Development of Bioinformatics Infrastructure for Genomics Research in H3Africa

Background: Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet’s role has evolved in response to changing needs from the consortium and the African bioinformatics community. Objectives: H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Methods and Results: Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training. Conclusions: For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa

SUSTAIN drilling at Surtsey volcano, Iceland, tracks hydrothermal and microbiological interactions in basalt 50 years after eruption

The 2017 Surtsey Underwater volcanic System for Thermophiles, Alteration processes and INnovative concretes (SUSTAIN) drilling project at Surtsey volcano, sponsored in part by the International Continental Scientific Drilling Program (ICDP), provides precise observations of the hydrothermal, geochemical, geomagnetic, and microbiological changes that have occurred in basaltic tephra and minor intrusions since explosive and effusive eruptions produced the oceanic island in 1963–1967. Two vertically cored boreholes, to 152 and 192 m below the surface, were drilled using filtered, UV-sterilized seawater circulating fluid to minimize microbial contamination. These cores parallel a 181 m core drilled in 1979. Introductory investigations indicate changes in material properties and whole-rock compositions over the past 38 years. A Surtsey subsurface observatory installed to 181 m in one vertical borehole holds incubation experiments that monitor in situ mineralogical and microbial alteration processes at 25–124 ∘C. A third cored borehole, inclined 55∘ in a 264∘ azimuthal direction to 354 m measured depth, provides further insights into eruption processes, including the presence of a diatreme that extends at least 100 m into the seafloor beneath the Surtur crater. The SUSTAIN project provides the first time-lapse drilling record into a very young oceanic basaltic volcano over a range of temperatures, 25–141 ∘C from 1979 to 2017, and subaerial and submarine hydrothermal fluid compositions. Rigorous procedures undertaken during the drilling operation protected the sensitive environment of the Surtsey Natural Preserve

Etude de l'effet de l'huile (nigella sativa)sur l'evolutin ponderale ,bilan nutritionnel et bilan lipidique chez les rats Wistar rendu obese

obesite est un probleme majeur de sante publique en ce 21eme siecles et la consommation d'aliments hypercaloriques riche en graisse et hydrate de carbone est considerer comme un facteur important,contribuant a l'exes de poid et a l'obesite ,les recherchers ecentes ont montres q'une supplimentation en acide gras polyinsatures (AGPI)tend a corriger et/ou a prevenir l'obesite . de ce fait,l'autre etude a porté sur l'incorporation,a un regime hypergras,l'huile fixe des graines de nigelle (nigella sativa l.)tres riche en AGPI (88,5%

Comparison of Local Analysis Strategies for Exudate Detection in Fundus Images

Diabetic Retinopathy (DR) is a severe and widely spread eye disease. Exudates are one of the most prevalent signs during the early stage of DR and an early detection of these lesions is vital to prevent the patient’s blindness. Hence, detection of exudates is an important diagnostic task of DR, in which computer assistance may play a major role. In this paper, a system based on local feature extraction and Support Vector Machine (SVM) classification is used to develop and compare different strategies for automated detection of exudates. The main novelty of this work is allowing the detection of exudates using non-regular regions to perform the local feature extraction. To accomplish this objective, different methods for generating superpixels are applied to the fundus images of E-OPHTA database and texture and morphological features are extracted for each of the resulting regions. An exhaustive comparison among the proposed methods is also carried out.This paper was supported by the European Union’s Horizon 2020 research and innovation programme under the Project GALAHAD [H2020-ICT2016-2017, 732613]. The work of Adri´an Colomer has been supported by the Spanish Government under a FPI Grant [BES-2014-067889]. We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Titan Xp GPU used for this research.Pereira, J.; Colomer, A.; Naranjo Ornedo, V. (2018). Comparison of Local Analysis Strategies for Exudate Detection in Fundus Images. En Intelligent Data Engineering and Automated Learning – IDEAL 2018. Springer. 174-183. https://doi.org/10.1007/978-3-030-03493-1_19S174183Sidibé, D., Sadek, I., Mériaudeau, F.: Discrimination of retinal images containing bright lesions using sparse coded features and SVM. Comput. Biol. Med. 62, 175–184 (2015)Zhou, W., Wu, C., Yi, Y., Du, W.: Automatic detection of exudates in digital color fundus images using superpixel multi-feature classification. IEEE Access 5, 17077–17088 (2017)Sinthanayothin, C., et al.: Automated detection of diabetic retinopathy on digital fundus images. Diabet. Med. 19(2), 105–112 (2002)Walter, T., Klein, J.C., et al.: A contribution of image processing to the diagnosis of diabetic retinopathy-detection of exudates in color fundus images of the human retina. IEEE Trans. Med. Imaging 21(10), 1236–1243 (2002)Ali, S., et al.: Statistical atlas based exudate segmentation. Comput. Med. Imaging Graph. 37(5–6), 358–368 (2013)Zhang, X., Thibault, G., Decencière, E., Marcotegui, B., et al.: Exudate detection in color retinal images for mass screening of diabetic retinopathy. Med. Image Anal. 18(7), 1026–1043 (2014)Li, H., Chutatape, O.: Automated feature extraction in color retinal images by a model based approach. IEEE Trans. Biomed. Eng. 51(2), 246–254 (2004)Welfer, D., Scharcanski, J., Marinho, D.R.: A coarse-to-fine strategy for automatically detecting exudates in color eye fundus images. Comput. Med. Imaging Graph. 34(3), 228–235 (2010)Giancardo, L., et al.: Exudate-based diabetic macular edema detection in fundus images using publicly available datasets. Med. Image Anal. 16(1), 216–226 (2012)Amel, F., Mohammed, M., Abdelhafid, B.: Improvement of the hard exudates detection method used for computer-aided diagnosis of diabetic retinopathy. Int. J. Image Graph. Signal Process. 4(4), 19 (2012)Akram, M.U., Khalid, S., Tariq, A., Khan, S.A., Azam, F.: Detection and classification of retinal lesions for grading of diabetic retinopathy. Comput. Biol. Med. 45, 161–171 (2014)Akram, M.U., Tariq, A., Khan, S.A., Javed, M.Y.: Automated detection of exudates and macula for grading of diabetic macular edema. Comput. Methods Programs Biomed. 114(2), 141–152 (2014)Machairas, V.: Waterpixels and their application to image segmentation learning. Ph.D. thesis, Université de recherche Paris Sciences et Lettres (2016)Shi, J., Malik, J.: Normalized cuts and image segmentation. IEEE Trans. Pattern Anal. Mach. Intell. 22(8), 888–905 (2000)Veksler, O., Boykov, Y., Mehrani, P.: Superpixels and supervoxels in an energy optimization framework. In: Daniilidis, K., Maragos, P., Paragios, N. (eds.) ECCV 2010. LNCS, vol. 6315, pp. 211–224. Springer, Heidelberg (2010). https://doi.org/10.1007/978-3-642-15555-0_16Comaniciu, D., Meer, P.: Mean shift: a robust approach toward feature space analysis. IEEE Trans. Pattern Anal. Mach. Intell. 24(5), 603–619 (2002)Levinshtein, A., Stere, A., Kutulakos, K.N., Fleet, D.J., Dickinson, S.J., Siddiqi, K.: TurboPixels: fast superpixels using geometric flows. IEEE Trans. Pattern Anal. Mach. 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Vanadium Carbide (V4C3) MXene as an Efficient Anode for Li-Ion and Na-Ion Batteries

Li-ion batteries (LIBs) and Na-ion batteries (SIBs) are deemed green and efficient electrochemical energy storage and generation devices; meanwhile, acquiring a competent anode remains a serious challenge. Herein, the density-functional theory (DFT) was employed to investigate the performance of V4C3 MXene as an anode for LIBs and SIBs. The results predict the outstanding electrical conductivity when Li/Na is loaded on V4C3. Both Li2xV4C3 and Na2xV4C3 (x = 0.125, 0.5, 1, 1.5, and 2) showed expected low-average open-circuit voltages of 0.38 V and 0.14 V, respectively, along with a good Li/Na storage capacity of (223 mAhg?1) and a good cycling performance. Furthermore, there was a low diffusion barrier of 0.048 eV for Li0.0625V4C3 and 0.023 eV for Na0.0625V4C3, implying the prompt intercalation/extraction of Li/Na. Based on the findings of the current study, V4C3-based materials may be utilized as an anode for Li/Na-ion batteries in future applications. 2022 by the authors.This work was financially funded by the authors express their gratitude for the support of the Researchers Supporting Project Number (RSP-2021/267) King Saud University, Riyadh, Saudi Arabia. This work is also supported by Scientific Research Fund of Hunan Provincial Education Department (No. 21B0637).Scopu

The effect of tobacco, XPC, ERCC2 and ERCC5 genetic variants in bladder cancer development

<p>Abstract</p> <p>Background</p> <p>In this work, we have conducted a case-control study in order to assess the effect of tobacco and three genetic polymorphisms in <it>XPC, ERCC2 and ERCC5 </it>genes (rs2228001, rs13181 and rs17655) in bladder cancer development in Tunisia. We have also tried to evaluate whether these variants affect the bladder tumor stage and grade.</p> <p>Methods</p> <p>The patients group was constituted of 193 newly diagnosed cases of bladder tumors. The controls group was constituted of non-related healthy subjects. The rs2228001, rs13181 and rs17655 polymorphisms were genotyped using a polymerase chain reaction-restriction fragment length polymorphism technique.</p> <p>Results</p> <p>Our data have reported that non smoker and light smoker patients (1-19PY) are protected against bladder cancer development. Moreover, light smokers have less risk for developing advanced tumors stage. When we investigated the effect of genetic polymorphisms in bladder cancer development we have found that ERCC2 and ERCC5 variants were not implicated in the bladder cancer occurrence. However, the mutated homozygous genotype for XPC gene was associated with 2.09-fold increased risk of developing bladder cancer compared to the control carrying the wild genotype (p = 0.03, OR = 2.09, CI 95% 1.09-3.99). Finally, we have found that the XPC, ERCC2 and ERCC5 variants don't affect the tumors stage and grade.</p> <p>Conclusion</p> <p>These results suggest that the mutated homozygous genotype for XPC gene was associated with increased risk of developing bladder. However we have found no association between rs2228001, rs13181 and rs17655 polymorphisms and tumors stage and grade.</p

Institutional investors and corporate governance

We provide a comprehensive overview of the role of institutional investors in corporate governance with three main components. First, we establish new stylized facts documenting the evolution and importance of institutional ownership. Second, we provide a detailed characterization of key aspects of the legal and regulatory setting within which institutional investors govern portfolio firms. Third, we synthesize the evolving response of the recent theoretical and empirical academic literature in finance to the emergence of institutional investors in corporate governance. We highlight how the defining aspect of institutional investors – the fact that they are financial intermediaries – differentiates them in their governance role from standard principal blockholders. Further, not all institutional investors are identical, and we pay close attention to heterogeneity amongst institutional investors as blockholders