A Target Restricted Assembly Method (TRAM) for Phylogenomics

While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications. Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes. This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon

Oncogenic viruses associated with vulva cancer in HIV-1 patients in Botswana

BACKGROUND: Oncoviruses such as HPV, KSHV, and EBV have been reported in patients with HIV infection and AIDS. How oncovirus-associated cancers rise in AIDS patients has not been fully established. The purpose of our study was to identify the viral agents in vulvar cancer and to assess their contribution to pathogenesis. METHOD: We retrospectively identified a total of 13 vulva tissue samples from HIV-1 positive and 9 vulvar samples from HIV-1 negative patients from the Botswana National Health Laboratory in Gaborone, Botswana, a Southern African country with a high incidence of HIV. We utilized PCR and IHC to identify HPV, EBV, KSHV, and JC virus in FFPE preserved tissue samples. RESULTS: Using the GP5(+)/GP6(+) primer set we detected several HPV types in tissue samples. EBV was detected in all of the positive cases (100%) and in most of the negative cases (89%). KSHV was detected in 39% of the HIV-1 positive samples and in 11% of the negative samples, and no JC virus was detected in any of the samples. Using IHC we demonstrated that LANA was expressed in 61% of the positive samples and in 44% of the negative samples. The ubiquitous EBV was more consistently expressed in negative cases (100%) than in positive cases (69%). Interestingly, the HPV-16 E6 transcript was detected in 56% of the negative samples compared to 31% of the positive samples. However, the cell cycle protein P21 used as a surrogate marker for HPV was detected in 77% of the positive samples and in 44% of the negative samples, while VEGF signals were similar in both positive (92%) and negative samples (89%). CONCLUSION: Our study, suggests that in Botswana, vulvar squamous cell carcinoma (VSCC) is associated with oncogenic viruses present in the niche but the contribution and progression may be regulated by HPV and other immunosuppressive infections that include HIV-1

The fourth industrial revolution and the future of the entrepreneurial university in South Africa

Globally, digital disruption has accelerated in the last few years. It is argued that this technological revolution would fundamentally alter our interactions with one another, our work, and our lives. The Fourth Industrial Revolution (4IR) can blur the boundaries between the physical and biological worlds. Although the extent of the effect is unclear, many anticipate massive changes in the economic and educational spheres. Given the close relationship between the economy and the drivers of entrepreneurship in universities, the survival of entrepreneurial universities remains contingent on the influence and preparedness of the 4IR. This review aimed to ascertain South African entrepreneurial universities’ readiness for the 4IR. Systematic literature analysis was adopted for this study; it draws on journal articles, books as wells as online publications relating to disruptive innovation, entrepreneurial universities and 4IR. The paper argues that there is a need for a radical overhaul of the current curriculum, as retraining lecturers to prepare for 4IR disruptions

DISRUPTION AT ITS PEAK: POCKMARK OF COVID-19 ON IMMIGRANT RETAIL BUSINESS IN SOUTH AFRICA

The Covid-19 pandemic has left a trail of untold damage in many countries, and there is no foreseeable end to its spread. Besides the loss of life, the impact of the virus on the economy and small businesses, in particular, is not yet clear. Even so, the policies aimed at containing the spread of the virus have exerted further pressure and uncertainty on the survival of small businesses in general and immigrant-owned businesses in particu­lar. This study explored the pockmark of C0VID-19 on immigrant retail businesses in selected outlets in West Rand, Johannesburg. A qualitative research approach was adopted as it best supports the exploratory intent of the study. The purposive sampling technique was utilised to draw participants for the study until a saturation point was attained. Data was collected through face-to-face interviews using unstructured, open-ended questions, with interviews recorded and transcribed. Atlas-ti 8 software was used to code, categorise and analyse the data to form themes and patterns, which helped to inform the outcome of the study. Findings indicate that none of the immigrant businesses was prepared for the pandemic and lockdown. Furthermore, it was found that most of the businesses may cease to exist due to cash fragility should the lockdown be extended for a longer period and the pandemic not abate soon. Despite the government having announced some palliative measures to help reduce the impact of the pandemic and lockdown on small businesses, results from this study indicate that immigrant businesses received no such support from the government

Cytokine and Chemokine Expression Profiles in HIV-1 Infected Patients With Ocular Surface Squamous Neoplasia From Botswana

Purpose: Ocular surface squamous neoplasia (OSSN) rate has increased in incidence with the HIV pandemic in Africa. Multiple factors including cellular and environmental can affect the pathogenesis of OSSN in HIV-infected patients. We will investigate anti-inflammatory cytokines, proinflammatory cytokines, and growth factor expression in sera and tissue samples of OSSN and pterygia for the potential link to the development of OSSN. Results: Antibody analysis showed significant changes in levels of pro-inflammatory cytokines, anti-inflammatory cytokines and growth factors in sera. Quantitative RT-PCR of tissues showed expression of inflammatory cytokines and chemokines associated with HIV infection and carcinogenesis. Conclusion: Our findings showed that dysregulation in expression of cytokines and growth factors in patients with multiple infections may contribute to pathogenesis of OSSN and pterygia. The data reinforces the significance of in depth analysis of immune function in HIV-1 OSSN patients with multiple viral infections that has potential for therapy and vaccine development

Etched distributed Bragg reflectors as three-dimensional photonic crystals: photonic bands and density of states

The photonic band dispersion and density of states (DOS) are calculated for the three-dimensional (3D) hexagonal structure corresponding to a distributed Bragg reflector patterned with a 2D triangular lattice of circular holes. Results for the Si/SiO$_2$ and GaAs/AlGaAs systems determine the optimal parameters for which a gap in the 2D plane occurs and overlaps the 1D gap of the multilayer. The DOS is considerably reduced in correspondence with the overlap of 2D and 1D gaps. Also, the local density of states (i.e., the DOS weighted with the squared electric field at a given point) has strong variations depending on the position. Both results imply substantial changes of spontaneous emission rates and patterns for a local emitter embedded in the structure and make this system attractive for the fabrication of a 3D photonic crystal with controlled radiative properties.Comment: 8 pages, 5 figures; to appear in Phys. Rev.

Wavelength dependent mechanism of phenolate photooxidation in aqueous solution

Phenolate photooxidation is integral to a range of biological processes, yet the mechanism of electron ejection has been disputed. Here, we combine femtosecond transient absorption spectroscopy, liquid-microjet photoelectron spectroscopy and high-level quantum chemistry calculations to investigate the photooxidation dynamics of aqueous phenolate following excitation at a range of wavelengths, from the onset of the S0-S1 absorption band to the peak of the S0-S2 band. We find that for λ ≥ 266 nm, electron ejection occurs from the S1 state into the continuum associated with the contact pair in which the PhO˙ radical is in its ground electronic state. In contrast, we find that for λ ≤ 257 nm, electron ejection also occurs into continua associated with contact pairs containing electronically excited PhO˙ radicals and that these contact pairs have faster recombination times than those containing PhO˙ radicals in their ground electronic state

Neural Networks for Information Retrieval

Machine learning plays a role in many aspects of modern IR systems, and deep learning is applied in all of them. The fast pace of modern-day research has given rise to many different approaches for many different IR problems. The amount of information available can be overwhelming both for junior students and for experienced researchers looking for new research topics and directions. Additionally, it is interesting to see what key insights into IR problems the new technologies are able to give us. The aim of this full-day tutorial is to give a clear overview of current tried-and-trusted neural methods in IR and how they benefit IR research. It covers key architectures, as well as the most promising future directions.Comment: Overview of full-day tutorial at SIGIR 201

Children of prisoners: exploring the impact of families' reappraisal of the role and status of the imprisoned parent on children's coping strategies

Qualitative data from a larger study on the impact of parental imprisonment in four countries found that children of prisoners face fundamentally similar psychological and social challenges. The ways that children cope, however, are influenced by the interpretative frame adopted by the adults around them, and by how issues of parental imprisonment are talked about in their families. This article argues that families have to reappraise their view of the imprisoned parent and then decide on their policy for how to deal with this publicly. Their approach may be based on openness and honesty or may emphasise privacy and secrecy, or a combination of these. Children are likely to be influenced by their parents'/carers' views, although these may cause conflict for them. Where parents/carers retain a positive view of the imprisoned parent, children are likely to benefit; where parents/carers feel issues of shame and stigma acutely, this is likely to be transmitted to their children. This is important for social workers and practitioners involved in supporting prisoners' families and for parenting programmes