dataesr/scientific-paragraphs-categorization huggingface dataset:
mirabile, are described as having small basidiomata, sessile endoperidial body, basidiospores 3. 5-5. 0 μm diam. , and lignicolous habit. Leprieur's revision of the original type collections of G. mirabile from French Guiana held at PC (PC0084351, Leprieur 849, 2 plates), not successfully sequenced, suggests that G. mirabile is a morphological synonym of G. schweinitzii. Since we have not been able to analyze the Japanese collections of Kasuya et al. [16]  we cannot ensure whether their morphology matches that of the PC vouchers of G. mirabile. However, all available photographs of the samples alleged to be G. mirabile at on-line TNS fungarium databases (including source materials of the sequences used in our analysis) are from specimens with small mycelial tufts in a slightly hirsute exoperidium (S6 Fig).
Subiculum and rhizomorphs with surface covered by crystals, with coarser and more irregular oblique prism shape. Mycelial layer composed of hyaline to yellowish, thinwalled hyphae (<1 μm), 1. 66-3. 04 μm diam, dextrinoid, lumen not evident. Hairs dark brown, thick-walled (0. 7-1. 0 μm. ), skeletal hyphae, 3. 2-4. 5 μm diam, strongly dextrinoid, sinuous, lumen not conspicuous. Fibrous layer composed of hyaline, sinuous, thick-walled hyphae (0. ´gica Guaribas, 11 Jul. 2015, leg. J. O. Sousa, J. F. Freitas-Neto (UFRN-Fungos 2759, ITS sequence GenBank KX761177 and LSU sequence GenBank KX761178). Remarks. This species is recognized by its yellowish exoperidium; with ephemeral, long (0. 5-2. 0 mm high), dark brown hairs; peristome delimited by a yellowish line; and basidiospores globose to subglobose, 2.
schweinitzii may be endemic, since the Pakaraima Mountains are an ecological barrier for many organisms  [44, 48, 49]. Keeping this in mind, the ten synonyms of Geastrum schweinitzii proposed by Ponce de Leon  [27]  need to be reassessed. Furthermore, some of the putative synonyms are from very distinct ecoregions  [5]  Fifteen samples with the morphology traditionally associated to the name G. schweinitzii, collected from widespread areas of the neotropical region, appear in clade XII in Fig  1 , illustrating a case of semi-cryptic species  [17, 18, 20, 21]  and evolutionary convergence in their morphology. Another case of semi-cryptic species of G. schweinitzii is G. baculicrystallum, the two species could be distinguished only by details in basidiospore size and ornamentation. Three ITS sequences from GenBank previously identified under the name G.
Comparative analyses were done including the following type collections: Geastrum hirsutum, BRAZIL-Pernambuco, Recife, Reserva Ecologica do Gurjau, 12 Jul. 2003, leg. I. G. Baseia (Ma-Fungi 67886 paratype); Geastrum pleosporum, CAMEROON, Centre Province, Department of Nyong & So'o, in the Mbalmayo forest reserve, 47 km South east of Yaounde, 16 Oct. 2002, leg. C. Douanla-Meli (MA-Fungi 56971 isotype); Geastrum pusillipilosum, BRAZIL, Paraı ´ba, Mamanguape, REBIO Guaribas, SEMA II, 26 Jun. 2014, leg. J. O. Sousa JM100 (UFRN-Fungos 2315 holotype, ITS sequence GenBank KX761175); Geastrum trichiferum PACA 15970, BPI 706088 (Rick's original collection), and BPI 706086; and Geastrum schweinitzii, SURINAME, (K (M) 180187 type, K(M) 180187 isotype).
Fig) with 862 steps (CI = 0. 572, RI = 0. 823, RC = 0. 471, HI = 0. 428). The ITS/LSU concatenated dataset included 28 samples with both ITS and LSU sequences, 1583 unambiguously aligned nucleotide positions: 1242 constant, 72 parsimony uninformative, and 269 parsimony-informative. Parsimony analyses resulted in a most parsimonious tree (S3 Fig) with 748 steps (CI = 0. 591, RI = 0. 779, RC = 0. 460, HI = 0. 409). Maximum likelihood analyses with the default model GTRCAT gave a best ITS tree with-lnL = -2,900. 087 (S2 Fig). Concatenated ITS/LSU likelihood analyses gave a best tree with-lnL = -4340. 387 (S4 Fig).
2 μm), subglobose to oval, 9. 4-16. 4 × 6. 4-10. 0 μm. Basidiospores brownish, subglobose, 3. 8-4. 5 × 3. 6-4. 4 μm (x = 4. 1 ± 0. 2 × 3. 9 ± 0. 2, Q m = 1. 04, n = 30), ornamentation inconspicuous under LM, verrucose under SEM, warts very small (0. 02-0. 08 μm high). Ecology and distribution. This species has a Neotropical distribution. Found in the biome Tropical & Subtropical Moist Broadleaf Forests of Brazil (Pernambuco coastal forests ecoregion), and French Guiana (Guianan lowland moist forests) on decaying wood with gregarious or caespitose growth. Additional material examined. BRAZIL, Paraı ´ba, Areia, Mata do Pau Ferro, 17 Jul. 2012, leg. D. S. Alfredo (UFRN-Fungos 1857 paratype, ITS sequence GenBank MH635018, LSU sequence Genbank MH635035). FRENCH GUIANA, Sau ¨l, Layon des Grands Arbres, 3 May 2008, leg.
8-5. 1 × 3. 7-4. 9 μm), with longer warts; the basidia differ, with clavate, pyriform to lageniform shapes in G. neoamericanum, and the crystals with rod shape in G. baculicrystallum. The bacullar crystals on the rhizomorphs, and more inconspicuous warts on the basidiospores in G. baculicrystallum can differentiate this species from G. schweinitzii; we can consider G. baculicrystallum a semi-cryptic species of G. schweinitzii. Geastrum brunneocapillatum J. O. Sousa, Accioly, M. P. Martı ´n & Baseia, sp. nov. , Fig 5, A1-A5, Mycobank MB 827086. Etymology. Referring to the dark brown hairs on the exoperidium. Holotype. Paraı ´ba, Mamanguape, Reserva Biologica de Guaribas, 26 Jun. 2014, leg. J. O. Sousa, Y. M. Nascimento & E. J. Souza JM101 (UFRN-Fungos 2286, ITS sequence GenBank MH634996, LSU sequence GenBank MH635029).
Additional material examined. BRAZIL, Paraı ´ba, Areia, Mata do Pau Ferro, Trilha Boa Vista, 21 Jul. 2014, leg. J. O. Sousa, D. S. Alfredo & E. J. Souza, JM117 (UFRN-Fungos 2834, paratype, ITS sequence GenBank MH634997). COSTA RICA, La Selva Biological Station, C. Ovrebo 2303 (UFRN-Fungos 2851, paratype, ITS sequence GenBank MH634998). Additional species examined. Geastrum hirsutum, BRAZIL-Pernambuco, Recife, Reserva Ecologica do Gurjau, 12 Jul. 2003, leg. I. G. Baseia (MA-Fungi 67886, paratype, ITS sequence GenBank MH538295) (Fig 5, B1-B5); Amazonas, Manaus, Reserva Florestal Adolfo Ducke, 02 Jul. 2014, leg. M. D. F. Santana (INPA 259950, ITS sequence GenBank MH634993 and LSU sequence GenBank MH635026). Geastrum pusillipilosum, BRAZIL. Paraı ´ba, Mamanguape, REBIO Guaribas, SEMA II, 26 Jun.
2014, leg. J. O. Sousa JM100 (UFRN-Fungos 2315, holotype, ITS sequence GenBank KX761175 and LSU sequence GenBank KX761176) (Fig 5, C1-C5); Ceara, Crato, Floresta Nacional do Araripe, 01 Apr. 2014, leg. R. J. Ferreira (UFRN-Fungos 2256, paratype, ITS sequence GenBank KX761180); Paraı ´ba, Mamanguape, Reserva Biolo.
P. -A. Moreau, C. Lecuru, sp. nov. , Fig 4, C1-C5 Mycobank MB 827090. Etymology. In honor to Dr. Courtecuisse, research scientist from France. Holotype. GUADELOUPE, Saint-Claude, Matouba, along the Victor Hugues trail, on litter of Cupressus cf. macrocarpa, leg. F. Hairie, 9 Sep. 2004 (LIP FH2004090503, ITS sequence Gen-Bank MH635003, LSU sequence GenBank MH635033). Diagnosis. This species is similar to G. baculicrystallum, but G. courtecuissei is distinguished by the presence of echinulate exoperidium and basidiospores with longer warts, conspicuous under LM. Another morphologically closel-related species is G. pleosporum, which has polymorphic basidiospores (4. 0-7. 0 × 3. 2-5. 0 μm), while, G. baculicrystallum has globose to subglobose basidiospores (3. 7-4. 9 μm diam). Description. Unexpanded basidiomata epigeous, light brown (N 10 Y 30 M 10 ), subglobose to citriform, 2.
8-5. 0 × 3. 7-4. 9 μm (x = 4. 1 ± 0. 4 × 4. 0 ± 0. 3, Q m = 1. 03, n = 30), ornamentation conspicuous in LM. Ecology and distribution. This species has a Neotropical distribution. Found in the biome Tropical & Subtropical Moist Broadleaf Forests of Argentina (Alto ParanaAtlantic forest ecoregion) and Guadeloupe Island (Leeward Islands moist forest ecoregion). Additional material examined. ARGENTINA, Puerto Iguazu, no date, leg. E. Grassi (MA-Fungi 83779, paratype, ITS sequence GenBank KF988437, LSU sequence GenBank KF988567). GUADELOUPE, Saint-Claude, Matouba, along the Victor Hugues trail, on litter of Cupressus cf. macrocarpa, 10 Aug. 2011, leg. P. -A. Moreau, LIP PAM/GUAD 11. 04, paratype, ITS sequence GenBank MH635002).
2013, J. O. Sousa & D. S Alfredo, JM64 (UFRN-Fungos 2149, paratype, ITS sequence GenBank MH635021, LSU sequence GenBank MH635039); Rio Grande do Norte, Parnamirim, Mata da Base Aerea de Natal, 23 Aug. 2007, leg. E. P. Fazolino (UFRN-Fungos 348, paratype, ITS sequence GenBank MH635019); Rondonia, Modulo Abunã, 25 Jun. 2014, leg. M. D. F. Santana (INPA 259949, paratype, ITS sequence GenBank MH635025, LSU sequence GenBank MH635041); Minas Gerais, Santa Rita do Sapucaı ´, Reserva Biologica Municipal Santa Rita Mı ´tzi Brandão, 2015, leg. D. S. Alfredo & P. Lavor, DSA279 (UFRN-Fungos 2850, paratype, ITS sequence GenBank MH635000, LSU sequence GenBank MH635032); Bahia, Ilheus, RPPN Mãe da Mata, 19 Dec. 2006, leg. J. L. Bezerra 858 (CEPEC 1391, paratype, ITS sequence GenBank MH635020). GUADELOUPE, Petit-Bourg, Carrère, Forêt departementalo-domaniale de Bois Sergeant, 21 Nov.
2006, leg. C. Lecuru (LIP CL/Guad 06. 010, paratype, ITS sequence GenBank MH635011); Petit-Bourg, Route forestière de Jules, domaine de Duclos, 24 Nov. 2006, leg. C. Lecuru (LIP CL/Guad 06. 056, paratype, ITS sequence GenBank MH635012). MARTINIQUE, Saint-Esprit, morne David, 23 Aug. 2004, leg. C. Lecuru (LIP CL/ Mart 04. 001, paratype, ITS sequence GenBank MH635013). FRENCH GUIANA, 1 Mar. 2012, leg. J. -L. Cheype (LIP JLC12030103, paratype, ITS sequence GenBank MH635014, LSU sequence GenBank MH635038); 2012, leg. M. Roy (LIP MR-GUY-12-004, paratype, ITS sequence GenBank MH635015).
P. -A. Moreau & C. Lecuru. sp. nov. , Fig 5, D1-D5, Mycobank MB 827092. Etymology. Named in reference to its reddish-coloured exoperidum. Holotype. MARTINIQUE, Le Prêcheur, Anse Couleuvre, path towards Anse Levrier, 17 Aug. 2012, leg. P. -A. Moreau (LIP PAM/Mart 12. 100, ITS sequence GenBank MH635010, LSU sequence GenBank MH635037).
Additional material examined. BRAZIL. Rio Grande do Norte, Baı ´a Formosa, Reserva Particular do Patrimonio Natural Mata Estrela, 09 Jun. 2009, leg. B. D. B Silva, I. G. Baseia, T. S. Cabral (UFRN-Fungos 1214, paratype, ITS sequence GenBank KJ127029, LSU sequence GenBank JQ683662); Acre, Floresta Nacional do Macauã, 29 Jan. 2016, leg. A. M. Ottoni, AMO 604 (UFRN-Fungos 2844, paratype, ITS sequence GenBank MH634999, LSU sequence GenBank MH635031). MARTINIQUE, Le Prêcheur, Anse Couleuvre, along the road, in secondary mesophytic forest, 25 Aug. 2008, leg. C. Lecuru (LIP CL/MART 08. 067B, paratype, ITS sequence GenBank MH635009, LSU sequence GenBank MH635035).
J. O. Sousa, Accioly, M. P. Martı ´n & Baseia, sp. nov. , Fig 4, D1-D5, Mycobank MB 827094. Etymology. Referring to the reddish pseudoparenchymatous layer and the small size of basidiomata. Holotype. MARTINIQUE, Le Prêcheur, anse Couleuvre, 1 Sep. 2003, leg. R. Courtecuisse (LIP RC/MART 03. 015, ITS sequence GenBank MH635006).
1-0. 5 μm high), slightly columnar, with planar to rounded tips, apiculus reduced surrounded by columnar processes. Ecology and distribution. This species has a Neotropical distribution. Found in the biomes Tropical & Subtropical Moist Broadleaf Forests of Brazil (Pernambuco coastal forests ecoregion) and Martinique Island (Windward Islands moist forests), and in the biome Mangroves of Panama(Southern Mesoamerican Pacific mangroves ecoregion) on decaying wood, fruiting is gregarious, rarely cespitose. Additional material examined. BRAZIL, Paraı ´ba, Areia, Mata do Pau Ferro, Trilha do Cumbe, 15 Jul. 2013, leg. J. O. Sousa, D. S. Alfredo & R. A Lima JM36 (UFRN-Fungos 2308, paratype, ITS sequence GenBank MH634994, LSU sequence GenBank MH635027). PANAMA, Coiba Island, 15 Nov. 1996, leg. F. Pando & M.
P. Nuñez (MA-Fungi 36141, paratype, ITS sequence GenBank KF988438, LSU sequence GenBank KF988568). MARTINIQUE, Le Robert, bois Pothau, 30 Aug. 2008, leg. C. Lecuru (LIP CL/MART 08. 112, paratype, ITS sequence Gen-Bank MH635007, LSU sequence GenBank MH635034).
Acknowledgments The analyses of specimens of the genus Geastrum Pers. from distinct neotropical localities ( Antilles Islands, Argentina, Brazil, Costa Rica, French Guiana, Suriname ) in this work was only possible thanks to the collaboration of taxonomic and systematic researchers from many institutions of the world:  Universitede Lille and Universitede Toulouse (France) ;  Real Jardı ´n Botanico de Madrid (RJB-CSIC, Spain) ;  Universidade Federal do Rio Grande do Norte  and  Universidade Federal da Bahia (Brazil). The authors would like to express their thanks to the  Coordenacão de Aperfeicoamento de Pessoal de Nı ´vel Superior  ( CAPES-Brazil ) for the PhD scholarships awarded to  Thiago Accioly  and  Julieth Sousa  ( PDSE-2017 ); to the  Conselho Nacional de Desenvolvimento Cientı ´fico e  Tecnologico (CNPq-Brazil ,  Projeto Pesquisador Visitante Especial   PVE/407474/2013-7 ,  Marı ´a P.
Martı  ´n and  Iuri G. Baseia ). The authors are also thank  Donis Alfredo  for the photos from Kew´s collections,  Dr. Clark Ovrebo  for the collection UFRN-Fungos 2851 from  Costa Rica ,  Angelia Ottoni  for the collection UFRN-Fungos 2844 from  Acre state, Brazil ,  Marian Glenn  for English revision, the curators of herbaria K, LIP and PC for having made collections available to them,  Jean-Louis Cheype ,  Regis Courtecuisse, Francois Hairie, Jean-Pierre Fiard and Melanie Roy  for providing interesting material from  French West Indies. We are grateful to  Sophie Manzi  for help with molecular labwork, and we also thank  Jonathan Dubousquet  and  Morgan Ada  who have contributed to this work by conducting some DNA extractions and amplifications at the laboratory EDB. The  French Laboratories of Excellence Labex TULIP  ( ANR-10-LABX-41 ;  ANR-11-IDEX-0002-02 ) and  Labex CEBA  ( ANR-10-LABX-25-01 ), the  National Forest Office (ONF, France) , the program  ANR E-TRICEL (National Research Agency, France)  and the  DREAL Martinique (France)  provided financial support for this study.
This work was supported by: ( TA and JS) Coordenacão de Aperfeicoamento de Pessoal de Nı ´vel Superior  ( CAPES-Brazil ) for the PhD scholarships awarded to  Thiago Accioly  and  Julieth Sousa  ( PDSE-2017 ); ( IGB and MPM) Conselho Nacional de Desenvolvimento Cientı ´fico e Tecnologico (CNPq-Brazil ,  Projeto Pesquisador Visitante Especial   PVE/407474/2013-7 ,  Marı ´a P. Martı  ´n and  Iuri G. Baseia ); (PAM, MR and MG) The  French Laboratories of Excellence Labex TULIP  ( ANR-10-LABX-41 ;  ANR-11-IDEX-0002-02 ) and  Labex CEBA  ( ANR-10-LABX-25-01 ), the  National Forest Office (ONF, France) , the program  ANR E-TRICEL (National Research Agency, France)  and the  DREAL Martinique (France)  provided financial support for this study.
In the EUROCAT database  [28, 31] , which collects data on congenital malformations in Europe, the rate of elective TOP for gonosomal abnormalities varies considerably among countries, even when the laws governing TOP are similar  [25]. There is also variability among PDCs within a given country  [26, 32]. Nevertheless, reasons for this observed variability are unclear and literature has not yet been explored if this difference is due to the profession of the * PCDs staff members, to local laws upon TOP or severity of antenatal signs. Neither has the variability of the decisions been quantified with precision regards to the decision for TOP. Overall rates of TOP hence compare heterogeneous prenatal situations. Indeed, studies compare overall rates of TOP for Turner syndrome  [25, 27, 28] : they do not distinguish which signs led to prenatal diagnosis.
We used a multi-level model in order to take into account the hierarchical cases (vignettes) nested within experts (of different specialties), in turn nested within centers. For the agreement analyses we used Excel (Microsoft Office, version 15. 0. 4737. 1003). For the multilevel model, we used the multilevel logistic model (melogit) of Stata software (Stata 13. 1, Texas, USA). This study was approved by the Ethical Review Committee « Comité d'éthique de la recherche en obstétrique et gynécologie » under the number CEROG OBS 2017-02-26. This research was found to conform to generally accepted scientific principles and medical research ethical standards by the upper stated institutional review board.
Acknowledgments We are thankful to  Adrien Teixera  and  Jacques Bou Khalil  for their technical help with the generation of Figures 1 and3, respectively. We sincerely thank  Takashi Irie ,  Kyoko Imai ,  Shigeki Matsubara ,  Taku Sakazume  and the  Hitachi team of Japan (Hitachi High-Technologies Corporation, Science & Medical Systems Business Group   24-14 , Nishishimbashi 1-chome, Minato-ku, Tokyo  105-8717 Japan ) for the collaborative study conducted together with  IHU Méditerranée Infection , and for the installation of a SU5000 microscope at  IHU Méditerranée Infection.
25 mm x 0. 25 μm; Phenomenex, France). Data were recorded and analysed by TotalChrom Workstation (Perkin-Elmer). S. aureus fatty acid peaks were detected between 12 and 32 min of elution, and identified with retention times of purified esterified fatty acid standards. were processed with the Zeiss ZEN software package using a 38 HE Green Fluorescent Protein filter (excitation wavelength 450/490 nm; beam splitter, 495 nm; emission, 500/550 nm) and 45 Texas Red filter (excitation: 540/580 nm; beam splitter, 585 nm; emission, 595-668 nm). The numbers of live (green) and permeabilized (red) cells were counted manually. Dividing cells and tetrads were counted as single entities. Tetrads and clusters containing both viable and permeabilized cells (in FA-Tric and SerFA-Tric samples) were classified in a separate "mixed" category.
Genomic DNA sequencing by Illumina HiSeq next generation sequencing was outsourced (GATC-Biotech, Konstanz, Germany). Coverage was estimated to be at least 70-fold for USA300 SerFA-Tric samples, and at least 400-fold for all other samples. The 2 x 150 paired-end reads were analysed using "Variation Analysis" method provided by Patricbrc. org. Bowtie2 (Patricbrc. org) was used to align sequences and SAMtools to identify SNPs  (8). SNPs that differed in non-antibiotictreated USA300 and Newman strains from those in the reference sequence (GenBank Nucleotide accession codes NC_007793. 1 and NC_009641 respectively) were subtracted prior to variant screening. Variants were identified as representing at least 80% of reads in sequences for which there were at least 10 reads. ACP assessment by immunoblotting.
Gels were then electro-transferred to PVDF membranes (0. 2 mm; BioRad; 75mA) for 3 h on a semi-dry transfer unit (Hoefer TE 70). Western blotting and exposure used an ECL kit (Perkin-Elmer) as per supplier's instructions. Rabbit anti-S. aureus ACP antibodies (2) were used at 1:1,300 dilution. Proteomic analyses of USA300 responses to anti-FASII. Four independent overnight BHI precultures of USA300 spa::Tn strain were used to inoculate BHI, FA, SerFA, FA-Tric, or SerFA-Tric media at OD600 = 0. 1. Culture extracts were prepared as described for Western blotting, and after verification of protein concentration and quality, 10 μg of each protein sample was short-run on SDS-PAGE. Further sample treatment by LC-MS/MS, and bioinformatics and statistical analyses of data are as described  (9). The reference genome GenBank Nucleotide accession code NC_007793.
Sheath gas, auxiliary gas and sweep gas flow rates were set at 20, 8 and 0 (arbitrary unit) respectively. Capillary temperature was set at 325°C and S-lens RF level at 60%. Analysis was performed in negative mode to obtain structural information on phosphatidylglycerol fatty chains. The mass spectrometer is equipped with two analyzers: a double linear ion trap (LTQ Velos Pro) for fragmentation at low resolution and an orbital trap (Orbitrap©) for high resolution detection. Detection was performed in full MS Scan with 100,000 resolution and data dependent MS 2 and MS 3 with collision induced dissociation (CID; collision energy set at 35). Chromatographic retention time was used for polar head identification by comparing to commercial standards. Phospholipid identification was performed using high resolution mass full scan to obtain the formula of the entire PG species (  14 ), and MS 2 /MS 3 fragmentation to obtain structural information about fatty acid chain composition of each species.
Acknowledgements Nebraska Transposon Mutant Library strains were generously provided by the  Network on Antimicrobial Resistance in Staphylococcus aureus , prepared by  BEI Resources, NIAID, NIH, USA. We are grateful to  P. Casedesus  ( Univ. Sevilla, Spain ),  B. Michel  and  P. Bouloc  ( I2BC, France ), and  P. Trieu-Cuot  ( Institut Pasteur, France ) for stimulating discussion of this work. We thank  M. Gaillard ,  A. Picart  ( I. Cochin ), and  M. Benard  (animal facility,  I. Cochin ) for expert assistance in animal studies, and  M. Gaillard  for data analyses;  M. Gohar  ( Micalis ) for advice in fluorescence microscopy studies; R. Boudjemaa,  E. Borezée-Durant ,  R. Briandet ,  J. Deschamps ,  D. Lechardeur , and  P. Gaudu  ( Micalis ) for frequent discussion. GK was funded by the  French  ministry; AP received a postdoctoral grant from the regional DIM-Malinf; LD, AW, and  M.
Data availability Genome sequence data have been deposited in the European Nucleotide Archive and can be accessed at http://www. ebi. ac. uk/ena/data/view/PRJEB24433. The complete list of proteins from the proteomic study will be made available on the Mendeley database (doi:10. 17632/9292c75797. 1) upon publication. The authors declare that all other data supporting the findings of this study are available within the article and its Supplementary Information files, or from the corresponding author upon request.
International Inflammatory Bowel Disease Genetics Consortium (IIBDGC)* Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics.
Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers. Crohn Disease (CD) is an inflammatory bowel disease (IBD) characterized by a chronic or relapsing inflammation of the gut with a prevalence of at least 0. 1% in most developed countries 1. It has been extensively studied by several groups, often in the context of the International IBD Genetics Consortium (IIBDGC), thus sharing common datasets and allowing comparisons between different approaches. CD is a complex genetic disorder caused by multiple genetic and environmental factors. A major goal of medical genetics is to accurately predict CD from these genetic and environmental parameters. In practice, we need to know risk factors, their effect sizes and how they interact.