Transforming RNA-Seq gene expression to track cancer progression in the multi-stage early to advanced-stage cancer development.

BACKGROUND: Cancer progression can be tracked by gene expression changes that occur throughout early-stage to advanced-stage cancer development. The accumulated genetic changes can be detected when gene expression levels in advanced-stage are less variable but show high variability in early-stage. Normalizing advanced-stage expression samples with early-stage and clustering of the normalized expression samples can reveal cancers with similar or different progression and provide insight into clinical and phenotypic patterns of patient samples within the same cancer. OBJECTIVE: This study aims to investigate cancer progression through RNA-Seq expression profiles across the multi-stage process of cancer development. METHODS: RNA-sequenced gene expression of Diffuse Large B-cell Lymphoma, Lung cancer, Liver cancer, Cervical cancer, and Testicular cancer were downloaded from the UCSC Xena database. Advanced-stage samples were normalized with early-stage samples to consider heterogeneity differences in the multi-stage cancer progression. WGCNA was used to build a gene network and categorized normalized genes into different modules. A gene set enrichment analysis selected key gene modules related to cancer. The diagnostic capacity of the modules was evaluated after hierarchical clustering. RESULTS: Unnormalized RNA-Seq gene expression failed to segregate advanced-stage samples based on selected cancer cohorts. Normalization with early-stage revealed the true heterogeneous gene expression that accumulates across the multi-stage cancer progression, this resulted in well segregated cancer samples. Cancer-specific pathways were enriched in the normalized WGCNA modules. The normalization method was further able to stratify patient samples based on phenotypic and clinical information. Additionally, the method allowed for patient survival analysis, with the Cox regression model selecting gene MAP4K1 in cervical cancer and Kaplan-Meier confirming that upregulation is favourable. CONCLUSION: The application of the normalization method further enhanced the accuracy of clustering of cancer samples based on how they progressed. Additionally, genes responsible for cancer progression were discovered.

Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues.

To elucidate cancer pathogenesis and its mechanisms at the molecular level, the collecting and characterization of large individual patient tissue cohorts are required. Since most pathology institutes routinely preserve biopsy tissues by standardized methods of formalin fixation and paraffin embedment, these archived FFPE tissues are important collections of pathology material that include patient metadata, such as medical history and treatments. FFPE blocks can be stored under ambient conditions for decades, while retaining cellular morphology, due to modifications induced by formalin. However, the effect of long-term storage, at resource-limited institutions in developing countries, on extractable protein quantity/quality has not yet been investigated. In addition, the optimal sample preparation techniques required for accurate and reproducible results from label-free LC-MS/MS analysis across block ages remains unclear. This study investigated protein extraction efficiency of 1, 5, and 10-year old human colorectal carcinoma resection tissue and assessed three different gel-free protein purification methods for label-free LC-MS/MS analysis. A sample size of n = 17 patients per experimental group (with experiment power = 0.7 and α = 0.05, resulting in 70% confidence level) was selected. Data were evaluated in terms of protein concentration extracted, peptide/protein identifications, method reproducibility and efficiency, sample proteome integrity (due to storage time), as well as protein/peptide distribution according to biological processes, cellular components, and physicochemical properties. Data are available via ProteomeXchange with identifier PXD017198. The results indicate that the amount of protein extracted is significantly dependent on block age (p < 0.0001), with older blocks yielding less protein than newer blocks. Detergent removal plates were the most efficient and overall reproducible protein purification method with regard to number of peptide and protein identifications, followed by the MagReSyn® SP3/HILIC method (with on-bead enzymatic digestion), and lastly the acetone precipitation and formic acid resolubilization method. Overall, the results indicate that long-term storage of FFPE tissues (as measured by methionine oxidation) does not considerably interfere with retrospective proteomic analysis (p > 0.1). Block age mainly affects initial protein extraction yields and does not extensively impact on subsequent label-free LC-MS/MS analysis results.

Cyber security education is as essential as "the three R's".

Smartphones have diffused rapidly across South African society and constitute the most dominant information and communication technologies in everyday use. That being so, it is important to ensure that all South Africans know how to secure their smart devices. Doing so requires a high level of security awareness and knowledge. As yet, there is no formal curriculum addressing cyber security in South African schools. Indeed, it seems to be left to universities to teach cyber security principles, and they currently only do this when students take computing-related courses. The outcome of this approach is that only a very small percentage of South Africans, i.e. those who take computing courses at university, are made aware of cyber security risks and know how to take precautions. In this paper we found that, because this group is overwhelmingly male, this educational strategy disproportionately leaves young South African women vulnerable to cyber-attacks. We thus contend that cyber security ought to be taught as children learn the essential "3 Rs"-delivering requisite skills at University level does not adequately prepare young South Africans for a world where cyber security is an essential skill. Starting to provide awareness and knowledge at primary school, and embedding it across the curriculum would, in addition to ensuring that people have the skills when they need them, also remove the current gender imbalance in cyber security awareness.

A weighted bootstrap approach to logistic regression modelling in identifying risk behaviours associated with sexual activity.

The latest population estimates released by Statistics South Africa indicate that 25.03% of all deaths in 2017 in South Africa were AIDS-related. Along with these results, it is also reported that 7.06% of the population were living with HIV, with the HIV-prevalence among youth (aged 15-24) at 4.64% for 2017 (STATSSA. (2018). Retrieved from Statistics South Africa: http://www.statssa.gov.za/publications/P0302/P03022017.pdf ). The data used in the study contained information related to the risk-taking behaviours associated with the sexual activity of entering first-year students at the University of the Western Cape. In this study, a logistic regression modelling procedure was carried out on those students that were determined to be sexually active, therefore, in the modelling procedure significant risk behaviours of sexually active first-year students could be identified. Of the 14 variables included in the modelling procedure, six were found to be significantly associated with sexually active students. The significant variables included; the age and race of the student, whether the student had ever taken an HIV test, the importance of religion in influencing the sexual behaviour of the student, whether the student consumed alcohol and lastly whether the student smoked. This study further investigated the impact of introducing sample weighting, bootstrap sampling as well as variable selection methods into the logistic regression modelling procedure. It is shown that incorporating these techniques into the modelling procedure produces logistic regression models that are more accurate and have an increased predictive capability. The bootstrapping procedure is shown to produce logistic regression models that are more accurate than those produced without a bootstrap procedure. A comparison between 200, 500 and 1000 bootstrap samples is also incorporated into the modelling procedure with the models produced from 200 bootstrap samples shown to be just as accurate those produced from 500 or 1000 bootstrap samples. Of the five variable selection methods used, it is shown that the Newton-Raphson and Fisher methods are unreliable in producing logistic regression models. The forward, backward and stepwise variable selection methods are shown to produce very similar results.

A weighted bootstrap approach to logistic regression modelling in identifying risk behaviours associated with sexual activity

The latest population estimates released by Statistics South Africa indicate that 25.03% of all deaths in 2017 in South Africa were AIDS-related. Along with these results, it is also reported that 7.06% of the population were living with HIV, with the HIV-prevalence among youth (aged 15­24) at 4.64% for 2017 (STATSSA. (2018). Retrieved from Statistics South Africa: http://www.statssa.gov.za/publications/P0302/P03022017.pdf). The data used in the study contained information related to the risk-taking behaviours associated with the sexual activity of entering first-year students at the University of the Western Cape. In this study, a logistic regression modelling procedure was carried out on those students that were determined to be sexually active, therefore, in the modelling procedure significant risk behaviours of sexually active first-year students could be identified. Of the 14 variables included in the modelling procedure, six were found to be significantly associated with sexually active students. The significant variables included; the age and race of the student, whether the student had ever taken an HIV test, the importance of religion in influencing the sexual behaviour of the student, whether the student consumed alcohol and lastly whether the student smoked. This study further investigated the impact of introducing sample weighting, bootstrap sampling as well as variable selection methods into the logistic regression modelling procedure. It is shown that incorporating these techniques into the modelling procedure produces logistic regression models that are more accurate and have an increased predictive capability. The bootstrapping procedure is shown to produce logistic regression models that are more accurate than those produced without a bootstrap procedure. A comparison between 200, 500 and 1000 bootstrap samples is also incorporated into the modelling procedure with the models produced from 200 bootstrap samples shown to be just as accurate those produced from 500 or 1000 bootstrap samples. Of the five variable selection methods used, it is shown that the Newton­Raphson and Fisher methods are unreliable in producing logistic regression models. The forward, backward and stepwise variable selection methods are shown to produce very similar results

Validity and reliability of the South African health promoting schools monitoring questionnaire.

Health promoting schools, as conceptualised by the World Health Organisation, have been developed in many countries to facilitate the health-education link. In 1994, the concept of health promoting schools was introduced in South Africa. In the process of becoming a health promoting school, it is important for schools to monitor and evaluate changes and developments taking place. The Health Promoting Schools (HPS) Monitoring Questionnaire was developed to obtain opinions of students about their school as a health promoting school. It comprises 138 questions in seven sections: socio-demographic information; General health promotion programmes; health related Skills and knowledge; Policies; Environment; Community-school links; and support Services. This paper reports on the reliability and face validity of the HPS Monitoring Questionnaire. Seven experts reviewed the questionnaire and agreed that it has satisfactory face validity. A test-retest reliability study was conducted with 83 students in three high schools in Cape Town, South Africa. The kappa-coefficients demonstrate mostly fair (κ-scores between 0.21 and 0.4) to moderate (κ-scores between 0.41 and 0.6) agreement between test-retest General and Environment items; poor (κ-scores up to 0.2) agreement between Skills and Community test-retest items, fair agreement between Policies items, and for most of the questions focussing on Services a fair agreement was found. The study is a first effort at providing a tool that may be used to monitor and evaluate students' opinions about changes in health promoting schools. Although the HPS Monitoring Questionnaire has face validity, the results of the reliability testing were inconclusive. Further research is warranted.

Correlates of gender characteristics, health and empowerment of women in Ethiopia.

BACKGROUND: The low status of women prevents them from recognizing and voicing their concerns about health needs. This study aimed to examine the relationship between gender characteristics, health and empowerment of women in an attempt to understand between 2005 and 2011. METHODS: Data from the Ethiopia Demographic and Health Survey (EDHS) 2005 and 2011 were used. Bivariate and multivariate analyses were used to determine the relative contribution of the predictor variables. The hypotheses tested in this study were that gender (men and women), health and empowerment of women in region are highly significant with women's education and work status. RESULTS: Study findings showed that the low status of women and their disempowerment are highly associated with poor health outcomes. In both 2005 and 2011 men school ages were positively associated with their attainment in primary education, whereas for women it was negatively related with their attainment in some education. In both 2005 and 2011 women in the richest wealth quintile had the highest odds ratio of relating to some education. The results show that the odds ratios of women with some education (within the richest wealth quintile) has improved from 6.39 (in 2005) to 10.90 (in 2011), whereas among men there has been a decrease from 10.33 (in 2005) to 2.13 (in 2011). The results indicated that in 2005 and 2011, when comparing the percentage distribution of both genders on employment status and type of occupation, the percentage of men who were employed was higher than women. The percentage of males who were engaged in the agricultural-type of occupation was higher than that of women. Men and women knowledge about family planning methods have been improved, yet, there are wider gender gaps in family planning users. CONCLUSIONS: The officials such as policy makers, planners, program managers and government and non-government organizations need to addressed. The issue of child marriages in order to minimize the number of girls who never attend school or drop out to become wives Planners should also work on improving family planning to empower women. There was a significant relationship between status of women and quality of healthy life, and this relationship appeared to differ by education and work status.

Trends in HIV risk behaviour of incoming first-year students at a South African university: 2007-2012.

The aim of the research on which this article is based was to understand the behavioural changes of the target student population over time to ensure that future prevention programmes are more effective in changing behaviour. This study reports on quantitative data collected at the University of the Western Cape over a six-year period between 2007 and 2012. All the students attending the orientation sessions and who were willing to complete the anonymous questionnaire during each of the six years were included in the study. Data were collected on the following aspects and subjects: sexual activity, age at first sexual encounter, number of sexual partners, condom usage, knowledge of how to use a condom, perceived ability to discuss condoms usage with a sexual partner, perception of HIV risk and HIV testing as well as the intention to be tested. Reported alcohol and drug usage, as well as depressive symptoms, was also recorded. The percentage of students reporting having had vaginal sex prior to entering university increased from 44% in 2007 to 51% in 2012 but, alarmingly, the consistent use of condoms decreased from 60% in 2007 to 51% in 2012. The average onset age of about 15.6 years for males and 16.7 years for females for vaginal sex did not change over the six-year period. No difference in smoking patterns or drug use was seen over the period of the study, but the number of entering students who indicated that they consumed alcohol increased significantly from 48% in 2007 to 58% in 2012. HIV testing increased from 19% in 2007 to 47% in 2012, whereas the intention to be tested showed no significant change over the period. Although students increasingly reported that they knew enough about HIV/AIDS (63% in 2007 and 69% in 2012), about a third reported suffering from AIDS fatigue. Prevention efforts targeted at those incoming first-year students who are not yet sexually active (about 45% in this study) should be developed and should take into account the multiplicity of factors that appear to influence their sexual debut.

Early loading of mandibular implants placed immediately after extraction: a 10-year prospective study of eight patients.

PURPOSE: This prospective study was undertaken to evaluate the 10-year implant survival rate as well as bone remodeling for immediately loaded anterior mandibular implants. MATERIALS AND METHODS: Patients with nonrestorable anterior mandibular teeth were enrolled. All mandibular teeth were extracted, and five rough-surfaced (titanium plasma spray) one-piece implants were placed, evenly spread between the mental foramina. All implants were immediately loaded with a provisional prosthesis. A definitive prosthesis was . RESULTS: Eight patients received 40 implants, 30 in extraction sockets and 10 in healed sites. All but two implants that did not achieve primary stability (35 Ncm) were immediately loaded. The progress of seven patients was evaluated after 10 years. The mean age at implant placement was 60 years, and the length of follow-up varied between 10.3 and 11.47 years. The results showed a 100% implant retention rate; however, clinically observed bone loss around two central implants led to consideration for future surgical intervention or removal. Average bone loss was < 1 mm, and little difference was noted between implants placed in healed sites and those placed in extraction sockets. Technical problems with the prostheses were confined to two patients; one patient had seven fractures and the other had one. CONCLUSION: Rough-surfaced implants placed in extraction sockets between the mental foramina and immediately loaded can be successful in the long term. Because only is recommended that this site be avoided when immediately loaded implants are to be used in the anterior mandible.

Correlates of sexual activity versus non-activity of incoming first-year students at a South African university.

In order to contribute to the design of more effective programmes to curb the spread of HIV at tertiary institutions, this study compares the profile of students who are sexually active versus those who are not yet sexually active when entering university. The study was conducted among three cohorts of first-year university students at the University of the Western Cape from 2007 to 2009. A range of correlates of sexual activity versus non-activity were explored using logistic regression analysis. The predicted probabilities of the logit link function depict marked differences between genders and racial groups. Males were more likely than females to be sexually active when entering university and the Black racial group was more likely than other racial groups to be sexually active. Risk-taking behaviours such as smoking, alcohol and drug use were shown to increase the likelihood of being sexually active when entering university, as did indicators of depression and suicidal ideation. The results indicate that religion plays an important role in influencing sexual behaviour, highlighting the important potential role that religious organisations can play in addressing HIV risk at tertiary institutions.

TB/HIV risk factors identified from a General Household Survey of South Africa in 2006.

The level of human immunodeficiency virus (HIV), tuberculosis (TB) as well as the co-infection TB/HIV in South Africa is among the highest in the world. TB is curable while HIV is not, yet the combination of both is a growing feature in the world. This study examined TB and HIV affecting people living in South Africa. Analyses have been undertaken based on data from the General Household Survey of South Africa in 2006. The study focused on respondents aged 15-49 years, corresponding to a total of 55,384 people composed of 25,859 males and 29,525 females. Among this population, 5935 people suffered from illness/injury, including 2469 (41.6%) males and 3466 (58.4%) females. Weighted multivariate logistic regression is performed on TB and/or HIV in association with the province, background characteristics of the target population, and selected socioeconomic and demographic variables included in the survey. In this study we focus on variables of health status and whether subjects suffered from TB and/or HIV. Findings of this investigation show that TB is the second most common cause of illness in the provinces of KwaZulu-Natal (KN) (9.1%), North West (5.4%) and Limpopo (4.2%). People who are married have a 50% lower risk compared to those currently not married to suffer from TB and/or HIV. Those with living spouses have a 5% lower risk to suffer from TB and/or HIV than those whose partners are not alive. This study concluded that rapid action is needed to curb the spread of TB and/or HIV to produce a healthy population. Therefore, follow-up care and special preventative measures are urgently needed in provinces with higher reported rates of TB and/or HIV such as KN.

Correlates of Sexual Activity Versus Non-Activity of Incoming First-Year Students at a South African University

In order to contribute to the design of more effective programmes to curb the spread of HIV at tertiary institutions; this study compares the profile of students who are sexually active versus those who are not yet sexually active when entering university. The study was conducted among three cohorts of first-year university students at the University of the Western Cape from 2007 to 2009. A range of correlates of sexual activity versus non-activity were explored using logistic regression analysis. The predicted probabilities of the logit link function depict marked differences between genders and racial groups. Males were more likely than females to be sexually active when entering university and the Black racial group was more likely than other racial groups to be sexually active. Risk-taking behaviours such as smoking; alcohol and drug use were shown to increase the likelihood of being sexually active when entering university; as did indicators of depression and suicidal ideation. The results indicate that religion plays an important role in influencing sexual behaviour; highlighting the important potential role that religious organisations can play in addressing HIV risk at tertiary institutions

Sexual-risk behaviour among sexually active first-year students at the University of the Western Cape, South Africa.

In South Africa, new HIV infections are concentrated among persons aged 15-24 years. The university population falls within this age group and are prone to higher-risk behaviours that place them at risk of acquiring HIV. In a study to assess this risk among sexually active students, we classified higher-risk sexual behaviours as not using condoms at every instance of sex, having had more than one sexual partner during the preceding 12 months, a relatively young age at first sexual intercourse (7-16 years), and experience of sexual violence and/or transactional sex. In total, 796 first-year students at the University of the Western Cape in Cape Town, South Africa, completed a self-administered questionnaire in 2006. The sample included 263 sexually active, unmarried students, aged 16 to 24 years. The responses showed that 62% did not use a condom for every instance of sex, 39% had two or more sexual partners in the previous 12 months, 53% had initiated sexual intercourse at a younger age (7-16 years), and 2% had ever exchanged money or gifts for sexual intercourse. Eight percent of the respondents said they did not give their consent or permission at initiation of first sexual intercourse. One in every 10 respondents claimed that they had ever been forced to have sexual intercourse, and 4% said that they had ever forced someone to have sexual intercourse. The sexually active students who reported an earlier age of initiation of sexual intercourse and having only one sexual partner during the last year were more likely to not use a condom every time, whereas the sexually active students that had experienced initiation of sexual intercourse while in an older age group (17-24 years) and who had two or more sexual partners in the last year were more likely to use a condom every time. Sexually active university students are in need of particular HIV-prevention interventions given their tendencies for poor condom usage and having multiple sexual partners.