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Transitive inferences

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https://www.readbyqxmd.com/read/28524679/transition-from-collisional-to-collisionless-regimes-in-interpenetrating-plasma-flows-on-the-national-ignition-facility
#1
J S Ross, D P Higginson, D Ryutov, F Fiuza, R Hatarik, C M Huntington, D H Kalantar, A Link, B B Pollock, B A Remington, H G Rinderknecht, G F Swadling, D P Turnbull, S Weber, S Wilks, D H Froula, M J Rosenberg, T Morita, Y Sakawa, H Takabe, R P Drake, C Kuranz, G Gregori, J Meinecke, M C Levy, M Koenig, A Spitkovsky, R D Petrasso, C K Li, H Sio, B Lahmann, A B Zylstra, H-S Park
A study of the transition from collisional to collisionless plasma flows has been carried out at the National Ignition Facility using high Mach number (M>4) counterstreaming plasmas. In these experiments, CD-CD and CD-CH planar foils separated by 6-10 mm are irradiated with laser energies of 250 kJ per foil, generating ∼1000  km/s plasma flows. Varying the foil separation distance scales the ion density and average bulk velocity and, therefore, the ion-ion Coulomb mean free path, at the interaction region at the midplane...
May 5, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28518200/multichromophoric-hybrid-species-made-of-perylene-bisimide-derivatives-and-ru-ii-and-os-ii-polypyridine-subunits
#2
Francesco Nastasi, Giuseppina La Ganga, Sebastiano Campagna, Zois Syrgiannis, Francesco Rigodanza, Stefania Vitale, Antonino Licciardello, Maurizio Prato
Herein, the synthesis and the photophysical and redox properties of a new perylene bisimide (PBI) species (L), bearing two 1,10-phenanthroline (phen) ligands at the two imide positions of the PBI, and its dinuclear Ru(ii) and Os(ii) complexes, [(bpy)2Ru(μ-L)Ru(bpy)2](PF6)4 (Ru2; bpy = 2,2'-bipyridine) and [(Me2-bpy)2Os(μ-L)Os(Me2-bpy)2](PF6)4 (Os2; Me2-bpy = (4,4'-dimethyl)-2,2'-bipyridine), are reported. The absorption spectra of the compounds are dominated by the structured bands of the PBI subunit due to the lowest-energy spin-allowed π-π* transition...
May 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28515314/the-mzidentml-data-standard-version-1-2-supporting-advances-in-proteome-informatics
#3
Juan Antonio Vizcaíno, Gerhard Mayer, Simon R Perkins, Harald Barsnes, Marc Vaudel, Yasset Perez-Riverol, Tobias Ternent, Julian Uszkoreit, Martin Eisenacher, Lutz Fischer, Juri Rappsilber, Eugen Netz, Mathias Walzer, Oliver Kohlbacher, Alexander Leitner, Robert J Chalkley, Fawaz Ghali, Salvador Martínez-Bartolomé, Eric W Deutsch, Andrew R Jones
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012 - capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (i) scores associated with localization of modifications on peptides; (ii) statistics performed at the level of peptides; (iii) identification of cross-linked peptides; and (iv) support for proteogenomics approaches...
May 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28514147/fragmentation-of-valence-and-core-shell-cl-2p-excited-c2cl4-molecule
#4
Antonio C F Santos, Michael Alistair MacDonald, Alexandre Braga Rocha, Narayana Perumal Appathurai, Marcelo M Sant'Anna, William Holetz, Ralph Wehlitz, Lucia Zuin
The dynamics of the photo-fragmentation pathways of tetrachloroethylene with photon energies from 15 eV up to 250 eV, encompassing the Cl 2p edge is presented. In order to distinguish the fragmentation channels, the ionic fragments were separated according to their mass to charge ratio, measured in coincidence with the photoelectrons, and collected as a function of the incident photon energy. Distinct minima or maxima are found in the partial ion yield in the region between 40 and 50 eV. These features are believed to be associated with the Cooper minimum which results from a molecular orbital with a strong atomic 3p subshell character...
May 17, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28513668/computational-analysis-of-site-differences-in-selective-aliphatic-c-h-hydroxylation-by-nonheme-iron-oxo-complexes
#5
Jian Wang, Yuan-Yuan Zhao, Po-Heng Lee
Selective C-H hydroxylation by nonheme iron complexes offers a promising method in the field of organic synthesis. Aliphatic C-H bond oxidation reactions of pivalate (R) catalyzed by [Fe(S,S-PDP)(CH3CN)2](2+) (CAT1) were examined using the density functional theory. Our calculations of the CH3CN solvent agree with the experimental findings. However, it was observed that the gas-phase results did not replicate selective C-H hydroxylation observed experimentally when CAT1 catalyzed hydrocarbon oxidations by H2O2via an HO-Fe(V)[double bond, length as m-dash]O oxidant (CAT1a)...
May 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28512037/understanding-behavior-under-nonverbal-transitive-inference-procedures-stimulus-control-topography-analyses
#6
Ann Galizio, Adam H Doughty, Dean C Williams, Kathryn J Saunders
Following training with verbal stimulus relations involving A is greater than B and B is greater than C, verbally-competent individuals reliably select A > C when asked "which is greater, A or C?" (i.e., verbal transitive inference). This result is easy to interpret. Nonhuman animals and humans with and without intellectual disabilities have been exposed to nonverbal transitive-inference procedures involving trained arbitrary stimulus relations. Following the training of A+B-, B+C-, C+D-, and D+E-, B reliably is selected over D (i...
May 13, 2017: Behavioural Processes
https://www.readbyqxmd.com/read/28509342/morphological-and-molecular-characterization-of-bysmatrum-subsalsum-dinophyceae-from-the-western-mediterranean-sea-reveals-the-existence-of-cryptic-species
#7
Sílvia Anglès, Albert Reñé, Esther Garcés, Antonella Lugliè, Nicola Sechi, Jordi Camp, Cecilia Teodora Satta
Bysmatrum subsalsum is a cosmopolitan dinoflagellate species that inhabits marine and transitional habitats. Despite its wide distribution, information on the morphological variability, phylogeny and ecology of B. subsalsum is scarce. In this study, we provide morphological and molecular data on B. subsalsum strains and wild cells from different locations in the Mediterranean Basin. The dynamics of cell abundances and the associated environmental conditions during a field bloom are also described. Genetic sequences of B...
May 16, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28508537/superorganismality-and-caste-differentiation-as-points-of-no-return-how-the-major-evolutionary-transitions-were-lost-in-translation
#8
Jacobus J Boomsma, Richard Gawne
More than a century ago, William Morton Wheeler proposed that social insect colonies can be regarded as superorganisms when they have morphologically differentiated reproductive and nursing castes that are analogous to the metazoan germ-line and soma. Following the rise of sociobiology in the 1970s, Wheeler's insights were largely neglected, and we were left with multiple new superorganism concepts that are mutually inconsistent and uninformative on how superorganismality originated. These difficulties can be traced to the broadened sociobiological concept of eusociality, which denies that physical queen-worker caste differentiation is a universal hallmark of superorganismal colonies...
May 15, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28505197/structure-of-ca2-binding-protein-6-from-entamoeba-histolytica-and-its-involvement-in-trophozoite-proliferation-regulation
#9
Deepshikha Verma, Aruna Murmu, Samudrala Gourinath, Alok Bhattacharya, Kandala V R Chary
Cell cycle of Entamoeba histolytica, the etiological agent of amoebiasis, follows a novel pathway, which includes nuclear division without the nuclear membrane disassembly. We report a nuclear localized Ca2+-binding protein from E. histolytica (abbreviated hereafter as EhCaBP6), which is associated with microtubules. We determined the 3D solution NMR structure of EhCaBP6, and identified one unusual, one canonical and two non-canonical cryptic EF-hand motifs. The cryptic EF-II and EF-IV pair with the Ca2+-binding EF-I and EF-III, respectively, to form a two-domain structure similar to Calmodulin and Centrin proteins...
May 15, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28497967/interactions-of-metal-based-and-ligand-based-electronic-spins-in-neutral-tripyrrindione-%C3%AF-dimers
#10
Ritika Gautam, Andrei V Astashkin, Tsuhen M Chang, Jason Shearer, Elisa Tomat
The ability of tetrapyrrolic macrocycles to stabilize unpaired electrons and engage in π-π interactions is essential for many electron-transfer processes in biology and materials engineering. Herein, we demonstrate that the formation of π dimers is recapitulated in complexes of a linear tripyrrolic analogue of naturally occurring pigments derived from heme decomposition. Hexaethyltripyrrindione (H3TD1) coordinates divalent transition metals (i.e., Pd, Cu, Ni) as a stable dianionic radical and was recently described as a robust redox-active ligand...
May 12, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28494150/non-destructive-redox-quantification-reveals-glassmaking-of-rare-french-gothic-stained-glasses
#11
Myrtille O J Y Hunault, Claudine Loisel, Fanny Bauchau, Quentin Lemasson, Claire Pacheco, Laurent Pichon, Brice Moignard, Karine Boulanger, Michel Hérold, Georges Calas, Isabelle Pallot-Frossard
The sophisticated colors of medieval glasses arise from their transition metal (TM) impurities, and capture information on the ancient glassmaking techniques. Beyond the glass chemical composition, the TM redox is also a key factor of the glass color but its quantification without any sampling is a challenge. We report the combination of non-destructive and non-invasive quantitative analyses of the chemical composition by PIXE-PIGE mappings and of the color and TM element speciation by optical absorption spectroscopy performed on a red-blue-purple striped glass from the stained glass windows of the Sainte-Chapelle in Paris (France) during its restoration...
May 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28489906/neocortical-activity-is-stimulus-and-scale-invariant
#12
Yahya Karimipanah, Zhengyu Ma, Jae-Eun Kang Miller, Rafael Yuste, Ralf Wessel
Mounting evidence supports the hypothesis that the cortex operates near a critical state, defined as the transition point between order (large-scale activity) and disorder (small-scale activity). This criticality is manifested by power law distribution of the size and duration of spontaneous cascades of activity, which are referred as neuronal avalanches. The existence of such neuronal avalanches has been confirmed by several studies both in vitro and in vivo, among different species and across multiple spatial scales...
2017: PloS One
https://www.readbyqxmd.com/read/28488774/fscn1-is-upregulated-by-snai2-and-promotes-epithelial-to-mesenchymal-transition-in-head-and-necksquamous-cell-carcinoma
#13
Lei Wang, YaoPeng Jia, ZengYu Jiang, Wei Gao, BinQuan Wang
In this study, we investigated whether there is any association between the expression of FSCN1 and SNAI2and the possible underlying mechanisms in head and neck squamous cell carcinoma (HNSC). In addition, we also investigated whether FSCN1 modulates epithelial to mesenchymal transition (EMT) in HNSC cells. Microarray data of dysregulated genes in HNSC was searched in GEO datasets. The association between FSCN1 expression and the 5-year/10-year overall survival (OS), as well as the correlation between the expression of FSCN1 and SOX2, MYBL2, SNAI2, STAT1 and SOX4 were analyzed based on data in TCGA HNSC cohort (TCGA-HNSC)...
May 10, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28488335/climate-change-and-human-colonization-triggered-habitat-loss-and-fragmentation-in-madagascar
#14
Jordi Salmona, Rasmus Heller, Erwan Quéméré, Lounès Chikhi
The relative effect of past climate fluctuations and anthropogenic activities on current biome distribution is subject to increasing attention, notably in biodiversity hotspots. In Madagascar, where humans arrived in the last ~4-5,000 years, the exact causes of the demise of large vertebrates that cohabited with humans is yet unresolved. The prevailing narrative holds that Madagascar was covered with forest before human arrival, and that the expansion of grasslands was the result of human driven deforestation...
May 10, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28485939/creating-quasi-two-dimensional-cluster-assembled-materials-through-self-assembly-of-a-janus-polyoxometalate-silsesquioxane-co-cluster
#15
Han Wu, Yu-Qi Zhang, Min-Biao Hu, Li-Jun Ren, Yue Lin, Wei Wang
Clusters are an important class of nanoscale molecules or superatoms that exhibit an amazing diversity in structure, chemical composition, shape, and functionality. Assembling two types of clusters is creating emerging cluster-assembled materials (CAMs). In this paper, we report an effective approach to produce quasi two-dimensional (2D) CAMs of two types of spherelike clusters, polyhedral oligomeric silsesquioxanes (POSS), and polyoxometalates (POM). To avoid macrophase separation between the two clusters, they are covalently linked to form a POM-POSS cocluster with Janus characteristics and a dumbbell shape...
May 15, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28479747/elucidation-of-the-sequential-transcriptional-activity-in-escherichia-coli-using-time-series-rna-seq-data
#16
Pui Shan Wong, Kosuke Tashiro, Satoru Kuhara, Sachiyo Aburatani
Functional genomics and gene regulation inference has readily expanded our knowledge and understanding of gene interactions with regards to expression regulation. With the advancement of transcriptome sequencing in time-series comes the ability to study the sequential changes of the transcriptome. Here, we present a new method to augment regulation networks accumulated in literature with transcriptome data gathered from time-series experiments to construct a sequential representation of transcription factor activity...
2017: Bioinformation
https://www.readbyqxmd.com/read/28479476/high-resolution-magnetic-resonance-imaging-reveals-nuclei-of-the-human-amygdala-manual-segmentation-to-automatic-atlas
#17
Z M Saygin, D Kliemann, J E Iglesias, A J W van der Kouwe, E Boyd, M Reuter, A Stevens, K Van Leemput, A McKee, M P Frosch, B Fischl, J C Augustinack
The amygdala is composed of multiple nuclei with unique functions and connections in the limbic system and to the rest of the brain. However, standard in vivo neuroimaging tools to automatically delineate the amygdala into its multiple nuclei are still rare. By scanning postmortem specimens at high resolution (100-150µm) at 7T field strength (n = 10), we were able to visualize and label nine amygdala nuclei (anterior amygdaloid, cortico-amygdaloid transition area; basal, lateral, accessory basal, central, cortical medial, paralaminar nuclei)...
May 4, 2017: NeuroImage
https://www.readbyqxmd.com/read/28475342/strongly-bound-sodium-dodecyl-sulfate-surrounding-single-wall-carbon-nanotubes
#18
Jia Xu, Robert Mueller, Eric Hazelbaker, Yang Zhao, Jean-Claude J Bonzongo, Justin G Clar, Sergey Vasenkov, Kirk J Ziegler
NMR techniques have been widely used to infer molecular structure, including surfactant aggregation. A combination of optical spectroscopy, proton NMR spectroscopy, and pulsed field gradient NMR (PFG NMR) is used to study the adsorption number for sodium dodecyl sulfate (SDS) with single-wall carbon nanotubes (SWCNTs). Distinct transitions in the NMR chemical shift of SDS are observed in the presence of SWCNTs. These transitions demonstrate that micelle formation is delayed by SWCNTs due to the adsorption of SDS on the nanotube surface...
May 9, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28473417/african-genomes-illuminate-the-early-history-and-transition-to-selfing-in-arabidopsis-thaliana
#19
Arun Durvasula, Andrea Fulgione, Rafal M Gutaker, Selen Irez Alacakaptan, Pádraic J Flood, Célia Neto, Takashi Tsuchimatsu, Hernán A Burbano, F Xavier Picó, Carlos Alonso-Blanco, Angela M Hancock
Over the past 20 y, many studies have examined the history of the plant ecological and molecular model, Arabidopsis thaliana, in Europe and North America. Although these studies informed us about the recent history of the species, the early history has remained elusive. In a large-scale genomic analysis of African A. thaliana, we sequenced the genomes of 78 modern and herbarium samples from Africa and analyzed these together with over 1,000 previously sequenced Eurasian samples. In striking contrast to expectations, we find that all African individuals sampled are native to this continent, including those from sub-Saharan Africa...
May 4, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28470722/estimation-and-simulation-of-foraging-trips-in-land-based-marine-predators
#20
Théo Michelot, Roland Langrock, Sophie Bestley, Ian D Jonsen, Theoni Photopoulou, Toby A Patterson
The behaviour of colony-based marine predators is the focus of much research globally. Large telemetry and tracking data sets have been collected for this group of animals, and are accompanied by many empirical studies that seek to segment tracks in some useful way, as well as theoretical studies of optimal foraging strategies. However, relatively few studies have detailed statistical methods for inferring behaviours in central place foraging trips. In this paper we describe an approach based on hidden Markov models, which splits foraging trips into segments labeled as "outbound", "search", "forage", and "inbound"...
May 4, 2017: Ecology
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