Bioinformatics and HIV Latency.

Despite effective treatment, HIV is not completely eliminated from the infected organism because of the existence of viral reservoirs. A major reservoir consists of infected resting CD4+ T cells, mostly of memory type, that persist over time due to the stable proviral insertion and a long cellular lifespan. Resting cells do not produce viral particles and are protected from viral-induced cytotoxicity or immune killing. However, these latently infected cells can be reactivated by stochastic events or by external stimuli. The present review focuses on novel genome-wide technologies applied to the study of integration, transcriptome, and proteome characteristics and their recent contribution to the understanding of HIV latency.

Lymphocytic Choriomeningitis Virus Differentially Affects the Virus-Induced Type I Interferon Response and Mitochondrial Apoptosis Mediated by RIG-I/MAVS.

Arenaviruses are important emerging human pathogens maintained by noncytolytic persistent infection in their rodent reservoir hosts. Despite high levels of viral replication, persistently infected carrier hosts show only mildly elevated levels of type I interferon (IFN-I). Accordingly, the arenavirus nucleoprotein (NP) has been identified as a potent IFN-I antagonist capable of blocking activation of interferon regulatory factor 3 (IRF3) via the retinoic acid inducible gene (RIG)-I/mitochondrial antiviral signaling (MAVS) pathway. Another important mechanism of host innate antiviral defense is represented by virus-induced mitochondrial apoptosis via RIG-I/MAVS and IRF3. In the present study, we investigated the ability of the prototypic Old World arenavirus lymphocytic choriomeningitis virus (LCMV) to interfere with RIG-I/MAVS-dependent apoptosis. We found that LCMV does not induce apoptosis at any time during infection. While LCMV efficiently blocked induction of IFN-I via RIG-I/MAVS in response to superinfection with cytopathic RNA viruses, virus-induced mitochondrial apoptosis remained fully active in LCMV-infected cells. Notably, in LCMV-infected cells, RIG-I was dispensable for virus-induced apoptosis via MAVS. Our study reveals that LCMV infection efficiently suppresses induction of IFN-I but does not interfere with the cell's ability to undergo virus-induced mitochondrial apoptosis as a strategy of innate antiviral defense. The RIG-I independence of mitochondrial apoptosis in LCMV-infected cells provides the first evidence that arenaviruses can reshape apoptotic signaling according to their needs. IMPORTANCE: Arenaviruses are important emerging human pathogens that are maintained in their rodent hosts by persistent infection. Persistent virus is able to subvert the cellular interferon response, a powerful branch of the innate antiviral defense. Here, we investigated the ability of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) to interfere with the induction of programmed cell death, or apoptosis, in response to superinfection with cytopathic RNA viruses. Upon viral challenge, persistent LCMV efficiently blocked induction of interferons, whereas virus-induced apoptosis remained fully active in LCMV-infected cells. Our studies reveal that the persistent virus is able to reshape innate apoptotic signaling in order to prevent interferon production while maintaining programmed cell death as a strategy for innate defense. The differential effect of persistent virus on the interferon response versus its effect on apoptosis appears as a subtle strategy to guarantee sufficiently high viral loads for efficient transmission while maintaining apoptosis as a mechanism of defense.

Rehufosfaattitehtaan raaka-ainesyöttöjen säätöpiirien kehitys

Diplomityö tehtiin Kemira Chemicals Oy:n Kokkolan tehtaiden rehufosfaattitehtaalla. Työn tavoitteena oli uusien reseptiohjauksien suunnittelu ja käyttöönotto sekä tasaussäiliön pinnansäädön ja rakeistusrummun suhdesäädön suunnittelu. Käyttöhenkilöstön koulutus uuteen prosessinohjaukseen kuului myös osaksi diplomityötä. Uuden reseptiohjauksen avulla pyrittiin saamaan prosessin ohjaus havainnollisemmaksi ja ennustettavammaksi käyttäjille, yhdenmukaistamaan käyttäjien ajotapaa sekä suunnitella tuotereseptit vastaamaan paremmin todellista tuotantoa. Uusi reseptiohjaus mahdollistaa myös lajikekohtaisten parametrien käytön ja hyväksi havaittujen ajoreseptien tallennuksen. Tasaussäiliön pinnankorkeuden säädön tavoitteena on poistaa tuotantokatkokset, jotka johtuivat säiliön tyhjenemisestä tai täyttymisestä. Rakeistusrummun suhdesäädön tavoitteena on reaktoriliemen ja kuiva-ainesyöttöjen oikean suhteen säilyttäminen. Uuden reseptiohjauksen käyttöönoton jälkeen ajoreseptit ovat vastanneet todellista tuotantoa ja tuotantovauhti on jäänyt pysyvästi korkeammalle tasolle. Tasaussäiliön pinnansäätö toimii suunnitellulla tavalla ja on myös otettu käyttöön. Reaktoriliemen ja kuivasyöttöjen suhdesäätö on testattu käytännössä ja toimii halutulla tavalla. Suhdesäädön paremman toiminnan kannalta epätarkkoja toimilaitteita tulisi kuitenkin uusia.

Probabilistic electrical resistivity tomography of a CO2 sequestration analog

Electrical resistivity tomography (ERT) is a well-established method for geophysical characterization and has shown potential for monitoring geologic CO2 sequestration, due to its sensitivity to electrical resistivity contrasts generated by liquid/gas saturation variability. In contrast to deterministic inversion approaches, probabilistic inversion provides the full posterior probability density function of the saturation field and accounts for the uncertainties inherent in the petrophysical parameters relating the resistivity to saturation. In this study, the data are from benchtop ERT experiments conducted during gas injection into a quasi-2D brine-saturated sand chamber with a packing that mimics a simple anticlinal geological reservoir. The saturation fields are estimated by Markov chain Monte Carlo inversion of the measured data and compared to independent saturation measurements from light transmission through the chamber. Different model parameterizations are evaluated in terms of the recovered saturation and petrophysical parameter values. The saturation field is parameterized (1) in Cartesian coordinates, (2) by means of its discrete cosine transform coefficients, and (3) by fixed saturation values in structural elements whose shape and location is assumed known or represented by an arbitrary Gaussian Bell structure. Results show that the estimated saturation fields are in overall agreement with saturations measured by light transmission, but differ strongly in terms of parameter estimates, parameter uncertainties and computational intensity. Discretization in the frequency domain (as in the discrete cosine transform parameterization) provides more accurate models at a lower computational cost compared to spatially discretized (Cartesian) models. A priori knowledge about the expected geologic structures allows for non-discretized model descriptions with markedly reduced degrees of freedom. Constraining the solutions to the known injected gas volume improved estimates of saturation and parameter values of the petrophysical relationship. (C) 2014 Elsevier B.V. All rights reserved.

Calcificações orbitárias incidentais na tomografia computadorizada

Estudamos, retrospectivamente, tomografias computadorizadas de órbita de 75 pacientes, de maneira a identificar a presença de calcificações incidentais (esclerais e do aparato troclear). Estes achados devem ser incluídos no vasto diagnóstico diferencial das calcificações orbitárias. A familiaridade com seus achados de imagem pode ajudar o radiologista a diferenciá-las do diagnóstico de corpo estranho orbitário.

The Depsipeptide Romidepsin Reverses HIV-1 Latency In Vivo.

UNLABELLED: Pharmacologically-induced activation of replication competent proviruses from latency in the presence of antiretroviral treatment (ART) has been proposed as a step towards curing HIV-1 infection. However, until now, approaches to reverse HIV-1 latency in humans have yielded mixed results. Here, we report a proof-of-concept phase Ib/IIa trial where 6 aviremic HIV-1 infected adults received intravenous 5 mg/m2 romidepsin (Celgene) once weekly for 3 weeks while maintaining ART. Lymphocyte histone H3 acetylation, a cellular measure of the pharmacodynamic response to romidepsin, increased rapidly (maximum fold range: 3.7-7.7 relative to baseline) within the first hours following each romidepsin administration. Concurrently, HIV-1 transcription quantified as copies of cell-associated un-spliced HIV-1 RNA increased significantly from baseline during treatment (range of fold-increase: 2.4-5.0; p = 0.03). Plasma HIV-1 RNA increased from <20 copies/mL at baseline to readily quantifiable levels at multiple post-infusion time-points in 5 of 6 patients (range 46-103 copies/mL following the second infusion, p = 0.04). Importantly, romidepsin did not decrease the number of HIV-specific T cells or inhibit T cell cytokine production. Adverse events (all grade 1-2) were consistent with the known side effects of romidepsin. In conclusion, romidepsin safely induced HIV-1 transcription resulting in plasma HIV-1 RNA that was readily detected with standard commercial assays demonstrating that significant reversal of HIV-1 latency in vivo is possible without blunting T cell-mediated immune responses. These finding have major implications for future trials aiming to eradicate the HIV-1 reservoir. TRIAL REGISTRATION: clinicaltrials.gov NTC02092116.

The High Prevalence and Diversity of Chlamydiales DNA within Ixodes ricinus Ticks Suggest a Role for Ticks as Reservoirs and Vectors of Chlamydia-Related Bacteria.

The Chlamydiales order is composed of nine families of strictly intracellular bacteria. Among them, Chlamydia trachomatis, C. pneumoniae, and C. psittaci are established human pathogens, whereas Waddlia chondrophila and Parachlamydia acanthamoebae have emerged as new pathogens in humans. However, despite their medical importance, their biodiversity and ecology remain to be studied. Even if arthropods and, particularly, ticks are well known to be vectors of numerous infectious agents such as viruses and bacteria, virtually nothing is known about ticks and chlamydia. This study investigated the prevalence of Chlamydiae in ticks. Specifically, 62,889 Ixodes ricinus ticks, consolidated into 8,534 pools, were sampled in 172 collection sites throughout Switzerland and were investigated using pan-Chlamydiales quantitative PCR (qPCR) for the presence of Chlamydiales DNA. Among the pools, 543 (6.4%) gave positive results and the estimated prevalence in individual ticks was 0.89%. Among those pools with positive results, we obtained 16S rRNA sequences for 359 samples, allowing classification of Chlamydiales DNA at the family level. A high level of biodiversity was observed, since six of the nine families belonging to the Chlamydiales order were detected. Those most common were Parachlamydiaceae (33.1%) and Rhabdochlamydiaceae (29.2%). "Unclassified Chlamydiales" (31.8%) were also often detected. Thanks to the huge amount of Chlamydiales DNA recovered from ticks, this report opens up new perspectives on further work focusing on whole-genome sequencing to increase our knowledge about Chlamydiales biodiversity. This report of an epidemiological study also demonstrates the presence of Chlamydia-related bacteria within Ixodes ricinus ticks and suggests a role for ticks in the transmission of and as a reservoir for these emerging pathogenic Chlamydia-related bacteria.

From Regional Landslide Detection to Site-Specific Slope Deformation Monitoring and Modelling Based on Active Remote Sensors

Landslide processes can have direct and indirect consequences affecting human lives and activities. In order to improve landslide risk management procedures, this PhD thesis aims to investigate capabilities of active LiDAR and RaDAR sensors for landslides detection and characterization at regional scales, spatial risk assessment over large areas and slope instabilities monitoring and modelling at site-specific scales. At regional scales, we first demonstrated recent boat-based mobile LiDAR capabilities to model topography of the Normand coastal cliffs. By comparing annual acquisitions, we validated as well our approach to detect surface changes and thus map rock collapses, landslides and toe erosions affecting the shoreline at a county scale. Then, we applied a spaceborne InSAR approach to detect large slope instabilities in Argentina. Based on both phase and amplitude RaDAR signals, we extracted decisive information to detect, characterize and monitor two unknown extremely slow landslides, and to quantify water level variations of an involved close dam reservoir. Finally, advanced investigations on fragmental rockfall risk assessment were conducted along roads of the Val de Bagnes, by improving approaches of the Slope Angle Distribution and the FlowR software. Therefore, both rock-mass-failure susceptibilities and relative frequencies of block propagations were assessed and rockfall hazard and risk maps could be established at the valley scale. At slope-specific scales, in the Swiss Alps, we first integrated ground-based InSAR and terrestrial LiDAR acquisitions to map, monitor and model the Perraire rock slope deformation. By interpreting both methods individually and originally integrated as well, we therefore delimited the rockslide borders, computed volumes and highlighted non-uniform translational displacements along a wedge failure surface. Finally, we studied specific requirements and practical issues experimented on early warning systems of some of the most studied landslides worldwide. As a result, we highlighted valuable key recommendations to design new reliable systems; in addition, we also underlined conceptual issues that must be solved to improve current procedures. To sum up, the diversity of experimented situations brought an extensive experience that revealed the potential and limitations of both methods and highlighted as well the necessity of their complementary and integrated uses.

Efeito do campo magnético na precipitação de parafinas

In the oil industry, the paraffination phenomenon is a major problem during oil production, displacement and treatment. Paraffin deposition in subsea flowlines, surface equipment, production string or even in the reservoir, can cause significant and increasing oil losses. To minimize paraffin precipitation, the application of magnetic field in the petroleum path has been suggested based on empiric studies. In this study, we assembled a labscale magnetic conditioner to determine the influence of magnetic field on the physical-chemical properties of two fluids : oil and a paraffin mixture. We observed that magnetic field reduce sample aparent viscosity due to crystal morphology alteration.

Automatização de um destilador d'água

A simple and inexpensive device to automate a water distilling apparatus is shown. It is composed by a magnetic floater placed in the water reservoir and a level control unit, which acts over the heating element circuit. In order to provide water saving, an electromagnetic valve is inserted in the water supply inlet. Some suggestions for the adaptation to other types of equipment are also offered.

LibraryThing as a library service. Assessment report

This report was requested by the Innovation and Marketing department of the ETHBibliotek, for the purpose of assessing the social cataloguing tool LibraryThing and its potential uses in an academic library.

One pot obtention of a tetrabutylammonium hydroxide solution for ironporphyrin-OH- interaction studies in organic solvents

In this work we report the obtention of a tetrabutylammonium hydroxide (TBAOH) solution in acetonitrile in a one pot process in order to study the interaction ironporphyrinOH- in non-aqueous systems. All the reactions were carried out under dry argon atmosphere to prevent the contamination of the solution with CO2, which leads to the formation of (TBA)2CO3.

Bordetella pertussis - Vaccination and Strain Variation

Pertussis or whooping cough is a highly contagious vaccine-preventable disease of the human respiratory tract caused by the Bordetella pertussis bacteria. In Finland, pertussis vaccinations were started in 1952 leading to a dramatic decrease in the morbidity and mortality. In the late 1990s, the incidence of pertussis increased despite the high vaccination coverage. Strain variation has been connected to the re-emergence of pertussis in countries with long history of pertussis vaccination. In 2005, the pertussis vaccine and the vaccination schedule were changed in Finland. The molecular epidemiology and the strain variation of the B. pertussis isolates were examined in Finland and in countries with similar (France) and different (Sweden) vaccination history. Continuous evolution of the B. pertussis population in Finland was observed since the 1950s, and the recently circulating isolates were antigenically different from the vaccine strains. Comparison of the circulating isolates from Finland, France and Sweden did not refer to significant differences. Certain type of strains noticed in France already in 1994 mainly caused the recent epidemics in Sweden (1999) and in Finland (2003-4). On several occasions, a new type of strains first appeared in Sweden and some years later in Finland. The B. pertussis isolates from the infants were shown to be similar to those from the other age groups. It is suggested that the strains originate from the same reservoir among adolescents and adults. The strain variation does not seem to have a major effect on the morbidity among recently vaccinated individuals, but it might play a role among those who are in the waning phase of immunity. The incidence of pertussis in Finland has remained low since the change of the vaccination programme. This might be related to the epidemic nature of pertussis and the near future will show the real effectiveness of the new vaccination programme. At present, many infants are infected because they are too young to be immunised with the current schedule. New strategies or vaccines are needed to protect those who are the most vulnerable.

Relações da atividade agropecuária com parâmetros físicos químicos da água

Water Quality Index (WQI) was used during summer and winter of 1994 and 1995 in the final section of Onça and Feijão streams, downstream Broa Reservoir (São Carlos/SP) to evaluate agricultural and catlleman effects. In Onça stream water quality was "acceptable" in winter and "inappropriate to conventional treatment" in the summer. In Feijão stream the water had an "excellent" quality in winter and "good" in the summer. A MANOVA (Multivariate Analysis of Variance) has used to discriminate seasons and streams. Correlation (p<0,05) among the variables was tested. Water temperature, turbidity, pH and fecal bacteria are highly correlated and can be one of the factors that cause WQI change by seasons.

Propulsor pneumático versátil e isento de pulsação para sistemas de análise em fluxo

Aquarium air pumps are proposed and evaluated as pneumatic liquid propulsion devices for flow injection and continuos flow analysis (FIA and CFA) systems. This kind of pump is widely available at a very low cost and it can sustain a pressure around of 4 psi (0.28 bar) indefinitely. By applying this air pressure onto a solution contained in a reservoir flask, it is possible to reach flow rates of up to 12.5 mL min-1 for circuits comprising reactors, made from 0.8 i.d. tubing with a length of 100 cm. The precise adjustment of flow rate below the maximum one can be made with a simplified needle valve or inserting in series a short length of capillary tube. The absence of flow pulsation is a definite advantage in comparison with peristaltic pumps, especially when amperometric detection is elected, as confirmed experimentally in FIA and CF applications.