An outstanding debt: Noel Pearson’s A Rightful Place. Race, Recognition and a more complete Commonwealth

‘A Rightful Place’ by Aboriginal lawyer and activist Noel Pearson traverses the contentious spheres of racial distinction and the psychology of anthropological categorisation with estimable fortitude. His historical and sociopolitical analysis highlights the parameters of ‘race’ within the Australian federal constitution and the distorting effect this has had on Indigenous Australians since its inception. Fiercely emotive language and personal narration is used to examine our troublesome history and the national scars created in the wake of western influence and British colonisation. We have deep reparations to account for - and it’s time to pay up

Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird

<p>Abstract</p> <p>Background</p> <p>With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (<it>Alligator mississippiensis</it>), painted turtle (<it>Chrysemys picta</it>) and emu (<it>Dromaius novaehollandiae</it>) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken.</p> <p>Results</p> <p>From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes.</p> <p>Conclusion</p> <p>Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.</p

Calderon, J-A., L. Demailly et S. Muller (dir), Aux Marges du Travail, Toulouse, Octarès Editions, 2016, 230 p.

L'ouvrage collectif consécutif aux JIST 2014 (Journées Internationales de Sociologie du Travail) invite à « décentrer le regard » sociologique sur les marges du travail. Définies surtout par ce qu'elles ne sont pas, ces dernières sont situées par rapport aux « centres », qu’elles ont vocation à questionner. Non exempte de présupposés théoriques, leur analyse gagne, selon les coordinateurs de l’ouvrage, à être circonstanciée et à sortir du prisme de la domination qui voudrait que la marge ne s..

Exploration of phylogenetic data using a global sequence analysis method

BACKGROUND: Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets. RESULTS: Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses – in particular explicit statements of homology inherent in character matrices – the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 γ-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers. CONCLUSION: The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis

Flow Moods: Recommending Music by Moods on Deezer

The music streaming service Deezer extensively relies on its Flow algorithm, which generates personalized radio-style playlists of songs, to help users discover musical content. Nonetheless, despite promising results over the past years, Flow used to ignore the moods of users when providing recommendations. In this paper, we present Flow Moods, an improved version of Flow that addresses this limitation. Flow Moods leverages collaborative filtering, audio content analysis, and mood annotations from professional music curators to generate personalized mood-specific playlists at scale. We detail the motivations, the development, and the deployment of this system on Deezer. Since its release in 2021, Flow Moods has been recommending music by moods to millions of users every day.Comment: 16th ACM Conference on Recommender Systems (RecSys 2022) - Industry pape

Track Mix Generation on Music Streaming Services using Transformers

This paper introduces Track Mix, a personalized playlist generation system released in 2022 on the music streaming service Deezer. Track Mix automatically generates "mix" playlists inspired by initial music tracks, allowing users to discover music similar to their favorite content. To generate these mixes, we consider a Transformer model trained on millions of track sequences from user playlists. In light of the growing popularity of Transformers in recent years, we analyze the advantages, drawbacks, and technical challenges of using such a model for mix generation on the service, compared to a more traditional collaborative filtering approach. Since its release, Track Mix has been generating playlists for millions of users daily, enhancing their music discovery experience on Deezer.Comment: RecSys 2023 - Industry track with oral presentatio

GOHTAM: a website for ‘Genomic Origin of Horizontal Transfers, Alignment and Metagenomics’

Motivation: This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies

The Evolution of Word Composition in Metazoan Promoter Sequence

The field of molecular evolution provides many examples of the principle that molecular differences between species contain information about evolutionary history. One surprising case can be found in the frequency of short words in DNA: more closely related species have more similar word compositions. Interest in this has often focused on its utility in deducing phylogenetic relationships. However, it is also of interest because of the opportunity it provides for studying the evolution of genome function. Word-frequency differences between species change too slowly to be purely the result of random mutational drift. Rather, their slow pattern of change reflects the direct or indirect action of purifying selection and the presence of functional constraints. Many such constraints are likely to exist, and an important challenge is to distinguish them. Here we develop a method to do so by isolating the effects acting at different word sizes. We apply our method to 2-, 4-, and 8-base-pair (bp) words across several classes of noncoding sequence. Our major result is that similarities in 8-bp word frequencies scale with evolutionary time for regions immediately upstream of genes. This association is present although weaker in intronic sequence, but cannot be detected in intergenic sequence using our method. In contrast, 2-bp and 4-bp word frequencies scale with time in all classes of noncoding sequence. These results suggest that different genomic processes are involved at different word sizes. The pattern in 2-bp and 4-bp words may be due to evolutionary changes in processes such as DNA replication and repair, as has been suggested before. The pattern in 8-bp words may reflect evolutionary changes in gene-regulatory machinery, such as changes in the frequencies of transcription-factor binding sites, or in the affinity of transcription factors for particular sequences