keyword
MENU ▼
Read by QxMD icon Read
search

Parallel processing

keyword
https://www.readbyqxmd.com/read/27933386/endoscopic-submucosal-dissection-specimens-in-early-colorectal-cancer-lateral-margins-macroscopic-techniques-and-possible-pitfalls
#1
Alicia Dessain, Christophe Snauwaert, Pamela Baldin, Pierre Deprez, Louis Libbrecht, Hubert Piessevaux, Anne Jouret-Mourin
Endoscopic submucosal dissection (ESD) allows en-bloc resection of superficial gastrointestinal tumors, providing specimens on which lateral margin analysis can be performed reliably. Positive lateral margins have been linked to higher rates of recurrence/residual tumor. There are no guidelines for macroscopic processing of lateral margins. Currently, most institutions use parallel lateral sections, which are difficult to interpret. We use perpendicular lateral sections, hypothesizing that it decreases potential artifactually positive lateral margins...
December 8, 2016: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/27932907/optimized-r-functions-for-analysis-of-ecological-community-data-using-the-r-virtual-laboratory-rvlab
#2
Constantinos Varsos, Theodore Patkos, Anastasis Oulas, Christina Pavloudi, Alexandros Gougousis, Umer Zeeshan Ijaz, Irene Filiopoulou, Nikolaos Pattakos, Edward Vanden Berghe, Antonio Fernández-Guerra, Sarah Faulwetter, Eva Chatzinikolaou, Evangelos Pafilis, Chryssoula Bekiari, Martin Doerr, Christos Arvanitidis
BACKGROUND: Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27932681/acute-intermittent-hypoxia-in-rats-activates-muscle-proteolytic-pathways-through-a-glucocorticoid-dependent-mechanism
#3
Franciele Przygodda, Leandro Henrique Manfredi, Juliano Machado, Dawit A P Gonçalves, Neusa Maria Zanon, Leni G H Bonagamba, Benedito H Machado, Isis do Carmo Kettelhut, Luiz C C Navegantes
Although it is well known that chronic hypoxia induces muscle wasting, the effects of intermit-tent hypoxia on skeletal muscle protein metabolism remains unclear. We hypothesized that acute intermittent hypoxia (AIH), a challenge that activates the hypothalamic-pituitary-adrenal axis, would alter muscle protein homeostasis through a glucocorticoid-dependent mechanism. Three-week-old rats were submitted to adrenalectomy (ADX) and exposed to 8 h of AIH (6% O2 for 40s at 9 min intervals). Animals were sacrificed and the soleus and extensor digitorum longus (EDL) muscles were harvested and incubated in vitro for measurements of protein turn-over...
December 8, 2016: Journal of Applied Physiology
https://www.readbyqxmd.com/read/27932271/deactivation-of-left-ventricular-assist-devices-differing-perspectives-of-cardiology-and-hospice-palliative-medicine-clinicians
#4
Colleen K McIlvennan, Sara E Wordingham, Larry A Allen, Daniel D Matlock, Jacqueline Jones, Shannon M Dunlay, Keith M Swetz
BACKGROUND: Beliefs around deactivation of a left ventricular assist device (LVAD) vary substantially between clinicians, institutions, and patients. Therefore, we sought to understand perspectives regarding LVAD deactivation among cardiology and hospice/palliative medicine (HPM) clinicians. METHODS AND RESULTS: We administered a 41-item survey via electronic mail to members of 3 cardiology and 1 HPM professional societies. A convergent parallel mixed methods design was used...
December 5, 2016: Journal of Cardiac Failure
https://www.readbyqxmd.com/read/27931250/tracing-the-origin-of-disseminated-tumor-cells-in-breast-cancer-using-single-cell-sequencing
#5
Jonas Demeulemeester, Parveen Kumar, Elen K Møller, Silje Nord, David C Wedge, April Peterson, Randi R Mathiesen, Renathe Fjelldal, Masoud Zamani Esteki, Koen Theunis, Elia Fernandez Gallardo, A Jason Grundstad, Elin Borgen, Lars O Baumbusch, Anne-Lise Børresen-Dale, Kevin P White, Vessela N Kristensen, Peter Van Loo, Thierry Voet, Bjørn Naume
BACKGROUND: Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate. Here, we apply single-cell sequencing to identify and trace the origin of DTCs in breast cancer. RESULTS: We sequence the genomes of 63 single cells isolated from six non-metastatic breast cancer patients...
December 9, 2016: Genome Biology
https://www.readbyqxmd.com/read/27930672/brain-connectivity-variation-topography-associated-with-working-memory
#6
Xiaofei Ma, Xiaolin Huang, Yun Ge, Yueming Hu, Wei Chen, Aili Liu, Hongxing Liu, Ying Chen, Bin Li, Xinbao Ning
Brain connectivity analysis plays an essential role in the research of working memory that involves complex coordination of various brain regions. In this research, we present a comprehensive view of trans-states brain connectivity variation based on continuous scalp EEG, extending beyond traditional stimuli-lock averaging or restriction to short time scales of hundreds of milliseconds after stimulus onset. The scalp EEG was collected under three conditions: quiet, memory, and control. The only difference between the memory and control conditions was that in the memory condition, subjects made an effort to retain information...
2016: PloS One
https://www.readbyqxmd.com/read/27929542/autophagy-and-epithelial-mesenchymal-transition-an-intricate-interplay-in-cancer
#7
REVIEW
Mila Gugnoni, Valentina Sancisi, Gloria Manzotti, Greta Gandolfi, Alessia Ciarrocchi
Autophagy and epithelial to mesenchymal transition (EMT) are major biological processes in cancer. Autophagy is a catabolic pathway that aids cancer cells to overcome intracellular or environmental stress, including nutrient deprivation, hypoxia and drugs effect. EMT is a complex transdifferentiation through which cancer cells acquire mesenchymal features, including motility and metastatic potential. Recent observations indicate that these two processes are linked in a complex relationship. On the one side, cells that underwent EMT require autophagy activation to survive during the metastatic spreading...
December 8, 2016: Cell Death & Disease
https://www.readbyqxmd.com/read/27929523/single-cell-barcoding-and-sequencing-using-droplet-microfluidics
#8
Rapolas Zilionis, Juozas Nainys, Adrian Veres, Virginia Savova, David Zemmour, Allon M Klein, Linas Mazutis
Single-cell RNA sequencing has recently emerged as a powerful tool for mapping cellular heterogeneity in diseased and healthy tissues, yet high-throughput methods are needed for capturing the unbiased diversity of cells. Droplet microfluidics is among the most promising candidates for capturing and processing thousands of individual cells for whole-transcriptome or genomic analysis in a massively parallel manner with minimal reagent use. We recently established a method called inDrops, which has the capability to index >15,000 cells in an hour...
January 2017: Nature Protocols
https://www.readbyqxmd.com/read/27929462/methods-to-examine-the-lymph-gland-and-hemocytes-in-drosophila-larvae
#9
Theresa A Reimels, Cathie M Pfleger
Many parallels exist between the Drosophila and mammalian hematopoietic systems, even though Drosophila lack the lymphoid lineage that characterize mammalian adaptive immunity. Drosophila and mammalian hematopoiesis occur in spatially and temporally distinct phases to produce several blood cell lineages. Both systems maintain reservoirs of blood cell progenitors with which to expand or replace mature lineages. The hematopoietic system allows Drosophila and mammals to respond to and to adapt to immune challenges...
November 28, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27928941/molecular-dynamics-analysis-of-the-structural-and-dynamic-properties-of-the-functionally-enhanced-hepta-variant-of-mouse-5-aminolevulinate-synthase
#10
Insung Na, Shelly DeForte, Bosko M Stojanovski, Gloria C Ferreira, Vladimir N Uversky
Heme biosynthesis, a complex, multistage, and tightly controlled process, starts with 5-aminolevulinate (ALA) production, which, in metazoa and certain bacteria, is a reaction catalyzed by 5-aminolevulinate synthase (ALAS), a pyridoxal 5'-phosphate (PLP)-dependent enzyme. Functional aberrations in ALAS are associated with several human diseases. ALAS can adopt open and closed conformations, with segmental rearrangements of a C-terminal, 16-amino acid loop and an α-helix regulating accessibility to the ALAS active site...
December 8, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27928514/a-microchip-for-high-throughput-axon-growth-drug-screening
#11
Hyun Soo Kim, Sehoon Jeong, Chiwan Koo, Arum Han, Jaewon Park
It has been recently known that not only the presence of inhibitory molecules associated with myelin but also the reduced growth capability of the axons limit mature central nervous system (CNS) axonal regeneration after injury. Conventional axon growth studies are typically conducted using multi-well cell culture plates that are very challenging to investigate localized effects of drugs and limited to low throughput. Unfortunately, there is currently no other in vitro tools that allow investigating localized axonal responses to biomolecules in high-throughput for screening potential drugs that might promote axonal growth...
July 2016: Micromachines
https://www.readbyqxmd.com/read/27927961/nasal-respiration-entrains-human-limbic-oscillations-and-modulates-cognitive-function
#12
Christina Zelano, Heidi Jiang, Guangyu Zhou, Nikita Arora, Stephan Schuele, Joshua Rosenow, Jay A Gottfried
: The need to breathe links the mammalian olfactory system inextricably to the respiratory rhythms that draw air through the nose. In rodents and other small animals, slow oscillations of local field potential activity are driven at the rate of breathing (∼2-12 Hz) in olfactory bulb and cortex, and faster oscillatory bursts are coupled to specific phases of the respiratory cycle. These dynamic rhythms are thought to regulate cortical excitability and coordinate network interactions, helping to shape olfactory coding, memory, and behavior...
December 7, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27927806/sleep-neurophysiological-dynamics-through-the-lens-of-multitaper-spectral-analysis
#13
REVIEW
Michael J Prerau, Ritchie E Brown, Matt T Bianchi, Jeffrey M Ellenbogen, Patrick L Purdon
During sleep, cortical and subcortical structures within the brain engage in highly structured oscillatory dynamics that can be observed in the electroencephalogram (EEG). The ability to accurately describe changes in sleep state from these oscillations has thus been a major goal of sleep medicine. While numerous studies over the past 50 years have shown sleep to be a continuous, multifocal, dynamic process, long-standing clinical practice categorizes sleep EEG into discrete stages through visual inspection of 30-s epochs...
January 2017: Physiology
https://www.readbyqxmd.com/read/27927200/tribbles-ortholog-nipi-3-and-bzip-transcription-factor-cebp-1-regulate-a-caenorhabditis-elegans-intestinal-immune-surveillance-pathway
#14
Deborah L McEwan, Rhonda L Feinbaum, Nicholas Stroustrup, Wilhelm Haas, Annie L Conery, Anthony Anselmo, Ruslan Sadreyev, Frederick M Ausubel
BACKGROUND: Many pathogens secrete toxins that target key host processes resulting in the activation of immune pathways. The secreted Pseudomonas aeruginosa toxin Exotoxin A (ToxA) disrupts intestinal protein synthesis, which triggers the induction of a subset of P. aeruginosa-response genes in the nematode Caenorhabditis elegans. RESULTS: We show here that one ToxA-induced C. elegans gene, the Tribbles pseudokinase ortholog nipi-3, is essential for host survival following exposure to P...
December 7, 2016: BMC Biology
https://www.readbyqxmd.com/read/27927177/initiator-trna-genes-template-the-3-cca-end-at-high-frequencies-in-bacteria
#15
David H Ardell, Ya-Ming Hou
BACKGROUND: While the CCA sequence at the mature 3' end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and Archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In Bacteria, tRNA genes template CCA sporadically. RESULTS: In order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database version 0...
December 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27927051/effect-of-berberine-on-ppar%C3%AE-no-signalling-pathway-in-vascular-smooth-muscle-cell-proliferation-induced-by-angiotensin-iv
#16
Hongmei Qiu, Yang Wu, Quanhua Wang, Changqing Liu, Lai Xue, Hong Wang, Qin Wu, Qingsong Jiang
CONTEXT: The available treatments for the abnormal proliferation of vascular smooth muscle cells (VSMCs) are still dismal. Berberine has been demonstrated to possess extensive medicine activity, yet relatively little is known about its effect on VSMCs proliferation. Many studies showed that PPARα and NO participated in the process of VSMCs proliferation. OBJECTIVE: To evaluate the effect of berberine and its possible influence on PPARα-NO pathway in angiotensin IV-stimulated VSMCs...
December 2017: Pharmaceutical Biology
https://www.readbyqxmd.com/read/27926917/implementation-of-syndromic-surveillance-systems-in-two-rural-villages-in-senegal
#17
Cédric Abat, Philippe Colson, Hervé Chaudet, Jean-Marc Rolain, Hubert Bassene, Aldiouma Diallo, Oleg Mediannikov, Florence Fenollar, Didier Raoult, Cheikh Sokhna
Infectious diseases still represent a major challenge for humanity. In this context, their surveillance is critical. From 2010 to 2016, two Point-Of-Care (POC) laboratories have been successfully implemented in the rural Saloum region of Senegal. In parallel, a homemade syndromic surveillance system called EPIMIC was implemented to monitor infectious diseases using data produced by the POC laboratory of the Timone hospital in Marseille, France. The aim of this study is to describe the steps necessary for implementing EPIMIC using data routinely produced by two POC laboratories (POC-L) established in rural Senegal villages...
December 7, 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27925748/role-of-the-%C3%AE-resonance-in-the-population-of-a-four-nucleon-state-in-the-56-fe%C3%A2-54-fe-reaction-at-relativistic-energies
#18
Zs Podolyák, C M Shand, N Lalović, J Gerl, D Rudolph, T Alexander, P Boutachkov, M L Cortés, M Górska, I Kojouharov, N Kurz, C Louchart, E Merchán, C Michelagnoli, R M Pérez-Vidal, S Pietri, D Ralet, M Reese, H Schaffner, Ch Stahl, H Weick, F Ameil, G de Angelis, T Arici, R Carroll, Zs Dombrádi, A Gadea, P Golubev, M Lettmann, C Lizarazo, D Mahboub, H Pai, Z Patel, N Pietralla, P H Regan, L G Sarmiento, O Wieland, E Wilson, B Birkenbach, B Bruyneel, I Burrows, L Charles, E Clément, F C L Crespi, D M Cullen, P Désesquelles, J Eberth, V González, T Habermann, L Harkness-Brennan, H Hess, D S Judson, A Jungclaus, W Korten, M Labiche, A Maj, D Mengoni, D R Napoli, A Pullia, B Quintana, G Rainovski, P Reiter, M D Salsac, E Sanchis, J J Valiente Dóbon
The ^{54}Fe nucleus was populated from a ^{56}Fe beam impinging on a Be target with an energy of E/A=500  MeV. The internal decay via γ-ray emission of the 10^{+} metastable state was observed. As the structure of this isomeric state has to involve at least four unpaired nucleons, it cannot be populated in a simple two-neutron removal reaction from the ^{56}Fe ground state. The isomeric state was produced in the low-momentum (-energy) tail of the parallel momentum (energy) distribution of ^{54}Fe, suggesting that it was populated via the decay of the Δ^{0} resonance into a proton...
November 25, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27925020/susceptibility-of-phytomonas-serpens-to-calpain-inhibitors-in-vitro-interference-on-the-proliferation-ultrastructure-cysteine-peptidase-expression-and-interaction-with-the-invertebrate-host
#19
Simone Santiago Carvalho de Oliveira, Diego de Souza Gonçalves, Aline Dos Santos Garcia-Gomes, Inês Correa Gonçalves, Sergio Henrique Seabra, Rubem Figueiredo Menna-Barreto, Angela Hampshire de Carvalho Santos Lopes, Claudia Masini D'Avila-Levy, André Luis Souza Dos Santos, Marta Helena Branquinha
A pleiotropic response to the calpain inhibitor MDL28170 was detected in the tomato parasite Phytomonas serpens. Ultrastructural studies revealed that MDL28170 caused mitochondrial swelling, shortening of flagellum and disruption of trans Golgi network. This effect was correlated to the inhibition in processing of cruzipain-like molecules, which presented an increase in expression paralleled by decreased proteolytic activity. Concomitantly, a calcium-dependent cysteine peptidase was detected in the parasite extract, the activity of which was repressed by pre-incubation of parasites with MDL28170...
December 1, 2016: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/27924861/size-specific-transfection-to-mammalian-cells-by-micropillar-array-electroporation
#20
Yingbo Zu, Shuyan Huang, Yang Lu, Xuan Liu, Shengnian Wang
Electroporation serves as a promising non-viral gene delivery approach, while its current configuration carries several drawbacks associated with high-voltage electrical pulses and heterogeneous treatment on individual cells. Here we developed a new micropillar array electroporation (MAE) platform to advance the electroporation-based delivery of DNA and RNA probes into mammalian cells. By introducing well-patterned micropillar array texture on the electrode surface, the number of pillars each cell faces varies with its plasma membrane surface area, despite their large population and random locations...
December 7, 2016: Scientific Reports
keyword
keyword
94192
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"