Short hairpin RNA-directed knockdown of epidermal growth factor receptor in human oesophageal squamous carcinoma cell lines

Epidermal growth factor receptor (EGFR) is a transmembrane receptor tyrosine kinase which activates, upon EGFR binding, a number of signaling pathways including the mitogenic protein kinase pathway (MAPK) and phosphatidylinositol 3-kinase cascade (PI3K). Over expression of EGFR is a common feature in variety of human cancers including lung, colorectal, breast, pancreatic and oesophageal cancers and results in autonomous cell growth, enhanced metastatic potential, tissue invasion and increased resistance to current cancer therapeutics. Thus EGFR has been identified as a potential target in cancer therapeutics. Using the RNA interference (RNAi) pathway, the aim was to specifically knockdown expression levels of endogeneous EGFR in human oesophageal squamous carcinoma cell (HOSCC) lines. The RNAi pathway was initiated through the transfection of three specifically designed short hairpin RNAs (shRNAs) against human EGFR. The shRNAs were specifically designed using bioinformatics tools and their individual knockdown efficacy determined through the introduction of an exogeneous based target reporter systems, psiCHECK and pcieGFP. Expression levels of EGFR were determined using Western blot analysis followed by densitometry. Knockdown of EGFR was achieved by all three EGFR shRNAs in the three HOSCC cell lines (WHCO1, WHCO5 and WHCO6) despite low transfection levels of ~10%. Greastest knockdown of EGFR (85%) was achieved by EGFR sh2 in WHCO5. EGFR sh2 and sh1 resulted in average knockdown of EGFR of ~ 65% in WHCO1 and WHCO5 respectively. Weakest knockdown of EGFR (~ 20%) was obtained by all three EGFR shRNAs following transfection of WHCO6. RNAi-based approaches therefore show substantial potential for the specific and efficient targeting of EGFR in human cancer cells

Founder virus envelope glycoproteins as novel oligomeric HIV-1 vaccine immunogens

A thesis submitted to Faculty of Health Sciences, University of the Witwatersrand, in fulfillment of the requirements for the degree of Doctor of Philosophy Johannesburg, March 2014The ability to induce a broadly neutralizing antibody (bNAb) response following vaccination is regarded as a crucial aspect in developing an effective vaccine targeting the human immunodeficiency virus type 1 (HIV-1). The bNAbs target the HIV-1 envelope glycoprotein (Env) which is exposed on the surface of the virion, thereby preventing cell entry. Previous work in our laboratory focused on the generation of a 2dCD4S60C molecule (a variant of the CD4 primary Env receptor) with higher affinity for HIV-1 Env through targeted disulphide exchange. This study reports on the design and construction of an HIV-1 subtype C founder virus consensus Env immunogen derived from newly transmitted/founder virus sequences, and the ability of the purified recombinant Env proteins (2dCD4S60C-liganded and unliganded) to induce a broadly neutralizing antibody response in small animals. A total of 1894 founder sequences from 80 HIV-1 subtype C infected patients were available and downloaded from the databases. A consensus sequence was generated for each of the patients, and this alignment was subsequently used to generate a founder virus consensus env sequence. The env sequence was used to create codon-optimized constructs encoding monomeric (gp120FVCm), dimeric (gp120FVCGCN4d) and trimeric (gp140FVCGCN4t(+) and gp140FVCGCN4t(-) founder virus conformations cloned into the pcDNA3.1(-) mammalian expression vector. All four Env constructs were successfully expressed in HEK293T mammalian cell culture. The 2dCD4S60C was expressed in E. coli BL21 (DE3) and purified by nickel affinity chromatography. Large scale expression and purification of the gp120, gp120GCN4 and gp140GCN4 +/- in the unliganded or 2dCD4S60C liganded state were purified by lectin affinity chromatography, followed by conformation and complex purification using size exclusion chromatography. Immunogens/immune complexes were evaluated by ELISA, SDS-PAGE, native PAGE and surface plasmon resonance, and confirmed they were functional and conformationally intact. Immunogenicity of each conformation alone or complexed to 2dCD4S60C was evaluated in rabbits. Breadth and potency of the rabbit sera was tested against 12 pseudoviruses (Tiers 1-3), derived from HIV-1 subtype B and C Env, using the PhenoSense Neutralizing antibody assay (Monogram Bioscience, Inc.). Minimal neutralizing breadth was obtained from animals immunized exclusively with Env conformations. However, animals that received the Env/2dCD4S60C complex showed extensive neutralizing capacity against all 12 viruses tested, including the tier 2 and 3 virus strains. End-point ELISA titer results revealed that the rabbits that were immunized with Env/2dCD4S60C produced both Env and 2dCD4S60C specific titers, but those directed towards 2dCD4 were on average 10x lower than the 2dCD4S60C control group. This implies a proportion of the NAb activity is directed towards conserved epitopes exposed on the Env/2dCD4S60C immunogens. Overall, these results show that the use of founder Env/2dCD4S60C complexes as vaccine immunogens dramatically improves the antibody neutralization breadth and magnitude as compared to founder Env or 2dCD4S60C alone. This level of broad neutralization has not been previously reported in the literature, and these results provide encouraging data to inform us of the best envelope vaccine immunogen to include in a preventative vaccine

Humanities and Engineering Perspectives on Music Transcription:

Music transcription is a process of creating a notation of musical sounds. It has been used as a basis for the analysis of music from a wide variety of cultures. Recent decades have seen an increasing amount of engineering research within the field of Music Information Retrieval that aims at automatically obtaining music transcriptions in Western staff notation. However, such approaches are not widely applied in research in ethnomusicology. This article aims to bridge interdisciplinary gaps by identifying aspects of proximity and divergence between the two fields. As part of our study, we collected manual transcriptions of traditional dance tune recordings by eighteen transcribers. Our method employs a combination of expert and computational evaluation of these transcriptions. This enables us to investigate the limitations of automatic music transcription (AMT) methods and computational transcription metrics that have been proposed for their evaluation. Based on these findings, we discuss promising avenues to make AMT more useful for studies in the Humanities. These are, first, assessing the quality of a transcription based on an analytic purpose; secondly, developing AMT approaches that are able to learn conventions concerning the transcription of a specific style; thirdly, a focus on novice transcribers as users of AMT systems; and, finally, considering target notation systems different from Western staff notation

Did they report it to stop it? A realist evaluation of the effect of an advertising campaign on victims’ willingness to report unwanted sexual behaviour

Tackling unwanted sexual behaviour (USB) on public transport is a concern for transit authorities across the world. However, high rates of underreporting mean a lack of reliable information about USB, presenting a key barrier to prevention. This paper presents a realist evaluation of an initiative called ‘Report It To Stop It’ (RITSI) implemented in London, UK, to tackle underreporting. RITSI aimed to encourage victims to report details of USB incidents to police and transit authorities through media campaigns. Results show that the initiative did increase reporting of USB and, that this increase was not due to a rise in the prevalence of USB. Crucially, there was no evidence of any increase in passengers’ fear of crime during the campaign activity. However, the impacts of this campaign were more pronounced in earlier waves, and on certain modes of transport. These findings demonstrate the importance of the context in motivating reporting behaviour change

The VocalNotes Dataset

The VocalNotes dataset is a collection of audio and annotations for excerpts of vocal performances from five musical traditions - Japanese Minyo, Chinese Hebei Bangzi opera, Russian traditional singing, Alpine yodel and Jewish Romaniote chant. For each tradition the dataset contains: about 10 minutes of audio; documentation for the songs from which annotated fragments originate; f0, independent onset, offset and note pitch annotations created by two or three experts; The dataset was created as part of the VocalNotes project [1]. It is released under CC-BY-NC-SA license and can be accessed by filling out a request form

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

In-play sports betting: a scoping study

Technology has changed the nature of gambling practices over the last decade and is continuing to do so. The online sports betting industry has become a rapidly growing sector of the global economy, with online sports betting contributing 37% of the annual online gambling market in Europe. There has been an integration of social and technological processes that has enabled the cultural saliency of contemporary online betting. One of the more newly introduced forms of online sports betting is in-play sports betting behaviour (the betting on events within a sporting event such as football and cricket). In-play sports betting features (such as 'cash out') are increasing in popularity amongst online gambling operators. A scoping study was carried out examining the evolution of this new form of gambling practice which included both a systematic literature review and the examination of 338 online gambling websites that offered sports betting. The present study identified a comprehensive list of what in-play betting features are currently being offered on online gambling websites as well as other information concerning in-play sports betting. A total of 16 academic papers and two 'grey literature' reports and were identified in the systematic review. Out of 338 online gambling websites that were visited, 26% of these offered at least on in-play betting feature. Results from the systematic review suggest that in-play sports betting has the potential to be more harmful than other ways of gambling because of the inherent structural characteristics

Heat stored in the Earth system:where does the energy go?

Human-induced atmospheric composition changes cause a radiative imbalance at the top of the atmosphere which is driving global warming. This Earth energy imbalance (EEI) is the most critical number defining the prospects for continued global warming and climate change. Understanding the heat gain of the Earth system – and particularly how much and where the heat is distributed – is fundamental to understanding how this affects warming ocean, atmosphere and land; rising surface temperature; sea level; and loss of grounded and floating ice, which are fundamental concerns for society. This study is a Global Climate Observing System (GCOS) concerted international effort to update the Earth heat inventory and presents an updated assessment of ocean warming estimates as well as new and updated estimates of heat gain in the atmosphere, cryosphere and land over the period 1960–2018. The study obtains a consistent long-term Earth system heat gain over the period 1971–2018, with a total heat gain of 358±37 ZJ, which is equivalent to a global heating rate of 0.47±0.1 W m−2. Over the period 1971–2018 (2010–2018), the majority of heat gain is reported for the global ocean with 89 % (90 %), with 52 % for both periods in the upper 700 m depth, 28 % (30 %) for the 700–2000 m depth layer and 9 % (8 %) below 2000 m depth. Heat gain over land amounts to 6 % (5 %) over these periods, 4 % (3 %) is available for the melting of grounded and floating ice, and 1 % (2 %) is available for atmospheric warming. Our results also show that EEI is not only continuing, but also increasing: the EEI amounts to 0.87±0.12 W m−2 during 2010–2018. Stabilization of climate, the goal of the universally agreed United Nations Framework Convention on Climate Change (UNFCCC) in 1992 and the Paris Agreement in 2015, requires that EEI be reduced to approximately zero to achieve Earth's system quasi-equilibrium. The amount of CO2 in the atmosphere would need to be reduced from 410 to 353 ppm to increase heat radiation to space by 0.87 W m−2, bringing Earth back towards energy balance. This simple number, EEI, is the most fundamental metric that the scientific community and public must be aware of as the measure of how well the world is doing in the task of bringing climate change under control, and we call for an implementation of the EEI into the global stocktake based on best available science. Continued quantification and reduced uncertainties in the Earth heat inventory can be best achieved through the maintenance of the current global climate observing system, its extension into areas of gaps in the sampling, and the establishment of an international framework for concerted multidisciplinary research of the Earth heat inventory as presented in this study. This Earth heat inventory is published at the German Climate Computing Centre (DKRZ, https://www.dkrz.de/, last access: 7 August 2020) under the DOI https://doi.org/10.26050/WDCC/GCOS_EHI_EXP_v2 (von Schuckmann et al., 2020)

In-play sports betting: a scoping study

Technology has changed the nature of gambling practices over the last decade and is continuing to do so. The online sports betting industry has become a rapidly growing sector of the global economy, with online sports betting contributing 37% of the annual online gambling market in Europe. There has been an integration of social and technological processes that has enabled the cultural saliency of contemporary online betting. One of the more newly introduced forms of online sports betting is in-play sports betting behaviour (the betting on events within a sporting event such as football and cricket). In-play sports betting features (such as 'cash out') are increasing in popularity amongst online gambling operators. A scoping study was carried out examining the evolution of this new form of gambling practice which included both a systematic literature review and the examination of 338 online gambling websites that offered sports betting. The present study identified a comprehensive list of what in-play betting features are currently being offered on online gambling websites as well as other information concerning in-play sports betting. A total of 16 academic papers and two 'grey literature' reports and were identified in the systematic review. Out of 338 online gambling websites that were visited, 26% of these offered at least on in-play betting feature. Results from the systematic review suggest that in-play sports betting has the potential to be more harmful than other ways of gambling because of the inherent structural characteristics

Plasma Biomarkers of Brain Atrophy in Alzheimer's Disease

Peripheral biomarkers of Alzheimer's disease (AD) reflecting early neuropathological change are critical to the development of treatments for this condition. The most widely used indicator of AD pathology in life at present is neuroimaging evidence of brain atrophy. We therefore performed a proteomic analysis of plasma to derive biomarkers associated with brain atrophy in AD. Using gel based proteomics we previously identified seven plasma proteins that were significantly associated with hippocampal volume in a combined cohort of subjects with AD (N = 27) and MCI (N = 17). In the current report, we validated this finding in a large independent cohort of AD (N = 79), MCI (N = 88) and control (N = 95) subjects using alternative complementary methods—quantitative immunoassays for protein concentrations and estimation of pathology by whole brain volume. We confirmed that plasma concentrations of five proteins, together with age and sex, explained more than 35% of variance in whole brain volume in AD patients. These proteins are complement components C3 and C3a, complement factor-I, γ-fibrinogen and alpha-1-microglobulin. Our findings suggest that these plasma proteins are strong predictors of in vivo AD pathology. Moreover, these proteins are involved in complement activation and coagulation, providing further evidence for an intrinsic role of these pathways in AD pathogenesis