STLV-1 co-infection is correlated with an increased SFV proviral load in the peripheral blood of SFV/STLV-1 naturally infected non-human primates

Simian T-Leukemia Virus type 1 and Simian Foamy Virus infect non-human primates. While STLV-1, as HTLV-1, causes Adult T-cell Leukemia/lymphoma, SFV infection is asymptomatic. Both retroviruses can be transmitted from NHPs to humans through bites that allow contact between infected saliva and recipient blood. Because both viruses infect CD4+ T-cells, they might interfere with each other replication, and this might impact viral transmission. Impact of STLV-1 co-infection on SFV replication was analyzed in 18 SFV-positive/STLV-1-negative and 18 naturally SFV/STLV-1 co-infected Papio anubis. Even if 9 animals were found STLV-1-positive in saliva, STLV-1 PVL was much higher in the blood. SFV proviruses were detected in the saliva of all animals. Interestingly, SFV proviral load was much higher in the blood of STLV-1/SFV co-infected animals, compared to STLV-1-negative animals. Given that soluble Tax protein can enter uninfected cells, we tested its effect on foamy virus promoter and we show that Tax protein can transactivate the foamy LTR. This demonstrates that true STLV-1 co-infection or Tax only has an impact on SFV replication and may influence the ability of the virus to be zoonotically transmitted as well as its ability to promote hematological abnormalities

Efficiency-Effectiveness Trade-offs in Recommendation Systems

Throughout the years, numerous recommendation algorithms have been developed to address the information filtering problem by leveraging users’ tastes through implicit or explicit feedback. In this paper, we present the work undertaken as part of a PhD thesis focused on exploring new evaluation dimensions centred around the efficiency-effectiveness trade-offs present in state-of-the-art recommendation systems. Firstly, we highlight the lack of efficiency-oriented studies and we formulate the research problem. Then, we propose a mapping of the design space and a classification of the recommendation algorithms/models with respect to salient attributes and characteristics. At the same time, we explain why and how assessing the recommendations on an accuracy versus training cost curve would advance the current knowledge in the area of evaluation, as well as open new research avenues for exploring parameter configurations within well-known algorithms. Finally, we make the case for a comprehensive methodology that incorporates predictive efficiency-effectiveness models, which illustrate the performance and behaviour of the recommendation systems under different recommendation tasks, while satisfying user-defined quality of service constraints and goals

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences

Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including

Calibration of NOMAD on ESA's ExoMars Trace Gas Orbiter: Part 2 – The Limb, Nadir and Occultation (LNO) channel

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).The Nadir and Occultation for MArs Discovery (NOMAD) instrument is a 3-channel spectrometer suite on the ESA ExoMars Trace Gas Orbiter. Since April 2018, when the nominal science mission began, it has been measuring the constituents of the Martian atmosphere. NOMAD contains three separate spectrometers, two of which operate in the infrared: the Solar Occultation (SO) channel makes only solar occultation observations, and therefore has the best resolving power (∼20,000) and a wider spectral region covering 2.2–4.3 ​μm. The Limb, Nadir and Occultation (LNO) channel covers the 2.2–3.8 ​μm spectral region and can operate in limb, nadir or solar occultation pointing modes. The Ultraviolet–VISible (UVIS) channel operates in the UV–visible region, from 200 to 650 ​nm, and can measure in limb, nadir or solar occultation modes like LNO. The LNO channel has a lower resolving power (∼10,000) than the SO channel, but is still typically an order of magnitude better than previous instruments orbiting Mars. The channel primarily operates in nadir-viewing mode, pointing directly down to the surface to measure the narrow atmospheric molecular absorption lines, clouds and surface features in the reflected sunlight. From the depth and position of the observed atmospheric absorption lines, the constituents of the Martian atmosphere and their column densities can be derived, leading to new insights into the processes that govern their distribution and transport. Surface properties can also be derived from nadir observations by observing the shape of the spectral continuum. Many calibration measurements were made prior to launch, on the voyage to Mars, and continue to be made in-flight during the science phase of the mission. This work, part 2, addresses the aspects of the LNO channel calibration that are not covered elsewhere, namely: the LNO ground calibration setup, the LNO occultation and nadir boresight pointing vectors, LNO detector characterisation and nadir/limb illumination pattern, instrument temperature effects, and finally the radiometric calibration of the LNO channel. An accompanying paper, part 1 (Thomas et al., 2021, this issue), addresses similar aspects for SO, the other infrared channel in NOMAD. A further accompanying paper (Cruz-Mermy et al., 2021, this issue) investigated the LNO radiometric calibration in more detail, approaching the work from a theoretical perspective. The two calibrations agree with each other to within 3%, validating each calibration method. © 2022 The Authors. Published by Elsevier Ltd.This project acknowledges funding by the Belgian Science Policy Office (BELSPO), with the financial and contractual coordination by the ESA Prodex Office (PEA 4000103401, 4000121493), by Spanish Ministry of Science and Innovation (MCIU) and by European funds under grants PGC2018-101836-B-I00 and ESP2017-87143-R (MINECO/FEDER), as well as by the UK Space Agency through grants ST/V002295/1, ST/V005332/1 and ST/S00145X/1 and ST/R001405/1 and Italian Space Agency through grant 2018-2-HH.0. This work was supported by the Belgian Fonds de la Recherche Scientifique – FNRS under grant number 30442502 (ET_HOME). The IAA/CSIC team acknowledges financial support from the State Agency for Research of the Spanish MCIU through the ‘Center of Excellence Severo Ochoa’ award for the Instituto de Astrofísica de Andalucía (SEV-2017-0709). SR thanks BELSPO for the FED-tWIN funding (Prf-2019-077 - RT-MOLEXO)

The Atmospheric Chemistry Suite (ACS) of Three Spectrometers for the ExoMars 2016 Trace Gas Orbiter

The Atmospheric Chemistry Suite (ACS) package is an element of the Russian contribution to the ESA-Roscosmos ExoMars 2016 Trace Gas Orbiter (TGO) mission. ACS consists of three separate infrared spectrometers, sharing common mechanical, electrical, and thermal interfaces. This ensemble of spectrometers has been designed and developed in response to the Trace Gas Orbiter mission objectives that specifically address the requirement of high sensitivity instruments to enable the unambiguous detection of trace gases of potential geophysical or biological interest. For this reason, ACS embarks a set of instruments achieving simultaneously very high accuracy (ppt level), very high resolving power (>10,000) and large spectral coverage (0.7 to 17 μm—the visible to thermal infrared range). The near-infrared (NIR) channel is a versatile spectrometer covering the 0.7–1.6 μm spectral range with a resolving power of ∼20,000. NIR employs the combination of an echelle grating with an AOTF (Acousto-Optical Tunable Filter) as diffraction order selector. This channel will be mainly operated in solar occultation and nadir, and can also perform limb observations. The scientific goals of NIR are the measurements of water vapor, aerosols, and dayside or night side airglows. The mid-infrared (MIR) channel is a cross-dispersion echelle instrument dedicated to solar occultation measurements in the 2.2–4.4 μm range. MIR achieves a resolving power of >50,000. It has been designed to accomplish the most sensitive measurements ever of the trace gases present in the Martian atmosphere. The thermal-infrared channel (TIRVIM) is a 2-inch double pendulum Fourier-transform spectrometer encompassing the spectral range of 1.7–17 μm with apodized resolution varying from 0.2 to 1.3 cm−1. TIRVIM is primarily dedicated to profiling temperature from the surface up to ∼60 km and to monitor aerosol abundance in nadir. TIRVIM also has a limb and solar occultation capability. The technical concept of the instrument, its accommodation on the spacecraft, the optical designs as well as some of the calibrations, and the expected performances for its three channels are described

Genetic Characterization of Human T-Cell Lymphotropic Virus Type 1 in Mozambique: Transcontinental Lineages Drive the HTLV-1 Endemic

Human T-cell lymphotropic virus type 1 (HTLV-1) is the causative agent of Adult T-Cell Leukemia/Lymphoma (ATL), the Tropical Spastic Paraparesis/HTLV-1-associated Myelopathy (TSP/HAM) and other inflammatory diseases, including dermatitis, uveitis, and myositis. It is estimated that 2–8% of the infected persons will develop a HTLV-1-associated disease during their lifetimes, frequently TSP/HAM. Thus far, there is not a specific treatment to this progressive and chronic disease. HTLV-1 has means of three transmission: (i) from mother to child during prolonged breastfeeding, (ii) between sexual partners and (iii) through blood transfusion. HTLV-1 has been characterized in 7 subtypes and the geographical distribution and the clinical impact of this infection is not well known, mainly in African population. HTLV-1 is endemic in sub-Saharan Africa. Mozambique is a country of southeastern Africa where TSP/HAM cases were reported. Recently, our group estimated the HTLV prevalence among Mozambican blood donors as 0.9%. In this work we performed a genetic analysis of HTLV-1 in blood donors and HIV/HTLV co-infected patients from Maputo, Mozambique. Our results showed the presence of three HTLV-1 clusters within the Cosmopolitan/Transcontinental subtype/subgroup. The differential rates of HIV-1/HTLV-1 co-infection in the three HTLV-1 clusters demonstrated the dynamic of the two viruses and the need for implementation of control measures focusing on both retroviruses

Trends in the prevalence and distribution of HTLV-1 and HTLV-2 infections in Spain

<p>Abstract</p> <p>Background</p> <p>Although most HTLV infections in Spain have been found in native intravenous drug users carrying HTLV-2, the large immigration flows from Latin America and Sub-Saharan Africa in recent years may have changed the prevalence and distribution of HTLV-1 and HTLV-2 infections, and hypothetically open the opportunity for introducing HTLV-3 or HTLV-4 in Spain. To assess the current seroprevalence of HTLV infection in Spain a national multicenter, cross-sectional, study was conducted in June 2009.</p> <p>Results</p> <p>A total of 6,460 consecutive outpatients attending 16 hospitals were examined. Overall, 12% were immigrants, and their main origin was Latin America (4.9%), Africa (3.6%) and other European countries (2.8%). Nine individuals were seroreactive for HTLV antibodies (overall prevalence, 0.14%). Evidence of HTLV-1 infection was confirmed by Western blot in 4 subjects (prevalence 0.06%) while HTLV-2 infection was found in 5 (prevalence 0.08%). Infection with HTLV types 1, 2, 3 and 4 was discarded by Western blot and specific PCR assays in another two specimens initially reactive in the enzyme immunoassay. All but one HTLV-1 cases were Latin-Americans while all persons with HTLV-2 infection were native Spaniards.</p> <p>Conclusions</p> <p>The overall prevalence of HTLV infections in Spain remains low, with no evidence of HTLV-3 or HTLV-4 infections so far.</p

Mechanisms of HTLV-1 persistence and transformation

Adult T-cell leukaemia (ATL) is caused by the human T-cell lymphotropic virus type 1 (HTLV-1). HTLV-1 has elaborated strategies to persist and replicate in the presence of a strong immune response. In this review, we summarise these mechanisms and their contribution to T-cell transformation and ATL development