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https://www.readbyqxmd.com/read/28211541/antibody-controlled-actuation-of-dna-based-molecular-circuits
#1
Wouter Engelen, Lenny H H Meijer, Bram Somers, Tom F A de Greef, Maarten Merkx
DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically...
February 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28209195/qualitative-exploration-of-why-people-repeatedly-attend-emergency-departments-for-alcohol-related-reasons
#2
Tom Parkman, Joanne Neale, Ed Day, Colin Drummond
BACKGROUND: Understanding why people repeatedly attend Emergency Departments (EDs) for alcohol-related reasons is an important prerequisite to identifying ways of reducing any unnecessary demands on hospital resources. We use Andersen's Behavioural Model of Health Services Use to explore factors that contributed to repeat ED attendances. METHODS: Qualitative interviews were conducted with 30 people who repeatedly attended EDs for alcohol-related reasons (≥10 attendances in the past 12 months)...
February 16, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/28208070/association-of-medial-prefrontal-resting-state-functional-connectivity-and-metacognitive-capacity-in-early-phase-psychosis
#3
Michael M Francis, Tom A Hummer, Bethany L Leonhardt, Jenifer L Vohs, Matt G Yung, Nicole F Mehdiyoun, Paul H Lysaker, Alan Breier
Metacognition refers to a range of cognitive processes that allow one to form complex ideas of self and others and to use this information to navigate psychosocial challenges. Several studies in both early-phase and prolonged schizophrenia have demonstrated not only that significant deficits in metacognitive ability are present, but importantly that they are associated with significant functional impairment and decreased quality of life. In spite of the importance of metacognitive impairment in schizophrenia, relatively little is known about the biological substrates that may contribute to this dysfunction...
February 8, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28207309/multilocus-sequence-typing-and-staphylococcal-protein-a-typing-revealed-novel-and-diverse-clones-of-methicillin-resistant-staphylococcus-aureus-in-seafood-and-the-aquatic-environment
#4
V Murugadas, C Joseph Toms, Sara A Reethu, K V Lalitha
Methicillin-resistant Staphylococcus aureus (MRSA) has been a global health concern since the 1960s, and isolation of this pathogen from food-producing animals has been increasing. However, little information is available on the prevalence of MRSA and its clonal characteristics in seafood and the aquatic environment. In this study, 267 seafood and aquatic environment samples were collected from three districts of Kerala, India. Staphylococcal protein A (spa) typing and multilocus sequence typing (MLST) was performed for 65 MRSA strains isolated from 20 seafood and aquatic environment samples...
February 16, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28202184/high-prevalence-of-same-sex-twins-in-patients-with-cloacal-exstrophy-support-for-embryological-association-with-monozygotic-twinning
#5
Brenna S Fullerton, Eric A Sparks, Amber M Hall, Cristine S Velazco, Biren P Modi, Dennis P Lund, Tom Jaksic, W Hardy Hendren
PURPOSE: Previous studies have hypothesized that cloacal exstrophy may be caused by errors early in embryological development related to monozygotic twinning. This study reports the prevalence of twins in a large cohort of patients with cloacal exstrophy. METHODS: Patients with cloacal exstrophy treated 1974-2015 were reviewed for reports of multiple gestation or conjoined twinning. The genetic sex of the patient and their twin, and any mention of anomaly in the twin were recorded...
January 30, 2017: Journal of Pediatric Surgery
https://www.readbyqxmd.com/read/28197091/axonpacking-an-open-source-software-to-simulate-arrangements-of-axons-in-white-matter
#6
Tom Mingasson, Tanguy Duval, Nikola Stikov, Julien Cohen-Adad
HIGHLIGHTS AxonPacking: Open-source software for simulating white matter microstructure.Validation on a theoretical disk packing problem.Reproducible and stable for various densities and diameter distributions.Can be used to study interplay between myelin/fiber density and restricted fraction. Quantitative Magnetic Resonance Imaging (MRI) can provide parameters that describe white matter microstructure, such as the fiber volume fraction (FVF), the myelin volume fraction (MVF) or the axon volume fraction (AVF) via the fraction of restricted water (fr)...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28195242/the-alternative-complement-pathway-is-dysregulated-in-patients-with-chronic-heart-failure
#7
Negar Shahini, Annika E Michelsen, Per H Nilsson, Karin Ekholt, Lars Gullestad, Kaspar Broch, Christen P Dahl, Pål Aukrust, Thor Ueland, Tom Eirik Mollnes, Arne Yndestad, Mieke C Louwe
The complement system, an important arm of the innate immune system, is activated in heart failure (HF). We hypothesized that HF patients are characterized by an imbalance of alternative amplification loop components; including properdin and complement factor D and the alternative pathway inhibitor factor H. These components and the activation product, terminal complement complex (TCC), were measured in plasma from 188 HF patients and 67 age- and sex- matched healthy controls by enzyme immunoassay. Our main findings were: (i) Compared to controls, patients with HF had significantly increased levels of factor D and TCC, and decreased levels of properdin, particularly patients with advanced clinical disorder (i...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28186996/harnessing-rna-sequencing-for-global-unbiased-evaluation-of-two-new-adjuvants-for-dendritic-cell-immunotherapy
#8
Till S M Mathan, Johannes Textor, Annette E Sköld, Inge Reinieren-Beeren, Tom van Oorschot, Mareke Brüning, Carl G Figdor, Sonja I Buschow, Ghaith Bakdash, I Jolanda M de Vries
Effective stimulation of immune cells is crucial for the success of cancer immunotherapies. Current approaches to evaluate the efficiency of stimuli are mainly defined by known flow cytometry-based cell activation or cell maturation markers. This method however does not give a complete overview of the achieved activation state and may leave important side effects unnoticed. Here, we used an unbiased RNA sequencing (RNA-seq)-based approach to compare the capacity of four clinical-grade dendritic cell (DC) activation stimuli used to prepare DC-vaccines composed of various types of DC subsets; the already clinically applied GM-CSF and Frühsommer meningoencephalitis (FSME) prophylactic vaccine and the novel clinical grade adjuvants protamine-RNA complexes (pRNA) and CpG-P...
February 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28186668/a-post-hoc-study-on-gene-panel-analysis-for-the-diagnosis-of-dystonia
#9
Martje E van Egmond, Coen H A Lugtenberg, Oebele F Brouwer, Maria Fiorella Contarino, Victor S C Fung, M Rebecca Heiner-Fokkema, Jacobus J van Hilten, Annemarie H van der Hout, Kathryn J Peall, Richard J Sinke, Emmanuel Roze, Corien C Verschuuren-Bemelmans, Michel A Willemsen, Nicole I Wolf, Marina A Tijssen, Tom J de Koning
BACKGROUND: Genetic disorders causing dystonia show great heterogeneity. Recent studies have suggested that next-generation sequencing techniques such as gene panel analysis can be effective in diagnosing heterogeneous conditions. The objective of this study was to investigate whether dystonia patients with a suspected genetic cause could benefit from the use of gene panel analysis. METHODS: In this post hoc study, we describe gene panel analysis results of 61 dystonia patients (mean age, 31 years; 72% young onset) in our tertiary referral center...
February 10, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28184209/theory-of-mind-is-impaired-in-mild-to-moderate-huntington-s-disease-independently-from-global-cognitive-functioning
#10
Giovanna Lagravinese, Laura Avanzino, Alessia Raffo De Ferrari, Roberta Marchese, Carlo Serrati, Paola Mandich, Giovanni Abbruzzese, Elisa Pelosin
Affective "Theory of Mind" (ToM) is the specific ability to represent own and others' emotional states and feelings. Previous studies examined affective ToM ability in patients with Huntington's disease (HD), using the "Reading the Mind in the Eyes test" (RMET). Results were consistent in showing difficulties in inferring complex mental states from photographs of people even in the early stage of HD. However, there has been no agreement as to whether or not cognitive impairments in HD population might have contributed to poor performance on the RMET test...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28181915/interlayer-vacancy-defects-in-aa-stacked-bilayer-graphene-density-functional-theory-predictions
#11
Amanda Vuong, Tom Trevethan, Christopher Latham, Chris Ewels, Doğan Erbahar, Patrick Briddon, Mark Rayson, Malcolm Heggie
AA-stacked graphite and closely related structures, where carbon atoms are located in registry in adjacent graphene layers, are a feature of graphitic systems including twisted and folded bilayer graphene, and turbostratic graphite. We present the results of <i>ab initio</i> density functional theory calculations performed to investigate the complexes that are formed from the binding of vacancy defects across neighbouring layers in AA-stacked bilayers. As with AB stacking, the carbon atoms surrounding lattice vacancies can form interlayer structures with sp<sup>2</sup> bonding that are lower in energy than in-plane reconstructions...
February 9, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28178278/advances-in-the-quantification-of-mitochondrial-function-in-primary-human-immune-cells-through-extracellular-flux-analysis
#12
Dequina Nicholas, Elizabeth A Proctor, Forum M Raval, Blanche C Ip, Chloe Habib, Eleni Ritou, Tom N Grammatopoulos, Devin Steenkamp, Hans Dooms, Caroline M Apovian, Douglas A Lauffenburger, Barbara S Nikolajczyk
Numerous studies show that mitochondrial energy generation determines the effectiveness of immune responses. Furthermore, changes in mitochondrial function may regulate lymphocyte function in inflammatory diseases like type 2 diabetes. Analysis of lymphocyte mitochondrial function has been facilitated by introduction of 96-well format extracellular flux (XF96) analyzers, but the technology remains imperfect for analysis of human lymphocytes. Limitations in XF technology include the lack of practical protocols for analysis of archived human cells, and inadequate data analysis tools that require manual quality checks...
2017: PloS One
https://www.readbyqxmd.com/read/28167931/the-active-component-of-aspirin-salicylic-acid-promotes-staphylococcus-aureus-biofilm-formation-in-a-pia-dependent-manner
#13
Cristian Dotto, Andrea Lombarte Serrat, Natalia Cattelan, María S Barbagelata, Osvaldo M Yantorno, Daniel O Sordelli, Monika Ehling-Schulz, Tom Grunert, Fernanda R Buzzola
Aspirin has provided clear benefits to human health. But salicylic acid (SAL) -the main aspirin biometabolite- exerts several effects on eukaryote and prokaryote cells. SAL can affect, for instance, the expression of Staphylococcus aureus virulence factors. SAL can also form complexes with iron cations and it has been shown that different iron chelating molecules diminished the formation of S. aureus biofilm. The aim of this study was to elucidate whether the iron content limitation caused by SAL can modify the S...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28167535/adaptation-of-a-genetic-screen-reveals-an-inhibitor-for-mitochondrial-protein-import-component-tim44
#14
Non Miyata, Zhiye Tang, Michael A Conti, Meghan E Johnson, Colin J Douglas, Samuel A Hasson, Robert Damoiseaux, Chia-En A Chang, Carla M Koehler
Diverse protein import pathways into mitochondria use translocons on the outer membrane (TOM) and inner membrane (TIM). We adapted a genetic screen, based on Ura3 mistargeting from mitochondria to the cytosol, to identify small molecules that attenuated protein import. Small molecule Mitochondrial import Blockers of the Carla Koehler laboratory (MitoBloCK, MB)-10 inhibited import of substrates that require the TIM23 translocon. Mutational analysis coupled with molecular docking and molecular dynamics modeling revealed that MB-10 binds to a specific pocket in the C-terminal domain of Tim44 of the Protein Associated Motor (PAM) complex...
February 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28161472/novel-serum-and-bile-protein-markers-predict-primary-sclerosing-cholangitis-disease-severity-and-prognosis
#15
Mette Vesterhus, Anders Holm, Johannes Roksund Hov, Ståle Nygård, Erik Schrumpf, Espen Melum, Liv Wenche Thorbjørnsen, Vemund Paulsen, Knut Lundin, Inge Dale, Odd Helge Gilja, Serge J L B Zweers, Morten Vatn, Frank G Schaap, Peter L M Jansen, Thor Ueland, Helge Røsjø, Bjørn Moum, Cyriel Y Ponsioen, Kirsten Muri Boberg, Martti Färkkilä, Tom H Karlsen, Fridtjof Lund-Johansen
BACKGROUND&AIMS: We aimed to identify novel protein biomarkers of disease severity and prognosis in primary sclerosing cholangitis (PSC). METHODS: Using a bead-based array targeting 63 proteins, we profiled a derivation panel of Norwegian endoscopic retrograde cholangiography-bile samples (55 PSC, 20 disease controls) and a Finnish validation panel (34 PSC, 10 disease controls). Selected identified proteins were measured in serum from two Norwegian PSC cohorts (n=167 [1992-2006] and n=138 [2008-2012]), inflammatory bowel disease (n=96) and healthy controls (n=100)...
February 1, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28154079/dna-pkcs-structure-suggests-an-allosteric-mechanism-modulating-dna-double-strand-break-repair
#16
Bancinyane L Sibanda, Dimitri Y Chirgadze, David B Ascher, Tom L Blundell
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a central component of nonhomologous end joining (NHEJ), repairing DNA double-strand breaks that would otherwise lead to apoptosis or cancer. We have solved its structure in complex with the C-terminal peptide of Ku80 at 4.3 angstrom resolution using x-ray crystallography. We show that the 4128-amino acid structure comprises three large structural units: the N-terminal unit, the Circular Cradle, and the Head. Conformational differences between the two molecules in the asymmetric unit are correlated with changes in accessibility of the kinase active site, which are consistent with an allosteric mechanism to bring about kinase activation...
February 3, 2017: Science
https://www.readbyqxmd.com/read/28125364/improving-oncology-quality-measurement-in-accountable-care-filling-gaps-with-cross-cutting-measures
#17
Tom Valuck, David Blaisdell, Donna P Dugan, Kimberly Westrich, Robert W Dubois, Robert S Miller, Mark McClellan
: Payment for health care services, including oncology services, is shifting from volume-based fee-for-service to value-based accountable care. The objective of accountable care is to support providers with flexibility and resources to reform care delivery, accompanied by accountability for maintaining or improving outcomes while lowering costs. These changes depend on health care payers, systems, physicians, and patients having meaningful measures to assess care delivery and outcomes and to balance financial incentives for lowering costs while providing greater value...
February 2017: Journal of Managed Care & Specialty Pharmacy
https://www.readbyqxmd.com/read/28123088/fluctuations-in-population-fecundity-drive-variation-in-demographic-connectivity-and-metapopulation-dynamics
#18
Max C N Castorani, Daniel C Reed, Peter T Raimondi, Filipe Alberto, Tom W Bell, Kyle C Cavanaugh, David A Siegel, Rachel D Simons
Demographic connectivity is vital to sustaining metapopulations yet often changes dramatically through time due to variation in the production and dispersal of offspring. However, the relative importance of variation in fecundity and dispersal in determining the connectivity and dynamics of metapopulations is poorly understood due to the paucity of comprehensive spatio-temporal data on these processes for most species. We quantified connectivity in metapopulations of a marine foundation species (giant kelp Macrocystis pyrifera) across 11 years and approximately 900 km of coastline by estimating population fecundity with satellite imagery and propagule dispersal using a high-resolution ocean circulation model...
January 25, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28122501/exact-p-values-for-pairwise-comparison-of-friedman-rank-sums-with-application-to-comparing-classifiers
#19
Rob Eisinga, Tom Heskes, Ben Pelzer, Manfred Te Grotenhuis
BACKGROUND: The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is typically of interest to conduct pairwise comparison tests. Current approaches to such tests rely on large-sample approximations, due to the numerical complexity of computing the exact distribution. These approximate methods lead to inaccurate estimates in the tail of the distribution, which is most relevant for p-value calculation...
January 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28122224/physical-model-for-stabilization-and-repair-of-trans-endothelial-apertures
#20
Eduard G Fedorov, Tom Shemesh
Bacterial toxins that disrupt the stability of contractile structures in endothelial cells promote the opening of large-scale apertures, thereby breaching the endothelium barrier. These apertures are formed by fusion of the basal and apical membranes into a tunnel that spans the height of the cell. Subsequent to the aperture formation, an active repair process, driven by a stimulated polymerization of actin, results in asymmetrical membrane protrusions and, ultimately, the closure of the aperture. Here, we propose a physics-based model for the generation, stabilization and repair of trans-endothelial apertures...
January 24, 2017: Biophysical Journal
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