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https://www.readbyqxmd.com/read/28637310/the-metagenomic-data-life-cycle-standards-and-best-practices
#1
Petra Ten Hoopen, Robert D Finn, Lars Ailo Bongo, Erwan Corre, Bruno Fosso, Folker Meyer, Alex Mitchell, Eric Pelletier, Graziano Pesole, Monica Santamaria, Nils Peder Willassen, Guy Cochrane
Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing.Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28636943/opa1-isoforms-in-the-hierarchical-organization-of-mitochondrial-functions
#2
Valentina Del Dotto, Prashant Mishra, Sara Vidoni, Mario Fogazza, Alessandra Maresca, Leonardo Caporali, J Michael McCaffery, Martina Cappelletti, Enrico Baruffini, Guy Lenaers, David Chan, Michela Rugolo, Valerio Carelli, Claudia Zanna
OPA1 is a GTPase that controls mitochondrial fusion, cristae integrity, and mtDNA maintenance. In humans, eight isoforms are expressed as combinations of long and short forms, but it is unclear whether OPA1 functions are associated with specific isoforms and/or domains. To address this, we expressed each of the eight isoforms or different constructs of isoform 1 in Opa1(-/-) MEFs. We observed that any isoform could restore cristae structure, mtDNA abundance, and energetic efficiency independently of mitochondrial network morphology...
June 20, 2017: Cell Reports
https://www.readbyqxmd.com/read/28636923/mechanosensitive-adhesion-explains-stepping-motility-in-amoeboid-cells
#3
Calina A Copos, Sam Walcott, Juan C Del Álamo, Effie Bastounis, Alex Mogilner, Robert D Guy
Cells employing amoeboid motility exhibit repetitive cycles of rapid expansion and contraction and apply coordinated traction forces to their environment. Although aspects of this process are well studied, it is unclear how the cell controls the coordination of cell length changes with adhesion to the surface. Here, we develop a simple model to mechanistically explain the emergence of periodic changes in length and spatiotemporal dynamics of traction forces measured in chemotaxing unicellular amoeba, Dictyostelium discoideum...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636892/topical-bioavailability-of-diclofenac-from-locally-acting-dermatological-formulations
#4
S F Cordery, A Pensado, W S Chiu, M Z Shehab, A L Bunge, M B Delgado-Charro, R H Guy
Assessment of the bioavailability of topically applied drugs designed to act within or beneath the skin is a challenging objective. A number of different, but potentially complementary, techniques are under evaluation. The objective of this work was to evaluate in vitro skin penetration and stratum corneum tape-stripping in vivo as tools with which to measure topical diclofenac bioavailability from three approved and commercialized products (two gels and one solution). Drug uptake into, and its subsequent clearance from, the stratum corneum of human volunteers was used to estimate the input rate of diclofenac into the viable skin layers...
June 18, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28636521/a-proposed-role-for-sepsis-in-the-pathogenesis-of-myocardial-calcification
#5
Guy Bower, Hutan Ashrafian, Simone Cappelletti, Liang Mei Lee, Leanne Harling, Costantino Ciallella, Mariarosaria Aromatario, Thanos Athanasiou
No abstract text is available yet for this article.
March 30, 2017: Acta Cardiologica
https://www.readbyqxmd.com/read/28636472/benign-tumors-of-the-parotid-gland-a-retrospective-study-of-339-patients
#6
Marie Quiriny, Cécile Dekeyser, Michel Moreau, Antoine Digonnet, Esther Willemse, Laurent Vanbel, Guy Andry
AIM: Among 339 patients operated for benign tumor of the parotid gland: the recurrences and the postoperative complications rates were compared WITH those published in literature. MATERIALS AND METHODS: About 339 patients operated: 274 primarily and 65 for recurrence or residual tumor. VARIABLES: sex, age, surgical techniques, pre- or postoperative radiotherapy, histology, size and localization of the tumors, disease free intervals, recurrences and postoperative complications...
February 10, 2017: Acta Chirurgica Belgica
https://www.readbyqxmd.com/read/28634789/detection-and-grading-of-prostate-cancer-using-temporal-enhanced-ultrasound-combining-deep-neural-networks-and-tissue-mimicking-simulations
#7
Shekoofeh Azizi, Sharareh Bayat, Pingkun Yan, Amir Tahmasebi, Guy Nir, Jin Tae Kwak, Sheng Xu, Storey Wilson, Kenneth A Iczkowski, M Scott Lucia, Larry Goldenberg, Septimiu E Salcudean, Peter A Pinto, Bradford Wood, Purang Abolmaesumi, Parvin Mousavi
PURPOSE  : Temporal Enhanced Ultrasound (TeUS) has been proposed as a new paradigm for tissue characterization based on a sequence of ultrasound radio frequency (RF) data. We previously used TeUS to successfully address the problem of prostate cancer detection in the fusion biopsies. METHODS  : In this paper, we use TeUS to address the problem of grading prostate cancer in a clinical study of 197 biopsy cores from 132 patients. Our method involves capturing high-level latent features of TeUS with a deep learning approach followed by distribution learning to cluster aggressive cancer in a biopsy core...
June 20, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28634194/zbp1-dai-ubiquitination-and-sensing-of-influenza-vrnps-activate-programmed-cell-death
#8
Sannula Kesavardhana, Teneema Kuriakose, Clifford S Guy, Parimal Samir, R K Subbarao Malireddi, Ashutosh Mishra, Thirumala-Devi Kanneganti
Innate sensing of influenza virus infection induces activation of programmed cell death pathways. We have recently identified Z-DNA-binding protein 1 (ZBP1) as an innate sensor of influenza A virus (IAV). ZBP1-mediated IAV sensing is critical for triggering programmed cell death in the infected lungs. Surprisingly, little is known about the mechanisms regulating ZBP1 activation to induce programmed cell death. Here, we report that the sensing of IAV RNA by retinoic acid inducible gene I (RIG-I) initiates ZBP1-mediated cell death via the RIG-I-MAVS-IFN-β signaling axis...
June 20, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28634095/comparative-effectiveness-and-safety-of-drug-prophylaxis-for-prevention-of-venous-thromboembolism-after-total-knee-arthroplasty
#9
Guy Cafri, Elizabeth W Paxton, Yuexin Chen, Craig T Cheetham, Michael K Gould, Janet Sluggett, Stefano A Bini, Monti Khatod
BACKGROUND: Rates of venous thromboembolism in contemporary studies of primary total knee arthroplasty (TKA) have been reported to be as high as 3.5%. Although drug prophylaxis is effective, the best option among these regimens is not well established. The purpose of this study was to evaluate the comparative effectiveness and safety of aspirin, low-molecular-weight heparin, synthetic pentasaccharide factor Xa inhibitors, and vitamin K antagonist. METHODS: Data were from a US total joint replacement registry, with 30,499 patients receiving unilateral TKA from May 16, 2006, to December 31, 2013...
May 31, 2017: Journal of Arthroplasty
https://www.readbyqxmd.com/read/28633195/survival-of-patients-with-cancer-starting-chronic-dialysis-data-from-kidney-and-cancer-registries-in-lower-normandy
#10
Clémence Béchade, Olivier Dejardin, Simona Bara, Véronique Bouvier, Anne-Valérie Guizard, Rémy De Mil, Xavier Troussard, Guy Launoy, Thierry Lobbedez
AIM: Cancer and chronic kidney disease are known to be associated. The way in which a history of cancer can influence outcome in dialysis is not well described. This work aimed to evaluate survival of cancer patients starting chronic dialysis after their diagnosis of cancer. METHODS: We merged data from cancer registries and a dialysis registry, and explored patients' charts. RESULTS: Between January 2001 and December 2008, 74 patients with incident cancer in the two-counties-study-area (Calvados and Manche) started chronic dialysis after their diagnosis of cancer...
June 20, 2017: Nephrology
https://www.readbyqxmd.com/read/28632775/unique-cellular-interactions-between-pancreatic-cancer-cells-and-the-omentum
#11
Valerya Feygenzon, Shelly Loewenstein, Nir Lubezky, Metsada Pasmanic-Chor, Osnat Sher, Joseph M Klausner, Guy Lahat
Pancreatic cancer is a common cause of cancer-related mortality. Omental spread is frequent and usually represents an ominous event, leading to patient death. Omental metastasis has been studied in ovarian cancer, but data on its role in pancreatic cancer are relatively scarce and the molecular biology of this process has yet to be explored. We prepared tissue explants from human omental fat, and used conditioned medium from the explants for various in vitro and in vivo experiments designed to evaluate pancreatic cancer development, growth, and survival...
2017: PloS One
https://www.readbyqxmd.com/read/28632774/short-term-eeg-dynamics-and-neural-generators-evoked-by-navigational-images
#12
Axelle Leroy, Carlos Cevallos, Ana-Maria Cebolla, Stéphanie Caharel, Bernard Dan, Guy Cheron
The ecological environment offered by virtual reality is primarily supported by visual information. The different image contents and their rhythmic presentation imply specific bottom-up and top-down processing. Because these processes already occur during passive observation we studied the brain responses evoked by the presentation of specific 3D virtual tunnels with respect to 2D checkerboard. For this, we characterized electroencephalograhy dynamics (EEG), the evoked potentials and related neural generators involved in various visual paradigms...
2017: PloS One
https://www.readbyqxmd.com/read/28631733/plastid-thylakoid-architecture-optimizes-photosynthesis-in-diatoms
#13
Serena Flori, Pierre-Henri Jouneau, Benjamin Bailleul, Benoit Gallet, Leandro F Estrozi, Christine Moriscot, Olivier Bastien, Simona Eicke, Alexander Schober, Carolina Río Bártulos, Eric Maréchal, Peter G Kroth, Dimitris Petroutsos, Samuel Zeeman, Cécile Breyton, Guy Schoehn, Denis Falconet, Giovanni Finazzi
Photosynthesis is a unique process that allows independent colonization of the land by plants and of the oceans by phytoplankton. Although the photosynthesis process is well understood in plants, we are still unlocking the mechanisms evolved by phytoplankton to achieve extremely efficient photosynthesis. Here, we combine biochemical, structural and in vivo physiological studies to unravel the structure of the plastid in diatoms, prominent marine eukaryotes. Biochemical and immunolocalization analyses reveal segregation of photosynthetic complexes in the loosely stacked thylakoid membranes typical of diatoms...
June 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28631719/erratum-changes-in-initial-copd-treatment-choice-over-time-and-factors-influencing-prescribing-decisions-in-uk-primary-care-a-real-world-study
#14
Kevin Gruffydd-Jones, Guy Brusselle, Rupert Jones, Marc Miravitlles, Michael Baldwin, Rebecca Stewart, Anna Rigazio, Emily Davis, Dorothy L Keininger, David Price
This corrects the article DOI: 10.1038/npjpcrm.2016.2.
June 8, 2017: NPJ Primary Care Respiratory Medicine
https://www.readbyqxmd.com/read/28631598/in-vitro-and-in-vivo-evidence-of-a-potential-a-h1n1-pdm09-antigenic-drift-mediated-by-escape-mutations-in-the-haemagglutinin-sa-antigenic-site
#15
Miguel Retamal, Yacine Abed, Chantal Rhéaume, Mariana Baz, Guy Boivin
Influenza A(H1N1)pdm09 virus continues to circulate worldwide without evidence of significant antigenic drift between 2009 and 2016. By using escape mutants, we previously identified six haemagglutinin (HA) changes (T80R, G143E, G158E, N159D, K166E and A198E) that were located within antigenic sites. Combinations of these mutations were introduced into the A(H1N1)pdm09 HA plasmid by mutagenesis. Reassortant 6 : 2 viruses containing both the HA and NA genes of the A(H1N1)pdm09 and the six internal gene segments of A/PR/8/34 were rescued by reverse genetics...
June 20, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28631497/cost-effectiveness-of-blinatumomab-versus-salvage-chemotherapy-in-relapsed-or-refractory-philadelphia-chromosome-negative-b-precursor-acute-lymphoblastic-leukemia-from-a-us-payer-perspective
#16
Thomas E Delea, Jordan Amdahl, Diana Boyko, May Hagiwara, Zachary F Zimmerman, Janet L Franklin, Ze Cong, Guy Hechmati, Anthony Stein
Objective To evaluate the cost-effectiveness of blinatumomab (Blincyto) versus standard of care (SOC) chemotherapy in adults with relapsed or refractory (R/R) Philadelphia-chromosome-negative (Ph-) B-precursor acute lymphoblastic leukemia (ALL) based on the results of the phase 3 TOWER study from a US healthcare payer perspective. Methods The Blincyto Global Economic Model (B-GEM), a partitioned survival model, was used to estimate the incremental cost-effectiveness ratio (ICER) of blinatumomab versus SOC. Response rates, event free survival (EFS), overall survival (OS), numbers of cycles of blinatumomab and SOC, and transplant rates were estimated from TOWER...
June 20, 2017: Journal of Medical Economics
https://www.readbyqxmd.com/read/28631117/multi-criteria-decision-analysis-to-model-ixodes-ricinus-habitat-suitability
#17
Raphaël Rousseau, Guy McGrath, Barry J McMahon, Sophie O Vanwambeke
Tick-borne diseases present a major threat to both human and livestock health throughout Europe. The risk of infection is directly related to the presence of its vector. Thereby it is important to know their distribution, which is strongly associated with environmental factors: the presence and availability of a suitable habitat, of a suitable climate and of hosts. The present study models the habitat suitability for Ixodes ricinus in Ireland, where data on tick distribution are scarce. Tick habitat suitability was estimated at a coarse scale (10 km) with a multi-criteria decision analysis (MCDA) method according to four different scenarios (depending on the variables used and on the weights granted to each of them)...
June 19, 2017: EcoHealth
https://www.readbyqxmd.com/read/28630998/annals-consult-guys-syncope-how-do-i-figure-this-one-out
#18
Geno J Merli, Howard H Weitz
No abstract text is available yet for this article.
June 20, 2017: Annals of Internal Medicine
https://www.readbyqxmd.com/read/28630937/high-precision-neural-decoding-of-complex-movement-trajectories-using-recursive-bayesian-estimation-with-dynamic-movement-primitives
#19
Guy Hotson, Ryan J Smith, Adam G Rouse, Marc H Schieber, Nitish V Thakor, Brock A Wester
Brain-machine interfaces (BMIs) are a rapidly progressing technology with the potential to restore function to victims of severe paralysis via neural control of robotic systems. Great strides have been made in directly mapping a user's cortical activity to control of the individual degrees of freedom of robotic end-effectors. While BMIs have yet to achieve the level of reliability desired for widespread clinical use, environmental sensors (e.g. RGB-D cameras for object detection) and prior knowledge of common movement trajectories hold great potential for improving system performance...
July 2016: IEEE Robotics and Automation Letters
https://www.readbyqxmd.com/read/28630736/abnormal-femoral-antetorsion-a-subtrochanteric-deformity
#20
Guy Waisbrod, Florian Schiebel, Martin Beck
Femoral rotational malalignment is associated with pain and functional disability and may be a contributing factor to hip impingement as well as to instability. In general, the deformity can be addressed surgically by rotational osteotomy. However, the anatomic location of the deformity is debated. The goal of the present study was to narrow down the anatomic site of deformity using the lesser trochanter (LT) as an additional landmark. One hundred and eight patients underwent computer tomography (CT)-based rotational analysis of their lower extremities...
July 2017: Journal of Hip Preservation Surgery
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