The draft genome sequence of Xanthomonas species strain Nyagatare, isolated from diseased bean in Rwanda.

types: Journal ArticleThis is a pre-copyedited, author-produced PDF of an article accepted for publication in FEMS following peer review. The version of record Aritua, V., Musoni, A., Kabeja, A., Butare, L., Mukamuhirwa, F., Gahakwa, D., . . . Smith, J. (2015). The draft genome sequence of Xanthomonas species strain Nyagatare, isolated from diseased bean in Rwanda, FEMS Microbiology Letters, 2015, Vol. 362, No. 4 pp. 1-4 is available online at: http://femsle.oxfordjournals.org/content/362/4/1.1.exploreWe announce the genome sequence for Xanthomonas species strain Nyagatare, isolated from beans showing unusual disease symptoms in Rwanda. This strain represents the first sequenced genome belonging to an as-yet undescribed Xanthomonas species known as species-level clade 1. It has at least 100 kb of genomic sequence that shows little or no sequence similarity to other xanthomonads, including a unique lipopolysaccharide synthesis gene cluster. At least one genomic region appears to have been acquired from relatives of Agrobacterium or Rhizobium species. The genome encodes homologues of only three known type-three secretion system effectors: AvrBs2, XopF1 and AvrXv4. Availability of the genome sequence will facilitate development of molecular tools for detection and diagnostics for this newly discovered pathogen of beans and facilitate epidemiological investigations of a potential causal link between this pathogen and the disease outbreak.Canadian International Development AgencyBBSRC SCPRI

Rwanda Nutrition, Markets and Gender Analysis 2015: An integrated approach towards alleviating malnutrition among vulnerable populations in Rwanda

The Nutrition, Markets and Gender (NMG) Survey was conducted in Rwanda to investigate the causes of malnutrition in children under 24 months. The NMG Survey was informed by the 2010 Demographic Health Survey (DHS) for Rwanda that gave some insight into the knowledge and trend of malnutrition in the country for the period 2005 to 2010. The DHS results indicated a 6 percent decline in stunting among children under the age of five years. The key findings from the 2014/2015 DHS that followed the same delineation as the DHS 2010 provided the most current status of malnutrition in Rwanda and showed further overall improvements in child growth outcomes with 37.9 percent of children under five years classified as stunted. These results again indicated a 6.3 percent decline in stunting among children under the age of five years for the period 2010 to 2015. This progressive trend is a testament to the country’s commitments to prioritise nutrition issues and nutrition programmes in its development agenda. The Government of Rwanda, through the Ministry of Health, has prioritised malaria control, nutrition education, and better public healthcare. However, in spite of the advancements made, the consensus is that high rates of chronic malnutrition among children still prevail. Thus a better understanding of risk factors that contribute to child malnutrition at the household level in Rwanda was needed to strengthen the fight against malnutrition in the country. The ‘Comprehensive Food Security and Vulnerability and Nutrition Analysis’ – CFSVA 2012 – report produced by the Ministry of Agriculture and Animal Resources (MINAGRI), the National Institute of Statistics of Rwanda (NISR) and the World Food Programme (WFP) acknowledged that vulnerable households are increasingly reliant on markets as a source of food; providing on average 65 percent of the food consumed by a household. It is therefore clear that household nutrition outcomes in such households are dependent on markets. In addition, it is widely accepted that gender dynamics influence decision-making in the household. Thus gender dynamics affect decisions related to food, care, markets, and health. Therefore this survey focused on nutrition, markets, and gender to determine the factors that influence the nutrition status of children under 24 months. Moreover, a disconnect between agricultural production and nutrition outcomes was revealed in the CFSVA 2012 report that indicated that the northern agricultural zones, considered the bread basket of the country, had stunting rates of up to 66 percent in children under 60 months

Pattern and clinical management of penile cancer in Rwanda

Introduction: Penile cancer is rare in developed countries but has a high prevalence in some developing countries. Surgery includes inguinal lymphadenectomy, which remains the mainstay treatment of the disease.Objective: This study reports on the epidemiological profile of penile cancer and clinical management options in Rwanda. Patients and methods: From January 2015 to June 2016, a multicenter cross-sectional, prospective cohort study was conducted involving all male patients presenting with penile cancer after two national radio campaigns and a Ministry of Health instruction to all district hospitals. All patients with positive biopsy were included. Surgical treatment aligned with published guidelines. Clinical characteristics, surgery, pathology, and early follow-up data were collected.Results: Over 18 consecutive months, 30 male patients were enrolled. The mean age was 60 years [range 33–83]. All patients were uncircumcised before symptom onset; 50% had phimosis and 20% were HIV- positive. The estimated prevalence of penile cancer in Rwanda was 0.37 per 100,000 men. At presentation, 96.7% of patients had a T2-4 disease and 43.3% were with clinically non-palpable inguinal lymph nodes (cNO). After penectomy, bilateral inguinal lymphadenectomy was performed in 10 (33.3%) patients (modified and radical in 16 and 4 limbs, respectively). Complications included surgical site infection (10%), lymphocele (10%), urethral meatus stenosis (6.7%), skin necrosis (3.3%) and two (6.7%) patients with metastatic disease died in hospital.Conclusion: Penile cancer is a rare but significant disease in Rwanda. Patients present with advanced disease. After treatment of the primary tumor, modified inguinal lymphadenectomy appears to be a safe method of cure and staging for patients with clinically impalpable inguinal lymph nodes. Our early results provide a compelling insight into this rare but serious disease

Visual Assessments of Functional Maps

Shape-matching is one central topic in Geometry Processing, with numerous important applications in Computer Graphics and shape analysis, such as shape registration, shape interpolation, modeling, information transfer and many others. A recent and successful class of shape-matching methods is based on the functional maps framework [OBCS*12] where the correspondences between the two surfaces is described in terms of a mapping between functions. Several effective approaches have been proposed to produce accurate and reliable functional maps, leading to need for a way to assess the quality of a given solution. In particular, standard quantitative evaluation methods focus mainly on the global matching error disregarding the annoying effects of wrong correspondences along the surface details. Therefore, in this context, it is very important to pair quantitative numeric evaluations with a visual, qualitative assessment. Although this is usually not recognized as a problem, the latter task is not trivial, and we argue that the commonly employed solutions suffer from important limitations. In this work, we offer a new visual evaluation method which is based on the transfer of the object-space normals across the two spaces and then visualize the resulting lighting. In spite of its simplicity, this method produces readable images that allow subtleties of the mapping to be discerned, and improve direct comparability of alternative results

Visual Assessments of Functional Maps

Shape-matching is one central topic in Geometry Processing, with numerous important applications in Computer Graphics and shape analysis, such as shape registration, shape interpolation, modeling, information transfer and many others. A recent and successful class of shape-matching methods is based on the functional maps framework [OBCS*12] where the correspondences between the two surfaces is described in terms of a mapping between functions. Several effective approaches have been proposed to produce accurate and reliable functional maps, leading to need for a way to assess the quality of a given solution. In particular, standard quantitative evaluation methods focus mainly on the global matching error disregarding the annoying effects of wrong correspondences along the surface details. Therefore, in this context, it is very important to pair quantitative numeric evaluations with a visual, qualitative assessment. Although this is usually not recognized as a problem, the latter task is not trivial, and we argue that the commonly employed solutions suffer from important limitations. In this work, we offer a new visual evaluation method which is based on the transfer of the object-space normals across the two spaces and then visualize the resulting lighting. In spite of its simplicity, this method produces readable images that allow subtleties of the mapping to be discerned, and improve direct comparability of alternative results.Symposium on Geometry Processing 2019- PostersPoster

Bioreactor design and implementation strategies for the cultivation of filamentous fungi and the production of fungal metabolites: from traditional methods to engineered systems

The production of fungal metabolites and conidia at an industrial scale requires an adequate yield at relatively low cost. To this end, many factors are examined and the design of the bioreactor to be used for the selected product takes a predominant place in the analysis. One approach to addressing the issue is to integrate the scaling-up procedure according to the biological characteristics of the microorganism considered, i.e. in our case filamentous fungi. Indeed, the scaling-up procedure is considered as one of the major bottlenecks in fermentation technology, mainly due to the near impossibility of reproducing the ideal conditions obtained in small reactors designed for research purposes when transposing them to a much larger production scale. The present review seeks to make the point regarding the bioreactor design and its implementation for cultivation of filamentous fungi and the production of fungal metabolites according to different developmental stages of fungi of industrial interest. Solid-state (semi-solid), submerged, fermentation and biofilm reactors are analyzed. The different bioreactor designs used for these three processes are also described at the technological level

CMH: Coordinates Manifold Harmonics for Functional Remeshing

In digital world reconstruction, 2-dimensional surface of real objects are often obtained as polygonal meshes after an acquisition procedure using 3D sensors. However, such representation requires several manual efforts from highly experts to correct the irregularity of tessellation and make it suitable for professional applications, such as those in the gaming or movie industry. Moreover, for modelling and animation purposes it is often required that the same connectivity is shared among two or more different shapes. In this paper we propose a new method that exploits a remeshing-by-matching approach where the observed noisy shape inherits a regular tessellation from a target shape which already satisfies the professional constraints. A fully automatic pipeline is introduced based on a variation of the functional mapping framework. In particular, a new set of basis functions, namely the Coordinates Manifold Harmonics (CMH), is properly designed for this tessellation transfer task. In our experiments an exhaustive quantitative and quality evaluation is reported for human body shapes in T-pose where the effectiveness of the proposed functional remeshing is clearly shown in comparison with other methods