| 1. |
- Razavi-Shearer, Devin M., et al.
(author)
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Adjusted estimate of the prevalence of hepatitis delta virus in 25 countries and territories
- 2024
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In: JOURNAL OF HEPATOLOGY. - 0168-8278 .- 1600-0641. ; 80:2, s. 232-242
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Journal article (peer-reviewed)abstract
- Background & Aims: Hepatitis delta virus (HDV) is a satellite RNA virus that requires the hepatitis B virus (HBV) for assembly and propagation. Individuals infected with HDV progress to advanced liver disease faster than HBV-monoinfected individuals. Recent studies have estimated the global prevalence of anti-HDV antibodies among the HBV-infected population to be 5-15%. This study aimed to better understand HDV prevalence at the population level in 25 countries/territories. Methods: We conducted a literature review to determine the prevalence of anti-HDV and HDV RNA in hepatitis B surface antigen (HBsAg)-positive individuals in 25 countries/territories. Virtual meetings were held with experts from each setting to discuss the findings and collect unpublished data. Data were weighted for patient segments and regional heterogeneity to estimate the prevalence in the HBV-infected population. The findings were then combined with The Polaris Observatory HBV data to estimate the anti-HDV and HDV RNA prevalence in each country/territory at the population level. Results: After adjusting for geographical distribution, disease stage and special populations, the anti-HDV prevalence among the HBsAg+ population changed from the literature estimate in 19 countries. The highest anti-HDV prevalence was 60.1% in Mongolia. Once adjusted for the size of the HBsAg+ population and HDV RNA positivity rate, China had the highest absolute number of HDV RNA+ cases. Conclusions: We found substantially lower HDV prevalence than previously reported, as prior meta-analyses primarily focused on studies conducted in groups/regions that have a higher probability of HBV infection: tertiary care centers, specific risk groups or geographical regions. There is large uncertainty in HDV prevalence estimates. The implementation of reflex testing would improve estimates, while also allowing earlier linkage to care for HDV RNA+ individuals. The logistical and economic burden of reflex testing on the health system would be limited, as only HBsAg+ cases would be screened.
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| 2. |
- Wiedorn, Max O., et al.
(author)
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Megahertz serial crystallography
- 2018
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In: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9
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Journal article (peer-reviewed)abstract
- The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a beta-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
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| 3. |
- Lambert-Niclot, S., et al.
(author)
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Antiretroviral resistance at virological failure in the NEAT 001/ANRS 143 trial: Raltegravir plus darunavir/ritonavir or tenofovir/emtricitabine plus darunavir/ritonavir as first-line ART
- 2016
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In: Journal of Antimicrobial Chemotherapy. - : Oxford University Press (OUP). - 1460-2091 .- 0305-7453. ; 71:4, s. 1056-1062
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Journal article (peer-reviewed)abstract
- Objectives: To describe the pattern of drug resistance at virological failure in the NEAT001/ANRS143 trial (first-line treatment with ritonavir-boosted darunavir plus either tenofovir/emtricitabine or raltegravir). Methods: Genotypic testing was performed at baseline for reverse transcriptase (RT) and protease genes and for RT, protease and integrase (IN) genes for patients with a confirmed viral load (VL) >50 copies/mL or any single VL >500 copies/mL during or after week 32. Results: A resistance test was obtained for 110/805 (13.7%) randomized participants qualifying for resistance analysis (61/401 of participants in the raltegravir arm and 49/404 of participants in the tenofovir/emtricitabine arm). No resistance-associated mutation (RAM) was observed in the tenofovir/emtricitabine plus darunavir/ritonavir arm, and all further analyses were limited to the raltegravir plus darunavir arm. In this group, 15/55 (27.3%) participants had viruses with IN RAMs (12 N155H alone, 1 N155H + Q148R, 1 F121Y and 1 Y143C), 2/53 (3.8%) with nucleotide analogue RT inhibitor RAMs (K65R, M41L) and 1/57 (1.8%) with primary protease RAM (L76V). The frequency of IN mutations at failure was significantly associated with baseline VL: 7.1% for a VL of TREND = 0.007). Of note, 4/15 participants with IN RAM had a VL <200 copies/mL at time of testing. Conclusions: In the NEAT001/ANRS143 trial, there was no RAM at virological failure in the standard tenofovir/emtricitabine plus darunavir/ritonavir regimen, contrasting with a rate of 29.5% (mostly IN mutations) in the raltegravir plus darunavir/ritonavir NRTI-sparing regimen. The cumulative risk of IN RAM after 96 weeks of follow-up in participants initiating ART with raltegravir plus darunavir/ritonavir was 3.9%.
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| 4. |
- Rudke, A. P., et al.
(author)
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Landscape changes over 30 years of intense economic activity in the upper Paraná River basin
- 2022
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In: Ecological Informatics. - : Elsevier BV. - 1574-9541. ; 72
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Journal article (peer-reviewed)abstract
- In this study, we show the complexity associated with the recent land cover changes by elucidating the paths of 30 years of changes in the Upper Paraná River Basin (UPRB), a region severely impacted by agricultural activity, one of the areas with the highest density in the production of hydroelectricity, biofuels and food in the world. In this sense, a post-classification comparison approach based on Landsat images was used to identify detailed ‘from-to’ paths behind those land cover changes. The most expressive changes were the expansion of Cropland and Forest areas and the reduction in savannas, with a net change of 17.9%, 4.1%, and −16.9% of the UPRB area, respectively. Cropland areas showed an expressive increase between 1985 and 2015, rising from 249,439 km2 (27.7%) to 412,909 km2 (45.9%). Forest areas increased from 149,389 km2 to 185,839 km2 in the period. Notably, for this class, an intense spatial dynamic of losses (7.5%) and gains (11.6%) took place between 1985 and 2015. This behavior is related to the disappearance of native vegetation fragments in some sub-basins, as well as to afforestation, reforestation, and/or forest restoration in others. The Cerrado (a typical tropical savanna in South America), the most impacted natural biome of the Basin, decreased from 21.9% of the UPRB in 1985 (196,746 km2) to only about 5% of the whole UPRB area in 2015. Grassland areas, mostly used for livestock, decreased from 271,827 km2 (30.2%) to 229,007 km2 (25.5%). This net decrease was associated with a reduction of 160,830 km2 (17.8%) and the appearance of 118,010 km2 (13.2%) in new areas, previously occupied by tropical savannas in 1985. In conclusion, economic factors were the main drivers for land cover changes, especially agriculture and livestock activities, besides forestry and hydroelectric energy production. In addition, Grassland areas that predominated on the left banks of the UPRB in 1985 retreated with the advance of Cropland areas, mainly due to the expansion of sugarcane for ethanol production, a biofuel widely used in Brazil. In turn, pasture areas migrated to the right bank and occupied a significant part of the Cerrado. Finally, our results demonstrate that the transition dynamics among land cover classes can involve complex political-economical mechanisms that are not always captured by remote sensing.
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| 5. |
- Rudke, A. P., et al.
(author)
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Mapping past landscapes using landsat data : Upper Paraná River Basin in 1985
- 2021
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In: Remote Sensing Applications: Society and Environment. - : Elsevier BV. - 2352-9385. ; 21
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Journal article (peer-reviewed)abstract
- During the last decades, the science of remote sensing of the Earth's surface has produced an enormous amount of data. In parallel, with the increase in computational capacity, several classification methods have been applied to the satellite retrievals. This timely combination allows recovering more accurate knowledge about the land cover maps of past times. Therefore, the main goal of this work was to develop a land cover product for the year 1985 in the Upper Paraná River Basin (UPRB-1985), one of the largest and most economically important river basins in the world. The land cover map was developed using a supervised classifier - SVM (Support Vector Machine) applied to data from Landsat TM (Thematic Mapper) sensor. The classification process was carried out based on 52 scenes collected during 1985 and a total of 17,040 training samples across the basin. Pixel and Object-based methods were used to classify Landsat scenes. The generated mapping accuracy was assessed using statistical criteria adopted in the literature - Global Accuracy and Kappa Index. The McNemar's test result showed no significant differences (at the 5% level) between the Pixel-based and Object-based classifications, even with the Object-based classification accuracy was slightly higher (Global Accuracy of 79.8%). However, some relationship between the relief and the classification approach was observed. In sub-basins with high slopes, the mean overall accuracy values of the Pixel-based classification approach were 13.1% higher than the Object-based approach. By mapping past land cover, this work is strategic information to understand ongoing processes, as well as to assess changes in land cover that have occurred over time and evaluate to what extent they explain the variability in the hydrology of the region.
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| 6. |
- Yefanov, Oleksandr, et al.
(author)
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Evaluation of serial crystallographic structure determination within megahertz pulse trains
- 2019
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In: Structural Dynamics. - : AMER INST PHYSICS. - 2329-7778. ; 6:6
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Journal article (peer-reviewed)abstract
- The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible results in unwanted structural changes due to either radiation damage or systematic effects on data quality. Here, separate structures from the first and subsequent pulses in the European XFEL pulse train were determined, showing that there is essentially no difference between structures determined from different pulses under currently available operating conditions at the European XFEL.
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