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Data visualization

Piotr Klukowski, Michal Augoff, Maciej Zieba, Maciej Drwal, Adam Gonczarek, Michal J Walczak
Motivation: Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy...
March 14, 2018: Bioinformatics
Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven
Summary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot...
March 14, 2018: Bioinformatics
Emmett Harrison, Paul B A Dhillon
INTRODUCTION: Rural family physicians are often required to meet a wide variety of medical service demands that are otherwise the responsibility of specialty physicians in urban centres. However, many rural physicians enjoy the practice variety and ability to meet patients' medical needs through this wider spectrum of care. We aimed to quantify and summarize the workload and clinical disorders seen by rural family physicians in Saskatchewan relative to urban family physicians. METHODS: We used Saskatchewan Ministry of Health billing data for 2015/16 to compare rural and urban care provision...
2018: Canadian Journal of Rural Medicine
Neil E O'Connell, Louise Marston, Sally Spencer, Lorraine H DeSouza, Benedict M Wand
BACKGROUND: This is an updated version of the original Cochrane Review published in 2010, Issue 9, and last updated in 2014, Issue 4. Non-invasive brain stimulation techniques aim to induce an electrical stimulation of the brain in an attempt to reduce chronic pain by directly altering brain activity. They include repetitive transcranial magnetic stimulation (rTMS), cranial electrotherapy stimulation (CES), transcranial direct current stimulation (tDCS), transcranial random noise stimulation (tRNS) and reduced impedance non-invasive cortical electrostimulation (RINCE)...
March 16, 2018: Cochrane Database of Systematic Reviews
Da Li, Yu-Ming Jiao, Liang Wang, Fu-Xin Lin, Jun Wu, Xian-Zeng Tong, Shuo Wang, Yong Cao
OBJECTIVE Surgical management of brainstem lesions is challenging due to the highly compact, eloquent anatomy of the brainstem. This study aimed to evaluate the safety and efficacy of preoperative diffusion tensor imaging (DTI) and diffusion tensor tractography (DTT) in brainstem cavernous malformations (CMs). METHODS A prospective randomized controlled clinical trial was performed by using stratified blocked randomization. The primary eligibility criterion of the study was being a surgical candidate for brainstem CMs (with informed consent)...
March 16, 2018: Journal of Neurosurgery
Hai Yan Huang, Shao Jian Lin, Wei Guo Zhao, Zhe Bao Wu
The aim of this study is to compare the efficacy of bromocriptine (BRC) versus cabergoline (CAB) in patients with giant prolactinomas. We searched MEDLINE, EMBASE, CENTRAL and Clinical for studies dated before March 1st, 2016, that used BRC or CAB for the treatment of patients with giant prolactinomas. Specific eligibility criteria were set to identify articles and cases. The selected articles were reviewed, and the data were extracted for analysis. The compared outcomes included tumor shrinkage, tumor response, normalization of prolactin (PRL) level, and visual field defect (VFD) improvement...
March 15, 2018: Metabolic Brain Disease
Loïc Peter, Marcel Tella-Amo, Dzhoshkun Ismail Shakir, George Attilakos, Ruwan Wimalasundera, Jan Deprest, Sébastien Ourselin, Tom Vercauteren
PURPOSE: The standard clinical treatment of Twin-to-Twin transfusion syndrome consists in the photo-coagulation of undesired anastomoses located on the placenta which are responsible to a blood transfer between the two twins. While being the standard of care procedure, fetoscopy suffers from a limited field-of-view of the placenta resulting in missed anastomoses. To facilitate the task of the clinician, building a global map of the placenta providing a larger overview of the vascular network is highly desired...
March 15, 2018: International Journal of Computer Assisted Radiology and Surgery
Quan Zhou, Li Hong, Jing Wang
PURPOSE: The aim of this study was to elucidate the molecular mechanisms and to identify the key genes and pathways for pelvic organ prolapse (POP) using bioinformatics analysis. METHODS: The microarray data for GSE53868 included 12 POP and 12 non-POP anterior vaginal wall samples. Differentially expressed genes (DEGs) were identified by GEO2R online tool. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the DAVID database, and a DEG-associated protein-protein interaction (PPI) network was constructed using STRING and visualized in Cytoscape...
March 15, 2018: Archives of Gynecology and Obstetrics
Andrew R Christiansen, Rami M Shorti, Cory D Smith, William C Prows, Jay T Bishoff
PURPOSE: Despite the increasing use of advanced 3D imaging techniques and 3D printing, these techniques have not yet been comprehensively compared in a surgical setting. The purpose of this study is to explore the effectiveness of five different advanced imaging modalities during a complex renal surgical procedure. METHODS: A patient with a horseshoe kidney and multiple large, symptomatic stones that had failed Extracorporeal Shock Wave Lithotripsy (ESWL) and ureteroscopy treatment was used for this evaluation...
March 15, 2018: World Journal of Urology
Masha Shulkin, Laura Pimpin, David Bellinger, Sarah Kranz, Wafaie Fawzi, Christopher Duggan, Dariush Mozaffarian
Background: Epidemiologic studies link maternal seafood and n-3 (ω-3) polyunsaturated fatty acid (PUFA) consumption with improved childhood cognitive development; trials show mixed results. Objective: We investigated effects of n-3 PUFA supplementation on child cognitive and visual outcomes. Methods: We systematically reviewed and meta-analyzed randomized controlled trials of n-3 PUFA supplementation in mothers or infants (age ≤2 y) and evaluated standardized measures of cognitive or visual development up to age 18 y...
March 1, 2018: Journal of Nutrition
Jonathan L Preston, Gabriela Holliman-Lopez, Megan C Leece
Purpose: Ultrasound visual feedback of the tongue is increasingly used as a component of speech therapy in clinical research and practice. The purpose is to offer a preliminary summary of the nature of participant-reported undesired effects related to ultrasound visual feedback. Method: Sixty-two participants across 3 sites (mean age = 11.9 years) and 38 parents responded to a 2-item verbal questionnaire following 14-16 hr of treatment regarding any aspects of the treatment they did not like...
March 15, 2018: American Journal of Speech-language Pathology
Yan Yang, Zhongyin Zhou, Rong Liu, Lu Chen, Hongyu Xiang, Na Chen
Endoscopic retrograde cholangiopancreatography (ERCP) is an important treatment for inoperable hilar cholangiocarcinoma (HCC). The aim of the present study as to evaluate the clinical value of three-dimensional visualization (3DV) and 3D printing (3DP) technologies for ERCP in patients with HCC. The clinical data of 15 patients with HCC admitted for ERCP were analyzed retrospectively, including 9 males and 6 females. Thin-sliced data of computed tomography and magnetic resonance cholangiopancreatography (MRCP) were acquired and imported into Mimics Innovation Suite v17...
April 2018: Experimental and Therapeutic Medicine
Colin P McNally, Alexander Eng, Cecilia Noecker, William C Gagne-Maynard, Elhanan Borenstein
The abundance of both taxonomic groups and gene categories in microbiome samples can now be easily assayed via various sequencing technologies, and visualized using a variety of software tools. However, the assemblage of taxa in the microbiome and its gene content are clearly linked, and tools for visualizing the relationship between these two facets of microbiome composition and for facilitating exploratory analysis of their co-variation are lacking. Here we introduce BURRITO , a web tool for interactive visualization of microbiome multi-omic data with paired taxonomic and functional information...
2018: Frontiers in Microbiology
Achim Fieß, Alexander Karl-Georg Schuster, Stefan Nickels, Heike M Elflein, Andreas Schulz, Manfred E Beutel, Maria Blettner, Norbert Pfeiffer
PURPOSE: Low birth weight (BW) is linked to impaired organ development in childhood, including altered ocular morphological and functional development. The aim of this study was to evaluate whether low BW has long-term effects on visual acuity and refraction in adulthood. METHODS: The Gutenberg Health Study is a population-based, observational cohort study in Germany, including 15 010 participants aged between 35 and 74 years. These participants were divided into three different BW groups (low: <2500 g; normal: between 2500 and 4000 g; and high: >4000 g)...
March 15, 2018: British Journal of Ophthalmology
Sébastien Chanoine, Margaux Sanchez, Isabelle Pin, Sofia Temam, Nicole Le Moual, Agnès Fournier, Christophe Pison, Jean Bousquet, Pierrick Bedouch, Marie-Christine Boutron-Ruault, Raphaëlle Varraso, Valérie Siroux
Multi-medication related to multimorbidity is common in the elderly with asthma. We aimed at comprehensively characterizing medications used by elderly women, and assessing how multi-medication impacts on asthma prognosis.We performed network-based analyses on drug administrative databases to visualize the prevalence of drug classes and their interconnections among 17,458 elderly women from the Asthma-E3N study, including 4,328 women with asthma. Asthma groups sharing similar medication profiles were identified by clustering method relying on all medications and were studied in association with adverse asthma events (uncontrolled asthma, attacks/exacerbations, and poor asthma-related quality of life)...
March 15, 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
C Liam Dwyer, Maximillian Soong, Alice Hunter, Jesse Dashe, Eric Tolo, N George Kasparyan
PURPOSE: We investigated whether written guidelines for surgeons and educational handouts for patients regarding safe and effective opioid use after hand surgery could reduce prescription sizes while achieving high patient satisfaction and a low refill rate. METHODS: All patients undergoing isolated carpal tunnel release or distal radius volar locked plating in a hand surgery group practice during a 6-month period were prospectively enrolled. Surgeons prescribed analgesics at their own discretion based on written guidelines...
March 12, 2018: Journal of Hand Surgery
Magdalena Kolasa, Joanna Solich, Agata Faron-Górecka, Dariusz Żurawek, Paulina Pabian, Sylwia Łukasiewicz, Maciej Kuśmider, Kinga Szafran-Pilch, Marta Szlachta, Marta Dziedzicka-Wasylewska
Recently, it has been shown that serotonin 5-HT1A receptor interacts with dopamine D2 receptor in vitro. However, the existence of 5-HT1A -D2 heteromers in native tissue remains unexplored. In the present study, we investigated 5-HT1A -D2 receptor heteromerization in mice treated acutely or chronically with paroxetine (10 mg/kg) or risperidone (0.05 mg/kg). Receptor heteromerization was visualized and quantified in the mouse brain by in situ proximity ligation assay (PLA). Additionally, we aimed to determine the cellular localization of 5-HT1A -D2 receptor heteromers in mouse adult primary neuronal cells by immunofluorescent staining with markers for astrocytes (GFAP) and neurons (NeuN and MAP2)...
March 12, 2018: Neuroscience
Ayesha Sohail, O A Bég, Zhiwu Li, Sebahattin Celik
The mathematics of imaging is a growing field of research and is evolving rapidly parallel to evolution in the field of imaging. Imaging, which is a sub-field of biomedical engineering, considers novel approaches to visualize biological tissues with the general goal of improving health. "Medical imaging research provides improved diagnostic tools in clinical settings and supports the development of drugs and other therapies. The data acquisition and diagnostic interpretation with minimum error are the important technical aspects of medical imaging...
March 12, 2018: Progress in Biophysics and Molecular Biology
Qihong Zou, Shuqin Zhou, Jing Xu, Zihui Su, Yuezhen Li, Yundong Ma, Hongqiang Sun, Changwei W Wu, Jia-Hong Gao
Rapid eye movement (REM) sleep has been frequently associated with dreaming. However, mounting evidence obtained from behavioral, pharmacological, and brain imaging studies suggests that REM sleep is not indicative of the dream report and may originate from diverse neural substrates in brain functionality. The aim of the current study was to investigate the functional systems associated with inter-individual differences in dream recall and REM sleep through assessments of the resting-state functional connectivity...
March 12, 2018: NeuroImage
Eli Gibson, Wenqi Li, Carole Sudre, Lucas Fidon, Dzhoshkun I Shakir, Guotai Wang, Zach Eaton-Rosen, Robert Gray, Tom Doel, Yipeng Hu, Tom Whyntie, Parashkev Nachev, Marc Modat, Dean C Barratt, Sébastien Ourselin, M Jorge Cardoso, Tom Vercauteren
BACKGROUND AND OBJECTIVES: Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this domain of application requires substantial implementation effort. Consequently, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups...
May 2018: Computer Methods and Programs in Biomedicine
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