486 research outputs found
A study of the genital microbiotas of black South African women and men: associations with human papillomavirus and HIV infections
No full textPersistent genital infection with oncogenic or high-risk human papillomavirus (HPV) is causally associated with cervical cancer in women and some penile cancers in men. The role of the complex genital microbiota in HPV infection has not been extensively addressed. This study characterised the genital microbiotas of heterosexually-active Black South African women and men, predominantly of the Xhosa ethnicity, recruited from a community in Cape Town, South Africa. The association of the genital microbiotas with prevalent HPV, HIV, demographic, behavioural, and clinical characteristics of the participants was examined. In Chapter 2 the bacterial communities in cervicovaginal samples from 62 HIVseronegative South African women were profiled by Ion Torrent PGM sequencing of the V4 hypervariable region of the bacterial 16S rRNA gene (IT-V4 method). The cervicovaginal microbiotas (CVMs) were found to cluster into three distinct community state types (CSTs): Lactobacillus iners-dominated CVMs (CST I (38.7%, 24/62)), unclassified Lactobacillusdominated CVMs (CST II (4.8%, 3/62)), and diverse CVMs (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. The majority of the women had nonLactobacillus-dominated CVMs. Lactobacilli are recognised as protective against sexually transmitted infections. Among the Lactobacillus species detected in the women, L. iners was the most prevalent and abundant. This species is recognised as the least protective amongst the vaginal lactobacilli. Women in CST I were more likely to be on hormonal contraception compared to women in CST III (relative risk (RR): 2.6 [95% CI 1.3-5.3]; p=0.005). Further research is required to confirm this association and to determine the biological mechanism. Microbiome research methodologies are constantly improving and in Chapter 3 the performance of two bacterial 16S rRNA gene amplicon-based methodologies were compared. The CVMs of 19 women were characterised using the IT-V4 method (Chapter 2) and using the Illumina 16S rRNA metagenomics method (IM-V3/V4 method). The latter method involves sequencing the V3 and V4 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. The two methods showed a high degree of correlation (r=0.89, p3, p3, p3, p 2, p<0.05) Men with BV-negative female sexual partners (66.5% (157/236)) had higher relative abundances of Lactobacillus in their penile microbiotas than men with BV-positive female partners (p=0.007). Atopobium, Sneathia, and Saccharofermentans were significantly more prevalent in men with BV-positive female partners than men with BV-negative partners (p<0.020). The main limitations of our study include relatively small sample size of women, insufficient participant information such as host genetics, other STIs (e.g., herpes simplex virus) and abnormal vaginal flora (e.g., aerobic vaginitis), using a less sensitive method to diagnose BV in women, and inherent biases evident in any retrospective study. Moreover, we did not adjust for confounding factors in our analysis due to the small sample size. Despite the underscored limitations, our findings provide insight into the baseline genital microbiotas of the Black South African women and men. The associations identified in this cross-sectional study between specific microbiota members and HPV infection, particularly the association between Sneathia and HPV/high-risk HPV infection, identified in both women and men, are hypothesis-generating and warrant further investigation. The study forms a critical starting point for future longitudinal confirmatory association studies and studies examining these bacteria as potential biomarkers or risk factors for HPV infection
Characterisation and evolutionary dynamics of ten novel Gammapapillomavirus types from South African penile swabs
No full textHuman papillomaviruses (HPVs) are genetically diverse, belonging to five distinct genera: Alpha, Beta, Gamma, Mu and Nu. We discovered ten novel Gammapapillomaviruses (Gamma-HPVs). Genomic characterisation and phylogenetic evaluation of the ten novel Gamma-HPV types were done: HPV211, HPV212, HPV213, HPV214, HPV215, HPV216, HPV219, HPV220, HPV221 and HPV222. These HPVs were previously identified in a study that was done on 218 penile samples (104 HIV negative and 114 HIV positive) using high throughput sequencing (Roche 454) of amplimers obtained using FAP59/64 primers which were designed to detect “cutaneous” or Beta- and Gamma-HPVs. Fifteen putative novel HPV types were identified from the short HPV L1 FAP fragments HPV211 (CT02, KY063000), HPV212 (CT03, KY063001), HPV213 (CT04, KY063002), HPV214 (CT06, KY063004), HPV215 (CT07, KY063005), HPV216 (CT12, KY063010), HPV219 (CT01, KY062999), HPV220 (CT08, KY063006), HPV221 (CT09, KY063007) and HPV222 (CT155, AY009886) with prevalences varying from 0.5% to 4.1% of men sampled. Multiple full genome clones for each novel type were generated through whole genome amplification, cloning and next generation sequencing. Complete genome sizes were: HPV211 (7253 bp), HPV212 (7208 bp), HPV213 (7096 bp), HPV214 (7357 bp), HPV215 (7186 bp), HPV216 (7233 bp), HPV219 (7108 bp), HPV220 (7381 bp), HPV221 (7326 bp) and HPV222 (7275 bp). Phylogenetically the novel Papillomaviruses (PVs) all clustered with Gamma-HPVs: HPV211 is most closely related to HPV168 (72% identity in the L1 nucleotide sequence) of the Gamma-8 species, HPV212 is most closely related to HPV144 (82.9%) of the Gamma-17 species, HPV213 is most closely related to HPV153 (71.8%) of the Gamma-13 species, HPV214 is most closely related to HPV103 (75.3%) of the Gamma-6 species, HPV215 and HPV216 are most closely related to HPV129 (76.8% and 79.2% respectively) of the Gamma-9 species. HPV219 is phylogenetically most closely related to HPV213 (87% identity in L1 gene) of the Gamma-13 species, HPV220 to HPV212 (72%) of Gamma-17, HPV221 to HPV142 (80%) of Gamma-10, HPV222 to HPV162 (73%) of Gamma-19. The novel HPV types demonstrated the classical genomic organisation of Gamma-HPVs, with seven open reading frames (ORFs) encoding five early (E1, E2, E4, E6 and E7) and two late (L1 and L2) proteins. Typical of Gamma-HPVs, the novel types all lacked the E5 ORF and HPV214 also lacked the E6 ORF. We further examined variation of the novel types in clinical specimens from which they were identified. All the clones of HPV211, HPV214, HPV216, HPV219 and HPV221 were identical and showed 100% pairwise identity. The clones of HPV213, HPV215, HPV212, HPV220 and HPV222 had several differences. Analysis of mismatches between the nine genomic clones of HPV212 showed a total of 67 mismatch positions that varied along the 7208 bp genome and all the clones were unique. Analysis of mismatches between the 10 genomic clones of HPV213 showed a total of 51 mismatch positions that varied along the 7096 bp genome and it had 5 unique clones. The 6 genomic clones of HPV215 showed a total of 50 mismatch positions along a 7186 bp genome and it had 3 identical and 3 different clones. HPV220 had 4 different genomic clones that showed 17 mismatch positions along a 7381 bp genome. The 5 different clones of HPV222 showed a total of 24 mismatch positions along the 7275 bp genome. Conserved domains observed among the novel types were the Zinc finger binding Domain and PDZ domains. A retinoblastoma binding protein (pRB) binding domain in the E7 protein was additionally identified in HPV214 and HPV222. PVs are thought to evolve slowly because they co-opt high-fidelity host cellular DNA polymerases for their replication. Despite extensive efforts to catalogue all the HPV species that infect humans, it is likely that many still remain undiscovered. We used the genome sequences of the ten novel viruses and related HPVs to analyse the evolutionary dynamics of these viruses at the whole genome and individual gene scales. We found statistically significant incongruences between the phylogenetic trees of different genes which imply gene-to-gene variation in the evolutionary processes underlying the diversification of Gamma-PVs. We were, however, only able to detect convincing evidence of a single recombination event which, on its own, cannot explain the observed incongruences between gene phylogenies. The divergence times of the last common ancestor (LCA) of the Alpha, Beta, Mu, Nu and Gamma genera was predicted to have existed between 49.7-58.5 million years ago before splitting into the five main lineages. The LCA of the presently sampled Gamma-PVs was predicted to have existed between 45.3 and 67.5 million years ago: approximately at the time when the simian and tarsier lineages of the primates diverged. The discovery, characterisation and classification of HPV211, HPV212, HPV213, HPV214, HPV215 HPV216, HPV219, HPV220, HPV221 and HPV222 add these novel types to the repertoire of the ever expanding Gamma-HPVs genus hence expanding our knowledge of these viruses
Understanding insertion and integration in a study abroad context: the case of English-speaking sojourners in France
No full textThis paper draws on a recent study of British students of languages undertaking a year abroad in France, in a variety of placements (as language teaching assistants, as exchange students, and as workplace interns). The data were gathered in the context of the 2011-2013 LANGSNAP project, a larger study undertaken which investigated both the language learning and social integration of British students spending an academic year abroad in France, Spain or Mexico Having made a positive choice to specialise in languages at university, and having already reached a relatively advanced level in French during their secondary school education, it could be assumed that these students were positively motivated to further develop their language skills, to deepen their intercultural understanding, and to integrate socially within the local society. Indeed, in pre-departure interviews (in French), the participating students unanimously expressed the wish to integrate and in particular to make French same-aged friends. The paper first of all presents an overview of the range of tools used to gather both quantitative and qualitative data on participants’ social integration. The paper then goes on to evaluate the degree of success of even such highly motivated participants in achieving this declared goal, and to consider social, sociolinguistic and personal factors which appear to influence the degree of social integration achieved by individual participants
A Study of Genital Human Papillomavirus (HPV) and Evaluation of HPV Testing for Cervical Cancer Screening in Women from the Eastern Cape Province, South Africa
No full textIntroduction: Human papillomavirus (HPV) infection is an important public health problem facing black African women. Persistent infection with high-risk (HR) HPV types is the key factor for the development of cervical cancer. Coinfection of HPV with other sexually transmitted pathogens contributes to the progression of cervical cancer. Preventative measures including screening for and treating pre-cancerous cervical lesions as well as HPV vaccination have been implemented in parts of South Africa. However, in the rural Eastern Cape Province there is limited information on the prevalence of HPV and the HPV types associated with cervical lesions. Two cohorts were chosen to study HPV in the Eastern Cape (South Africa), a community clinic, and a referral hospital for treatment of cervical lesions. This study aimed at determining the prevalence of HPV, risk factors of HPV, coinfection of HPV with sexually transmitted pathogens and evaluate the performance of a number of HPV tests for HPV detection and cervical cancer screening. The objectives of the study were: • To investigate the prevalence of HR-HPV and factors associated with HR-HPV infection among women from rural Eastern Cape, South Africa. • To investigate the distribution of HPV genotypes among women with cervical intraepithelial lesions according to HIV status from Eastern Cape Province, South Africa. • To investigate HR-HPV prevalence and compare agreement between cliniciancollected and self-collected genital specimens as well as two different HPV tests on clinician-collected samples. • To investigate the prevalence of sexually transmitted pathogens and co-infection of with HR-HPV infection among women from rural Eastern Cape Province, South Africa. Methods: A total of 741 participants were recruited from the Mbekweni Community Clinic (N=417) and the Nelson Mandela Hospital Referral Clinic (N=324) located in the OR Tambo municipality of the Eastern Cape Province. Clinician-collected cervical scrapes from women attending the Community Clinic were screened for HR-HPV prevalence and HR-HPV viral load using Hybrid Capture 2 (HC-2, Qiagen Inc., Gaithersburg, MD; USA); Cervical clinician-collected and vaginal self-collected specimens of women with or without abnormal cytology from both study cohorts were also screened for HR-HPV infection using hpVIR real-time PCR. HPV typing of clinician-collected cervical specimens from women with cervical intraepithelial neoplasia grades 2 and 3 (CIN 2 / 3) was done using Direct Flow Chip HPV kit (Master Diagnostica, Spain). Cervical specimens from the Community Clinic (N=205) were also tested for sexually transmitted infections (STIs) namely Chlamydia trachomatis: CT, Haemophilus ducreyi, Herpes Simplex Virus type 2, Neisseria gonorrhoeae: NG, Treponema pallidum, and Trichomonas vaginalis: TV) and pathobionts (Ureaplasma spp: (UP), Mycoplasma genitalium: MG, and Mycoplasma hominis: MH) using the STD Direct Flow Chip kit (Master Diagnostica, Spain). The univariate and multivariate analysis was used to determine the correlation between HPV infection and potential behavioural risk factors using STATA 14.2 (Stata Corp, College Station, Texas). A chi squared test was used determine the difference in estimated HR-HPV prevalence between self-collected and clinician-collected samples. STIs prevalence and association with behavioural risk factors were analysed using GraphPad Prism v6.01 (GraphPad Software, Inc., San Diego, CA). Results: Of the 417 women from the community clinic, HR-HPV prevalence was significantly higher in HIV-positive women compared to HIV-negative women (40.6%, 63/155 vs 21.4%, 56/262, p< 0.0001). Among women referred to Nelson Mandela Hospital with cervical intraepithelial lesions, HPV prevalence was observed to be significantly higher in HIV-positive than HIV-positive women (98.0% vs 89.1%, p=0.012). Similarly, HIV-positive women (65.3%, 96/147) had higher multiple HPV infections than HIV-negative women (47.8%, 22/46; p=0.034). HPV35 (23.9%), HPV58 (23.9%), HPV45 (19.6%), and HPV16 (17.3%) were the most frequently detected HPV types in CIN2, while HPV35 (22.5%), HPV16 (21.8%), HPV33 (15.6%), HPV58 (14.3%) were commonly detected in women with CIN3 regardless of HIV status. HR-HPV prevalence in clinician-collected samples was equivalent to self-collected samples from both study sites, the community clinic (26.4% vs 27.9%, p=0.601) and the referral clinic (83.6% vs 79.9%, p=0.222). HR-HPV positivity between self-collected and clinician-collected samples showed an agreement of 86.9% for community clinic (k=0.669) and 91.4% for referral clinic (k=0.711). The distribution of HR-HPV genotypes was similar between self-collected and clinician-collected samples from both study sites. The agreement of HR-HPV genotypes between self-collected and clinician ranged from moderate to almost perfect (0.571-0.888). A majority of women reported a high positive response of acceptance for self-collection (community-based clinic: 77.2% and referral clinic: 83.0%). HR-HPV detection agreement between hpVIR real-time PCR and HC-2 was almost perfect (87.7%, k=0.754). The prevalence of the six traditional STIs (CT, TV, NG, HSV-2, TP, and Haemophilus ducreyi) was high (22.9%, 47/205). TV was the most frequently detected STI (15.6%, 32/205). UP (70.2%, 144/205) and MH (36.6%, 47/205) were the most frequently identified pathobionts. Multiple infections/coinfections with more than two STIs/pathobionts was found in 52.7% (108/205) of women with UP/MH (26.9%) and UP/HPV (21.3%) the frequently identified coinfections. HR-HPV infection was significantly associated with HIV infection (p=0.017) and HSV-2 (p=0.026). Conclusion: This study shows that HIV infection and sexual behaviour increased the risk of HPV infection among women from the community clinic. HIV-positive women had significantly higher HPV viral load and multiple HPV type infections compared with HIV-negative women with or without cervical lesions. Since HIV positive women are at higher risk of HPV infection they need to continue to be screened more regularly for cervical lesions and treated when appropriate. In addition, the high prevalence of HPV in the community of HIV negative women indicates that a robust cervical screening programme is needed to implement the cervical screening policy of South Africa. Thus, the women get the allocated three cervical smears in a life time. Distribution of HPV types was similar among women with CIN2 & 3 with HPV35 being the most frequently detected HPV type regardless of HIV status. This highlights the importance for the inclusion of HPV-35 in the next generation of HPV prophylactic vaccines. The findings of this study add to the limited information on genital HPV infection in women from this province. Moreover, our data now acts as a baseline/reference data for future investigations. The data will also contribute to discussions on HPV testing as the primary screening strategy for cervical cancer and HPV vaccination in South Africa. The hpVIR real-time PCR test between self-collected and clinician-collected specimens showed comparable agreement for the detection of HPV infection. The type-specific concordance between self-collected and clinician-collected showed moderate to an excellent agreement, indicating that self-collection can be utilised as the alternative screening tool for cervical cancer. The participants showed a high positive response for the self-collection method, indicating that introducing this method can positively impact the cervical cancer screening program. However, hpVIR real-time PCR is an in-house test which is not practical to introduce on a large scale in South Africa. Therefore, future research should be done to determine what other HPV tests could be done on these types of specimens. Presently, syndromic management is used to treat STI at clinics in South Africa. The high prevalence of sexually transmitted pathogens necessitates the need to enhance the current screening methods for these pathogens
From technical to teachable: Tone and vowel length
No full textLanguage documentation and description in their many forms (e.g., word lists, dictionaries and grammars, discourse representations, or audio/visual recordings) often for academic purposes of research, in and of themselves cannot save a language. They do, however, comprise a critical facet of the revitalization enterprise. Challenges come when these sources of information are overly technical and inaccessible to communities working to revitalize the language (Penfield & Tucker 2011; Rice 2011; Hinton 2001) and are perceived as only preservation oriented. This presentation discusses ways in which meeting community needs for teaching can be addressed through documentation designed to be mutually beneficial. Examples come from a revitalization effort focused on tone and vowel length in Cherokee.
Understanding the distinctive features of tone and vowel length in the Cherokee language without available resources has been challenging for second language learners whether in the classroom or studying on their own. With no corresponding audio and written examples for the learners, teachers, or researchers to refer to, learners felt limited. Responding to this community need, documentation served to specifically feed into teaching through a close interface between the different foci of documenting and creating educationally helpful tools. The collaborative aspect of the project brought together speakers, second language users, linguists, educational specialists, and others with a vested interest in taking documentation beyond preservation to facilitating teaching.
Documentation and acoustic analysis resulted in data about pitch and vowel length including visual representations (AUTHOR submitted). This technical info contributed toward a better understanding of the nature of Cherokee tone and vowel length. To convert this information to a useful form for language learning, we built on the idea that improving ability to receptively identify tones can generalize to production (Wang et al. 1999). Research indicates that the complexity of and confusion about input associated with tones can be lessened by providing visual pitch contours with written forms accompanying audio materials (e.g., Liu, et al. 2011) and also by presenting tones in pairs (e.g., Wang et al. 1999).
The resulting “teachable” component kept linguistics jargon to a minimum and incorporated visual representations in PowerPoint lectures with embedded audio that could be used by teachers plus allow learners to practice on their own. Constant input from teachers and learners helped guide the documentation process so it would result in information valuable to revitalization efforts – thus, teaching needs helped determine the direction the documentation work.
REFERENCES
AUTHOR. Submitted. “Collaborative Documentation and Revitalization of Cherokee Tone.” Language Documentation and Conservation.
Penfield, S.D. & Tucker, B.V. 2011. “From Documenting to Revitalizing an Endangered Language: Where do Applied Linguists Fit?” Language and Education, 25(4), 291-305.
Rice, S. 2011. “Applied Field Linguistics: Delivering Linguistic Training to Speakers of Endangered Languages.” Language and Education, 25(4), 319-338.
Hinton, L. 2001. “Audio-Video Documentation” In L. Hinton and K. Hale (Eds.), The Green Book of Language Revitalization in Practice, 265-271. San Diego, CA: Academic Press.
Wang, Y. Spence, M., Jongman, A., & Sereno, J. 1999. “Training American Listeners to Perceive Mandarin Tones.” Journal of the Acoustical Society of America, 106(6), 3649-3658.
Liu, Y., Wang, M., Perfetti, C.A., Brubaker, B., Wu, S., & MacWhinney, B. 2011. “Learning a Tonal Language by Attending to the Tone: An In-Vivo Experiment.” Language Learning, 61(4), 1119-1141
ACT Family Violence Intervention Program review
No full textThis paper reports on a review of the Australian Capital Territory’s Family Violence Intervention Program, which provides an interagency response to family violence matters.
The scope of the review was to analyse the program’s activities and outcomes using 2007–08 data provided by participating agencies, supported by in-depth interviews with key stakeholders including victims whose matters had been finalised in court. After the completion of this report, additional data from 2008–09 and 2009–10 was made available by some Family Violence Intervention Program (FVIP) participating agencies. Although not within the scope of this evaluation, these data pointed to some preliminary improvements in the FVIP
Philosophical and Psychological Housecleaning: A Mathematical Framework for Cognitive-Emotional Maintenance Across Lifespan Development
No full textThis theoretical paper presents a mathematical framework for philosophical and psychological housecleaning as an essential component of lifespan development. The framework emerged from an intellectual exercise called "Connect Four"—a methodology I have refined over three decades of application—linking any concept to psychology, philosophy, and consilience. When applied to the mundane concept of "housecleaning" suggested by co-author Tracy L. Boether, unexpected theoretical richness emerged. Drawing support from existing empirical literature on cognitive accumulation (Murre & Dros, 2015), rumination (Nolen-Hoeksema et al., 2008), and treatment resistance (Taylor et al., 2012), we develop a theoretical model for understanding cognitive-emotional maintenance processes. We define the cognitive space Ψ as a theoretical quadruple (B, E, M, τ) representing beliefs, emotions, memories, and temporal ordering. Based on empirical findings that information intake exceeds forgetting rates, we propose that cognitive accumulation follows A(t) = A₀ + ∫₀ᵗ [I(s) - D(s)]ds. We theoretically distinguish between toxic elements T ⊂ Ψ requiring elimination (metaphorically "mold") and dormant valuable elements V ⊂ Ψ requiring revitalization (metaphorically "dust"). The theoretical housecleaning operator H: Ψ → Ψ' is formalized as Ψ' = (Ψ \ T) ∪ R(V), representing elimination and revitalization processes. Drawing from treatment resistance literature, we hypothesize that maintenance difficulty increases exponentially: D(t) = D₀e^(λt), suggesting optimal quarterly maintenance intervals. The mathematical framework demonstrates internal consistency and formal rigor, providing precision in theoretical statements, constraints on theoretical proliferation, and generation of non-obvious predictions. We acknowledge seven major challenges to the framework—from metaphorical oversimplification to cultural bias—and propose specific research pathways to address each. The paper presents both real-life applications of the Connect Four methodology across three decades and a defense of mathematical formalization in theoretical psychology. While entirely theoretical and speculative, this framework demonstrates how consilience can transform everyday concepts into formal theoretical structures, providing a mathematical language for understanding cognitive maintenance that may guide future empirical research
Philosophical and Psychological Housecleaning: A Mathematical Framework for Cognitive-Emotional Maintenance Across Lifespan Development
No full textThis theoretical paper presents a mathematical framework for philosophical and psychological housecleaning as an essential component of lifespan development. The framework emerged from an intellectual exercise called "Connect Four"—a methodology I have refined over three decades of application—linking any concept to psychology, philosophy, and consilience. When applied to the mundane concept of "housecleaning" suggested by co-author Tracy L. Boether, unexpected theoretical richness emerged. Drawing support from existing empirical literature on cognitive accumulation (Murre & Dros, 2015), rumination (Nolen-Hoeksema et al., 2008), and treatment resistance (Taylor et al., 2012), we develop a theoretical model for understanding cognitive-emotional maintenance processes. We define the cognitive space Ψ as a theoretical quadruple (B, E, M, τ) representing beliefs, emotions, memories, and temporal ordering. Based on empirical findings that information intake exceeds forgetting rates, we propose that cognitive accumulation follows A(t) = A₀ + ∫₀ᵗ [I(s) - D(s)]ds. We theoretically distinguish between toxic elements T ⊂ Ψ requiring elimination (metaphorically "mold") and dormant valuable elements V ⊂ Ψ requiring revitalization (metaphorically "dust"). The theoretical housecleaning operator H: Ψ → Ψ' is formalized as Ψ' = (Ψ \ T) ∪ R(V), representing elimination and revitalization processes. Drawing from treatment resistance literature, we hypothesize that maintenance difficulty increases exponentially: D(t) = D₀e^(λt), suggesting optimal quarterly maintenance intervals. The mathematical framework demonstrates internal consistency and formal rigor, providing precision in theoretical statements, constraints on theoretical proliferation, and generation of non-obvious predictions. We acknowledge seven major challenges to the framework—from metaphorical oversimplification to cultural bias—and propose specific research pathways to address each. The paper presents both real-life applications of the Connect Four methodology across three decades and a defense of mathematical formalization in theoretical psychology. While entirely theoretical and speculative, this framework demonstrates how consilience can transform everyday concepts into formal theoretical structures, providing a mathematical language for understanding cognitive maintenance that may guide future empirical research
Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits
No full textAbstract Background Human papillomavirus (HPV) is the aetiological agent for cervical cancer and genital warts. Concurrent HPV and HIV infection in the South African population is high. HIV positive (+) women are often infected with multiple, rare and undetermined HPV types. Data on HPV incidence and genotype distribution are based on commercial HPV detection kits, but these kits may not detect all HPV types in HIV + women. The objectives of this study were to (i) identify the HPV types not detected by commercial genotyping kits present in a cervical specimen from an HIV positive South African woman using next generation sequencing, and (ii) determine if these types were prevalent in a cohort of HIV-infected South African women. Methods Total DNA was isolated from 109 cervical specimens from South African HIV + women. A specimen within this cohort representing a complex multiple HPV infection, with 12 HPV genotypes detected by the Roche Linear Array HPV genotyping (LA) kit, was selected for next generation sequencing analysis. All HPV types present in this cervical specimen were identified by Illumina sequencing of the extracted DNA following rolling circle amplification. The prevalence of the HPV types identified by sequencing, but not included in the Roche LA, was then determined in the 109 HIV positive South African women by type-specific PCR. Results Illumina sequencing identified a total of 16 HPV genotypes in the selected specimen, with four genotypes (HPV-30, 74, 86 and 90) not included in the commercial kit. The prevalence’s of HPV-30, 74, 86 and 90 in 109 HIV positive South African women were found to be 14.6%, 12.8%, 4.6% and 8.3% respectively. Conclusions Our results indicate that there are HPV types, with substantial prevalence, in HIV positive women not being detected in molecular epidemiology studies using commercial kits. The significance of these types in relation to cervical disease remains to be investigated.</p
Effects of estrous stage and time of day on prepulse inhibition in female rats
No full textPrepulse inhibition (PPI) of the acoustic startle response is a measure of sensory motor gating, and is affected in various neuropsychiatric disorders. Although PPI has been used extensively to study both the neural effects of such conditions, as well as in the search for animal models, a number of critical issues have been encountered. Published methods for testing PPI vary widely across many parameters, two of the most common being the phase of the light/dark cycle during which the subjects are tested and the inclusion or exclusion of females. While previous research has attempted to clarify the effect of these factors, results for both human and animal studies have often been contradictory. This study investigated the relevance of the estrous cycle and time of day as variables that may influence PPI in adult female Sprague-Dawley rats. Results indicate that PPI is not affected by estrous phase, but may be affected by the time of day of testing, particularly at higher prepulse levels. At the 86 dBs prepulse level, rats tested during the light phase of the light/dark cycle displayed significantly lowered PPI as compared to the animals tested during the dark phase. Additionally, other measures such as baseline startle, habituation and activity during testing did not vary across the estrous or light cycles. These findings indicate that while estrous phase does not have any effect on PPI in female Sprague-Dawley rats when tested under these parameters, the time of day during which testing occurs does have the potential to alter PPI.Accession Number: 18621080. Date Created: 20080804. Date Completed: 20081024. Update Code: 20081217. Publication Type: Journal Article; Research Support, Non-U.S. Gov't. Journal ID: 7905558. Publication Model: Print-Electronic. Cited Medium: Print. NLM ISO Abbr: J. Neurosci. MethodsSource type: Electronic(1
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