Susceptibility and adaptation to human TRIM5α alleles at positive selected sites in HIV-1 capsid.

Numerous in vitro studies attribute to human TRIM5α some modest anti-HIV-1 activity and human population studies suggest some differential effect of TRIM5α polymorphisms on disease progression. If the activity of TRIM5α were relevant in vivo, it could result in positive selection on the viral capsid. To address this issue, we identified 10 positively selected sites in HIV-1 capsid from multiple viral strains and generated 17 clade B viruses carrying a minor (i.e. low frequency) residue or an alanine at those positions. All recombinant viruses were susceptible to the modest effect of common human TRIM5α and allelic variants R136Q, and H419Y; H43Y and G249D TRIM5α were generally inactive. Increased sensitivity to TRIM5α was observed for some capsid variants, suggesting that minor residues are selected against in human populations. On the other hand, the modest potency of human TRIM5α does not translate in escape mutations in the viral capsid.

Aggregate material formulated with MSWI bottom ash and APC fly ash for use as secondary building material

The main goal of this paper is to obtain a granular material formulated with Municipal Solid Waste Incinerarion (MSWI) bottom ash (BA) and air pollution control (APC) ash to be used as secondary building material. Previously, an optimum concrete mixture using both MSWI residues as aggregates was formulated. A compromise between the environmental behaviour and the economy of the process was considered. Unconfined compressive strength and abrasion resistance values were measured in order to evaluate the mechanical properties. From these results, the granular mixture was not suited for certain applications owing to the high BA/APC content and low cement percentages used to reduce the costs of the final product. Nevertheless, the leaching test performed showed that the concentrations of all heavy metals were below the limits established by the current Catalan legislation for their reutilization. Therefore, the material studied might be mainly used in embankments, where high mechanical properties are not needed and environmental safety is assured.

Building a Better Future.... Together, We Can: Iowa's Program and Budget Fiscal Years 2016-2017, January 2015

Governor Terry E. Branstad's FY2016-17 budget in brief

Corruption in building the image of politics in television news broadcasts

This work analyses the political news of eight Spanish television channels in order to see what image is built of politics, and particularly how the news of corruption affects the image of politics in Spanish news broadcasts. Different cases of corruption such as Gürtel, Palma Arena and those associated with judge Baltasar Garzón in his final stage in office, occupy part of the study. A new methodology is therefore proposed that enables the quality of the political information emitted from inside and outside the political content of the news programmes to be observed. Particular attention is paid to the news broadcasts of Televisión Española and Cuatro as those which offer a more balanced view of politics, and channels such as La Sexta, which give priority to a narrative construction of politics in the news programmes around causes of corruption.

A Framework for Building Hypercubes Using MapReduce

The European Space Agency's Gaia mission will create the largest and most precise three dimensional chart of our galaxy (the Milky Way), by providing unprecedented position, parallax, proper motion, and radial velocity measurements for about one billion stars. The resulting catalogue will be made available to the scientific community and will be analyzed in many different ways, including the production of a variety of statistics. The latter will often entail the generation of multidimensional histograms and hypercubes as part of the precomputed statistics for each data release, or for scientific analysis involving either the final data products or the raw data coming from the satellite instruments. In this paper we present and analyze a generic framework that allows the hypercube generation to be easily done within a MapReduce infrastructure, providing all the advantages of the new Big Data analysis paradigmbut without dealing with any specific interface to the lower level distributed system implementation (Hadoop). Furthermore, we show how executing the framework for different data storage model configurations (i.e. row or column oriented) and compression techniques can considerably improve the response time of this type of workload for the currently available simulated data of the mission. In addition, we put forward the advantages and shortcomings of the deployment of the framework on a public cloud provider, benchmark against other popular solutions available (that are not always the best for such ad-hoc applications), and describe some user experiences with the framework, which was employed for a number of dedicated astronomical data analysis techniques workshops.

A Framework for Building Hypercubes Using MapReduce

The European Space Agency's Gaia mission will create the largest and most precise three dimensional chart of our galaxy (the Milky Way), by providing unprecedented position, parallax, proper motion, and radial velocity measurements for about one billion stars. The resulting catalogue will be made available to the scientific community and will be analyzed in many different ways, including the production of a variety of statistics. The latter will often entail the generation of multidimensional histograms and hypercubes as part of the precomputed statistics for each data release, or for scientific analysis involving either the final data products or the raw data coming from the satellite instruments. In this paper we present and analyze a generic framework that allows the hypercube generation to be easily done within a MapReduce infrastructure, providing all the advantages of the new Big Data analysis paradigmbut without dealing with any specific interface to the lower level distributed system implementation (Hadoop). Furthermore, we show how executing the framework for different data storage model configurations (i.e. row or column oriented) and compression techniques can considerably improve the response time of this type of workload for the currently available simulated data of the mission. In addition, we put forward the advantages and shortcomings of the deployment of the framework on a public cloud provider, benchmark against other popular solutions available (that are not always the best for such ad-hoc applications), and describe some user experiences with the framework, which was employed for a number of dedicated astronomical data analysis techniques workshops.

Iowa Veterans Home Building A Future On The Foundation Of Our Past FY 2012 Annual,

Annual report for the Iowa Veterans Home. To provide a continuum of care to Iowa’s veterans and their spouses in an environment focusing on individualized services to enhance their quality of life.

Growth rate and wood properties of Norway spruce cutting clones on different sites

[Abstract]

Practical Data Collection: Establishing Methods and Procedures for Measuring Water Clarity and Turbidity of Storm Water Run-Off from Active Major Highway Construction Sites, 2014

In anticipation of regulation involving numeric turbidity limit at highway construction sites, research was done into the most appropriate, affordable methods for surface water monitoring. Measuring sediment concentration in streams may be conducted a number of ways. As part of a project funded by the Iowa Department of Transportation, several testing methods were explored to determine the most affordable, appropriate methods for data collection both in the field and in the lab. The primary purpose of the research was to determine the exchangeability of the acrylic transparency tube for water clarity analysis as compared to the turbidimeter.

Identification of in vitro phosphorylation sites in the growth cone protein SCG10. Effect Of phosphorylation site mutants on microtubule-destabilizing activity.

SCG10 is a neuron-specific, membrane-associated protein that is highly concentrated in growth cones of developing neurons. Previous studies have suggested that it is a regulator of microtubule dynamics and that it may influence microtubule polymerization in growth cones. Here, we demonstrate that in vivo, SCG10 exists in both phosphorylated and unphosphorylated forms. By two-dimensional gel electrophoresis, two phosphoisoforms were detected in neonatal rat brain. Using in vitro phosphorylated recombinant protein, four phosphorylation sites were identified in the SCG10 sequence. Ser-50 and Ser-97 were the target sites for protein kinase A, Ser-62 and Ser-73 for mitogen-activated protein kinase and Ser-73 for cyclin-dependent kinase. We also show that overexpression of SCG10 induces a disruption of the microtubule network in COS-7 cells. By expressing different phosphorylation site mutants, we have dissected the roles of the individual phosphorylation sites in regulating its microtubule-destabilizing activity. We show that nonphosphorylatable mutants have increased activity, whereas mutants in which phosphorylation is mimicked by serine-to-aspartate substitutions have decreased activity. These data suggest that the microtubule-destabilizing activity of SCG10 is regulated by phosphorylation, and that SCG10 may link signal transduction of growth or guidance cues involving serine/threonine protein kinases to alterations of microtubule dynamics in the growth cone.

Prepupal Building Behavior in Drosophila melanogaster and Its Evolution under Resource and Time Constraints.

Structures built by animals are a widespread and ecologically important 'extended phenotype'. While its taxonomic diversity has been well described, factors affecting short-term evolution of building behavior within a species have received little experimental attention. Here we describe how, given the opportunity, wandering Drosophila melanogaster larvae often build long tunnels in agar substrates and embed their pupae within them. These embedded larvae are characterized by a longer egg-to-pupariation developmental time than larvae that pupate on the surface. Assuming that such building behaviors are likely to be energetically costly and/or time consuming, we hypothesized that they should evolve to be less pronounced under resource or time limitation. In accord with this prediction, larvae from populations evolved for 160 generations under a regime that combines larval malnutrition with limited developmental time dug shorter tunnels than larvae from control unselected populations. However, the proportion of larvae that embedded before pupation did not differ between the malnutrition-adapted and control populations, suggesting that tunnel length and likelihood of embedding before pupation are controlled by different genetic loci. The behaviors exhibited by wandering larvae of Drosophila melanogaster prior to pupation offer a model system to study evolution of animal building behaviors because the tunneling and embedding phenotypes are simple, facultative and highly variable.

Quantitative modelling of transcription factor binding sites

Abstract One of the most important issues in molecular biology is to understand regulatory mechanisms that control gene expression. Gene expression is often regulated by proteins, called transcription factors which bind to short (5 to 20 base pairs),degenerate segments of DNA. Experimental efforts towards understanding the sequence specificity of transcription factors is laborious and expensive, but can be substantially accelerated with the use of computational predictions. This thesis describes the use of algorithms and resources for transcriptionfactor binding site analysis in addressing quantitative modelling, where probabilitic models are built to represent binding properties of a transcription factor and can be used to find new functional binding sites in genomes. Initially, an open-access database(HTPSELEX) was created, holding high quality binding sequences for two eukaryotic families of transcription factors namely CTF/NF1 and LEFT/TCF. The binding sequences were elucidated using a recently described experimental procedure called HTP-SELEX, that allows generation of large number (> 1000) of binding sites using mass sequencing technology. For each HTP-SELEX experiments we also provide accurate primary experimental information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, and assembled clone sequences of binding sequences. The database also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols.The database is available at http://wwwisrec.isb-sib.ch/htpselex/ and and ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex. The Expectation-Maximisation(EM) algorithm is one the frequently used methods to estimate probabilistic models to represent the sequence specificity of transcription factors. We present computer simulations in order to estimate the precision of EM estimated models as a function of data set parameters(like length of initial sequences, number of initial sequences, percentage of nonbinding sequences). We observed a remarkable robustness of the EM algorithm with regard to length of training sequences and the degree of contamination. The HTPSELEX database and the benchmarked results of the EM algorithm formed part of the foundation for the subsequent project, where a statistical framework called hidden Markov model has been developed to represent sequence specificity of the transcription factors CTF/NF1 and LEF1/TCF using the HTP-SELEX experiment data. The hidden Markov model framework is capable of both predicting and classifying CTF/NF1 and LEF1/TCF binding sites. A covariance analysis of the binding sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism. We next tested the LEF1/TCF model by computing binding scores for a set of LEF1/TCF binding sequences for which relative affinities were determined experimentally using non-linear regression. The predicted and experimentally determined binding affinities were in good correlation.

Building Environmental Management System for Laboratory Products Manufacturing Company according ISO 14001-standard

Tutkielman tavoitteena on rakentaa toimiva ympäristöjärjestelmä Thermo Fisher Scientific Oy:lle. Tutkimuksen tarkoituksena on myös löytää kahdelle täysin erilaiselle toiminnalle yhtenäinen ympäristöjärjestelmä, jonka avulla pystytään ottamaan huomioon molempien toimipaikkojen hieman erilaiset vaatimukset. Lisäksi tavoitteena on muodostaa ympäristöjärjestelmälle oma organisaatio, jonka avulla ympäristöjärjestelmän integrointi yrityksen prosesseihin voidaan suorittaa sujuvasti. Aluksi tutkimusongelmaa lähestytään teoreettisesta näkökulmasta,jossa tarkastellaan ympäristöjärjestelmän historiaa, rakennetta, etuja sekä ISO 14001–standardin rakennetta ja sen etenemistä ympäristöjärjestelmän rakentamisen yhteydessä aina kolmannen osapuolen sertifiointiin asti. Empiria osa alkaa alustavalla ympäristökatselmuksella, jossa selvitetään ympäristöasioiden hoidon nykytaso ja luodaan pohja koko ympäristöjärjestelmän luomiselle, jonka vankimpana perustana on ympäristöpolitiikka. Johdon hyväksymä ympäristöpolitiikka varmistaa johdon sitoutumisen järjestelmään. Ympäristöjärjestelmän toimintarakenteen muodostaminen kahdelle erilaiselle toiminnalle onnistui tutkimuksessa kiitettävästi. Se miten ympäristöjärjestelmä toimii todellisuudessa, tullaan näkemään käytännön kokemuksien yhteydessä.

Customer References as Marketing Practice in Company Web sites - Content and Discourse Analysis

Työn tarkoituksena oli tutkia sisältö- ja diskurssianalyysin avulla kuinka yritykset viestivät asiakasreferenssejä verkkosivuillaan. Työssä keskityttiin tutkimaan yritysten referenssikuvausten teemoja ja diskursseja, sekä sitä kuinka referenssisuhde rakentuu diskursiivisesti referenssikuvauksissa. Tutkimukseen valittiin kolme suomalaista ICT-alan yritystä: Nokia, TietoEnator ja F-Secure. Aineisto koostuu 140:stä yritysten WWW-sivuilta kerätystä referenssikuvauksesta. Sisältöanalyysin tuloksena havaittiin, että referenssikuvaukset keskittyvät kuvaamaan yksittäisiä tuote- tai projektitoimituksia referenssiasiakkaille kyseisten asiakassuhteiden valossa. Analyysin tuloksena tunnistettiin kolme diskurssia: hyötydiskurssi, sitoutumisen diskurssi sekä teknologisen eksperttiyden diskurssi. Diskurssit paljastavat referenssikuvausten retoriset keinot ja konstruoivat referenssisuhteen ja toimittajan subjektiposition eri näkökulmista. Pääpaino referenssikuvauksissa on toimittajan ratkaisun tuomissa hyödyissä. Diskurssit tuottavat referenssisuhteesta kuvan hyötyjä tuovana ja läheisenä asiakassuhteena, joka tarjoaa väylän ulkopuolisiin kyvykkyyksiin ja teknologioihin. Toimittaja esitetään referenssikuvauksissa diskurssista riippuen hyötyjen tuojana, luotettavana partnerina sekä kokeneena eksperttinä. Referenssiasiakas sen sijaan esitetään vain yhdestä näkökulmasta stereotyyppisesti tärkeänä ja tyytyväisenä asiakkaana.

The building blocks of the full body ownership illusion

Previous work has reported that it is not difficult to give people the illusion of ownership over an artificial body, providing a powerful tool for the investigation of the neural and cognitive mechanisms underlying body perception and self consciousness. We present an experimental study that uses immersive virtual reality (IVR) focused on identifying the perceptual building blocks of this illusion. We systematically manipulated visuotactile and visual sensorimotor contingencies, visual perspective, and the appearance of the virtual body in order to assess their relative role and mutual interaction. Consistent results from subjective reports and physiological measures showed that a first person perspective over a fake humanoid body is essential for eliciting a body ownership illusion. We found that the illusion of ownership can be generated when the virtual body has a realistic skin tone and spatially substitutes the real body seen from a first person perspective. In this case there is no need for an additional contribution of congruent visuotactile or sensorimotor cues. Additionally, we found that the processing of incongruent perceptual cues can be modulated by the level of the illusion: when the illusion is strong, incongruent cues are not experienced as incorrect. Participants exposed to asynchronous visuotactile stimulation can experience the ownership illusion and perceive touch as originating from an object seen to contact the virtual body. Analogously, when the level of realism of the virtual body is not high enough and/or when there is no spatial overlap between the two bodies, then the contribution of congruent multisensory and/or sensorimotor cues is required for evoking the illusion. On the basis of these results and inspired by findings from neurophysiological recordings in the monkey, we propose a model that accounts for many of the results reported in the literature.