809 research outputs found
Efficient k-mer based curation of raw sequence data: application in Drosophila suzukii
No full textPreprint version 2 of this article (Gautier, 2023a, https://doi.org/10.1101/2023.04.18.537389) has been peer-reviewed and recommended by Peer Community In Genomics (Galtier, 2023, https://doi.org/10.24072/pci.genomics.100244).The Clark and Clark-l k–mer databases and the (cleaned) assemblies used to build them have been made publicly available from the Data INRAE repository (Gautier, 2023b, https ://doi.org/10 . 57745/HYTIBH). The compressed archive also contains scripts used to run Clark and Clark-l analyses and parse the results. All sequencing data analyzed in this study are publicly available under the accession IDs reported in Tables 1, S2 and S3. Supplementary Tables S1 to S5 and Supplementary Figures S1 to S5 are available online with the latest preprint version of the manuscript (Gautier, 2023a, https://doi.org/10.1101/2023.04.18.537389).International audienceSeveral studies have highlighted the presence of contaminated entries in public sequence repositories, calling for special attention to the associated metadata. Here, we propose and evaluate a fast and efficient k–mer-based approach to assess the degree of mislabeling or contamination. We applied it to high-throughput whole-genome raw sequence data for 236 Ind-Seq and 22 Pool-Seq samples of the invasive species Drosophila suzukii. We first used Clark software to build a dictionary of species-discriminating k–mers from the curated assemblies of 29 target drosophilid species (including D. melanogaster, D. simulans, D. subpulchrella, or D. biarmipes) and 12 common drosophila pathogens and commensals (including Wolbachia). Counting the number of k–mers composing each query sample sequence that matched a discriminating k–mer from the dictionary provided a simple criterion for assignment to target species and evaluation of the entire sample. Analyses of a wide range of samples, representative of both target and other drosophilid species, demonstrated very good performance of the proposed approach, both in terms of run time and accuracy of sequence assignment. Of the 236 D. suzukii individuals, five were reassigned to D. simulans and eleven to D. subpulchrella. Another four showed moderate to substantial microbial contamination. Similarly, among the 22 Pool-Seq samples analyzed, two from the native range were found to be contaminated with 1 and 7 D. subpulchrella individuals, respectively (out of 50), and one from Europe was found to be contaminated with 5 to 6 D. immigrans individuals (out of 100). Overall, the present analysis allowed the definition of a large curated dataset consisting of > 60 population samples representative of the worldwide genetic diversity, which may be valuable for further population genetics studies on D. suzukii. More generally, while we advocate careful sample identification and verification prior to sequencing, the proposed framework is simple and computationally efficient enough to be included as a routine post-hoc quality check prior to any data analysis and prior to data submission to public repositories
Peperomia robusta G. Mathieu 2020, sp. nov.
No full textPeperomia robusta G. Mathieu, sp. nov. (Fig. 2, 3). Holotypus: MADAGASCAR. Reg. Alaotra-Mangoro [Prov. Toamasina]: Zahamena NP, NW border, 7 km SE of Antanandavao, along trail to camp 1 (1300 m N of campsite), 17°29'41"S 48°43'59"E, 1300 m, 26.IX.2001, Mathieu 446 (BR [BR000000916063]!; iso-: B [B100001403]!, G [G00341878]!, MO-5662979!, TAN!). Peperomia robusta G. Mathieu differs by the pilose indument from P. portulacoides (Lam.) A. Dietr., an essentially glabrous species, and from P. pedunculata C. DC., of which the indument is characterized by short erect trichomes. Perennial terrestrial herb, occasionally epiphytic, up to 40(–50) cm tall. Stem simple or 1–3 branched, erect or basally decumbent, terete, up to 8 mm diam. at the base, internodes 4–8 cm, pilose, dark red. Leaves opposite or 3–4-verticilate; petiole 8–10 mm long, pilose, red; lamina coriaceous to succulent, broad obovate, sometimes elliptic, 3–7 × 2–4 cm, smallest at the base of the stem, length/width ratio ca 1.6, apex rounded, base obtuse to acute or cuneate, 3-nerved, often only central nerve distinct, slightly impressed adaxially, both sides loosely pilose (usually more dense abaxially or at the nerves) or glabrescent, rather dark dull green adaxially, pale green abaxially, margin entire, ciliate, more dense in the apical half. Inflorescence 1 terminal spadix or 2–3(–4) together; peduncle 1 –2 cm long, basally pilose; rachis 5– 10 cm long, glabrous, loosely to moderately densely flowered, floral bracts orbicular or slightly elliptic. Fruit globose, ca. 0.5 mm diam., subbasally attached, entirely covered with sticky papillae, individual papilla longer than wide, style wide conical, horseshoe shaped ridge around subapical stigma, highest adaxially, open abaxially, conical pseudopedicellate when mature. Etymology. – The specific epithet refers to the general habit of the plant. It is one of the largest Peperomia species of Madagascar. Distribution and habitat. – The new species is endemic to North-East Madagascar from the National Park of Zahamena to the Loky-Manambato Protected Area (Daraina) where it occurs in medium altitude moist evergreen forests at an elevation of 700–1400 m. Because of its distribution and the number of currently known collections it is not considered as a rare species. Conservation status. – Peperomia robusta is known from 15 locations, all but two are encompassed in the protected area network (Anjanaharibe Sud, COMATSA Nord, Corridor Ankeniheny Zahamena, Loky Manambato, Manongarivo, Marojejy, Masoala and Zahamena). With an Extent of Occurrence (EOO) of c. 59,000 km ², an Area of Occupancy (AOO) of 60 km ² and no current threats, P. robusta is assigned a status of “Least Concern” [LC] using the IUCN Red List Categories and Criteria (IUCN, 2012). Notes. – Peperomia robusta resembles P. portulacoides, which is essentially glabrous. However, varieties of the latter species with indument have been published: P. portulacoides var. pilosa Baker from the Seychelles and P. portulacoides var. hirtella Wawra from Sri Lanka. Var. pilosa shows a short, erect indument. Its synonimization with P. tomentosa (Vahl) A. Dietr. (FRIEDMANN, 2011: 78) is questionable. Peperomia tomentosa not only exhibits a villous indument but is also distinct in its (sub)sessile leaves. Var. hirtella shows much smaller leaves (1–1.5 cm long). It is only known from its type collection and probably belongs to P. heyneana Miq. Peperomia robusta has to be distinguished from P. pedunculata, known from La Réunion, which does show an indument, characterized however by short erect trichomes. Moreover, the leaves of that species are smaller, 2–4(–5) cm long, elliptic, and usually show an obtuse apex. At last, there is some resemblance in general habit with P. mantadiana G. Mathieu. That is a glabrous species showing elliptic-lanceolate leaves. Peperomia robusta is considered as belonging to Peperomia subg. Micropiper, as it is the case with P. portulacoides and P. pedunculata (FRENZKE et al., 2015). Paratypi. – MADAGASCAR. Reg. Alaotra-Mangoro [Prov. Toamasina]: Mount Ankaroka, [17 °48'S 48°32'E], 1200 –1400 m, X.1937, Humbert 17511 (P); Zahamena AP, massif de l’Andrangovalo, [17°40'S 48°45'E], 1200–1300 m, X.1937, Humbert 17755 (P); ibid. loco, entre les rivière Sahatavy et Sivora, 17 °36'34"S 48°47 '10"E, 709 m, 2.X.2001, Ratovoson 547 (MO). Reg. Analanjirofo [Prov. Toamasina]: Masoala NP, N ridge of Ambohitsitondroinan’Mahalevona, 25°26'16"S 49°57'22"E, 1190 m, 23.II.2003, Lowry 6126 (MO, P). Reg. Atsinanana [Prov. Toamasina]: Rahobevava massif, [17°59'59"S 48°46'57"E], 1250 m, 12.III.1951, Cours 4330 (P, TAN). Reg DIANA [Prov. Antsiranana]: Manongarivo, 14°02'S 48°18'E, 1050 m, 15.XI.1994, Gautier 2555 (BR, G, TAN). Reg SAVA [Prov. Antsiranana]: Marojejy massif, NE side, [14°25'S 49°43'E], 800–1200 m, 25.I.–25.II.1949, Humbert 23165 (BR, P); ibid. loco, W side, 1000–1200 m, 9.XI.–2.XII.1939, Humbert 31394 (P); vallée inférieure de l’Androranga, Mt Anjenabe, [14°17'S 49°46'E], 1100–1130 m, 3–7.XII.1950, Humbert 24161bis (P); Marojejy PA, along E trail to summit, 14°26'20"S 49°44'50"E, 1150 m, 25.X.2001, Mathieu 485 (BR, MO, P, TAN); Distr. Vohemar, forêt de Binara, Daraina, 13°16'38"S 49°35'21"E, 1012 m, 20.XI.2005, Nusbaumer 1639 (BR, G, K, MO, TEF); Distr. Andapa, forêt de Betaolana, 11 km NW of Ambodiangezoka (camp 2), 14°36'22"S 49°25'30"E, 1200 m, 22.X.1999, Rakotomalaza 2025 (G); Marojejy, 14°29'S 49°38'E, 1300–1500 m, 21–22.I.1994, Rasoavimbahoaka 17 (MO, TAN); Andranomilolo, forêt située env. 13 km à l’W d’Andranopositra, 14°19'21"S 49°17'46"E, 1380 m, 7.XI.2006, Ravelonarivo 1955 (BR, MO, P, TAN).Published as part of Mathieu, Guido, 2020, Endemic Peperomia (Piperaceae) novelties from eastern Madagascar, pp. 75-82 in Candollea 75 (1) on page 78, DOI: 10.15553/c2020v751a7, http://zenodo.org/record/572481
Just Making It Up: Structure and Spontaneity in Music and Teaching. An interview with W.A. Mathieu by Noam Lemish
No full textWilliam Allaudin Mathieu (born in 1937) is a consummate musician, a pianist, composer, author, and teacher — and, in my view, one of the most influential musicians of his generation. In his early twenties he composed music for the Kenton and Ellington Big Bands, was the founding musical director of the famed Second City of Chicago (Improv Theater) and was a pioneer in the 1960s of the application of theater improvisation games into the musical sphere. He is the author of four influential books, including the best selling "The Listening Book" (1991). In a teaching career spanning more than fifty years, Mathieu has been an important influence and guide to many musicians worldwide. As I demonstrate throughout this essay, W.A. Mathieu reminds us that in highlighting the world of improvisation we must be careful not to romanticize spontaneity, for doing so might well involve our falling into the trap of dualistic thinking that separates if not excludes such activity from composition. Overall, Mathieu implores us to reflect deeply about false dichotomies as improvisation/composition, and by extension think more broadly about the perils of dualistic thinking in general. In exploring themes in discussion of improvisation, I highlight some of the ways in which we can begin to draw connections between Mathieu’s ideas and the usefulness of improvisation to pedagogy in music education and beyond
Renal insufficiency, a frequent complication with age in oral-facial-digital syndrome type I.
No full textpeer reviewedSaal S, Faivre L, Aral B, Gigot N, Toutain A, Van Maldergem L, Destree A, Maystadt I, Cosyns J-P, Jouk P-S, Loeys B, Chauveau D, Bieth E, Layet V, Mathieu M, Lespinasse J, Teebi A, Franco B, Gautier E, Binquet C, Masurel-Paulet A, Mousson C, Gouyon J-B, Huet F, Thauvin-Robinet C. Renal insufficiency, a frequent complication with age in oral-facial-digital syndrome type I. The oral-facial-digital syndrome type I (OFD I) is characterized by multiple congenital malformations of the face, oral cavity and digits. A polycystic kidney disease (PKD) is found in about one-third of patients but long-term outcome and complications are not well described in the international literature. Renal findings have been retrospectively collected in a cohort of 34 females all carrying a pathogenic mutation in the OFD1 gene with ages ranging from 1 to 65 years. Twelve patients presented with PKD - 11/16 (69%) if only adults were considered -with a median age at diagnosis of 29 years [IQR (interquartile range) = (23.5-38)]. Among them, 10 also presented with renal impairment and 6 were grafted (median age = 38 years [IQR = (25-48)]. One grafted patient under immunosuppressive treatment died from a tumor originated from a native kidney. The probability to develop renal failure was estimated to be more than 50% after the age of 36 years. Besides, neither genotype-phenotype correlation nor clinical predictive association with renal failure could be evidenced. These data reveal an unsuspected high incidence rate of the renal impairment outcome in OFD I syndrome. A systematic ultrasound (US) and renal function follow-up is therefore highly recommended for all OFD I patients
Development and test of a universal FPGA-based Arc Detector for accelerating cavities at the facility for Antiproton and Ion Research FAIR [10.08.2011]
No full textOnTEAM metadata: GDSID: DOC-2011-Nov-83; Attribute ID: LIBRARY-thesis_ma-2011-001; Title: [GSI Ma 2011-01] Development and test of a universal FPGA-based Arc Detector for accelerating cavities at the facility for Antiproton and Ion Research FAIR [10.08.2011]; Author(s): Omet, Mathieu; Corporate author(s): ; Publication date: 20111116; Creator: manton; Creation date: 16.11.2011 16:02:19; Change date: 16.11.2011 16:44:09; Access: Welt; Attribute type: Text.Thesis.MA; Directory path: ['GSI Publications', 'GSI as Publisher']; Attribute path: ['Infrastructure', 'Library and Documentation', 'thesis_ma', 'Added in 2011']; File name(s): ['DOC-2011-Nov-83-1.pdf']; File title(s): ['']; File access: ['GSI-intern'
L’industria in epoca preindustriale? Riflessioni su “L’industrie au village” di Catherine Verna
No full textThe book published by French medievalist Catherine Verna L’industrie au village (2017) raises a double question: on the one hand because it uses the term industry in reference to the Middle Ages, and on the other because it associates the same term with the village, i.e. rurality, whereas medieval industry – at least for those who think it is possible to talk about industry during these times – is traditionally associated with cities rather than the countryside. In the introduction of the book, Verna conducts a historiographical review of the concept of industry, limited to only French medievalists. This paper endeavors a similar review but focused on Italian historiography, illustrating how the concept of industry appears no clearer to Italian medievalists than it does to French ones. In addition, it discusses the definition of industry proposed by Verna – in order to determine whether it is appropriate or not to talk about “industry in the pre-industrial times” – and analyzes what the author means by the expression “industry in the village”. In particular, it pays attention to the concepts of small town and industrial district developed by Verna within her case study (the Pyrenean village of Arles-sur-Tech and the Vallespir localities in the 14th and 15th centuries), i.e. two concepts that constitute valuable interpretive keys for the history of medieval and modern Italy
La Cour de cassation et le législateur : ou comment avoir le dernier mot
No full textInternational audienceA propos de l'arrêt de l'Assemblée plénière de la Cour de cassation du 23 janvier 2004 (D. 2004, p. 1108, note P.-Y. Gautier
Preliminary Analysis of the PreFlexMS Molten Salt Once-Through Steam Generator Dynamics and Control Strategy
No full textEfficient k-mer based curation of raw sequence data: application in Drosophila suzukii
No full textSeveral studies have highlighted the presence of contaminated entries in public sequence repositories, calling for special attention to the associated metadata. Here, we propose and evaluate a fast and efficient k–mer-based approach to assess the degree of mislabeling or contamination. We applied it to high-throughput whole-genome raw sequence data for 236 Ind-Seq and 22 Pool-Seq samples of the invasive species Drosophila suzukii. We first used Clark software to build a dictionary of species-discriminating k–mers from the curated assemblies of 29 target drosophilid species (including D. melanogaster, D. simulans, D. subpulchrella, or D. biarmipes) and 12 common drosophila pathogens and commensals (including Wolbachia). Counting the number of k–mers composing each query sample sequence that matched a discriminating k–mer from the dictionary provided a simple criterion for assignment to target species and evaluation of the entire sample. Analyses of a wide range of samples, representative of both target and other drosophilid species, demonstrated very good performance of the proposed approach, both in terms of run time and accuracy of sequence assignment. Of the 236 D. suzukii individuals, five were reassigned to D. simulans and eleven to D. subpulchrella. Another four showed moderate to substantial microbial contamination. Similarly, among the 22 Pool-Seq samples analyzed, two from the native range were found to be contaminated with 1 and 7 D. subpulchrella individuals, respectively (out of 50), and one from Europe was found to be contaminated with 5 to 6 D. immigrans individuals (out of 100). Overall, the present analysis allowed the definition of a large curated dataset consisting of > 60 population samples representative of the worldwide genetic diversity, which may be valuable for further population genetics studies on D. suzukii. More generally, while we advocate careful sample identification and verification prior to sequencing, the proposed framework is simple and computationally efficient enough to be included as a routine post-hoc quality check prior to any data analysis and prior to data submission to public repositories
Energy and Waste
No full textThe Anthropocene epoch is defined by the profound impacts of human activity on natural ecosystems. Industrial processing of raw materials produces vast quantities of man-made matter including materials, wastes, and residues, which Harpet (2001) termed the rudosphere. Monsaingeon (2017) further introduced the term poubellocene to characterize this era of waste and a wasteful world (UNEP 2024). In France, the article L541-1 from the Environment Code defines waste as “any residue from a production, transformation, or use process, any substance, material, product, or more generally any good or piece of furniture that is abandoned or that its holder intends to abandon.” In other words, the term waste is generic, qualifying any element that is abandoned
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