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https://www.readbyqxmd.com/read/28819787/flexible-semi-parametric-regression-of-state-occupational-probabilities-in-a-multistate-model-with-right-censored-data
#1
Chathura Siriwardhana, K B Kulasekera, Somnath Datta
Inference for the state occupation probabilities, given a set of baseline covariates, is an important problem in survival analysis and time to event multistate data. We introduce an inverse censoring probability re-weighted semi-parametric single index model based approach to estimate conditional state occupation probabilities of a given individual in a multistate model under right-censoring. Besides obtaining a temporal regression function, we also test the potential time varying effect of a baseline covariate on future state occupation...
August 17, 2017: Lifetime Data Analysis
https://www.readbyqxmd.com/read/28819768/maternal-obesity-is-associated-with-gut-microbial-metabolic-potential-in-offspring-during-infancy
#2
Tomás Cerdó, Alicia Ruiz, Ruy Jáuregui, Hatim Azaryah, Francisco José Torres-Espínola, Luz García-Valdés, M Teresa Segura, Antonio Suárez, Cristina Campoy
Children born to obese mothers are at increased risk for obesity, but the mechanisms behind this association are not fully understood. Our study aimed to investigate differences in the functions encoded by the microbiome of infants at 18 months of age when the transition from early infant-feeding to solid family foods is established. To investigate the impact of maternal prepregnancy body mass index on infants' gut microbiome, faecal samples from infants born to normoweight (n = 21) and obese mothers (n = 18) were analysed by 16S rRNA gene sequencing and a functional-inference-based microbiome analysis...
August 17, 2017: Journal of Physiology and Biochemistry
https://www.readbyqxmd.com/read/28814035/decoding-of-individual-finger-movements-from-surface-emg-signals-using-vector-autoregressive-hierarchical-hidden-markov-models-varhhmm
#3
Nebojsa Malesevic, Dimitrije Markovic, Gunter Kanitz, Marco Controzzi, Christian Cipriani, Christian Antfolk
In this paper we present a novel method for predicting individual fingers movements from surface electromyography (EMG). The method is intended for real-time dexterous control of a multifunctional prosthetic hand device. The EMG data was recorded using 16 single-ended channels positioned on the forearm of healthy participants. Synchronously with the EMG recording, the subjects performed consecutive finger movements based on the visual cues. Our algorithm could be described in following steps: extracting mean average value (MAV) of the EMG to be used as the feature for classification, piece-wise linear modeling of EMG feature dynamics, implementation of hierarchical hidden Markov models (HHMM) to capture transitions between linear models, and implementation of Bayesian inference as the classifier...
July 2017: IEEE ... International Conference on Rehabilitation Robotics: [proceedings]
https://www.readbyqxmd.com/read/28808680/early-formation-of-planetary-building-blocks-inferred-from-pb-isotopic-ages-of-chondrules
#4
Jean Bollard, James N Connelly, Martin J Whitehouse, Emily A Pringle, Lydie Bonal, Jes K Jørgensen, Åke Nordlund, Frédéric Moynier, Martin Bizzarro
The most abundant components of primitive meteorites (chondrites) are millimeter-sized glassy spherical chondrules formed by transient melting events in the solar protoplanetary disk. Using Pb-Pb dates of 22 individual chondrules, we show that primary production of chondrules in the early solar system was restricted to the first million years after the formation of the Sun and that these existing chondrules were recycled for the remaining lifetime of the protoplanetary disk. This finding is consistent with a primary chondrule formation episode during the early high-mass accretion phase of the protoplanetary disk that transitions into a longer period of chondrule reworking...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28802449/living-with-an-autonomous-spatiotemporal-home-heating-system-exploration-of-the-user-experiences-ux-through-a-longitudinal-technology-intervention-based-mixed-methods-approach
#5
Martin Kruusimagi, Sarah Sharples, Darren Robinson
Rising energy demands place pressure on domestic energy consumption, but savings can be delivered through home automation and engaging users with their heating and energy behaviours. The aim of this paper is to explore user experiences (UX) of living with an automated heating system regarding experiences of control, understanding of the system, emerging thermal behaviours, and interactions with the system as this area is not sufficiently researched in the existing homes setting through extended deployment. We present a longitudinal deployment of a quasi-autonomous spatiotemporal home heating system in three homes...
November 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/28789556/optical-determination-of-the-electronic-coupling-and-intercalation-geometry-of-thiazole-orange-homodimer-in-dna
#6
Paul D Cunningham, William P Bricker, Sebastián A Díaz, Igor L Medintz, Mark Bathe, Joseph S Melinger
Sequence-selective bis-intercalating dyes exhibit large increases in fluorescence in the presence of specific DNA sequences. This property makes this class of fluorophore of particular importance to biosensing and super-resolution imaging. Here we report ultrafast transient anisotropy measurements of resonance energy transfer (RET) between thiazole orange (TO) molecules in a complex formed between the homodimer TOTO and double-stranded (ds) DNA. Biexponential homo-RET dynamics suggest two subpopulations within the ensemble: 80% intercalated and 20% non-intercalated...
August 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28778052/interaction-of-levofloxacin-with-lung-surfactant-at-the-air-water-interface
#7
Stephanie Ortiz-Collazos, Evelina D Estrada-López, Alline A Pedreira, Paulo H S Picciani, Osvaldo N Oliveira, Andre S Pimentel
The molecular-level interaction of levofloxacin with lung surfactant was investigated using Langmuir monolayers and atomistic molecular dynamics (MD) simulations. In the simulation, the DPPC/POPC mixed monolayer was used as a lung surfactant model and the molecules of levofloxacin were placed at the air-lipid interface to mimic the adsorption process on the lung surfactant model. The simulation results indicate that amphoteric levofloxacin expands the lung surfactant, also stabilizing the film for levofloxacin fractions until 10% w/w at least...
July 27, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28776995/effect-of-interfacial-alloying-versus-volume-scaling-on-auger-recombination-in-compositionally-graded-semiconductor-quantum-dots
#8
Young-Shin Park, Jaehoon Lim, Nikolay S Makarov, Victor I Klimov
Auger recombination is a nonradiative three-particle process wherein the electron-hole recombination energy dissipates as a kinetic energy of a third carrier. Auger decay is enhanced in quantum-dot (QD) forms of semiconductor materials compared to their bulk counterparts. Because this process is detrimental to many prospective applications of the QDs, the development of effective approaches for suppressing Auger recombination has been an important goal in the QD field. One such approach involves "smoothing" of the confinement potential, which suppresses the intraband transition involved in the dissipation of the electron-hole recombination energy...
August 4, 2017: Nano Letters
https://www.readbyqxmd.com/read/28754764/plastome-sequences-of-an-ancient-fern-lineage-reveal-remarkable-changes-in-gene-content-and-architecture
#9
Paulo H Labiak, Kenneth G Karol
PREMISE OF THE STUDY: Comparative analyses of plastid genomes have suggested that gene order and content are relatively stable across the main groups of land plants, with significant changes rarely reported. We examine plastome organization and RNA editing in ferns and report changes that add valuable information on plastome evolution in land plants. METHODS: Using next-generation sequencing methods, we fully sequenced plastomes from three species of Schizaeaceae, and compared their plastomes with other groups of land plants to study changes in gene composition, plastome architecture, and putative RNA editing sites...
July 28, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28741177/birth-birth-death-processes-and-their-computable-transition-probabilities-with-biological-applications
#10
Lam Si Tung Ho, Jason Xu, Forrest W Crawford, Vladimir N Minin, Marc A Suchard
Birth-death processes track the size of a univariate population, but many biological systems involve interaction between populations, necessitating models for two or more populations simultaneously. A lack of efficient methods for evaluating finite-time transition probabilities of bivariate processes, however, has restricted statistical inference in these models. Researchers rely on computationally expensive methods such as matrix exponentiation or Monte Carlo approximation, restricting likelihood-based inference to small systems, or indirect methods such as approximate Bayesian computation...
July 24, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28739577/common-pitfalls-and-mistakes-in-the-set-up-analysis-and-interpretation-of-results-in-network-meta-analysis-what-clinicians-should-look-for-in-a-published-article
#11
Anna Chaimani, Georgia Salanti, Stefan Leucht, John R Geddes, Andrea Cipriani
OBJECTIVE: Several tools have been developed to evaluate the extent to which the findings from a network meta-analysis would be valid; however, applying these tools is a time-consuming task and often requires specific expertise. Clinicians have little time for critical appraisal, and they need to understand the key elements that help them select network meta-analyses that deserve further attention, optimising time and resources. This paper is aimed at providing a practical framework to assess the methodological robustness and reliability of results from network meta-analysis...
July 24, 2017: Evidence-based Mental Health
https://www.readbyqxmd.com/read/28733657/a-gene-network-regulated-by-fgf-signalling-during-ear-development
#12
Maryam Anwar, Monica Tambalo, Ramya Ranganathan, Timothy Grocott, Andrea Streit
During development cell commitment is regulated by inductive signals that are tightly controlled in time and space. In response, cells activate specific programmes, but the transcriptional circuits that maintain cell identity in a changing signalling environment are often poorly understood. Specification of inner ear progenitors is initiated by FGF signalling. Here, we establish the genetic hierarchy downstream of FGF by systematic analysis of many ear factors combined with a network inference approach. We show that FGF rapidly activates a small circuit of transcription factors forming positive feedback loops to stabilise otic progenitor identity...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729554/comparison-of-traditional-and-new-generation-dna-markers-declares-high-genetic-diversity-and-differentiated-population-structure-of-wild-almond-species
#13
Karim Sorkheh, Mehrana Koohi Dehkordi, Sezai Ercisli, Attila Hegedus, Júlia Halász
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724627/using-step-width-to-compare-locomotor-biomechanics-between-extinct-non-avian-theropod-dinosaurs-and-modern-obligate-bipeds
#14
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
#15
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
#16
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
#17
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
#18
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...
September 1, 2017: Life Sciences
https://www.readbyqxmd.com/read/28702673/unexpected-thermal-annealing-effects-on-the-viscosity-of-polymer-nanocomposites
#19
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...
August 9, 2017: Soft Matter
https://www.readbyqxmd.com/read/28699065/n-protonated-isomers-and-coulombic-barriers-to-dissociation-of-doubly-protonated-ala8arg
#20
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
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