29,145 results match your criteria Biomedical physics & engineering express[Journal]


Neuro4Neuro: A neural network approach for neural tract segmentation using large-scale population-based diffusion imaging.

Neuroimage 2020 May 31:116993. Epub 2020 May 31.

Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands.

Subtle changes in white matter (WM) microstructure have been associated with normal aging and neurodegeneration. To study these associations in more detail, it is highly important that the WM tracts can be accurately and reproducibly characterized from brain diffusion MRI. In addition, to enable analysis of WM tracts in large datasets and in clinical practice it is essential to have methodology that is fast and easy to apply. Read More

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http://dx.doi.org/10.1016/j.neuroimage.2020.116993DOI Listing

Whole-heart, ungated, free-breathing, cardiac-phase-resolved myocardial perfusion MRI by using Continuous Radial Interleaved simultaneous Multi-slice acquisitions at sPoiled steady-state (CRIMP).

Magn Reson Med 2020 Jun 3. Epub 2020 Jun 3.

Utah Center for Advanced Imaging Research (UCAIR), Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, Utah, USA.

Purpose: To develop a whole-heart, free-breathing, non-electrocardiograph (ECG)-gated, cardiac-phase-resolved myocardial perfusion MRI framework (CRIMP; Continuous Radial Interleaved simultaneous Multi-slice acquisitions at sPoiled steady-state) and test its quantification feasibility.

Methods: CRIMP used interleaved radial simultaneous multi-slice (SMS) slice groups to cover the whole heart in 9 or 12 short-axis slices. The sequence continuously acquired data without magnetization preparation, ECG gating or breath-holding, and captured multiple cardiac phases. Read More

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http://dx.doi.org/10.1002/mrm.28337DOI Listing

A Comprehensive Evaluation of the Copying Process of a Complex Figure in Early- and Late-Onset Alzheimer's Disease: Quantitative Analysis of Digital Pen Data.

J Med Internet Res 2020 May 13. Epub 2020 May 13.

Center for Neuroscience, Korea Institute of Science and Technology, Seoul, KR.

Background: The Rey-Osterrieth Complex Figure Test (RCFT) is a neuropsychological test that is widely used to assess visual memory and visuoconstructional deficits in patients with cognitive impairment including Alzheimer's disease (AD). AD patients have an increased tendency for extraordinary behaviors in the RCFT for selecting the drawing area, organizing the figure, and deciding the order of images, among other activities. However, the conventional scoring system based on pen and paper has limited ability to reflect these detailed behaviors. Read More

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http://dx.doi.org/10.2196/18136DOI Listing

Investigating the accuracy and precision of TE-dependent versus multi-echo QSM using Laplacian-based methods at 3 T.

Magn Reson Med 2020 Jun 3. Epub 2020 Jun 3.

Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.

Purpose: Multi-echo gradient-recalled echo acquisitions for QSM enable optimizing the SNR for several tissue types through multi-echo (TE) combination or investigating temporal variations in the susceptibility (potentially reflecting tissue microstructure) by calculating one QSM image at each TE (TE-dependent QSM). In contrast with multi-echo QSM, applying Laplacian-based methods (LBMs) for phase unwrapping and background field removal to single TEs could introduce nonlinear temporal variations (independent of tissue microstructure) into the measured susceptibility. Here, we aimed to compare the effect of LBMs on the QSM susceptibilities in TE-dependent versus multi-echo QSM. Read More

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http://dx.doi.org/10.1002/mrm.28331DOI Listing

Electron density and effective atomic number estimation in a maximum a posteriori framework for dual-energy computed tomography.

Med Phys 2020 Jun 3. Epub 2020 Jun 3.

Département de physique, Université de Montréal, Complexe des sciences, 1375 Avenue Thérèse-Lavoie-Roux, Montréal, Québec, H2V 0B3, Canada.

Purpose: The stoichiometric calibration method for dual-energy CT (DECT) proposed by Bourque et al. (Phys. Med. Read More

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http://dx.doi.org/10.1002/mp.14309DOI Listing

Determination of Diagnostic Reference Level in Routine Examinations of Digital Radiography in Mazandaran Province.

Radiat Prot Dosimetry 2020 Jun 3. Epub 2020 Jun 3.

Department of Medical Physics Radiobiology and Radiation Protection, School of Medicine, Babol University of Medical Sciences, Babol, Iran.

Introduction: The main purpose of this study was to determine the diagnostic reference level (DRL) for routine digital radiography examinations in Mazandaran province.

Materials And Methods: Thirteen digital radiographic examinations at 18 high-patient-load radiography centres were investigated. The indirect dosimetry method was performed based on the IAEA report. Read More

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http://dx.doi.org/10.1093/rpd/ncaa074DOI Listing

An MRI contrast agent based on a zwitterionic metal-chelating polymer for hepatorenal angiography and tumor imaging.

J Mater Chem B 2020 Jun 3. Epub 2020 Jun 3.

Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Bei Yi Jie 2, Zhong Guan Cun, Beijing 100190, China. and School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.

MRI contrast agents such as paramagnetic Gd(iii)-chelates, can improve the ability of MRI in differentiating diseased and healthy tissues, and have been widely used in clinical diagnosis. However, the enhancement effect of small molecular MRI contrast agents is unsatisfied due to their relative high rotation rates. Furthermore, the small molecular contrast agents also suffer from the short blood half-life and nonspecific extracellular diffusion in tissues, which also restricts their applications. Read More

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http://dx.doi.org/10.1039/d0tb00893aDOI Listing

Elevated amyloidoses of human IAPP and amyloid beta by lipopolysaccharide and their mitigation by carbon quantum dots.

Nanoscale 2020 Jun 3. Epub 2020 Jun 3.

ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia. and Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China.

Type 2 diabetes (T2D) and Alzheimer's disease (AD) represent two most prevalent amyloid diseases with a significant global burden. Pathologically, T2D and AD are characterized by the presence of amyloid plaques consisting primarily of toxic human islet amyloid polypeptide (IAPP) and amyloid beta (Aβ). It has been recently revealed that the gut microbiome plays key functions in the pathological progression of neurological disorders through the production of bacterial endotoxins, such as lipopolysaccharide (LPS). Read More

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http://dx.doi.org/10.1039/d0nr02710cDOI Listing

Application of Mitochondrially Targeted Nanoconstructs to Neoadjuvant X-ray-Induced Photodynamic Therapy for Rectal Cancer.

ACS Cent Sci 2020 May 24;6(5):715-726. Epub 2020 Apr 24.

ARC Centre of Excellence for Nanoscale Biophotonics, Graduate School of Biomedical Engineering, University of New South Wales, Kensington, New South Wales 2052, Australia.

In this work, we brought together two existing clinical techniques used in cancer treatment-X-ray radiation and photodynamic therapy (PDT), whose combination termed X-PDT uniquely allows PDT to be therapeutically effective in deep tissue. To this end, we developed mitochondrially targeted biodegradable polymer poly(lactic--glycolic acid) nanocarriers incorporating a photosensitizer verteporfin, ultrasmall (2-5 nm) gold nanoparticles as radiation enhancers, and triphenylphosphonium acting as the mitochondrial targeting moiety. The average size of the nanocarriers was about 160 nm. Read More

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http://dx.doi.org/10.1021/acscentsci.9b01121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7256935PMC

Simple, sensitive and specific quantification of diamine oxidase activity in complex matrices using newly discovered fluorophores derived from natural substrates.

Inflamm Res 2020 Jun 1. Epub 2020 Jun 1.

Department of Clinical Pharmacology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.

Objective: To measure diamine oxidase (DAO) activity with high sensitivity in complex matrices like plasma or tissue extracts radioactive putrescine or horseradish peroxidase (HRP)/hydrogen peroxide (HO) coupling must be used. The use of radioactive material should be avoided and HRP/HO coupling is compromised by antioxidants.

Methods And Results: Condensation of ortho-aminobenzaldehyde (oABA) with delta-1-pyrroline and delta-1-piperideine, the autocyclization products of the DAO-oxidized natural substrates putrescine and cadaverine, generates new quinazoline fluorophores with absorption and excitation maxima of 430 and 460 nm, respectively, and peak emission at 620 nm. Read More

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http://dx.doi.org/10.1007/s00011-020-01359-5DOI Listing

Association Between Structure-function Characteristics and Visual Field Outcomes in Glaucoma Subjects with Intraocular Pressure Reduction After Trabeculectomy.

J Glaucoma 2020 Jun 1. Epub 2020 Jun 1.

Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.

Precis: Improvements in post-trabeculectomy visual field outcomes were found to be significantly associated with pre-operative nerve fiber layer thickness parameters extracted from the sectorized structure-function relationship, baseline visual field and severity of glaucoma.

Objective: To determine whether the pre-operative structure-function relationship helps to predict visual outcomes at one-year post-trabeculectomy.

Patients And Methods: 91 eyes from 87 participants who successfully underwent trabeculectomy were included in our study. Read More

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http://dx.doi.org/10.1097/IJG.0000000000001550DOI Listing

Correlation of Iodine Quantification and FDG Uptake in Early Therapy Response Assessment of Non-small Cell Lung Cancer: Possible Benefit of Dual-energy CT Scan as an Integral Part of PET/CT Examination.

Anticancer Res 2020 Jun;40(6):3459-3468

Department of Imaging Methods, Faculty of Medicine in Pilsen, Charles University and University Hospital in Pilsen, Pilsen, Czech Republic.

Aim: To compare iodine-related and fluorine-18 fluorodeoxyglucose (F-FDG) parameters during staging of lung cancer as well as during early follow-up, while investigating potential use and possible substitutability in the assessment of therapeutic response or prediction.

Patients And Methods: Patients (n=45) with confirmed lung cancer underwent F-FDG positron-emission tomography (PET) using single-source dual-energy computed tomography was performed for staging and early follow-up. Correlation of FDG uptake and iodine-related parameters was assessed and comparison with therapy response was performed. Read More

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http://dx.doi.org/10.21873/anticanres.14332DOI Listing

Classification Model to Estimate MIB-1 (Ki 67) Proliferation Index in NSCLC Patients Evaluated With F-FDG-PET/CT.

Anticancer Res 2020 Jun;40(6):3355-3360

Thoracic Surgery Unit, Azienda Ospedaliera "S. Maria", Terni, Italy.

Background/aim: Proliferation biomarkers such as MIB-1 are strong predictors of clinical outcome and response to therapy in patients with non-small-cell lung cancer, but they require histological examination. In this work, we present a classification model to predict MIB-1 expression based on clinical parameters from positron emission tomography.

Patients And Methods: We retrospectively evaluated 78 patients with histology-proven non-small-cell lung cancer (NSCLC) who underwent F-FDG-PET/CT for clinical examination. Read More

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http://dx.doi.org/10.21873/anticanres.14318DOI Listing

Comparison of the osteoblastic activity of low elastic modulus Ti-24Nb-4Zr-8Sn alloy and pure titanium modified by physical and chemical methods.

Mater Sci Eng C Mater Biol Appl 2020 Aug 25;113:111018. Epub 2020 Apr 25.

Central Laboratory, Peking University School and Hospital of Stomatology, #22 Zhongguancun South Avenue, Haidian District, Beijing 100081, China. Electronic address:

Ti-24Nb-4Zr-8Sn (Ti2448) alloy is a novel low elastic modulus β-titanium alloy without toxic elements. It also has the advantage of high strength, so it has potential application prospects for implantation. To develop its osteogenic effects, it can be modified by electrochemical, and physical processes. Read More

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http://dx.doi.org/10.1016/j.msec.2020.111018DOI Listing

Effective killing of bacteria under blue-light irradiation promoted by green synthesized silver nanoparticles loaded on reduced graphene oxide sheets.

Mater Sci Eng C Mater Biol Appl 2020 Aug 21;113:110984. Epub 2020 Apr 21.

Laboratory of Nanomaterials and Applied Nanotechnology (LNNA), Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil. Electronic address:

Graphene oxide (GO) materials loaded with silver nanoparticles (AgNPs) have drawn considerable attention due to their capacity to efficiently inactivate bacteria though a multifaceted mechanism of action, as well as for presenting a synergetic effect against bacteria when compared to the activity of AgNPs and GO alone. In this investigation, we present an inexpensive and environmentally-friendly method for synthesizing reduced GO sheets coated with silver nanoparticles (AgNPs/r-GO) using a coffee extract solution as a green reducing agent. The physical and chemical properties of the produced materials were extensively characterized by scanning electron microscopy (SEM), field-emission gun transmission electron microscopy (FEG-TEM), ultraviolet and visible absorption (UV-Vis), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), inductively coupled plasma-optical emission spectroscopy (ICP-OES) and ion release determination. Read More

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http://dx.doi.org/10.1016/j.msec.2020.110984DOI Listing

SRC Tyrosine Kinase Inhibitor and X-rays Combined Effect on Glioblastoma Cell Lines.

Int J Mol Sci 2020 May 30;21(11). Epub 2020 May 30.

UNICAEN, CEA, CNRS, ISTCT/CERVOxy Group, GIP Cyceron, Normandie University, 14074 Caen, France.

Glioblastoma (GBM) is one of the most lethal types of tumor due to its high recurrence level in spite of aggressive treatment regimens involving surgery, radiotherapy and chemotherapy. Hypoxia is a feature of GBM, involved in radioresistance, and is known to be at the origin of treatment failure. The aim of this work was to assess the therapeutic potential of a new targeted c-SRC inhibitor molecule, named Si306, in combination with X-rays on the human glioblastoma cell lines, comparing normoxia and hypoxia conditions. Read More

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http://dx.doi.org/10.3390/ijms21113917DOI Listing

RNA Sequencing-Based Identification of Ganglioside GD2-Positive Cancer Phenotype.

Biomedicines 2020 May 30;8(6). Epub 2020 May 30.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho- Maklaya St., 117997 Moscow, Russia.

The tumor-associated ganglioside GD2 represents an attractive target for cancer immunotherapy. GD2-positive tumors are more responsive to such targeted therapy, and new methods are needed for the screening of GD2 molecular tumor phenotypes. In this work, we built a gene expression-based binary classifier predicting the GD2-positive tumor phenotypes. Read More

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http://dx.doi.org/10.3390/biomedicines8060142DOI Listing

Probing the Electron Transfer between iLOV Protein and Ag Nanoparticles.

Molecules 2020 May 29;25(11). Epub 2020 May 29.

Institute of Micro/Nano Photonic Materials and Application, School of Physics and Electronics, Henan University, Kaifeng 475004, China.

Nanomaterials have been widely used in biomedical sciences; however, the mechanism of interaction between nanoparticles and biomolecules is still not fully understood. In the present study, we report the interaction mechanism between differently sized Ag nanoparticles and the improved light-oxygen-voltage (iLOV) protein. The steady-state and time-resolved fluorescence results demonstrated that the fluorescence intensity and lifetime of the iLOV protein decreased upon its adsorption onto Ag nanoparticles, and this decrease was dependent upon nanoparticle size. Read More

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http://dx.doi.org/10.3390/molecules25112544DOI Listing

Employing Nanostructured Scaffolds to Investigate the Mechanical Properties of Adult Mammalian Retinae Under Tension.

Int J Mol Sci 2020 May 29;21(11). Epub 2020 May 29.

Soft Matter Physics Division and Biotechnology & Biomedical Group, Peter-Debye-Institute for Soft Matter Physics, Leipzig University, Linnéstr. 5, 04103 Leipzig, Germany.

Numerous eye diseases are linked to biomechanical dysfunction of the retina. However, the underlying forces are almost impossible to quantify experimentally. Here, we show how biomechanical properties of adult neuronal tissues such as porcine retinae can be investigated under tension in a home-built tissue stretcher composed of nanostructured TiO scaffolds coupled to a self-designed force sensor. Read More

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http://dx.doi.org/10.3390/ijms21113889DOI Listing

Oxygen-Releasing Antibacterial Nanofibrous Scaffolds for Tissue Engineering Applications.

Polymers (Basel) 2020 May 29;12(6). Epub 2020 May 29.

Center of Nanotechnology, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Lack of suitable auto/allografts has been delaying surgical interventions for the treatment of numerous disorders and has also caused a serious threat to public health. Tissue engineering could be one of the best alternatives to solve this issue. However, deficiency of oxygen supply in the wounded and implanted engineered tissues, caused by circulatory problems and insufficient angiogenesis, has been a rate-limiting step in translation of tissue-engineered grafts. Read More

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http://dx.doi.org/10.3390/polym12061233DOI Listing

On-demand generation of singlet oxygen from a smart graphene complex for the photodynamic treatment of cancer cells.

Biomater Sci 2014 Oct 4;2(10):1412-1418. Epub 2014 Jul 4.

CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China.

Graphene oxide (GO) has been proven to be a highly efficient long-range quencher for various fluorescence processes, which intrinsically work through a photophysical mechanism similar to that of singlet oxygen generation (SOG). Under our hypothesis that GO may be capable of quenching the SOG process, here we design and synthesize a novel nanocomplex consisting of GO, a photosensitizer and an aptamer. We demonstrate that GO is an ideal SOG controller, which can reversibly quench and recover SOG depending on the interaction intensity between GO and a photosensitizer. Read More

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http://dx.doi.org/10.1039/c4bm00143eDOI Listing
October 2014

Evaluating reconstruction algorithms for respiratory motion guided acquisition.

Phys Med Biol 2020 Jun 2. Epub 2020 Jun 2.

Radiation Physics Laboratory, Sydney Medical School, University of Sydney, NSW 2006, Camperdown, New South Wales, 2039, AUSTRALIA.

Conventional thoracic 4DCBCT scans take 1,320 projections over 4 minutes. This paper investigates which reconstruction algorithms best leverage Respiratory-Motion-Guided (RMG) acquisition in order to reduce scan time and dose while maintaining image quality. We investigated a 200 projection, on average 1-minute RMG acquisition. Read More

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http://dx.doi.org/10.1088/1361-6560/ab98d3DOI Listing

Programming cell pyroptosis with biomimetic nanoparticles for solid tumor immunotherapy.

Biomaterials 2020 May 28;254:120142. Epub 2020 May 28.

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China. Electronic address:

Immunotherapy shows remarkable efficacy in treating several types of cancer such as melanoma, leukemia, and lung carcinoma, but its therapeutic effect for most solid tumors is still limited. Various cancer therapies, such as chemotherapy, radiotherapy and phototherapy, kill solid tumors through non-inflammatory apoptosis or ablation, rather than making solid tumors immunogenic. As a highly-inflammatory programmed cell death (PCD), pyroptosis provides a great opportunity to alleviate immunosuppression and promote a systemic immune response in treating solid tumors. Read More

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http://dx.doi.org/10.1016/j.biomaterials.2020.120142DOI Listing

Real-time Detection of Aortic Valve in Echocardiography using Convolutional Neural Networks.

Curr Med Imaging 2020 ;16(5):584-591

Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Jalan Universiti, Kuala Lumpur 50603, Malaysia.

Background: Valvular heart disease is a serious disease leading to mortality and increasing medical care cost. The aortic valve is the most common valve affected by this disease. Doctors rely on echocardiogram for diagnosing and evaluating valvular heart disease. Read More

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http://dx.doi.org/10.2174/1573405615666190114151255DOI Listing
January 2020

Photoprogrammable Mesogenic Soft Helical Architectures: A Promising Avenue toward Future Chiro-Optics.

Adv Mater 2020 Jun 2:e1905318. Epub 2020 Jun 2.

Advanced Materials and Liquid Crystal Institute and Chemical Physics Interdisciplinary Program, Kent State University, Kent, OH, 44242, USA.

Mesogenic soft materials, having single or multiple mesogen moieties per molecule, commonly exhibit typical self-organization characteristics, which promotes the formation of elegant helical superstructures or supramolecular assemblies in chiral environments. Such helical superstructures play key roles in the propagation of circularly polarized light and display optical properties with prominent handedness, that is, chiro-optical properties. The leveraging of light to program the chiro-optical properties of such mesogenic helical soft materials by homogeneously dispersing photosensitive chiral material into an achiral soft system or covalently connecting photochromic moieties to the molecules has attracted considerable attention in terms of materials, properties, and potential applications and has been a thriving topic in both fundamental science and application engineering. Read More

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http://dx.doi.org/10.1002/adma.201905318DOI Listing

Variability in the analysis of a single neuroimaging dataset by many teams.

Authors:
Rotem Botvinik-Nezer Felix Holzmeister Colin F Camerer Anna Dreber Juergen Huber Magnus Johannesson Michael Kirchler Roni Iwanir Jeanette A Mumford R Alison Adcock Paolo Avesani Blazej M Baczkowski Aahana Bajracharya Leah Bakst Sheryl Ball Marco Barilari Nadège Bault Derek Beaton Julia Beitner Roland G Benoit Ruud M W J Berkers Jamil P Bhanji Bharat B Biswal Sebastian Bobadilla-Suarez Tiago Bortolini Katherine L Bottenhorn Alexander Bowring Senne Braem Hayley R Brooks Emily G Brudner Cristian B Calderon Julia A Camilleri Jaime J Castrellon Luca Cecchetti Edna C Cieslik Zachary J Cole Olivier Collignon Robert W Cox William A Cunningham Stefan Czoschke Kamalaker Dadi Charles P Davis Alberto De Luca Mauricio R Delgado Lysia Demetriou Jeffrey B Dennison Xin Di Erin W Dickie Ekaterina Dobryakova Claire L Donnat Juergen Dukart Niall W Duncan Joke Durnez Amr Eed Simon B Eickhoff Andrew Erhart Laura Fontanesi G Matthew Fricke Shiguang Fu Adriana Galván Remi Gau Sarah Genon Tristan Glatard Enrico Glerean Jelle J Goeman Sergej A E Golowin Carlos González-García Krzysztof J Gorgolewski Cheryl L Grady Mikella A Green João F Guassi Moreira Olivia Guest Shabnam Hakimi J Paul Hamilton Roeland Hancock Giacomo Handjaras Bronson B Harry Colin Hawco Peer Herholz Gabrielle Herman Stephan Heunis Felix Hoffstaedter Jeremy Hogeveen Susan Holmes Chuan-Peng Hu Scott A Huettel Matthew E Hughes Vittorio Iacovella Alexandru D Iordan Peder M Isager Ayse I Isik Andrew Jahn Matthew R Johnson Tom Johnstone Michael J E Joseph Anthony C Juliano Joseph W Kable Michalis Kassinopoulos Cemal Koba Xiang-Zhen Kong Timothy R Koscik Nuri Erkut Kucukboyaci Brice A Kuhl Sebastian Kupek Angela R Laird Claus Lamm Robert Langner Nina Lauharatanahirun Hongmi Lee Sangil Lee Alexander Leemans Andrea Leo Elise Lesage Flora Li Monica Y C Li Phui Cheng Lim Evan N Lintz Schuyler W Liphardt Annabel B Losecaat Vermeer Bradley C Love Michael L Mack Norberto Malpica Theo Marins Camille Maumet Kelsey McDonald Joseph T McGuire Helena Melero Adriana S Méndez Leal Benjamin Meyer Kristin N Meyer Glad Mihai Georgios D Mitsis Jorge Moll Dylan M Nielson Gustav Nilsonne Michael P Notter Emanuele Olivetti Adrian I Onicas Paolo Papale Kaustubh R Patil Jonathan E Peelle Alexandre Pérez Doris Pischedda Jean-Baptiste Poline Yanina Prystauka Shruti Ray Patricia A Reuter-Lorenz Richard C Reynolds Emiliano Ricciardi Jenny R Rieck Anais M Rodriguez-Thompson Anthony Romyn Taylor Salo Gregory R Samanez-Larkin Emilio Sanz-Morales Margaret L Schlichting Douglas H Schultz Qiang Shen Margaret A Sheridan Jennifer A Silvers Kenny Skagerlund Alec Smith David V Smith Peter Sokol-Hessner Simon R Steinkamp Sarah M Tashjian Bertrand Thirion John N Thorp Gustav Tinghög Loreen Tisdall Steven H Tompson Claudio Toro-Serey Juan Jesus Torre Tresols Leonardo Tozzi Vuong Truong Luca Turella Anna E van 't Veer Tom Verguts Jean M Vettel Sagana Vijayarajah Khoi Vo Matthew B Wall Wouter D Weeda Susanne Weis David J White David Wisniewski Alba Xifra-Porxas Emily A Yearling Sangsuk Yoon Rui Yuan Kenneth S L Yuen Lei Zhang Xu Zhang Joshua E Zosky Thomas E Nichols Russell A Poldrack Tom Schonberg

Nature 2020 Jun 20;582(7810):84-88. Epub 2020 May 20.

Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.

Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses. The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. Read More

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http://dx.doi.org/10.1038/s41586-020-2314-9DOI Listing

Macromolecular modeling and design in Rosetta: recent methods and frameworks.

Authors:
Julia Koehler Leman Brian D Weitzner Steven M Lewis Jared Adolf-Bryfogle Nawsad Alam Rebecca F Alford Melanie Aprahamian David Baker Kyle A Barlow Patrick Barth Benjamin Basanta Brian J Bender Kristin Blacklock Jaume Bonet Scott E Boyken Phil Bradley Chris Bystroff Patrick Conway Seth Cooper Bruno E Correia Brian Coventry Rhiju Das René M De Jong Frank DiMaio Lorna Dsilva Roland Dunbrack Alexander S Ford Brandon Frenz Darwin Y Fu Caleb Geniesse Lukasz Goldschmidt Ragul Gowthaman Jeffrey J Gray Dominik Gront Sharon Guffy Scott Horowitz Po-Ssu Huang Thomas Huber Tim M Jacobs Jeliazko R Jeliazkov David K Johnson Kalli Kappel John Karanicolas Hamed Khakzad Karen R Khar Sagar D Khare Firas Khatib Alisa Khramushin Indigo C King Robert Kleffner Brian Koepnick Tanja Kortemme Georg Kuenze Brian Kuhlman Daisuke Kuroda Jason W Labonte Jason K Lai Gideon Lapidoth Andrew Leaver-Fay Steffen Lindert Thomas Linsky Nir London Joseph H Lubin Sergey Lyskov Jack Maguire Lars Malmström Enrique Marcos Orly Marcu Nicholas A Marze Jens Meiler Rocco Moretti Vikram Khipple Mulligan Santrupti Nerli Christoffer Norn Shane Ó'Conchúir Noah Ollikainen Sergey Ovchinnikov Michael S Pacella Xingjie Pan Hahnbeom Park Ryan E Pavlovicz Manasi Pethe Brian G Pierce Kala Bharath Pilla Barak Raveh P Douglas Renfrew Shourya S Roy Burman Aliza Rubenstein Marion F Sauer Andreas Scheck William Schief Ora Schueler-Furman Yuval Sedan Alexander M Sevy Nikolaos G Sgourakis Lei Shi Justin B Siegel Daniel-Adriano Silva Shannon Smith Yifan Song Amelie Stein Maria Szegedy Frank D Teets Summer B Thyme Ray Yu-Ruei Wang Andrew Watkins Lior Zimmerman Richard Bonneau

Nat Methods 2020 Jun 1. Epub 2020 Jun 1.

Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Read More

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http://dx.doi.org/10.1038/s41592-020-0848-2DOI Listing

Deletion of Perilipin 5 Protects Against Hepatic Injury in Nonalcoholic Fatty Liver Disease via Missing Inflammasome Activation.

Cells 2020 May 28;9(6). Epub 2020 May 28.

Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, 52074 Aachen, Germany.

Nonalcoholic fatty liver disease (NAFLD) is a leading cause of chronic liver diseases with an increasing prevalence due to rising rates of obesity, metabolic syndrome and type II diabetes. Untreated NAFLD may progress to steatohepatitis (NASH) and ultimately liver cirrhosis. NAFLD is characterized by lipid accumulation, and when sufficient excess lipids are obtained, irreversible liver injury may follow. Read More

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http://dx.doi.org/10.3390/cells9061346DOI Listing

1,4-Disubstituted 1-1,2,3-Triazoles for Renal Diseases: Studies of Viability, Anti-Inflammatory, and Antioxidant Activities.

Int J Mol Sci 2020 May 28;21(11). Epub 2020 May 28.

Department of Chemistry, College of Science, Sultan Qaboos University, P.O. Box 36, Al-Khod 123, Sultanate of Oman.

Inflammation is a hallmark of many metabolic diseases. We previously showed that ferrocene-appended 1-1,2,3-triazole hybrids inhibit nitric oxide (NO) production in in vitro models of lipopolysaccharide-induced inflammation in the BV-2 cell. In the present study, we explored the viability, anti-inflammatory, and antioxidant potential of ferrocene-1-1,2,3-triazole hybrids using biochemical assays in rat mesangial cells (RMCs). Read More

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http://dx.doi.org/10.3390/ijms21113823DOI Listing
May 2020
2.862 Impact Factor

Engineering Sub-Cellular Targeting Strategies to Enhance Safe Cytosolic Silica Particle Dissolution in Cells.

Pharmaceutics 2020 May 28;12(6). Epub 2020 May 28.

Grupo de Nanomedicina, Instituto Valdecilla-IDIVAL, Herrera Oria s/n, 39011 Santander, Spain.

Mesoporous silica particles (MSP) are major candidates for drug delivery systems due to their versatile, safe, and controllable nature. Understanding their intracellular route and biodegradation process is a challenge, especially when considering their use in neuronal repair. Here, we characterize the spatiotemporal intracellular destination and degradation pathways of MSP upon endocytosis by HeLa cells and NSC-34 motor neurons using confocal and electron microscopy imaging together with inductively-coupled plasma optical emission spectroscopy analysis. Read More

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http://dx.doi.org/10.3390/pharmaceutics12060487DOI Listing

Towards a more precise therapy in cancer: Exploring epigenetic complexity.

Curr Opin Chem Biol 2020 May 29;57:41-49. Epub 2020 May 29.

Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain; Epigenetic Therapies Group, Experimental and Clinical Hematology Program (PHEC), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain. Electronic address:

A plethora of preclinical evidences suggests that pharmacological targeting of epigenetic dysregulation is a potent strategy to combat human diseases. Nevertheless, the implementation of epidrugs in clinical practice is very scarce and mainly limited to haematological malignancies. In this review, we discuss cutting-edge strategies to foster the chemical design, the biological rationale and the clinical trial development of epidrugs. Read More

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http://dx.doi.org/10.1016/j.cbpa.2020.04.008DOI Listing

Impact of total variation minimization in volume rendering visualization of breast tomosynthesis data.

Comput Methods Programs Biomed 2020 May 23;195:105534. Epub 2020 May 23.

Faculdade de Ciências, Instituto de Biofísica e Engenharia Biomédica, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.

Background And Objective: Total Variation (TV) minimization algorithms have achieved great attention due to the virtue of decreasing noise while preserving edges. The purpose of this work is to implement and evaluate two TV minimization methods in 3D. Their performance is analyzed through 3D visualization of digital breast tomosynthesis (DBT) data with volume rendering. Read More

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http://dx.doi.org/10.1016/j.cmpb.2020.105534DOI Listing

Multi-parametric artificial neural network fitting of phase-cycled balanced steady-state free precession data.

Magn Reson Med 2020 Jun 1. Epub 2020 Jun 1.

High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.

Purpose: Standard relaxation time quantification using phase-cycled balanced steady-state free precession (bSSFP), eg, motion-insensitive rapid configuration relaxometry (MIRACLE), is subject to a considerable underestimation of tissue T and T due to asymmetric intra-voxel frequency distributions. In this work, an artificial neural network (ANN) fitting approach is proposed to simultaneously extract accurate reference relaxation times (T , T ) and robust field map estimates ( , ΔB ) from the bSSFP profile.

Methods: Whole-brain bSSFP data acquired at 3T were used for the training of a feedforward ANN with N = 12, 6, and 4 phase-cycles. Read More

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http://dx.doi.org/10.1002/mrm.28325DOI Listing

Molecular docking and dynamics simulations studies of OmpATb identifies four potential novel natural product-derived anti-Mycobacterium tuberculosis compounds.

Comput Biol Med 2020 May 23;122:103811. Epub 2020 May 23.

Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana; Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA.

The outer membrane protein A (OmpATb) of Mycobacterium tuberculosis is a virulence factor that neutralizes the host pH to impede the uptake of hydrophilic antitubercular drugs. Identifying natural compounds with the potential to inhibit OmpATb could allow circumvention of the porin-like activities of OmpATb. Four potential leads comprising ZINC000003958185, ZINC000000157405, ZINC000000001392 and ZINC000034268676 were obtained by virtual screening of 6394 diverse natural products. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2020.103811DOI Listing
May 2020
1.240 Impact Factor

Correction: Modulated podosome patterning in osteoclasts by fullerenol nanoparticles disturbs the bone resorption for osteoporosis treatment.

Nanoscale 2020 Jun 1. Epub 2020 Jun 1.

Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, P.R. China.

Correction for 'Modulated podosome patterning in osteoclasts by fullerenol nanoparticles disturbs the bone resorption for osteoporosis treatment' by Kui Chen et al., Nanoscale, 2020, 12, 9359-9365, DOI: 10.1039/D0NR01625J. Read More

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http://dx.doi.org/10.1039/d0nr90114hDOI Listing

Optical Biopsy of the Upper GI Tract Using Fluorescence Lifetime and Spectra.

Front Physiol 2020 13;11:339. Epub 2020 May 13.

School of Biomedical Engineering, Faculty of Engineering, McMaster University, Hamilton, ON, Canada.

Screening and surveillance for gastrointestinal (GI) cancers by endoscope guided biopsy is invasive, time consuming, and has the potential for sampling error. Tissue endogenous fluorescence spectra contain biochemical and physiological information, which may enable real-time, objective diagnosis. We first briefly reviewed optical biopsy modalities for GI cancer diagnosis with a focus on fluorescence-based techniques. Read More

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http://dx.doi.org/10.3389/fphys.2020.00339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237753PMC

Increasing Doxorubicin Loading in Lipid-Shelled Perfluoropropane Nanobubbles a Simple Deprotonation Strategy.

Front Pharmacol 2020 12;11:644. Epub 2020 May 12.

Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States.

Drug delivery to solid tumors using echogenic nanobubbles (NBs) and ultrasound (US) has recently gained significant interest. The approach combines attributes of nanomedicine and the enhanced permeation and retention (EPR) effect with the documented benefits of ultrasound to improve tumor drug distribution and treatment outcomes. However, optimized drug loading strategies, the drug-carrying capacity of NBs and their drug delivery efficiency have not been explored in depth and remain unclear. Read More

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http://dx.doi.org/10.3389/fphar.2020.00644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7235281PMC

Assessment of skin dose in breast cancer radiotherapy: on-phantom measurement and Monte Carlo simulation.

Rep Pract Oncol Radiother 2020 May-Jun;25(3):456-461. Epub 2020 Mar 18.

Comprehensive Cancer Centers of Nevada, Las Vegas, Nevada, USA.

Aim: The main purpose of the present study is assessment of skin dose in breast cancer radiotherapy.

Background: Accurate assessment of skin dose in radiotherapy can provide useful information for clinical considerations.

Materials And Methods: A RANDO phantom was irradiated using a 6 MV Siemens Primus linac with medial and tangential radiotherapy fields for simulating breast cancer treatment. Read More

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http://dx.doi.org/10.1016/j.rpor.2020.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7244887PMC

Sodium in the Relapsing-Remitting Multiple Sclerosis Spinal Cord: Increased Concentrations and Associations With Microstructural Tissue Anisotropy.

J Magn Reson Imaging 2020 Jun 1. Epub 2020 Jun 1.

NMR Research Unit, Queen Square MS Centre, UCL Queen Square Institute of Neurology, Faculty of Brain Sciences, University College London, London, UK.

Background: Associations between brain total sodium concentration, disability, and disease progression have recently been reported in multiple sclerosis. However, such measures in spinal cord have not been reported.

Purpose: To measure total sodium concentration (TSC) alterations in the cervical spinal cord of people with relapsing-remitting multiple sclerosis (RRMS) and a control cohort using sodium MR spectroscopy (MRS). Read More

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http://dx.doi.org/10.1002/jmri.27201DOI Listing

Longer duration electroencephalogram arousals have a better relationship with impaired vigilance and health status in obstructive sleep apnoea.

Sleep Breath 2020 May 30. Epub 2020 May 30.

Department of Respiratory & Sleep Medicine, Princess Alexandra Hospital, Brisbane, Australia.

Purpose: Obstructive sleep apnoea (OSA) is a prevalent sleep disorder with significant health consequences. Sleep fragmentation is a feature of OSA and is often determined by the arousal index (ArI), a metric based on the electroencephalograph (EEG). The ArI has a weak correlation with neurocognitive outcomes in OSA patients. Read More

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http://dx.doi.org/10.1007/s11325-020-02110-4DOI Listing

Definition of internal target volumes based on planar X-ray fluoroscopic images for lung and hepatic stereotactic body radiation therapy. Comparison to inhale/exhale CT technique.

J Appl Clin Med Phys 2020 May 30. Epub 2020 May 30.

Department of Medical Physics, Hospital Universitario Ramón y Cajal, Madrid, Spain.

Purpose: To compare tumor motion amplitudes measured with 2D fluoroscopic images (FI) and with an inhale/exhale CT (IECT) technique MATERIALS AND METHODS: Tumor motion of 52 patients (39 lung patients and 13 liver patients) was obtained with both FI and IECT. For FI, tumor detection and tracking was performed by means of a software developed by the authors. Motion amplitude and, thus, internal target volume (ITV), were defined to cover the positions where the tumor spends 95% of the time. Read More

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http://dx.doi.org/10.1002/acm2.12914DOI Listing

Author Correction: Water molecular structure underpins extreme desiccation tolerance of the resurrection plant Haberlea rhodopensis.

Sci Rep 2020 May 29;10(1):9061. Epub 2020 May 29.

Abiotic Stress, AgroBioinstitute, Agricultural Academy, 8 Dragan Tzankov Blvd., 1164, Sofia, Bulgaria.

An amendment to this paper has been published and can be accessed via a link at the top of the paper. Read More

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http://dx.doi.org/10.1038/s41598-020-66185-5DOI Listing

MR-guided proton therapy: a review and a preview.

Radiat Oncol 2020 May 29;15(1):129. Epub 2020 May 29.

Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität München, Garching, Germany.

Background: The targeting accuracy of proton therapy (PT) for moving soft-tissue tumours is expected to greatly improve by real-time magnetic resonance imaging (MRI) guidance. The integration of MRI and PT at the treatment isocenter would offer the opportunity of combining the unparalleled soft-tissue contrast and real-time imaging capabilities of MRI with the most conformal dose distribution and best dose steering capability provided by modern PT. However, hybrid systems for MR-integrated PT (MRiPT) have not been realized so far due to a number of hitherto open technological challenges. Read More

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http://dx.doi.org/10.1186/s13014-020-01571-xDOI Listing

Biocompatible Magnetic Fluids of Co-Doped Iron Oxide Nanoparticles with Tunable Magnetic Properties.

Nanomaterials (Basel) 2020 May 27;10(6). Epub 2020 May 27.

Department Hematology and Oncology, Jena University Hospital, D-07747 Jena, Germany.

Magnetite (FeO) particles with a diameter around 10 nm have a very low coercivity (H) and relative remnant magnetization (M/M), which is unfavorable for magnetic fluid hyperthermia. In contrast, cobalt ferrite (CoFeO) particles of the same size have a very high H and M/M, which is magnetically too hard to obtain suitable specific heating power (SHP) in hyperthermia. For the optimization of the magnetic properties, the Fe ions of magnetite were substituted by Co step by step, which results in a Co doped iron oxide inverse spinel with an adjustable Fe substitution degree in the full range of pure iron oxide up to pure cobalt ferrite. Read More

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http://dx.doi.org/10.3390/nano10061019DOI Listing

A nonuniform projection distribution CT method for solitary lung nodule follow-up: personal previous lung image-guided, patchwise, low-rank constrained imaging.

Phys Med Biol 2020 May 29. Epub 2020 May 29.

Department of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200040, Shanghai, CHINA.

In this paper, a nonuniform projection distribution (NUPD) CT method is proposed for the region-of-interest-specific examination in the solitary lung nodule follow-up application in order to reduce redundant X-ray projections exposed on normal tissues. The method exploits personal previous lung CT scan information to design a nonuniform X-ray projection modulation scheme where X-rays are sparsely modulated over the areas outside of the nodule in each projection view. The nonuniform projection modulation scheme could obstruct 71. Read More

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http://dx.doi.org/10.1088/1361-6560/ab97e6DOI Listing

Live-cell imaging in the era of too many microscopes.

Curr Opin Cell Biol 2020 May 26;66:34-42. Epub 2020 May 26.

MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK. Electronic address:

At the time of this writing, searching Google Scholar for 'light-sheet microscopy' returns almost 8500 results; over three-quarters of which were published in the last 5 years alone. Searching for other advanced imaging methods in the last 5 years yields similar results: 'super-resolution microscopy' (>16 000), 'single-molecule imaging' (almost 10 000), SPIM (Single Plane Illumination Microscopy, 5000), and 'lattice light-sheet' (1300). The explosion of new imaging methods has also produced a dizzying menagerie of acronyms, with over 100 different species of 'light-sheet' alone, from SPIM to UM (Ultra microscopy) to SiMView (Simultaneous MultiView) to iSPIM (inclined SPIM, not to be confused with iSPIM, inverted SPIM). Read More

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http://dx.doi.org/10.1016/j.ceb.2020.04.008DOI Listing

MS-SMART study: systematic sampling bias concerns - Authors' reply.

Lancet Neurol 2020 Jun 26;19(6):479-480. Epub 2020 May 26.

Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.

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http://dx.doi.org/10.1016/S1474-4422(20)30149-6DOI Listing

Cellular Uptake of Active Particles.

Phys Rev Lett 2020 May;124(19):198102

State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.

Active particles are widely recognized to potentially revolutionize technologies in numerous biomedical applications. However, the physical origin behind cellular uptake of these particles in the nonequilibrium state remains scarcely understood. Here we combine Brownian dynamics simulation as well as theoretical analysis to provide the criterion for cellular uptake of active particles, related to various physical attributes. Read More

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http://dx.doi.org/10.1103/PhysRevLett.124.198102DOI Listing

Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2.

J Med Microbiol 2020 May 29. Epub 2020 May 29.

Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA.

The emergence of SARS-CoV-2 has taken humanity off guard. Following an outbreak of SARS-CoV in 2002, and MERS-CoV about 10 years later, SARS-CoV-2 is the third coronavirus in less than 20 years to cross the species barrier and start spreading by human-to-human transmission. It is the most infectious of the three, currently causing the COVID-19 pandemic. Read More

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http://dx.doi.org/10.1099/jmm.0.001203DOI Listing