Methods for Generating Complex Networks with Selected Structural Properties for Simulations: A Review and Tutorial for Neuroscientists

Many simulations of networks in computational neuroscience assume completely homogenous random networks of the Erdös–Rényi type, or regular networks, despite it being recognized for some time that anatomical brain networks are more complex in their connectivity and can, for example, exhibit the “scale-free” and “small-world” properties. We review the most well known algorithms for constructing networks with given non-homogeneous statistical properties and provide simple pseudo-code for reproducing such networks in software simulations. We also review some useful mathematical results and approximations associated with the statistics that describe these network models, including degree distribution, average path length, and clustering coefficient. We demonstrate how such results can be used as partial verification and validation of implementations. Finally, we discuss a sometimes overlooked modeling choice that can be crucially important for the properties of simulated networks: that of network directedness. The most well known network algorithms produce undirected networks, and we emphasize this point by highlighting how simple adaptations can instead produce directed networks

Prescription for Progress: NN/LM New England Region Subcontractor Outreach Activities

The mission of the National Network of Libraries of Medicine (NN/LM®) is to advance the progress of medicine and improve the public health by providing all U.S. health professionals equal access to biomedical information and by improving the public\u27s access to information to enable them to make informed decisions about their health. The Program is coordinated by the National Library of Medicine and carried out through a nationwide network of health science libraries, public Libraries, and information centers. Under contract with NLM, Regional Medical Libraries continue their efforts strengthen the Network to reach under served health professionals in rural and inner city areas, public health professionals, and special populations. NN/LM members work with a variety of intermediaries, including health care providers, public health professionals, public librarians, educators, community organizations, health advocacy groups, faith-based organizations, and self-help groups, to reach members of the public. The Regional Medical Library for the New England Region is the Lamar Soutter Library at the University of Massachusetts Medical School in Worcester, Massachusetts. The New England Region of 516 members includes 16 Resource Libraries, over 360 hospital and academic libraries, and over 100 public libraries

Covalent bond shortening and distortion induced by pressurization of thorium, uranium, and neptunium tetrakis aryloxides

Covalency involving the 5f orbitals is regularly invoked to explain the reactivity, structure and spectroscopic properties of the actinides, but the ionic versus covalent nature of metal-ligand bonding in actinide complexes remains controversial. The tetrakis 2,6-di-tert-butylphenoxide complexes of Th, U and Np form an isostructural series of crystal structures containing approximately tetrahedral MO(4) cores. We show that up to 3 GPa the Th and U crystal structures show negative linear compressibility as the OMO angles distort. At 3 GPa the angles snap back to their original values, reverting to a tetrahedral geometry with an abrupt shortening of the M-O distances by up to 0.1 Å. The Np complex shows similar but smaller effects, transforming above 2.4 GPa. Electronic structure calculations associate the M-O bond shortening with a change in covalency resulting from increased contributions to the M-O bonding by the metal 6d and 5f orbitals, the combination promoting MO(4) flexibility at little cost in energy

On thermodynamic modeling and the role of the second law of thermodynamics in geophysics

The article contains a brief review of elements of thermodynamic modeling in theoretical geophysics. We motivate the existence of the second law of thermodynamics in macroscopic theoretical physics and demonstrate its evaluation. In particular we show its consequences in the construction of constitutive laws for a two-component poroelastic medium. This construction is also related to microstructural properties verified by means of the second law

The 3rd Global Summit of Research Institutes for Disaster Risk Reduction: Expanding the Platform for Bridging Science and Policy Making

The Global Alliance of Disaster Research Institutes held its 3rd Global Summit of Research Institutes for Disaster Risk Reduction at the Disaster Prevention Research Institute, Kyoto University, Japan, 19–21 March, 2017. The Global Alliance seeks to contribute to enhancing disaster risk reduction (DRR) and disaster resilience through the collaboration of research organizations around the world. The summit aim was to expand the platform for bridging science and policy making by evaluating the evidence base needed to meet the expected outcomes and actions of the Sendai Framework for Disaster Risk Reduction 2015–2030 and its Science and Technology Roadmap. The summit reflected the international nature of collaborative research and action. A pre-conference questionnaire filled out by Global Alliance members identified 323 research projects that are indicative of current research. These were categorized to support seven parallel discussion sessions related to the Sendai Framework priorities for action. Four discussion sessions focused on research that aims to deepen the understanding of disaster risks. Three cross-cutting sessions focused on research that is aimed at the priorities for action on governance, resilience, and recovery. Discussion summaries were presented in plenary sessions in support of outcomes for widely enhancing the science and policy of DRR

A CD317/tetherin–RICH2 complex plays a critical role in the organization of the subapical actin cytoskeleton in polarized epithelial cells

CD317/tetherin is a lipid raft–associated integral membrane protein with a novel topology. It has a short N-terminal cytosolic domain, a conventional transmembrane domain, and a C-terminal glycosyl-phosphatidylinositol anchor. We now show that CD317 is expressed at the apical surface of polarized epithelial cells, where it interacts indirectly with the underlying actin cytoskeleton. CD317 is linked to the apical actin network via the proteins RICH2, EBP50, and ezrin. Knocking down expression of either CD317 or RICH2 gives rise to the same phenotype: a loss of the apical actin network with concomitant loss of apical microvilli, an increase in actin bundles at the basal surface, and a reduction in cell height without any loss of tight junctions, transepithelial resistance, or the polarized targeting of apical and basolateral membrane proteins. Thus, CD317 provides a physical link between lipid rafts and the apical actin network in polarized epithelial cells and is crucial for the maintenance of microvilli in such cells

Water in cratonic lithosphere : calibrating laboratory-determined models of electrical conductivity of mantle minerals using geophysical and petrological observations

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 13 (2012): Q06010, doi:10.1029/2012GC004055.Measurements of electrical conductivity of “slightly damp” mantle minerals from different laboratories are inconsistent, requiring geophysicists to make choices between them when interpreting their electrical observations. These choices lead to dramatically different conclusions about the amount of water in the mantle, resulting in conflicting conclusions regarding rheological conditions; this impacts on our understanding of mantle convection, among other processes. To attempt to reconcile these differences, we test the laboratory-derived proton conduction models by choosing the simplest petrological scenario possible – cratonic lithosphere – from two locations in southern Africa where we have the most complete knowledge. We compare and contrast the models with field observations of electrical conductivity and of the amount of water in olivine and show that none of the models for proton conduction in olivine proposed by three laboratories are consistent with the field observations. We derive statistically model parameters of the general proton conduction equation that satisfy the observations. The pre-exponent dry proton conduction term (σ0) and the activation enthalpy (ΔHwet) are derived with tight bounds, and are both within the broader 2σ errors of the different laboratory measurements. The two other terms used by the experimentalists, one to describe proton hopping (exponent r on pre-exponent water content Cw) and the other to describe H2O concentration-dependent activation enthalpy (term αCw1/3 added to the activation energy), are less well defined and further field geophysical and petrological observations are required, especially in regions of higher temperature and higher water content.The SAMTEX data were acquired through funding provided by the Continental Dynamics program of the U.S. National Science Foundation (grant EAR0455242 to RLE), the South African Department of Science and Technology (grant to South African Council for Geoscience), and Science Foundation Ireland (grant 05/RGP/GEO001 to AGJ) plus financial and/or logistical support provided by all members of the SAMTEX consortium. JF was initially supported by an IRCSET grant to AGJ for the TopoMed project (TopoMed: Plate reorganization in the western Mediterranean: Lithospheric causes and topographic consequences) within the European Science Foundation’s TOPOEUROPE EUROCORES (http://www.esf.org/activities/eurocores/ running-programmes/topo-europe.html), and subsequently by an SFI PI grant (10/IN.1/I3022) to AGJ for IRETHERM (www.iretherm.ie).2012-12-1

Gene Targeting Implicates Cdc42 GTPase in GPVI and Non-GPVI Mediated Platelet Filopodia Formation, Secretion and Aggregation

Background: Cdc42 and Rac1, members of the Rho family of small GTPases, play critical roles in actin cytoskeleton regulation. We have shown previously that Rac1 is involved in regulation of platelet secretion and aggregation. However, the role of Cdc42 in platelet activation remains controversial. This study was undertaken to better understand the role of Cdc42 in platelet activation. Methodology/Principal Findings: We utilized the Mx-cre;Cdc42 lox/lox inducible mice with transient Cdc42 deletion to investigate the involvement of Cdc42 in platelet function. The Cdc42-deficient mice exhibited a significantly reduced platelet count than the matching Cdc42 +/+ mice. Platelets isolated from Cdc42 2/2, as compared to Cdc42 +/+, mice exhibited (a) diminished phosphorylation of PAK1/2, an effector molecule of Cdc42, (b) inhibition of filopodia formation on immobilized CRP or fibrinogen, (c) inhibition of CRP- or thrombin-induced secretion of ATP and release of P-selectin, (d) inhibition of CRP, collagen or thrombin induced platelet aggregation, and (e) minimal phosphorylation of Akt upon stimulation with CRP or thrombin. The bleeding times were significantly prolonged in Cdc42 2/2 mice compared with Cdc42 +/+ mice. Conclusion/Significance: Our data demonstrate that Cdc42 is required for platelet filopodia formation, secretion an