This paper describes a highly efficient method for lossless compression of volumetric sets of medical images, such as CTs or MRIs. The proposed method, referred to as 3-D-MRP, is based on the ...principle of minimum rate predictors (MRPs), which is one of the state-of-the-art lossless compression technologies presented in the data compression literature. The main features of the proposed method include the use of 3-D predictors, 3-D-block octree partitioning and classification, volume-based optimization, and support for 16-b-depth images. Experimental results demonstrate the efficiency of the 3-D-MRP algorithm for the compression of volumetric sets of medical images, achieving gains above 15% and 12% for 8- and 16-bit-depth contents, respectively, when compared with JPEG-LS, JPEG2000, CALIC, and HEVC, as well as other proposals based on the MRP algorithm.
The incidence of dengue has grown dramatically in recent decades worldwide, especially in Southeast Asia and the Americas with substantial transmission in 2014-2015. Yet the mechanisms underlying the ...spatio-temporal circulation of dengue virus (DENV) serotypes at large geographical scales remain elusive. Here we investigate the co-circulation in Asia of DENV serotypes 1-3 from 1956 to 2015, using a statistical framework that jointly estimates migration history and quantifies potential predictors of viral spatial diffusion, including socio-economic, air transportation and maritime mobility data. We find that the spread of DENV-1, -2 and -3 lineages in Asia is significantly associated with air traffic. Our analyses suggest the network centrality of air traffic hubs such as Thailand and India contribute to seeding dengue epidemics, whilst China, Cambodia, Indonesia, and Singapore may establish viral diffusion links with multiple countries in Asia. Phylogeographic reconstructions help to explain how growing air transportation networks could influence the dynamics of DENV circulation.
This paper proposes a two-stage high-order intrablock prediction method for light field image coding. This method exploits the spatial redundancy in lenslet light field images by predicting each ...image block, through a geometric transformation applied to a region of the causal encoded area. Light field images comprise an array of microimages that are related by complex geometric transformations that cannot be efficiently compensated by state-of-the-art image coding techniques, which are usually based on low-order translational prediction models. The two-stage nature of the proposed method allows us to choose the order of the prediction model most suitable for each block, ranging from pure translations to projective or bilinear transformations, optimized according to an appropriate rate-distortion criterion. The proposed higher order intrablock prediction approach was integrated into a high efficiency video coding (HEVC) codec and evaluated for both unfocused and focused light field camera models, using different resolutions and microlens arrays. Experimental results show consistent bitrate savings, which can go up to 12.62%, when compared to a lower order intrablock prediction solution and 49.82% when compared to HEVC still picture coding.
In December 2013, an outbreak of Chikungunya virus (CHIKV) caused by the Asian genotype was notified in the Caribbean. The outbreak has since spread to 38 regions in the Americas. By September 2014, ...the first autochthonous CHIKV infections were confirmed in Oiapoque, North Brazil, and in Feira de Santana, Northeast Brazil.
We compiled epidemiological and clinical data on suspected CHIKV cases in Brazil and polymerase-chain-reaction-based diagnostic was conducted on 68 serum samples from patients with symptom onset between April and September 2014. Two imported and four autochthonous cases were selected for virus propagation, RNA isolation, full-length genome sequencing, and phylogenetic analysis. We then followed CDC/PAHO guidelines to estimate the risk of establishment of CHIKV in Brazilian municipalities.
We detected 41 CHIKV importations and 27 autochthonous cases in Brazil. Epidemiological and phylogenetic analyses indicated local transmission of the Asian CHIKV genotype in Oiapoque. Unexpectedly, we also discovered that the ECSA genotype is circulating in Feira de Santana. The presumed index case of the ECSA genotype was an individual who had recently returned from Angola and developed symptoms in Feira de Santana. We estimate that, if CHIKV becomes established in Brazil, transmission could occur in 94% of municipalities in the country and provide maps of the risk of importation of each strain of CHIKV in Brazil.
The etiological strains associated with the early-phase CHIKV outbreaks in Brazil belong to the Asian and ECSA genotypes. Continued surveillance and vector mitigation strategies are needed to reduce the future public health impact of CHIKV in the Americas.
In Brazil, Dengue (DENV) and Zika (ZIKV) viruses are reported as being transmitted exclusively by Aedes aegypti in urban settings. This study established the vectors and viruses involved in an ...arbovirus outbreak that occurred in 2019 in a rural area of Espírito Santo state, Brazil. Mosquitoes collected were morphologically identified, sorted in samples, and submitted to molecular analysis for arboviruses detection. Phylogenetic reconstruction was performed for the viral sequence obtained. All 393 mosquitoes were identified as Aedes albopictus. DENV-1 genotype V was present in one sample and another sample was positive for ZIKV. The DENV-1 clustered with viruses that have circulated in previous years in large urban centers of different regions in Brazil. This is the first report of A. albopictus infected by DENV and ZIKV during an outbreak in a rural area in Brazil, indicating its involvement in arboviral transmission. The DENV-1 strain found in the A. albopictus was not new in Brazil, being involved previously in epidemics related to A. aegypti, suggesting the potential to A. albopictus in transmitting viruses already circulating in the Brazilian population. This finding also indicates the possibility of these viruses to disperse across urban and rural settings, imposing additional challenges for the control of the diseases.
The World Health Organization has declared Zika virus an international public health emergency. Knowledge of Zika virus genomic epidemiology is currently limited due to challenges in obtaining and ...processing samples for sequencing. The ZiBRA project is a United Kingdom-Brazil collaboration that aims to improve this situation using new sequencing technologies.
•We compared the new REGA version 3, with other seven subtyping tools.•Reproducibility was 100% with similarity-based tools and statistical-based tools.•Sensitivity and specificity was ∼ 96% with ...seven tools for B and C subtypes.•COMET, jpHMM, REGAv3 and SCUEAL had the best performance for other pure subtypes.•Performance was variable for CRFs, but COMET and REGAv3 identified most of them.
To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3).
HIV-1 pol sequences (PR+RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. The performance of these tools, for pol, and for PR and RT separately, was compared in terms of reproducibility, sensitivity and specificity with respect to the gold standard which was manual phylogenetic analysis of the pol region.
The sensitivity and specificity for subtypes B and C was more than 96% for seven tools, but was variable for other subtypes such as A, D, F and G. With regard to the most common circulating recombinant forms (CRFs), the sensitivity and specificity for CRF01_AE was ∼99% with statistical-based tools, with phylogenetic-based tools and with Stanford, one of the similarity based tools. CRF02_AG was correctly identified for more than 96% by COMET, REGAv3, Stanford and STAR. All the tools reached a specificity of more than 97% for most of the subtypes and the two main CRFs (CRF01_AE and CRF02_AG). Other CRFs were identified only by COMET, REGAv2, REGAv3, and SCUEAL and with variable sensitivity. When analyzing sequences for PR and RT separately, the performance for PR was generally lower and variable between the tools. Similarity and statistical-based tools were 100% reproducible, but this was lower for phylogenetic-based tools such as REGA (∼99%) and SCUEAL (∼96%).
REGAv3 had an improved performance for subtype B and CRF02_AG compared to REGAv2 and is now able to also identify all epidemiologically relevant CRFs. In general the best performing tools, in alphabetical order, were COMET, jpHMM, REGAv3, and SCUEAL when analyzing pure subtypes in the pol region, and COMET and REGAv3 when analyzing most of the CRFs. Based on this study, we recommend to confirm subtyping with 2 well performing tools, and be cautious with the interpretation of short sequences.
This paper proposes a novel light field image compression approach with viewpoint scalability and random access functionalities. Although current state-of-the-art image coding algorithms for light ...fields already achieve high compression ratios, there is a lack of support for such functionalities, which are important for ensuring compatibility with different displays/capturing devices, enhanced user interaction and low decoding delay. The proposed solution enables various encoding profiles with different flexible viewpoint scalability and random access capabilities, depending on the application scenario. When compared to other state-of-the-art methods, the proposed approach consistently presents higher bitrate savings (44% on average), namely when compared to pseudo-video sequence coding approach based on HEVC. Moreover, the proposed scalable codec also outperforms MuLE and WaSP verification models, achieving average bitrate saving gains of 37% and 47%, respectively. The various flexible encoding profiles proposed add fine control to the image prediction dependencies, which allow to exploit the tradeoff between coding efficiency and the viewpoint random access, consequently, decreasing the maximum random access penalties that range from 0.60 to 0.15, for lenslet and HDCA light fields.
In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis ...revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than reported.
The Zika virus has emerged as a global public health concern. Its rapid geographic expansion is attributed to the success of
mosquito vectors, but local epidemiological drivers are still poorly ...understood. Feira de Santana played a pivotal role in the Chikungunya epidemic in Brazil and was one of the first urban centres to report Zika infections. Using a climate-driven transmission model and notified Zika case data, we show that a low observation rate and high vectorial capacity translated into a significant attack rate during the 2015 outbreak, with a subsequent decline in 2016 and fade-out in 2017 due to herd-immunity. We find a potential Zika-related, low risk for microcephaly per pregnancy, but with significant public health impact given high attack rates. The balance between the loss of herd-immunity and viral re-importation will dictate future transmission potential of Zika in this urban setting.
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