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https://www.readbyqxmd.com/read/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#1
Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R J Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence)...
2017: PloS One
https://www.readbyqxmd.com/read/28851437/development-and-use-of-a-content-search-strategy-for-retrieving-studies-on-patients-views-and-preferences
#2
Anna Selva, Ivan Solà, Yuan Zhang, Hector Pardo-Hernandez, R Brian Haynes, Laura Martínez García, Tamara Navarro, Holger Schünemann, Pablo Alonso-Coello
BACKGROUND: Identifying scientific literature addressing patients' views and preferences is complex due to the wide range of studies that can be informative and the poor indexing of this evidence. Given the lack of guidance we developed a search strategy to retrieve this type of evidence. METHODS: We assembled an initial list of terms from several sources, including the revision of the terms and indexing of topic-related studies and, methods research literature, and other relevant projects and systematic reviews...
August 30, 2017: Health and Quality of Life Outcomes
https://www.readbyqxmd.com/read/28802455/from-control-to-causation-validating-a-complex-systems-model-of-running-related-injury-development-and-prevention
#3
A Hulme, P M Salmon, R O Nielsen, G J M Read, C F Finch
INTRODUCTION: There is a need for an ecological and complex systems approach for better understanding the development and prevention of running-related injury (RRI). In a previous article, we proposed a prototype model of the Australian recreational distance running system which was based on the Systems Theoretic Accident Mapping and Processes (STAMP) method. That model included the influence of political, organisational, managerial, and sociocultural determinants alongside individual-level factors in relation to RRI development...
November 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/28728059/iterative-variational-mode-decomposition-based-automated-detection-of-glaucoma-using-fundus-images
#4
Shishir Maheshwari, Ram Bilas Pachori, Vivek Kanhangad, Sulatha V Bhandary, U Rajendra Acharya
Glaucoma is one of the leading causes of permanent vision loss. It is an ocular disorder caused by increased fluid pressure within the eye. The clinical methods available for the diagnosis of glaucoma require skilled supervision. They are manual, time consuming, and out of reach of common people. Hence, there is a need for an automated glaucoma diagnosis system for mass screening. In this paper, we present a novel method for an automated diagnosis of glaucoma using digital fundus images. Variational mode decomposition (VMD) method is used in an iterative manner for image decomposition...
September 1, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28653181/laparoscopic-sleeve-gastrectomy-for-the-management-of-type-1-diabetes-mellitus
#5
Salman Al Sabah, Eliana Al Haddad, Talal H Muzaffar, Ahmad Almulla
BACKGROUND: The prevalence of obesity is on a continuous rise worldwide, with major studies clearly correlating obesity with the development of chronic metabolic disorders including type 2 diabetes. Bariatric surgery has proven to be beneficial in the management of this condition; however, a limited number of studies exist on its effect on type 1 diabetes. OBJECTIVE: The objective of this study is to evaluate the outcome of laparoscopic sleeve gastrectomy for the management of patients with type 1 diabetes (DM1)...
June 26, 2017: Obesity Surgery
https://www.readbyqxmd.com/read/28651096/predicting-actions-from-subtle-preparatory-movements
#6
Maryam Vaziri-Pashkam, Sarah Cormiea, Ken Nakayama
To study how people anticipate others' actions, we designed a competitive reaching task. Subjects faced each other separated by a Plexiglas screen and their finger movements in 3D space were recorded with sensors. The first subject (Attacker) was instructed to touch one of two horizontally arranged targets on the screen. The other subject (Blocker) touched the same target as quickly as possible. Average finger reaction times (fRTs) were fast, much faster than reactions to a dot moving on the screen in the same manner as the Attacker's finger...
November 2017: Cognition
https://www.readbyqxmd.com/read/28637243/nanopore-sequencing-data-analysis-state-of-the-art-applications-and-challenges
#7
Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data...
June 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28583024/reach-out-churches-a-community-based-participatory-research-pilot-trial-to-assess-the-feasibility-of-a-mobile-health-technology-intervention-to-reduce-blood-pressure-among-african-americans
#8
Lesli E Skolarus, Joan Cowdery, Mackenzie Dome, Sarah Bailey, Jonggyu Baek, James Brian Byrd, Sarah E Hartley, Staci C Valley, Sima Saberi, Natalie C Wheeler, Mollie McDermott, Rebecca Hughes, Krithika Shanmugasundaram, Lewis B Morgenstern, Devin L Brown
Innovative strategies are needed to reduce the hypertension epidemic among African Americans. Reach Out was a faith-collaborative, mobile health, randomized, pilot intervention trial of four mobile health components to reduce high blood pressure (BP) compared to usual care. It was designed and tested within a community-based participatory research framework among African Americans recruited and randomized from churches in Flint, Michigan. The purpose of this pilot study was to assess the feasibility of the Reach Out processes...
June 1, 2017: Health Promotion Practice
https://www.readbyqxmd.com/read/28569436/sociodemographic-physical-mental-and-social-factors-in-the-cessation-of-breastfeeding-before-6-months-a-systematic-review
#9
REVIEW
Elisabeth Mangrio, Karin Persson, Ann-Cathrine Bramhagen
BACKGROUND: The World Health Organization recommends exclusive breastfeeding as the main source of nutrition for infants during their first 6 months of life. However, despite this well-known recommendation, not all mothers breastfeed, whether partly or fully, during this time. OBJECTIVE: The aim of this systematic literature review was to compile evidence regarding sociodemographic, physical, mental and social factors that influence breastfeeding mothers to stop breastfeeding before the infant reaches 6 months...
June 1, 2017: Scandinavian Journal of Caring Sciences
https://www.readbyqxmd.com/read/28542006/an-efficient-affordable-optically-stimulated-luminescent-osl-annealer
#10
Sara A Abraham, Samuel J Frank, Kimberlee J Kearfott
Optically stimulated luminescent (OSL) dosimeters are devices used for measuring doses of ionizing radiation. Signal is stored within an OSL material so that when stimulated with light, light of a specific wavelength is emitted in proportion to the integrated ionizing radiation dose. Each interrogation of the material results in the loss of a small fraction of signal, thus allowing multiple interrogations leading to more accurate measurements of dose. In order to reuse a dosimeter, the residual signals from prior doses must be taken into account and subtracted from current readings, adding uncertainty to any future measurements...
July 2017: Health Physics
https://www.readbyqxmd.com/read/28521708/implementation-and-evaluation-of-a-technology-system-to-improve-safety-of-the-oncohematology-medication-practices
#11
Maria Teresa Aznar Saliente, Mauricio Martínez Ramírez, Maria Amparo Talens Bolós, Paola Herraiz Robles, Nuria Bujadón Querejeta, Maria Dolores Camacho Romera, L P Martínez, Manuel Bonete Sánchez, Borja Marcos Ribes, Maria Teresa Martínez Lazcano, Francisco Martínez Granados
OBJECTIVE The objective of the study was to describe the process of implementing a technology system to improve safety and quality in all processes involved in the treatment with parenteral antineoplastic agents within an interdisciplinary team and to analyze the errors detected and avoided thanks to this system at the different stages of the process. MATERIALS AND METHODS Observational and retrospective study where the implementation of an expert technology system in all phases of the therapeutic process is described: prescription, validation, preparation and administration of drugs, in which errors found in the different phases are analysed...
May 18, 2017: Current Drug Safety
https://www.readbyqxmd.com/read/28458053/overexpression-of-ebola-virus-envelope-gp1-protein
#12
Zhongcheng Zou, John Misasi, Nancy Sullivan, Peter D Sun
Ebola virus uses its envelope GP1 and GP2 for viral attachment and entry into host cells. Due to technical difficulty expressing full-length envelope, many structural and functional studies of Ebola envelope protein have been carried out primarily using GP1 lacking its mucin-like domain. As a result, the viral invasion mechanisms involving the mucin-like domain are not fully understood. To elucidate the role of the mucin-like domain of GP1 in Ebola-host attachment and infection and to facilitate vaccine development, we constructed a GP1 expression vector containing the entire attachment region (1-496)...
July 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28437940/rydberg-atom-based-radio-frequency-electrometry-using-frequency-modulation-spectroscopy-in-room-temperature-vapor-cells
#13
Santosh Kumar, Haoquan Fan, Harald Kübler, Akbar J Jahangiri, James P Shaffer
Rydberg atom-based electrometry enables traceable electric field measurements with high sensitivity over a large frequency range, from gigahertz to terahertz. Such measurements are particularly useful for the calibration of radio frequency and terahertz devices, as well as other applications like near field imaging of electric fields. We utilize frequency modulated spectroscopy with active control of residual amplitude modulation to improve the signal to noise ratio of the optical readout of Rydberg atom-based radio frequency electrometry...
April 17, 2017: Optics Express
https://www.readbyqxmd.com/read/28419062/single-center-study-investigating-foreign-language-acquisition-at-school-in-children-adolescents-and-young-adults-with-uni-or-bilateral-cochlear-implants-in-the-swiss-german-population
#14
Renske Beeres-Scheenstra, Claudia Ohnsorg, Claudia Candreia, Sybille Heinzmann, Susana Castellanos, Nicola De Min, Thomas E Linder
OBJECTIVE: To evaluate foreign language acquisition at school in cochlear implant patients. STUDY DESIGN: Cohort study. SETTING: CI center. PATIENTS: Forty three cochlear implants (CI) patients (10-18 yr) were evaluated. CI nonusers and patients with CI-explantation, incomplete datasets, mental retardation, or concomitant medical disorders were excluded. INTERVENTION(S): Additional data (type of schooling, foreign language learning, and bilingualism) were obtained with questionnaires...
July 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28390838/super-resolution-microscopy-approaches-to-nuclear-nanostructure-imaging
#15
Christoph Cremer, Aleksander Szczurek, Florian Schock, Amine Gourram, Udo Birk
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca...
July 1, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28249518/development-of-x-ray-ccd-camera-based-x-ray-micro-ct-system
#16
Partha S Sarkar, N K Ray, Manoj K Pal, Ravi Baribaddala, Ashish Agrawal, Y Kashyap, A Sinha, S C Gadkari
Availability of microfocus X-ray sources and high resolution X-ray area detectors has made it possible for high resolution microtomography studies to be performed outside the purview of synchrotron. In this paper, we present the work towards the use of an external shutter on a high resolution microtomography system using X-ray CCD camera as a detector. During micro computed tomography experiments, the X-ray source is continuously ON and owing to the readout mechanism of the CCD detector electronics, the detector registers photons reaching it during the read-out period too...
February 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28089896/characterization-and-expression-analysis-of-a-chitinase-gene-pmchi-4-from-black-tiger-shrimp-penaeus-monodon-under-pathogen-infection-and-ambient-ammonia-nitrogen-stress
#17
Kaimin Zhou, Falin Zhou, Jianhua Huang, Qibin Yang, Song Jiang, Lihua Qiu, Lishi Yang, Caiyan Zhu, Shigui Jiang
Chitinase is a multi-gene family, which play important physiological roles in crustaceans, involved in several biological processes, including digestion, molting and defense against viruses. In the present study, a chitinase-4 gene (PmChi-4) was cloned from Penaeus monodon by rapid amplification of cDNA ends (RACE). The full length of PmChi-4 cDNA was 2178 bp, including an 1815 bp open reading frame (ORF) which encoded 604 amino acid residues. The predicted PmChi-4 protein was 67.7 kDa and shared 61%-88% identity with the type of Chi-4s from other crustaceans...
March 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28078776/performance-of-the-forenseq-tm-dna-signature-prep-kit-on-highly-degraded-samples
#18
Paolo Fattorini, Carlo Previderé, Ilaria Carboni, Giorgio Marrubini, Solange Sorçaburu-Cigliero, Pierangela Grignani, Barbara Bertoglio, Paolo Vatta, Ugo Ricci
Next generation sequencing (NGS) is the emerging technology in forensic genomics laboratories. It offers higher resolution to address most problems of human identification, greater efficiency and potential ability to interrogate very challenging forensic casework samples. In this study, a trial set of DNA samples was artificially degraded by progressive aqueous hydrolysis, and analyzed together with the corresponding unmodified DNA sample and control sample 2800 M, to test the performance and reliability of the ForenSeq(TM) DNA Signature Prep kit using the MiSeq Sequencer (Illumina)...
April 2017: Electrophoresis
https://www.readbyqxmd.com/read/28048775/mo-fg-campus-tep1-04-pseudo-in-vivo-dose-verification-of-a-new-mono-isocentric-technique-for-the-treatment-of-multiple-brain-metastases
#19
E P Pappas, N Papanikolaou, G Kalaitzakis, T Boursianis, D Makris, V Lahanas, I Genitsarios, S Stathakis, L Watts, T Maris, E Pappas
PURPOSE: To validate dose calculation and delivery accuracy of a recently introduced mono-isocentric technique for the treatment of multiple brain metastases in a realistic clinical case. METHODS: Anonymized CT scans of a patient were used to model a hollow phantom that duplicates anatomy of the skull. A 3D printer was used to construct the phantom of a radiologically bone-equivalent material. The hollow phantom was subsequently filled with a polymer gel 3D dosimeter which also acted as a water-equivalent material...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/27986645/cardiopulmonary-resuscitation-training-by-avatars-a-qualitative-study-of-medical-students-experiences-using-a-multiplayer-virtual-world
#20
Johan Creutzfeldt, Leif Hedman, Li Felländer-Tsai
BACKGROUND: Emergency medical practices are often team efforts. Training for various tasks and collaborations may be carried out in virtual environments. Although promising results exist from studies of serious games, little is known about the subjective reactions of learners when using multiplayer virtual world (MVW) training in medicine. OBJECTIVE: The objective of this study was to reach a better understanding of the learners' reactions and experiences when using an MVW for team training of cardiopulmonary resuscitation (CPR)...
December 16, 2016: JMIR Serious Games
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