3D Imaging on heterogeneous surfaces on laterite drill core materials

The SOLSA project aims to construct an analytical expert system for on-line-on-mine-real-time mineralogical and geochemical analyses on sonic drilled cores. A profilometer is indispensable to obtain reliable and quantitative data from RGB and hyperspectral cameras, and to get 3D definition of close-to-surface objects such as rheology (grain shape, grain size, fractures and vein systems), material hardness and porosities. Optical properties of minerals can be analyzed by focusing on the reflectance. Preliminary analyses were performed with the commercial scan control profilometer MI-CRO-EPSILON equipped with a blue 405 nm laser on a conveyor belt (depth resolution: 10 μm; surface resolution: 30x30 μm2 (maximum resolution; 1m drill core/4 min). Drill core parts and rocks with 4 different surface roughness states: (1) sonic drilled, (2) diamond saw-cut, polished at (3) 6 mm and (4) 0.25 μm were measured (see also abstract Duée et al. this volume). The ΜICRO- EPSILON scanning does not detect such small differences of surface roughness states. Profilometer data can also be used to access rough mineralogical identification of some mineral groups like Fe-Mg silicates, quartz and feldspars). Drill core parts from a siliceous mineralized breccia and laterite with high and deep porosity and fractures were analyzed. The determination of holes’ convexity and fractures) is limited by the surface/depth ratio. Depending on end-user’s needs, parameters such as fracture densities and mineral content should be combined, and depth and surface resolutions should be optimized, to speed up “on-line-on-mine-real- time” mineral and chemical analyses in order to reach the target of about 80 m/day of drilled core

Efficient long-term open-access data archiving in mining industries

Efficient data collection, analysis and preservation are needed to accomplish adequate business decision making. Long-lasting and sustainable business operations, such as mining, add extra requirements to this process: data must be reliably preserved over periods that are longer than that of a typical software life-cycle. These concerns are of special importance for the combined on-line-on-mine-real-time expert system SOLSA (http://www.solsa-mining.eu/) that will produce data not only for immediate industrial utilization, but also for the possible scientific reuse. We thus applied the experience of scientific data publishing to provide efficient, reliable, long term archival data storage. Crystallography, a field covering one of the methods used in the SOLSA expert system, has long traditions of archiving and disseminating crystallographic data. To that end, the Crystallographic Interchange Framework (CIF, [1]) was developed and is maintained by the International Union of Crystallography (IUCr). This framework provides rich means for describing crystal structures and crystallographic experiments in an unambiguous, human- and machine- readable way, in a standard that is independent of the underlying data storage technology. The Crystallography Open Database (COD, [2]) has been successfully using the CIF framework to maintain its open-access crystallographic data collection for over a decade [3,4]. Since the CIF framework is extensible it is possible to use it for other branches of knowledge. The SOLSA system will generate data using different methods of material identification: XRF, XRD, Raman, IR and DRIFT spectroscopy. For XRD, the CIF is usable out-of-the-box, since we can rely on extensive data definition dictionaries (ontologies) developed by the IUCr and the crystallographic community. For spectroscopic techniques such dictionaries, to our best knowledge, do not exist; thus, the SOLSA team is developing CIF dictionaries for spectroscopic techniques to be used in the SOLSA expert system. All dictionaries will be published under liberal license and communities are encourage to join the development, reuse and extend the dictionaries where necessary. These dictionaries will enable access to open data generated by SOLSA by all interested parties. The use of the common CIF framework will ensure smooth data exchange among SOLSA partners and seamless data publication from the SOLSA project

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

Impact of oocytes with CLCG on ICSI outcomes and their potential relation to pesticide exposure

Abstract Background Oocyte quality is a key limiting factor in female fertility which is primarily reflected in morphological features. Centrally located cytoplasm granulation (CLCG) is one type of cytoplasmic dimorphism exhibited by oocytes that could be linked to pesticide exposure with a significant risk of decreased ICSI outcomes. Methods This retrospective study included 633 women who were part of an intracytoplasmic spermatozoa injection (ICSI) program between 2009 and 2011. The participants lived in the Picardy region of France and had been exposed to pesticides. The participants were divided in two groups based on prevalence of oocytes with CLCG (LCLCG [n = 83]: low prevalence of oocytes with CLCG under 25%. HCLCG [n = 68]: high prevalence of CLCG over 75%). The embryological and clinical outcomes were analysed for both groups and were calculated using the difference between the two values. Results Results for couples with HCLCG compared to LCLCG showed a decrease in embryo cleavage, ongoing pregnancy, and live birth rates (82%, 14%, 13% vs 99%, 32%, 30%, respectively).The early miscarriage rate was increased (47% vs 11%), with an OR of 3.1 (95%CI [2.1–4.1]). Due to high pesticide exposure (over 3000 g/ha), there is a higher risk of a resulting disturbed oocyte cohort with a high prevalence of CLCG over 75%. Conclusion The high prevalence of oocytes with CLCG over 75% has a negative effect on embryos and the general ICSI clinical outcomes. Furthermore, a putative association between pesticide exposure and risk of CLCG was identified, justifying the need for further research and a potential need to find alternative assisted reproductive technologies for these couples. Trial registration Tabacfertimasc. ID number: ID2011-A00634–37 ; registered 2011/2/

Impact of heterogeneities and surface roughness on pXRF, pIR, XRD and Raman analyses: Challenges for on-line, real-time combined mineralogical and chemical analyses on drill cores and implication for “high speed” Ni-laterite exploration

International audienceOn-line, real-time chemical and mineralogical analyses on drill cores are highly demanded by mining companies. However, they are a challenge because of drill core surface state and sample heterogeneities. We selected four rock samples: highly porous, siliceous breccia and serpentinized harzburgite coming from the base of a nickel laterite profile in New Caledonia which were sonic drilled, and fine grained, homogeneous sandstone and coarse grained granite which were diamond drilled and provided by Eijkelkamp Sonic Drill with unknown origin. The samples were analysed at five surface states (diamond or sonic drilled, cut as squares, polished at 6 and 0.25 μm, powdered <80 μm) by portable XRF spectroscopy (pXRF) in mining and soil modes and portable infrared spectroscopy (pIR, Visible and Near Infrared-Short Wave Infrared range (VNIR-SWIR)). A total of 52 pXRF and 200 pIR analyses were performed per sample at each surface state. This study shows that the surface state has minor influence on the results of the portable instruments. By comparing pIR and pXRF results with laboratory devices (Raman spectroscopy, XRD with Rietveld refinement, XRF spectroscopy and ICP-AES), we evidence the lower and less accurate information obtained from handheld instruments in terms of chemistry and mineralogy. The porosity and grain size effect on the measurement need to be taken into consideration for on-line drill core analyses. We show that the combination of complementary analytical techniques helps to overcome the drawbacks of the core texture and of the precision of portable instruments in order to define the regions of interest (ROI) for mining companies. We also demonstrate that a precise pXRF calibration is mandatory and that the concentration of light elements (Si, Mg), even if not accurate, shows sufficient contrast along the lateritic profile for ROI definition

Impact of heterogeneities and surface roughness on pXRF, pIR, XRD and Raman analyses: Challenges for on-line, real-time combined mineralogical and chemical analyses on drill cores and implication for “high speed” Ni-laterite exploration

International audienc