888 research outputs found
Isolation of three novel rat and mouse papillomaviruses and their genomic characterization.
Despite a growing knowledge about the biological diversity of papillomaviruses (PV), only little is known about non-human PV in general and about PV mice models in particular. We cloned and sequenced the complete genomes of two novel PV types from the Norway rat (Rattus norvegicus; RnPV2) and the wood mouse (Apodemus sylvaticus; AsPV1) as well as a novel variant of the recently described MmuPV1 (originally designated as MusPV) from a house mouse (Mus musculus; MmuPV1 variant). In addition, we conducted phylogenetic analyses using a systematically representative set of 79 PV types, including the novel sequences. As inferred from concatenated amino acid sequences of six proteins, MmuPV1 variant and AsPV1 nested within the Beta+Xi-PV super taxon as members of the Pi-PV. RnPV2 is a member of the Iota-PV that has a distant phylogenetic position from Pi-PV. The phylogenetic results support a complex scenario of PV diversification driven by different evolutionary forces including co-divergence with hosts and adaptive radiations to new environments. PV types particularly isolated from mice and rats are the basis for new animal models, which are valuable to study PV induced tumors and new treatment options
Developing an HPV Infection Risk Prediction Model for Adult Females
According to the Centers for Disease Control and Prevention (CDC), nearly one in four people are currently infected with human papillomavirus (HPV) in the United States. Although most people with HPV never experience symptoms, there is a risk of developing different types of HPV-related cancers after infection. These cancers and other related diseases result in almost $8 billion spent annually for treatment. Currently, all boys and girls ages 11 or 12 years are recommended to receive HPV vaccination. Catch-up vaccines are recommended for males and females through the age of 21 and 26, respectively, if they did not get vaccinated previously. However, the uptake rates among young adult females remain low in the United States.
This research seeks to create a risk prediction model with a focus on adult females that will assist these individuals to estimate the risk of HPV infection based on demographic, sexual behavior, and lifestyle factors. The focus of this thesis is on the impact diet and exercise have on risk of infection. A variety of predictive models were applied to the data collected to determine the best fit. These models include logistic regression, lasso regression, ridge regression, elastic net regression, and the random forest algorithm.
Our results corroborate findings in other studies. Similar factors are recognized as significant such as sexual partners, age at first sexual activity, alcohol use, smoking habits, poverty level, and marital status. This study also found daily nutrition and sedentary activity has a significant role in HPV infection but was not able to show significance of daily exercise due to data constraints
Evolution and Taxonomic Classification of Human Papillomavirus 16 (HPV16)-Related Variant Genomes: HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67
Human papillomavirus 16 (HPV16) species group (alpha-9) of the Alphapapillomavirus genus contains HPV16, HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. These HPVs account for 75% of invasive cervical cancers worldwide. Viral variants of these HPVs differ in evolutionary history and pathogenicity. Moreover, a comprehensive nomenclature system for HPV variants is lacking, limiting comparisons between studies.DNA from cervical samples previously characterized for HPV type were obtained from multiple geographic regions to screen for novel variants. The complete 8 kb genomes of 120 variants representing the major and minor lineages of the HPV16-related alpha-9 HPV types were sequenced to capture maximum viral heterogeneity. Viral evolution was characterized by constructing phylogenic trees based on complete genomes using multiple algorithms. Maximal and viral region specific divergence was calculated by global and pairwise alignments. Variant lineages were classified and named using an alphanumeric system; the prototype genome was assigned to the A lineage for all types.The range of genome-genome sequence heterogeneity varied from 0.6% for HPV35 to 2.2% for HPV52 and included 1.4% for HPV31, 1.1% for HPV33, 1.7% for HPV58 and 1.1% for HPV67. Nucleotide differences of approximately 1.0% - 10.0% and 0.5%-1.0% of the complete genomes were used to define variant lineages and sublineages, respectively. Each gene/region differs in sequence diversity, from most variable to least variable: noncoding region 1 (NCR1) /noncoding region 2 (NCR2) >upstream regulatory region (URR)> E6/E7 > E2/L2 > E1/L1.These data define maximum viral genomic heterogeneity of HPV16-related alpha-9 HPV variants. The proposed nomenclature system facilitates the comparison of variants across epidemiological studies. Sequence diversity and phylogenies of this clinically important group of HPVs provides the basis for further studies of discrete viral evolution, epidemiology, pathogenesis and preventative/therapeutic interventions
Identification of Human Papillomavirus Type 58 Lineages and the Distribution Worldwide
Background. Human papillomavirus type 58 (HPV-58) accounts for a much higher proportion of cervical cancers in East Asia than other types. A classification system of HPV-58, which is essential for molecular epidemiological study, is lacking. Methods and results. This study analyzed the sequences of 401 isolates collected from 15 countries and cities. The 268 unique concatenated E6-E7-E2-E5-L1-LCR sequences that comprised 57% of the whole HPV-58 genome showed 4 distinct clusters. L1 and LCR produced tree topologies that best resembled the concatenated sequences and thus are the most appropriate surrogate regions for lineage classification. Moreover, short fragments from L1 (nucleotides 6014–6539) and LCR (nucleotides 7257–7429 and 7540–52) were found to contain sequence signatures informative for lineage identification. Lineage A was the most prevalent lineage across all regions. Lineage C was more frequent in Africa than elsewhere, whereas lineage D was more prevalent in Africa than in Asia. Among lineage A variants, sublineage A2 dominated in Africa, the Americas, and Europe, but not in Asia. Sublineage A1, which represents the prototype that originated from a patient with cancer, was rare worldwide except in Asia. Conclusions. HPV-58 can be classified into 4 lineages that show some degree of ethnogeographic predilection in distribution. The evolutionary, epidemiological, and pathological characteristics of these lineages warrant further study
Radiomics strategies for risk assessment of tumour failure in head-and-neck cancer
Quantitative extraction of high-dimensional mineable data from medical images
is a process known as radiomics. Radiomics is foreseen as an essential
prognostic tool for cancer risk assessment and the quantification of
intratumoural heterogeneity. In this work, 1615 radiomic features (quantifying
tumour image intensity, shape, texture) extracted from pre-treatment FDG-PET
and CT images of 300 patients from four different cohorts were analyzed for the
risk assessment of locoregional recurrences (LR) and distant metastases (DM) in
head-and-neck cancer. Prediction models combining radiomic and clinical
variables were constructed via random forests and imbalance-adjustment
strategies using two of the four cohorts. Independent validation of the
prediction and prognostic performance of the models was carried out on the
other two cohorts (LR: AUC = 0.69 and CI = 0.67; DM: AUC = 0.86 and CI = 0.88).
Furthermore, the results obtained via Kaplan-Meier analysis demonstrated the
potential of radiomics for assessing the risk of specific tumour outcomes using
multiple stratification groups. This could have important clinical impact,
notably by allowing for a better personalization of chemo-radiation treatments
for head-and-neck cancer patients from different risk groups.Comment: (1) Paper: 33 pages, 4 figures, 1 table; (2) SUPP info: 41 pages, 7
figures, 8 table
EpidemiologĂa molecular y análisis filogenĂ©tico de la infecciĂłn por el virus del papiloma humano en mujeres con lesiones cervicales y cáncer en la regiĂłn litoral del Ecuador
The aim of the present study was to gather information regarding the molecular epidemiology of Human papillomavirus (HPV) and related risk factors in a group of women with low- and high-grade cervical lesions and cancer from the coastal region of Ecuador. In addition, we studied the evolution of HPV variants from the most prevalent types and provided a temporal framework for their emergence, which may help to trace the source of dissemination within the region. We analyzed 166 samples, including 57 CIN1, 95 CIN2/3 and 14 cancer cases. HPV detection and typing was done by PCR-sequencing (MY09/MY11). HPV variants and estimation of the time to most recent common ancestor (tMRCA) was assessed through phylogeny and coalescence analysis. HPV DNA was found in 54.4% of CIN1, 74.7% of CIN2/3 and 78.6% of cancer samples. HPV16 (38.9%) and HPV58 (19.5%) were the most prevalent types. Risk factors for the development of cervical lesions/cancer were the following: three or more pregnancies (OR = 4.3), HPV infection (OR = 3.7 for high-risk types; OR = 3.5 for HPV16), among others. With regard to HPV evolution, HPV16 isolates belonged to lineages A (69%) and D (31%) whereas HPV58 isolates belonged only to lineage A. The period of emergence of HPV16 was in association with human populations (tMRCA = 91. 052 years for HPV16A and 27. 000 years for HPV16D), whereas HPV58A preceded Homo sapiens evolution (322. 257 years). This study provides novel data on HPV epidemiology and evolution in Ecuador, which will be fundamental in the vaccine era.Fil: Bedoya Pilozo, Cesar H.. Escuela Superior PolitĂ©cnica del Litoral; Ecuador. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Medina MagĂĽes, Lex G.. Escuela Superior PolitĂ©cnica del Litoral; EcuadorFil: Espinosa GarcĂa, Maylen. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Sánchez, Martha. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Parrales Valdiviezo, Johanna V.. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Molina, Denisse. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Ibarra, MarĂa A.. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Quimis Ponce, MarĂa. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: España, Karool. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Párraga Macias, Karla E.. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Cajas Flores, Nancy V.. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Solon, Orlando A.. Instituto Nacional de Investigaciones en Salud PĂşblica; Ecuador. Universidad Agraria del Ecuador; EcuadorFil: Robalino Penaherrera, Jorge A.. Instituto Nacional de Investigaciones en Salud PĂşblica; EcuadorFil: Chedraui, Peter. Hospital Gineco-ObstĂ©trico Enrique C. Sotomayor; EcuadorFil: Escobar, Saul. Universidad CatĂłlica de Guayaquil; EcuadorFil: Loja Chango, Rita D.. Universidad CatĂłlica de Guayaquil; EcuadorFil: Ramirez Morán, Cecibel. Universidad CatĂłlica de Guayaquil; EcuadorFil: Espinoza Caicedo, Jasson. Universidad CatĂłlica de Guayaquil; EcuadorFil: Sánchez Giler, Sunny. Universidad Especialidades EspĂritu Santo. Facultad de Ciencias MĂ©dicas; EcuadorFil: Limia, Celia M.. Instituto de Medicina Tropical Pedro Kouri; CubaFil: Alemán, Yoan. Instituto de Medicina Tropical Pedro Kouri; CubaFil: Soto, Yudira. Instituto de Medicina Tropical Pedro Kouri; CubaFil: Kouri, Vivian. Instituto de Medicina Tropical Pedro Kouri; CubaFil: Culasso, AndrĂ©s Carlos Alberto. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Centro CientĂfico TecnolĂłgico Conicet - Nordeste; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y BioquĂmica. Departamento de MicrobiologĂa, InmunologĂa y BiotecnologĂa. Cátedra de VirologĂa; ArgentinaFil: Badano, Ines. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Centro CientĂfico TecnolĂłgico Conicet - Nordeste; Argentina. SecretarĂa de EducaciĂłn Superior, Ciencia, TecnologĂa e InnovaciĂłn; Ecuador. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, QuĂmicas y Naturales. Laboratorio de BiologĂa Molecular Aplicada; Argentin
Refining The Staging Scheme For Human Papillomavirus-Related Oropharyngeal Carcinoma
Current TNM staging system derived empirically from human papillomavirus (HPV) unrelated oropharyngeal cancer (OPC) has been shown inadequate to predict survival for HPV-related OPC. This study used three recursive partitioning algorithms, Classification Trees (CART), Conditional Inference Trees (CTree) and Model-based Recursive Partitioning (MOB) to derive a new staging scheme based on data from the National Cancer Data Base (NCDB). The derived staging systems were compared to the current system using the criteria such as hazard consistency within staging groups, hazard discrimination between groups, predictive ability and balance of distribution across groups. A total of 5,712 patients were included in the analysis. The staging system derived using the model-based recursive partitioning (MOB) has the best predictive ability and overall performance. It separates patients into four stages: Stage I (T1-2N0-2a), Stage II (T1-2N2b-3), Stage III (T3), and Stage IV (T4). Stage V is reserved for metastatic patients (M1). The theoretical advantages for the MOB algorithm of fitting the local parametric model in each node and adjusting for covariates affecting survival were confirmed with empirical analysis. Thus MOB algorithm is recommended for future TNM cancer staging studies
Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer
A thorough understanding of virus diversity in wildlife provides epidemiological baseline information about pathogens. In this study, eye swab samples were obtained from semi-domesticated reindeer (Rangifer tarandus tarandus) in Norway during an outbreak of infectious eye disease, possibly a very early stage of infectious keratoconjunctivitis (IKC). Large scale molecular virus screening, based on host nucleic acid depletion, sequence-independen
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