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Chikungunya virus has caused millions of cases worldwide over the past 20 years, with recent outbreaks in Kedougou region in the southeastern Senegal, West Africa. Genomic characterization highlights that an ongoing epidemic in Kedougou in 2023 is not due to an introduction event but caused by the re-emergence of an endemic strain evolving linearly in a sylvatic context.

Abstract The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.

This article studies the action of predators and the predator-dependent functional response in the fishery resource model. We employ the Atangana–Baleanu–Caputo fractional derivative to study the proposed fractional fishery resource model in the presence of predators with Crowley–Martin functional response. We present a theoretical and numerical analysis of the governing nonlinear differential equations of the model consisting of the biomass density of the fish population inside the unrestricted fishing zone, the biomass density of the fish population inside the reserve or restricted fishing zone, and the predator population. Using the fixed point theory and nonlinear analysis, we establish the existence and uniqueness results of the proposed ABC fractional fishery resource model. We establish stability analysis of the fishery model using the Ulam–Hyers stability approach. The numerical scheme of the fractional Adams–Bashforth method is provided and the approximate solutions for the model under consideration are given and discussed. We observe that an increase in the fish capturing rates increases the size of the predator population and reduces the fish subpopulations. To maintain a high number of fish species, we recommend a control measure to reduce the fish capturing rate by the predators.

Résumé: Les manuscrits islamiques de la région du Fouta Djalon (Guinée) ont fait l’objet de recherche et de publication depuis une période relativement récente. Cependant, une grande partie de ces manuscrits conservée par de propriétaires privés reste à explorer. Dans le but de découvrir et d’étudier davantage de manuscrits, des recherches documentaires suivies des enquêtes de terrains et d’entretiens ont été menés dans la région courant 2022 et 2023. Cet article présente les résultats des recherches qui ont permis de découvrir plusieurs manuscrits importants pour la compréhension de l’histoire et de réalités socioculturelles du Fouta Djalon au XIXe et début du XXe siècle. Il rappelle que ce patrimoine documentaire est un gisement qui mérite toute l’attention de la communauté scientifique et des décideurs. Mots-clés : manuscrits, islamiques, arabe, Fouta Djalon, conservation

Bovine tuberculosis (bTB) is a zoonotic disease that is commonly transmitted via inhaling aerosols, drinking unpasteurized milk, and eating raw meat. We use a fractional-order model with the Caputo sense to examine the evolution of bovine tuberculosis transmission in human and animal populations, including a vaccine compartment for humans. We derived and obtained the threshold quantity R0 to ascertain the illness state. We established conditions guaranteeing the asymptotic stability of the equilibria (locally and globally). Sensitivity analysis was conducted to identify the factors that govern the dynamics of tuberculosis. The study demonstrates that the rate of human-to-animal transmission of tuberculosis and environmental pollution and the rate of bTB transmission between animals all affect tuberculosis transmission. However, as vaccination rates increase and fewer individuals consume contaminated environment products (such as meat, milk, and other dairy products), the disease becomes less common in humans. To manage bovine TB, it is advised that information programmes be implemented, the environment be monitored, infected persons be treated, contaminated animals be vaccinated, and contaminated animals be quarantined. The usefulness of the discovered theoretical results is demonstrated through numerical experiments.

Hepatitis E virus (HEV) is one of the emerging zoonotic diseases in Sub-Saharan Africa. Domestic pigs are considered to be the main reservoir for this infectious disease. A third of the world’s population is thought to have been exposed to the virus. The zoonotic transmission of the HEV raises serious zoonotic and food safety concerns for the general public. This is a major public health issue in both developed and developing countries. The World Health Organization (WHO) estimated that 44,000 people died in 2015 as a result of HEV infection. East and South Asia have the highest prevalence of this disease overall. In this study, we proposed, developed, and analyzed the transmission routes of the infection using a fractional-order derivative approach. The existence, stability, and uniqueness of solutions were established using the approach and concept in Banach space. Local and global stability was determined using the Hyers–Ulam (HU) stability approach. Numerical simulation was conducted using existing parameter values, and it was established that, as the susceptible human population declines, the number of infected human populations rises with a change in fractional order θ^. When the susceptible pig population increases, the number of infected pig populations rises with a change in θ^. It was observed that a few variations in the fractional derivative order did not alter the function’s overall behavior with the results of numerical simulations. Moreover, as the number of recovered human populations increases, there is a corresponding increase in the population of recovered pigs with a change in θ^. The exponential increase in the infected pig population can be controlled by treatment of the infected pigs and prevention of the susceptible pigs. The authors recommend policymakers, and stakeholders prioritize the fight against the virus by enforcing the prevention of humans and treatment of infected pigs. The model can be extended to optimal control and cost-effectiveness analysis to determine the most effective control strategy that comes with less cost in the combat of the disease.

Abstract Background Lung ultrasound is a non-invasive tool available at the bedside for the assessment of critically ill patients. The objective of this study was to evaluate the usefulness of lung ultrasound in assessing the severity of SARS-CoV-2 infection in critically-ill patients in a low-income setting. Methods We conducted a 12-month observational study in a university hospital intensive care unit (ICU) in Mali, on patients admitted for COVID-19 as diagnosed by a positive polymerase chain reaction for SARS-CoV-2 and/or typical lung computed tomography scan findings. Results The inclusion criteria was met by 156 patients with a median age of 59 years. Almost all patients (96%) had respiratory failure at admission and many needed respiratory support (121/156, 78%). The feasibility of lung ultrasound was very good, with 1802/1872 (96%) quadrants assessed. The reproducibility was good with an intra-class correlation coefficient of elementary patterns of 0.74 (95% CI 0.65, 0.82) and a coefficient of repeatability of lung ultrasound score

Abstract Background In cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array. Results We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS. Conclusions Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.

Dengue virus is becoming a major public health threat worldwide, principally in Africa. From 2016 to 2020, 23 outbreaks were reported in Africa, principally in West Africa. In Senegal, dengue outbreaks have been reported yearly since 2017. Data about the circulating serotypes and their spatial and temporal distribution were limited to outbreaks that occurred between 2017 and 2018. Herein, we describe up-to-date molecular surveillance of circulating DENV serotypes in Senegal between 2019 to 2023 and their temporal and spatial distribution around the country. For this purpose, suspected DENV-positive samples were collected and subjected to dengue detection and serotyping using RT-qPCR methods. Positive samples were used for temporal and spatial mapping. A subset of DENV+ samples were then sequenced and subjected to phylogenetic analysis. Results show a co-circulation of three DENV serotypes with an overall predominance of DENV-3. In terms of abundance, DENV-3 is followed by DENV-1, with scarce cases of DENV-2 from February 2019 to February 2022. Interestingly, data show the extinction of both serotype 1 and serotype 2 and the only circulation of DENV-3 from March 2022 to February 2023. At the genotype level, the analysis shows that sequenced strains belong to same genotype as previously described: Senegalese DENV-1 strains belong to genotype V, DENV-2 strains to the cosmopolitan genotype, and DENV-3 strains to Genotype III. Interestingly, newly obtained DENV 1–3 sequences clustered in different clades within genotypes. This co-circulation of strains belonging to different clades could have an effect on virus epidemiology and transmission dynamics. Overall, our results highlight DENV serotype replacement by DENV-3, accompanied by a wider geographic distribution, in Senegal. These results highlight the importance of virus genomic surveillance and call for further viral fitness studies using both in vitro and in vivo models, as well as in-depth phylogeographic studies to uncover the virus dispersal patterns across the country.

The 10th and largest Ebola virus disease epidemic in the Democratic Republic of the Congo (DRC) was declared in North Kivu Province in August 2018 and ended in June 2020. We describe and evaluate an Early Warning, Alert and Response System (EWARS) implemented in the Beni health zone of DRC during August 5, 2018–June 30, 2020. During this period, 194,768 alerts were received, of which 30,728 (15.8%) were validated as suspected cases. From these, 801 confirmed and 3 probable cases were detected. EWARS showed an overall good performance: sensitivity and specificity >80%, nearly all (97%) of alerts investigated within 2 hours of notification, and good demographic representativeness. The average cost of the system was US $438/case detected and US $1.8/alert received. The system was stable, despite occasional disruptions caused by political insecurity. Our results demonstrate that EWARS was a cost-effective component of the Ebola surveillance strategy in this setting.

At the end of the 2013–2016 Ebola virus disease outbreak in Guinea, we implemented an alert system for early detection of Ebola resurgence among survivors. Survivors were asked to report health alerts in their household and provide body fluid specimens for laboratory testing. During April–September 2016, a total of 1,075 (88%) of 1,215 survivors participated in the system; follow up occurred at a median of 16 months after discharge (interquartile range 14–18 months). Of these, 784 acted as focal points and reported 1,136 alerts (including 4 deaths among survivors). A total of 372 (91%) of 408 eligible survivors had >1 semen specimen tested; of 817 semen specimens, 5 samples from 4 survivors were positive up to 512 days after discharge. No lochia (0/7) or breast milk (0/69) specimens tested positive. Our findings underscore the importance of long-term monitoring of survivors’ semen samples in an Ebola-affected country.

Near-infrared spectroscopy (NIR) is a non-destructive, fast, and low-cost method to measure the grain quality of different cereals. However, the feasibility for determining the critical biochemicals, related to the classifications for food, feed, and fuel products are not adequately investigated. Fourier-transform (FT) NIR was applied in this study to determine the eight biochemicals in four types of sorghum samples: hulled grain flours, hull-less grain flours, whole grains, and grain flours. A total of 20 hybrids of sorghum grains were selected from the two locations in China. Followed by FT-NIR spectral and wet-chemically measured biochemical data, partial least squares regression (PLSR) was used to construct the prediction models. The results showed that sorghum grain morphology and sample format affected the prediction of biochemicals. Using NIR data of grain flours generally improved the prediction compared with the use of NIR data of whole grains. In addition, using the spectra of whole grains enabled comparable predictions, which are recommended when a non-destructive and rapid analysis is required. Compared with the hulled grain flours, hull-less grain flours allowed for improved predictions for tannin, cellulose, and hemicellulose using NIR data. This study aimed to provide a reference for the evaluation of sorghum grain biochemicals for food, feed, and fuel without destruction and complex chemical analysis.

Abstract Background The ninth outbreak of Ebola Virus Disease (EVD) in the Democratic Republic of the Congo occurred in Équateur Province from 8 May-24 July 2018. A system of health facility (HF)-based active case finding (ACF) was implemented in Mbandaka, a regional capital with four confirmed EVD cases, following completion of contact tracing. The goal of this HF-based ACF system was to look for undetected EVD cases among patients that visited HFs beginning one week prior to the system’s implementation. Methods From 23 June – 24 July 2018, ACF teams visited HFs in Mbandaka and reviewed all medical records as far back as 17 June for any consultations meeting the suspected EVD case definition. The teams then assessed whether to validate these as suspected EVD cases based on factors such as recovery, epidemiological links, and their clinical judgement. ACF teams also assessed HFs’ awareness of EVD symptoms and the process for alerting suspected cases. We calculated descriptive statistics regarding the characteristics of reviewed consultations, alert cases, and visited HFs. We also used univariate and multivariate random effects logistic regression models to evaluate the impact of repeated ACF visits to the same HF on the staff’s awareness of EVD. Results ACF teams reviewed 37,746 consultations, of which 690 met the definition of a suspected case of EVD. Two were validated as suspected EVD cases and transferred to the Ebola Treatment Unit for testing; both tested negative. Repeated ACF visits to the same HF were significantly associated with improved EVD awareness (p

BackgroundNeonatal mortality in Guinea accounts for about 30% of all fatalities in children younger than five years. Countrywide, specialized neonatal intensive care is provided in one single clinic with markedly limited resources. To implement targeted measures, prospective data on patient characteristics and factors of neonatal death are needed.ObjectiveTo determine the rates of morbidity and mortality, to describe clinical characteristics of admitted newborns requiring intensive care, to assess the quality of disease management, and to identify factors contributing to neonatal mortality.MethodsProspective observational cohort study of newborns admitted to the hospital between mid-February and mid-March 2019 after birth in other institutions. Data were collected on maternal/prenatal history, delivery, and in-hospital care via convenience sampling. Associations of patient characteristics with in-hospital death were assessed using cause-specific Cox proportional-hazards models.ResultsHalf of the 168 admitted newborns underwent postnatal cardiopulmonary resuscitation. Reasons for admission included respiratory distress (49.4%), poor postnatal adaptation (45.8%), prematurity (46.2%), and infections (37.1%). 101 newborns (61.2%) arrived in serious/critical general condition; 90 children (53.9%) showed clinical signs of neurological damage. Quality of care was poor: Only 59.4% of the 64 newborns admitted with hypothermia were externally heated; likewise, 57.1% of 45 jaundiced infants did not receive phototherapy. Death occurred in 56 children (33.3%) due to birth asphyxia (42.9%), prematurity (33.9%), and sepsis (12.5%). Newborns in serious/critical general condition at admission had about a fivefold higher hazard to die than those admitted in good condition (HR 5.21 95%-CI 2.42-11.25, p = ConclusionNeonatal mortality was strikingly high. Birth asphyxia, prematurity, and infection accounted for 89.3% of death, aggravated by poor quality of in-hospital care. Children with serious general condition at admission had poor chances of survival. The whole concept of perinatal care in Guinea requires reconsideration.

Images available on online sharing platforms have a high probability of being modified, with additional global transformations such as compression, resizing or filtering covering the possible alteration. Such manipulations impose many constraints on forgery detection algorithms. This article presents a framework improving robustness for image forgery detection. The most important step of our framework is to take into account the image quality corresponding to the chosen application. Therefore, we relied on a camera identification model based on convolutional neural networks. Lossy compression such as JPEG being considered as the most common type of intentional or inadvertent concealment of image forgery, that leads us to experiment our proposal on this manipulation. Thus, our trained CNN is fed with a mixture of different qualities of compressed and uncompressed images. Experimental results showed the importance of this step to improve the effectiveness of our approach against recent literature approaches. To better interpret our trained CNN, we proposed an in-depth supervision by first a visualization of the layer and an experimental analysis of the influence of the learned features. This analysis led us to a more robust and accurate framework. Finally, we applied this improved system on an image forgery detection application and showed some promising results.

A considerable number of metrics can be used to evaluate the performance of machine learning algorithms. While much work is dedicated to the study and improvement of data quality and models’ performance, much less research is focused on the study of these evaluation metrics, their intrinsic relationship, the interplay of the influence among the metrics, the models, the data, and the environments and conditions in which they are to be applied. While some works have been conducted on general machine learning tasks such as classification, fewer efforts have been dedicated to more complex problems such as object detection and image segmentation, in which the evaluation of performance can vary drastically depending on the objectives and domains of application. Working in an agricultural context, specifically on the problem of the automatic detection of plants in proximal sensing images, we studied twelve evaluation metrics that we used to evaluate three image segmentation models recently presented in the literature. After a unified presentation of these metrics, we carried out an exploratory analysis of their relationships using a correlation analysis, a clustering of variables, and two factorial analyses (namely principal component analysis and multiple factorial analysis). We distinguished three groups of highly linked metrics and, through visual inspection of the representative images of each group, identified the aspects of segmentation that each group evaluates. The aim of this exploratory analysis was to provide some clues to practitioners for understanding and choosing the metrics that are most relevant to their agricultural task.

Abstract Background Due to its chemical composition and abundance, lignocellulosic biomass is an attractive feedstock source for global bioenergy production. However, chemical composition variations interfere with the success of any single methodology for efficient bioenergy extraction from diverse lignocellulosic biomass sources. Although chemical component distributions could guide process design, they are difficult to obtain and vary widely among lignocellulosic biomass types. Therefore, expensive and laborious “one-size-fits-all” processes are still widely used. Here, a non-destructive and rapid analytical technology, near-infrared spectroscopy (NIRS) coupled with multivariate calibration, shows promise for addressing these challenges. Recent advances in molecular spectroscopy analysis have led to methodologies for dual-optimized NIRS using sample subset partitioning and variable selection, which could significantly enhance the robustness and accuracy of partial least squares (PLS) calibration models. Using this methodology, chemical components and theoretical ethanol yield (TEY) values were determined for 70 sweet and 77 biomass sorghum samples from six sweet and six biomass sorghum varieties grown in 2013 and 2014 at two study sites in northern China. Results Chemical components and TEY of the 147 bioenergy sorghum samples were initially analyzed and compared using wet chemistry methods. Based on linear discriminant analysis, a correct classification assignment rate (either sweet or biomass type) of 99.3% was obtained using 20 principal components. Next, detailed statistical analysis demonstrated that partial optimization using sample set partitioning based on joint X–Y distances (SPXY) for sample subset partitioning enhanced the robustness and accuracy of PLS calibration models. Finally, comparisons between five dual-optimized strategies indicated that competitive adaptive reweighted sampling coupled with the SPXY (CARS-SPXY) was the most efficient and effective method for improving predictive performance of PLS multivariate calibrations. Conclusions As a dual-optimized methodology, sample subset partitioning combined with variable selection is an efficient and straightforward strategy to enhance the accuracy and robustness of NIRS models. This knowledge should facilitate generation of improved lignocellulosic biomass feedstocks for bioethanol production. Moreover, methods described here should have wider applicability for use with feedstocks incorporating multispecies biomass resource streams.

Abstract Background By the end of the 2013–2016 West African Ebola Virus Disease (EVD) outbreaks, a total of 3814 cases (probable and confirmed) and 2544 deaths were reported in Guinea. Clearly, surveillance activities aiming at stopping human-to-human transmission have been the breakthrough of EVD outbreak management, but their application has been at times easier said than done. This article presents five confirmed or probable EVD cases that arose in Conakry towards the end of the Guinea epidemic, which demonstrate flaws in surveillance and follow-up. Case presentation For case 1, safe burial requirements were not followed. For cases 1 and 2, negative Polymerase Chain Reaction (PCR) results were interpreted as no infection. For the first case, the sample may have not been taken properly while for the second the disease was possibly at its early stage. Case 3 was stopped at a border health checkpoint and despite her high temperature she was allowed to continue the bus journey. For case 4, an oral swab sample was supposedly taken after death but could not be found for retrospective testing. Despite characteristic symptomatology, case 5 was not identified as a suspect case for as long as 3 weeks. Conclusion In epidemic contexts, health systems must be able to track all samples of suspect cases and deaths, regardless of their laboratory results. Social mobilization in communities and training in health care facilities must be strengthened at the tail of an outbreak, to avoid the natural slackening of disease surveillance, in particular for long-lasting and deadly epidemics.

Objectives To assess the impact of refresher training of healthcare workers (HCWs) in infection prevention and control (IPC), ensuring consistent adequate supplies and availability of IPC kits and carrying out weekly monitoring of IPC performance in healthcare facilities (HCFs)Design This was a before and after comparison studySettings This study was conducted from June to July 2018 during an Ebola virus disease (EVD) outbreak in Equateur Province in the Democratic Republic of the Congo (DRC).Participants 48 HCFsInterventions HCWs capacity building in basic IPC, IPC kit donation and IPC mentoring.Primary outcome measures IPC scoreResults 48 HCFs were evaluated and 878 HCWs were trained, of whom 437 were women and 441 were men. The mean IPC score at baseline was modestly higher in hospitals (8%) compared with medical centres (4%) and health centres (4%), respectively. The mean IPC score at follow-up significantly increased to 50% in hospitals, 39% in medical centres and 36% in health centres (p value

Les envenimations ophidiennes constituent un problème de santé publique en Afrique, entrainant 20 000 décès annuels. Cette mortalité traduit les difficultés de prise en charge des complications en particuliers hémorragiques. Nous rapportons le cas de Mr SL 35 ans, agriculteur, victime d'une morsure de vipère entrainant un syndrome hémorragique, suivi d'un abdomen aigu d'installation progressive. L'échographie objectivait un épanchement de grande abondance, dont la ponction ramenait du sang incoagulable. Devant la reconstitution de l'hémopéritoine après trois doses de sérum antivenimeux et la coagulation des prélèvements sur tube sec, une laparotomie exploratrice était réalisée à J9. Elle a retrouvé un hématome retro péritonéal bombant dans le méso-colon et qui s'écoulait dans la cavité péritonéale. Le geste a consisté à une évacuation de 1500ml de sang, et un toilettage au sérum physiologique. Les suites opératoires ont été simples. Le patient était transféré en secteur d'hospitalisation de chirurgie à J3 post opératoire puis sortie d'hôpital à J19.

In October 2015, a new case of Ebola virus disease in Guinea was detected. Case investigation, serology, and whole-genome sequencing indicated possible transmission of the virus from an Ebola virus disease survivor to another person and then to the case-patient reported here. This transmission chain over 11 months suggests slow Ebola virus evolution.

The largest recorded Ebola virus disease epidemic began in March 2014; as of July 2015, it continued in 3 principally affected countries: Guinea, Liberia, and Sierra Leone. Control efforts include contact tracing to expedite identification of the virus in suspect case-patients. We examined contact tracing activities during September 20–December 31, 2014, in 2 prefectures of Guinea using national and local data about case-patients and their contacts. Results show less than one third of case-patients (28.3% and 31.1%) were registered as contacts before case identification; approximately two thirds (61.1% and 67.7%) had no registered contacts. Time to isolation of suspected case-patients was not immediate (median 5 and 3 days for Kindia and Faranah, respectively), and secondary attack rates varied by relationships of persons who had contact with the source case-patient and the type of case-patient to which a contact was exposed. More complete contact tracing efforts are needed to augment control of this epidemic.

Human Ebola infection is characterized by a paralysis of the immune system. A signature of αβ T cells in fatal Ebola infection has been recently proposed, while the involvement of innate immune cells in the protection/pathogenesis of Ebola infection is unknown. Aim of this study was to analyze γδ T and NK cells in patients from the Ebola outbreak of 2014-2015 occurred in West Africa, and to assess their association with the clinical outcome.Nineteen Ebola-infected patients were enrolled at the time of admission to the Ebola Treatment Centre in Guinea. Patients were divided in two groups on the basis of the clinical outcome. The analysis was performed by using multiparametric flow cytometry established by the European Mobile Laboratory in the field. A low frequency of Vδ2 T-cells was observed during Ebola infection, independently from the clinical outcome. Moreover, Vδ2 T-cells from Ebola patients massively expressed CD95 apoptotic marker, suggesting the involvement of apoptotic mechanisms in Vδ2 T-cell loss. Interestingly, Vδ2 T-cells from survivors expressed an effector phenotype and presented a lower expression of the CTLA-4 exhaustion marker than fatalities, suggesting a role of effector Vδ2 T-cells in the protection. Furthermore, patients with fatal Ebola infection were characterized by a lower NK cell frequency than patients with non fatal infection. In particular, both CD56bright and CD56dim NK frequency were very low both in fatal and non fatal infections, while a higher frequency of CD56neg NK cells was associated to non-fatal infections. Finally, NK activation and expression of NKp46 and CD158a were independent from clinical outcome.Altogether, the data suggest that both effector Vδ2 T-cells and NK cells may play a role in the complex network of protective response to EBOV infection. Further studies are required to characterize the protective effector functions of Vδ2 and NK cells.

BackgroundThe ongoing West African Ebola epidemic began in December 2013 in Guinea, probably from a single zoonotic introduction. As a result of ineffective initial control efforts, an Ebola outbreak of unprecedented scale emerged. As of 4 May 2015, it had resulted in more than 19,000 probable and confirmed Ebola cases, mainly in Guinea (3,529), Liberia (5,343), and Sierra Leone (10,746). Here, we present analyses of data collected during the outbreak identifying drivers of transmission and highlighting areas where control could be improved.Methods and findingsOver 19,000 confirmed and probable Ebola cases were reported in West Africa by 4 May 2015. Individuals with confirmed or probable Ebola ("cases") were asked if they had exposure to other potential Ebola cases ("potential source contacts") in a funeral or non-funeral context prior to becoming ill. We performed retrospective analyses of a case line-list, collated from national databases of case investigation forms that have been reported to WHO. These analyses were initially performed to assist WHO's response during the epidemic, and have been updated for publication. We analysed data from 3,529 cases in Guinea, 5,343 in Liberia, and 10,746 in Sierra Leone; exposures were reported by 33% of cases. The proportion of cases reporting a funeral exposure decreased over time. We found a positive correlation (r = 0.35, p < 0.001) between this proportion in a given district for a given month and the within-district transmission intensity, quantified by the estimated reproduction number (R). We also found a negative correlation (r = -0.37, p < 0.001) between R and the district proportion of hospitalised cases admitted within ≤4 days of symptom onset. These two proportions were not correlated, suggesting that reduced funeral attendance and faster hospitalisation independently influenced local transmission intensity. We were able to identify 14% of potential source contacts as cases in the case line-list. Linking cases to the contacts who potentially infected them provided information on the transmission network. This revealed a high degree of heterogeneity in inferred transmissions, with only 20% of cases accounting for at least 73% of new infections, a phenomenon often called super-spreading. Multivariable regression models allowed us to identify predictors of being named as a potential source contact. These were similar for funeral and non-funeral contacts: severe symptoms, death, non-hospitalisation, older age, and travelling prior to symptom onset. Non-funeral exposures were strongly peaked around the death of the contact. There was evidence that hospitalisation reduced but did not eliminate onward exposures. We found that Ebola treatment units were better than other health care facilities at preventing exposure from hospitalised and deceased individuals. The principal limitation of our analysis is limited data quality, with cases not being entered into the database, cases not reporting exposures, or data being entered incorrectly (especially dates, and possible misclassifications).ConclusionsAchieving elimination of Ebola is challenging, partly because of super-spreading. Safe funeral practices and fast hospitalisation contributed to the containment of this Ebola epidemic. Continued real-time data capture, reporting, and analysis are vital to track transmission patterns, inform resource deployment, and thus hasten and maintain elimination of the virus from the human population.

BackgroundThe case fatality ratio (CFR) of Ebola virus disease (EVD) can vary over time and space for reasons that are not fully understood. This makes it difficult to define the baseline CFRs needed to evaluate treatments in the absence of randomized controls. Here, we investigate whether viremia in EVD patients may be used to evaluate baseline EVD CFRs.Methods and findingsWe analyzed the laboratory and epidemiological records of patients with EVD confirmed by reverse transcription PCR hospitalized in the Conakry area, Guinea, between 1 March 2014 and 28 February 2015. We used viremia and other variables to model the CFR. Data for 699 EVD patients were analyzed. In the week following symptom onset, mean viremia remained stable, and the CFR increased with viremia, V, from 21% (95% CI 16%-27%) for low viremia (V < 104.4 copies/ml) to 53% (95% CI 44%-61%) for intermediate viremia (104.4 ≤ V < 105.2 copies/ml) and 81% (95% CI 75%-87%) for high viremia (V ≥ 105.2 copies/ml). Compared to adults (15-44 y old [y.o.]), the CFR was larger in young children (0-4 y.o.) (odds ratio [OR]: 2.44; 95% CI 1.02-5.86) and older adults (≥ 45 y.o.) (OR: 2.84; 95% CI 1.81-4.46) but lower in children (5-14 y.o.) (OR: 0.46; 95% CI 0.24-0.86). An order of magnitude increase in mean viremia in cases after July 2014 compared to those before coincided with a 14% increase in the CFR. Our findings come from a large hospital-based study in Conakry and may not be generalizable to settings with different case profiles, such as with individuals who never sought care.ConclusionsViremia in EVD patients was a strong predictor of death that partly explained variations in CFR in the study population. This study provides baseline CFRs by viremia group, which allow appropriate adjustment when estimating efficacy in treatment studies. In randomized controlled trials, stratifying analysis on viremia groups could reduce sample size requirements by 25%. We hypothesize that monitoring the viremia of hospitalized patients may inform the ability of surveillance systems to detect EVD patients from the different severity strata.

From February to August 2003, 38 persons were infected with Crimean-Congo hemorrhagic fever (CCHF) virus in Mauritania; 35 of these persons were residents of Nouakchott. The first patient was a young woman who became ill shortly after butchering a goat. She transmitted the infection to 15 persons in the hospital where she was admitted and four members of her family. In Nouakchott, two disease clusters and 11 isolated cases were identified. The case-fatality ratio was 28.6%. Of the patients not infected by the first case-patient, almost half were butchers, which suggests that the primary mode of animal-to-human transmission was direct contact with blood of infected animals. The hospital outbreak alerted health authorities to sporadic cases that occurred in the following weeks, which would have probably gone otherwise unnoticed. Studies must be conducted to determine the potential risk for continued sporadic outbreaks of CCHF in humans and to propose prevention measures.

In October 2003, 9 human cases of hemorrhagic fever were reported in 3 provinces of Mauritania, West Africa. Test results showed acute Rift Valley fever virus (RVFV) infection, and a field investigation found recent circulation of RVFV with a prevalence rate of 25.5% (25/98) and 4 deaths among the 25 laboratory-confirmed case-patients. Immunoglobulin M against RVFV was found in 46% (25/54) of domestic animals. RVFV was also isolated from the mosquito species Culex poicilipes. Genetic comparison of virion segments indicated little variation among the strains isolated. However, phylogenetic studies clearly demonstrated that these strains belonged to the East-Central African lineage for all segments. To our knowledge, this is the first time viruses of this lineage have been observed in an outbreak in West Africa. Whether these strains were introduced or are endemic in West Africa remains to be determined.

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Abstract Introduction In sub-Saharan Africa (SSA), the clinical and progressive diagnostic certainty of AIDS dementia is difficult to establish due to under-medicalization and delays in consultation and especially the diversity of etiologies of demented states. Material and methods We carried out a retrospective study of 196 patients hospitalized for dementia syndrome between 2016 and 2021 in the neurology department of the University Hospital of Conakry. The criteria labeled in this study are those retained by the DSM-IV and the classification of the American Academy of Neurology (AAN) developed in accordance with the WHO. Results HIV etiology was identified in patients aged 44–67 years (17 women and 19 men). The clinical picture was dominated by severe cognitive disorders, slowed ideation, memory disorders and reduced motor skills associated with personality changes. Neurological examination revealed dysphoric disorders in most patients, sphincter abnormalities in 13 cases and labio-lingual tremor in 11 cases. Diagnosis was based on positive serological tests for HIV1 antibodies (25 cases) and HIV2 antibodies (1 case) using the Elisa and Western blot techniques, and the presence of discretely hypercellular CSF. Magnetic resonance imaging contributed to the diagnosis, showing diffuse white matter abnormalities with hyper signals on T2-weighted or FLAIR sequences. Conclusion This study shows a non-stereotype clinical picture of AIDS dementia requiring a differential diagnosis with other infectious dementias. These results are important for the therapeutic and prognostic discussion.

Abstract In today’s race to find ways to produce cheap and green hydrogen, the natural hydrogen wells in Bourakebougou offer a promising solution and are a good example of how H2 can be produced in the natural environment. Not only has one well been successfully exploited to generate electricity for the local village, but twenty-four other exploratory boreholes have also demonstrated the presence of natural H2 in the surrounding area. The Bourakebougou H2 field offers a unique opportunity for geoscientists to determine the key characteristics of natural hydrogen reservoirs. This paper presents the coring, logging, and geochemistry studies that were performed to better characterize the nature of the Bourakebougou H2-bearing reservoirs. The shallowest main reservoir, in which there is the highest content of H2, is made of dolomitic carbonate (Neoproterozoic cap carbonate). These carbonates are largely karstified and show a high degree of heterogeneity in porosity (0.21–14.32%). Based on the analysis of the drilling imagery of the carbonated reservoirs, the accumulation of hydrogen occurs in the karst (void) representing a secondary porosity in the rock matrix. Other reservoirs, especially the deepest ones, are porous sandstone rocks with much more homogeneous porosities (4.52–6.37%) compared to the massive carbonates. For the wells analysed, the neutron tool reacted in a specific way when there is the presence of hydrogen. Hence, it stands out as being the primary tool to detect the presence of natural hydrogen beyond simple gas logging. When comparing a H2 reservoir system to classical oil and gas reservoir systems, the results show that the hydrogen reservoir is a dynamic system that is progressively recharged in H2-rich gas at the production timescale.

Background: The prevalence of non-tuberculous mycobacteria (NTM) has been increasing worldwide in both developed and developing countries. NTM infection is clinically indistinguishable from tuberculosis and therefore poses significant challenges in patient management, especially in patients chronically treated for pulmonary TB. In this study, we evaluated a new highly sensitive Multiplex MTB/NTM assay that can differentiate M. tuberculosis complex (MTBC) from all NTM, including the treatable and most common NTM, M. avium complex (MAC). Methods: We developed and optimized a new open- Multiplex MTB/NTM assay with two gene-targets for MTBC (IS6110/senX3-regX3) and two targets for MAC (IS1311/DT1) with samples spiked with stored strains and testing 20 replicates. Patients with presumptive TB and NTM were enrolled at the Respiratory Disease Department of The University Teaching Hospital of Point G, in Mali. Findings: In the development stage, the new assay showed a high analytic performance with 100% detections of MTBC and MAC at only 5 colony forming units (CFUs). Overall, without the treatment failure cases, the Multiplex assay and the Xpert showed a sensitivity, specificity, PPV and NPV of 83·3% [66·4-92·6], 96·6% [88·6-99·0], 92·5% [82·3-96·5] and 92·2% [82·7-96·5] and the Xpert had values of 96·7% [83·3-99·4], 80·0% [68·2-88·1], 70·7 [55·5-82·3] and 97·9% [89·3-99·6], respectively. The Multiplex assay successfully detected all (5/5) the MAC cases. Interpretation: Our new Multiplex assay demonstrates better specificity than Xpert for all group studied, in addition to detecting potential NTM cases. The assay could therefore complement the widely used Xpert assay and enhance discrimination of TB and NTM infections. Funding: This work was supported by the National Institutes of Health (R03AI137674, U54EB027049, D43TW010350 and UM1AI069471) and Northwestern University's Institute for Global Health Catalyzer Fund.

La dysplasie fibreuse osseuse (DFO) est une maladie osseuse bénigne, congénitale et rare, dans laquelle l´os normal est remplacé par du tissu fibro-osseux entraînant des lésions osseuses déformantes. Tous les os peuvent être concernés, cependant la localisation crânio-faciale se particularise par ses manifestations cliniques, son évolution et ses difficultés thérapeutiques. L´objectif de notre travail était de décrire les aspects diagnostiques, thérapeutiques et évolutifs des DFO crânio-faciales. Nous rapportons six observations de patients suivis au service d´ORL de l´Hôpital Principal de Dakar pour DFO crânio-faciale. L´âge moyen des patients était de 26,16 ans avec des extrêmes de 11 et 58 ans. Le sexe féminin était prédominant dans 83% des cas. Les circonstances de découverte étaient dominées par la déformation osseuse. Un patient a consulté pour obstruction nasale unilatérale avec épistaxis. Le scanner a permis dans tous les cas de faire le diagnostic et le bilan topographique. Deux patientes ont bénéficié d´un traitement chirurgical. Un cas de récidive a été observé. La DFO crânio-faciale est une pathologie osseuse rare qui peut se manifester par de graves troubles sensoriels et fonctionnels. Elle pose de réelles difficultés thérapeutiques et fait appel à une bonne collaboration interdisciplinaire.

Abstract Background The PR1MaC study was conducted to evaluate the integration of Chronic Disease Prevention and Management services into primary care practices and was reported effective. The aim of this study was to further explore the effects of the PR1MaC intervention on patients and their family. Methods We conducted a qualitative study embedded in a randomized controlled trial. The trial was implemented in eight primary health care practices in the Saguenay region, Quebec, Canada. The interdisciplinary patient-centred team-based intervention included self-management support and a motivational approach. We conducted focus groups and semi-directed individual interviews with patients, family members and healthcare professionals. Results Perceived positive effects can be grouped into six major themes: awareness, improved knowledge, improved motivation and empowerment, adoption of healthy behaviours, improvement of health status and improvement of quality of life. On the negative side, some participants reported lack of sustainability of newly acquired benefits in the months following the intervention. Conclusions Integrating chronic disease prevention and management services into primary care settings had impacts on patients and their family members. These findings are consistent with findings that were reported in the quantitative study. Further studies should address longterm sustainabilility in terms of benefits for the patients. Trial registration ClinicalTrials.gov, no.: NCT01319656.

Le rétrécissement urétral est une pathologie dont l'étiologie et la prise en charge varient selon le contexte. L'objectif de l'étude était de procéder à une analyse des aspects épidémiologiques, étiologique et thérapeutique du rétrécissement urétral dans notre contexte. Il s'agit d'une étude transversale longitudinale portant sur les cas de rétrécissement urétral acquis admis dans notre service entre mars 2014-février 2016. Age moyen: 24,5ans (10 et 81 ans). Le diagnostic fut confirmé par l'Uretro-Cystographie Rétrograde et Mictionnelle (UCRM). La longueur moyenne du rétrécissement était de 2,28cm (0,5-5cm). Les modalités thérapeutiques adoptées: la Résection Anastomose Termino-Terminale (RAT-T); la Dilatation Urétrale Rétrograde Itérative (DURI) etc. L'évaluation du résultat 6-15 mois postopératoire; satisfaisant en l'absence de récidive, RPM ≤30cc et un jet urinaire fort et mauvais en cas de récidive de dysurie ou RPM ≥100cc. Le RU occupe 7,14% de nos activités urologiques. La plus part de nos patients sont des cultivateurs provenant de la zone rurale. Les antécédents d'urétrite répétée ont été le plus souvent évoqués par nos patients et 78,57% d'entre eux étaient des hommes mariés dont 91% polygames. Les patients ont consulté surtout pour dysurie soit 50% de l'effectif et 50,01% de nos patients ce sont présentés avec une infection urinaire secondaire dont le germe prédominant est Escherichia coli. L'étiologie infectieuse a été la plus dominante soit 56,52%. La portion la plus atteinte a été l'urètre bulbaire soit 45,60% des cas. La RAT-T a été la technique la plus utilisée soit 39,13%. Globalement nous avons eu 85,65% de bon résultat et 13,04% d'échec; les taux de succès les plus élevés ont été obtenus avec la résection anastomotique soit 94,44% respectivement. Le rétrécissement urétral reste une pathologie fréquente chez les jeunes. L'étiologie infectieuse demeure la plus dominante dans notre contexte. L'accent doit être mis sur la prévention et la Prise en Charge (PEC) efficace et efficiente des Infections Sexuellement Transmissible (IST).

La plaie carotidienne lors du cathétérisme jugulaire veineux est un accident rare mais pouvant être dramatique. Nous rapportons un cas d'hématome cervical compressif avec hémothorax survenu à la suite d'une plaie de l'artère carotide commune au décours d'un cathétérisme veineux jugulaire interne. Le diagnostic et la prise en charge de ce type de complication sont discutés.