Application of Multivariate Analysis in the Evaluation of Metals Distribution in Soil from Awwal Mining Site Kebbi, Nigeria

Multivariate statistical techniques such as principal component analysis (PCA), factor analysis (FA), and hierarchical cluster analysis (HCA) were utilized for the evaluation of metal distribution and variations in the soil at Awwal mining site. PCA was used to determine a reduced number of three principal components (PC) indicating about 82% of the total variation in the soil samples. The result of FA justifies the results of the PCA obtained. HCA classified the soil samples at the sites into two clusters, with cluster one having the higher metal levels, while cluster two had low metal levels but characterized with dominant toxic heavy metals (As and Pb). The results of the multivariate analysis showed that natural percentage abundance in soil and mineral composition of the mining ores were the main sources of the metals under study. Due to high metal levels in the soils, disposal and management of the mining waste/tailings and rehabilitation of the mining site after closure of mining should be done with care and caution to avoid leaching of the toxic metals to surface and underground water for the protection of health and safety of the neighboring community. Keywords: Soil, Metals, Mining, Multivariate analysis, Awwal

Efficient N-to-M Checkpointing Algorithm for Finite Element Simulations

In this work, we introduce a new algorithm for N-to-M checkpointing in finite element simulations. This new algorithm allows efficient saving/loading of functions representing physical quantities associated with the mesh representing the physical domain. Specifically, the algorithm allows for using different numbers of parallel processes for saving and loading, allowing for restarting and post-processing on the process count appropriate to the given phase of the simulation and other conditions. For demonstration, we implemented this algorithm in PETSc, the Portable, Extensible Toolkit for Scientific Computation, and added a convenient high-level interface into Firedrake, a system for solving partial differential equations using finite element methods. We evaluated our new implementation by saving and loading data involving 8.2 billion finite element degrees of freedom using 8,192 parallel processes on ARCHER2, the UK National Supercomputing Service

Profiling ascidian promoters as the primordial type of vertebrate promoter

<p>Abstract</p> <p>Background</p> <p>CpG islands are observed in mammals and other vertebrates, generally escape DNA methylation, and tend to occur in the promoters of widely expressed genes. Another class of promoter has lower G+C and CpG contents, and is thought to be involved in the spatiotemporal regulation of gene expression. Non-vertebrate deuterostomes are reported to have a single class of promoter with high-frequency CpG dinucleotides, suggesting that this is the original type of promoter. However, the limited annotation of these genes has impeded the large-scale analysis of their promoters.</p> <p>Results</p> <p>To determine the origins of the two classes of vertebrate promoters, we chose <it>Ciona intestinalis</it>, an invertebrate that is evolutionarily close to the vertebrates, and identified its transcription start sites genome-wide using a next-generation sequencer. We indeed observed a high CpG content around the transcription start sites, but their levels in the promoters and background sequences differed much less than in mammals. The CpG-rich stretches were also fairly restricted, so they appeared more similar to mammalian CpG-poor promoters.</p> <p>Conclusions</p> <p>From these data, we infer that CpG islands are not sufficiently ancient to be found in invertebrates. They probably appeared early in vertebrate evolution via some active mechanism and have since been maintained as part of vertebrate promoters.</p

The X-ray luminosity function of Active Galactic Nuclei in the redshift interval z=3-5

We combine deep X-ray survey data from the Chandra observatory and the wide-area/shallow XMM-XXL field to estimate the AGN X-ray luminosity function in the redshift range z=3-5. The sample consists of nearly 340 sources with either photometric (212) or spectroscopic (128) redshift in the above range. The combination of deep and shallow survey fields provides a luminosity baseline of three orders of magnitude, Lx(2-10keV)~1e43-1e46erg/s at z>3. We follow a Bayesian approach to determine the binned AGN space density and explore their evolution in a model-independent way. Our methodology accounts for Poisson errors in the determination of X-ray fluxes and uncertainties in photometric redshift estimates. We demonstrate that the latter is essential for unbiased measurement of space densities. We find that the AGN X-ray luminosity function evolves strongly between the redshift intervals z=3-4 and z=4-5. There is also suggestive evidence that the amplitude of this evolution is luminosity dependent. The space density of AGN with Lx<1e45erg/s drops by a factor of 5 between the redshift intervals above, while the evolution of brighter AGN appears to be milder. Comparison of our X-ray luminosity function with that of UV/optical selected QSOs at similar redshifts shows broad agreement at bright luminosities, Lx>1e45erg/s. The faint-end slope of UV/optical luminosity functions however, is steeper than for X-ray selected AGN. This implies that the type-I AGN fraction increases with decreasing luminosity at z>3, opposite to trends established at lower redshift. We also assess the significance of AGN in keeping the hydrogen ionised at high redshift. Our X-ray luminosity function yields ionising photon rate densities that are insufficient to keep the Universe ionised at redshift z>4. A source of uncertainty in this calculation is the escape fraction of UV photons for X-ray selected AGN.Comment: MNRAS accepte

Epitaxial contact Andreev reflection spectroscopy of NbN/Co₂FeSi layered devices

We investigated the spin polarization P of Co-based Heusler alloy Co2FeSi by epitaxial contact Andreev reflection (ECAR) spectroscopy using epitaxially grown superconductor NbN and Heusler alloy Co2FeSi layered devices. Ferromagnetic Co2FeSi possesses the highest Curie temperature (TC ? 1100 K) and the largest spontaneous magnetic moment (ps ? 6 μB) in the class of Heusler alloys. The ECAR measurements revealed that the P value of Co2FeSi was 54 ± 2% with a finite barrier parameter Z, indicating that an intrinsic P value in ECAR spectroscopy would exceed reported values in point-contact Andreev reflection spectroscopy. We therefore established not only the epitaxial integration of ferromagnetic Co2FeSi with superconductor NbN on an MgO substrate but also the fabrication and evaluation techniques of their ECAR devices. This highly versatile superconducting spintronic system enables fundamental superconducting spintronic studies, and it is also a candidate for practical superconducting spintronic devices

Mitochondrial Genetic Diversity and its Determinants in Island Melanesia

For a long time, many physical anthropologists and human geneticists considered Island Melanesian populations to be genetically impoverished, dominated by the effects of random genetic drift because of their small sizes, internally very homogeneous, and therefore of little relevance in reconstructing past human migrations. This view is changing. Here we present the developing detailed picture of mitochondrial DNA (mtDNA) variation in eastern New Guinea and Island Melanesia that reflects linguistic distinctions within the region as well as considerable island-by-island isolation. It also appears that the patterns of variation reflect marital migration distinctions between bush and beach populations. We have identified a number of regionally specific mtDNA variants. We also question the widely accepted hypothesis that the mtDNA variant referred to as the ‘Polynesian Motif’ (or alternatively the ‘Austronesian Motif’) developed outside this region somewhere to the west. It may well have first appeared among certain non-Austronesian speaking groups in eastern New Guinea or the Bismarcks. Overall, the developing mtDNA pattern appears to be more easily reconciled with that of other genetic and biometric variables

社団法人神緑会事業報告1

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario

Alarming rates of virological failure and HIV-1 drug resistance amongst adolescents living with perinatal HIV in both urban and rural settings: evidence from the EDCTP READY-study in Cameroon

Objectives: Adolescents living with perinatal HIV infection (ALPHI) experience persistently high mortality rates, particularly in resource-limited settings. It is therefore clinically important for us to understand the therapeutic response, acquired HIV drug resistance (HIVDR) and associated factors among ALPHI, according to geographical location. Methods: A study was conducted among consenting ALPHI in two urban and two rural health facilities in the Centre Region of Cameroon. World Health Organization (WHO) clinical staging, self-reported adherence, HIVDR early warning indicators (EWIs), immunological status (CD4 count) and plasma viral load (VL) were assessed. For those experiencing virological failure (VF, VL&nbsp;≥&nbsp;1000 copies/mL), HIVDR testing was performed and interpreted using the Stanford HIV Drug Resistance Database v.8.9-1. Results: Of the 270 participants, most were on nonnucleoside reverse transcriptase inhibitor (NNRTI)-based regimens (61.7% urban vs. 82.2% rural), and about one-third were poorly adherent (30.1% vs. 35.1%). Clinical failure rates (WHO-stage III/IV) in both settings were&nbsp;&lt;&nbsp;15%. In urban settings, the immunological failure (IF) rate (CD4 &nbsp;&lt;&nbsp;250 cells/μL) was 15.8%, statistically associated with late adolescence, female gender and poor adherence. The VF rate was 34.2%, statistically associated with poor adherence and NNRTI-based antiretroviral therapy. In the rural context, the IF rate was 26.9% and the VF rate was 52.7%, both statistically associated with advanced clinical stages. HIVDR rate was over 90% in both settings. EWIs were delayed drug pick-up, drug stock-outs and suboptimal viral suppression. Conclusions: Poor adherence, late adolescent age, female gender and advanced clinical staging worsen IF. The VF rate is high and consistent with the presence of HIVDR in both settings, driven by poor adherence, NNRTI-based regimen and advanced clinical staging