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Nanomaterials: Look at the Earth
Get PDFNanotechnology promises to be the greatest technological breakthrough in history, doing for our control of matter what computers did for our control of information. The origins of nanoscience can be traced to clay mineralogy and crystallography when it was discovered that clay minerals were crystalline and of micrometer size. The unit cell dimensions of clay minerals are in nanometer scale in all three axes (x, y, and z). The advantages of clays are: (i) their ordered arrangements, (ii) their large adsorption capacity, (iii) their shielding against sunlight (ultraviolet radiation), (iv) their ability to concentrate organic chemicals, and (v) their ability to serve as polymerization templates. Clay minerals in nanoforms played a catalytic role in the synthesis of the ribosome in RNA that led to genesis of life on Earth. The history of Earth suggests that the late Precambrian oxygenation led to the inception of a ‘clay mineral factory’ that triggered the radical evolutionary diversification of Neoproterozoic life due to enhanced burial of organic carbon. High activity clays protected organic matter from reoxygenation, allowing a corresponding quantity of O2 to accumulate in the environment. The inseparable association of clays with lifeforms makes them most desirable in manufacturing nanoparticles. Clays have been extensively used in industry, but as concern for environmental sustainability grows, clay minerals find new takers from all conceivable forms of industries. Nanotechnology literature is flooded with clay-polymers for their possible use in high strength material manufacturing, for ecological life support systems, removal of contaminants from water and wastes, and as catalysts in chemical reactions to reduce energy consumption
Expression cartography of human tissues using self organizing maps
Get PDFBackground: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.
Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion, exocrine, epithelium, sexual reproduction, muscle, immune system and nervous tissues). SOM mapping reduces the dimension of expression data from ten thousands of genes to a few thousands of metagenes where each metagene acts as representative of a minicluster of co-regulated single genes. Tissue-specific and common properties shared between groups of tissues emerge as a handful of localized spots in the tissue maps collecting groups of co-regulated and co-expressed metagenes. The functional context of the spots was discovered using overrepresentation analysis with respect to pre-defined gene sets of known functional impact. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. Analysis techniques normally used at the gene-level such as two-way hierarchical clustering provide a better signal-to-noise ratio and a better representativeness of the method if applied to the metagenes. Metagene-based clustering analyses aggregate the tissues into essentially three clusters containing nervous, immune system and the remaining tissues. 
Conclusions: The global view on the behavior of a few well-defined modules of correlated and differentially expressed genes is more intuitive and more informative than the separate discovery of the expression levels of hundreds or thousands of individual genes. The metagene approach is less sensitive to a priori selection of genes. It can detect a coordinated expression pattern whose components would not pass single-gene significance thresholds and it is able to extract context-dependent patterns of gene expression in complex data sets.

Molecular modelling and Function Prediction of hABH7, human homologue of _E. coli_ ALKB7
Get PDFHuman homologues of ALKB protein have shown the prime role in DNA damaging drugs, used for cancer therapy. Little is known about structure and function of hABH7, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeller 9v7 to predict the 3D structure of the hABH7 protein. The tertiary structure model of hABH7, ALKBH7.B99990002.pdb was predicted and evaluated. Validation results showed 97.8% residues in favored and additional allowed regions of Ramachandran plots. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, presence of a Phe120-Gly121-Gly122 conserved pattern in the functional domain was detected. In the predicted structural model of hABH7, amino acid residues, Arginine at 57, 58, 59 and 60 along with tyrosine at 61 were predicted in RNA binding sites of the model. The predicted and validated model of human homologue hABH7 resulting from this study may unveil the mechanism of DNA damage repair in humans and accelerate the research on designing appropriate inhibitors aiding in chemotherapy and cancer related diseases
Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1
Get PDFThe Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in the MIASE guidelines. SED-ML allows one to define the model to use, the experimental task to run, and which result to produce
Herd Immunity/Herd Infection: Cultural Artifacts of Marginalization and the Dynamics of AIDS
Get PDFWe examine conditions under which high prevalence of infectious disease can become endemic within a community, in effect constituting a state of 'herd infection' inverse to epidemiological herd immunity. For something like AIDS, under such circumstances, a single behavioral lapse or adverse accident will probably be a death sentence
Anthropogenic Renourishment Feedback on Shorebirds: a Multispecies Bayesian Perspective
Get PDFIn this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some possible geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping Plover	(PP)	(Charadrius	melodus )	and	Red	Knot	(RK)	(Calidris	canutus ).	Additionally, we investigated the potential differences between the SP breeding and wintering distributions using only regional-scale physiognomic variables and the recorded occur- rences. To quantify the relationship between past renourishment projects and shorebird species we used a Monte Carlo procedure to sample from the posterior distribution of the binomial probabilities that a region is not a nesting or a wintering ground conditional on the occurrence of a beach replenishment intervention in the same and the previous year. The results indicate that it was 2.3, 3.1, and 0.8 times more likely that a region was not a wintering ground following a year with a renourishment intervention for the SP, PP and RK respectively. For the SP it was 2.5. times more likely that a region was not a breeding ground after a renourishment event. Through a maximum entropy principle model we observed small differences in the habitat use of the SP during the breeding and the wintering season. However the habitats where RK was observed appeared quite different. While ecological niche models at the macro-scale are useful for determining habitat suitability ranges, the characterization of the species’ local niche is fundamentally important for adopting concrete multi-species management scenarios. Maintaining and creating optimal suitable habitats for SP characterized by sparse low vegetation in the foredunes areas, and uneven/low-slope beach surfaces, is the proposed conservation scenario to convert anthropic beach restorations and SP populations into a positive feedback without impacting other threatened shorebird species
Replacement and late formation of atmospheric N2 on undifferentiated Titan by impacts
Get PDFSaturn’s moon, Titan, has remarkable surface features—a massive N2 atmosphere and hydrological cycle of CH4—that are often compared with that of Earth^1^. However, the origin and evolution of Titan’s atmosphere remains largely unknown. The proposed formation mechanisms for Titan’s N2 require a prolonged, warm proto-atmosphere during accretion^2-4^. These mechanisms accordingly would not have worked efficiently if Titan stayed cold, as indicated by the incompletely differentiated interior observed by Cassini^5^. Because formation of a massive secondary atmosphere on a planetary body would associate with a major differentiation of its sold body during accretion^6–8^, the presence of such an atmosphere on undifferentiated cold Titan poses a serious dilemma on our view of how planetary bodies develop atmospheres. Here we propose a new mechanism for the post-accretion formation of Titan’s N2 to resolve this problem: conversion and replenishment of N2 from NH3 contained in Titan by impacts during the late heavy bombardment (LHB)^9^. Our results show that Titan, regardless of its thermal history, would acquire sufficient N2 to account for the current atmosphere during the LHB and that most of the pre-LHB atmosphere would have replaced by impact-induced N2. This is the first scenario capable of generating a N2-rich and nearly primordial Ar-free atmosphere on undifferentiated cold Titan. We also suggest that Titan’s N2 was delivered from a different source in the solar nebula compared with Earth and that the origins of N2 on Titan and Triton are fundamentally different with that of N2 on Pluto
Attention induces dynamic changes in coherence between monkey area V1 and V4
No full textNeurons receive a vast number of synaptic inputs at the same time. To successfully process a relevant piece of information, a neuron needs to select relevant, while suppressing irrelevant signals. In order to dynamically route a meaningful set of signals through processing pathways, neurons need to have a fast and flexible mechanism to change their effective connectivity. Here, we hypothesize that attention changes effective connectivity by modulating the synchrony between neuronal populations.
We investigated whether attention dynamically changes effective connectivity between area V4 neurons and their V1 input. Single unit activity, multi unit activity and local field potentials (LFP) were recorded simultaneously from macaque monkeys’ areas V1 and V4. While maintaining their gaze on a fixation spot, the monkeys had to attend to one of two continuously morphing shapes and respond to reoccurrence of the initial sample shape in the attended stream. Size and position of the shapes were adjusted such that both fitted into a single V4 receptive field (RF) while covering two separate, non-overlapping V1 RFs.
We found strong phase-coherence of gamma-band LFPs between the V1 populations responding to the attended stimulus and the V4 population. At the same time, V1 populations responding to the unattended stimulus showed only weak LFP phase-coherence with the V4 population. Furthermore, spike-triggered averages (STAs) of at least 40% of the recording pairs revealed that spikes recorded from area V4 were precisely timed with respect to the phase of the gamma oscillation in the upstream area V1. More importantly, almost all these cases showed an increased effect with attention. These results support the hypothesis that attention induces dynamic changes in the effective connectivity between two anatomically hard-wired neuronal populations by selectively modulating synchrony
OpenCOR
No full textA description of the OpenCOR project. What has been done so far, the choices that were made, etc., as well as the direction in which we are heading
The influence of different excipients and storage procedures on hCG (human Corionic Gonadotropin) as evidenced by spectrophotometry
No full textOur studies concluded that changes in either PH, temperature, electrolytes, excipients, alcohol or silver modify the chemical structure of hCG as evidenced by UV-Spectrophotometry