In the Central African Republic (CAR), poultry production primarily relies on indigenous chicken (Gallus gallus domesticus) as a raw genetic resource that has never been characterised despite its great genetic and economic potential in rural and periurban areas. The present study assessed the genetic diversity of native chicken in CAR using 16 microsatellite markers. Blood samples were randomly collected on FTA filter cards from 205 adult native chickens from two agroecological zones out of four in CAR, including 102 from the forest and 103 from the savannah. Sixteen microsatellite markers could amplify, giving a coverage rate of 61.54% of the SSR panel used. A low but positive Fis mean value (0.16) suggested a low inbreeding and a weak reduction in Heterozygosity of individuals due to non-random mating within each population. Overall genetic diversity (0.54), Heterozygosity (0.45) and allele frequency (0.61) confirmed a moderate to high genetic variation within the CAR indigenous chicken population. The molecular variance was more significant within individuals (81%) than among individuals (16%) and between populations (3%). Evanno’s method shows that the likely number of sub-populations is 2 as influenced by the agroecological zone while Structure showed admixture between the two populationsdespite the low observed inbreeding. These results suggest a weak structuring of the CAR native chicken population and great possibilities for selection and genetic improvement. However, SSR markers are neutral and further studies need to be done using functional markers to detect functional and productivity genes relevant to disease resistance, environmental resilience and production traits. En République Centrafricaine (RCA), la production avicole repose principalement sur la poule locale dite indigène (Gallus gallus domesticus). Cette ressource n’a jamais été génétiquement caractérisée malgré l’énorme potentiel économique découlant de son exploitation en milieu rural et périurbain. Cette étude avait pour but d’évaluer la diversité génétique de la poule locale en RCA par génotypage à l’aide de 16 marqueurs microsatellites. Des échantillons de sang ont été prélevés au hasard sur 205 sujets adultes provenant de deux des quatre zones agroécologiques de RCA, dont 102 en zone forestière et 103 en savane. Les résultats ont révélé que 16 marqueurs microsatellites ont été amplifiés avec un taux d’amplification de 61,54 % des marqueurs recommandés pour l’espèce poule. La valeur moyenne du Fis a été faible et positive (0,16) suggérant une faible consanguinité et une faible réduction de l’hétérozygotie. La diversité génétique globale (0,54), l’hétérozygotie moyen (0,45) et la fréquence allélique élevée (0,61) ont confirmé une variabilité génétique modérée à élevée au sein de la population de poule locale de la RCA. La variance moléculaire au sein de l’individu a été très élevée (81 %) qu’entre individus (16 %) et entre populations (3 %). La méthode d’Evanno montre que le nombre probable de sous-populations est de 2, tandis que la structure génétique a confirmé un brassage de deux sous populations et une faible consanguinité observée. Ces résultats suggèrent une faible structuration de la population de poules originaires de RCA et une possibilité de sélection et d’amélioration génétique. Cependant, les microsatellites étant des marqueurs neutres, des études supplémentaires doivent être réalisées à l’aide des marqueurs fonctionnels pour détecter les gènes utiles en vue de l’amélioration des performances de production et d’adaptabilité .

Theileria annulata, which causes tropical theileriosis, is a major impediment to improving cattle production in Sudan. Tropical theileriosis disease is prevalent in the north and central regions of Sudan. Outbreaks of the disease have been observed outside the known endemic areas, in east and west regions of the country, due to changes in tick vector distribution and animal movement. A live schizont attenuated vaccination based on tissue culture technology has been developed to control the disease. The parasite in the field as well as the vaccine strain need to be genotyped before the vaccinations are practiced, in order to be able to monitor any breakthrough or breakdown, if any, after the deployment of the vaccine in the field. Nine microsatellite markers were used to genotype 246 field samples positive for T. annulata DNA and the vaccine strain. North and central populations have a higher multiplicity of infection than east and west populations. The examination of principal components showed two sub-structures with a mix of all four populations in both clusters and the vaccine strain used being aligned with left-lower cluster. Only the north population was in linkage equilibrium, while the other populations were in linkage disequilibrium, and linkage equilibrium was found when all samples were regarded as single population. The genetic identity of the vaccine and field samples was 0.62 with the north population and 0.39 with west population. Overall, genetic investigations of four T. annulata populations in Sudan revealed substantial intermixing, with only two groups exhibiting regional origin independence. In the four geographically distant regions analyzed, there was a high level of genetic variation within each population. The findings show that the live schizont attenuated vaccine, Atbara strain may be acceptable for use in all Sudanese regions where tropical theileriosis occurs.

The live infection and treatment (ITM) vaccination procedure using the trivalent Muguga cocktail is increasingly being used to control East Coast fever, with potential implications for Theileria parva population genetic structure in the field. Transmission of the Kiambu V T. parva component to unvaccinated cattle has previously been described in Uganda. We monitored the T. parva carrier state in vaccinated and control animals on a farm in West Kenya where an ITM stabilate derived from the Kenyan T. parva Marikebuni stock was evaluated for field efficacy. A nested PCR-based Marikebuni-specific marker identified a carrier state in nine of ten vaccinated animals, detectable for a period of two years. We used 22 variable number tandem repeat (VNTR) markers to determine multilocus genotypes (MLGs) of 19 T. parva schizont-infected lymphocyte isolates derived from cattle and field ticks. Two isolates from unimmunized cattle were identical to the Marikebuni vaccination stock. Two cattle isolates were identical to a Muguga cocktail component Kiambu V. Seven isolates from ticks exhibited MLGs that were identical to the Serengeti/Muguga vaccine stocks. Six cattle and two tick-derived stocks exhibited unique MLGs. The data strongly suggest transmission of immunizing genotypes, from Marikebuni vaccine-induced carrier cattle to unimmunized cattle. It is possible that genotypes similar to those in the Muguga cocktail are present in the field in Western Kenya. An alternative hypothesis is that these parasites may have originated from vaccine trial sites in Eastern Uganda. If correct, this suggests that T. parva stocks used for immunization can potentially be disseminated 125 km beyond the immediate vaccination site. Regardless of their origin, the data provide evidence that genotypes similar to those in the Muguga cocktail are circulating in the field in East Africa, alleviating concerns about dissemination of 'alien' T. parva germplasm through live vaccination.

An extensive knowledge of a system's failures is crucial for identifying areas where the reliability of the system can benefit from improvements, as well as informing the design of new systems. Moreover, relationships between faults and failures can be used to enhance the maintenance of the system. In this paper we present a taxonomy of failure modes of the Joint European Torus (JET) Remote Handling System (RHS). This system is used during maintenance and enhancements of in-vessel systems, and consists of two transporters (articulated booms) and a two-armed manipulator, along with a number of supporting systems. In this work we first present a failure taxonomy suitable for our specific system, and then we use a clustering approach to introduce example failure modes into the taxonomy. The presented failures have been collected during commissioning and operations over a period of over 5 years. Cataloged failures are extracted from the logs produced by the control system and from the daily log books recorded by the system operator.

International students have faced unique challenges during the COVID-19 Pandemic. This essay shares three stories from African women doctoral students who are scholarship recipients under the Regional Scholarship and Innovation Fund. They are conducting cutting-edge research in Science, Technology, Engineering, and Mathematics (STEM) towards their PhD degrees and have found themselves in a foreign land during the pandemic. Their stories illustrate the pandemic's impacts on their personal lives and research productivity and their immense resilience in the face of challenges brought on by the pandemic.

This paper presents results of JET ITER-like wall L-mode experiments in hydrogen and deuterium (D) plasmas, dedicated to the study of the isotope dependence of ion heat transport by determination of the ion critical gradient and stiffness by varying the ion cyclotron resonance heating power deposition. When no strong role of fast ions in the plasma core is expected, the main difference between the two isotope plasmas is determined by the plasma edge and the core behavior is consistent with a gyro-Bohm scaling. When the heating power (and the fast ion pressure) is increased, in addition to the difference in the edge region, also the plasma core shows substantial changes. The stabilization of ion heat transport by fast ions, clearly visible in D plasmas, appears to be weaker in H plasmas, resulting in a higher ion heat flux in H with apparent anti-gyro-Bohm mass scaling. The difference is found to be caused by the different fast ion pressure between H and D plasmas, related to the heating power settings and to the different fast ion slowing down time, and is completely accounted for in non-linear gyrokinetic simulations. The application of the TGLF quasi-linear model to this set of data is also discussed.

The present paper offers an overview of the potential of ion cyclotron resonance heating (ICRH) or radio frequency heating for the DEMO machine. It is found that various suitable heating schemes are available. Similar to ITER and in view of the limited bandwidth of about 10 MHz that can be achieved to ensure optimal functioning of the launcher, it is proposed to make core second harmonic tritium heating the key ion heating scheme, assisted by fundamental cyclotron heating He-3 in the early phase of the discharge; for the present design of DEMO-with a static magnetic field strength of B-o = 5.855 T-that places the T and 3He layers in the core for f = 60 MHz and suggests centering the bandwidth around that main operating frequency. In line with earlier studies for hot, dense plasmas in large-size magnetic confinement machines, it is shown that good single pass absorption is achieved but that the size as well as the operating density and temperature of the machine cause the electrons to absorb a non-negligible fraction of the power away from the core when core ion heating is aimed at. Current drive and alternative heating options are briefly discussed and a dedicated computation is done for the traveling wave antenna, proposed for DEMO in view of its compatibility with substantial antenna-plasma distances. The various tasks that ICRH can fulfill are briefly listed. Finally, the impact of transport and the sensitivity of the obtained results to changes in the machine parameters is commented on.

The need for predictive capabilities greater than 95% with very limited false alarms are demanding requirements for reliable disruption prediction systems in tokamaks such as JET or, in the near future, ITER.The prediction of an upcoming disruption must be provided sufficiently in advance in order to apply effective disruption avoidance or mitigation actions to prevent the machine from being damaged.In this paper, following the typical machine learning workflow, a generative topographic mapping (GTM) of the operational space of JET has been built using a set of disrupted and regularly terminated discharges.In order to build the predictive model, a suitable set of dimensionless, machine-independent, physics-based features have been synthesized, which make use of 1D plasma profile information, rather than simple zero-D time series.The use of such predicting features, together with the power of the GTM in fitting the model to the data, obtains, in an unsupervised way, a 2D map of the multi-dimensional parameter space of JET, where it is possible to identify a boundary separating the region free from disruption from the disruption region.In addition to helping in operational boundaries studies, the GTM map can also be used for disruption prediction exploiting the potential of the developed GTM toolbox to monitor the discharge dynamics.Following the trajectory of a discharge on the map throughout the different regions, an alarm is triggered depending on the disruption risk of these regions.The proposed approach to predict disruptions has been evaluated on a training and an independent test set and achieves very good performance with only one tardive detection and a limited number of false detections.The warning times are suitable for avoidance purposes and, more important, the detections are consistent with physical causes and mechanisms that destabilize the plasma leading to disruptions.

Malignant theileriosis of sheep and goats caused by Theileria lestoquardi is considered to be among the most important tick borne diseases in the Sudan. Information on the prevalence of the disease in different parts of the Sudan is limited. The purpose of this study was to estimate the prevalence of the disease in five states of the Sudan using molecular and serological assays. A total of 393 blood and serum samples from clinically asymptomatic sheep were analysed using nested reverse line blot (nRLB) and loop mediated isothermal amplification (LAMP), as well as an enzyme-linked immunosorbent assay (ELISA). The results indicated a sero-prevalence of 33.8% while RLB and LAMP assays revealed molecular prevalences of 29.5 and 22.6% respectively. The prevalence of Theileria lestoquardi varied significantly according to the geographical origin of the infected animals, whereas age and gender did not have a significant effect. RLB data indicated that T. lestoquardi usually occurred as a co-infection with the non-pathogenic Theileria ovis. Using RLB as a gold standard, a sensitivity of 68.1% and a specificity of 96.4% were recorded for LAMP and a sensitivity of 75.9% and a specificity of 83.8% for ELISA. The Kappa coefficient between nRLB and LAMP indicated a significant level of agreement (0.692), but only moderate concordance (0.572) between nRLB and ELISA. The results of the present study confirm and extend earlier findings regarding the widespread of T. lestoquardi infections in sheep in the Sudan. The data provide evidence that should enable the veterinary authorities to deploy appropriate control measures.

The First Mirror Test for ITER has been carried out in JET with mirrors exposed during: (i) the third ILW campaign (ILW-3, 2015-2016, 23.33 h plasma) and (ii) all three campaigns, i.e. ILW-1 to ILW-3: 2011-2016, 63,52 h in total. All mirrors from main chamber wall show no significant changes of the total reflectivity from the initial value and the diffuse reflectivity does not exceed 3% in the spectral range above 500 nm. The modified layer on surface has very small amount of impurities such as D, Be, C, N, O and Ni. All mirrors from the divertor (inner, outer, base under the bulk W tile) lost reflectivity by 20-80% due to the beryllium-rich deposition also containing D, C, N, O, Ni and W. In the inner divertor N reaches 5 x 10(17) cm(-2), W is up to 4.3 x 10(17) cm(-2), while the content of Ni is the greatest in the outer divertor: 3.8 x 10(17) cm(-2). Oxygen-18 used as the tracer in experiments at the end of ILW-3 has been detected at the level of 1.1 x 10(16) cm(-2). The thickness of deposited layer is in the range of 90 nm to 900 nm. The layer growth rate in the base (2.7 pm s(-1)) and inner divertor is proportional to the exposure time when a single campaign and all three are compared. In a few cases, on mirrors located at the cassette mouth, flaking of deposits and erosion occurred.

The analysis of the polarimetry measurements has the aim of validating models (De Marco and Segre 1972 Plasma Phys. 14 245), with a careful attention to the clarification of their limits of application. In this paper a new approximation method is introduced, the so-called special constant Omega direction (SCOD), which gives an analytical solution to the polarimetry exact Stokes model equations. The available approximate solutions (including SCOD) of the polarimetry propagation equations are presented, compared and their application limits determined, using a reference tokamak configuration, which is a simplified equilibrium for a circular tokamak. The SCOD approximation is compared successfully to the Stokes model in the context also of equilibria evaluated for two JET discharges. The approximation methods are analytical or very simple mathematical expressions which can also be used in equilibrium codes for their optimization.

The morphological diversity of African ticks of the genus Rhipicephalus and subgenus Boophilus have been studied in detail. However, their taxonomy remains poorly resolved with limited molecular studies performed to improve inter-species discrimination. Herein, ribosomal cytochrome c oxidase I (COI), 12S ribosomal DNA (12S rDNA) and nuclear ribosomal DNA internal transcriber spacer 2 (ITS2) were analyzed in Rhipicephalus tick populations in Kenya. While the morphological and molecular criteria separated R. e. evertsi, R. pulchellus and R. appendiculatus from other members of the genus, except the morphologically similar sibling species R. zambeziensis, this was not the case for other tick populations. COI sequences of Rhipicephalus ticks from Ruma National Park (RNP) in Southwestern Kenya, that were morphologically similar to R. praetextatus/R. simus, a formed distinct clade and barcode gap group. 12S rDNA haplotypes of this population were 99% identical to a GenBank accession of R. muhsamae which is thought to be endemic in West and Central Africa. However, the ITS2 locus indicated that the RNP samples were genetically closest to ticks identified morphologically as R. praetextatus. The COI and 12S rDNA haplotype sequences of R. praetextatus clustered closely with R. simus reference sequences though the two species occurred in distinct barcode gap groups. Our results suggest that the R. simus/R. praetextatus/R. muhsamae comprise a closely related tick species complex found across sub-Saharan Africa and includes the yet to be described RNP population. More studies on the biology, ecology and genomics of all life stages of tick species in the complex may clarify their taxonomic status. A continent-wide study that combines morphology, DNA marker sequencing and emerging methods, such as mass spectrometry and whole-genome resequencing may reveal the diversity and distribution of taxa within the genus Rhipicephalus in sub-Saharan Africa.

This paper outlines an approach towards improved rigour in tokamak turbulence transport model validation within integrated modelling. Gaussian process regression (GPR) techniques were applied for profile fitting during the preparation of integrated modelling simulations allowing for rigourous sensitivity tests of prescribed initial and boundary conditions as both fit and derivative uncertainties are provided. This was demonstrated by a JETTO integrated modelling simulation of the JET ITER-like-wall H-mode baseline discharge #92436 with the QuaLiKiz quasilinear turbulent transport model, which is the subject of extrapolation towards a deuterium-tritium plasma. The simulation simultaneously evaluates the time evolution of heat, particle, and momentum fluxes over similar to 10 confinement times, with a simulation boundary condition at rho(tor) = 0.85. Routine inclusion of momentum transport prediction in multi-channel flux-driven transport modelling is not standard and is facilitated here by recent developments within the QuaLiKiz model. Excellent agreement was achieved between the fitted and simulated profiles for n(e), T-e, T-i, and Omega(tor) within 2 sigma, but the simulation underpredicts the mid-radius Ti and overpredicts the core n(e) and T-e profiles for this discharge. Despite this, it was shown that this approach is capable of deriving reasonable inputs, including derivative quantities, to tokamak models from experimental data. Furthermore, multiple figures-of-merit were defined to quantitatively assess the agreement of integrated modelling predictions to experimental data within the GPR profile fitting framework.

Mountain bongo (Tragelaphus euryceros isaaci) from Kenya were exported to zoological institutions in North America and Europe in the 1970s and 1980s. In the following 20-30 years bongo numbers declined in Kenya and the Mountain Bongo Repatriation Project was launched. This resulted in 18 adult bongo, descendants of the original translocated bongo, being repatriated from the United States to Kenya in 2004. These newly arrived bongo were inadvertently exposed to heavy tick infestation on release in a conservancy on the slopes of Mount Kenya. Mortality and morbidity occurred during the third week after arrival. Theileria sp. infection was apparent from the history, clinical signs, and necropsy findings, and Theileria-like parasites were detected microscopically in samples from sick and dead animals. Four bongo died before the outbreak was controlled. In order to identify the Theileria parasite conclusively, molecular amplification techniques were used. A combination of reverse line blotting, with small subunit ribosomal RNA (SSU rRNA) polymerase chain reaction (PCR) amplification and nucleotide sequencing, identified the protozoan parasite Theileria taurotragi, suggesting this as the most probable cause of mortality and morbidity in the repatriated bongo.

ERO is a 3D Monte-Carlo impurity transport and plasma-surface interaction code. In 2011 it was applied for the ITER first wall (FW) life time predictions [1] (critical blanket module BM11). After that the same code was significantly improved during its application to existing fusion-relevant plasma devices: the tokamak JET equipped with an ITER-like wall and linear plasma device PISCES-B. This has allowed testing the sputtering data for beryllium (Be) and showing that the "ERO-min" fit based on the large (50%) deuterium (D) surface content is well suitable for plasma-wetted areas (D plasma). The improved procedure for calculating of the effective sputtering yields for each location along the plasma-facing surface using the recently developed semi-analytical sheath approach was validated. The re-evaluation of the effective yields for BM11 following the similar revisit of the JET data has indicated significant increase of erosion and motivated the current re-visit of ERO simulations.

Measurements of neutron streaming through penetrations in biological shields are being carried out at JET fusion device by means of thermoluminescence (TL) detectors with the objective to validate the neutronics codes and nuclear data widely applied in ITER nuclear analyses in a real fusion environment. TLDs response due to the neutron component of the radiation field is related to the neutron fluence in a well-defined neutron energy spectrum. Therefore, a TLDs calibration in real fusion radiation fields is necessary to allow neutron fluence from TL measurements at JET to be more precisely calculated. Hence, a MCP-N and MCP-7 TLDs produced at the IFJ PAN in Kraków were calibrated at the ENEA facilities of Frascati and Casaccia laboratories. The obtained results have been analysed and new calibration factors are proposed. The detection system based on TLDs developed and calibrated for JET experiments can then be generally applied not only to fusion neutron fields, but also to ITER to monitor the neutron fluence outside the biological shield.

Experimental observations in JET tokamak plasmas and gyrokinetic simulations point to an important role, for electron heat transport, of electron-scale instabilities and of their interaction with ion-scale instabilities. Since these effects are maximized for strong electron heating and ion-scale modes close to marginal stability, these findings are of high relevance for ITER plasmas, featuring both conditions. Gyrokinetic and quasi-linear transport models accounting for multi-scale effects are assessed against JET experimental results.

HomePlant DiseaseVol. 103, No. 1First Report of East African Cassava Mosaic Virus-Uganda Infecting the Nile Tulip Tree in Western Kenya PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of East African Cassava Mosaic Virus-Uganda Infecting the Nile Tulip Tree in Western KenyaM. Kyallo, E. M. Ateka, J. Ndunguru, M. O. Ssemakula, R. A. Skilton, S. M. Kiarie, and P. SseruwagiM. Kyallo†Corresponding author: M. Kyallo; E-mail: E-mail Address: m.kyallo@cgiar.orghttp://orcid.org/0000-0001-9426-8152Search for more papers by this author, E. M. AtekaSearch for more papers by this author, J. NdunguruSearch for more papers by this author, M. O. SsemakulaSearch for more papers by this author, R. A. SkiltonSearch for more papers by this author, S. M. KiarieSearch for more papers by this author, and P. SseruwagiSearch for more papers by this authorAffiliationsAuthors and Affiliations M. Kyallo † , Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya E. M. Ateka , Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya J. Ndunguru , Mikocheni Agricultural Research Institute, Eastern Zone, Dar es Salaam, Tanzania M. O. Ssemakula , School of Agricultural Sciences, Makerere University, Kampala, Uganda R. A. Skilton , International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya S. M. Kiarie , Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya P. Sseruwagi , Mikocheni Agricultural Research Institute, Eastern Zone, Dar es Salaam, Tanzania. Published Online:29 Oct 2018https://doi.org/10.1094/PDIS-07-18-1133-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Whitefly-transmitted cassava mosaic begomoviruses (CMBs; family Geminiviridae; genus Begomovirus) are viruses with bipartite genomes (components referred to as DNA-A and DNA-B) containing a conserved (between the two components) noncoding sequence known as the common region (CR) required for DNA replication and transcription (Fondong 2013). CMBs cause cassava mosaic disease (CMD), a major limitation to cassava production in sub-Saharan Africa. In Kenya, CMD is associated with the begomoviruses East African cassava mosaic virus (EACMV), African cassava mosaic virus (ACMV), East African cassava mosaic Kenya virus, and East African cassava mosaic Zanzibar virus, as well as several recombinant viruses, such as the virulent EACMV-Uganda (EACMV-UG) that so far occurs only in western Kenya (Nyongesa Were et al. 2016). Within the CMB-cassava pathosystem, various noncassava plant species may play an epidemiological role as virus reservoirs for the whitefly vector Bemisia tabaci (Alabi et al. 2008). In May 2017, leaf samples were collected from three plants exhibiting virus-like symptoms including mosaic, mottling, twisted leaves, and reduction in leaf surface area as well as from two nonsymptomatic plants belonging to the family Bignoniaceae growing in three cassava fields in western Kenya. Total genomic DNA was extracted from leaf samples using the ZR Plant/Seed DNA MiniPrep kit as per the manufacturer’s instructions (Zymo Research Corp., U.S.A.). The identity of the plant species was confirmed as Markhamia lutea by phenotypic characteristics and by polymerase chain reaction (PCR) amplification, Sanger sequencing, and BLASTn analysis of the chloroplast rubisco large-chain gene using the primer pair RbcLa-F (5′-ATGTCACCACAAACAGAGACTAAAGC-3′)/RbcLa-R (5′-GTAAAATCAAGTCCACCRCG-3′). Samples were screened by PCR with the diagnostic primer pairs JSP001/JSP002 for ACMV, JSP001/JSP003 for EACMV (Fondong et al. 2000), and UV AL1-F1/ACMV CP-R3 for EACMV-UG (Zhou et al. 1997). Samples from nonsymptomatic plants did not yield amplification products, confirming absence of viral infection. A 1,650-bp fragment of the expected size was amplified from one symptomatic sample with the primer pair UV AL1-F1/ACMV CP-R3, suggesting the presence of EACMV-UG. To confirm the positive PCR result, the genome of the virus was enriched by rolling-circle amplification (RCA) using a TempliPhi 100 RCA Kit (GE Healthcare, U.S.A.). The library was prepared using the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, U.S.A.) according to the manufacturer’s instructions and sequenced using an Illumina MiSeq platform with the MiSeq Reagent Kit version 3 (600 cycles) (Illumina, U.S.A.). Following de novo sequence assembly, 344 and 89 paired-end reads aligned to generate two contigs identified by BLASTn search as the DNA-A and DNA-B of a bipartite virus. The nucleotide sequences were deposited in GenBank as accession numbers MF974568 and MH379641. The 2,798-nucleotide (nt) DNA-A and 2,774-nt DNA-B had an approximately 160-nt EACMV-like CR with 53%-nt sequence identity. DNA-A shared 99% nucleotide sequence identity with the DNA-A of an EACMV-UG isolate (AJ717522) from western Kenya, whereas the DNA-B was closely related to another EACMV-UG isolate (AJ704962) from western Kenya at 97% nucleotide sequence identity. To the best of our knowledge, this is the first report of occurrence of EACMV-UG in a species of the family Bignoniaceae. Further investigations are required to determine the epidemiological significance of M. lutea in the CMB-cassava pathosystem.References:Alabi, O. J., et al. 2008. Arch. Virol. 153:1743. https://doi.org/10.1007/s00705-008-0169-8 Crossref, ISI, Google ScholarFondong, V. N. 2013. Mol. Plant Pathol. 14:635. https://doi.org/10.1111/mpp.12032 Crossref, ISI, Google ScholarFondong, V. N., et al. 2000. J. Gen. Virol. 81:287. https://doi.org/10.1099/0022-1317-81-1-287 Crossref, ISI, Google ScholarNyongesa Were, M., et al. 2016. Plant 4:108. https://doi.org/10.11648/j.plant.20160406.18 Crossref, Google ScholarZhou, X., et al. 1997. J. Gen. Virol. 78:2101. https://doi.org/10.1099/0022-1317-78-8-2101 Crossref, ISI, Google ScholarFunding: Funding was provided by the Bill and Melinda Gates Foundation (grant no. OPP1052391). Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.DetailsFiguresLiterature CitedRelated Vol. 103, No. 1 January 2019SubscribeISSN:0191-2917e-ISSN:1943-7692 Metrics Article History Issue Date: 4 Jan 2019Published: 29 Oct 2018First Look: 26 Jul 2018Accepted: 24 Jul 2018 Page: 164 InformationCopyright © 2018 The Author(s).This is an open access article distributed under the CC BY 4.0 International license.FundingBill and Melinda Gates FoundationGrant/Award Number: OPP1052391Cited byEast African cassava mosaic virusCABI Compendium, Vol. CABI Compendium

This paper presents the first application to real JET data of the new equilibrium code NICE which enables the consistent resolution of the inverse equilibrium reconstruction problem in the framework of non-linear free-boundary equilibrium coupled to the Stokes model equation for polarimetry. The conducted numerical experiments enable first of all to validate NICE by comparing it to the well-established EFIT code on 4 selected high performance shots. Secondly the results indicate that the fit to polarimetry measurements clearly benefits from the use of Stokes vector measurements compared to the classical case of Faraday measurements, and that the reconstructed p' and ff' profiles are better constrained with smaller error bars and are closer to the profiles reconstructed by EFTM, the EFIT JET code using internal MSE constraints.

Plasma tomography consists of reconstructing a two-dimensional radiation profile of a poloidal cross section of a fusion device based on line-integrated measurements along several lines of sight. The reconstruction process is computationally intensive, and in practice, only a few reconstructions are usually computed per pulse. In this work, we trained a deep neural network based on a large collection of sample tomograms that have been produced at JET over several years. Once trained, the network is able to reproduce those results with high accuracy. More importantly, it can compute all the tomographic reconstructions for a given pulse in just a few seconds. This makes it possible to visualize several phenomena—such as plasma heating, disruptions, and impurity transport—over the course of the entire pulse.