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https://www.readbyqxmd.com/read/28724627/using-step-width-to-compare-locomotor-biomechanics-between-extinct-non-avian-theropod-dinosaurs-and-modern-obligate-bipeds
#1
P J Bishop, C J Clemente, R E Weems, D F Graham, L P Lamas, J R Hutchinson, J Rubenson, R S Wilson, S A Hocknull, R S Barrett, D G Lloyd
How extinct, non-avian theropod dinosaurs locomoted is a subject of considerable interest, as is the manner in which it evolved on the line leading to birds. Fossil footprints provide the most direct evidence for answering these questions. In this study, step width-the mediolateral (transverse) distance between successive footfalls-was investigated with respect to speed (stride length) in non-avian theropod trackways of Late Triassic age. Comparable kinematic data were also collected for humans and 11 species of ground-dwelling birds...
July 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28714942/palaeo-leaf-economics-reveal-a-shift-in-ecosystem-function-associated-with-the-end-triassic-mass-extinction-event
#2
W K Soh, I J Wright, K L Bacon, T I Lenz, M Steinthorsdottir, A C Parnell, J C McElwain
Climate change is likely to have altered the ecological functioning of past ecosystems, and is likely to alter functioning in the future; however, the magnitude and direction of such changes are difficult to predict. Here we use a deep-time case study to evaluate the impact of a well-constrained CO2-induced global warming event on the ecological functioning of dominant plant communities. We use leaf mass per area (LMA), a widely used trait in modern plant ecology, to infer the palaeoecological strategy of fossil plant taxa...
July 17, 2017: Nature Plants
https://www.readbyqxmd.com/read/28709213/when-memory-pays-discord-in-hidden-markov-models
#3
Emma Lathouwers, John Bechhoefer
When is keeping a memory of observations worthwhile? We use hidden Markov models to look at phase transitions that emerge when comparing state estimates in systems with discrete states and noisy observations. We infer the underlying state of the hidden Markov models from the observations in two ways: through naive observations, which take into account only the current observation, and through Bayesian filtering, which takes the history of observations into account. Defining a discord order parameter to distinguish between the different state estimates, we explore hidden Markov models with various numbers of states and symbols and varying transition-matrix symmetry...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28709197/picosecond-time-resolved-measurements-of-dense-plasma-line-shifts
#4
C R Stillman, P M Nilson, S T Ivancic, I E Golovkin, C Mileham, I A Begishev, D H Froula
Picosecond time-resolved x-ray spectroscopy is used to measure the spectral line shift of the 1s2p-1s^{2} transition in He-like Al ions as a function of the instantaneous plasma conditions. The plasma temperature and density are inferred from the Al He_{α} complex using a nonlocal-thermodynamic-equilibrium atomic physics model. The experimental spectra show a linearly increasing redshift for electron densities of 1-5×10^{23}cm^{-3}. The measured line shifts are broadly consistent with a generalized analytic line-shift model based on calculations of a self-consistent field ion-sphere model...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28705469/systematic-prioritization-of-functional-hotspot-in-rig-1-domains-using-pattern-based-conventional-molecular-dynamic-simulation
#5
P Raghuraman, R Jesu Jaya Sudan, J Lesitha Jeeva Kumari, C Sudandiradoss
BACKGROUND: Retinoic acid inducible gene 1 (RIG-1), multi-domain protein has a role-play in detecting viral nucleic acids and stimulates the antiviral response. Dysfunction of this protein due to mutations makes the route vulnerable to viral diseases. AIM: Identification of functional hotspots that maintains conformational stability in RIG-1 domains. METHODS: In this study, we employed a systematic in silico strategy on RIG-1 protein to understand the mechanism of structural changes upon mutation...
July 10, 2017: Life Sciences
https://www.readbyqxmd.com/read/28702673/unexpected-thermal-annealing-effects-on-the-viscosity-of-polymer-nanocomposites
#6
Fei Chen, Koshu Takatsuji, Dan Zhao, Xuanji Yu, Sanat K Kumar, Ophelia K C Tsui
The effects of thermal annealing, 12-50 K above the glass transition temperature, on the zero-shear viscosity, η, of polymer nanocomposites (PNCs) and the corresponding host polymers were studied. For all specimens, including neat and 4 wt% dioctyl phthalate (DOP)-plasticized polystyrene (PS), neat poly(methyl methacrylate) (PMMA), and PNCs containing bare and grafted silica nanoparticles in neat and DOP-plasticized PS, the η increased with time initially, and only asymptotically approached a steady-state value after thermal annealing for ∼100 to ∼200 h...
July 12, 2017: Soft Matter
https://www.readbyqxmd.com/read/28699065/n-protonated-isomers-and-coulombic-barriers-to-dissociation-of-doubly-protonated-ala8arg
#7
Fredrik Haeffner, Karl K Irikura
Collision-induced dissociation (or tandem mass spectrometry, MS/MS) of a protonated peptide results in a spectrum of fragment ions that is useful for inferring amino acid sequence. This is now commonplace and a foundation of proteomics. The underlying chemical and physical processes are believed to be those familiar from physical organic chemistry and chemical kinetics. However, first-principles predictions remain intractable because of the conflicting necessities for high accuracy (to achieve qualitatively correct kinetics) and computational speed (to compensate for the high cost of reliable calculations on such large molecules)...
July 11, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28695860/dna-conformational-transitions-inferred-from-re-evaluation-of-m-fo-d-fc-electron-density-maps
#8
Tomoko Sunami, Toshiyuki Chatake, Hidetoshi Kono
Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packaging etc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28693450/transition-to-parenthood-in-the-neonatal-care-unit-a-qualitative-study-and-conceptual-model-designed-to-illuminate-parent-and-professional-views-of-the-impact-of-webcam-technology
#9
Susan Kerr, Caroline King, Rhona Hogg, Kerri McPherson, Janet Hanley, Maggie Brierton, Sean Ainsworth
BACKGROUND: Complications during pregnancy, childbirth and/or the postnatal period may result in the admission of a baby to a neonatal unit (NNU). While the survival and long-term prospects of high-risk infants are enhanced by admission, the enforced separation of the parent and child may have psychological consequences for both. There is a need to develop and evaluate interventions to help parents 'feel closer' to their infants in circumstances where they are physically separated from them...
July 11, 2017: BMC Pediatrics
https://www.readbyqxmd.com/read/28691367/the-photoinduced-trans-to-cis-phase-transition-of-polycrystalline-azobenzene-at-low-irradiances-occurs-in-the-solid-state
#10
Ujjal Bhattacharjee, Daniel Freppon, Long Men, Javier Vela, Emily A Smith, Jacob W Petrich
The ability to produce large-scale, reversible structural changes in a variety of materials by photoexcitation of a wide variety of azobenzene derivatives has been recognized for almost two decades. Because photoexcitation of trans-azobenzene produces the cis isomer in solution, it has generally been inferred that the macroscopic structural changes occurring in materials are also initiated by a similar large-amplitude, trans-to-cis isomerization. This work provides the first demonstration that a trans-to-cis photoisomerization occurs in polycrystalline azobenzene, and is consistent with the previously hypothesized nature of the trigger in the photoactuated mechanisms of the materials in question...
July 9, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28682091/a-quantum-probability-framework-for-human-probabilistic-inference
#11
Jennifer S Trueblood, James M Yearsley, Emmanuel M Pothos
There is considerable variety in human inference (e.g., a doctor inferring the presence of a disease, a juror inferring the guilt of a defendant, or someone inferring future weight loss based on diet and exercise). As such, people display a wide range of behaviors when making inference judgments. Sometimes, people's judgments appear Bayesian (i.e., normative), but in other cases, judgments deviate from the normative prescription of classical probability theory. How can we combine both Bayesian and non-Bayesian influences in a principled way? We propose a unified explanation of human inference using quantum probability theory...
July 6, 2017: Journal of Experimental Psychology. General
https://www.readbyqxmd.com/read/28680063/bi-2212-1t-tas2-van-der-waals-junctions-interplay-of-proximity-induced-high-t-c-superconductivity-and-cdw-order
#12
Ang J Li, Xiaochen Zhu, G R Stewart, Arthur F Hebard
Understanding the coexistence, competition and/or cooperation between superconductivity and charge density waves (CDWs) in the transition metal dichalcogenides (TMDs) is an elusive goal which, when realized, promises to reveal fundamental information on this important class of materials. Here, we use four-terminal current-voltage measurements to study the Van der Waals interface between freshly exfoliated flakes of the high-T c superconductor, Bi-2212, and the CDW-dominated TMD layered material, 1T-TaS2. For highly transparent barriers, there is a pronounced Andreev reflection feature providing evidence for proximity-induced high-T c superconductivity in 1T-TaS2 with a surprisingly large energy gap (~20 meV) equal to half that of intrinsic Bi-2212 (~40 meV)...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28679721/the-importance-of-offshore-origination-revealed-through-ophiuroid-phylogenomics
#13
Guadalupe Bribiesca-Contreras, Heroen Verbruggen, Andrew F Hugall, Timothy D O'Hara
Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome...
July 12, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28674260/relaxin-ameliorates-renal-fibrosis-and-expression-of-endothelial-cell-transition-markers-in-rats-of-isoproterenol-induced-heart-failure
#14
Gaoshu Zheng, Jiejie Cai, Xingxing Chen, Lingzhi Chen, Wenhua Ge, Xi Zhou, Hao Zhou
There may be cardio-renal interactions in rats of isoproterenol-induced heart failure, which may be associated with renal fibrosis and endothelial-to-mesenchymal transition (EndMT). Since its discovery, relaxin (RLX) which was regarded as a reproductive hormone for a long time, is recently considered an effective antifibrotic hormone in cardiac and renal fibrosis. We studied whether RLX diminished renal fibrosis in rats of isoproterenol (Iso)-induced heart failure and investigated the mechanism. Fifty male Sprague-Dawley rats were separated into five groups for treatment: control; Iso subcutaneously injection to induce heart failure, which led to renal fibrosis; RLX subcutaneously injection at low, medium and high dose (0...
2017: Biological & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28672160/origin-of-the-retroviruses-when-where-and-how
#15
REVIEW
Alexander Hayward
Retroviruses are a virus family of considerable medical and veterinary importance. Additionally, it is now clear that endogenous retroviruses (ERVs) comprise significant portions of vertebrate genomes. Until recently, very little was known about the deep evolutionary origins of retroviruses. However, advances in genomics and bioinformatics have opened the way for great strides in understanding. Recent research employing a wide variety of bioinformatic approaches has demonstrated that retroviruses evolved during the early Palaeozoic Era, between 460 and 550 million years ago, providing the oldest inferred date estimate for any virus group...
June 30, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28670785/constraining-the-timing-of-the-great-oxidation-event-within-the-rubisco-phylogenetic-tree
#16
B Kacar, V Hanson-Smith, Z R Adam, N Boekelheide
Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components...
July 3, 2017: Geobiology
https://www.readbyqxmd.com/read/28662317/clonestimate-a-bayesian-method-for-quantifying-rates-of-clonality-of-populations-genotyped-at-two-time-steps
#17
Ronan Becheler, Jean-Pierre Masson, Sophie Arnaud-Haond, Fabien Halkett, Stéphanie Mariette, Marie-Laure Guillemin, Myriam Valero, Christophe Destombe, Solenn Stoeckel
Partial clonality is commonly used in Eukaryotes and has large consequences for their evolution and ecology. Assessing accurately the relative importance of clonal versus sexual reproduction matters for studying and managing such species. Here, we proposed a Bayesian approach, ClonEstiMate, to infer rates of clonality c from populations sampled twice over a short time interval, ideally one generation time. The method relies on the likelihood of the transitions between genotype frequencies of ancestral and descendent populations, using an extended Wright-Fisher model explicitly integrating reproductive modes...
June 29, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28659714/celltrans-an-r-package-to-quantify-stochastic-cell-state-transitions
#18
Thomas Buder, Andreas Deutsch, Michael Seifert, Anja Voss-Böhme
Many normal and cancerous cell lines exhibit a stable composition of cells in distinct states which can, e.g., be defined on the basis of cell surface markers. There is evidence that such an equilibrium is associated with stochastic transitions between distinct states. Quantifying these transitions has the potential to better understand cell lineage compositions. We introduce CellTrans, an R package to quantify stochastic cell state transitions from cell state proportion data from fluorescence-activated cell sorting and flow cytometry experiments...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28644666/frictional-resistance-within-the-wake-of-frictional-rupture-fronts
#19
Ilya Svetlizky, Elsa Bayart, Gil Cohen, Jay Fineberg
Frictional resistance to slip, τ, is determined by the real area of contact, A, and the shear strength of the contacts forming the frictional interface. We perform simultaneous high-speed local measurements of τ and A at the tail of propagating rupture fronts. Rate dependence is investigated over 2 orders of magnitude of local slip velocities which reach up to ∼1  m/s. A critical slip velocity is observed that signifies a transition in the frictional behavior: enhanced velocity weakening of A and τ...
June 9, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28642015/convergent-and-unidirectional-evolution-of-extremely-long-aedeagi-in-the-largest-feather-mite-genus-proctophyllodes-acari-proctophyllodidae-evidence-from-comparative-molecular-and-morphological-phylogenetics
#20
Pavel B Klimov, Sergey V Mironov, Barry M OConnor
Proctophyllodid feather mites (400+ species) are permanent (full-time) symbionts commonly occurring on passerine birds. Phenotypic evolution of these mites appears to be greatly influenced by characters related to reproduction (>87.5% of a total of 32 taxonomically important discrete characters) and male genitalic characters (21.9%). Because sexual selection could the major evolutionary driver in this system, we test the theoretical expectation that genitalic or sexually dimorphic characters should evolve more rapidly and divergently then other characters...
June 19, 2017: Molecular Phylogenetics and Evolution
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