20 research outputs found
An Approach to a New Network Security Architecture of Nuclear and Research Facilities
With the growth of information technology (IT) systems, network security is rapidly becoming a critical business concern. Due to the interconnectivity of IT systems, a comprehensive description of all of the key elements and relationships that make up an organization2019;s network security is needed, which can be referred as network security architecture. The value of this architecture is often questioned by organizations in terms of its practical application. This paper has presents a new approach to the network security architecture by using the Zachman Framework capabilities. The network security architecture of nuclear and academic facilities academic centers is discussed to show how a conceptual model can be applied to a real organization. This new approach makes any Local Area Network LAN more secure and more flexible than any conventional security procedures without affecting the performance of the LAN. Applying Zachman matrix provides the answers to what data assets the nuclear and research facilities controls, how they are used, and where they are located
Bahr El-Baqar drain system / Egypt environmental studies on water quality. Part I: Bilbeis drain / Bahr El-Baqar drain
Multi-parametric MR Imaging Biomarkers Associated to Clinical Outcomes in Gliomas: A Systematic Review
[EN] Purpose: To systematically review evidence regarding the association of multi-parametric biomarkers with clinical outcomes and their capacity to explain relevant subcompartments of gliomas.
Materials and Methods: Scopus database was searched for original journal papers from January 1st, 2007 to February 20th , 2017 according to PRISMA. Four hundred forty-nine abstracts of papers were reviewed and scored independently by two out of six authors. Based on those papers we analyzed associations between biomarkers, subcompartments within the tumor lesion, and clinical outcomes. From all the articles analyzed, the twenty-seven papers with the highest scores were highlighted to represent the evidence about MR imaging biomarkers associated with clinical outcomes. Similarly, eighteen studies defining subcompartments within the tumor region were also highlighted to represent the evidence of MR imaging biomarkers. Their reports were critically appraised according to the QUADAS-2 criteria.
Results: It has been demonstrated that multi-parametric biomarkers are prepared for surrogating diagnosis, grading, segmentation, overall survival, progression-free survival, recurrence, molecular profiling and response to treatment in gliomas. Quantifications and radiomics features obtained from morphological exams (T1, T2, FLAIR, T1c), PWI (including DSC and DCE), diffusion (DWI, DTI) and chemical shift imaging (CSI) are the preferred MR biomarkers associated to clinical outcomes. Subcompartments relative to the peritumoral region, invasion, infiltration, proliferation, mass effect and pseudo flush, relapse compartments, gross tumor volumes, and high-risk regions have been defined to characterize the heterogeneity. For the majority of pairwise cooccurrences, we found no evidence to assert that observed co-occurrences were significantly different from their expected co-occurrences (Binomial test with False Discovery Rate correction, alpha=0.05). The co-occurrence among terms in the studied papers was found to be driven by their individual prevalence and trends in the literature.
Conclusion: Combinations of MR imaging biomarkers from morphological, PWI, DWI and CSI exams have demonstrated their capability to predict clinical outcomes in different management moments of gliomas. Whereas morphologic-derived compartments have been mostly studied during the last ten years, new multi-parametric MRI approaches have also been proposed to discover specific subcompartments of the tumors. MR biomarkers from those subcompartments show the local behavior within the heterogeneous tumor and may quantify the prognosis and response to treatment of gliomas.This work was supported by the Spanish Ministry for Investigation, Development and Innovation project with identification number DPI2016-80054-R.Oltra-Sastre, M.; Fuster García, E.; Juan -Albarracín, J.; Sáez Silvestre, C.; Perez-Girbes, A.; Sanz-Requena, R.; Revert-Ventura, A.... (2019). Multi-parametric MR Imaging Biomarkers Associated to Clinical Outcomes in Gliomas: A Systematic Review. Current Medical Imaging Reviews. 15(10):933-947. https://doi.org/10.2174/1573405615666190109100503S9339471510Louis D.N.; Perry A.; Reifenberger G.; The 2016 world health organization classification of tumors of the central nervous system: a summary. Acta Neuropathol 2016,131(6),803-820Ostrom Q.T.; Gittleman H.; Fulop J.; CBTRUS statistical report: primary brain and central nervous system tumors diagnosed in the United States in 2008-2012. Neuro-oncol 2015,17(Suppl. 4),iv1-iv62Yachida S.; Jones S.; Bozic I.; Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 2010,467(7319),1114-1117Gerlinger M.; Rowan A.J.; Horswell S.; Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012,366(10),883-892Sottoriva A.; Spiteri I.; Piccirillo S.G.M.; Intratumor heterogeneityin human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci USA 2013,110(10),4009-4014Whiting P.F.; Rutjes A.W.; Westwood M.E.; QUADAS-2: a revised tool for the quality assessment of diagnostic accuracy studies. Ann Intern Med 2011,155(8),529-536Stupp R.; Mason W.P.; van den Bent M.J.; Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N Engl J Med 2005,352(10),987-996Ponte K.F.; Berro D.H.; Collet S.; In vivo relationship between hypoxia and angiogenesis in human glioblastoma: a multimodal imaging study. J Nucl Med 2017,58(10),1574-1579Pope W.B.; Kim H.J.; Huo J.; Recurrent glioblastoma multiforme: ADC histogram analysis predicts response to bevacizumab treatment. Radiology 2009,252(1),182-189Mörén L.; Bergenheim A.T.; Ghasimi S.; Brännström T.; Johansson M.; Antti H.; Metabolomic screening of tumor tissue and serum in glioma patients reveals diagnostic and prognostic information. Metabolites 2015,5(3),502-520Prager A.J.; Martinez N.; Beal K.; Omuro A.; Zhang Z.; Young R.J.; Diffusion and perfusion MRI to differentiate treatment-related changes including pseudoprogression from recurrent tumors in high-grade gliomas with histopathologic evidence. AJNR Am J Neuroradiol 2015,36(5),877-885Kickingereder P.; Burth S.; Wick A.; Radiomic profiling of glioblastoma: identifying an imaging predictor of patient survival with improved performance over established clinical and radiologic risk models. Radiology 2016,280(3),880-889Yoo R-E.; Choi S.H.; Cho H.R.; Tumor blood flow from arterial spin labeling perfusion MRI: a key parameter in distinguishing high-grade gliomas from primary cerebral lymphomas, and in predicting genetic biomarkers in high-grade gliomas. J Magn Reson Imaging 2013,38(4),852-860Liberman G.; Louzoun Y.; Aizenstein O.; Automatic multi-modal MR tissue classification for the assessment of response to bevacizumab in patients with glioblastoma. Eur J Radiol 2013,82(2),e87-e94Ramadan S.; Andronesi O.C.; Stanwell P.; Lin A.P.; Sorensen A.G.; Mountford C.E.; Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma. Radiology 2011,259(2),540-549Xintao H.; Wong K.K.; Young G.S.; Guo L.; Wong S.T.; Support vector machine multi-parametric MRI identification of pseudoprogression from tumor recurrence in patients with resected glioblastoma. J Magn Reson Imaging 2011,33(2),296Ingrisch M.; Schneider M.J.; Nörenberg D.; Radiomic Analysis reveals prognostic information in T1-weighted baseline magnetic resonance imaging in patients with glioblastoma. Invest Radiol 2017,52(6),360-366Ulyte A.; Katsaros V.K.; Liouta E.; Prognostic value of preoperative dynamic contrast-enhanced MRI perfusion parameters for high-grade glioma patients. Neuroradiology 2016,58(12),1197-1208O’Neill A.F.; Qin L.; Wen P.Y.; de Groot J.F.; Van den Abbeele A.D.; Yap J.T.; Demonstration of DCE-MRI as an early pharmacodynamic biomarker of response to VEGF Trap in glioblastoma. J Neurooncol 2016,130(3),495-503Kickingereder P.; Bonekamp D.; Nowosielski M.; Radiogenomics of glioblastoma: machine learning-based classification of molecular characteristics by using multiparametric and multiregional mr imaging features. Radiology 2016,281(3),907-918Roberto S-R.; Antonio R-V.; Luis M-B.; Angel A-B.; Gracián G-M.; Quantitative mr perfusion parameters related to survival time in high-grade gliomas. European Radiology 2013,23(12),3456-3465Jain R.; Poisson L.; Narang J.; Genomic mapping and survival prediction in glioblastoma: molecular subclassification strengthened by hemodynamic imaging biomarkers. Radiology 2013,267(1),212-220Fathi K.A.; Mohseni M.; Rezaei S.; Bakhshandehpour G.; Saligheh R.H.; Multi-parametric (ADC/PWI/T2-W) image fusion approach for accurate semi-automatic segmentation of tumorous regions in glioblastoma multiforme. MAGMA 2015,28(1),13-22Caulo M.; Panara V.; Tortora D.; Data-driven grading of brain gliomas: a multiparametric MR imaging study. Radiology 2014,272(2),494-503Alexiou G.A.; Zikou A.; Tsiouris S.; Comparison of diffusion tensor, dynamic susceptibility contrast MRI and (99m)Tc-Tetrofosmin brain SPECT for the detection of recurrent high-grade glioma. Magn Reson Imaging 2014,32(7),854-859Van Cauter S.; De Keyzer F.; Sima D.M.; Integrating diffusion kurtosis imaging, dynamic susceptibility-weighted contrast-enhanced MRI, and short echo time chemical shift imaging for grading gliomas. Neuro-oncol 2014,16(7),1010-1021Seeger A.; Braun C.; Skardelly M.; Comparison of three different MR perfusion techniques and MR spectroscopy for multiparametric assessment in distinguishing recurrent high-grade gliomas from stable disease. Acad Radiol 2013,20(12),1557-1565Chawalparit O.; Sangruchi T.; Witthiwej T.; Diagnostic performance of advanced mri in differentiating high-grade from low-grade gliomas in a setting of routine service. J Med Assoc Thai 2013,96(10),1365-1373Li Y.; Lupo J.M.; Parvataneni R.; Survival analysis in patients with newly diagnosed glioblastoma using pre- and postradiotherapy MR spectroscopic imaging. Neuro-oncol 2013,15(5),607-617Shankar J.J.S.; Woulfe J.; Silva V.D.; Nguyen T.B.; Evaluation of perfusion CT in grading and prognostication of high-grade gliomas at diagnosis: a pilot study. AJR Am J Roentgenol 2013,200(5)Zinn P.O.; Mahajan B.; Sathyan P.; Radiogenomic mapping of edema/cellular invasion MRI-phenotypes in glioblastoma multiforme. PLoS One 2011,6(10)Matsusue E.; Fink J.R.; Rockhill J.K.; Ogawa T.; Maravilla K.R.; Distinction between glioma progression and post-radiation change by combined physiologic MR imaging. Neuroradiology 2010,52(4),297-306Juan-Albarracín J.; Fuster-Garcia E.; Manjón J.V.; Automated glioblastoma segmentation based on a multiparametric structured unsupervised classification. PLoS One 2015,10(5)Itakura H.; Achrol A.S.; Mitchell L.A.; Magnetic resonance image features identify glioblastoma phenotypic subtypes with distinct molecular pathway activities. Sci Transl Med 2015,7(303)Ion-Margineanu A.; Van Cauter S.; Sima D.M.; Tumour relapse prediction using multiparametric MR data recorded during follow-up of GBM patients. BioMed Res Int 2015,2015Durst C.R.; Raghavan P.; Shaffrey M.E.; Multimodal MR imaging model to predict tumor infiltration in patients with gliomas. Neuroradiology 2014,56(2),107-115Yoon J.H.; Kim J.H.; Kang W.J.; Grading of cerebral glioma with multi-parametric MR Imaging and 18F-FDG-PET: concordance and accuracy. European Radiol 2014,24(2),380-389Demerath T.; Simon-Gabriel C.P.; Kellner E.; Mesoscopic imaging of glioblastomas: are diffusion, perfusion and spectroscopic measures influenced by the radiogenetic phenotype? Neuroradiol J 2017,30(1),36-47Qin L.; Li X.; Stroiney A.; Advanced MRI assessment to predict benefit of anti-programmed cell death 1 protein immunotherapy response in patients with recurrent glioblastoma. Neuroradiology 2017,59(2),135-145Boult J.K.R.; Borri M.; Jury A.; Investigating intracranial tumour growth patterns with multiparametric MRI incorporating Gd-DTPA and USPIO-enhanced imaging. NMR Biomed 2016,29(11),1608-1617Server A.; Kulle B.; Gadmar Ø.B.; Josefsen R.; Kumar T.; Nakstad P.H.; Measurements of diagnostic examination performance using quantitative apparent diffusion coefficient and proton MR spectroscopic imaging in the preoperative evaluation of tumor grade in cerebral gliomas. Eur J Radiol 2011,80(2),462-470Chang P.D.; Chow D.S.; Yang P.H.; Filippi C.G.; Lignelli A.; Predicting glioblastoma recurrence by early changes in the apparent diffusion coefficient value and signal intensity on FLAIR images. AJR Am J Roentgenol 2017,208(1),57-65Yi C.; Shangjie R.; Volume of high-risk intratumoralsubregions at multi-parametric MR imaging predicts overall survival and complements molecular analysis of glioblastoma. Eur Radiol 2017,27,3583-3592Khalifa J.; Tensaouti F.; Chaltiel L.; Identification of a candidate biomarker from perfusion MRI to anticipate glioblastoma progression after chemoradiation. Eur Radiol 2016,26(11),4194-4203Prateek P.; Jay P.; Partovi S.; Madabhushi A.; Tiwari P.; Radiomic features from the peritumoral brain parenchyma on treatment-naïve multi-parametric MR imaging predict long versus short-term survival in glioblastomamultiforme: preliminary findings. Eur Radiol 2017,27(10),4188-4197Lemasson B.; Chenevert T.L.; Lawrence T.S.; Impact of perfusion map analysis on early survival prediction accuracy in glioma patients. Transl Oncol 2013,6(6),766-774Inano R.; Oishi N.; Kunieda T.; Visualization of heterogeneity and regional grading of gliomas by multiple features using magnetic resonance-based clustered images. Sci Rep 2016,6,30344Delgado-Goñi T.; Ortega-Martorell S.; Ciezka M.; MRSI-based molecular imaging of therapy response to temozolomide in preclinical glioblastoma using source analysis. NMR Biomed 2016,29(6),732-743Cui Y.; Tha K.K.; Terasaka S.; Prognostic imaging biomarkers in glioblastoma: development and independent validation on the basis of multiregion and quantitative analysis of MR images. Radiology 2016,278(2),546-553Price S.J.; Young A.M.H.; Scotton W.J.; Multimodal MRI can identify perfusion and metabolic changes in the invasive margin of glioblastomas. J Magn Reson Imaging 2016,43(2),487-494Sauwen N.; Acou M.; Van Cauter S.; Comparison of unsupervised classification methods for brain tumor segmentation using multi-parametric MRI. Neuroimage Clin 2016,12,753-764Jena A.; Taneja S.; Gambhir A.; Glioma recurrence versus radiation necrosis: single-session multiparametric approach using simultaneous O-(2-18F-Fluoroethyl)-L-Tyrosine PET/MRI. Clin Nucl Med 2016,41(5),e228-e236Kim H.S.; Goh M.J.; Kim N.; Choi C.G.; Kim S.J.; Kim J.H.; Which combination of MR imaging modalities is best for predicting recurrent glioblastoma? Study of diagnostic accuracy and reproducibility. Radiology 2014,273(3),831-843Christoforidis G.A.; Yang M.; Abduljalil A.; “Tumoral pseudoblush” identified within gliomas at high-spatial-resolution ultrahigh-field-strength gradient-echo MR imaging corresponds to microvascularity at stereotactic biopsy. Radiology 2012,264(1),210-217Wang S.; Kim S.; Chawla S.; Differentiation between glioblastomas, solitary brain metastases, and primary cerebral lymphomas using diffusion tensor and dynamic susceptibility contrast-enhanced MR imaging. AJNR Am J Neuroradiol 2011,32(3),507-514Hanahan D.; Weinberg R.A.; Hallmarks of cancer: the next generation. Cell 2011,144(5),646-674Macdonald D.R.; Cascino T.L.; Schold S.C.; Cairncross J.G.; Response criteria for phase II studies of supratentorial malignant glioma. J Clin Oncol 1990,8(7),1277-1280Wen P.Y.; Macdonald D.R.; Reardon D.A.; Updated response assessment criteria for high-grade gliomas: response assessment in neuro-oncology working group. J Clin Oncol 2010,28(11),1963-1972Sorensen A.G.; Batchelor T.T.; Wen P.Y.; Zhang W-T.; Jain R.K.; Response criteria for glioma. Nat Clin Pract Oncol 2008,5(11),634-644Rosenkrantz A.B.; Friedman K.; Chandarana H.; Current status of hybrid PET/MRI in oncologic imaging. AJR Am J Roentgenol 2016,206(1),162-172Castiglioni I.; Gallivanone F.; Canevari C.; Hybrid PET/MRI for In vivo imaging of cancer: current clinical experiences and recent advances. Curr Med Imaging 2016,12,106Mainta I.C.; Perani D.; Delattre B.M.A.; FDG PET/MR imaging in major neurocognitive disorders. Curr Alzheimer Res 2017,14,186-197Marner L.; Henriksen O.M.; Lundemann M.; Larsen V.A.; Law I.; Clinical PET/MRI in neurooncology: opportunities and challenges from a single-institution perspective. Clin Transl Imaging 2017,5(2),135-149R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria; 2015. Available from: https://www.R-project.org
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
Use of GIS as a supporting tool for environmental risk assessment and emergency response plans
Although occurrence of disasters cannot be prevented completely, it is possible to minimize their hazards by taking precautions and applying effective emergency response plans. In addition to measures taken to reduce economical and human losses, an environmental dimension is required in these plans to control environmental pollution and lessen possible adverse effects on both ecosystems and human health, which in the long term may cost much more than direct disaster losses. Technological accidents triggered by natural disasters are one of the most important factors increasing the environmental damage. Therefore, it is of utmost importance to prepare regional plans considering both natural and technological disasters and aiming the coordination and resource sharing between the related authorities, institutions and factories. Geographical Information Systems (GIS) are powerful tools having comprehensive data query, analysis, and visualization capabilities, and they may facilitate preparation of such emergency plans. In this paper, the role of GIS in emergency response plans is explained. A case study from Turkey utilizing GIS extensively for regional environmental emergency planning is given and problems that can be faced in developing countries are discussed