Evolutionary optimization of classifiers and features for single-trial EEG Discrimination

Background  

State-of-the-art signal processing methods are known to detect information in single-trial event-related EEG data, a crucial aspect in development of real-time applications such as brain computer interfaces. This paper investigates one such novel approach, evaluating how individual classifier and feature subset tailoring affects classification of single-trial EEG finger movements. The discrete wavelet transform was used to extract signal features that were classified using linear regression and non-linear neural network models, which were trained and architecturally optimized with evolutionary algorithms. The input feature subsets were also allowed to evolve, thus performing feature selection in a wrapper fashion. Filter approaches were implemented as well by limiting the degree of optimization.     

A switch‐off fluorescence probe towards Pb(II) and cu(II) ions based on a calix[4]pyrrole bearing amino‐quinoline group

A new fluorescence receptor calix[4]pyrrole‐N‐(quinoline‐8‐yl) acetamide (CAMQ) containing a pyrrolic ring connected via the meso‐position was synthesized, purified and characterized by elemental analysis, NMR and mass spectroscopy. This compound was examined for its fluorescence properties towards different metal ions e.g. Ag(I), Hg(II), Co(II), Ca(II), Ni(II), Zn(II), Cr(II), Ba(II), Fe(II), Cu(II), Pb(II)and Mg(II) ions by spectrophotometry and spectrofluorometry. It was concluded that the compound (CAMQ) possessed significantly enhanced selectivity for Pb(II) and Cu(II) ions in dimethyl sulfoxide (DMSO) even at very low concentrations (1 μM). It exhibit ‘turn‐on’ fluorescence when exposed to Pb(II) and Cu(II) and did so in preference to other metal ions. The binding constants, stoichiometry and quantum yields have been determined. The quenching mechanism was assessed using the Stern–Volmer equation and was also discussed.     

Regulation of Stomatal Defense by Air Relative Humidity

It has long been observed that environmental conditions play crucial roles in modulating immunity and disease in plants and animals. For instance, many bacterial plant disease outbreaks occur after periods of high humidity and rain. A critical step in bacterial infection is entry into the plant interior through wounds and natural openings, such as stomata, which are adjustable microscopic pores in the epidermal tissue. Several studies have shown that stomatal closure is an integral part of the plant immune response to reduce pathogen invasion. In this study, we found that high humidity can effectively compromise Pseudomonas syringae-triggered stomatal closure in both Phaseolus vulgaris and Arabidopsis (Arabidopsis thaliana), which is accompanied by early up-regulation of the jasmonic acid (JA) pathway and simultaneous down-regulation of salicylic acid (SA) pathway in guard cells. Furthermore, SA-dependent response, but not JA-dependent response, is faster in guard cells than in whole leaves, suggesting that the SA signaling in guard cells may be independent from other cell types. Thus, we conclude that high humidity, a well-known disease-promoting environmental condition, acts in part by suppressing stomatal defense and is linked to hormone signaling in guard cells.The phyllosphere is one of the most diverse niches for microbe inhabitation. Numerous bacteria can survive and proliferate on the surface of the plant without causing any harm (Lindow and Brandl, 2003). However, for a bacterial pathogen to cause disease, it must penetrate through the plant epidermis and be able to survive and proliferate inside the plant. The mode and mechanism of penetration into the plant tissue is a critical step for infection, especially for bacterial pathogens that rely on natural openings and accidental wounds on the plant surface to colonize internal tissues (Misas-Villamil et al., 2013). Stomata are an example of such openings, providing one of the main routes through which the foliar pathogen Pseudomonas syringae transitions from avirulent epiphytic to virulent endophytic lifestyles (Melotto et al., 2008). This abundant opening in the epidermal tissue is not a passive port that allows unrestricted entry of microbes. It has been shown that plants are able to respond to human and plant bacterial pathogens by actively closing the stomatal pore (McDonald and Cahill, 1999; Melotto et al., 2006; Gudesblat et al., 2009; Zhang et al., 2010; Roy et al., 2013; Arnaud and Hwang, 2015), a phenomenon described as stomatal immunity (Sawinski et al., 2013). Several lines of evidence point to the complexity of this response and show that stomatal closure is an integral basal plant defense mechanism to restrict the invasion of pathogenic bacteria into plant tissues (Ali et al., 2007; Melotto et al., 2008; Zhang et al., 2008; Gudesblat et al., 2009). However, certain bacterial pathogens, such as Xanthomonas campestris pv campestris (Gudesblat et al., 2009), P. syringae pv syringae (Pss) B728a (Schellenberg et al., 2010), and P. syringae pvs tabaci, tomato, and maculicola (Melotto et al., 2006), can successfully cause disease by producing toxins that overcome stomatal immunity. Specifically, P. syringae pv tomato (Pst) DC3000 uses coronatine (COR) as such a toxin.In this study, we focused on elucidating environmental regulation of stomatal-based defense against bacterial invasion. Changes in environmental conditions, such as air relative humidity (RH), light, and carbon dioxide concentration regulate guard cell turgidity that consequently alters stomatal aperture size and the basic functions of stomata in plants, i.e. exchange of photosynthetic gases and regulation of water loss by transpiration (Zelitch, 1969; Schroeder et al., 2001; Fan et al., 2004). In natural conditions, plants are exposed to both biotic and abiotic stresses, and guard cells need to prioritize their response to the simultaneous occurrence of these stresses. For instance, it is a common observation that severe outbreaks of bacterial disease in the field are often associated with periods of heavy rain or high air humidity (Goode and Sasser, 1980). Mechanical wounding of plant tissues by rain might be one way that allows pathogens to bypass the stomatal route and gain unprecedented access to the plant interior. Additionally, the formation of large bacterial aggregates under high humidity on the leaf surface (Monier and Lindow, 2004) and splashing of bacteria during rain may also contribute to the spreading of disease at a higher rate. Interestingly, to ensure infection in the laboratory, researchers commonly expose plants to very high humidity for an extended period after surface inoculation. Here, we demonstrate that high RH compromises stomatal defense in Arabidopsis (Arabidopsis thaliana) and common bean (Phaseolus vulgaris) against P. syringae, allowing more bacteria to enter the leaf tissue and contributing to severe infections. Compromised bacterial-triggered stomatal closure due to high RH is accompanied by changes in plant hormone signaling in Arabidopsis. Specifically, high RH leads to activation of the jasmonic acid (JA) signaling pathway and down-regulation of the salicylic acid (SA) signaling in guard cells. These results connect plant physiology with epidemiology and advance the current understanding of foliar bacterial infection in plants.     

A Systematic Screen of FDA-Approved Drugs for Inhibitors of Biological Threat Agents

Background

The rapid development of effective medical countermeasures against potential biological threat agents is vital. Repurposing existing drugs that may have unanticipated activities as potential countermeasures is one way to meet this important goal, since currently approved drugs already have well-established safety and pharmacokinetic profiles in patients, as well as manufacturing and distribution networks. Therefore, approved drugs could rapidly be made available for a new indication in an emergency.

Methodology/Principal Findings

A large systematic effort to determine whether existing drugs can be used against high containment bacterial and viral pathogens is described. We assembled and screened 1012 FDA-approved drugs for off-label broad-spectrum efficacy against Bacillus anthracis; Francisella tularensis; Coxiella burnetii; and Ebola, Marburg, and Lassa fever viruses using in vitro cell culture assays. We found a variety of hits against two or more of these biological threat pathogens, which were validated in secondary assays. As expected, antibiotic compounds were highly active against bacterial agents, but we did not identify any non-antibiotic compounds with broad-spectrum antibacterial activity. Lomefloxacin and erythromycin were found to be the most potent compounds in vivo protecting mice against Bacillus anthracis challenge. While multiple virus-specific inhibitors were identified, the most noteworthy antiviral compound identified was chloroquine, which disrupted entry and replication of two or more viruses in vitro and protected mice against Ebola virus challenge in vivo.

Conclusions/Significance

The feasibility of repurposing existing drugs to face novel threats is demonstrated and this represents the first effort to apply this approach to high containment bacteria and viruses.     

The automation and evaluation of nested clade phylogeographic analysis

Nested clade phylogeographic analysis (NCPA) is a popular method for reconstructing the demographic history of spatially distributed populations from genetic data. Although some parts of the analysis are automated, there is no unique and widely followed algorithm for doing this in its entirety, beginning with the data, and ending with the inferences drawn from the data. This article describes a method that automates NCPA, thereby providing a framework for replicating analyses in an objective way. To do so, a number of decisions need to be made so that the automated implementation is representative of previous analyses. We review how the NCPA procedure has evolved since its inception and conclude that there is scope for some variability in the manual application of NCPA. We apply the automated software to three published datasets previously analyzed manually and replicate many details of the manual analyses, suggesting that the current algorithm is representative of how a typical user will perform NCPA. We simulate a large number of replicate datasets for geographically distributed, but entirely random-mating, populations. These are then analyzed using the automated NCPA algorithm. Results indicate that NCPA tends to give a high frequency of false positives. In our simulations we observe that 14% of the clades give a conclusive inference that a demographic event has occurred, and that 75% of the datasets have at least one clade that gives such an inference. This is mainly due to the generation of multiple statistics per clade, of which only one is required to be significant to apply the inference key. We survey the inferences that have been made in recent publications and show that the most commonly inferred processes (restricted gene flow with isolation by distance and contiguous range expansion) are those that are commonly inferred in our simulations. However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy.     

Binding of isoxazole and pyrazole derivatives of curcumin with the activator binding domain of novel protein kinase C

The protein kinase C (PKC) family of serine/threonine kinases is an attractive drug target because of its involvement in the regulation of various cellular functions, including cell growth, differentiation, metabolism, and apoptosis. The endogenous PKC activator diacylglycerol contains two long carbon chains, which are attached to the glycerol moiety via ester linkage. Natural product curcumin (1), the active constituent of Curcuma L., contains two carbonyl and two hydroxyl groups. It modulates PKC activity and binds to the activator binding site (Majhi et al., Bioorg. Med. Chem.2010, 18, 1591). To investigate the role of the carbonyl and hydroxyl groups of curcumin in PKC binding and to develop curcumin derivatives as effective PKC modulators, we synthesized several isoxazole and pyrazole derivatives of curcumin (2-6), characterized their absorption and fluorescence properties, and studied their interaction with the activator-binding second cysteine-rich C1B subdomain of PKCδ, PKCε and PKCθ. The EC(50)s of the curcumin derivatives for protein fluorescence quenching varied in the range of 3-25 μM. All the derivatives showed higher binding with the PKCθC1B compared with PKCδC1B and PKCεC1B. Fluorescence emission maxima of 2-5 were blue shifted in the presence of the C1B domains, confirming their binding to the protein. Molecular docking revealed that hydroxyl, carbonyl and pyrazole ring of curcumin (1), pyrazole (2), and isoxazole (4) derivatives form hydrogen bonds with the protein residues. The present result shows that isoxazole and pyrazole derivatives bind to the activator binding site of novel PKCs and both carbonyl and hydroxy groups of curcumin play roles in the binding process, depending on the nature of curcumin derivative and the PKC isotype used.     

Cloning, expression and purification of the DNA binding domain of RFX protein

The RFX DNA binding domain (DBD) is a novel highly conserved motif belonging to a large number of dimer DNA binding proteins which have diverse regulatory functions in eukaryotic organisms. To characterize this novel motif, a 78mer polypeptide corresponding to the DBD of human hRFX (hrfX1/DBD), a prototypical member of the RFX family has been cloned and overproduced in Escherichia coli. A purification procedure using cation exchange chromatography has also been developed.     

Bromobenzofurans : a new class of potent, non-peptide antagonists of angiotensin II

This paper describes the synthesis and pharmacology of a novel series of benzofurans which are antagonists of angiotensin II. One of these, the bromobenzofuran 11b, is a potent (apparent pK_B=9.8) and specific antagonist of angiotensin II which, after oral administration (10mg/Kg), causes marked and long-lasting ( > 24h) falls in blood pressure in renal hypertensive rats.     

Inhibition of metalloprotease botulinum serotype A from a pseudo-peptide binding mode to a small molecule that is active in primary neurons

An efficient research strategy integrating empirically guided, structure-based modeling and chemoinformatics was used to discover potent small molecule inhibitors of the botulinum neurotoxin serotype A light chain. First, a modeled binding mode for inhibitor 2-mercapto-3-phenylpropionyl-RATKML (K(i) = 330 nM) was generated, and required the use of a molecular dynamic conformer of the enzyme displaying the reorientation of surface loops bordering the substrate binding cleft. These flexible loops are conformationally variable in x-ray crystal structures, and the model predicted that they were pivotal for providing complementary binding surfaces and solvent shielding for the pseudo-peptide. The docked conformation of 2-mercapto-3-phenylpropionyl-RATKML was then used to refine our pharmacophore for botulinum serotype A light chain inhibition. Data base search queries derived from the pharmacophore were employed to mine small molecule (non-peptidic) inhibitors from the National Cancer Institute's Open Repository. Four of the inhibitors possess K(i) values ranging from 3.0 to 10.0 microM. Of these, NSC 240898 is a promising lead for therapeutic development, as it readily enters neurons, exhibits no neuronal toxicity, and elicits dose-dependent protection of synaptosomal-associated protein (of 25 kDa) in a primary culture of embryonic chicken neurons. Isothermal titration calorimetry showed that the interaction between NSC 240898 and the botulinum A light chain is largely entropy-driven, and occurs with a 1:1 stoichiometry and a dissociation constant of 4.6 microM.     

Identification of small molecule inhibitors of anthrax lethal factor

The virulent spore-forming bacterium Bacillus anthracis secretes anthrax toxin composed of protective antigen (PA), lethal factor (LF) and edema factor (EF). LF is a Zn-dependent metalloprotease that inactivates key signaling molecules, such as mitogen-activated protein kinase kinases (MAPKK), to ultimately cause cell death. We report here the identification of small molecule (nonpeptidic) inhibitors of LF. Using a two-stage screening assay, we determined the LF inhibitory properties of 19 compounds. Here, we describe six inhibitors on the basis of a pharmacophoric relationship determined using X-ray crystallographic data, molecular docking studies and three-dimensional (3D) database mining from the US National Cancer Institute (NCI) chemical repository. Three of these compounds have K(i) values in the 0.5-5 microM range and show competitive inhibition. These molecular scaffolds may be used to develop therapeutically viable inhibitors of LF.