An investigation of impact breakage of rocks using the split Hopkinson pressure bar

Discrete element methods (DEM) are being used to provide detailed impact histories of the particles in comminution devices, such as mills. To match this immense detail of information, far more informative breakage tests than those that are generally conducted are now required. The split Hopkinson pressure bar apparatus is used in this study, as it allows the calculation of breakage forces and absorbed energies. The geometry of rock particles has been identified as significant, so this project undertook to identify the influence of shape on the breakage pattern of blue stone. Comparisons are then made between the breakage pattern of angular rocks and rounded, milled rocks for single impact fracture and consecutive impact loading at low energy. Results of this experiment indicate that although breakage for both geometries occurs over a similar energy range, rounded particles have the greater probability of fracture because they absorb more of the impact energy for a given loading. Size distributions of progeny show that five pebbles or more are sufficient to predict the distribution of most particles in small energy regimes. Cumulative impact testing shows that considerably more energy is required to break a rock through cumulative damage than through a single impact—this is of considerable importance in the light of the indications from DEM simulations that most breakage in a mill will be from cumulative damage rather than single impact breakage

QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

SUMMARY: Next-generation sequencing (NGS) enables reliable detection of resistance mutations in minority variants of human immunodeficiency virus type 1 (HIV-1). There is paucity of evidence for the association of minority resistance to treatment failure, and this requires evaluation. However, the tools for analyzing HIV-1 drug resistance (HIVDR) testing data are mostly web-based which requires uploading data to webservers. This is a challenge for laboratories with internet connectivity issues and instances with restricted data transfer across networks. We present QuasiFlow, a pipeline for reproducible analysis of NGS-based HIVDR testing data across different computing environments. Since QuasiFlow entirely depends on command-line tools and a local copy of the reference database, it eliminates challenges associated with uploading HIV-1 NGS data onto webservers. The pipeline takes raw sequence reads in FASTQ format as input and generates a user-friendly report in PDF/HTML format. The drug resistance scores obtained using QuasiFlow were 100% and 99.12% identical to those obtained using web-based HIVdb program and HyDRA web respectively at a mutation detection threshold of 20%. AVAILABILITY AND IMPLEMENTATION: QuasiFlow and corresponding documentation are publicly available at https://github.com/AlfredUg/QuasiFlow. The pipeline is implemented in Nextflow and requires regular updating of the Stanford HIV drug resistance interpretation algorithm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online

High Levels of Acquired HIV Drug Resistance Following Virological Nonsuppression in HIV-Infected Women from a High-Risk Cohort in Uganda.

HIV drug resistance (HIVDR) is of increasing health concern, especially among key populations. We investigated the prevalence of virological suppression (VS), prevalence and correlates of HIVDR in HIV-infected women, enrolled in a high-risk cohort. We enrolled 267 women initiated on first-line antiretroviral therapy (ART) between 2015 and 2018. Participants' plasma samples were analyzed for HIV RNA viral load (VL) and genotypic resistance testing was performed on those with VL nonsuppression (defined as VL ≥1,000 copies/mL). We used the Stanford HIVDR database-algorithm to assess HIVDR mutations and logistic regression to assess risk factors for VL nonsuppression and HIVDR. We observed an overall VS prevalence of 76.0% (203/267) and detected respective acquired drug resistance prevalence to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTIs) of 81.3% [confidence interval (CI) 67.4-91.1] and 45.8% (CI 31.4-60.8) among the 48 successfully genotyped VL nonsuppressors. NNRTI mutations were observed in 81.3% (39/48) of the genotyped participants and 45.8% (22/48) had both NRTI and NNRTI mutations. The mutation K103N was detected in 62.5% (30/48) of participants, 41.7% (20/48) had M184V/I, 14.6% had K65R, and 12.5% (6/48) had thymidine analog mutations (TAMs). None of the analyzed potential risk factors, including age and duration on ART, was significantly correlated with VL nonsuppression or HIVDR. Although high levels of NNRTI mutations support the transition to dolutegravir, the presence of NRTI mutations, especially TAMs, may compromise dolutegravir-based regimens or other second-line ART options. The moderate VS prevalence and high HIVDR prevalence therefore call for timely ART switching and intensive adherence counseling

The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Power draw estimations in experimental tumbling mills using PEPT

Positron Emission Particle Tracking (PEPT) was employed to reconstruct the motion of mono-sized glass beads in an experimental tumbling mill run in batch mode. In each case, the derived trajectory field of a representative tracer particle was used to determine the charge power draw at steady state operation. Two approaches for calculating power draw were considered: the torque of the centre of mass about the mill centre, and the time averaged torque contribution per discrete grid cell summed over the volume of the mill. Results were compared across different operating conditions and particle sizes to measured power

Developing a 3D mineral texture quantification method of drill core for geometallurgy

CITATION: Voigt, M.J. et al. 2019. Developing a 3D mineral texture quantification method of drill core for geometallurgy. Journal of the Southern African Institute of Mining and Metallurgy, 119(4):347-353. doi:10.17159/2411-9717/590/2019The original publication is available at https://www.saimm.co.za/publications/journal-papersMineral texture is a critical factor which controls ore variability and is an important attribute in geometallurgy. In relation to downstream processes, it affects the fracture pattern during breakage, where rock strength is inherently a function of mineral texture. Because of the subjective nature of mineral texture, it has not been easy to quantify, especially in the context of a measurement suitable for use in geometallurgical programmes. The aim of this paper is to present the first steps in developing a 3D mineral texture quantification method for drill core and to assess its sensitivity to differences in rock strength using a case study. The methodology includes classifying the textural information using the 3D grey level co-occurrence matrices (GLCM) and X-ray computed tomography (XCT) coupled method. Rock strength tests were performed using the split Hopkinson pressure bar (SHPB). The case study investigates a heterogeneous polymetallic sulphide deposit and a homogeneous shale subdivided into three ’mineral textural types’. The variability is largely captured by the GLCM matrices, and preliminary trends can be observed where the shale is finer grained and has a higher yield strength in comparison with the coarser grained polymetallic sulphide ore.https://www.saimm.co.za/publications/journal-papersPublisher’s versio