Right for the Right Reason: Training Agnostic Networks

We consider the problem of a neural network being requested to classify images (or other inputs) without making implicit use of a "protected concept", that is a concept that should not play any role in the decision of the network. Typically these concepts include information such as gender or race, or other contextual information such as image backgrounds that might be implicitly reflected in unknown correlations with other variables, making it insufficient to simply remove them from the input features. In other words, making accurate predictions is not good enough if those predictions rely on information that should not be used: predictive performance is not the only important metric for learning systems. We apply a method developed in the context of domain adaptation to address this problem of "being right for the right reason", where we request a classifier to make a decision in a way that is entirely 'agnostic' to a given protected concept (e.g. gender, race, background etc.), even if this could be implicitly reflected in other attributes via unknown correlations. After defining the concept of an 'agnostic model', we demonstrate how the Domain-Adversarial Neural Network can remove unwanted information from a model using a gradient reversal layer.Comment: Author's original versio

Dwell-time computation for stability of switched systems with time delays

Cataloged from PDF version of article.The aim of this study is to find an improved dwell time that guarantees the stability of switched systems with heterogeneous constant time-delays. Piecewise Lyapunov-Krasovkii functionals are used for each candidate system to investigate the stability of the switched time-delayed system. Under the assumption that each candidate system is stable for small delay values, a sufficient condition for dwell-time that guarantees the asymptotic stability is derived. Numerical examples are given to compare the results with the previously obtained dwell-time bounds. © The Institution of Engineering and Technology 2013

Screening of medicinal plant extracts as novel DNA gyrase inhibitors

Bioactivities of a number of medicinal plants; Alkanna tinctoria (L.) Tausch, Alnus glutinosa (L.) Gaertn., Calamintha nepeta Willk. and C. nepeta, Centaurea iberica Trevir. ex Spreng., Citrus paradisi Macfad., C. paradisi, Citrus sinensis (L.) Osbeck, Colutea cilicica Boiss. & Balansa, Cotinus coggygria Scop., Cuscuta arvensis Beyr. ex Engelm., Equisetum palustre L., Lapsana communis L., Laurus nobilis L., Olea europea L., Plantago major L., Rhus coriaria L, Salvia verticillata L., Sambucus ebulus L., Sedum acre L, Thymus capitatus (L.) Hoffmanns. & Link, T. capitatus, Thymbra spicata L., T. spicata (n: 20), which are used for the prevention and treatment of diverse diseases, were investigated. The antimicrobial activities of extracts were evaluated using broth microdilution assay. The cytotoxicities of extracts were investigated on HeLa cell line by MTT assay. Statistical analysis was performed using GraphPad Prism (5.0). The effects of the extracts, which have the highest antimicrobial activity, on the Escherichia coli and Staphylococcus aureus DNA gyrase gene expression were determined by using quantitative reverse transcription polymerase chain reaction (qRT-PCR). The MICs (µg/ml) of extracts were determined as 32-64, 2-128, 8-128,1-128, 4-128 against Gram-positive, Gram-negative bacteria, yeasts, dermatophytes, and Mycobacterium spp., respectively. No cytotoxicity has been observed in plant extracts tested. DNA gyrase activity was determined for T. capitatus-SFE (128 µg/mL) and L. nobilis-Hx (128 µg/mL) extracts according to the inhibition of DNA gyrase gene expression. Overall, T. capitatus-SFE and L. nobilis-Hx are good candidates for further antimicrobial studies.

Theory of biopolymer stretching at high forces

We provide a unified theory for the high force elasticity of biopolymers solely in terms of the persistence length, $\xi_p$, and the monomer spacing, $a$. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the Worm-like Chain (WLC) is a better model. We show that $\xi_p$ can be estimated from the force extension curve (FEC) at the extension $x\approx 1/2$ (normalized by the contour length of the biopolymer). After validating the theory using simulations, we provide a quantitative analysis of the FECs for a diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and unstructured PEVK domain of titin) for $x \ge 1/2$. The success of a specific polymer model (FJC or WLC) to describe the FEC of a given biopolymer is naturally explained by the theory. Only by probing the response of biopolymers over a wide range of forces can the $f$-dependent elasticity be fully described.Comment: 20 pages, 4 figure

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease

PMCID: PMC3710212This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

The new COST Action European Venom Network (EUVEN)—synergy and future perspectives of modern venomics

Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging and pursued by different teams lacking connection with each other. This lack of coordination hampers the full development of venom investigation and applications. The COST Action CA19144–European Venom Network was recently launched to promote synergistic interactions among different stakeholders and foster venom research at the European level

Green function techniques in the treatment of quantum transport at the molecular scale

The theoretical investigation of charge (and spin) transport at nanometer length scales requires the use of advanced and powerful techniques able to deal with the dynamical properties of the relevant physical systems, to explicitly include out-of-equilibrium situations typical for electrical/heat transport as well as to take into account interaction effects in a systematic way. Equilibrium Green function techniques and their extension to non-equilibrium situations via the Keldysh formalism build one of the pillars of current state-of-the-art approaches to quantum transport which have been implemented in both model Hamiltonian formulations and first-principle methodologies. We offer a tutorial overview of the applications of Green functions to deal with some fundamental aspects of charge transport at the nanoscale, mainly focusing on applications to model Hamiltonian formulations.Comment: Tutorial review, LaTeX, 129 pages, 41 figures, 300 references, submitted to Springer series "Lecture Notes in Physics

Comparative effect of N-substituted dehydroamino acids and alpha-tocopherol on rat liver lipid peroxidation activities

Free radical damage has been associated with a growing number of diseases and conditions, such as autoimmune diseases, neurodegenerative disorders and multiple types of cancer. Some dehydroamino acids and corresponding peptides can function as radical scavengers. In this study the in vitro effects on rat liver lipid peroxidation levels of fourteen N-substituted dehydroamino acid derivatives and alpha-tocopherol were investigated. alpha-Tocopherol is a powerful antioxidant that is beneficial in the treatment of many free radical related diseases. The results indicated that all the compounds showed very good inhibitory effect on the lipid peroxidation compound with alpha-tocopherol at 1 mM concentrations and the inhibition rate was in the range of 70-79 % with the exception of compound 5. At 0.1 mM concentrations compounds 1, 2 and 9 were found more active than alpha-tocopherol. The results confirmed that molecules such as dehydroamino acids which have reactive double bonds can act as a guard in vitro against oxidants.- (undefined