Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

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

Prospects for Direct Natural Gas Conversion to Petrochemical Feedstocks

Natural gas, due to its abundance and low cost, is a major future source as a feedstock for the petroleum and chemical industry. For strategic or economic reasons, it may be undesirable to transport natural gas to potential markets or to use it for transportation fuels. This provides an incentive to investigate various routes to convert natural gas to higher hydrocarbons. Methane, which accounts for over 60% of natural gas, is used today as a source of hydrogen, for ammonia production and to manufacture methanol through steam reforming to the synthesis gas mixtures. However, direct methane conversion to higher hydrocarbon has a high economic incentive as a result of bypassing the synthesis gas step.Recent process development studies have investigated various options for the conversion of natural gas to valuable hydrocarbons. This paper discusses the prospects for direct natural gas conversion by three routes: oxidative coupling to ethylene and higher hydrocarbons, oxidation to methanol or formaldehyde. and oxidation to aromatics by nitrous oxide. Current research activities in the area of natural gas oxidation are reviewed in terms of process conditions, reactor design, catalyst performance in terms of methane conversion and selectivities to various products. Future challenges in reactor and process design for methane oxidation are highlighted

Depositional environments and an apparent age for the Geci meta-limestones : constraints on the geological history of northern Mozambique

Strongly contrasting rocks were juxtaposed during the long tectonometamorphic history of the Mozambique Orogenic Belt in northern Mozambique. The latest depositional event was expressed by accumulation of marine sediments, which were subsequently mildly metamorphosed and tectonically juxtaposed with granulite facies complexes. The low-grade metasedimentary rocks comprise the Geci group which was mapped, and studied petrographically, geochemically and isotopically in order to provide constraints on the depositional environments, age and latest history of the Mozambique Orogenic Belt. The group occurs as several large, tectonically dissected, intensively sheared, folded and mylonitised, SW–NE trending lenses within Unango Complex granulite rocks. In places, primary depositional features are well preserved. The dominant rocks are calcarenites, dolarenites, calcite matrix-supported and dolostone clast-supported carbonate breccias forming beds with erosional bases, normal and reverse graded bedding, and well-developed Bouma sequences. Dolomicritic, microbial and oolitic dolostone clasts were apparently derived from the margin of a shallow-water carbonate platform and redeposited by turbidity currents on a continental slope with calcareous sedimentation. The Geci meta-carbonate rocks have low SiO2 and Al2O3 contents. MgO/CaO ratios fluctuate between 0.05 and 0.70 averaging 0.15 ± 0.18 (1σ, n = 111). Acid-soluble constituents have moderate concentrations of Fe (777 ± 310 ppm), Mn (131 ± 85 ppm) and Sr (566 ± 145). Mn/Sr ratios are relatively low (0.26 ± 0.19), δ13C and δ18O values are invariably high, with only moderate scatter: +4.0 ± 0.6% V-PDB and 25.8 ± 0.5% V-SMOW, respectively. The least altered 87Sr/86Sr ratio of calcite is 0.70708, whereas dolomite is enriched in 87Sr with the lowest ratio of 0.70730. The least-altered 87Sr/86Sr and δ13C ratios suggest an apparent depositional age of either 595–585 or 630–625 Ma. This provides a lower age limit for juxtaposition of the low-grade Geci group rocks and granulite facies rocks of the Unango Complex

Trojan Horse Infection Detection in Cloud Based Environment Using Machine Learning

Cloud computing technology is known as a distributed computing network, which consists of a large number of servers connected via the internet. This technology involves many worthwhile resources, such as applications, services, and large database storage. Users have the ability to access cloud services and resources through web services. Cloud computing provides a considerable number of benefits, such as effective virtualized resources, cost efficiency, self-service access, flexibility, and scalability. However, many security issues are present in cloud computing environment. One of the most common security challenges in the cloud computing environment is the trojan horses. Trojan horses can disrupt cloud computing services and damage the resources, applications, or virtual machines in the cloud structure. Trojan horse attacks are dangerous, complicated and very difficult to be detected. In this research, eight machine learning classifiers for trojan horse detection in a cloud-based environment have been investigated. The accuracy of the cloud trojan horses detection rate has been investigated using dynamic analysis, Cukoo sandbox, and the Weka data mining tool. Based on the conducted experiments, the SMO and Multilayer Perceptron have been found to be the best classifiers for trojan horse detection in a cloud-based environment. Although SMO and Multilayer Perceptron have achieved the highest accuracy rate of 95.86%, Multilayer Perceptron has outperformed SMO in term of Receiver Operating Characteristic (ROC) area

Isotope chemostratigraphy of marbles in northeastern Mozambique: Apparent depositional ages and tectonostratigraphic implications

Marbles are minor but characteristic components of metasedimentary units within nappes in the Pan-African Mozambique Belt in NE Mozambique. Metasedimentary units remain largely undated, and carbon and strontium isotope stratigraphy of marbles has been used for indirect dating of the depositional history in this part of the Mozambique Belt. Sixty-nine samples from nine occurrences of dolomite, calcite and magnesite marbles in the Montepuez, Xixano, Lalamo, Ocua and Nampula metamorphic complexes were analysed for major and trace elements, and a subset of 39 samples for C, O and Sr isotopes. The least altered δ¹³C values range from −3.5 to +7.1‰ (V-PDB) and ⁸⁷Sr/⁸⁶Sr ratios from 0.70504 to 0.70671. These values are considered as the best proxy to seawater composition at the time of deposition. The apparent deposition ages, derived from available seawater evolution curves, range from c. 1250 to c. 660 Ma. An age of 1250–910 Ma is obtained from a tripartite marble unit in the Montepuez Complex which is exposed in the Montepuez quarries. Five other age-groups are represented by marble units with apparent depositional ages of 800–750 Ma (Xixano North), 800–660 Ma (Montepuez West), c. 750 Ma (Nampula), c. 740 Ma (Xixano South and Lalamo), and 740–670 Ma (Montepuez East). The data suggest that: (i) Pan-African nappes in NE Mozambique include Neoproterozoic and probable Mesoproterozoic sediments; (ii) Neoproterozoic rocks of the Xixano and Nampula complexes might have different ancestry and were tectonically juxtaposed during the Neoproterozoic Pan-African orogeny