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Automated Software Engineering[Journal] Publications | PubFacts

127,381 results match your criteria Automated Software Engineering[Journal]


Quantitation of vitamin K1 in serum using online SPE-LC-MS/MS and the challenges of working with vitamin K.

J Chromatogr B Analyt Technol Biomed Life Sci 2019 Apr 7;1117:41-48. Epub 2019 Apr 7.

Department of Clinical Biochemistry and Immunology, Lillebaelt Hospital, Vejle, Denmark.

Vitamin K1 (phylloquinone) is one of the vitamin Ks. Several studies have previously investigated the role of vitamin K1 status in respect to disease, but without consistent results. Since vitamin K deficiency has been associated with different disease states it is important to develop a biochemical analysis with sufficient sensitivity and a low limit of quantitation (LOQ). Read More

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https://linkinghub.elsevier.com/retrieve/pii/S15700232183176
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http://dx.doi.org/10.1016/j.jchromb.2019.04.010DOI Listing
April 2019
1 Read

Quantitative Characterization of α-Synuclein Aggregation in Living Cells through Automated Microfluidics Feedback Control.

Cell Rep 2019 Apr;27(3):916-927.e5

Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy. Electronic address:

Aggregation of α-synuclein and formation of inclusions are hallmarks of Parkinson's disease (PD). Aggregate formation is affected by cellular environment, but it has been studied almost exclusively in cell-free systems. We quantitatively analyzed α-synuclein inclusion formation and clearance in a yeast cell model of PD expressing either wild-type (WT) α-synuclein or the disease-associated A53T mutant from the galactose (Gal)-inducible promoter. Read More

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http://dx.doi.org/10.1016/j.celrep.2019.03.081DOI Listing

Potential Technologies Review - A hybrid information retrieval framework to accelerate demand-pull innovation in biomedical engineering.

Res Synth Methods 2019 Apr 17. Epub 2019 Apr 17.

Science Management, Institute of Applied Medical Engineering, RWTH Aachen University, Aachen, Germany.

Launching biomedical innovations based on clinical demands instead of translating basic research findings to practice reduces the risk that the results will not fit the clinical routine. To realize this type of innovation, a meta-analysis of the body of research is necessary to reveal demand-matching concepts. However, both the data deluge and the narrow time constraints for innovation make it impossible to perform such reviews manually. Read More

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http://dx.doi.org/10.1002/jrsm.1350DOI Listing

Protective effect of alpha-lipoic acid against apical periodontitis-induced cardiac injury in rats.

Eur J Oral Sci 2019 Apr 17. Epub 2019 Apr 17.

Department of Biochemistry, Faculty of Veterinary Medicine, Near East University, Nicosia, Mersin 10, Turkey.

This study was designed to assess the possible protective effect of alpha-lipoic acid (ALA) on apical periodontitis (AP)-induced cardiac injury. Wistar albino rats were randomized into four groups: control; ALA; AP; and ALA + AP. Rats of the control and ALA groups were not endodontically treated, but saline and ALA (100 mg kg ) were administered. Read More

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http://dx.doi.org/10.1111/eos.12618DOI Listing

Longitudinal evaluation of visual function and structure for detection of subclinical Ethambutol-induced optic neuropathy.

PLoS One 2019 17;14(4):e0215297. Epub 2019 Apr 17.

Department of Ophthalmology, Hallym University College of Medicine, Seoul, Republic of Korea.

Purpose: To longitudinally evaluate the visual function and structure of patients taking ethambutol by various modalities and identify useful tests for detection of subclinical ethambutol-induced optic toxicity.

Methods: This retrospective study enrolled 84 patients with newly diagnosed tuberculosis treated with ethambutol. Best-corrected visual acuity (BCVA), color vision, contrast sensitivity, fundus and retinal nerve fiber layer (RNFL) photography, automated visual field (VF) test, and optical coherence tomography (OCT) were performed: prior to starting; every month during administration, and 1 month after stoppage. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215297PLOS
April 2019
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Viable and necrotic tumor assessment from whole slide images of osteosarcoma using machine-learning and deep-learning models.

PLoS One 2019 17;14(4):e0210706. Epub 2019 Apr 17.

The University of Texas Southwestern Medical Center, Dallas, TX, United States of America.

Pathological estimation of tumor necrosis after chemotherapy is essential for patients with osteosarcoma. This study reports the first fully automated tool to assess viable and necrotic tumor in osteosarcoma, employing advances in histopathology digitization and automated learning. We selected 40 digitized whole slide images representing the heterogeneity of osteosarcoma and chemotherapy response. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210706PLOS

Increase in the diagnosis of mycobacteremia after the implementation of semi-automated blood culture at a Brazilian public health laboratory.

Rev Soc Bras Med Trop 2019 Apr 11;52:e20180267. Epub 2019 Apr 11.

Departamento de Biologia Médica, Seção de Micobactérias, Laboratório de Saúde Pública Dr. Giovanni Cysneiros, Goiânia, GO, Brasil.

Introduction: The prevalence of hematogenous dissemination of mycobacteria is high in immunosuppressed patients. The isolation of mycobacteria in culture remains the standard procedure.

Methods: This is a cross-sectional study based on the results of solid (Löwenstein-Jensen medium) and semi-automated liquid (BACTEC 9240) blood cultures, obtained from the Lacen-GO database. Read More

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http://dx.doi.org/10.1590/0037-8682-0267-2018DOI Listing

Impact of Automated Time-released Reminders on Patient Preparedness for Colonoscopy.

J Clin Gastroenterol 2019 Apr 15. Epub 2019 Apr 15.

Division of Gastroenterology, Hepatology and Endoscopy.

Goals: To evaluate the effect of an automated time-released colonoscopy reminder program on preparation quality and the rates of canceled procedures.

Background: Patients missing colonoscopy appointments or arriving with inadequate bowel preparations result in delays in care and increase in health care costs.

Study: We initiated a quality improvement program which included switching to a split-dose preparation and delivering preparation instructions and appointment reminders via text messages and emails sent with an automated time-released HIPAA-compliant software platform. Read More

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http://dx.doi.org/10.1097/MCG.0000000000001211DOI Listing

Inadequate diagnostics: the case to move beyond the bacilli for detection of meningitis due to Mycobacterium tuberculosis.

J Med Microbiol 2019 Apr 17. Epub 2019 Apr 17.

3 University of Minnesota, Minneapolis, MN, USA.

Tuberculosis (TB) meningitis is extremely difficult to diagnose due to its pauci-bacillary disease nature and new techniques are needed. Improved test sensitivity would allow for greater clinician confidence in diagnostic testing and has the potential to improve patient outcomes. Traditional microbiologic and molecular tests for TB meningitis focus on detection of TB bacilli and are inadequate. Read More

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http://dx.doi.org/10.1099/jmm.0.000975DOI Listing

Detection by flow cytometry of anti-neutrophil cytoplasmic antibodies in a novel approach based on neutrophil extracellular traps.

Autoimmunity 2018 Sep;51(6):288-296

a Department of Internal Medicine 1 - Gastroenterology, Pneumology and Endocrinology , Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen , Erlangen , Germany.

Background: Anti-neutrophil-cytoplasmic antibodies (ANCA) are auto-antibodies directed against components of neutrophil granulocytes and may be found in various inflammatory conditions, like small-vessel vasculitis or ulcerative colitis (UC). Routine ANCA screening is performed on ethanol-fixed neutrophils using indirect immunofluorescence technique. Yet, how neutrophil granule proteins become available to immunologic presentation is a matter of debate. Read More

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http://dx.doi.org/10.1080/08916934.2018.1527317DOI Listing
September 2018

Three-dimensional Therapy Needle Applicator Segmentation for Ultrasound-guided Focal Liver Ablation.

Med Phys 2019 Apr 17. Epub 2019 Apr 17.

Department of Medical Biophysics.

Purpose: Minimally invasive procedures, such as microwave ablation, are becoming first-line treatment options for early-stage liver cancer due to lower complication rates and shorter recovery times than conventional surgical techniques. Although these procedures are promising, one reason preventing widespread adoption is inadequate local tumour ablation leading to observations of higher local cancer recurrence compared to conventional procedures. Poor ablation coverage has been associated with two-dimensional (2D) ultrasound (US) guidance of the therapy needle applicators and has stimulated investigation into the use of three-dimensional (3D) US imaging for these procedures. Read More

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http://dx.doi.org/10.1002/mp.13548DOI Listing

Towards a standard MRI protocol for multiple sclerosis across the UK.

Br J Radiol 2019 Apr 17:20180926. Epub 2019 Apr 17.

7 Department of Diagnostic and Interventional Neuroradiology, Hannover Medical School , Hannover , Germany.

Multiple sclerosis (MS) is a chronic inflammatory demyelinating and degenerative disease of the central nervous system. It is the most common non-traumatic cause of chronic disability in young adults. An early and accurate diagnosis, and effective disease modifying treatment (DMT) are key elements of optimum care for people with MS (pwMS). Read More

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http://dx.doi.org/10.1259/bjr.20180926DOI Listing

HbA1c and retinal arteriolar narrowing in children with type 1 diabetes: the DEAR-Kids study.

Pediatr Diabetes 2019 Apr 16. Epub 2019 Apr 16.

Department of General Paediatrics, Adolescent Medicine and Neonatology, Medical Centre, Faculty of Medicine, University of Freiburg, Freiburg, Germany.

Background/objective: Microvascular alterations play a key role in the development of diabetes complications. Retinal vessel analysis is a unique method to examine microvascular changes in brain derived vessels.

Subjects/methods: 67 pediatric and adolescent type 1 diabetes patients and 58 healthy control persons (mean age 12. Read More

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http://dx.doi.org/10.1111/pedi.12858DOI Listing

A 2D laser rangefinder scans dataset of standard EUR pallets.

Data Brief 2019 Jun 22;24:103837. Epub 2019 Mar 22.

Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genoa, Italy.

In the past few years, the technology of automated guided vehicles (AGVs) has notably advanced. In particular, in the context of factory and warehouse automation, different approaches have been presented for detecting and localizing pallets inside warehouses and shop-floor environments. In a related research paper Mohamed et al. Read More

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http://dx.doi.org/10.1016/j.dib.2019.103837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449777PMC

Development of a Clinical Decision Support System for Pediatric Abdominal Pain in Emergency Department Settings Across Two Health Systems Within the HCSRN.

EGEMS (Wash DC) 2019 Apr 12;7(1):15. Epub 2019 Apr 12.

Children's MN, Department of Pediatric Emergency Medicine, Minneapolis, Minnesota, US.

Background: Appendicitis is a common surgical emergency in children, yet diagnosis can be challenging. An electronic health record (EHR) based, clinical decision support (CDS) system called Appy CDS was designed to help guide management of pediatric patients with acute abdominal pain within the Health Care Systems Research Network (HCSRN).

Objectives: To describe the development and implementation of a clinical decision support tool (Appy CDS) built independently but synergistically at two large HCSRN affiliated health systems using well-established platforms, and to assess the tool's Triage component, aiming to identify pediatric patients at increased risk for appendicitis. Read More

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http://dx.doi.org/10.5334/egems.282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460497PMC

Step-by-step Descemet's membrane endothelial keratoplasty surgery.

Taiwan J Ophthalmol 2019 Jan-Mar;9(1):18-26

Cornea Services, Devers Eye Institute, Portland, OR, USA.

With the success of Descemet's stripping automated endothelial keratoplasty (DSAEK) technique providing better outcomes in visual prognosis and theoretically lower rejection rate than penetrating keratoplasty, DSAEK dominated the realm of endothelial keratoplasty for the past decade. However, Descemet's membrane endothelial keratoplasty (DMEK) has become more and more popular worldwide due to its even lower rejection rate, faster visual recovery, better visual outcome, and lower long-term endothelial loss. In this article, we demonstrate the techniques and nuances of DMEK surgery in detail for corneal specialists who are beginning their DMEK surgeries. Read More

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http://dx.doi.org/10.4103/tjo.tjo_108_18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6432849PMC

Automated analysis of small RNA datasets with RAPID.

PeerJ 2019 10;7:e6710. Epub 2019 Apr 10.

Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.

Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. Read More

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https://peerj.com/articles/6710
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http://dx.doi.org/10.7717/peerj.6710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462184PMC
April 2019
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virMine: automated detection of viral sequences from complex metagenomic samples.

PeerJ 2019 10;7:e6695. Epub 2019 Apr 10.

Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.

Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. Read More

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https://peerj.com/articles/6695
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http://dx.doi.org/10.7717/peerj.6695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462185PMC
April 2019
1 Read

Evaluation of the early warning, alert and response system after Cyclone Winston, Fiji, 2016.

Bull World Health Organ 2019 Mar 18;97(3):178-189C. Epub 2019 Jan 18.

Division of Pacific Technical Support, World Health Organization, Suva, Fiji.

Objective: To assess the performance of an early warning, alert and response system (EWARS) developed by the World Health Organization (WHO) - EWARS in a Box - that was used to detect and control disease outbreaks after Cyclone Winston caused destruction in Fiji on 20 February 2016.

Methods: Immediately after the cyclone, Fiji's Ministry of Health and Medical Services, supported by WHO, started to implement EWARS in a Box, which is a smartphone-based, automated, early warning surveillance system for rapid deployment during health emergencies. Both indicator-based and event-based surveillance were employed. Read More

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http://dx.doi.org/10.2471/BLT.18.211409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6453321PMC

Phenotyping ciliary dynamics and coordination in response to CFTR-modulators in Cystic Fibrosis respiratory epithelial cells.

Nat Commun 2019 Apr 16;10(1):1763. Epub 2019 Apr 16.

Biological and Soft Systems Sector, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK.

Personalized approaches for systematically assessing ciliary beat dynamics and for drug testing would improve the challenging task of diagnosing and treating respiratory disorders. In this pilot study, we show how multiscale differential dynamic microscopy (multi-DDM) can be used to characterize collective ciliary beating in a non-biased automated manner. We use multi-DDM to assess the efficacy of different CFTR-modulating drugs in human airway epithelial cells derived from subjects with cystic fibrosis (ΔF508/ΔF508 and ∆F508/-) based on ciliary beat frequency and coordination. Read More

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http://www.nature.com/articles/s41467-019-09798-3
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http://dx.doi.org/10.1038/s41467-019-09798-3DOI Listing
April 2019
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Microfluidic multipoles theory and applications.

Nat Commun 2019 Apr 16;10(1):1781. Epub 2019 Apr 16.

Institut de Génie Biomédical, École Polytechnique de Montréal, Montréal, QC, H3T 1J4, Canada.

Microfluidic multipoles (MFMs) have been realized experimentally and hold promise for "open-space" biological and chemical surface processing. Whereas convective flow can readily be predicted using hydraulic-electrical analogies, the design of advanced microfluidic multipole is constrained by the lack of simple, accurate models to predict mass transport within them. In this work, we introduce the complete solutions to mass transport in multipolar microfluidics based on the iterative conformal mapping of 2D advection-diffusion around a simple edge into dipoles and multipolar geometries, revealing a rich landscape of transport modes. Read More

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http://dx.doi.org/10.1038/s41467-019-09740-7DOI Listing

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.

Genome Res 2019 Apr 16. Epub 2019 Apr 16.

Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA.

Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we developed and validated a clinical mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, generate an automated summary of detected pathogens, and provide a graphical user interface for evaluating and interpreting results. Read More

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http://dx.doi.org/10.1101/gr.238170.118DOI Listing

Estimation of early life endogenous surfactant pool and CPAP failure in preterm neonates with RDS.

Respir Res 2019 Apr 16;20(1):75. Epub 2019 Apr 16.

Division of Pediatrics and Neonatal Critical Care, Medical Center "A.Béclère", South Paris University Hospitals, AP-HP, Paris, France.

Background: It is not known if the endogenous surfactant pool available early in life is associated with the RDS clinical course in preterm neonates treated with CPAP. We aim to clarify the clinical factors affecting surfactant pool in preterm neonates and study its association with CPAP failure.

Methods: Prospective, pragmatic, blind, cohort study. Read More

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http://dx.doi.org/10.1186/s12931-019-1040-zDOI Listing

A novel approach to neuraxial anesthesia: application of an automated ultrasound spinal landmark identification.

BMC Anesthesiol 2019 Apr 16;19(1):57. Epub 2019 Apr 16.

Department of Women's Anaesthesia, KK Women's and Children's Hospital, Singapore, Singapore.

Background: Neuraxial procedures are commonly performed for therapeutic and diagnostic indications. Currently, they are typically performed via palpation-guided surface landmark. We devised a novel intelligent image processing system that identifies spinal landmarks using ultrasound images. Read More

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http://dx.doi.org/10.1186/s12871-019-0726-6DOI Listing

Outcomes of Psychoeducation and a Text Messaging Adherence Intervention Among Individuals With Hypertension and Bipolar Disorder.

Psychiatr Serv 2019 Apr 17:appips201800482. Epub 2019 Apr 17.

Department of Psychiatry, Case Western Reserve University School of Medicine, Cleveland (Levin, Sajatovic, Rahman, Aebi, Cassidy, Blixen, Klein, Fuentes-Casiano); Neurological and Behavioral Outcomes Center (Levin, Sajatovic, Tatsuoka, Blixen) and Department of Medicine (Rahman), University Hospitals Cleveland Medical Center, Cleveland; Department of Psychiatry, University of California, San Diego, La Jolla (Depp, Cushman, Johnston, Moore); Department of Psychology, Cleveland State University, Cleveland (Eskew).

Objective: This study evaluated the feasibility, acceptability, and preliminary efficacy of psychoeducation plus an automated text messaging intervention (Individualized Texting for Adherence Building-Cardiovascular [iTAB-CV]) to improve adherence to antihypertensives and bipolar disorder medication.

Methods: After a psychoeducation program, iTAB-CV was administered for 2 months. In month 1, participants received one educational-motivational and one mood rating text daily. Read More

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http://dx.doi.org/10.1176/appi.ps.201800482DOI Listing

Convolutional Neural Network for Breathing Phase Detection in Lung Sounds.

Sensors (Basel) 2019 Apr 15;19(8). Epub 2019 Apr 15.

Department of Computer Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.

We applied deep learning to create an algorithm for breathing phase detection in lung sound recordings, and we compared the breathing phases detected by the algorithm and manually annotated by two experienced lung sound researchers. Our algorithm uses a convolutional neural network with spectrograms as the features, removing the need to specify features explicitly. We trained and evaluated the algorithm using three subsets that are larger than previously seen in the literature. Read More

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http://dx.doi.org/10.3390/s19081798DOI Listing

Human-Associated Indicator Bacteria and Human-Specific Viruses in Surface Water: A Spatial Assessment with Implications on Fate and Transport.

Environ Sci Technol 2018 Nov 15;52(21):12162-12171. Epub 2018 Oct 15.

U.S. Geological Survey, Upper Midwest Water Science Center , 8505 Research Way , Middleton , Wisconsin 53562 , United States.

Hydrologic, seasonal, and spatial variability of sewage contamination was studied at six locations within a watershed upstream from water reclamation facility (WRF) effluent to define relative loadings of sewage from different portions of the watershed. Fecal pollution from human sources was spatially quantified by measuring two human-associated indicator bacteria (HIB) and eight human-specific viruses (HSV) at six stream locations in the Menomonee River watershed in Milwaukee, Wisconsin from April 2009 to March 2011. A custom, automated water sampler, which included HSV filtration, was deployed at each location and provided unattended, flow-weighted, large-volume (30-913 L) sampling. Read More

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http://dx.doi.org/10.1021/acs.est.8b03481DOI Listing
November 2018

Guidance on prevention of unintended and accidental radiation exposures in nuclear medicine.

J Radiol Prot 2019 Apr 16. Epub 2019 Apr 16.

Australian Radiation Protection and Nuclear Safety Agency, Yallambie, Victoria, AUSTRALIA.

Nuclear medicine (NM) procedures for diagnosis and treatment of disease are performed routinely in hospitals throughout the world. These involve preparation and administration to patients of pharmaceuticals labelled with radioactive material. There is potential for incidents to occur, involving unintended exposures of patients or staff members, throughout all stages of a procedure. Read More

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http://iopscience.iop.org/article/10.1088/1361-6498/ab19d8
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http://dx.doi.org/10.1088/1361-6498/ab19d8DOI Listing
April 2019
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Determination of adsorbable organically bound fluorine (AOF) and adsorbable organically bound halogens as sum parameters in aqueous environmental samples using combustion ion chromatography (CIC).

Sci Total Environ 2019 Apr 6;673:384-391. Epub 2019 Apr 6.

Hessian State Laboratory, Glarusstrasse 6, D-65203 Wiesbaden, Germany.

Because of their toxicity and biomagnification potential individual perfluoroalkyl and polyfluoroalkyl substances (PFAS) are regularly examined in food and environmental matrices by LC-MS/MS. The combustion ion chromatography (CIC) can be used to determine adsorbable organic fluorine (AOF) in aqueous samples. This report describes the optimization and validation of an automated, robust, cost-efficient and rapid CIC method for the determination of AOF. Read More

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http://dx.doi.org/10.1016/j.scitotenv.2019.04.068DOI Listing

Automated DNA hybridization transfer with movable super-paramagnetic microbeads in a microflow reactor.

Biosens Bioelectron 2019 Apr 11;135:30-35. Epub 2019 Apr 11.

Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164, Sofia, Bulgaria. Electronic address:

An automated DNA hybridization transfer in a microflow reactor is demonstrated by moving paramagnetic beads between two spatially separate solutions with different pH values. The microbeads-based microfluidic platform is fully automated and programmable. It employs a robust chemical procedure for specific DNA hybridization transfer in microfluidic devices under isothermal conditions based on reversible pH alterations. Read More

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http://dx.doi.org/10.1016/j.bios.2019.04.014DOI Listing

Glucosamine-6-phosphate synthase inhibiting C3-β-cholesterol tethered spiro heterocyclic conjugates: Synthesis and their insight of DFT and docking study.

Bioorg Chem 2019 Apr 9;88:102920. Epub 2019 Apr 9.

Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia. Electronic address:

A series of novel covalent cholesterol-spiro pyrrolidine/pyrrolizidine heterocyclic hybrids possessing biologically active oxindole, indanedione, and acenaphthylene-1-one have been synthesized by the reaction of C3-β-cholesteroalacrylate with heterocyclic di- and tri-ketones. All the sixteen compounds were obtained as a single isomer in good yield through a stereo- and regio- selective 1,3-dipolar cycloaddition methodology. Stereochemistry of the spiranic cycloadducts has been established by spectroscopic analysis and the regioselectivity outcome of the spiro adducts has been accomplished by DFT calculations at B3LYP/6-31G (d,p) level study. Read More

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http://dx.doi.org/10.1016/j.bioorg.2019.102920DOI Listing

A new cryo-EM system for single particle analysis.

J Struct Biol 2019 Apr 13. Epub 2019 Apr 13.

Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, Hyogo, Japan. Electronic address:

A new cryo-EM system has been investigated for single particle analysis of protein structures. The system provides parallel illumination of a highly-coherent 300 kV electron beam from a cold-field emission gun, and boosts image contrast with an in-column energy filter and a hole-free phase plate. It includes motorized cryo-sample loading and automated liquid-nitrogen filling for cooling multiple samples. Read More

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http://dx.doi.org/10.1016/j.jsb.2019.04.011DOI Listing

Commonly used fluoroquinolones cross-react with urine drug screens for opiates, buprenorphine, and amphetamines.

Clin Biochem 2019 Apr 13. Epub 2019 Apr 13.

Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1301 Medical Center Drive, Nashville, TN 37232, United States.

Objectives: Fluoroquinolone antibiotics are commonly used in the treatment of infections and have previously been confirmed to cross-react with previous generations of opiates immunoassays. In this work we evaluated the cross-reactivity of the three fluoroquinolones in use at our institution with a panel of 10 urine drug screens.

Design And Methods: Drug preparations of levofloxacin, ciprofloxacin, and moxifloxacin that were designed for intravenous delivery were added to drug-free urine at varying concentrations. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00099120193009
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http://dx.doi.org/10.1016/j.clinbiochem.2019.04.009DOI Listing
April 2019
2 Reads

Studies on long term behavioural changes in group-housed rat models of brain and spinal cord injury using an automated home cage recording system.

J Neurosci Methods 2019 Apr 13. Epub 2019 Apr 13.

Centre for Neuroscience, Surgery and Trauma, Centre for Trauma Sciences, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom; Biological Services, Queen Mary University of London, London, United Kingdom. Electronic address:

Background: Neurotrauma patients face major neurological sequelae. The failure in the preclinical-to-clinical translation of candidate therapies could be due to poor evaluation of rodent behaviours after neurotrauma.

New Method: A home cage automated system was used to study the long term behaviour of individual rats with traumatic brain injury (TBI), spinal cord injury (SCI) and non-CNS injured controls, whilst group-housed in their home cages. Read More

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http://dx.doi.org/10.1016/j.jneumeth.2019.04.005DOI Listing

GNrep mouse: A reporter mouse for front-rear cell polarity.

Genesis 2019 Apr 16:e23299. Epub 2019 Apr 16.

Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.

Cell migration is essential during development, regeneration, homeostasis, and disease. Depending on the microenvironment, cells use different mechanisms to migrate. Yet, all modes of migration require the establishment of an intracellular front-rear polarity axis for directional movement. Read More

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http://dx.doi.org/10.1002/dvg.23299DOI Listing

A real-time road detection method based on reorganized lidar data.

PLoS One 2019 16;14(4):e0215159. Epub 2019 Apr 16.

School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China.

Road Detection is a basic task in automated driving field, in which 3D lidar data is commonly used recently. In this paper, we propose to rearrange 3D lidar data into a new organized form to construct direct spatial relationship among point cloud, and put forward new features for real-time road detection tasks. Our model works based on two prerequisites: (1) Road regions are always flatter than non-road regions. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215159PLOS
April 2019
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Concentrations of Intra-erythrocyte Folate, Serum Vitamin B12, and Hemoglobin in Women of Childbearing Age and Associated Factors.

J Am Coll Nutr 2019 Apr 16:1-7. Epub 2019 Apr 16.

a Centro de Ciências da Saúde/Departamento de Nutrição , Universidade Federal de Pernambuco , Recife - PE , Brazil.

Objective: The aim was to verify the relations among intra-erythrocyte folate, serum vitamin B12, and hemoglobin concentrations in women of childbearing age and their association with several socioeconomic and demographic variables, nutritional status, and food consumption in the city of Recife, Northeastern Brazil.

Methods: This was a cross-sectional study with a random sample of 1,210 women of childbearing age from the city of Recife. Concentrations of serum vitamin B12 and intra-erythrocyte folate were analyzed by immunoassay and hemoglobin concentrations by automated determination. Read More

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http://dx.doi.org/10.1080/07315724.2019.1592725DOI Listing

HistoQC: An Open-Source Quality Control Tool for Digital Pathology Slides.

JCO Clin Cancer Inform 2019 Apr(3):1-7

1 Case Western Reserve University, Cleveland, OH.

Purpose: Digital pathology (DP), referring to the digitization of tissue slides, is beginning to change the landscape of clinical diagnostic workflows and has engendered active research within the area of computational pathology. One of the challenges in DP is the presence of artefacts and batch effects, unintentionally introduced during both routine slide preparation (eg, staining, tissue folding) and digitization (eg, blurriness, variations in contrast and hue). Manual review of glass and digital slides is laborious, qualitative, and subject to intra- and inter-reader variability. Read More

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http://dx.doi.org/10.1200/CCI.18.00157DOI Listing

A new method using machine learning for automated image analysis applied to chip-based digital assays.

Analyst 2019 Apr 16. Epub 2019 Apr 16.

Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, College of Control Science and Engineering, Zhejiang University, Hangzhou 310027, P. R. China. and College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P.R. China.

Chip-based digital assays such as the digital polymerase chain reaction (digital PCR), digital loop-mediated amplification (digital LAMP), digital enzyme-linked immunosorbent assay (digital ELISA) and digital proximity ligation assay (digital PLA) need high-throughput quantification of the captured fluorescence image data. However, traditional methods that are mainly based on image segmentation using either a fixed threshold or an automated hard threshold failed to extract valid signals over a broad range of image characteristics. In this study, we introduce a new method for automated image analysis to extract signals applied to chip-based digital assays. Read More

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http://xlink.rsc.org/?DOI=C9AN00149B
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http://dx.doi.org/10.1039/c9an00149bDOI Listing
April 2019
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NOVEL SURGICAL TECHNIQUE TO REMOVE RETAINED SUBFOVEAL PERFLUOROCARBON LIQUID.

Retin Cases Brief Rep 2019 Apr 10. Epub 2019 Apr 10.

Department of Ophthalmology and Vision Sciences, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada.

Purpose: To describe a novel surgical technique to remove retained subfoveal perfluorocarbon liquid (PFCL).

Methods: After setting up for 23-G pars plana vitrectomy, a 38-G flexible-tip macular hydrodissection cannula connected to the automated viscous fluid infusion kit was used to create a small retinotomy approximately 700 μm to 800 μm inferior to the fovea and induce macular detachment involving the retained PFCL bubble. The flexible cannula was bent at its junction with the shaft and was carefully advanced through the same retinotomy into the subretinal space to access and directly aspirate the retained subfoveal PFCL bubble. Read More

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http://dx.doi.org/10.1097/ICB.0000000000000875DOI Listing

Automatic Hand Skeletal Shape Estimation from Radiographs.

IEEE Trans Nanobioscience 2019 Apr 12. Epub 2019 Apr 12.

Rheumatoid arthritis (RA) is an autoimmune disease whose common manifestation involves the slow destruction of joint tissue, damage that is visible in a radiograph. Over time, this damage causes pain and loss of functioning which depends, to some extent, on the spatial deformation induced by the joint damage. Building an accurate model of the current deformation and predicting potential future deformations is an important component of treatment planning. Read More

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http://dx.doi.org/10.1109/TNB.2019.2911026DOI Listing

A Roadmap for Foundational Research on Artificial Intelligence in Medical Imaging: From the 2018 NIH/RSNA/ACR/The Academy Workshop.

Radiology 2019 Apr 16:190613. Epub 2019 Apr 16.

From the Department of Radiology, Stanford University, Stanford, CA 94305 (C.P.L., M.P.L.); Department of Radiology, Grandview Medical Center, Birmingham, Ala (B.A.); Department of Radiology, Mayo Clinic, Rochester, Minn (B.J.E.); Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Mass (J.K.C.); GE Healthcare, Chicago, Ill (K.B.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pa (T.S.C., J.D.R.); Department of Radiology, Thomas Jefferson University Hospital, Philadelphia, Pa (A.E.F.); Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY (D.S.M.); Biomedical Imaging Center, Rensselaer Polytechnic Institute, Troy, NY (G.W.); and National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Washington, DC (K.K.).

Imaging research laboratories are rapidly creating machine learning systems that achieve expert human performance using open-source methods and tools. These artificial intelligence systems are being developed to improve medical image reconstruction, noise reduction, quality assurance, triage, segmentation, computer-aided detection, computer-aided classification, and radiogenomics. In August 2018, a meeting was held in Bethesda, Maryland, at the National Institutes of Health to discuss the current state of the art and knowledge gaps and to develop a roadmap for future research initiatives. Read More

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http://dx.doi.org/10.1148/radiol.2019190613DOI Listing

Hand Extension Robot Orthosis (HERO) Glove: Development and Testing with Stroke Survivors with Severe Hand Impairment.

IEEE Trans Neural Syst Rehabil Eng 2019 Apr 11. Epub 2019 Apr 11.

The Hand Extension Robot Orthosis (HERO) Glove was iteratively designed with occupational therapists and stroke survivors to enable stroke survivors with severe hand impairment to grasp and stabilize everyday objects, while being portable, lightweight, and easy to set up and use. The robot consists of a batting glove with artificial tendons embedded into the glove's fingers. The tendons are pulled and pushed by a linear actuator to extend and flex the fingers. Read More

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http://dx.doi.org/10.1109/TNSRE.2019.2910011DOI Listing

Global quantification of intact proteins via chemical isotope labeling and mass spectrometry.

J Proteome Res 2019 Apr 16. Epub 2019 Apr 16.

Although thousands of intact proteins can be feasibly identified in recent years, global quantification of intact proteins is still challenging. Herein, we develop a high-throughput strategy for global intact protein quantification based on chemical isotope labeling. The isotope incorporation efficiency is as high as 99. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00071
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http://dx.doi.org/10.1021/acs.jproteome.9b00071DOI Listing
April 2019
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Enzymatically-catalyzed CO -H O equilibration for oxygen isotope analyses of aqueous samples.

Rapid Commun Mass Spectrom 2019 Apr 15. Epub 2019 Apr 15.

School of Geography and Earth Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L83 4K1, Canada.

Rationale: The classic CO -H O equilibration method is a very popular technique for the measurement of the oxygen isotope composition of aqueous samples in stable isotope geochemistry. This study examined whether enzymatically-controlled CO -H O equilibration by carbonic anhydrase (CA) could reduce the time for oxygen isotope equilibrium between CO and H O at 25 °C.

Methods: Four types of aqueous samples containing CA were equilibrated with CO gases using a continuous flow isotope ratio mass spectrometer equipped with an automated gas sample collection device. Read More

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http://dx.doi.org/10.1002/rcm.8458DOI Listing

Morning Surge and Peak Morning Ambulatory Blood Pressure Versus Automated Office Blood Pressure in Predicting Cardiovascular Disease.

High Blood Press Cardiovasc Prev 2019 Apr 15. Epub 2019 Apr 15.

Department of Cardiology, Georgetown University and Veterans Affairs Medical Center, Athens, Greece.

Introduction: Automated office blood pressure (AOBP) has been recently shown to predict equally well to ambulatory blood pressure (ABP), conventional office blood pressure (OBP) and home blood pressure (HBP), cardiovascular (CV) events among hypertensives.

Aim: To compare AOBP recording and ABP monitoring in order to evaluate morning blood pressure (BP) peak in predicting CV events and deaths in hypertensives.

Methods: We assessed 236 initially untreated hypertensives, examined between 2009 and 2013. Read More

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http://link.springer.com/10.1007/s40292-019-00315-7
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http://dx.doi.org/10.1007/s40292-019-00315-7DOI Listing
April 2019
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Correction to: A Machine-Learning Algorithm to Optimise Automated Adverse Drug Reaction Detection from Clinical Coding.

Drug Saf 2019 Apr 15. Epub 2019 Apr 15.

Department of Clinical Pharmacology, Austin Health, Level 5, Lance Townsend Building, Studley Rd, Heidelberg, VIC, 3084, Australia.

CK: Principal Investigator. CM and CK were responsible for the study design and conception; all authors were responsible for acquisition and validation of the data; CM was responsible for analysis and interpretation of the data; and all authors contributed to reviewing drafts of the manuscript and approved the final version for publication. Read More

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http://dx.doi.org/10.1007/s40264-019-00820-7DOI Listing

Automated registration of magnetic resonance imaging and optoacoustic tomography data for experimental studies.

Neurophotonics 2019 Apr 3;6(2):025001. Epub 2019 Apr 3.

University of Zurich and ETH Zurich, Institute for Biomedical Engineering, Zurich, Switzerland.

Multimodal imaging combining optoacoustic tomography (OAT) with magnetic resonance imaging (MRI) enables spatiotemporal resolution complementarity, improves accurate quantification, and thus yields more insights into physiology and pathophysiology. However, only manual landmark based coregistration of OAT-MRI has been used so far. We developed a toolbox (RegOA), which frames an automated registration pipeline to align OAT with high-field MR images based on mutual information. Read More

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http://dx.doi.org/10.1117/1.NPh.6.2.025001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446211PMC

Determination of the chemical components and phospholipids of velvet antler using UPLC/QTOF-MS coupled with UNIFI software.

Exp Ther Med 2019 May 12;17(5):3789-3799. Epub 2019 Mar 12.

Department of Natural Medicinal Chemistry, School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China.

Velvet antler, which exhibits immune and growth enhancing effects, is commonly used in a variety of Asian health care products, but its complex components remain unknown. The current study analyzed extracts using ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry in the MS mode. Automated detection and data filtering were performed using UNIFI software and peaks were compared with a proprietary scientific library (Traditional Medicine Library; TML). Read More

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http://dx.doi.org/10.3892/etm.2019.7372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447902PMC

Outcome of Descemet membrane endothelial keratoplasty for graft failure after Descemet stripping automated endothelial keratoplasty.

Clin Ophthalmol 2019 25;13:553-559. Epub 2019 Mar 25.

Department of Ophthalmology, Goethe-University, Frankfurt am Main, Germany,

Purpose: To investigate the efficacy and safety of Descemet membrane endothelial keratoplasty (DMEK) for corneal decompensation following primary Descemet stripping automated endothelial keratoplasty (DSAEK).

Methods: This was a retrospective case series of 15 patients that underwent DMEK surgery for corneal decompensation after failed DSAEK. Main outcome parameter was corrected distance visual acuity (CDVA) after DMEK and DSAEK. Read More

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http://dx.doi.org/10.2147/OPTH.S194185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438261PMC