Taxonomic diversity of benthic macroinvertebrates along the Oum Er Rbia River (Morocco): implications for water quality bio-monitoring using indicator species

The macroinvertebrates of the Oum Er Rbia River were studied from samples collected seasonally from September 2015 to September 2016 at 10 sampling sites. The macroinvertebrates found during the sampling period were distributed into twelve orders. The most abundant order was diptera, having 9618 individuals, followed by the order Ephemeroptera with 2985 individuals. Coleoptera, odonates and crustaceans represent only a small fraction of the total fauna. Hydropsyche, Chironomidae sp. and Simuliidae are numerically more inventoried. The composition and distribution of the species were directly or indirectly affected by the physicochemical variables and the quality of the habitat. Correspondence analysis results showed that habitat quality and quality of water represented species distribution patterns and species can be used as indicators to assess the quality of the Oum Er Rbia River system. Habitat management along the Oum Er Rbia river should be aimed at preserving native species, especially during the summer, when the biotope requirements are optimal. The results obtained in this study showed an alarming situation of the water quality of the Oum Er Rbia River and particularly in downstream segment. To solve this problem, we recommend the development of the wastewater discharge of Khenifra and Kasba Tadla and the purification of wastewater before it is discharged into the river

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

Background: The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research consortium funded by the US National Institutes of Health and the UK Wellcome Trust, aimed at using genomics to study and improve the health of Africans. A key role of H3ABioNet is to support H3Africa projects by building bioinformatics infrastructure such as portable and reproducible bioinformatics workflows for use on heterogeneous African computing environments. Processing and analysis of genomic data is an example of a big data application requiring complex interdependent data analysis workflows. Such bioinformatics workflows take the primary and secondary input data through several computationally-intensive processing steps using different software packages, where some of the outputs form inputs for other steps. Implementing scalable, reproducible, portable and easy-to-use workflows is particularly challenging. Results: H3ABioNet has built four workflows to support (1) the calling of variants from high-throughput sequencing data; (2) the analysis of microbial populations from 16S rDNA sequence data; (3) genotyping and genome-wide association studies; and (4) single nucleotide polymorphism imputation. A week-long hackathon was organized in August 2016 with participants from six African bioinformatics groups, and US and European collaborators. Two of the workflows are built using the Common Workflow Language framework (CWL) and two using Nextflow. All the workflows are containerized for improved portability and reproducibility using Docker, and are publicly available for use by members of the H3Africa consortium and the international research community. Conclusion: The H3ABioNet workflows have been implemented in view of offering ease of use for the end user and high levels of reproducibility and portability, all while following modern state of the art bioinformatics data processing protocols. The H3ABioNet workflows will service the H3Africa consortium projects and are currently in use. All four workflows are also publicly available for research scientists worldwide to use and adapt for their respective needs. The H3ABioNet workflows will help develop bioinformatics capacity and assist genomics research within Africa and serve to increase the scientific output of H3Africa and its Pan-African Bioinformatics Network

Epidemiological characteristics of childhood urolithiasis in Morocco

Objectives: Due to the increase observed in the incidence of pediatric urolithiasis in the world, and the scarcity of studies of this pathology in Morocco, we assessed whether epidemiological characteristics of pediatric urolithiasis have a similar profile like in developed countries further we tried to assess the prevalence of this pathology among children in Hassan II University-Hospital of Fez. Subjects and methods: Between January 2003 to November 2013, 104 pediatric patients with urolithiasis were presented to Hassan II University-Hospital of Fez. Eighty one were boys and 23 girls. Patients were referred from different regions of Moroccan states. Results: Out of 104 children diagnosed with urolithiasis, 5 patients with positive family history of renal stones, and 12 were recurrent (12%). Their age varied between 8 months and 15 years old, with a mean age of 7.86 ± 4. The sex ratio was 3.5:1 boys to girls. Clinical presentations were dominated by micturition disorder (59%), abdominal or flank pain (28%), nephritic colic (22%), hematuria (22%) and urinary tract infection (13%). Stones were located in the upper urinary tract in 62.5% of cases. Stones were treated by surgery in 89 cases (89%), and with ESWL in only 2 cases (2%). Over these years of study, a prevalence of 0.83% of childhood urolithiasis was calculated. Conclusions: This preliminary study represents only a region of the country, so more epidemiological analyses should be done. Stone analysis should be performed more frequently, and patients must be presented at earlier stages, before any development of renal failure

A 1000-year-old case of Klinefelter's syndrome diagnosed by integrating morphology, osteology, and genetics.

Xavier Roca-Rada, Sofia Tereso, Adam B Rohrlach, André Brito, Matthew P Williams, Cláudia Umbelino, Francisco Curate, Ira W Deveson, Yassine Souilmi, António Amorim, Pedro C Carvalho, Bastien Llamas, João C Teixeir

Response to the Technical Comment by John Hawkes

Our paper about the impacts of the Laschamps Geomagnetic Excursion 42,000 years ago has provoked considerable scientific and public interest, particularly in the so-called Adams Event associated with the initial transition of the magnetic poles. Although we welcome the opportunity to discuss our new ideas, Hawks’ assertions of misrepresentation are especially disappointing given his limited examination of the material

Response to comment on “a global environmental crisis 42,000 years ago”

Our study on the exact timing and the potential climatic, environmental, and evolutionary consequences of the Laschamps Geomagnetic Excursion has generated the hypothesis that geomagnetism represents an unrecognized driver in environmental and evolutionary change. It is important for this hypothesis to be tested with new data, and encouragingly, none of the studies presented by Picin et al. undermine our model

Response to the Technical Comment by Andrea Picin et al.

Our study on the exact timing, and potential climatic, environmental and evolutionary consequences of the Laschamps Geomagnetic Excursion has generated a novel hypothesis that geomagnetism represents an unrecognised driver in environmental and evolutionary change (1). It is important that this is tested with new data, and encouragingly, none of the studies presented by Picin et al. (2) undermine our model

Response to comment on “a global environmental crisis 42,000 years ago”

Our paper about the impacts of the Laschamps Geomagnetic Excursion 42,000 years ago has provoked considerable scientific and public interest, particularly in the so-called Adams Event associated with the initial transition of the magnetic poles. Although we welcome the opportunity to discuss our new ideas, Hawks’ assertions of misrepresentation are especially disappointing given his limited examination of the material