Algebraic Comparison of Partial Lists in Bioinformatics

The outcome of a functional genomics pipeline is usually a partial list of genomic features, ranked by their relevance in modelling biological phenotype in terms of a classification or regression model. Due to resampling protocols or just within a meta-analysis comparison, instead of one list it is often the case that sets of alternative feature lists (possibly of different lengths) are obtained. Here we introduce a method, based on the algebraic theory of symmetric groups, for studying the variability between lists ("list stability") in the case of lists of unequal length. We provide algorithms evaluating stability for lists embedded in the full feature set or just limited to the features occurring in the partial lists. The method is demonstrated first on synthetic data in a gene filtering task and then for finding gene profiles on a recent prostate cancer dataset

Building solids inside nano-space: from confined amorphous through confined solvate to confined ‘metastable’ polymorph

The nanocrystallisation of complex molecules inside mesoporous hosts and control over the resulting structure is a significant challenge. To date the largest organic molecule crystallised inside the nano-pores is a known pharmaceutical intermediate – ROY (259.3 g mol1). In this work we demonstrate smart manipulation of the phase of a larger confined pharmaceutical – indomethacin (IMC, 357.8 g mol1), a substance with known conformational flexibility and complex polymorphic behaviour. We show the detailed structural analysis and the control of solid state transformations of encapsulated molecules inside the pores of mesoscopic cellular foam (MCF, pore size ca. 29 nm) and controlled pore glass (CPG, pore size ca. 55 nm). Starting from confined amorphous IMC we drive crystallisation into a confined methanol solvate, which upon vacuum drying leads to the stabilised rare form V of IMC inside the MCF host. In contrast to the pure form, encapsulated form V does not transform into a more stable polymorph upon heating. The size of the constraining pores and the drug concentration within the pores determine whether the amorphous state of the drug is stabilised or it recrystallises into confined nanocrystals. The work presents, in a critical manner, an application of complementary techniques (DSC, PXRD, solid-state NMR, N2 adsorption) to confirm unambiguously the phase transitions under confinement and offers a comprehensive strategy towards the formation and control of nano-crystalline encapsulated organic solids

A statistical analysis of Pc1–2 waves at a near-cusp station in Antarctica

Abstract A statistical study of Pc1–2 waves at southern polar latitudes is presented. Ultra-low frequency geomagnetic field measurements collected at the Italian station Mario Zucchelli (Terra Nova Bay, Antarctica, altitude-adjusted corrected geomagnetic latitude 80°S, MLT = UT − 8) from 2003 to 2010 corresponding with the declining phase of solar cycle 23 and the onset of the solar cycle 24 are used. The long data series allows us to analyze the solar cycle, seasonal and magnetic local time dependence and investigate the possible generation processes related to the solar wind–magnetosphere interaction. We found that during the day, Pc1–2 waves occur around local magnetic noon and midnight. Polarized waves show an almost linear polarization, suggesting a wave propagation along a meridional ionospheric waveguide, from the injection region up to the latitude of Terra Nova Bay. The origin of the waves appears to be due to substorm/stormrelated instabilities and, in the dayside, to solar wind compressions of the magnetopause. Based on these results, we propose a simple model to estimate Pc1–2 power variations depending on geomagnetic activity and solar wind density

Micro-computed tomography (μ-CT) as a potential tool to assess the effect of dynamic coating routes on the formation of biomimetic apatite layers on 3D-plotted biodegradable polymeric scaffolds

This work studies the influence of dynamic biomimetic coating procedures on the growth of bonelike apatite layers at the surface of starch/polycaprolactone (SPCL) scaffolds produced by a 3D-plotting technology. These systems are newly proposed for bone Tissue Engineering applications. After generating stable apatite layers through a sodium silicate-based biomimetic methodology the scaffolds were immersed in Simulated Body Fluid solutions (SBF) under static, agitation and circulating flow perfusion conditions, for different time periods. Besides the typical characterization techniques, Micro-Computed Tomography analysis (μ-CT) was used to assess scaffold porosity and as a new tool for mapping apatite content. 2D histomorphometric analysis was performed and 3D virtual models were created using specific softwares for CT reconstruction. By the proposed biomimetic routes apatite layers were produced covering the interior of the scaffolds, without compromising their overall morphology and interconnectivity. Dynamic conditions allowed for the production of thicker apatite layers as consequence of higher mineralizing rates, when comparing with static conditions. μ-CT analysis clearly demonstrated that flow perfusion was the most effective condition in order to obtain well-defined apatite layers in the inner parts of the scaffolds. Together with SEM, this technique was a useful complementary tool for assessing the apatite content in a non-destructive way

Penerapan Lean Canvas Pada Startup Pembelajaran Bahasa Inggris Lunchat

Lunchat merupakan sebuah startup di bidang pendidikan yang menciptakan sebuah aplikasi kursus bahasa Inggris berbasis website yang dapat mempermudah masyarakat Indonesia dalam belajar bahasa Inggris. Tujuan dari penelitian ini adalah untuk menentukan dan mempertajam model bisnis yang diterapkan di startup Lunchat. Metode pengembangan sistem yang digunakan pada penelitian ini adalah menggunakan metode lean canvas sebagai analisis bisnis. Dengan penerapan lean canvas dapat memudahkan pembuat dalam melakukan proses validasi, karena dapat melihat model bisnis secara keseluruhan, sehingga dapat mengurangi resiko dalam melakukan bisnis. Hal ini karena antara produk atau jasa yang ditawarkan sesuai dengan yang diinginkan oleh pasar. Hasil dari implementasi startup Lunchat menjadikan suatu peluang yang menjanjikan untuk memperluas sektor usaha sehingga Lunchat dapat bersaing di era Industry 4.0 ini

A case study of correspondence between Pc1 activity and ionospheric irregularities at polar latitudes

A possible driver of precipitation of magnetospheric energetic electrons in the high-latitude atmosphere is represented by electromagnetic ion-cyclotron (EMIC) magnetospheric waves. The precipitating particles produce variations, by collision, in the ionized component of the atmosphere, altering its chemistry and electrical conductivity, with a significant impact on the atmospheric processes. In this framework, it would be significant to find experimental evidence of a correspondence between ionospheric electron density irregularities and the occurrence of Ultra-Low-Frequency (ULF) Pc1 geomagnetic pulsations, i.e., the ground signatures of EMIC waves, at high latitudes. In this work, we face this subject by considering a specific case study occurred on 22 February 2007 during quiet magnetospheric conditions. The study is based on the analysis of simultaneous ULF geomagnetic field and Total Electron Content (TEC) measurements recorded at Mario Zucchelli Station in Antarctica. We show that Pc1 pulsations occur in correspondence to solar wind pressure increases and that, at the same time, the ionosphere is characterized by the presence of ionospheric irregularities. We suggest that a possible link between the Pc1 activity and the ionospheric irregularities may be energetic electron precipitations, driven by EMIC waves generated in the compressed magnetosphere, which produce density variations in the ionized component of the atmosphere. [Figure not available: see fulltext.]

Adsorption at cell surface and cellular uptake of silica nanoparticles with different surface chemical functionalizations: impact on cytotoxicity

International audienceSilica nanoparticles are particularly interesting for medical applications because of the high inertness and chemical stability of silica material. However, at the nanoscale their innocuousness must be carefully verified before clinical use. The aim of this study was to investigate the in vitro biological toxicity of silica nanoparticles depending on their surface chemical functionalization. To that purpose, three kinds of 50 nm fluorescent silica-based nanoparticles were synthesized: 1) sterically stabilized silica nanoparticles coated with neutral polyethylene glycol (PEG) molecules, 2) positively charged silica nanoparticles coated with amine groups and 3) negatively charged silica nanoparticles coated with carboxylic acid groups. RAW 264.7 murine macrophages were incubated for 20 hours with each kind of nanoparticles. Their cellular uptake and adsorption at the cell membrane were assessed by a fluorimetric assay and cellular responses were evaluated in terms of cytotoxicity, pro-inflammatory factor production and oxidative stress. Results showed that the highly positive charged nanoparticle, were the most adsorbed at cell surface and triggered more cytotoxicity than other nanoparticles types. To conclude, this study clearly demonstrated that silica nanoparticles surface functionalization represents a key parameter in their cellular uptake and biological toxicity

Application of RAPD markers in hybrid verification in coconut

Abstract -Coconut palms are classified into two majo

Biomimetic self-assembling copolymer-hydroxyapatite nanocomposites with the nanocrystal size controlled by citrate

Citrate binds strongly to the surface of calcium phosphate (apatite) nanocrystals in bone and is thought to prevent crystal thickening. In this work, citrate added as a regulatory element enabled molecular control of the size and stability of hydroxyapatite (HAp) nanocrystals in synthetic nanocomposites, fabricated with self-assembling block copolymer templates. The decrease of the HAp crystal size within the polymer matrix with increasing citrate concentration was documented by solid-state nuclear magnetic resonance (NMR) techniques and wide-angle X-ray diffraction (XRD), while the shapes of HAp nanocrystals were determined by transmission electron microscopy (TEM). Advanced NMR techniques were used to characterize the interfacial species and reveal enhanced interactions between mineral and organic matrix, concomitant with the size effects. The surface-to-volume ratios determined by NMR spectroscopy and long-range 31P{1H} dipolar dephasing show that 2, 10, and 40 mM citrate changes the thicknesses of the HAp crystals from 4 nm without citrate to 2.9, 2.8, and 2.3 nm, respectively. With citrate concentrations comparable to those in body fluids, HAp nanocrystals of sizes and morphologies similar to those in avian and bovine bones have been produced

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

Cellular signal transduction generally involves cascades of post-translational protein modifications that rapidly catalyze changes in protein-DNA interactions and gene expression. High-throughput measurements are improving our ability to study each of these stages individually, but do not capture the connections between them. Here we present an approach for building a network of physical links among these data that can be used to prioritize targets for pharmacological intervention. Our method recovers the critical missing links between proteomic and transcriptional data by relating changes in chromatin accessibility to changes in expression and then uses these links to connect proteomic and transcriptome data. We applied our approach to integrate epigenomic, phosphoproteomic and transcriptome changes induced by the variant III mutation of the epidermal growth factor receptor (EGFRvIII) in a cell line model of glioblastoma multiforme (GBM). To test the relevance of the network, we used small molecules to target highly connected nodes implicated by the network model that were not detected by the experimental data in isolation and we found that a large fraction of these agents alter cell viability. Among these are two compounds, ICG-001, targeting CREB binding protein (CREBBP), and PKF118–310, targeting β-catenin (CTNNB1), which have not been tested previously for effectiveness against GBM. At the level of transcriptional regulation, we used chromatin immunoprecipitation sequencing (ChIP-Seq) to experimentally determine the genome-wide binding locations of p300, a transcriptional co-regulator highly connected in the network. Analysis of p300 target genes suggested its role in tumorigenesis. We propose that this general method, in which experimental measurements are used as constraints for building regulatory networks from the interactome while taking into account noise and missing data, should be applicable to a wide range of high-throughput datasets.National Science Foundation (U.S.) (DB1-0821391)National Institutes of Health (U.S.) (Grant U54-CA112967)National Institutes of Health (U.S.) (Grant R01-GM089903)National Institutes of Health (U.S.) (P30-ES002109