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https://www.readbyqxmd.com/read/28333201/new-statistical-criteria-detect-phylogenetic-bias-caused-by-compositional-heterogeneity
#1
David A Duchêne, Sebastian Duchêne, Simon Y W Ho
In statistical phylogenetic analyses of DNA sequences, models of evolutionary change commonly assume that base composition is stationary through time and across lineages. This assumption is violated by many data sets, but it is unclear whether the magnitude of these violations is sufficient to mislead phylogenetic inference. We investigated the impacts of compositional heterogeneity on phylogenetic estimates using a method for assessing model adequacy. Based on a detailed simulation study, we found that common frequentist criteria are highly conservative, such that the model is often rejected when the phylogenetic estimates do not show clear signs of bias...
February 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28325024/balance-quality-assessment-as-an-early-indicator-of-physical-frailty-in-older-people
#2
Aly Chkeir, Doha Safieddine, D Bera, M Collart, J L Novella, M Drame, David J Hewson, Jacques Duchene
Frailty is an increasingly common geriatric condition that results in an increased risk of adverse health outcomes such as falls. The most widely-used means of detecting frailty is the Fried phenotype, which includes several objective measures such as grip strength and gait velocity. One method of screening for falls is to measure balance, which can be done by a range of techniques including the assessment of the Centre of Pressure (CoP) during a balance assessment. The Balance Quality Tester (BQT) is a device based on a commercial bathroom scale that can evaluate balance quality...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28286806/assessment-of-cellular-redox-state-using-nad-p-h-fluorescence-intensity-and-lifetime
#3
Thomas S Blacker, Tunde Berecz, Michael R Duchen, Gyorgy Szabadkai
NADH and NADPH are redox cofactors, primarily involved in catabolic and anabolic metabolic processes respectively. In addition, NADPH plays an important role in cellular antioxidant defence. In live cells and tissues, the intensity of their spectrally-identical autofluorescence, termed NAD(P)H, can be used to probe the mitochondrial redox state, while their distinct enzyme-binding characteristics can be used to separate their relative contributions to the total NAD(P)H intensity using fluorescence lifetime imaging microscopy (FLIM)...
January 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28273061/neanderthal-behaviour-diet-and-disease-inferred-from-ancient-dna-in-dental-calculus
#4
Laura S Weyrich, Sebastian Duchene, Julien Soubrier, Luis Arriola, Bastien Llamas, James Breen, Alan G Morris, Kurt W Alt, David Caramelli, Veit Dresely, Milly Farrell, Andrew G Farrer, Michael Francken, Neville Gully, Wolfgang Haak, Karen Hardy, Katerina Harvati, Petra Held, Edward C Holmes, John Kaidonis, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Patrick Semal, Arkadiusz Soltysiak, Grant Townsend, Donatella Usai, Joachim Wahl, Daniel H Huson, Keith Dobney, Alan Cooper
Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment...
March 8, 2017: Nature
https://www.readbyqxmd.com/read/28265814/a-comparative-study-of-the-sensitivity-of-diffusion-related-parameters-obtained-from-diffusion-tensor-imaging-diffusional-kurtosis-imaging-q-space-analysis-and-bi-exponential-modelling-in-the-early-disease-course-24%C3%A2-h-of-hyperacute-6%C3%A2-h-ischemic-stroke-patients
#5
Gaëtan Duchêne, Frank Peeters, André Peeters, Thierry Duprez
OBJECTIVES: To compare the sensitivity and early temporal changes of diffusion parameters obtained from diffusion tensor imaging (DTI), diffusional kurtosis imaging (DKI), q-space analysis (QSA) and bi-exponential modelling in hyperacute stroke patients. MATERIALS AND METHODS: A single investigational acquisition allowing the four diffusion analyses was performed on seven hyperacute stroke patients with a 3T system. The percentage change between ipsi- and contralateral regions were compared at admission and 24 h later...
March 6, 2017: Magma
https://www.readbyqxmd.com/read/28262838/galectin-3-is-a-non-classic-rna-binding-protein-that-stabilizes-the-mucin-muc4-mrna-in-the-cytoplasm-of-cancer-cells
#6
Lucie Coppin, Audrey Vincent, Frédéric Frénois, Belinda Duchêne, Fatima Lahdaoui, Laurence Stechly, Florence Renaud, Céline Villenet, Isabelle Van Seuningen, Emmanuelle Leteurtre, Johann Dion, Cyrille Grandjean, Françoise Poirier, Martin Figeac, Delphine Delacour, Nicole Porchet, Pascal Pigny
Pancreatic cancer cells express high levels of MUC1, MUC4 and MUC16 mRNAs that encode membrane-bound mucins. These mRNAs share unusual features such as a long half-life. However, it remains unknown how mucin mRNA stability is regulated. Galectin-3 (Gal-3) is an endogenous lectin playing important biological functions in epithelial cells. Gal-3 is encoded by LGALS3 which is up-regulated in pancreatic cancer. Despite the absence of a RNA-recognition motif, Gal-3 interacts indirectly with pre-mRNAs in the nucleus and promotes constitutive splicing...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28227723/balance-quality-assessment-as-an-early-indicator-of-physical-frailty-in-older-people
#7
Aly Chkeir, Doha Safieddine, D Bera, M Collart, J L Novella, M Drame, David J Hewson, Jacques Duchene, Aly Chkeir, Doha Safieddine, D Bera, M Collart, J L Novella, M Drame, David J Hewson, Jacques Duchene, J L Novella, David J Hewson, Jacques Duchene, M Collart, Aly Chkeir, D Bera, M Drame, Doha Safieddine
Frailty is an increasingly common geriatric condition that results in an increased risk of adverse health outcomes such as falls. The most widely-used means of detecting frailty is the Fried phenotype, which includes several objective measures such as grip strength and gait velocity. One method of screening for falls is to measure balance, which can be done by a range of techniques including the assessment of the Centre of Pressure (CoP) during a balance assessment. The Balance Quality Tester (BQT) is a device based on a commercial bathroom scale that can evaluate balance quality...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28217242/investigating-state-restriction-in-fluorescent-protein-fret-using-time-resolved-fluorescence-and-anisotropy
#8
Thomas S Blacker, WeiYue Chen, Edward Avezov, Richard J Marsh, Michael R Duchen, Clemens F Kaminski, Angus J Bain
Most fluorescent proteins exhibit multiexponential fluorescence decays, indicating a heterogeneous excited state population. FRET between fluorescent proteins should therefore involve multiple energy transfer pathways. We recently demonstrated the FRET pathways between EGFP and mCherry (mC), upon the dimerization of 3-phosphoinositide dependent protein kinase 1 (PDK1), to be highly restricted. A mechanism for FRET restriction based on a highly unfavorable κ(2) orientation factor arising from differences in donor-acceptor transition dipole moment angles in a far from coplanar and near static interaction geometry was proposed...
January 26, 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
https://www.readbyqxmd.com/read/28204787/inference-of-evolutionary-jumps-in-large-phylogenies-using-levy-processes
#9
Pablo Duchen, Christoph Leuenberger, Sandor M Szilagyi, Luke Harmon, Jonathan Eastman, Manuel Schweizer, Daniel Wegmann
No abstract text is available yet for this article.
February 16, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28178344/comparative-analysis-estimates-the-relative-frequencies-of-co-divergence-and-cross-species-transmission-within-viral-families
#10
Jemma L Geoghegan, Sebastián Duchêne, Edward C Holmes
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28158426/neutrophils-orchestrate-post-myocardial-infarction-healing-by-polarizing-macrophages-towards-a-reparative-phenotype
#11
Michael Horckmans, Larisa Ring, Johan Duchene, Donato Santovito, Maximilian J Schloss, Maik Drechsler, Christian Weber, Oliver Soehnlein, Sabine Steffens
No abstract text is available yet for this article.
January 14, 2017: European Heart Journal
https://www.readbyqxmd.com/read/28132899/pathological-consequences-of-micu1-mutations-on-mitochondrial-calcium-signalling-and-bioenergetics
#12
Gauri Bhosale, Jenny Sharpe, Amanda Koh, Antonina Kouli, Gyorgy Szabadkai, Michael R Duchen
Loss of function mutations of the protein MICU1, a regulator of mitochondrial Ca(2+) uptake, cause a neuronal and muscular disorder characterised by impaired cognition, muscle weakness and an extrapyramidal motor disorder. We have shown previously that MICU1 mutations cause increased resting mitochondrial Ca(2+) concentration ([Ca(2+)]m). We now explore the functional consequences of MICU1 mutations in patient derived fibroblasts in order to clarify the underlying pathophysiology of this disorder. We propose that deregulation of mitochondrial Ca(2+) uptake through loss of MICU1 raises resting [Ca(2+)]m, initiating a futile Ca(2+) cycle, whereby continuous mitochondrial Ca(2+) influx is balanced by Ca(2+) efflux through the sodium calcium exchanger (NLCXm)...
January 26, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28111024/mitochondrial-dysfunction-and-neurodegeneration-in-lysosomal-storage-disorders
#13
REVIEW
Nicoletta Plotegher, Michael R Duchen
Lysosomal storage disorders (LSDs) are rare inherited debilitating and often fatal disorders. Caused by mutations affecting lysosomal proteins, LSDs are characterized by the accumulation of undegraded material in lysosomes and by lysosomal dysfunction. Although LSDs are multisystemic diseases, the majority display neurologic symptoms and neurodegeneration. Only recently has a role emerged for mitochondrial dysfunction in the pathophysiology of LSDs, suggesting an impact of lysosomal dysfunction on mitochondria...
January 19, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28006956/findings-and-impact-of-early-imaging-after-partial-nephrectomy
#14
Ryan W Tubre, William P Parker, Travis Dum, Tim Walmann, Zachary Hamilton, Moben Mirza, David A Duchene
INTRODUCTION: American Urological Association guidelines for surveillance of renal-cell carcinoma after partial nephrectomy recommend imaging within 3-12 months of surgery. Imaging following partial nephrectomy may be difficult to interpret due to the surgical defect, the use of surgical material, and normal postoperative fluid collections. Our primary objective was to evaluate the frequency of indeterminate postoperative imaging results and how those radiographic findings altered patient management...
March 2017: Journal of Endourology
https://www.readbyqxmd.com/read/27977811/large-scale-phylogenomic-analysis-reveals-the-complex-evolutionary-history-of-rabies-virus-in-multiple-carnivore-hosts
#15
Cécile Troupin, Laurent Dacheux, Marion Tanguy, Claude Sabeta, Hervé Blanc, Christiane Bouchier, Marco Vignuzzi, Sebastián Duchene, Edward C Holmes, Hervé Bourhy
The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27941941/potentiation-of-amitriptyline-anti-hyperalgesic-like-action-by-astroglial-connexin-43-inhibition-in-neuropathic-rats
#16
Tiffany Jeanson, Adeline Duchêne, Damien Richard, Sylvie Bourgoin, Christèle Picoli, Pascal Ezan, Franck Mouthon, Christian Giaume, Michel Hamon, Mathieu Charvériat
Antidepressants, prescribed as first line treatment of neuropathic pain, have a limited efficacy and poorly tolerated side effects. Because recent studies pointed out the implication of astroglial connexins (Cx) in both neuropathic pain and antidepressive treatment, we investigated whether their blockade by mefloquine could modulate the action of the tricyclic antidepressant amitriptyline. Using primary cultures, we found that both mefloquine and amitriptyline inhibited Cx43-containing gap junctions, and that the drug combination acted synergically...
December 12, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27939314/17-th-century-variola-virus-reveals-the-recent-history-of-smallpox
#17
Ana T Duggan, Maria F Perdomo, Dario Piombino-Mascali, Stephanie Marciniak, Debi Poinar, Matthew V Emery, Jan P Buchmann, Sebastian Duchêne, Rimantas Jankauskas, Margaret Humphreys, G Brian Golding, John Southon, Alison Devault, Jean-Marie Rouillard, Jason W Sahl, Olivier Dutour, Klaus Hedman, Antti Sajantila, Geoffrey L Smith, Edward C Holmes, Hendrik N Poinar
Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1-4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4-9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4-6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone...
December 19, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27939264/preconception-health-behaviours-a-scoping-review
#18
REVIEW
Kirsti I Toivonen, Kirsten A Oinonen, Katelyn M Duchene
Preconception health refers to the health of males and females at any point in time prior to a potential pregnancy. A goal of preconception health research is to use preventive behaviour and healthcare to optimize the health of future offspring that result from both planned and unplanned pregnancies. This paper briefly reviews evidence of the importance of various preconception health behaviours, and examines the extent to which specific preconception health behaviours have been included in recent studies of such knowledge, behaviours, and intentions...
March 2017: Preventive Medicine
https://www.readbyqxmd.com/read/27916992/gene-editing-for-duchenne-muscular-dystrophy-using-the-crispr-cas9-technology-the-importance-of-fine-tuning-the-approach
#19
Jacques P Tremblay, Jean-Paul Iyombe-Engembe, Benjamin Duchêne, Dominique L Ouellet
No abstract text is available yet for this article.
November 2016: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/27899576/the-nuclear-and-organellar-trna-derived-rna-fragment-population-in-arabidopsis-thaliana-is-highly-dynamic
#20
Valérie Cognat, Geoffrey Morelle, Cyrille Megel, Stéphanie Lalande, Jean Molinier, Timothée Vincent, Ian Small, Anne-Marie Duchêne, Laurence Maréchal-Drouard
In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed...
November 28, 2016: Nucleic Acids Research
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