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https://www.readbyqxmd.com/read/28228094/sfreemap-a-simulation-free-tool-for-stochastic-mapping
#1
Diego Pasqualin, Marcos Barbeitos, Fabiano Silva
BACKGROUND: Stochastic mapping is frequently used in comparative biology to simulate character evolution, enabling the probabilistic computation of statistics such as number of state transitions along a tree and distribution of states in its internal nodes. Common implementations rely on Continuous-time Markov Chain simulations whose parameters are difficult to adjust and subjected to inherent inaccuracy. Thus, researchers must run a large number of simulations in order to obtain adequate estimates...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28228023/reconciling-transition-path-time-and-rate-measurements-in-reactions-with-large-entropic-barriers
#2
Dmitrii E Makarov
Recent experiments and simulation studies showed that protein/DNA folding barriers inferred from folding rates or from potentials of mean force are often much higher than the barriers estimated from the distributions of transition path times. Here a toy model is used to explain a possible origin of this effect: It is shown that when the transition in question involves an entropic barrier, the one-dimensional Langevin model commonly used to interpret experimental data, while adequately predicting the transition rate, fails to describe the properties of the subset of the trajectories that form the transition path ensemble; the latter may still be describable in terms of a one-dimensional model, but with a different potential, just as observed experimentally...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28227647/a-feasibility-study-of-depth-image-based-intent-recognition-for-lower-limb-prostheses
#3
Huseyin Atakan Varol, Yerzhan Massalin, Huseyin Atakan Varol, Yerzhan Massalin, Huseyin Atakan Varol, Yerzhan Massalin
This paper presents our preliminary work on a depth camera based intent recognition system intended for future use in robotic prosthetic legs. The approach infers the activity mode of the subject for standing, walking, running, stair ascent and stair descent modes only using data from the depth camera. Depth difference images are also used to increase the performance of the approach by discriminating between static and dynamic instances. After confidence map based filtering, simple features such as mean, maximum, minimum and standard deviation are extracted from rectangular regions of the frames...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28216511/global-kinetoplastea-phylogeny-inferred-from-a-large-scale-multigene-alignment-including-parasitic-species-for-better-understanding-transitions-from-a-free-living-to-a-parasitic-lifestyle
#4
Euki Yazaki, Sohta A Ishikawa, Keitaro Kume, Akira Kumagai, Takashi Kamaishi, Goro Tanifuji, Tetsuo Hashimoto, Yuji Inagaki
All members of the order Trypanosomatida known to date are parasites that are most likely descendants of a free-living ancestor. Trypanosomatids are an excellent model to assess the transition from a free-living to a parasitic lifestyle, because a large amount of experimental data has been accumulated for well-studied members that are harmful to humans and livestock (Trypanosoma spp. and Leishmania spp.). However, recent advances in our understanding of the diversity of trypanosomatids and their close relatives (i...
February 20, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28214993/scaleus-semantic-web-services-integration-for-biomedical-applications
#5
Pedro Sernadela, Lorena González-Castro, José Luís Oliveira
In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web...
April 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28211249/improving-the-interpretability-of-climate-landscape-metrics-an-ecological-risk-analysis-of-japan-s-marine-protected-areas
#6
Jorge García Molinos, Shintaro Takao, Naoki H Kumagai, Elvira S Poloczanska, Michael T Burrows, Masahiko Fujii, Hiroya Yamano
Conservation efforts strive to protect significant swaths of terrestrial, freshwater and marine ecosystems from a range of threats. As climate change becomes an increasing concern, these efforts must take into account how resilient protected spaces will be in the face of future drivers of change such as warming temperatures. Climate landscape metrics, which signal the spatial magnitude and direction of climate change, support a convenient initial assessment of potential threats to and opportunities within ecosystems to inform conservation and policy efforts where biological data are not available...
February 17, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28183976/deterministic-entanglement-generation-from-driving-through-quantum-phase-transitions
#7
Xin-Yu Luo, Yi-Quan Zou, Ling-Na Wu, Qi Liu, Ming-Fei Han, Meng Khoon Tey, Li You
Many-body entanglement is often created through the system evolution, aided by nonlinear interactions between the constituting particles. These very dynamics, however, can also lead to fluctuations and degradation of the entanglement if the interactions cannot be controlled. Here, we demonstrate near-deterministic generation of an entangled twin-Fock condensate of ~11,000 atoms by driving a arubidium-87 Bose-Einstein condensate undergoing spin mixing through two consecutive quantum phase transitions (QPTs)...
February 10, 2017: Science
https://www.readbyqxmd.com/read/28167884/pathological-status-of-pyricularia-angulata-causing-blast-and-pitting-disease-of-banana-in-eastern-india
#8
Sangeetha Ganesan, Hari Shankar Singh, Srinivas Petikam, Debasish Biswal
Incidence of leaf blast on nursery plants and pitting disease on maturing banana bunches has been recorded in banana plantations during rainy season in Eastern India during 2014 to 2015. Taxonomical identification as well as DNA sequence analysis of the internal transcribed spacer region of fungus isolated from affected tissue culture derived plantlets and fruits confirmed the pathogen to be Pyricularia angulata Hashioka "in both the cases". Koch's postulates were proved on young plantlets as well as on maturing fruits of cv...
February 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28153470/from-hiv-infection-to-therapeutic-response-a-population-based-longitudinal-hiv-cascade-of-care-study-in-kwazulu-natal-south-africa
#9
Noah Haber, Frank Tanser, Jacob Bor, Kevindra Naidu, Tinofa Mutevedzi, Kobus Herbst, Kholoud Porter, Deenan Pillay, Till Bärnighausen
BACKGROUND: Standard approaches to estimation of losses in the HIV cascade of care are typically cross-sectional and do not include the population stages before linkage to clinical care. We used indiviual-level longitudinal cascade data, transition by transition, including population stages, both to identify the health-system losses in the cascade and to show the differences in inference between standard methods and the longitudinal approach. METHODS: We used non-parametric survival analysis to estimate a longitudinal HIV care cascade for a large population of people with HIV residing in rural KwaZulu-Natal, South Africa...
January 30, 2017: Lancet HIV
https://www.readbyqxmd.com/read/28137461/investigating-the-effects-of-erythrosine-b-on-amyloid-fibril-formation-derived-from-lysozyme
#10
Chun-Tien Kuo, Yi-Lin Chen, Wei-Tse Hsu, Su-Chun How, Yu-Hong Cheng, Shu-Shun Hsueh, Hwai-Shen Liu, Ta-Hsien Lin, Josephine W Wu, Steven S-S Wang
Formation of amyloid fibrils has been associated with at least 30 different protein aggregation diseases. The 129-residue polypeptide hen lysozyme, which is structurally homologous to human lysozyme, has been demonstrated to exhibit amyloid fibril-forming propensity in vitro. This study is aimed at exploring the influence of erythrosine B on the in vitro amyloid fibril formation of hen lysozyme at pH 2.0 and 55°C using ThT binding assay, transmission electron microscopy, far-UV circular dichroism absorption spectroscopy, 1-anilinonaphthalene-8-sulfonic acid fluorescence spectroscopy, and synchronous fluorescence study...
January 27, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28128205/microwave-photon-fock-state-generation-by-stimulated-raman-adiabatic-passage
#11
Shavindra P Premaratne, F C Wellstood, B S Palmer
The deterministic generation of non-classical states of light, including squeezed states, Fock states and Bell states, plays an important role in quantum information processing and exploration of the physics of quantum entanglement. Preparation of these non-classical states in resonators is non-trivial due to their inherent harmonicity. Here we use stimulated Raman adiabatic passage to generate microwave photon Fock states in a superconducting circuit quantum electrodynamics system comprised of a fixed-frequency transmon qubit in a three-dimensional microwave cavity at 20 mK...
January 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/28126515/post-eocene-climate-change-across-continental-australia-and-the-diversification-of-australasian-spiny-trapdoor-spiders-idiopidae-arbanitinae
#12
Michael G Rix, Steven J B Cooper, Karen Meusemann, Seraina Klopfstein, Sophie E Harrison, Mark S Harvey, Andrew D Austin
The formation and spread of the Australian arid zone during the Neogene was a profoundly transformative event in the biogeographic history of Australia, resulting in extinction or range contraction in lineages adapted to mesic habitats, as well as diversification and range expansion in arid-adapted taxa (most of which evolved from mesic ancestors). However, the geographic origins of the arid zone biota are still relatively poorly understood, especially among highly diverse invertebrate lineages, many of which are themselves poorly documented at the species level...
January 23, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28121133/probing-the-structural-mechanism-of-partial-agonism-in-glycine-receptors-using-the-fluorescent-artificial-amino-acid-anap
#13
Ming S Soh, Argel Estrada-Mondragon, Nela Durisic, Angelo Keramidas, Joseph W Lynch
The efficacy of an agonist at a pentameric ligand-gated ion channel is determined by the rate at which it induces a conformational change from the resting closed state to a preopen ("flip") state. If the ability of an agonist to promote this isomerization is sufficiently low, then it becomes a partial agonist. As partial agonists at pentameric ligand-gated ion channels show considerable promise as therapeutics, understanding the structural basis of the resting-flip-state isomerization may provide insight into therapeutic design...
February 2, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28120839/signatures-of-human-european-palaeolithic-expansion-shown-by-resequencing-of-non-recombining-x-chromosome-segments
#14
Pierpaolo Maisano Delser, Rita Neumann, Stéphane Ballereau, Pille Hallast, Chiara Batini, Daniel Zadik, Mark A Jobling
Human genetic diversity in Europe has been extensively studied using uniparentally inherited sequences (mitochondrial DNA (mtDNA) and the Y chromosome), which reveal very different patterns indicating sex-specific demographic histories. The X chromosome, haploid in males and inherited twice as often from mothers as from fathers, could provide insights into past female behaviours, but has not been extensively investigated. Here, we use HapMap single-nucleotide polymorphism data to identify genome-wide segments of the X chromosome in which recombination is historically absent and mutations are likely to be the only source of genetic variation, referring to these as phylogeographically informative haplotypes on autosomes and X chromosome (PHAXs)...
January 25, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28116490/comprehensive-and-accurate-tracking-of-carbon-origin-of-lc-tandem-mass-spectrometry-collisional-fragments-for-13-c-mfa
#15
Jannick Kappelmann, Bianca Klein, Petra Geilenkirchen, Stephan Noack
In recent years the benefit of measuring positionally resolved (13)C-labeling enrichment from tandem mass spectrometry (MS/MS) collisional fragments for improved precision of (13)C-Metabolic Flux Analysis ((13)C-MFA) has become evident. However, the usage of positional labeling information for (13)C-MFA faces two challenges: (1) The mass spectrometric acquisition of a large number of potentially interfering mass transitions may hamper accuracy and sensitivity. (2) The positional identity of carbon atoms of product ions needs to be known...
January 23, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28114901/cryptic-diversity-geographical-endemism-and-allopolyploidy-in-ne-pacific-seaweeds
#16
João Neiva, Ester A Serrão, Laura Anderson, Peter T Raimondi, Neusa Martins, Licínia Gouveia, Cristina Paulino, Nelson C Coelho, Kathy Ann Miller, Daniel C Reed, Lydia B Ladah, Gareth A Pearson
BACKGROUND: Molecular markers are revealing a much more diverse and evolutionarily complex picture of marine biodiversity than previously anticipated. Cryptic and/or endemic marine species are continually being found throughout the world oceans, predominantly in inconspicuous tropical groups but also in larger, canopy-forming taxa from well studied temperate regions. Interspecific hybridization has also been found to be prevalent in many marine groups, for instance within dense congeneric assemblages, with introgressive gene-flow being the most common outcome...
January 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28114025/ventral-tegmental-area-dopamine-neurons-firing-model-reveals-prenatal-nicotine-induced-alterations
#17
Andrei Dragomir, Yasemin M Akay, Die Zhang, Metin Akay
The dopamine (DA) neurons found in the Ventral Tegmental Area (VTA) are widely involved in the addiction and natural reward circuitry of the brain. Their firing patterns were shown to be important modulators of dopamine release and repetitive burst-like firing activity was highlighted as a major firing pattern of DA neurons in the VTA. In the present study we use a state space model to characterize the DA neurons firing patterns, and trace transitions of neural activity through bursting and non-bursting states...
December 6, 2016: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28113626/saliency-transfer-a-correspondence-based-approach-for-saliency-detection
#18
Wenguan Wang, Jianbing Shen, Ling Shao, Fatih Porikli
In this paper, we show that large annotated datasets datasets have great potential to provide strong priors for saliency estimation rather than merely serving for benchmark evaluations. To this end, we present a novel image saliency detection method called saliency transfer. Given an input image, we first retrieve a support set of best matches from the large database of saliency annotated images. Then, we assign the transitional saliency scores by warping the support set annotations onto the input image according to computed dense correspondences...
August 19, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28105958/dmirnet-inferring-direct-microrna-mrna-association-networks
#19
Minsu Lee, HyungJune Lee
BACKGROUND: MicroRNAs (miRNAs) play important regulatory roles in the wide range of biological processes by inducing target mRNA degradation or translational repression. Based on the correlation between expression profiles of a miRNA and its target mRNA, various computational methods have previously been proposed to identify miRNA-mRNA association networks by incorporating the matched miRNA and mRNA expression profiles. However, there remain three major issues to be resolved in the conventional computation approaches for inferring miRNA-mRNA association networks from expression profiles...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28097055/comprehensive-transcriptome-analysis-provides-new-insights-into-nutritional-strategies-and-phylogenetic-relationships-of-chrysophytes
#20
Daniela Beisser, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, Jens Boenigk
BACKGROUND: Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms...
2017: PeerJ
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