background: Positron emission tomography (PET) imaging is a non-invasive method to visualize and quantify the tumor microenvironment. This study aimed to explore the feasibility of F-AIF-NOTA-E[PEG-c(RGDfk)] (denoted as F-RGD) PET quantitative parameters to distinguish the angiogenesis in colorectal cancer (CRC) mice which has different metastatic potential.

Methods: Twenty LoVo and twenty LS174T of CRC liver metastases animal models were established by implantation of human CRC cell lines via intrasplenic injection. Read More

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A 3D cine-MRI acquisition technique and image analysis framework to quantify bowel motion demonstrated in gynecological cancer patients.

Med Phys 2021 Mar 19. Epub 2021 Mar 19.

Department of Radiation Oncology, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.

Purpose: Magnetic resonance imaging (MRI) is increasingly used in radiation oncology for target delineation and radiotherapy treatment planning, for example, in patients with gynecological cancers. As a consequence of pelvic radiotherapy, a part of the bowel is irradiated, yielding risk of bowel toxicity. Existing dose-effect models predicting bowel toxicity are inconclusive and bowel motion might be an important confounding factor. Read More

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Quantifying Bolus Residue and Its Risks in Children: A Videofluoroscopic Study.

Am J Speech Lang Pathol 2021 Mar 18;30(2):687-696. Epub 2021 Mar 18.

Department of Surgery, The University of Auckland, New Zealand.

Purpose Postswallow residue is a clinical sign of swallow impairment and has shown a strong association with aspiration. Videofluoroscopy (videofluoroscopic study of swallowing [VFSS]) is commonly used to visualize oropharyngeal swallowing and to identify pharyngeal residue. However, subjective binary observation (present or absent) fails to provide important information on volume or location and lacks objectivity and reproducibility. Read More

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Ursolic acid inhibits multi-species biofilms developed by Streptococcus mutans, Streptococcus sanguinis, and Streptococcus gordonii.

Arch Oral Biol 2021 Mar 15;125:105107. Epub 2021 Mar 15.

State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China. Electronic address:

Objective: The current study aimed to assess the antimicrobial activity of ursolic acid (UA) against multi-species biofilms formed by Streptococcus mutans, Streptococcus sanguinis, and Streptococcus gordonii, as well as to measure its biocompatibility.

Methods: Crystal violet staining, CFU counting, CCK-8 assays and scanning electron microscopy (SEM) were applied to investigate the effect of UA on multi-species biofilms. UA's effect on exopolysaccharides (EPS) production was measured using confocal laser scanning microscopy (CLSM) and the anthrone-sulfuric acid method. Read More

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Advanced therapeutic inhalation aerosols of a Nrf2 activator and RhoA/Rho kinase (ROCK) inhibitor for targeted pulmonary drug delivery in pulmonary hypertension: design, characterization, aerosolization, 2D/3D human lung cell cultures, and efficacy.

Ther Adv Respir Dis 2021 Jan-Dec;15:1753466621998245

Skaggs Pharmaceutical Sciences Center, The University of Arizona College of Pharmacy, Tucson, AZ, USA.

Inhalable nanostructured microparticles of simvastatin, a Nrf2 activator and RhoA/Rho kinase (ROCK) inhibitor, were rationally designed for targeted pulmonary delivery as dry powder inhalers (DPIs) for the treatment of pulmonary hypertension (PH). Advanced particle engineering design technology was employed to develop inhalable dry powders using different dilute feed concentrations and spray drying pump rates. Several analytical techniques were used comprehensively to characterize the physicochemical properties of the resulting powders. Read More

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Advanced imaging and labelling methods to decipher brain cell organization and function.

Nat Rev Neurosci 2021 Apr 12;22(4):237-255. Epub 2021 Mar 12.

University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.

The brain is arguably the most complex organ. The branched and extended morphology of nerve cells, their subcellular complexity, the multiplicity of brain cell types as well as their intricate connectivity and the scattering properties of brain tissue present formidable challenges to the understanding of brain function. Neuroscientists have often been at the forefront of technological and methodological developments to overcome these hurdles to visualize, quantify and modify cell and network properties. Read More

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Molecular Force Measurement with Tension Sensors.

Annu Rev Biophys 2021 Mar 12. Epub 2021 Mar 12.

Department of Quantitative Cell Biology, Institute of Molecular Cell Biology, University of Münster, Münster D-48149, Germany; email:

The ability of cells to generate mechanical forces, but also to sense, adapt to, and respond to mechanical signals, is crucial for many developmental, postnatal homeostatic, and pathophysiological processes. However, the molecular mechanisms underlying cellular mechanotransduction have remained elusive for many decades, as techniques to visualize and quantify molecular forces across individual proteins in cells were missing. The development of genetically encoded molecular tension sensors now allows the quantification of piconewton-scale forces that act upon distinct molecules in living cells and even whole organisms. Read More

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Study of Mesenchymal Stem Cell-Mediated Mitochondrial Transfer in In Vitro Models of Oxidant-Mediated Airway Epithelial and Smooth Muscle Cell Injury.

Methods Mol Biol 2021 ;2269:93-105

National Heart and Lung Institute, Imperial College London, London, UK.

Mesenchymal stem cells (MSCs) have emerged as an attractive candidate for cell-based therapy. In the past decade, many animal and pilot clinical studies have demonstrated that MSCs are therapeutically beneficial for the treatment of obstructive lung diseases such as asthma and chronic obstructive pulmonary disease (COPD). However, due to the scarcity of adult human MSCs, human-induced pluripotent stem cells mesenchymal stem cells (iPSCs) are now increasingly used as a source of MSCs. Read More

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Assessment and Management of HIV Distal Sensory Peripheral Neuropathy: Understanding the Symptoms.

J Nurse Pract 2020 Apr 20;16(4):276-280. Epub 2020 Mar 20.

Studies in Symptom Management New York University / NYU Meyers.

Distal sensory peripheral neuropathy (HIV-DSP) affects upwards of 50% of people living with HIV. Causing often debilitating symptoms of tingling, numbness and burning, HIV-DSP can result in disability, unemployment and low quality of life. Comorbidities further complicate nursing care, heightening risk of polypharmacy and symptom exacerbation. Read More

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Fluorescent Polysome Profiling in .

Bio Protoc 2020 Sep 5;10(17):e3742. Epub 2020 Sep 5.

Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA.

An important but often overlooked aspect of gene regulation occurs at the level of protein translation. Many genes are regulated not only by transcription but by their propensity to be recruited to actively translating ribosomes (polysomes). Polysome profiling allows for the separation of unbound 40S and 60S subunits, 80S monosomes, and actively translating mRNA bound by two or more ribosomes. Read More

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September 2020

A Novel Function of TLR2 and MyD88 in the Regulation of Leukocyte Cell Migration Behavior During Wounding in Zebrafish Larvae.

Front Cell Dev Biol 2021 15;9:624571. Epub 2021 Feb 15.

Institute of Biology, Leiden University, Leiden, Netherlands.

Toll-like receptor (TLR) signaling via myeloid differentiation factor 88 protein (MyD88) has been indicated to be involved in the response to wounding. It remains unknown whether the putative role of MyD88 in wounding responses is due to a control of leukocyte cell migration. The aim of this study was to explore whether TLR2 and MyD88 are involved in modulating neutrophil and macrophage cell migration behavior upon zebrafish larval tail wounding. Read More

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February 2021

Whole-mount staining coupled to a UV-inducible basal cell carcinoma murine model.

STAR Protoc 2021 Mar 5;2(1):100329. Epub 2021 Feb 5.

The University of Queensland, UQ Diamantina Institute, Brisbane, QLD, Australia.

The origin of basal cell carcinomas (BCC) remains elusive. This protocol combines the use of an ultraviolet (UV)-inducible BCC murine model (K14CrexPtch) and an optimized protocol for florescent whole-mount cytokeratin 17 immunostaining to address the spatiotemporal dynamics of BCC formation. The high-resolution three-dimensional confocal images are an excellent tool to visualize and quantify the distribution of skin cancers at a given time point. Read More

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Epicardial fat and coronary artery disease: Role of cardiac imaging.

Atherosclerosis 2021 03 16;321:30-38. Epub 2021 Feb 16.

Department of Cardiovascular Imaging, Centro Cardiologico Monzino, IRCCS, Milan, Italy. Electronic address:

Epicardial adipose tissue (EAT) represents the fat depot located between the myocardium and the visceral pericardial layer. Far from being an inert tissue, EAT has been recognized as secreting a large amount of bioactive molecules called adipokines, which have numerous exocrine and paracrine effects. Recent evidence demonstrates that pericoronary adipose tissue (PCAT) - the EAT directly surrounding the coronary arteries - has a complex bidirectional interaction with the underlying vascular wall. Read More

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Characterization of ultrasound-mediated delivery of trastuzumab to normal and pathologic spinal cord tissue.

Sci Rep 2021 Feb 24;11(1):4412. Epub 2021 Feb 24.

Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Rm M7-302, Toronto, ON, M4N 3M5, Canada.

Extensive studies on focused ultrasound (FUS)-mediated drug delivery through the blood-brain barrier have been published, yet little work has been published on FUS-mediated drug delivery through the blood-spinal cord barrier (BSCB). This work aims to quantify the delivery of the monoclonal antibody trastuzumab to rat spinal cord tissue and characterize its distribution within a model of leptomeningeal metastases. 10 healthy Sprague-Dawley rats were treated with FUS + trastuzumab and sacrificed at 2-h or 24-h post-FUS. Read More

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February 2021

Entering a new era of quantifying glutamate clearance in health and disease.

J Neurosci Res 2021 Feb 22. Epub 2021 Feb 22.

Faculty of Medicine, Division of Biomedical Sciences, Memorial University of Newfoundland, St. John's, NL, Canada.

Glutamate transporter proteins, expressed on both neurons and glia, serve as the main gatekeepers that dictate the spatial and temporal actions of extracellular glutamate. Glutamate is essential to the function of the healthy brain yet paradoxically contributes to the toxicity associated with many neurodegenerative diseases. Rapid transporter-mediated glutamate uptake, primarily occurring at astrocytic processes, tightens the efficiency of excitatory network activity and prevents toxic glutamate build-up in the extracellular space. Read More

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February 2021

Visualization of probiotics via epifluorescence microscopy and fluorescence in situ hybridization (FISH).

J Microbiol Methods 2021 Mar 14;182:106151. Epub 2021 Feb 14.

Biological Sciences Department, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA.

Aerobic plate counts, the standard for bacterial enumeration in the probiotic industry, can be biased towards fast-growing organisms that replicate on synthetic media and can significantly underestimate total bacterial abundance. Culture-independent approaches such as fluorescence in situ hybridization (FISH) hold promise as a means to rapidly and accurately enumerate bacteria in probiotic products. In addition, FISH has the potential to more accurately represent bacterial growth dynamics in the environment in which products are applied without imposing additional growth constraints that are required for enumeration via plate counts. Read More

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