Implementation of the e-SUS Primary Care Strategy: an analysis based on official data.

OBJETIVE: Analyze the implementation of the strategy e-SUS Atenção Básica (e-SUS AB - e-SUS Primary Care) in Brazil between the first years of the system, from 2013 to 2019. METHODS: This is a quantitative, descriptive, and exploratory study. We considered official data from the Ministry of Health, submitted by Brazilian municipalities, in the period from April 2013 to December 2019. We categorized the municipalities as 'not implemented', 'initial implementation', 'partial implementation' and 'implemented' according to the criteria defined in this study. We also verified whether the type of municipality, according to the IBGE classification, influenced the degree of implementation of the e-SUS AB strategy. We performed descriptive analyses and investigated the association between the degrees of implementation of e-SUS AB and the typology of the IBGE classification and characterization of rural and urban spaces. RESULTS: The implementation increased in the analyzed period. The implementation status of the e-SUS AB strategy in 2019 was 'implemented' in 20.2% (1,117) of the municipalities, 'partial implementation' in 32.9% (1,819), 'initial implementation' in 39.1% (2,159) and 'not implemented' in 7.8% (432). The South and Southeast regions presented the best implementation situation in all years, and the states of Rio Grande do Sul, São Paulo and Santa Catarina reached a higher percentage of municipalities with 'implemented' status in 2019. CONCLUSIONS: We confirmed the progress in the implementation of the e-SUS AB strategy over the years. Most of the municipalities are between the status 'initial implementation' and 'partial implementation'. Therefore, we conclude that investments in technological resources, training of professionals, and support are necessary to qualify the implementation and use of information systems in the country, especially for the e-SUS AB strategy.

Morphological and Transcriptional Changes in Human Bone Marrow During Natural Plasmodium vivax Malaria Infections.

BACKGROUND: The presence of Plasmodium vivax malaria parasites in the human bone marrow (BM) is still controversial. However, recent data from a clinical case and experimental infections in splenectomized nonhuman primates unequivocally demonstrated the presence of parasites in this tissue. METHODS: In the current study, we analyzed BM aspirates of 7 patients during the acute attack and 42 days after drug treatment. RNA extracted from CD71+ cell suspensions was used for sequencing and transcriptomic analysis. RESULTS: We demonstrated the presence of parasites in all patients during acute infections. To provide further insights, we purified CD71+ BM cells and demonstrated dyserythropoiesis and inefficient erythropoiesis in all patients. In addition, RNA sequencing from 3 patients showed that genes related to erythroid maturation were down-regulated during acute infections, whereas immune response genes were up-regulated. CONCLUSIONS: This study thus shows that during P. vivax infections, parasites are always present in the BM and that such infections induced dyserythropoiesis and ineffective erythropoiesis. Moreover, infections induce transcriptional changes associated with such altered erythropoietic response, thus highlighting the importance of this hidden niche during natural infections.

Implementation of the e-SUS Primary Care Strategy: an analysis based on official data / Implantação da Estratégia e-SUS Atenção Básica: uma análise fundamentada em dados oficiais

ABSTRACT OBJETIVE Analyze the implementation of the strategy e-SUS Atenção Básica (e-SUS AB - e-SUS Primary Care) in Brazil between the first years of the system, from 2013 to 2019. METHODS This is a quantitative, descriptive, and exploratory study. We considered official data from the Ministry of Health, submitted by Brazilian municipalities, in the period from April 2013 to December 2019. We categorized the municipalities as 'not implemented', 'initial implementation', 'partial implementation' and 'implemented' according to the criteria defined in this study. We also verified whether the type of municipality, according to the IBGE classification, influenced the degree of implementation of the e-SUS AB strategy. We performed descriptive analyses and investigated the association between the degrees of implementation of e-SUS AB and the typology of the IBGE classification and characterization of rural and urban spaces. RESULTS The implementation increased in the analyzed period. The implementation status of the e-SUS AB strategy in 2019 was 'implemented' in 20.2% (1,117) of the municipalities, 'partial implementation' in 32.9% (1,819), 'initial implementation' in 39.1% (2,159) and 'not implemented' in 7.8% (432). The South and Southeast regions presented the best implementation situation in all years, and the states of Rio Grande do Sul, São Paulo and Santa Catarina reached a higher percentage of municipalities with 'implemented' status in 2019. CONCLUSIONS We confirmed the progress in the implementation of the e-SUS AB strategy over the years. Most of the municipalities are between the status 'initial implementation' and 'partial implementation'. Therefore, we conclude that investments in technological resources, training of professionals, and support are necessary to qualify the implementation and use of information systems in the country, especially for the e-SUS AB strategy.

RESUMO OBJETIVO Analisar a implantação da estratégia e-SUS Atenção Básica (e-SUS AB) no Brasil entre os anos iniciais do sistema, de 2013 até 2019. MÉTODOS Trata-se de um estudo quantitativo, descritivo e exploratório. Foram considerados os dados oficiais do Ministério da Saúde, enviados pelos municípios brasileiros, no período de abril de 2013 a dezembro de 2019. Os municípios foram categorizados como 'não implantado', 'implantação inicial', 'implantação parcial' e 'implantado', de acordo com os critérios definidos neste estudo. Verificou-se também se o tipo de município, segundo a classificação do IBGE, influenciou no grau de implantação da estratégia e-SUS AB. Foram realizadas análises descritivas e investigada a associação entre os graus de implantação do e-SUS AB e a tipologia da classificação e caracterização dos espaços rurais e urbanos do IBGE. RESULTADOS O grau de implantação aumentou no período analisado. A situação de implantação da estratégia e-SUS AB, em 2019, foi 'implantado' em 20,2% (1.117) dos municípios, 'implantação parcial' em 32,9% (1.819), 'implantação inicial' 39,1% (2.159) e a situação 'não implantado' foi atribuída em 7,8% (432). As regiões Sul e Sudeste apresentaram a melhor situação de implantação em todos os anos e os estados do Rio Grande do Sul, São Paulo e Santa Catarina alcançaram um maior percentual de municípios com a situação 'implantado' em 2019. CONCLUSÕES Houve avanço na implantação da estratégia e-SUS AB ao longo dos anos. A maior parte dos municípios encontra-se entre o status 'implantação inicial' e 'implantação parcial'. Com isso, conclui-se que ainda são necessários investimentos em recursos tecnológicos, treinamento de profissionais e suporte para qualificar a implantação e uso de sistemas de informação no país, especialmente para a estratégia e-SUS AB.

Rethinking Cervical Cancer Screening in Brazil Post COVID-19: A Global Opportunity to Adopt Higher Impact Strategies.

The World Health Organization global call to eliminate cervical cancer encourages countries to consider introducing or improving cervical cancer screening programs. Brazil's Unified Health System (SUS) is among the world's largest public health systems offering free cytology testing, follow-up colposcopy, and treatment. Yet, health care networks across the country have unequal infrastructure, human resources, equipment, and supplies resulting in uneven program performance and large disparities in cervical cancer incidence and mortality. An effective screening program needs multiple strategies feasible for each community's reality, facilitating coverage and follow-up adherence. Prioritizing those at highest risk with tests that better stratify risk will limit inefficiencies, improving program impact across different resource settings. Highly sensitive human papillomavirus (HPV)-DNA testing performs better than cytology and, with self-collection closer to homes and workplaces, improves access, even in remote regions. Molecular triage strategies like HPV genotyping can identify from the same self-collected sample, those at highest risk requiring follow-up. If proven acceptable, affordable, cost-effective, and efficient in the Brazilian context, these strategies would increase coverage while removing the need for speculum exams for routine screening and reducing follow-up visits. SUS could implement a nationwide organized program that accommodates heterogenous settings across Brazil, informing a variety of screening programs worldwide.

Moving towards a strategy to accelerate cervical cancer elimination in a high-burden city-Lessons learned from the Amazon city of Manaus, Brazil.

The World Health Organization Call to Eliminate Cervical Cancer resonates in cities like Manaus, Brazil, where the burden is among the world's highest. Manaus has offered free cytology-based screening since 1990 and HPV immunization since 2013, but the public system is constrained by many challenges and performance is not well-defined. We obtained cervical cancer prevention activities within Manaus public health records for 2019 to evaluate immunization and screening coverage, screening by region and neighborhood, and the annual Pink October screening campaign. We estimated that among girls and boys age 14-18, 85.9% and 64.9% had 1+ doses of HPV vaccine, higher than rates for age 9-13 (73.4% and 43.3%, respectively). Of the 90,209 cytology tests performed, 24.9% were outside the target age and the remaining 72,230 corresponded to 40.1% of the target population (one-third of women age 25-64). The East zone had highest screening coverage (49.1%), highest high-grade cytology rate (2.5%) and lowest estimated cancers (38.1/100,000) compared with the South zone (32.9%, 1.8% and 48.5/100,000, respectively). Largest neighborhoods had fewer per capita screening locations, resulting in lower coverage. During October, some clinics successfully achieved higher screening volumes and high-grade cytology rates (up to 15.4%). Although we found evidence of some follow-up within 10 months post-screening for 51/70 women (72.9%) with high-grade or worse cytology, only 18 had complete work-up confirmed. Manaus has successfully initiated HPV vaccination, forecasting substantial cervical cancer reductions by 2050. With concerted efforts during campaigns, some clinics improved screening coverage and reached high-risk women. Screening campaigns in community locations in high-risk neighborhoods using self-collected HPV testing can achieve widespread coverage. Simplifying triage and treatment with fewer visits closer to communities would greatly improve follow-up and program effectiveness. Achieving WHO Cervical Cancer Elimination goals in high-burden cities will require major reforms for screening and simpler follow-up and treatment.

The First Contact of Human Dendritic Cells With Trypanosoma cruzi Reveals Response to Virus as an Unexplored Central Pathway.

Chagas disease is a debilitating and neglected disease caused by the protozoan Trypanosoma cruzi. Soon after infection, interactions among T. cruzi and host innate immunity cells can drive/contribute to disease outcome. Dendritic cells (DCs), present in all tissues, are one of the first immune cells to interact with Trypanosoma cruzi metacyclic trypomastigotes. Elucidating the immunological events triggered immediately after parasite-human DCs encounter may aid in understanding the role of DCs in the establishment of infection and in the course of the disease. Therefore, we performed a transcriptomic analysis of a 12 h interaction between T. cruzi and MoDCs (monocyte-derived DCs) from three human donors. Enrichment analyses of the 468 differentially expressed genes (DEGs) revealed viral infection response as the most regulated pathway. Additionally, exogenous antigen processing and presentation through MHC-I, chemokine signaling, lymphocyte co-stimulation, metallothioneins, and inflammasome activation were found up-regulated. Notable, we were able to identify the increased gene expression of alternative inflammasome sensors such as AIM2, IFI16, and RIG-I for the first time in a T. cruzi infection. Both transcript and protein expression levels suggest proinflammatory cytokine production during early T. cruzi-DCs contact. Our transcriptome data unveil antiviral pathways as an unexplored process during T. cruzi-DC initial interaction, disclosing a new panorama for the study of Chagas disease outcomes.

Transcriptional Remodeling Patterns in Murine Dendritic Cells Infected with Paracoccidioides brasiliensis: More Is Not Necessarily Better.

Most people infected with the fungus Paracoccidioides spp. do not get sick, but approximately 5% develop paracoccidioidomycosis. Understanding how host immunity determinants influence disease development could lead to novel preventative or therapeutic strategies; hence, we used two mouse strains that are resistant (A/J) or susceptible (B10.A) to P. brasiliensis to study how dendritic cells (DCs) respond to the infection. RNA sequencing analysis showed that the susceptible strain DCs remodeled their transcriptomes much more intensely than those from the resistant strain, agreeing with a previous model of more intense innate immunity response in the susceptible strain. Contrastingly, these cells also repress genes/processes involved in antigen processing and presentation, such as lysosomal activity and autophagy. After the interaction with P. brasiliensis, both DCs and macrophages from the susceptible mouse reduced the autophagy marker LC3-II recruitment to the fungal phagosome compared to the resistant strain cells, confirming this pathway's repression. These results suggest that impairment in antigen processing and presentation processes might be partially responsible for the inefficient activation of the adaptive immune response in this model.

Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies.

BACKGROUND: Anti-CD3 immunotherapy was initially approved for clinical use for renal transplantation rejection prevention. Subsequently, new generations of anti-CD3 antibodies have entered clinical trials for a broader spectrum of therapeutic applications, including cancer and autoimmune diseases. Despite their extensive use, little is known about the exact mechanism of these molecules, except that they are able to activate T cells, inducing an overall immunoregulatory and tolerogenic behavior. To better understand the effects of anti-CD3 antibodies on human T cells, PBMCs were stimulated, and then, we performed RNA-seq assays of enriched T cells to assess changes in their gene expression profiles. In this study, three different anti-CD3 antibodies were used for the stimulation: two recombinant antibody fragments, namely, a humanized and a chimeric FvFc molecule, and the prototype mouse mAb OKT3. RESULTS: Gene Ontology categories and individual immunoregulatory markers were compared, suggesting a similarity in modulated gene sets, mainly those for immunoregulatory and inflammatory terms. Upregulation of interleukin receptors, such as IL2RA, IL1R, IL12RB2, IL18R1, IL21R and IL23R, and of inhibitory molecules, such as FOXP3, CTLA4, TNFRSF18, LAG3 and PDCD1, were also observed, suggesting an inhibitory and exhausted phenotype. CONCLUSIONS: We used a deep transcriptome sequencing method for comparing three anti-CD3 antibodies in terms of Gene Ontology enrichment and immunological marker expression. The present data showed that both recombinant antibodies induced a compatible expression profile, suggesting that they might be candidates for a closer evaluation with respect to their therapeutic value. Moreover, the proposed methodology is amenable to be more generally applied for molecular comparison of cell receptor dependent antibody therapy.

Exploring the molecular complexity of Triatoma dimidiata sialome.

Triatoma dimidiata, a Chagas disease vector widely distributed along Central America, has great capability for domestic adaptation as the majority of specimens caught inside human dwellings or in peridomestic areas fed human blood. Exploring the salivary compounds that overcome host haemostatic and immune responses is of great scientific interest. Here, we provide a deeper insight into its salivary gland molecules. We used high-throughput RNA sequencing to examine in depth the T. dimidiata salivary gland transcriptome. From >51 million reads assembled, 92.21% are related to putative secreted proteins. Lipocalin is the most abundant gene family, confirming it is an expanded family in Triatoma genus salivary repertoire. Other putatively secreted members include phosphatases, odorant binding protein, hemolysin, proteases, protease inhibitors, antigen-5 and antimicrobial peptides. This work expands the previous set of functionally annotated sequences from T. dimidiata salivary glands available in NCBI from 388 to 3815. Additionally, we complemented the salivary analysis through proteomics (available data via ProteomeXchange with identifier PXD008510), disclosing the set complexity of 119 secreted proteins and validating the transcriptomic results. Our large-scale approach enriches the pharmacologically active molecules database and improves our knowledge about the complexity of salivary compounds from haematophagous vectors and their biological interactions. SIGNIFICANCE: Several haematophagous triatomine species can transmit Trypanosoma cruzi, the etiological agent of Chagas disease. Due to the reemergence of this disease, new drugs for its prevention and treatment are considered priorities. For this reason, the knowledge of vector saliva emerges as relevant biological finding, contributing to the design of different strategies for vector control and disease transmission. Here we report the transcriptomic and proteomic compositions of the salivary glands (sialome) of the reduviid bug Triatoma dimidiata, a relevant Chagas disease vector in Central America. Our results are robust and disclosed unprecedented insights into the notable diversity of its salivary glands content, revealing relevant anti-haemostatic salivary gene families. Our work expands almost ten times the previous set of functionally annotated sequences from T. dimidiata salivary glands available in NCBI. Moreover, using an integrated transcriptomic and proteomic approach, we showed a correlation pattern of transcription and translation processes for the main gene families found, an important contribution to the research of triatomine sialomes. Furthermore, data generated here reinforces the secreted proteins encountered can greatly contribute for haematophagic habit, Trypanosoma cruzi transmission and development of therapeutic agent studies.

A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts.

BACKGROUND: In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed when analyzing this data is distinguishing between long non-coding RNAs (lncRNAs) and protein coding transcripts (PCTs). Thus, we present a Support Vector Machine (SVM) based method to distinguish lncRNAs from PCTs, using features based on frequencies of nucleotide patterns and ORF lengths, in transcripts. METHODS: The proposed method is based on SVM and uses the first ORF relative length and frequencies of nucleotide patterns selected by PCA as features. FASTA files were used as input to calculate all possible features. These features were divided in two sets: (i) 336 frequencies of nucleotide patterns; and (ii) 4 features derived from ORFs. PCA were applied to the first set to identify 6 groups of frequencies that could most contribute to the distinction. Twenty-four experiments using the 6 groups from the first set and the features from the second set where built to create the best model to distinguish lncRNAs from PCTs. RESULTS: This method was trained and tested with human (Homo sapiens), mouse (Mus musculus) and zebrafish (Danio rerio) data, achieving 98.21%, 98.03% and 96.09%, accuracy, respectively. Our method was compared to other tools available in the literature (CPAT, CPC, iSeeRNA, lncRNApred, lncRScan-SVM and FEELnc), and showed an improvement in accuracy by ≈3.00%. In addition, to validate our model, the mouse data was classified with the human model, and vice-versa, achieving ≈97.80% accuracy in both cases, showing that the model is not overfit. The SVM models were validated with data from rat (Rattus norvegicus), pig (Sus scrofa) and fruit fly (Drosophila melanogaster), and obtained more than 84.00% accuracy in all these organisms. Our results also showed that 81.2% of human pseudogenes and 91.7% of mouse pseudogenes were classified as non-coding. Moreover, our method was capable of re-annotating two uncharacterized sequences of Swiss-Prot database with high probability of being lncRNAs. Finally, in order to use the method to annotate transcripts derived from RNA-seq, previously identified lncRNAs of human, gorilla (Gorilla gorilla) and rhesus macaque (Macaca mulatta) were analyzed, having successfully classified 98.62%, 80.8% and 91.9%, respectively. CONCLUSIONS: The SVM method proposed in this work presents high performance to distinguish lncRNAs from PCTs, as shown in the results. To build the model, besides using features known in the literature regarding ORFs, we used PCA to identify features among nucleotide pattern frequencies that contribute the most in distinguishing lncRNAs from PCTs, in reference data sets. Interestingly, models created with two evolutionary distant species could distinguish lncRNAs of even more distant species.

Modulation of the immune response by Fonsecaea pedrosoi morphotypes in the course of experimental chromoblastomycosis and their role on inflammatory response chronicity.

A common theme across multiple fungal pathogens is their ability to impair the establishment of a protective immune response. Although early inflammation is beneficial in containing the infection, an uncontrolled inflammatory response is detrimental and may eventually oppose disease eradication. Chromoblastomycosis (CBM), a cutaneous and subcutaneous mycosis, caused by dematiaceous fungi, is capable of inducing a chronic inflammatory response. Muriform cells, the parasitic form of Fonsecaea pedrosoi, are highly prevalent in infected tissues, especially in long-standing lesions. In this study we show that hyphae and muriform cells are able to establish a murine CBM with skin lesions and histopathological aspects similar to that found in humans, with muriform cells being the most persistent fungal form, whereas mice infected with conidia do not reach the chronic phase of the disease. Moreover, in injured tissue the presence of hyphae and especially muriform cells, but not conidia, is correlated with intense production of pro-inflammatory cytokines in vivo. High-throughput RNA sequencing analysis (RNA-Seq) performed at early time points showed a strong up-regulation of genes related to fungal recognition, cell migration, inflammation, apoptosis and phagocytosis in macrophages exposed in vitro to muriform cells, but not conidia. We also demonstrate that only muriform cells required FcγR and Dectin-1 recognition to be internalized in vitro, and this is the main fungal form responsible for the intense inflammatory pattern observed in CBM, clarifying the chronic inflammatory reaction observed in most patients. Furthermore, our findings reveal two different fungal-host interaction strategies according to fungal morphotype, highlighting fungal dimorphism as an important key in understanding the bipolar nature of inflammatory response in fungal infections.

A Deep Insight into the Sialome of Rhodnius neglectus, a Vector of Chagas Disease.

BACKGROUND: Triatomines are hematophagous insects that act as vectors of Chagas disease. Rhodnius neglectus is one of these kissing bugs found, contributing to the transmission of this American trypanosomiasis. The saliva of hematophagous arthropods contains bioactive molecules responsible for counteracting host haemostatic, inflammatory, and immune responses. METHODS/PRINCIPAL FINDINGS: Next generation sequencing and mass spectrometry-based protein identification were performed to investigate the content of triatomine R. neglectus saliva. We deposited 4,230 coding DNA sequences (CDS) in GenBank. A set of 636 CDS of proteins of putative secretory nature was extracted from the assembled reads, 73 of them confirmed by proteomic analysis. The sialome of R. neglectus was characterized and serine protease transcripts detected. The presence of ubiquitous protein families was revealed, including lipocalins, serine protease inhibitors, and antigen-5. Metalloproteases, disintegrins, and odorant binding protein families were less abundant. CONCLUSIONS/SIGNIFICANCE: The data presented improve our understanding of hematophagous arthropod sialomes, and aid in understanding hematophagy and the complex interplay among vectors and their vertebrate hosts.

Knowledge-based reasoning to annotate noncoding RNA using multi-agent system.

Noncoding RNAs (ncRNAs) have been focus of intense research over the last few years. Since characteristics and signals of ncRNAs are not entirely known, researchers use different computational tools together with their biological knowledge to predict putative ncRNAs. In this context, this work presents ncRNA-Agents, a multi-agent system to annotate ncRNAs based on the output of different tools, using inference rules to simulate biologists' reasoning. Experiments with data from the fungus Saccharomyces cerevisiae allowed to measure the performance of ncRNA-Agents, with better sensibility, when compared to Infernal, a widely used tool for annotating ncRNA. Besides, data of the Schizosaccharomyces pombe and Paracoccidioides brasiliensis fungi identified novel putative ncRNAs, which demonstrated the usefulness of our approach. NcRNA-Agents can be be found at: http://www.biomol.unb.br/ncrna-agents.

Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring.

A Bacillus cereus strain, FT9, isolated from a hot spring in the midwest region of Brazil, had its entire genome sequenced.

Genetic diversity of hepatitis C virus quasispecies in chronic renal failure patients in Midwest Brazil.

Hepatitis C virus (HCV) quasispecies constitute a dynamic population in a continuous process of variation and selection. To investigate effect of the immune system on the genetic variability of HCV, we compared the hypervariable region 1 (HVR1) of immunosuppressed patients with chronic renal failure (CRF group) to immunocompetent patients with HCV chronic infection (control group). The HVR1 from ten samples of each group was amplified, cloned and sequenced. The HCV quasispecies from the control group had a higher frequency of variable sites in HVR1 (83.9 % vs 59.3 %, p < 0.05), as well as a greater diversity within (intra-patient) and between samples, compared to the CRF group. The clustering of the majority of the quasispecies of the CRF group in the phylogenetic tree also showed the limited diversity of the quasispecies in immunosuppressed patients. Moreover, a higher variability of amino acids at positions 384, 386, 391, 394, 397, 398, 400, 405 and 410 was observed in the control group than in the CRF group, which showed a greater variability only at position 388 (p < 0.05). These data corroborates the hypothesis that the major selective pressure factor is the immune system, which promotes a high degree of diversity in the viral progeny and contributes to a constant evolution of HCV.

A mouse variable gene fragment binds to DNA independently of the BCR context: a possible role for immature B-cell repertoire establishment.

B-cell maturation occurs in several steps and requires constant stimulus for its continuing development. From the emergence of the pre-B-cell receptor, signal transduction stimulates and supports B-cell development. Current viewpoints indicate that both positive selection pressure for autoantigens and tonic signaling constitutively stimulate B-cell maturation. In this work, we tested for the presence of a putative DNA binding site in a variable gene segment in a germline configuration, independently of VDJ recombination. After a survey of the public antibody databases, we chose a single mouse heavy variable gene segment that is highly represented in anti-nucleic acid antibodies and tested it for ssDNA binding. A phage display approach was used to search for intrinsic binding to oligo deoxythymidine. The results revealed that binding to an antigen can be influenced by the use of a specific DNA binding V[Formula: see text] gene segment. Our data support the idea that some variable genes have intrinsic reactivity towards specific types of endogenous autoantigens, and this property may contribute to the establishment of the immature B-cell repertoire.

Geographical distribution and oncogenic risk association of human papillomavirus type 58 E6 and E7 sequence variations.

Human papillomavirus (HPV) 58 accounts for a notable proportion of cervical cancers in East Asia and parts of Latin America, but it is uncommon elsewhere. The reason for such ethnogeographical predilection is unknown. In our study, nucleotide sequences of E6 and E7 genes of 401 HPV58 isolates collected from 15 countries/cities across four continents were examined. Phylogenetic relationship, geographical distribution and risk association of nucleotide sequence variations were analyzed. We found that the E6 genes of HPV58 variants were more conserved than E7. Thus, E6 is a more appropriate target for type-specific detection, whereas E7 is more appropriate for strain differentiation. The frequency of sequence variation varied geographically. Africa had significantly more isolates with E6-367A (D86E) but significantly less isolates with E6-203G, -245G, -367C (prototype-like) than other regions (p ≤ 0.003). E7-632T, -760A (T20I, G63S) was more frequently found in Asia, and E7-793G (T74A) was more frequent in Africa (p < 0.001). Variants with T20I and G63S substitutions at E7 conferred a significantly higher risk for cervical intraepithelial neoplasia grade III and invasive cervical cancer compared to other HPV58 variants (odds ratio = 4.44, p = 0.007). In conclusion, T20I and/or G63S substitution(s) at E7 of HPV58 is/are associated with a higher risk for cervical neoplasia. These substitutions are more commonly found in Asia and the Americas, which may account for the higher disease attribution of HPV58 in these areas.

Complete genome sequence of Mycobacterium massiliense.

Mycobacterium massiliense is a rapidly growing bacterium associated with opportunistic infections. The genome of a representative isolate (strain GO 06) recovered from wound samples from patients who underwent arthroscopic or laparoscopic surgery was sequenced. To the best of our knowledge, this is the first announcement of the complete genome sequence of an M. massiliense strain.

Clustering rfam 10.1: clans, families, and classes.

The Rfam database contains information about non-coding RNAs emphasizing their secondary structures and organizing them into families of homologous RNA genes or functional RNA elements. Recently, a higher order organization of Rfam in terms of the so-called clans was proposed along with its "decimal release". In this proposition, some of the families have been assigned to clans based on experimental and computational data in order to find related families. In the present work we investigate an alternative classification for the RNA families based on tree edit distance. The resulting clustering recovers some of the Rfam clans. The majority of clans, however, are not recovered by the structural clustering. Instead, they get dispersed into larger clusters, which correspond roughly to well-described RNA classes such as snoRNAs, miRNAs, and CRISPRs. In conclusion, a structure-based clustering can contribute to the elucidation of the relationships among the Rfam families beyond the realm of clans and classes.