Enhancement of rhizocompetence in pathogenic bacteria removal of a constructed wetland system

Preprin

Etiology, epidemiology and clinical characteristics of acute moderate-to-severe diarrhea in children under 5 years of age hospitalized in a referral pediatric hospital in Rabat, Morocco

The objective of the study was to describe the etiology, epidemiology, and clinical characteristics of the principal causes of acute infectious diarrhea requiring hospitalization among children under 5 years of age in Rabat, Morocco. A prospective study was conducted from March 2011 to March 2012, designed to describe the main pathogens causing diarrhea in hospitalized children >2 months and less than 5 years of age. Among the 122 children included in the study, Enteroaggregative E. coli (EAEC) and rotavirus were the main etiologic causes of diarrhea detected. Twelve (9.8%) children were referred to the intensive care unit, while 2, presenting infection by EAEC and EAEC plus a Shigella sonnei respectively, developed a hemolytic uremic syndrome. Additionally, 6 (4.9%) deaths occurred with EAEC being isolated in four of these cases. Diarrheogenic E. coli and rotavirus play a significant role as the two main causes of severe diarrhea while other pathogens such as norovirus or parasites seem to have a minimal contribution. Surveillance and prevention programs to facilitate early recognition and improved management of potentially life-threatening diarrhea-episodes are needed

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Adding 6 months of androgen deprivation therapy to postoperative radiotherapy for prostate cancer: a comparison of short-course versus no androgen deprivation therapy in the RADICALS-HD randomised controlled trial

Background Previous evidence indicates that adjuvant, short-course androgen deprivation therapy (ADT) improves metastasis-free survival when given with primary radiotherapy for intermediate-risk and high-risk localised prostate cancer. However, the value of ADT with postoperative radiotherapy after radical prostatectomy is unclear. Methods RADICALS-HD was an international randomised controlled trial to test the efficacy of ADT used in combination with postoperative radiotherapy for prostate cancer. Key eligibility criteria were indication for radiotherapy after radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to radiotherapy alone (no ADT) or radiotherapy with 6 months of ADT (short-course ADT), using monthly subcutaneous gonadotropin-releasing hormone analogue injections, daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as distant metastasis arising from prostate cancer or death from any cause. Standard survival analysis methods were used, accounting for randomisation stratification factors. The trial had 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 80% to 86% (hazard ratio [HR] 0·67). Analyses followed the intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov, NCT00541047. Findings Between Nov 22, 2007, and June 29, 2015, 1480 patients (median age 66 years [IQR 61–69]) were randomly assigned to receive no ADT (n=737) or short-course ADT (n=743) in addition to postoperative radiotherapy at 121 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 9·0 years (IQR 7·1–10·1), metastasis-free survival events were reported for 268 participants (142 in the no ADT group and 126 in the short-course ADT group; HR 0·886 [95% CI 0·688–1·140], p=0·35). 10-year metastasis-free survival was 79·2% (95% CI 75·4–82·5) in the no ADT group and 80·4% (76·6–83·6) in the short-course ADT group. Toxicity of grade 3 or higher was reported for 121 (17%) of 737 participants in the no ADT group and 100 (14%) of 743 in the short-course ADT group (p=0·15), with no treatment-related deaths. Interpretation Metastatic disease is uncommon following postoperative bed radiotherapy after radical prostatectomy. Adding 6 months of ADT to this radiotherapy did not improve metastasis-free survival compared with no ADT. These findings do not support the use of short-course ADT with postoperative radiotherapy in this patient population

Duration of androgen deprivation therapy with postoperative radiotherapy for prostate cancer: a comparison of long-course versus short-course androgen deprivation therapy in the RADICALS-HD randomised trial

Background Previous evidence supports androgen deprivation therapy (ADT) with primary radiotherapy as initial treatment for intermediate-risk and high-risk localised prostate cancer. However, the use and optimal duration of ADT with postoperative radiotherapy after radical prostatectomy remains uncertain. Methods RADICALS-HD was a randomised controlled trial of ADT duration within the RADICALS protocol. Here, we report on the comparison of short-course versus long-course ADT. Key eligibility criteria were indication for radiotherapy after previous radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to add 6 months of ADT (short-course ADT) or 24 months of ADT (long-course ADT) to radiotherapy, using subcutaneous gonadotrophin-releasing hormone analogue (monthly in the short-course ADT group and 3-monthly in the long-course ADT group), daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as metastasis arising from prostate cancer or death from any cause. The comparison had more than 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 75% to 81% (hazard ratio [HR] 0·72). Standard time-to-event analyses were used. Analyses followed intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov , NCT00541047 . Findings Between Jan 30, 2008, and July 7, 2015, 1523 patients (median age 65 years, IQR 60–69) were randomly assigned to receive short-course ADT (n=761) or long-course ADT (n=762) in addition to postoperative radiotherapy at 138 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 8·9 years (7·0–10·0), 313 metastasis-free survival events were reported overall (174 in the short-course ADT group and 139 in the long-course ADT group; HR 0·773 [95% CI 0·612–0·975]; p=0·029). 10-year metastasis-free survival was 71·9% (95% CI 67·6–75·7) in the short-course ADT group and 78·1% (74·2–81·5) in the long-course ADT group. Toxicity of grade 3 or higher was reported for 105 (14%) of 753 participants in the short-course ADT group and 142 (19%) of 757 participants in the long-course ADT group (p=0·025), with no treatment-related deaths. Interpretation Compared with adding 6 months of ADT, adding 24 months of ADT improved metastasis-free survival in people receiving postoperative radiotherapy. For individuals who can accept the additional duration of adverse effects, long-course ADT should be offered with postoperative radiotherapy. Funding Cancer Research UK, UK Research and Innovation (formerly Medical Research Council), and Canadian Cancer Society

Processus de complexification des systèmes productifs : de nouvelles dynamiques et trajectoires de developpement pour les MENA

MENA countries is today, at the center of ambitious economic stakes mainly in regional integration and structural transformation. However, the Arab States of this region have suffered great shortcomings and vulnerability in the economic and productive system in the aftermath of massive political, economic, social and popular upheavals and upheavals. These shocks present a number of new challenges. The main objective of this thesis is to study the new dynamics of the structural transformation process in order to propose new development trajectories for these countries. In this context, we address issues related to the spatial determinants and effects of this process, the relationship between economic complexity and air pollution on the one hand, and economic complexity and inequalities on the other education. For this, we consider a dynamic panel of 133 countries covering an important and recent period (1984 to 2014). Using recent data and integrating previously little used parameters, we highlight particular characteristics of the process of complexification of productive systems. From a general point of view, the results reveal that the productivity performance of productive systems is very heterogeneous within MENA countries and that their determinants depend on the characteristics of the economies. The large disparities observed are explained, beyond the significant effect of per capita income, by a deficiency in the institutional system, particularly in terms of access to innovation, but also to the abundance of natural resources or the attractiveness of foreign direct investment. Beyond the individual characteristics of economies, spatial analysis shows that geographical factors such as urbanization rate, trade agreements, but especially spatial location play a very important role in the process of structural transformation.We also bring, thanks to the tools derived from classical mechanics, answers to the limits of traditional economic models which are difficult to demonstrate the existence of a process of accelerating economic development.La région MENA est aujourd’hui, au centre d’ambitieux enjeux économiques essentiellement en matière d’intégration régionale et de transformation structurelle. Toutefois, les Etats Arabes de cette région ont présenté des défaillances et une vulnérabilité importante dans le système économique et productif au lendemain des mouvements et des bouleversements politiques, économiques, sociales et populaires de très grande ampleur. Ces chocs apportent un lot de nouveaux défis à relever. L’objectif principal de cette thèse est d’étudier les nouvelles dynamiques du processus de transformation structurelle afin de proposer de nouvelles trajectoires de développement pour ces pays. Dans cette optique, nous abordons les questions liées aux déterminants et aux effets spatiaux de ce processus, à la relation entre d’une part la complexité économique et la pollution de l’air, et d’autre part, la complexité économique et les inégalités de genre en éducation. Pour cela, nous considérons un panel dynamique de 133 pays qui couvre une période longue et récente (1984 à 2014). En utilisant des données récentes et en intégrant des paramètres jusque-là peu utilisés, nous mettons en évidence des caractéristiques particulières du processus de complexification des systèmes productifs. D’un point de vue général, les résultats révèlent que les performances en matière de complexification des systèmes productifs sont très hétérogènes au sein des pays MENA et que leurs déterminants dépendent des caractéristiques des économies. Les fortes disparités observées s’expliquent, au-delà de l’effet significatif du revenu par habitant, par une carence dans le système institutionnel, éducatif en particulier dans l’accès à l’innovation, mais aussi à l’abondance des ressources naturelles ou encore à l’attractivité des investissements directs étrangers. Au-delà des caractéristiques individuelles des économies, l’analyse spatiale montre que des facteurs géographiques tels que le taux d’urbanisation, les accords commerciaux, et la localisation spatiale jouent un rôle très important dans le processus de transformation structurelle. Nous apportons également, grâce aux outils tirés de la mécanique classique, des réponses aux limites des modèles économiques traditionnels qui peinent à démontrer l’existence d’un processus d’accélération du développement économique

L'effet de la complexité économique sur la pollution de l'air : une autre approche de la courbe environnementale de Kuznets

International audienceL'objectif de cet article est de mettre en évidence, au-delà de l'effet du PIB par habitant, le rôle majeur de l'évolution des transformations structurelles sur le niveau de pollution de l'air (émissions de CO2/tête), en reprenant autrement le modèle de la courbe environnementale de Kuznets, estimé sur un échantillon de 133 pays de 1984 à 2014. L'influence des changements structurels sur la pollution est évaluée de manière originale par un indice de complexité économique. La diminution relative de la pollution à partir d'un certain seuil, particulièrement perceptible dans les pays à revenu élevé, résulte davantage d'une large transformation structurelle que du niveau de développement, même s'il peut exister un certain lien entre eux. Nous montrons que l'accroissement de la complexité économique permet plus rapidement d'atteindre le seuil de retournement du niveau de pollution que l'accroissement du PIB/tête. Ce résultat laisse apparaître que pour réduire la pollution, le mode de croissance et les spécialisations productives sont plus importants que la croissance elle-même et le niveau de développement économique atteint

Three essays on company based savings plans and shared capitalism

La région MENA est aujourd’hui, au centre d’ambitieux enjeux économiques essentiellement en matière d’intégration régionale et de transformation structurelle. Toutefois, les Etats Arabes de cette région ont présenté des défaillances et une vulnérabilité importante dans le système économique et productif au lendemain des mouvements et des bouleversements politiques, économiques, sociales et populaires de très grande ampleur. Ces chocs apportent un lot de nouveaux défis à relever. L’objectif principal de cette thèse est d’étudier les nouvelles dynamiques du processus de transformation structurelle afin de proposer de nouvelles trajectoires de développement pour ces pays. Dans cette optique, nous abordons les questions liées aux déterminants et aux effets spatiaux de ce processus, à la relation entre d’une part la complexité économique et la pollution de l’air, et d’autre part, la complexité économique et les inégalités de genre en éducation. Pour cela, nous considérons un panel dynamique de 133 pays qui couvre une période longue et récente (1984 à 2014). En utilisant des données récentes et en intégrant des paramètres jusque-là peu utilisés, nous mettons en évidence des caractéristiques particulières du processus de complexification des systèmes productifs. D’un point de vue général, les résultats révèlent que les performances en matière de complexification des systèmes productifs sont très hétérogènes au sein des pays MENA et que leurs déterminants dépendent des caractéristiques des économies. Les fortes disparités observées s’expliquent, au-delà de l’effet significatif du revenu par habitant, par une carence dans le système institutionnel, éducatif en particulier dans l’accès à l’innovation, mais aussi à l’abondance des ressources naturelles ou encore à l’attractivité des investissements directs étrangers. Au-delà des caractéristiques individuelles des économies, l’analyse spatiale montre que des facteurs géographiques tels que le taux d’urbanisation, les accords commerciaux, et la localisation spatiale jouent un rôle très important dans le processus de transformation structurelle. Nous apportons également, grâce aux outils tirés de la mécanique classique, des réponses aux limites des modèles économiques traditionnels qui peinent à démontrer l’existence d’un processus d’accélération du développement économique.MENA countries is today, at the center of ambitious economic stakes mainly in regional integration and structural transformation. However, the Arab States of this region have suffered great shortcomings and vulnerability in the economic and productive system in the aftermath of massive political, economic, social and popular upheavals and upheavals. These shocks present a number of new challenges. The main objective of this thesis is to study the new dynamics of the structural transformation process in order to propose new development trajectories for these countries. In this context, we address issues related to the spatial determinants and effects of this process, the relationship between economic complexity and air pollution on the one hand, and economic complexity and inequalities on the other education. For this, we consider a dynamic panel of 133 countries covering an important and recent period (1984 to 2014). Using recent data and integrating previously little used parameters, we highlight particular characteristics of the process of complexification of productive systems. From a general point of view, the results reveal that the productivity performance of productive systems is very heterogeneous within MENA countries and that their determinants depend on the characteristics of the economies. The large disparities observed are explained, beyond the significant effect of per capita income, by a deficiency in the institutional system, particularly in terms of access to innovation, but also to the abundance of natural resources or the attractiveness of foreign direct investment. Beyond the individual characteristics of economies, spatial analysis shows that geographical factors such as urbanization rate, trade agreements, but especially spatial location play a very important role in the process of structural transformation.We also bring, thanks to the tools derived from classical mechanics, answers to the limits of traditional economic models which are difficult to demonstrate the existence of a process of accelerating economic development