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https://www.readbyqxmd.com/read/28088763/scater-pre-processing-quality-control-normalization-and-visualization-of-single-cell-rna-seq-data-in-r
#1
Davis J McCarthy, Kieran R Campbell, Aaron T L Lun, Quin F Wills
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. RESULTS: We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28088237/association-between-diabetes-mellitus-and-multi-drug-resistant-tuberculosis-a-protocol-for-a-systematic-review-and-meta-analysis
#2
Balewgizie Sileshi Tegegne, Tesfa Dejenie Habtewold, Melkamu Merid Mengesha, Johannes G M Burgerhof
INTRODUCTION: Multi-drug-resistant tuberculosis (MDR-TB) has emerged as a challenge to global tuberculosis (TB) control and remains a major public health concern in many countries. Diabetes mellitus (DM) is an increasingly recognized comorbidity that can both accelerate TB disease and complicate its treatment. The aim of this study is to summarize available evidence on the association of DM and MDR-TB among TB patients and to provide a pooled estimate of risks. METHODS: All studies published in English before October 2016 will be searched using comprehensive search strings through PubMed, EMBASE, Web of Science, and WHO Global Health Library databases which have reported the association of DM and MDR-TB in adults with TB (age > =15)...
January 14, 2017: Systematic Reviews
https://www.readbyqxmd.com/read/28088226/use-of-an-intraoperative-navigation-system-for-retrieving-a-broken-dental-instrument-in-the-mandible-a-case-report
#3
Shintaro Sukegawa, Takahiro Kanno, Akane Shibata, Kenichi Matsumoto, Yuka Sukegawa-Takahashi, Kyosuke Sakaida, Yoshihiko Furuki
BACKGROUND: A fracture of root canal instruments, with a fractured piece protruding beyond the apex, is a troublesome incident during an endodontic treatment. Locating and retrieving them represents a challenge to maxillofacial surgeons because it is difficult to access due to the proximity between the foreign body and vital structures. Although safe and accurate for surgery, radiographs and electromagnetic devices do not provide a precise three-dimensional position. In contrast, computer-aided navigation provides a correlation between preoperatively collected data and intraoperatively encountered anatomy...
January 15, 2017: Journal of Medical Case Reports
https://www.readbyqxmd.com/read/28088178/health-related-quality-of-life-and-associated-factors-in-functionally-independent-older-people
#4
Mónica Machón, Isabel Larrañaga, Miren Dorronsoro, Kalliopi Vrotsou, Itziar Vergara
BACKGROUND: Health-related quality of life (HRQL) is a key indicator of elderly people's health status that can be affected by different factors. However, little is known about which variables are associated with it in functionally independent elderly people. The aim of this project was to study HRQL and a wide variety of health, lifestyle, social and contextual aspects and their relation to HRQL in a sample of functionally independent, non-cognitively impaired community-dwelling adults, over 65 years of age, from a northern region of Spain...
January 14, 2017: BMC Geriatrics
https://www.readbyqxmd.com/read/28088063/verbal-and-musical-short-term-memory-variety-of-auditory-disorders-after-stroke
#5
Catherine Hirel, Norbert Nighoghossian, Yohana Lévêque, Salem Hannoun, Lesly Fornoni, Sébastien Daligault, Patrick Bouchet, Julien Jung, Barbara Tillmann, Anne Caclin
Auditory cognitive deficits after stroke may concern language and/or music processing, resulting in aphasia and/or amusia. The aim of the present study was to assess the potential deficits of auditory short-term memory for verbal and musical material after stroke and their underlying cerebral correlates with a Voxel-based Lesion Symptom Mapping approach (VLSM). Patients with an ischemic stroke in the right (N=10) or left (N=10) middle cerebral artery territory and matched control participants (N=14) were tested with a detailed neuropsychological assessment including global cognitive functions, music perception and language tasks...
January 11, 2017: Brain and Cognition
https://www.readbyqxmd.com/read/28087996/grating-lobes-suppression-by-adding-virtual-receiving-subaperture-in-synthetic-aperture-imaging
#6
Janusz Wojcik, Marcin Lewandowski, Norbert Żołek
A method of suppression of grating lobes is presented, analyzed, and verified. The method is based on creating a Virtual Receiving Subaperture (VRS) by adding virtual transducer elements not existing in the physical layout of the receiver. The VRS channels are filled with data based on signals from real channels. The analytical model of the synthetic aperture imaging system's impulse response is presented to describe the properties of the VRS. The model shows a reduction of the receiving grating lobes' amplitude (with a comparison to the main lobe's amplitude) by a magnitude equal to the number of receiving transducer elements...
December 21, 2016: Ultrasonics
https://www.readbyqxmd.com/read/28087578/distinct-binding-of-pet-ligands-pbb3-and-av-1451-to-tau-fibril-strains-in-neurodegenerative-tauopathies
#7
Maiko Ono, Naruhiko Sahara, Katsushi Kumata, Bin Ji, Ruiqing Ni, Shunsuke Koga, Dennis W Dickson, John Q Trojanowski, Virginia M-Y Lee, Mari Yoshida, Isao Hozumi, Yasumasa Yoshiyama, John C van Swieten, Agneta Nordberg, Tetsuya Suhara, Ming-Rong Zhang, Makoto Higuchi
Diverse neurodegenerative disorders are characterized by deposition of tau fibrils composed of conformers (i.e. strains) unique to each illness. The development of tau imaging agents has enabled visualization of tau lesions in tauopathy patients, but the modes of their binding to different tau strains remain elusive. Here we compared binding of tau positron emission tomography ligands, PBB3 and AV-1451, by fluorescence, autoradiography and homogenate binding assays with homologous and heterologous blockades using tauopathy brain samples...
January 12, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28087243/using-deep-learning-to-investigate-the-neuroimaging-correlates-of-psychiatric-and-neurological-disorders-methods-and-applications
#8
REVIEW
Sandra Vieira, Walter H L Pinaya, Andrea Mechelli
Deep learning (DL) is a family of machine learning methods that has gained considerable attention in the scientific community, breaking benchmark records in areas such as speech and visual recognition. DL differs from conventional machine learning methods by virtue of its ability to learn the optimal representation from the raw data through consecutive nonlinear transformations, achieving increasingly higher levels of abstraction and complexity. Given its ability to detect abstract and complex patterns, DL has been applied in neuroimaging studies of psychiatric and neurological disorders, which are characterised by subtle and diffuse alterations...
January 10, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28086991/does-waterfall-aerosol-influence-mucosal-immunity-and-chronic-stress-a-randomized-controlled-clinical-trial
#9
Carina Grafetstätter, Martin Gaisberger, Johanna Prossegger, Markus Ritter, Predrag Kolarž, Christina Pichler, Josef Thalhamer, Arnulf Hartl
BACKGROUND: The specific microclimate of alpine waterfalls with high levels of ionized water aerosols has been suggested to trigger beneficial immunological and psychological effects. In the present three-armed randomized controlled clinical study, we focused on effects on (i) immunological reagibility, on (ii) physiological stress responses, and on (iii) stress-related psychological parameters. METHODS: People with moderate to high stress levels (n = 65) spent an active sojourn with daily hiking tours in the National Park Hohe Tauern (Großkirchheim, Austria)...
January 13, 2017: Journal of Physiological Anthropology
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#10
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086781/effects-of-the-intradiscal-implantation-of-stromal-vascular-fraction-plus-platelet-rich-plasma-in-patients-with-degenerative-disc-disease
#11
Comella Kristin, Silbert Robert, Parlo Michelle
BACKGROUND: Stromal vascular fraction (SVF) can easily be obtained from a mini-lipoaspirate procedure of fat tissue and platelet rich plasma (PRP) can be obtained from peripheral blood. The SVF contains a mixture of cells including ADSCs and growth factors and has been depleted of the adipocyte (fat cell) population. We evaluated the safety and efficacy of administering SVF and PRP intra-discally into patients with degenerative disc disease. METHODS: A total of 15 patients underwent a local tumescent liposuction procedure to remove approximately 60 ml of fat tissue...
January 13, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28081581/differences-in-gene-expression-and-gene-associations-in-epicardial-fat-compared-to-subcutaneous-fat
#12
J Yim, S W Rabkin
Epicardial adipose tissue (EAT) plays a role in cardiac physiology and may contribute to the development of coronary artery disease. Our objective was to determine whether there was a significant difference in gene expression in EAT compared to subcutaneous adipose tissue (SAT) and to identify potential relationships. MEDLINE and EMBASE were searched using the key terms "Epicardial Adipose Tissue" or "Epicardial Fat" in combination with "RNA", "mRNA", or "gene". The entry criteria were studies that presented primary data including expression levels of mRNA in human EAT compared with SAT and an expression of variance (SD)...
January 12, 2017: Hormone and Metabolic Research, Hormon- und Stoffwechselforschung, Hormones et Métabolisme
https://www.readbyqxmd.com/read/28081518/development-of-a-biometric-method-to-estimate-age-on-hand-radiographs
#13
Floriane Remy, Gabriela Hossu, Romain Cendre, Emilien Micard, Laurence Mainard-Simard, Jacques Felblinger, Laurent Martrille, Loïc Lalys
Age estimation of living individuals aged less than 13, 18 or 21 years, which are some relevant legal ages in most European countries, is currently problematic in the forensic context. Thus, numerous methods are available for legal authorities, although their efficiency can be discussed. For those reasons, we aimed to propose a new method, based on the biometric analysis of hand bones. 451 hand radiographs of French individuals under the age of 21 were retrospectively analyzed. This total sample was divided into three subgroups bounded by the relevant legal ages previously mentioned: 0-13, 13-18 and 18-21 years...
December 23, 2016: Forensic Science International
https://www.readbyqxmd.com/read/28080110/spoken-words-can-make-the-invisible-visible-testing-the-involvement-of-low-level-visual-representations-in-spoken-word-processing
#14
Markus Ostarek, Falk Huettig
The notion that processing spoken (object) words involves activation of category-specific representations in visual cortex is a key prediction of modality-specific theories of representation that contrasts with theories assuming dedicated conceptual representational systems abstracted away from sensorimotor systems. In the present study, we investigated whether participants can detect otherwise invisible pictures of objects when they are presented with the corresponding spoken word shortly before the picture appears...
January 12, 2017: Journal of Experimental Psychology. Human Perception and Performance
https://www.readbyqxmd.com/read/28079737/dexmedetomidine-reduces-perioperative-opioid-consumption-and-postoperative-pain-intensity-in-neurosurgery-a-meta-analysis
#15
Yi Liu, Feng Liang, Xiaochen Liu, Xinxin Shao, Nan Jiang, Xiaoliang Gan
BACKGROUND: Dexmedetomidine (DEX) has been administered to patients during neurosurgery. Some studies have found that DEX could reduce perioperative opioid consumption and postoperative pain intensity. However, no firm conclusions have been reached. The purpose of this meta-analysis was to assess the efficacy of DEX for managing pain in neurosurgical patients. MATERIALS AND METHODS: A comprehensive literature review was conducted to identify randomized controlled trials (RCTs) focusing on the effects of DEX on perioperative opioid consumption and postoperative pain intensity in patients undergoing neurosurgery...
January 10, 2017: Journal of Neurosurgical Anesthesiology
https://www.readbyqxmd.com/read/28079249/fractal-analysis-of-visual-search-activity-for-mass-detection-during-mammographic-screening
#16
Folami Alamudun, Hong-Jun Yoon, Kathleen B Hudson, Garnetta Morin-Ducote, Tracy Hammond, Georgia D Tourassi
PURPOSE: The objective of this study is to assess the complexity of human visual search activity during mammographic screening using fractal analysis and to investigate its relationship with case and reader characteristics. METHODS: The study was performed for the task of mammographic screening with simultaneous viewing of four coordinated breast views as typically done in clinical practice. Eye-tracking data and diagnostic decisions collected for 100 mammographic cases (25 normal, 25 benign, 50 malignant) and 10 readers (three board certified radiologists and seven radiology residents), formed the corpus data for this study...
January 12, 2017: Medical Physics
https://www.readbyqxmd.com/read/28079128/parallel-meta-3-comprehensive-taxonomical-and-functional-analysis-platform-for-efficient-comparison-of-microbial-communities
#17
Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, Xiaoquan Su
The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078966/visual-and-cross-modal-cues-increase-the-identification-of-overlapping-visual-stimuli-in-balint-s-syndrome
#18
Daniela D'Imperio, Michele Scandola, Valeria Gobbetto, Cristina Bulgarelli, Matteo Salgarello, Renato Avesani, Valentina Moro
INTRODUCTION: Cross-modal interactions improve the processing of external stimuli, particularly when an isolated sensory modality is impaired. When information from different modalities is integrated, object recognition is facilitated probably as a result of bottom-up and top-down processes. The aim of this study was to investigate the potential effects of cross-modal stimulation in a case of simultanagnosia. METHOD: We report a detailed analysis of clinical symptoms and an (18)F-fluorodeoxyglucose (FDG) brain positron emission tomography/computed tomography (PET/CT) study of a patient affected by Balint's syndrome, a rare and invasive visual-spatial disorder following bilateral parieto-occipital lesions...
January 12, 2017: Journal of Clinical and Experimental Neuropsychology
https://www.readbyqxmd.com/read/28078672/determinants-for-drug-survival-of-methotrexate-in-patients-with-psoriasis-split-for-different-reasons-of-discontinuation-results-of-the-prospective-mtx-capture
#19
M Otero, J van den Reek, M Seyger, P Van Der Kerkhof, W Kievit, E de Jong
BACKGROUND: Methotrexate is a widely used treatment for psoriasis. It is important to gain insight into the reasons for discontinuation of methotrexate and determinants for drug survival. OBJECTIVES: To describe 5-year drug survival for methotrexate in patients with psoriasis split for different reasons of discontinuation, and to identify determinants for drug survival. METHODS: Data were extracted from a prospective psoriasis registry of patients treated with methotrexate (MTX-CAPTURE)...
January 12, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/28078573/setting-things-straight-a-comparison-of-measures-of-saccade-trajectory-deviation
#20
Luke Tudge, Eugene McSorley, Stephan A Brandt, Torsten Schubert
In eye movements, saccade trajectory deviation has often been used as a physiological operationalization of visual attention, distraction, or the visual system's prioritization of different sources of information. However, there are many ways to measure saccade trajectories and to quantify their deviation. This may lead to noncomparable results and poses the problem of choosing a method that will maximize statistical power. Using data from existing studies and from our own experiments, we used principal components analysis to carry out a systematic quantification of the relationships among eight different measures of saccade trajectory deviation and their power to detect the effects of experimental manipulations, as measured by standardized effect size...
January 11, 2017: Behavior Research Methods
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