CONTEST : a Controllable Test Matrix Toolbox for MATLAB

Large, sparse networks that describe complex interactions are a common feature across a number of disciplines, giving rise to many challenging matrix computational tasks. Several random graph models have been proposed that capture key properties of real-life networks. These models provide realistic, parametrized matrices for testing linear system and eigenvalue solvers. CONTEST (CONtrollable TEST matrices) is a random network toolbox for MATLAB that implements nine models. The models produce unweighted directed or undirected graphs; that is, symmetric or unsymmetric matrices with elements equal to zero or one. They have one or more parameters that affect features such as sparsity and characteristic pathlength and all can be of arbitrary dimension. Utility functions are supplied for rewiring, adding extra shortcuts and subsampling in order to create further classes of networks. Other utilities convert the adjacency matrices into real-valued coefficient matrices for naturally arising computational tasks that reduce to sparse linear system and eigenvalue problems

Upregulation of the Coagulation Factor VII Gene during Glucose Deprivation Is Mediated by Activating Transcription Factor 4

Background: Constitutive production of blood coagulation proteins by hepatocytes is necessary for hemostasis. Stressful conditions trigger adaptive cellular responses and delay processing of most proteins, potentially affecting plasma levels of proteins secreted exclusively by hepatocytes. We examined the effect of glucose deprivation on expression of coagulation proteins by the human hepatoma cell line, HepG2. Methodology/Principal Findings: Expression of coagulation factor VII, which is required for initiation of blood coagulation, was elevated by glucose deprivation, while expression of other coagulation proteins decreased. Realtime PCR and ELISA demonstrated that the relative percentage expression +/− SD of steady-state F7 mRNA and secreted factor VII antigen were significantly increased (from 100+/−15% to 188+/−27% and 100+/−8.8% to 176.3+/−17.3% respectively, p<0.001) at 24 hr of treatment. The integrated stress response was induced, as indicated by upregulation of transcription factor ATF4 and of additional stress-responsive genes. Small interfering RNAs directed against ATF4 potently reduced basal F7 expression, and prevented F7 upregulation by glucose deprivation. The response of the endogenous F7 gene was replicated in reporter gene assays, which further indicated that ATF4 effects were mediated via interaction with an amino acid response element in the F7 promoter. Conclusions/Significance: Our data indicated that glucose deprivation enhanced F7 expression in a mechanism reliant on prior ATF4 upregulation primarily due to increased transcription from the ATF4 gene. Of five coagulation protein genes examined, only F7 was upregulated, suggesting that its functions may be important in a systemic response to glucose deprivation stress

Long-term (25-year) survival after renal homotransplantation - The world experience

A follow-up is provided for 64 patients treated with renal transplantation at the University of Colorado before 31 March 1964. The 25-year survival was 15/64 (23.4%) and 14 patients (22%) are still alive after 25 1/2 to 27 years. There are 9 other survivors in the world from this era, distributed in 4 American and 2 European centers. All of the 25-year survivors received their grafts from living related donors

Subgraphs and network motifs in geometric networks

Many real-world networks describe systems in which interactions decay with the distance between nodes. Examples include systems constrained in real space such as transportation and communication networks, as well as systems constrained in abstract spaces such as multivariate biological or economic datasets and models of social networks. These networks often display network motifs: subgraphs that recur in the network much more often than in randomized networks. To understand the origin of the network motifs in these networks, it is important to study the subgraphs and network motifs that arise solely from geometric constraints. To address this, we analyze geometric network models, in which nodes are arranged on a lattice and edges are formed with a probability that decays with the distance between nodes. We present analytical solutions for the numbers of all 3 and 4-node subgraphs, in both directed and non-directed geometric networks. We also analyze geometric networks with arbitrary degree sequences, and models with a field that biases for directed edges in one direction. Scaling rules for scaling of subgraph numbers with system size, lattice dimension and interaction range are given. Several invariant measures are found, such as the ratio of feedback and feed-forward loops, which do not depend on system size, dimension or connectivity function. We find that network motifs in many real-world networks, including social networks and neuronal networks, are not captured solely by these geometric models. This is in line with recent evidence that biological network motifs were selected as basic circuit elements with defined information-processing functions.Comment: 9 pages, 6 figure

High-gain nonlinear observer for simple genetic regulation process

High-gain nonlinear observers occur in the nonlinear automatic control theory and are in standard usage in chemical engineering processes. We apply such a type of analysis in the context of a very simple one-gene regulation circuit. In general, an observer combines an analytical differential-equation-based model with partial measurement of the system in order to estimate the non-measured state variables. We use one of the simplest observers, that of Gauthier et al., which is a copy of the original system plus a correction term which is easy to calculate. For the illustration of this procedure, we employ a biological model, recently adapted from Goodwin's old book by De Jong, in which one plays with the dynamics of the concentrations of the messenger RNA coding for a given protein, the protein itself, and a single metabolite. Using the observer instead of the metabolite, it is possible to rebuild the non-measured concentrations of the mRNA and the proteinComment: 9 pages, one figur

The Meteoric Ni Layer in the Upper Atmosphere

The first global atmospheric model of Ni (WACCM-Ni) has been developed to understand recent observations of the mesospheric Ni layer by ground-based resonance lidars. The three components of the model are: the Whole Atmospheric Community Climate Model (WACCM6); a meteoric input function derived by coupling an astronomical model of dust sources in the solar system with a chemical meteoric ablation model; and a comprehensive set of neutral, ion-molecule, and photochemical reactions pertinent to the chemistry of Ni in the upper atmosphere. In order to achieve closure on the chemistry, the reaction kinetics of three important reactions were first studied using a fast flow tube with pulsed laser ablation of a Ni target, yielding k(NiO + O) = (4.6 ± 1.4) × 10−11, k(NiO + CO) = (3.0 ± 0.5) × 10−11, and k(NiO2 + O) = (2.5 ± 1.2) × 10−11 cm3 molecule−1 s−1 at 294 K. The photodissociation rate of NiOH was computed to be J(NiOH) = 0.02 s−1. WACCM-Ni simulates satisfactorily the observed neutral Ni layer peak height and width, and Ni+ measurements from rocket-borne mass spectrometry. The Ni layer is predicted to have a similar seasonal and latitudinal variation as the Fe layer, and its unusually broad bottom-side compared with Fe is caused by the relatively fast NiO + CO reaction. The quantum yield for photon emission from the Ni + O3 reaction, observed in the nightglow, is estimated to be between 6% and 40%. ©2020. The Authors

The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data

We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different types of data pertinent to anatomy, such as gene expression patterns and phenotype information, which will contribute to an integrated description of biological phenomena in the mouse

Tunable SNAP Microresonators via Internal Ohmic Heating

We demonstrate a thermally tunable Surface Nanoscale Axial Photonics (SNAP) platform. Stable tuning is achieved by heating a SNAP structure fabricated on the surface of a silica capillary with a metal wire positioned inside. Heating a SNAP microresonator with a uniform wire introduces uniform variation of its effective radius which results in constant shift of its resonance wavelengths. Heating with a nonuniform wire allows local nanoscale variation of the capillary effective radius, which enables differential tuning of the spectrum of SNAP structures as well as creation of temporary SNAP microresonators that exist only when current is applied. As an example, we fabricate two bottle microresonators coupled to each other and demonstrate differential tuning of their resonance wavelengths into and out of degeneracy with precision better than 0.2 pm. The developed approach is beneficial for ultraprecise fabrication of tunable ultralow loss parity-time symmetric, optomechanical, and cavity QED devices

'Dressage Is Full of Queens!' Masculinity, Sexuality and Equestrian Sport

Attitudes towards sexuality are changing and levels of cultural homophobia decreasing, yet there remain very few openly gay men within sport. As a proving ground for heteromasculinity, sport has traditionally been a hostile environment for gay men. This article is based on an ethnographic study within a sporting subworld in which gay men do appear to be accepted: equestrian sport. Drawing on inclusive masculinity theory, equestrian sport is shown to offer an unusually tolerant environment for gay men in which heterosexual men of all ages demonstrate low levels of homophobia. Inclusive masculinity theory is a useful framework for exploring the changing nature of masculinities and this study demonstrates that gay men are becoming increasingly visible and accepted within once unreceptive locales, such as sport and rural communities. However, this more tolerant attitude is purchased at the expense of a subordinated feminine Other, perpetuating the dominance of men within competitive sport. © The Author(s) 2012