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https://www.readbyqxmd.com/read/29223137/sysmex-uf-1000i-flow-cytometer-to-screen-urinary-tract-infections-the-uriscam-multicentre-study
#1
O Herráez, M A Asencio, R Carranza, M M Jarabo, M Huertas, O Redondo, A Arias, S Jiménez-Álvarez, S Solís, P Zamarrón, M S Illescas, M A Galán
The new Sysmex UF-1000i analyzer - which incorporates bacteria morphology distinction - allows to automatically screen samples to be cultured at microbiology laboratories. We have evaluated the feasibility and accuracy of Sysmex UF-1000i to screen urine tract infections (UTIs). A total amount of 2,468 urine samples from six Spanish hospitals were analysed. Demographic and clinical data such as age, gender, source and sample type, preserving conditions, cytometer parameters (bacteria, leucocytes, and bacteria morphology) as well as urine culture results (gold standard) were recorded...
December 9, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/29222764/optimization-of-multi-omic-genome-scale-models-methodologies-hands-on-tutorial-and-perspectives
#2
Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
Genome-scale metabolic models are valuable tools for assessing the metabolic potential of living organisms. Being downstream of gene expression, metabolism is increasingly being used as an indicator of the phenotypic outcome for drugs and therapies. We here present a review of the principal methods used for constraint-based modelling in systems biology, and explore how the integration of multi-omic data can be used to improve phenotypic predictions of genome-scale metabolic models. We believe that the large-scale comparison of the metabolic response of an organism to different environmental conditions will be an important challenge for genome-scale models...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222590/technical-accuracy-of-the-integration-of-an-external-ultrasonography-system-into-a-navigation-platform-effects-of-ultrasonography-probe-registration-and-target-detection
#3
Frederic A Wanis, Lars Wessels, Marcus H T Reinges, Eberhard Uhl, Andreas Jödicke
BACKGROUND: Intraoperative navigated ultrasonography has reached clinical acceptance, while published data for the accuracy of some systems are missing. We technically quantified and optimised the accuracy of the integration of an external ultrasonography system into a BrainLab navigation system. METHODS: A high-end ultrasonography system (Elegra; Siemens, Erlangen, Germany) was linked to a navigation system (Vector Vision; BrainLab, Munich, Germany). In vitro accuracy and precision was calculated from differences between a real world target (high-precision crosshair phantom) and the ultrasonography image of this target in the navigation coordinate system...
December 8, 2017: Acta Neurochirurgica
https://www.readbyqxmd.com/read/29222462/a-translational-model-to-determine-rodent-s-age-from-human-foetal-age
#4
Yoshiyuki Ohmura, Yasuo Kuniyoshi
To understand the prenatal origin of developmental and psychiatric disorders, studies in laboratory animals are imperative. However, the developmental pace differs between humans and animals; hence, corresponding human ages must be estimated to infer the most vulnerable developmental timings in humans. Because rats and mice are extensively used as models in developmental research, a correspondence between human foetal ages and rodents' ages must be precisely determined; thus, developing a translational model is of utmost importance...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221834/emotion-and-sex-of-facial-stimuli-modulate-conditional-automaticity-in-behavioral-and-neuronal-interference-in-healthy-men
#5
Nils Kohn, Guillén Fernández
Our surrounding provides a host of sensory input, which we cannot fully process without streamlining and automatic processing. Levels of automaticity differ for different cognitive and affective processes. Situational and contextual interactions between cognitive and affective processes in turn influence the level of automaticity. Automaticity can be measured by interference in Stroop tasks. We applied an emotional version of the Stroop task to investigate how stress as a contextual factor influences the affective valence-dependent level of automaticity...
December 5, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/29221640/threshold-based-segmentation-of-fluorescent-and-chromogenic-images-of-microglia-astrocytes-and-oligodendrocytes-in-fiji
#6
Sinead Healy, Jill McMahon, Peter Owens, Peter Dockery, Una FitzGerald
BACKGROUND: Image segmentation is often imperfect, particularly in complex image sets such z-stack micrographs of slice cultures and there is a need for sufficient details of parameters used in quantitative image analysis to allow independent repeatability and appraisal. NEW METHOD: For the first time, we have critically evaluated, quantified and validated the performance of different segmentation methodologies using z-stack images of ex vivo glial cells. The BioVoxxel toolbox plugin, available in FIJI, was used to measure the relative quality, accuracy, specificity and sensitivity of 16 global and 9 local threshold automatic thresholding algorithms...
December 5, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/29221286/automatic-lung-rads%C3%A2-classification-with-a-natural-language-processing-system
#7
Sebastian E Beyer, Brady J McKee, Shawn M Regis, Andrea B McKee, Sebastian Flacke, Gilan El Saadawi, Christoph Wald
Background: Our aim was to train a natural language processing (NLP) algorithm to capture imaging characteristics of lung nodules reported in a structured CT report and suggest the applicable Lung-RADS™ (LR) category. Methods: Our study included structured, clinical reports of consecutive CT lung screening (CTLS) exams performed from 08/2014 to 08/2015 at an ACR accredited Lung Cancer Screening Center. All patients screened were at high-risk for lung cancer according to the NCCN Guidelines®...
September 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29221042/image-processing-pipeline-for-segmentation-and-material-classification-based-on-multispectral-high-dynamic-range-polarimetric-images
#8
Miguel Ángel Martínez-Domingo, Eva M Valero, Javier Hernández-Andrés, Shoji Tominaga, Takahiko Horiuchi, Keita Hirai
We propose a method for the capture of high dynamic range (HDR), multispectral (MS), polarimetric (Pol) images of indoor scenes using a liquid crystal tunable filter (LCTF). We have included the adaptive exposure estimation (AEE) method to fully automatize the capturing process. We also propose a pre-processing method which can be applied for the registration of HDR images after they are already built as the result of combining different low dynamic range (LDR) images. This method is applied to ensure a correct alignment of the different polarization HDR images for each spectral band...
November 27, 2017: Optics Express
https://www.readbyqxmd.com/read/29220621/quality-of-life-in-australian-adults-aged-50-years-and-over-data-using-the-schedule-for-the-evaluation-of-individual-quality-of-life-seiqol-dw
#9
Sofia Robleda, Nancy A Pachana
OBJECTIVES: This study explored unique and personal domains associated with quality of life (QOL) in 153 mid-aged and older Australian adults over age 50, using an innovative measure of individualized QOL, the Schedule for the Evaluation of Individual Quality of Life (SEIQOL-DW). METHODS: Demographic measures as well as the SEIQOL-DW were administered. The qualitative responses on this scale were analyzed by Leximancer, a text analysis program that extracts semantic meaning and relational information automatically from text...
October 27, 2017: Clinical Gerontologist
https://www.readbyqxmd.com/read/29220476/egenpub-a-text-mining-system-for-extending-computationally-mapped-bibliography-for-uniprot-knowledgebase-by-capturing-centrality
#10
Ruoyao Ding, Emmanuel Boutet, Damien Lieberherr, Michel Schneider, Michael Tognolli, Cathy H Wu, K Vijay-Shanker, Cecilia N Arighi
UniProt Knowledgebase (UniProtKB) is a publicly available database with access to a vast amount of protein sequence and functional information. To widen the scope of the publications associated with a protein entry, UniProt has introduced the computationally mapped additional bibliography section, which includes literature collected from external sources. In this article, we describe a text mining system, eGenPub, which selects articles that are 'about' specific proteins and allows automatic identification of additional bibliography for given UniProt protein entries...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220462/first-steps-in-automatic-summarization-of-transcription-factor-properties-for-regulondb-classification-of-sentences-about-structural-domains-and-regulated-processes
#11
Carlos-Francisco Méndez-Cruz, Socorro Gama-Castro, Citlalli Mejía-Almonte, Marco-Polo Castillo-Villalba, Luis-José Muñiz-Rascado, Julio Collado-Vides
RegulonDB, http://regulondb.ccg.unam.mx.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220414/detection-of-spontaneous-pulse-using-the-acceleration-signals-acquired-from-cpr-feedback-sensor-in-a-porcine-model-of-cardiac-arrest
#12
Liang Wei, Gang Chen, Zhengfei Yang, Tao Yu, Weilun Quan, Yongqin Li
BACKGROUND: Reliable detection of return of spontaneous circulation with minimal interruptions of chest compressions is part of high-quality cardiopulmonary resuscitation (CPR) and routinely done by checking pulsation of carotid arteries. However, manual palpation was time-consuming and unreliable even if performed by expert clinicians. Therefore, automated accurate pulse detection with minimal interruptions of chest compression is highly desirable during cardiac arrest especially in out-of-hospital settings...
2017: PloS One
https://www.readbyqxmd.com/read/29220401/contour-recognition-of-complex-leaf-shapes
#13
Giacomo Diaz
The leaf shape is an important taxonomic character. Compared to the classic morphological leaf features such as veins, margin indentations, sinuses, etc., the shape is simpler to obtain by using the 'magic wand' or other contouring tools that are available in most of imaging applications. The only exception is when leaves develop large lobes that get in touch or overlap each other, as the presence of hidden or closed portions of the leaf border precludes the application of automatic methods and forces the leaf contour to be traced manually...
2017: PloS One
https://www.readbyqxmd.com/read/29219084/an-improved-bayesian-network-method-for-reconstructing-gene-regulatory-network-based-on-candidate-auto-selection
#14
Linlin Xing, Maozu Guo, Xiaoyan Liu, Chunyu Wang, Lei Wang, Yin Zhang
BACKGROUND: The reconstruction of gene regulatory network (GRN) from gene expression data can discover regulatory relationships among genes and gain deep insights into the complicated regulation mechanism of life. However, it is still a great challenge in systems biology and bioinformatics. During the past years, numerous computational approaches have been developed for this goal, and Bayesian network (BN) methods draw most of attention among these methods because of its inherent probability characteristics...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29219018/gender-differences-in-knee-joint-congruity-quantified-from-mri-a-validation-study-with-data-from-center-for-clinical-and-basic-research-and-osteoarthritis-initiative
#15
Sudhakar Tummala, Dieuwke Schiphof, Inger Byrjalsen, Erik B Dam
Objective Gender is a risk factor in the onset of osteoarthritis (OA). The aim of the study was to investigate gender differences in contact area (CA) and congruity index (CI) in the medial tibiofemoral (MTF) joint in 2 different cohorts, quantified automatically from magnetic resonance imaging (MRI). Design The CA and CI markers were validated on 2 different data sets from Center for Clinical and Basic Research (CCBR) and Osteoarthritis Initiative (OAI). The CCBR cohort consisted of 159 subjects and the OAI subcohort consisted of 1,436 subjects...
January 2018: Cartilage
https://www.readbyqxmd.com/read/29218918/annotating-gene-sets-by-mining-large-literature-collections-with-protein-networks
#16
Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W Huang, Jiawei Han, Jian Peng, Trey Ideker
Analysis of patient genomes and transcriptomes routinely recognizes new gene sets associated with human disease. Here we present an integrative natural language processing system which infers common functions for a gene set through automatic mining of the scientific literature with biological networks. This system links genes with associated literature phrases and combines these links with protein interactions in a single heterogeneous network. Multiscale functional annotations are inferred based on network distances between phrases and genes and then visualized as an ontology of biological concepts...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218877/automated-disease-cohort-selection-using-word-embeddings-from-electronic-health-records
#17
Benjamin S Glicksberg, Riccardo Miotto, Kipp W Johnson, Khader Shameer, Li Li, Rong Chen, Joel T Dudley
Accurate and robust cohort definition is critical to biomedical discovery using Electronic Health Records (EHR). Similar to prospective study designs, high quality EHR-based research requires rigorous selection criteria to designate case/control status particular to each disease. Electronic phenotyping algorithms, which are manually built and validated per disease, have been successful in filling this need. However, these approaches are time-consuming, leading to only a relatively small amount of algorithms for diseases developed...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218521/applying-microfluidic-systems-to-study-effects-of-glucose-at-single-cell-level
#18
Niek Welkenhuysen, Caroline B Adiels, Mattias Goksör, Stefan Hohmann
Microfluidic systems in combination with microscopy (e.g., fluorescence) can be a powerful tool to study, at single-cell level, the behavior and morphology of biological cells after uptake of glucose. Here, we briefly discuss the advantages of using microfluidic systems. We further describe how microfluidic systems are fabricated and how they are utilized. Finally, we discuss how the large amount of data can be analyzed in a "semi-automatic" manner using custom-made software. In summary, we provide a guide to how to use microfluidic systems in single-cell studies...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29218460/a-novel-adaptive-deformable-model-for-automated-optic-disc-and-cup-segmentation-to-aid-glaucoma-diagnosis
#19
Muhammad Salman Haleem, Liangxiu Han, Jano van Hemert, Baihua Li, Alan Fleming, Louis R Pasquale, Brian J Song
This paper proposes a novel Adaptive Region-based Edge Smoothing Model (ARESM) for automatic boundary detection of optic disc and cup to aid automatic glaucoma diagnosis. The novelty of our approach consists of two aspects: 1) automatic detection of initial optimum object boundary based on a Region Classification Model (RCM) in a pixel-level multidimensional feature space; 2) an Adaptive Edge Smoothing Update model (AESU) of contour points (e.g. misclassified or irregular points) based on iterative force field calculations with contours obtained from the RCM by minimising energy function (an approach that does not require predefined geometric templates to guide auto-segmentation)...
December 7, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/29218415/timing-of-cortical-activation-during-spontaneous-swallowing
#20
Erin Kamarunas, Rachel Mulheren, Katie Palmore, Christy Ludlow
Saliva accumulation in the oropharynx generates an automatic pattern of swallowing in the brainstem in animals. Previous fMRI studies have found that spontaneous saliva and water swallows in humans evoked activation following swallow onset in both precentral motor and postcentral somatosensory cortical regions. Using event-related averaging of continuous functional near infrared spectroscopy (fNIRS), we examined cortical hemodynamic responses (HDR) from 5 s before to 35 s after spontaneous reflexive saliva swallow onset in the lateral postcentral somatosensory and precentral motor regions in both hemispheres in healthy volunteers...
December 7, 2017: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
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