dataesr/scientific-paragraphs-categorization huggingface dataset:
Based on a comprehensive information package (e. g. notification C/NL/13/02, additional datasets, initial assessment report by the Netherlands), the GMO Panel concludes that the molecular characterisation data establish that carnation FLO-40685-2 contains inserts in four loci, consisting of three expression cassettes responsible for the intended trait (purple flower colour), conferred by the dfr and f3 0 5 0 h genes, and the herbicide tolerance, conferred by the mutated als gene. The stability of the newly introduced trait was observed over multiple vegetative generations. Carnation flowers have a long history of use as ornamentals. Carnation FLO-40685-2 differs from its parental variety in that it synthesises different levels of anthocyanins in the petals, e. g. an increased content of delphinidin and cyanidin (common pigments in many ornamental flowers and food plants).
1-biotin, anti-CD8-biotin, anti-CD5-biotin, anti-CD5-FITC, and anti-CD93-APC from eBioscience; anti-CD59-biotin from BMA Biomedical (Augst, Switzerland); anti-IgM-PE, -FITC or -APC, and SA-PE from Jackson ImmunoResearch; anti-rabbit IgG (HϩL)biotin from Vector Laboratories (Burlingame, CA); SA-Alexa Fluor 405 and anti-rat IgG-Qdot 605 from Invitrogen (Carlsbad, CA). Lin Ϫ cells were defined by staining with a mixture of antibodies for mature hematopoietic lineage marker including CD3⑀, CD11b, CD59, CD71, Gr-1, NK1. 1, TCR␣␤, TCR␥␦, CD8, and IgM. Cells were analyzed with a FACSCalibur and FACS LSR II (BD Biosciences) and FlowJo software (TreeStar, Ashland, OR). ELISA-ELISAs of sera were performed as described  (33). Briefly, polystyrene plates (MaxiSorb; Nunc, Rochester, NY) were coated ON at 37 °C with the following antigens: dsDNA (100 ng/ml in 25 mM citrate buffer, pH 5.
The primers for Spi1  (11) , Prmd1 and Xbp1  (14) , Slpi  (35) , Tyrobp  (36) , Pirb (37), Mcl1  (38) , Ikzf1, and Hprt  (22)  were used as described. Microarray Analysis-Total RNA was extracted with the RNeasy Micro kit (Qiagen). RNA quality was verified with a 2100 Bioanalyzer (Agilent, Santa Clara, CA). Biotinylated single strand cDNA targets were prepared from 150 ng of total RNA with the Ambion WT Expression Kit and the Affymetrix GeneChip WT Terminal Labeling Kit. After fragmentation and end-labeling, 1. 9 g of cDNAs were hybridized to Affymetrix GeneChip Mouse Gene 1. 0 ST arrays using standard procedures. Raw data were processed with the Robust Multiarray Average (RMA) algorithm. Microarray data are available in the GEO Data Bank (GSE 75827). Chromatin Immunoprecipitation and ChIP-Sequencing-The ChIP protocol was adapted from the Millipore ChIP Assay Kit (17-295) with minor modifications and described  (25).
Acknowledgments-We thank  A. S. Korganow  and  P. Soulas-Sprauel  for discussions;  K. Dorshkind  for the S17 cells;  M. Reth  for the IL-7 cDNA-transfected J558L cells;  M. Dalod  for the Flt3L cDNAtransfected B16 cells;  A. M. Knapp  for help with ELISAs;  V. Alunni ,  C. Thibault , and  D. Dembélé  for help with microarray experiments and data analysis;  C. Ebel  for flow cytometry; W. Magnant for help with mouse bleeding;  M. Gendron  and  S. Falcone  for animal husbandry.
* This work was supported by the  Agence Nationale de la Recherche  ( ANR-11-BSV3-018 ), the  Institut National du Cancer  (INCa # 2011-144 ), the  Ligue Nationale Contre le Cancer  (Equipe labellisée 2006 -2012, 2015-2017, to S. C. and P. K. ),  Fondation Arthritis Courtin  (2013),  Fondation ARC  (# PJA20141201922 ),  Fondation de France  (# 201400047508 ), and institutional funds from the  Institut National de la Santé et de la Recherche Médicale (INSERM) , the  Centre National de la Recherche Scientifique (CNRS) , the  Hôpitaux Universitaires de Strasbourg , the  ANR-10-LABX-0030-INRT , the  Laboratory of Excellence Medalis  ( ANR-10-LABX-0034 ), the EquipEx program  I2MC  ( ANR-11-EQPX-022 ), the  Initiative of Excellence (IdEx) ,  University of Strasbourg. The authors declare that they have no competing financial interests.
Results The incidence of all severe clinical events was 111 per 1000 person-years (95% CI 84 to 145) during the first 6 months. After 6 months, the incidence decreased and remained stable within the range of 40-58 events per 1000 patient-years. The largest decrease in incidence rates was among male patients and those aged ≥40 years when agalsidase β was initiated. Conclusions Contrary to the expected increased incidence of severe clinical events with time, adult patients with Fabry disease had decreased incidence of severe clinical events after 6 months treatment with agalsidase β 1 mg/kg every 2 weeks. Trial registration number NCT00196742.
Not unexpectedly, therefore, serious Fabry disease-related clinical events have occurred in these patients despite ERT  16- 18  and the use of ERT for patients with advanced kidney disease has been questioned. 19 The key question, however, is not if ERT completely prevents severe clinical events in patients with Fabry disease, but whether ERT reduces the incidence and/or progression of severe clinical events. Given the difficulty and ethical concerns of conducting long-term placebo-controlled clinical trials in patients with Fabry disease, patient registry data are needed to gain insights into the effect of ERT on the incidence rates of severe clinical events. In this study, we analysed data from adult patients with Fabry disease enrolled in the Fabry Registry (ClinicalTrials. gov identifier: NCT00196742) with the objective of determining trends in the incidence of severe, potentially life-threatening clinical events over time in patients receiving up to 5 years treatment with agalsidase β, at a dose of 1 mg/kg every 2 weeks.
Ile317Thr (I317T), p. Arg301Gln (R301Q); n=56),  [20] [21] [22] [23] [24] [25]  as reported in the 'fabrydatabase. org' Fabry mutation database,  26 27  were excluded from the analysis. The 'fabry-database. org' database of clinical phenotypes, genotypes and structures of mutant GLAs has been built by the research group led by Dr H Sakuraba in order to help researchers and clinicians who study Fabry disease. The database currently contains more than 640 different mutations. 27 oreover, individuals with non-pathogenic Fabry gene polymorphisms ( p. Asp313Tyr (D313Y), p. Arg118Cys (R118C); n=3)  [28] [29] [30]  were excluded. No patients in the cohort had a p. Ala143Thr or IVS4+919G>A mutation, or the polymorphism p. Glu66Gln (E66Q). The analysis population included: (1) patients with mutations categorised in the 'fabry-database.
Finally, Cox proportional hazards regression models were used to evaluate the impact of risk factors associated with severe clinical events, including a severe non-renal event prior to first ERT, age at agalsidase β initiation and gender. The small number of excluded individuals with Fabry gene polymorphisms or later-onset variant mutations did not allow for a meaningful separate analysis of these groups to assess time to treatment benefit in these groups. Statistical analyses were performed using SAS statistical software V. 9. 2 (SAS Institute, Cary, North Carolina, USA). An α level of 0. 05 was used as the criterion for statistical significance.
5 g/g (54% vs 38%), LVH (79% vs 37%), arrhythmias (30% vs 17%), systolic blood pressure >130 mm Hg (47% vs 35%) and diastolic blood pressure >80 mm Hg (46% vs 30%) compared with those who started ERT at age <40 years. Missense (42%) and nonsense mutations (14%) were most commonly reported, followed by frameshift mutations (10%). Genotype data were not available for 27% of the patients (see online supplementary table  S1 ). Four hundred patients had mutations categorised in the 'fabry-database. org' database as being associated with classic Fabry disease, whereas 365 patients had mutations not entered or classified in this database. 27 pe and timing of first severe clinical events following initiation of ERT Overall, 177 of 1044 (17%) patients had a severe clinical event within 5 years of agalsidase β treatment initiation: 120 events occurred in 641 male patients (19%) and 57 events occurred in 403 women (14%).
While our findings emphasise the importance of starting ERT at a relatively young age, we also clearly demonstrate a benefit of ERT in older patients with Fabry disease with more advanced disease who better represent the majority of patients reported to date. 19 49 abry disease is a clinically heterogeneous disease and little is known about the natural progression of Fabry disease in patients with later-onset variant mutations and reference studies in which ERT-treated patients with these mutations and classically affected patients have been analysed separately are lacking. Therefore, the main analysis population was restricted to patients with mutations categorised as being associated with classic Fabry disease, patients with mutations not entered or classified in the 'fabrydatabase. org' database, 27 and patients for whom mutations were not reported in the Fabry Registry (27% of the patients); even though these mutations were not recorded in the Fabry registry, the treating physicians classified these patients as 'classical' Fabry disease.
Furthermore, although the Fabry Registry provides a recommended schedule of assessments, patients and their treating physicians ultimately determine the timing of assessments and the time intervals at which they are carried out. Local standards of care may differ between treatment sites and across all time points, especially with respect to the use of vasculoprotective and renoprotective adjunctive therapies. Thus, clinical data may be incomplete for some patients and some assessments or events may be under-reported; additionally, some patients may be lost to follow-up. The absolute event rates are low overall, so that caution is warranted in interpreting the event rate in any individual short interval, as the CIs for the incidence rates are increased for short follow-up intervals. Serum-mediated inhibition of ERTs is emerging as an important issue particularly in male patients with classic Fabry disease.
Acknowledgements The authors thank the patients who agreed to participate in the Fabry Registry, as well as the physicians and research coordinators who have entered clinical data on behalf of these patients. The authors thank colleagues at  Genzyme , a  Sanofi company , for medical input ( Wytske Kingma ), epidemiological advice (  Judy Kempf  ), programming support ( Badari Gudivada ) and copy editing (Cheryl Lathrop). The authors received editorial/writing support in the preparation of this manuscript provided by  Niina Nuottamo of Excerpta Medica , funded by  Genzyme , and  Hans Ebels of Genzyme , a Sanofi company. The authors were responsible for all content and editorial decisions, and received no honoraria related to the preparation of this publication. Contributors Analysis and interpretation of data: AO, SSM and DGW.
Drafting the article: AO and DGW. All authors contributed to acquisition of data, reviewing and revising the article critically for important intellectual content, final approval of the version to be published, agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. Funding This research was funded by  Genzyme , a Sanofi company. AO was supported by  ISCIII   REDINREN RD012/0021  and  Intensification FEDER  funds. Competing interests AO is a consultant for  Genzyme  and has received speaker fees from  Shire HGT. AA is a member of the North American Fabry  Registry Board  and has received speaker fees for lectures on Fabry disease from  Genzyme. DGB is a member of the North American Fabry  Registry Board  and has received speaker fees for lectures on Fabry disease and for clinical studies from  Genzyme ,  Shire HGT and Amicus Therapeutics.
Targeted exome sequencing (TES) and bioinformatic analysis A multiplex amplicon panel (Fluidigm Access Array) was created to analyze all coding and non-coding exons of the 10 USH genes and the USH2 modifier gene PDZD7. 4 Exons recently identified by retina-specific transcript analysis were included. 26 The amplicons also covered a minimum of 25-bp intronic sequence flanking each exon to facilitate the detection of sequence variants that affect splice sites. The USH2A intronic region harboring the mutation c. 7595-2144A4G was also included. 27 The primers were designed based on the design program Primer3. 28, 29 A total of 1268 primer pairs (sequences available on request) were chosen to produce amplicons with an average length of 165 bp. Forty-eight pools of primer pairs were created such that each primer pair was represented twice per assay in independent pools, and each pool of primers contained a unique combination of 47-48 different primer pairs.
Each PCR was then controlled on a Fragment Analyzer (AATI, Ankeny, IA, USA), and quantified to create an equimolar pool of the 96 samples. This pool was again purified with AMPure, and loaded onto a Fragment Analyzer or Bioanalyzer (Agilent, Santa Clara, CA, USA) to verify the profile by comparing it with the expected profile. This pool was sequenced on a HiSeq 2000 sequencer (Illumina, San Diego, CA, USA). For each sample, a total of 313 Mb reads were sequenced per 108 kb of analyzed genome, which represents a 2900 × coverage. Raw sequencing data were processed for bioinformatics analysis through the Illumina pipeline (CASAVA1. 8. 2), using the ELANDv2 algorithm for sequence alignment (multiseed and gapped) and the sequence of each amplicon as reference. Variants were called if they met the following criteria: (1) a read depth superior to five with no ambiguous reading, and (2) an allelic frequency inferior to 0.
3% in all the following public variant databases: dbSNP132, Hapmap, 1000 Genomes, Exome Variant Server, Exome Aggregation Consortium (http://exac. broadinstitute. org/), Usher-specific Leiden Open Variation Database(https://grenada. lumc. nl/LOVD2/Usher_montpellier/home. php), and Deafness Variation Database (http://deafnessvariationdatabase. org/). They were then ranked according to their expected negative impact on the resulting gene product. Nonsense variants and small deletions or insertions inducing a frameshift of the coding sequence were considered the most damaging, as they necessarily alter the amino-acid sequence of the protein. The pathogenicity of missense and splice-site variants was estimated using the following prediction algorithms: PolyPhen2, SIFT, and Mutation Taster for missence variants, and NNSplice, ESEfinder, Max Ent Scan, Gene Splicer, and Human Splicing Finder for splice-site variants.
Comparative genome hybridization (CGH) using SNP arrays CytoSNP-12 arrays (Illumina, San Diego, CA, USA), which contain 300 000 polymorphic markers including 200 000 SNPs spread throughout the human genome, were used to assess the zygosity of USH genes in patients, when no mutation or only a monoallelic mutation was detected by TES. The samples were processed using the Infinium assay as previously described  30  and the results analyzed using Illumina Genome Studio software. An internal reference was created using the clustering algorithm Illumina Gentrain 2. 0 on the SNP profiles from 96 samples that were processed during the same run. The SNP profiles were analyzed by comparing the log R ratio (where the R ratio is the sample copy number over the reference copy number) and B allele frequency (BAF).
qPCR analysis Quantitative real-time PCR was performed using a SYBR Green PCR master mix (Applied Biosystems, Foster city, CA, USA) and specific primers were designed using the program Primer3,  28, 29  such that the amplicon length did not exceed 200 bp (primer sequences available on request). The PCR reactions were performed in duplicate using two different amounts of genomic DNA (10 ng and 2 ng, in 5 μl) in a final volume of 20 μl, including 0. 2 μl of each primer (20 μM final concentration), 4. 6 μl of nuclease free water, and 10 μl of power SYBR Green PCR master mix. Positive and negative (no DNA template) controls were used in each run. PCR amplification was performed in a 96-well plate format on a 7500 Fast Real-Time PCR machine (Applied Biosystems) using the following conditions: 2 min at 50 °C, 10 min at 95 °C, 40 cycles (15 s at 95 °C and 1 min at 60 °C), 15 s at 95 °C, 1 min at 60 °C, and 15 s at 95 °C.
The final dissociation step was included at the end of the PCR program to generate melting curves and assess primer specificity. 31 Relative quantification was performed using the ΔΔC T method to normalize the number of USH gene copies to those of the housekeeping gene GAPDH. 32, 33 ference sequences for mutation nomenclature and exon numbering All pathogenic or presumably pathogenic variants identified in the USH genes have been deposited in the 'Leiden Open Variation Database'.
In this article, the nomenclature of all sequence variants and exon numbering refer to the following genomic and cDNA reference sequences [NG_ and NM_ NCBI accession numbers, respectively]: MYO7A [NG_009086. 1, NM_000 260. 3]; USH1C [NG_011883. 1, NM_153676. 3]; CDH23 [NG_008835. 1, NM_022124. 5]; PCDH15 [NG_009191. 1, NM_001142769. 1 (CD2. 1 transcript)]; USH1G [NG_007882. 1, NM_173477. 4]; CIB2 [NG_033006. 1, NM_001301224. 1]; USH2A [NG_009497. 1, NM_206933. 2]; ADGRV1 [NG_007083. 1, NM_032119. 1]; WHRN/DFNB31 [NG_016700. 1, NM_015404. 3]; PDZD7 [NG_028030. 1, NM_001195263. 1]; USH3A [NG_009168. 1, NM_174878. 2 (transcript a), NM_052995. 2 (transcript c)].
ACKNOWLEDGEMENTS We are grateful to the patients and their families for their participation in the study. DNA samples included in this study originated from the NeuroSensCol** DNA bank, part of the  BioCollections network  for research in neuroscience (PI: JA Sahel, co-PI: I Audo, in partnership with the  CHNO des Quinze-Vingts, Inserm  and the  CNRS) , and the  Tuebingen RetDis biobank (PI: B Wissinger, co-PI S Kohl ). This work was supported by the  European Union Seventh Framework Programme  under the grant agreement  HEALTH-F2-2010-242013  ( TREATRUSH ),  ANR-15-RHUS-001  ( LIGHT4DEAF ),  LHW-Stiftung ,  Fondation Raymonde & Guy Strittmatter ,  FAUN Stiftung ,  Conny Maeva Charitable Foundation ,  Fondation Orange ,  Fondation BNP Paribas ,  LABEX Lifesenses  [ ANR-10-LABX-65 ], 'the  Foundation Fighting Blindness Paris Center  Grant', and the  Slovenian research agency  ( ARRS P3-0333 ).
g. , applicable policies, taxonomy [reptile database], trade statistics [EUROSTAT], and conservation status [IUCN Red List]). Case studies are presented from the following countries and regions: Australia, Central America, China, Galapagos Islands (Ecuador), Germany, Europe, India, Indonesia (Kalimantan), Islamic Republic of Iran, Japan, Madagascar, Mexico, New Zealand, the Philippines, South Africa, Sri Lanka, Vietnam, Western Africa, and Western Asia. The European Union (EU) plays a major role in reptile trade. Between 2004 and 2014 (the period under study), the EU member states officially reported the import of 20,788,747 live reptiles. This review suggests that illegal trade activities involve species regulated under CITES, as well as species that are not CITES-regulated but nationally protected in their country of origin and often openly offered for sale in the EU.
Methods The primary methodological approach for this review was extensive, global-scale consultation with experts who have relevant, long-term experience addressing reptile trade issues. These experts include: scientists, officers of conservation agencies, conservationists, and enforcement and customs officials. Contributing authors provided examples of unsustainable and illegal trade activities regarding the collection of, and international trade in, live reptiles within their regions of expertise. This information was supported by a comprehensive review of the published literature as well as anecdotal unpublished information that was made available by relevant administrative bodies. Information available for non-CITES species in trade (e. g. , Annex D species of the EWTR) was filtered from the IUCN Red List database.
Additional data sources including grey literature, reptile fairs, wholesaler and retail shop lists, and species' lists of private collectors were included. Furthermore, data extracted from several online databases (see below) augmented the results and conclusions of this review: • CITES Trade database (http://trade. cites. org/): Searches entered for all reptile taxa in Appendices I-III for the year range 2004-2014 using trade terms "live" and "eggs (live)" and the relevant taxa (genus or species). Queries were structured to capture data regarding major exporting and importing countries, species, quantities, and sources.
3. 3). A survey by  Nijman and Shepherd (2009)  found that all specimens of the emerald tree monitor (Varanus prasinus) and Timor monitor (Varanus timorensis) exported by Indonesia in 2006 as captive-bred were in fact wild-caught. According to field data collected between 2009 and 2011,  Lyons and Natusch (2011)  suggested that 80% of green tree pythons (Morelia viridis) exported by Indonesia claimed as captive-bred were in fact from the wild. Large-scale laundering of this kind has also been documented for Madagascan chameleons, which were channelled via Lebanon and Kazakhstan to escape quotas for wild-caught specimens and temporary trade suspensions  (Todd, 2011). Additional examples include the Princely spiny-tailed lizard (Uromastyx princeps) and the Omani spiny-tailed lizard (Uromastyx thomasi), both listed under CITES Appendix II since 1977.
In addition, specimens sourced from ranching operations include various loopholes. There appears to be no facility in any of these three countries that demonstrate a wellestablished captive breeding operation for any species. Thus, it can be confidently assumed that all specimens documented by the CITES trade database that are "officially" declared as exports (as well as those that are non-officially exported) from West Africa are in fact wild animals. This type of trade has had a substantial impact on wild populations of P. regius from Benin and Ghana due to gravid female export. In the last 15 years fecundity and mean body size of females has decreased substantially. Average clutch sizes of 15-18 eggs have decreased to 10-12 eggs (at least n = 5 females examined each year). Body size has decreased from around 1.
, 2013). In this case, molecular tools were also used to produce a forensic report that contributed to sentencing the illegal smuggler to four years in prison, as he was found guilty under Articles of the Ecuadorian Criminal Code. In 2014, the Galápagos National Park started a program aimed at detecting and uncovering the network of illegal traffickers operating in Galápagos. The UNEP-WCMC CITES trade database (2015) confirms that Ecuador has never declared export of live specimens of C. subcristatus or A. cristatus for commercial trade. Nevertheless, two live land iguanas and three live marine iguanas were officially exported from Mali to Switzerland in 2011 and 2012, respectively, labelled as "captive-bred" and for private purposes. In 2014, the Swiss CITES management authority issued export permits to Uganda for these animals, which for all practical purposes laundered these animals into the pet trade, and opened the door for additional smuggling events, claiming captive breeding.
Two range-restricted species, V. boehmei (CITES Appendix II) and the non-CITES listed Philippine pit viper (Trimeresurus mcgregori), exemplify this issue. Both species are classified as data deficient (DD) in the IUCN Red List, and are in fact heavily impacted by the international pet trade  (Bennett and Sweet, 2010; Koch et al. , 2013; Sy et al. , 2009). EU authorities should be aware of frequency in which some traders fraudulently declare their animals to have been bred in captivity. This can in reality represent individuals taken directly from the wild or the offspring of a gravid female giving birth or laying eggs soon after a smuggling event. Further, even for the truly captive bred individuals that are nationally protected in their native range and for which legal exports have never been permitted, the question on the legality of their breeding stock remains.