OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity.

OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of gene diversity and orthology is the most precise way of bridging gene functional knowledge with the rapidly expanding universe of genomic sequences. OrthoDB samples the most diverse organisms with the best quality genomics data to provide the leading coverage of species diversity.

BUSCO: Assessing Genomic Data Quality and Beyond.

Evaluation of the quality of genomic "data products" such as genome assemblies or gene sets is of critical importance in order to recognize possible issues and correct them during the generation of new data. It is equally essential to guide subsequent or comparative analyses with existing data, as the correct interpretation of the results necessarily requires knowledge about the quality level and reliability of the inputs. Using datasets of near universal single-copy orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy of genomic data by providing biologically meaningful metrics based on expected gene content.

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.

Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here, we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying data sets in sync with the OrthoDB v10 release.

Sustainability determinants of the Burkinabe performance-based financing project.

Purpose: A performance-based financing (PBF) pilot project was implemented in 2011 in Burkina Faso. After more than five years of implementation (data collection in 2016), the project's sustainability was not guaranteed. This study's objective is to assess this project's sustainability in 2016 by identifying the presence/absence of different determinants of sustainability according to the conceptual framework of Seppey (2017).

Scaling-Up Performance-Based Financing in Burkina Faso: From PBF to User Fees Exemption Strategic Purchasing.

Background: Numerous countries have undertaken performance-based financing (PBF) reforms to improve quality and quantity of healthcare services. However, only few reforms have successfully managed to achieve the different scale-up phases. In Burkina Faso, a pilot project was implemented, but was put on hold before being scaled.

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g.

LEMMI: a continuous benchmarking platform for metagenomics classifiers.

Studies of microbiomes are booming, along with the diversity of computational approaches to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. A swift evaluation of newly published methods and their improvements against established tools is necessary to reduce the time between the methods' release and their adoption in microbiome analyses. The LEMMI platform offers a novel approach for benchmarking software dedicated to metagenome composition assessments based on read classification.

Re-thinking global and public health projects during the COVID-19 pandemic context: Considerations and recommendations for early- and not-so-early-career researchers.

This commentary aims to provide a glimpse into some of the early and continuing impacts of the COVID-19 pandemic on our global and public health projects: research in low-resourced settings; research with vulnerable populations, such as asylum seekers, Indigenous communities, children, and mental health service users; and research with healthcare professionals, frontline workers, and health planners. In the early context of restrictions caused by COVID-19, this commentary highlights our research setbacks and challenges, and the ways in which we are adapting research methodologies, while considering ethical implications related to the pandemic and their impacts on conducting global and public health research. As we learn to become increasingly aware of some of our limitations in the face of the pandemic, some positives are also worth highlighting: we are mobilizing our training and research skills to participate in COVID-19 projects and to disseminate knowledge on COVID-19, including through papers such as this one.

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles.

Background: The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals.

BUSCO: Assessing Genome Assembly and Annotation Completeness.

Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the ability to evaluate their completeness using a biologically meaningful approach. Here, we describe the use of the BUSCO tool suite to assess the completeness of genomes, gene sets, and transcriptomes, using their gene content as a complementary method to common technical metrics.

Using BUSCO to Assess Insect Genomic Resources.

The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships among different species or orders and to build "omics" resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of critical importance to understanding the potential limitations on the types of questions that these data can be reliably used to address.

Validation d'un questionnaire auto-administré sur les valeurs en politique publique de santé.

Objectives: The aims of this article are to describe the development of a self-administered questionnaire assessing the core values in the field of public health ( radardesvaleurs.com ) and to report the results of a study testing the questionnaire's test-retest reliability, internal consistency and construct validity.

Method: A 24-item questionnaire grounded in the conceptual framework of Shalom H.

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.

Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.

Donor-funded project's sustainability assessment: a qualitative case study of a results-based financing pilot in Koulikoro region, Mali.

Background: Results-based financing (RBF) is emerging as a new alternative to finance health systems in many African countries. In Mali, a pilot project was conducted to improve demand and supply of health services through financing performance in targeted services. No study has explored the sustainability process of such a project in Africa.

Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders.

Insects comprise the most diverse and successful animal group with over one million described species that are found in almost every terrestrial and limnic habitat, with many being used as important models in genetics, ecology, and evolutionary research. Genome sequencing projects have greatly expanded the sampling of species from many insect orders, but genomic resources for species of certain insect lineages have remained relatively limited to date. To address this paucity, we sequenced the genome of the banded demoiselle, Calopteryx splendens, a damselfly (Odonata: Zygoptera) belonging to Palaeoptera, the clade containing the first winged insects.

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs.

OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations.

The role of transportation to access maternal care services for women in rural Bangladesh and Burkina Faso: A mixed methods study.

Objective: To understand the role of transportation in accessing health care during pregnancy, delivery, and the postpartum period among women in rural Bangladesh and Burkina Faso.

Methods: An exploratory mixed methods study was conducted in Mymensingh district in Bangladesh and Kaya district in Burkina Faso. We recruited 300 women from Bangladesh and 340 from Burkina Faso with a delivery outcome within one year of interview.

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand.

The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. In order to better understand the adaptive response of cells during a transition to contaminated material, we analyzed here the genome and short-term (1 h) changes in genome-wide gene expression of the BTEX-degrading bacterium Pseudomonas veronii 1YdBTEX2 in non-sterile soil and liquid medium, both in presence or absence of toluene.

Once daily mometasone furoate aqueous nasal spray is as effective as twice daily beclomethasone dipropionate for treating perennial allergic rhinitis patients.

Background: Perennial allergic rhinitis is chronic and persistent, may lead to a constellation of secondary complaints including sinusitis, mouth-breathing, and some symptoms resembling a permanent cold, and often requires constant medical intervention. Well-tolerated nasal corticosteroids, alone or in combination with antihistamines, have been found to be very effective in treating this condition.

Objective: To compare the effectiveness and tolerability of mometasone furoate aqueous suspension, a new once daily nasal spray, to placebo vehicle and to beclomethasone dipropionate, administered twice daily, in patients with perennial allergic rhinitis.

Comparative randomised clinical study of tolerability and efficacy of Rhinomer Force 3 versus a reference product in post-operative care of the nasal fossae after endonasal surgery.

Twenty-eight patients undergoing rhinologic surgery were enrolled in a clinical study to compare two post-operative cleansing preparations. Patients were asked to wash their nasal fossae for 1 month, either with Rhinomer, a cleansing preparation of isotonic, sterile, undiluted sea water, presented in slightly pressurised bottle with neither CFC nor preservative, or with Prorhinel, a marketed solution containing an antiseptic agent. Patients were randomly allocated to treatment beginning 2 days after surgery.

Facial thermography during nasal provocation tests with histamine and allergen.

Changes of skin temperature (T degree) of the nose area during nasal provocation tests with histamine and allergen were followed by means of an infrared thermography camera. By a colimator system in which temperatures measured on a given surface can be integrated and averaged, thermography allows the continuous and quantitative recording of the temperature during the whole procedure in a completely noninvasive way. In 10 normal subjects, increasing doses of histamine induced a dose-dependent rise of the nose external temperature.

Clinical evaluation of a new in-vitro assay for specific IgE, the immuno CAP system.

The Pharmacia CAP system is a new assay for specific IgE characterized by a new solid phase (hydrophilic polymer encased in a capsule). The CAP results were compared to those of the Phadebas IgE RAST and skin-prick tests (SPT) performed in 145 subjects suffering from rhinitis and/or asthma with eight common inhalant allergens (total number of tests = 1160). Concording CAP/RAST results were found in 91% of the tests.

Effects of terfenadine and pseudoephedrine, alone and in combination in a nasal provocation test and in perennial rhinitis.

The effects of terfenadine and pseudoephedrine, alone and in combination, have been assessed in a nasal provocation test and in perennial rhinitis. In a double-blind, placebo-controlled cross-over nasal provocation test, twelve men allergic to grass pollen were treated with two daily doses of placebo, terfenadine 60 mg, pseudoephedrine 120 mg, or the combination of the two, for 2 days preceding each test. The allergic reaction threshold, based on rhinorrhoea, sneezing and nasal inspiratory peak flow rate, was raised significantly both by terfenadine and pseudoephedrine, and their effects appeared additive (repeated measures analysis of variance).