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https://www.readbyqxmd.com/read/28742346/molecular-dynamics-of-double-stranded-xylo-nucleic-acid-xylona
#1
Amutha Ramaswamy, Daryna Smyrnova, Mattheus Froeyen, Mohitosh Maiti, Piet Herdewijn, Arnout Ceulemans
Xylo-nucleic acid (XyloNA) is a synthetic analogue of ribo-nucleic acid (RNA), where the ribose sugar has been replaced by xylose. We present a Molecular Dynamics study of the conformational evolution of XyloNA double strand oligomers derived from A-RNA through the substitution of beta-ᴅ-ribofuranose by beta-ᴅ-xylofuranose and having lengths of 8, 16 and 29 base pairs, using a set of independent all-atom simulations performed at various time scales ranging from 55 to 100 ns, , with one long 500 ns simulation of the 29-mer...
July 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28740912/effect-of-variations-in-atelectasis-on-tumor-displacement-during-radiation-therapy-for-locally-advanced-lung-cancer
#2
Nathan Tennyson, Elisabeth Weiss, William Sleeman, Mihaela Rosu, Nuzhat Jan, Geoffrey D Hugo
PURPOSE: Atelectasis (AT), or collapsed lung, is frequently associated with central lung tumors. We investigated the variation of atelectasis volumes during radiation therapy and analyzed the effect of AT volume changes on the reproducibility of the primary tumor (PT) position. METHODS AND MATERIALS: Twelve patients with lung cancer who had AT and 10 patients without AT underwent repeated 4-dimensional fan beam computed tomography (CT) scans during radiation therapy per protocols that were approved by the institutional review board...
January 2017: Advances in Radiation Oncology
https://www.readbyqxmd.com/read/28739479/emergency-department-visits-after-lumbar-spine-surgery-are-associated-with-lower-hcahps-scores
#3
Jay M Levin, Robert D Winkelman, Gabriel A Smith, Joseph E Tanenbaum, Roy Xiao, Thomas E Mroz, Michael P Steinmetz
BACKGROUND: Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) surveys are used to assess the quality of the patient experience following an inpatient stay. HCAHPS scores are used to determine reimbursement for hospital systems and incentivize spine surgeons nationwide. There are conflicting data detailing whether early readmission or other post-discharge complications are associated with patient responses on the HCAHPS survey. Currently, the association between post-discharge ED visits and HCAHPS scores following lumbar spine surgery is unknown...
July 21, 2017: Spine Journal: Official Journal of the North American Spine Society
https://www.readbyqxmd.com/read/28738222/thinking-inside-the-box-spatial-frames-of-reference-for-drawing-in-williams-syndrome-and-typical-development
#4
Kerry D Hudson, Emily K Farran
BACKGROUND: Successfully completing a drawing relies on the ability to accurately impose and manipulate spatial frames of reference for the object that is being drawn and for the drawing space. Typically developing (TD) children use cues such as the page boundary as a frame of reference to guide the orientation of drawn lines. Individuals with Williams syndrome (WS) typically produce incohesive drawings; this is proposed to reflect a local processing bias. AIMS: Across two studies, we provide the first investigation of the effect of using a frame of reference when drawing simple lines and shapes in WS and TD groups (matched for non-verbal ability)...
July 21, 2017: Research in Developmental Disabilities
https://www.readbyqxmd.com/read/28733464/lineage-tracing-of-epithelial-cells-in-developing-teeth-reveals-two-strategies-for-building-signaling-centers
#5
Wei Du, Jimmy Kuang-Hsien Hu, Wen Du, Ophir D Klein
An important event in organogenesis is the formation of signaling centers, which are clusters of growth-factor secreting cells. In the case of tooth development, sequentially formed signaling centers known as the initiation knot (IK) and the enamel knot (EK) regulate morphogenesis. However, despite the importance of signaling centers, their origin, as well as the fate of the cells composing them, remain open questions. Here, using lineage tracing of distinct epithelial populations, we found that the EK of the mouse incisor is derived de novo from a group of SRY-box 2 (Sox2)-expressing cells in the posterior half of the tooth germ...
July 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28732065/direct-targets-of-pstat5-signalling-in-erythropoiesis
#6
Kevin R Gillinder, Hugh Tuckey, Charles C Bell, Graham W Magor, Stephen Huang, Melissa D Ilsley, Andrew C Perkins
Erythropoietin (EPO) acts through the dimeric erythropoietin receptor to stimulate proliferation, survival, differentiation and enucleation of erythroid progenitor cells. We undertook two complimentary approaches to find EPO-dependent pSTAT5 target genes in murine erythroid cells: RNA-seq of newly transcribed (4sU-labelled) RNA, and ChIP-seq for pSTAT5 30 minutes after EPO stimulation. We found 302 pSTAT5-occupied sites: ~15% of these reside in promoters while the rest reside within intronic enhancers or intergenic regions, some >100kb from the nearest TSS...
2017: PloS One
https://www.readbyqxmd.com/read/28732024/4-nitrophenylsulfonyl-piperazines-mitigate-radiation-damage-to-multiple-tissues
#7
Ewa D Micewicz, Kwanghee Kim, Keisuke S Iwamoto, Josephine A Ratikan, Genhong Cheng, Gayle M Boxx, Robert D Damoiseaux, Julian P Whitelegge, Piotr Ruchala, Christine Nguyen, Prabhat Purbey, Joseph Loo, Gang Deng, Michael E Jung, James W Sayre, Andrew J Norris, Dörthe Schaue, William H McBride
Our ability to use ionizing radiation as an energy source, as a therapeutic agent, and, unfortunately, as a weapon, has evolved tremendously over the past 120 years, yet our tool box to handle the consequences of accidental and unwanted radiation exposure remains very limited. We have identified a novel group of small molecule compounds with a 4-nitrophenylsulfonamide (NPS) backbone in common that dramatically decrease mortality from the hematopoietic acute radiation syndrome (hARS). The group emerged from an in vitro high throughput screen (HTS) for inhibitors of radiation-induced apoptosis...
2017: PloS One
https://www.readbyqxmd.com/read/28731639/exploring-family-home-food-environments-household-resources-needed-to-utilise-weekly-deliveries-of-free-fruits-and-vegetables
#8
Sophie A Carty, Louise A Mainvil, John D Coveney
AIM: An adapted ethnographic approach was used to explore household factors that influence family fruit and vegetable consumption when access and cost barriers are removed. 'Structural' barriers, such as food affordability and accessibility, are likely to influence fruit and vegetable consumption in disadvantaged households, but households may require additional resources (human and social) to increase consumption. METHODS: Five low-income and five high-income households with children (N = 39 individuals) were observed in their home environment for three months...
April 2017: Nutrition & Dietetics: the Journal of the Dietitians Association of Australia
https://www.readbyqxmd.com/read/28727686/fbxw7-regulates-disc1-stability-via-the-ubiquitin-proteosome-system
#9
K Yalla, C Elliott, J P Day, J Findlay, S Barratt, Z A Hughes, L Wilson, E Whiteley, M Popiolek, Y Li, J Dunlop, R Killick, D R Adams, N J Brandon, M D Houslay, B Hao, G S Baillie
Disrupted in schizophrenia 1 (DISC1) is a multi-functional scaffolding protein that has been associated with neuropsychiatric disease. The role of DISC1 is to assemble protein complexes that promote neural development and signaling, hence tight control of the concentration of cellular DISC1 in neurons is vital to brain function. Using structural and biochemical techniques, we show for we believe the first time that not only is DISC1 turnover elicited by the ubiquitin proteasome system (UPS) but that it is orchestrated by the F-Box protein, FBXW7...
July 20, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28727073/technical-note-valuation-of-an-enteric-methane-emissions-measurement-system-for-cattle
#10
E M Andreini, M S Calvo-Lorenzo, C J Richards, J E White, S E Place
Through the process of enteric fermentation, cattle produce methane (CH), a potent greenhouse gas (GHG). Growing public concern about climate change has increased the need for accurate methods of measuring CH emissions from cattle directly to improve emission inventories and evaluate emissions mitigation techniques. The present study evaluated a ventilated head box system capable of measuring CH and carbon dioxide (CO) emissions, and oxygen (O) consumption from cattle. Six Holstein heifers were used to measure CH and CO emissions and O consumption from 2 ad libitum intake measurement periods (ADAPT and ADLIB) and 1 measurement period (RESTRICT) with intake restricted to 2% of BW on a DM basis...
June 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28724977/therapeutic-targeting-of-hmgb1-during-experimental-sepsis-modulates-the-inflammatory-cytokine-profile-to-one-associated-with-improved-clinical-outcomes
#11
Natalie E Stevens, Marianne J Chapman, Cara K Fraser, Tim R Kuchel, John D Hayball, Kerrilyn R Diener
Sepsis remains a significant health burden and a major clinical need exists for therapeutics to dampen the excessive and uncontrolled immune activation. Nuclear protein high mobility group box protein 1 (HMGB1) is released following cell death and is a late mediator in sepsis pathogenesis. While approaches targeting HMGB1 have demonstrated reduced mortality in pre-clinical models of sepsis, the impact of HMGB1 blockade on the complex septic inflammatory milieu and the development of subsequent immunosuppression remain enigmatic...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724350/a-random-effects-meta-analysis-model-with-box-cox-transformation
#12
Yusuke Yamaguchi, Kazushi Maruo, Christopher Partlett, Richard D Riley
BACKGROUND: In a random effects meta-analysis model, true treatment effects for each study are routinely assumed to follow a normal distribution. However, normality is a restrictive assumption and the misspecification of the random effects distribution may result in a misleading estimate of overall mean for the treatment effect, an inappropriate quantification of heterogeneity across studies and a wrongly symmetric prediction interval. METHODS: We focus on problems caused by an inappropriate normality assumption of the random effects distribution, and propose a novel random effects meta-analysis model where a Box-Cox transformation is applied to the observed treatment effect estimates...
July 19, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/28714680/correction-to-discovery-of-pyrazolo-1-5-a-pyrimidine-b-cell-lymphoma-6-bcl6-binders-and-optimization-to-high-affinity-macrocyclic-inhibitors
#13
William McCoull, Roman D Abrams, Erica Anderson, Kevin Blades, Peter Barton, Matthew Box, Jonathan Burgess, Kate Byth, Qing Cao, Claudio Chuaqui, Rodrigo J Carbajo, Tony Cheung, Erin Code, Andrew D Ferguson, Shaun Fillery, Nathan O Fuller, Eric Gangl, Ning Gao, Matthew Grist, David Hargreaves, Martin R Howard, Jun Hu, Paul D Kemmitt, Jennifer E Nelson, Nichole O'Connell, D Bryan Prince, Piotr Raubo, Philip B Rawlins, Graeme R Robb, Junjie Shi, Michael J Waring, David Whittaker, Marta Wylot, Xiahui Zhu
No abstract text is available yet for this article.
July 27, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28713345/experimental-study-and-ann-dual-time-scale-perturbation-model-of-electrokinetic-properties-of-microbiota
#14
Yong Liu, Cristian R Munteanu, Carlos Fernandez-Lozano, Alejandro Pazos, Tao Ran, Zhiliang Tan, Yizun Yu, Chuanshe Zhou, Shaoxun Tang, Humberto González-Díaz
The electrokinetic properties of the rumen microbiota are involved in cell surface adhesion and microbial metabolism. An in vitro study was carried out in batch culture to determine the effects of three levels of special surface area (SSA) of biomaterials and four levels of surface tension (ST) of culture medium on electrokinetic properties (Zeta potential, ξ; electrokinetic mobility, μe), fermentation parameters (volatile fatty acids, VFAs), and ST over fermentation processes (ST-a, γ). The obtained results were combined with previously published data (digestibility, D; pH; concentration of ammonia nitrogen, c(NH3-N)) to establish a predictive artificial neural network (ANN) model...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28711053/representations-in-neural-network-based-empirical-potentials
#15
Ekin D Cubuk, Brad D Malone, Berk Onat, Amos Waterland, Efthimios Kaxiras
Many structural and mechanical properties of crystals, glasses, and biological macromolecules can be modeled from the local interactions between atoms. These interactions ultimately derive from the quantum nature of electrons, which can be prohibitively expensive to simulate. Machine learning has the potential to revolutionize materials modeling due to its ability to efficiently approximate complex functions. For example, neural networks can be trained to reproduce results of density functional theory calculations at a much lower cost...
July 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28710722/organosulfur-compound-protects-against-memory-decline-induced-by-scopolamine-through-modulation-of-oxidative-stress-and-na-k-atpase-activity-in-mice
#16
Fernanda D da Silva, Mikaela P Pinz, Renata L de Oliveira, Karline C Rodrigues, Francine R Ianiski, Mariana M Bassaco, Claudio C Silveira, Cristiano R Jesse, Silvane S Roman, Ethel A Wilhelm, Cristiane Luchese
The present study investigated the possible effect of BMMS in protecting against memory impairment in an Alzheimer's disease model induced by scopolamine in mice. Another objective was to evaluate the involvement of oxidative stress and Na(+)/K(+) ATPase activity in cerebral cortex and hippocampus of mice. Male Swiss mice were divided into four groups: groups I and III received canola oil (10 ml/kg, intragastrically (i.g.)), while groups II and IV received BMMS (10 mg/kg, i.g.). Thirty minutes after treatments, groups III and IV received scopolamine (1 mg/kg, intraperitoneal (i...
July 14, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28709622/genipin-protects-d-galactosamine-and-lipopolysaccharide-induced-hepatic-injury-through-suppression-of-the-necroptosis-mediated-inflammasome-signaling
#17
Min-Jong Seo, Jeong-Min Hong, Seok-Joo Kim, Sun-Mee Lee
Acute liver failure (ALF) is a life-threatening syndrome resulting from massive inflammation and hepatocyte death. Necroptosis, a programmed cell death controlled by receptor-interacting protein kinase (RIP) 1 and RIP3, has been shown to play an important role in regulating inflammation via crosstalk between other intracellular signaling. The inflammasome is a major intracellular multiprotein that induces inflammatory responses by mediating immune cell infiltration, thus potentiating injury. Genipin, a major active compound of the gardenia fruit, exhibits anti-inflammatory, antioxidant, and anti-apoptotic properties...
July 11, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28709260/pneumatic-fractures-in-confined-granular-media
#18
Fredrik K Eriksen, Renaud Toussaint, Antoine L Turquet, Knut J Måløy, Eirik G Flekkøy
We perform experiments where air is injected at a constant overpressure P_{in}, ranging from 5 to 250 kPa, into a dry granular medium confined within a horizontal linear Hele-Shaw cell. The setup allows us to explore compacted configurations by preventing decompaction at the outer boundary, i.e., the cell outlet has a semipermeable filter such that beads are stopped while air can pass. We study the emerging patterns and dynamic growth of channels in the granular media due to fluid flow, by analyzing images captured with a high speed camera (1000 images/s)...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28705897/cas9-mediated-excision-of-nematostella-brachyury-disrupts-endoderm-development-pharynx-formation-and-oral-aboral-patterning
#19
Marc D Servetnick, Bailey Steinworth, Leslie S Babonis, David Simmons, Miguel Salinas-Saavedra, Mark Q Martindale
The mesoderm was a key novelty in animal evolution, though we understand little of how mesoderm arose. brachyury, the founding member of the T-box gene family, is a key gene in chordate mesoderm development. However, the brachyury gene was present in the common ancestor of fungi and animals, long before mesoderm appeared. To explore ancestral roles of brachyury prior to the evolution of definitive mesoderm, we excised the gene using CRISPR/Cas9 in the diploblastic cnidarian Nematostella vectensisNvbrachyury is normally expressed in precursors of the pharynx, which separates endoderm from ectoderm...
July 13, 2017: Development
https://www.readbyqxmd.com/read/28705607/noise-induced-hearing-loss-induces-loudness-intolerance-in-a-rat-active-sound-avoidance-paradigm-asap
#20
Senthilvelan Manohar, Jaclyn Spoth, Kelly Radziwon, Benjamin D Auerbach, Richard Salvi
Hyperacusis is a loudness hypersensitivity disorder in which moderate-intensity sounds are perceived as extremely loud, aversive and/or painful. To assess the aversive nature of sounds, we developed an Active Sound Avoidance Paradigm (ASAP) in which rats altered their place preference in a Light/Dark shuttle box in response to sound. When no sound (NS) was present, rats spent more than 95% of the time in the Dark Box versus the transparent Light Box. However, when a 60 or 90 dB SPL noise (2-20 kHz, 2-8 kHz, or 16-20 kHz bandwidth) was presented in the Dark Box, the rats'' preference for the Dark Box significantly decreased...
July 8, 2017: Hearing Research
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