dataesr/scientific-paragraphs-categorization huggingface dataset:
A. Data and task The RepLab dataset contains users manually labeled by specialists from Llorente & Cuenca 3  , a leading Spanish e-Reputation firm. These users were annotated according to their perceived real-world (offline) influence, and not by considering specifically their Twitter account. The annotation is binary: a user is either Influencer or Not-Influencer. The dataset contains a training set of 2500 users, including 796 Influencers, and a testing set of 4500 users, including 1563 Influencers. It also contains the 600 last tweets of each user at the crawling time. Given the low number of real Influencers, the RepLab organizers modeled the issue as a search problem restrained to the Automotive and Banking domains. In other words, the dataset was split in two, depending on the main activity domain of the considered users.
The performance is considered for each domain (Banking and Automotive), as well as averaged over both domains. It gives an overview of the system ability to recover information from each class. Ramirez et al. do not use any baseline to assess their results. Nevertheless, the imbalance between the influencer (31%) and non-influencer (69%) in the dataset leads to a strong noninformative baseline which simply consists in putting all users in the majority class (non-influencers).
We thus turn to non-linear classifiers under the form of kernelized SVMs (RBF, Polynomial and Sigmoid kernels). We used the logistic regression trained with each scalar feature alone, as well as with all combinations of scalar features within each category defined by us (as described in Tables I and II), and with all scalar features at once. Furthermore, we considered separately users from the two domains considered in the dataset: Banking and Automative. Regarding Feature 29 (terms weighting) we investigated two user-profile definitions: User-as-document  [41]  (noted UaD in Non-in uential In uential the rest of the article) and Bag-of-tweets (BoT). With the UaD approach, all tweets from each user belonging to a given class are merged to create one large document. Users are then compared by computing the similarity between both corresponding documents.
However, this did not result in good performances. But this path can still be further explored, by using other graph measures, or different methods to build the cooccurrence matrix, for instance by considering higher order word neighborhoods, or even word triplets. Moreover, our results are valid only for the considered dataset. This means they are restricted to the domains it describes (Automotive and Banking), and also they are only as good as the manual annotation of the data. Actually, in RepLab 2014  [19] , the organizers were not able to conclude on significant differences between certain participants due to the number of considered domains. This point should be solved quickly though, through the 2015 edition of PAN 4.
Crystallization and Data Collection-The purified complex proteins were crystallized using a sitting drop vapor diffusion method with a 1:1 mixture of sample and reservoir solution. Crystals appeared in the reservoir buffer containing 0. 1 M Tris, pH 8. 5, 0. 2 M Li 2 SO 4 , and 30% PEG4K after 1 week at 18 °C and were frozen in a cryoprotectant consisting of the reservoir solution supplemented with 20% PEG400. Data were collected on the BL17U1 station at the Shanghai Synchrotron Radiation Facility (SSRF) and processed using the HKL2000 and XDS software programs  (32, 33). Structure Determination and Refinement-The crystal structures were determined by the molecular replacement program PHASER (34) using the two PDZ domain structures of GRASP65 as an initial search model. Model building and iterative refinement were then performed with the COOT and PHENIX refinement programs  (35, 36).
The Interaction of GRASP65 and GM130 in Golgi Stacking val, and 1000 rpm stirring speed. The data were analyzed and fitted using the MicroCal Origin software suite. Native and SDS-PAGE-The affinity-purified recombinant GM130 coiled-coil domain (amino acids 447 to 897) was analyzed by 6% native and SDS-PAGE. The sample buffers consisted of the native loading buffer (with neither SDS nor a reducing agent) and the SDS loading buffer, respectively. The resulting gels were stained with Coomassie Blue. Cell Culture, Transfection, and Image Capture-HeLa cells were grown in RPMI 1640 medium containing 10% fetal bovine serum and maintained at 37 °C in a 5% CO 2 incubator. Transient transfection was performed with TurboFect (Thermo Scientific) according to the manufacturer's specifications. At 24 h after transfection, the cells were washed twice with PBS and fixed with Immunol Staining Fix Solution (Beyotime, China) at room temperature for 15 min.
Acknowledgments-The x-ray data were collected at the BL17U1 beamline of the  Shanghai Synchrotron Radiation Facility. We are grateful to  Prof. Jiahuai Han  for the plasmids;  Youxing Jiang ,  Nam Nguyen , and  Mingdong Huang  for their thoughtful discussions and reviews of the manuscript; and  Jinping Xue  for helping with confocal microscopy.
* This work was supported by the  National Natural Science Foundation of China  Grant  31370738 , the  One Hundred Person Project of the Chinese Academy of Sciences , the  National Science Foundation of Fujian Province  ( 2013J01150 ) and  Campus France  ( PHC CAI YUANPEI 2013 , Project  26203WD ). The authors declare that they have no conflict of interest with the contents of this article. The atomic coordinates and structure factors (code  4REY ) have been deposited in the Protein Data Bank (http://wwpdb. org/).
Isolation of cultures, morphological and molecular characterization of strains and phylogenetic inference resulted in descriptions of several new species (e. g. Eikrem 1996; Eikrem & Edvardsen 1999; Eikrem & Throndsen 1999 ). These investigations also pointed at the need for a revised taxonomy of the order Prymnesiales, where the genus Chrysochromulina, shown to be paraphyletic, was split between five genera and two families  (Edvardsen et al. 2011). Chrysochromulina sensu lato will here be used to mean species assigned to Chrysochromulina in publications before 2011. The abundance of Chrysochromulina spp. sensu lato in the Skagerrak was in the years following the bloom monitored by light microscopy in Norway (algeinfo. imr. no) and Sweden (AlgAware, www. smhi. se). Twelve years of monitoring data from one locality off Arendal, S Norway, revealed that Chrysochromulina spp.
Water samples and environmental data Water samples from 1 m depth were taken monthly in outer Oslofjorden at station OF2 (59. 19 N, 10. 69 E, Fig. 1 ) in the period September 2009-June 2011 (for sampling dates see Table  S1 , Supporting information). Sea water was collected in Niskin bottles attached to a rosette. Water temperature, conductivity (as a measure of salinity) and fluorescence by depth were measured directly on site using a CTD (Falmouth Scientific Inc. , Cataumet, MA, USA) attached to the Niskin rosette. Samples for chlorophyll a (Chl a) and nutrient measurements were collected at 1, 2, 4, 8, 12, 16, 20 and 40 m depth. For Chl a measurements, 100-500 mL was filtered onto glass-fibre filters (GF/F 25 mm; Whatman, Kent, UK) in two replicates. Filters were transferred to cryo-vials and immediately frozen in liquid N 2.
3À ), dissolved inorganic nitrogen (taken to be the sum of [NO 3 À ] and [NO 2 À ]) and silicate (SiO 4 4À ) concentrations were determined with a 2-Channel Autoanalyzer 3 (Bran + Luebbe, Norderstedt, Germany), with Autoanalyzer application Methods no. respectively (Seal Analytical, Germany). The upper mixed layer (z mix = from surface to pycnocline) was determined by inspecting the density profiles (calculated from temperature and salinity) visually. To incorporate information about the part of the water column likely to influence the conditions at 1 m depth, the hydrographical and chemical data were averaged over z mix. Irradiance (I; lmol photons/m 2 /s) depth profiles were determined at metre intervals with a LI-192 Underwater Quantum Sensor and a deck sensor connected to LI-250A Light Meters (LI-COR, Lincoln, NE, USA), and in addition, Secchi depth was measured.
Change in proportional read abundance of an OTU may not be a reliable indication of change in absolute abundance of ribosomes, because the proportion of reads of one OTU depends on the proportional abundance of the others (e. g. Gifford et al. 2011). If the absolute number of ribosomes from one species is the same in two samples, but the total number of haptophyte ribosomes is different between the two samples, the proportional abundance of this species will not be the same in the two samples. The OTU data set was therefore transformed to presence-absence prior to the ordination analyses. To visualize the similarity in OTU composition between the samples, we did a nonmetric multidimensional scaling (NMDS) of Jaccard distances between the samples  (Oksanen 2011). NMDS ordination was performed with the 'ordinate' function in the phyloseq package in R  (McMurdie & Holmes 2013) , with metaMDS method for ordination.
S1, Supporting information). Nonrandom co-occurring OTU pairs (both positive and negative associations) were identified with the Pairs program  (Ulrich 2008) , using a null model with fixed rows and column constraints to randomize the presence/absence matrix. The C-score was used as measure of pairwise co-occurrence. The procedure was repeated 10 times, and nonrandom co-occurring pairs found in at least nine replicates were considered robust associations  (Lentendu et al. 2014 ) and visualized using the R IGRAPH package  (Csardi & Nepusz 2006). Jaccard distance between OTUs can be used as a measure of distance/co-occurrence between OTUs  (Borcard et al. 2011). As a simple assessment of the relationship between genetic distance and seasonal distribution profile, we plotted Jaccard OTU distances against sequence similarity, calculated in BIOEDIT  (Hall 1999) , for all Prymnesiales OTUs occurring in >5 samples.
Data accessibility The raw. sff files from 454 pyrosequencing have been deposited in the Sequence Read Archive with Accession no. PRJEB5541, http://www. ebi. ac. uk/ena/data/view/ PRJEB5541. Environmental data including the flow cytometry counts, the reference alignment, the. tre file of the reference haptophyte tree, a fasta file with the aligned OTUs, the table with taxonomic assignment of each OTU and the read abundance OTU table are deposited in Dryad, doi:10. 5061/dryad. b8d21.
Acknowledgements Financial support was given by the  Research Council of Norway  through Grant  190307 HAPTODIV  to  ESE, BE , WE, TVJ and  RAS , by  ASSEMBLE FP7  grant agreement no. 227799 funding research stay for  ESE at the Station Biologique de Roscoff (SBR) , by the  EU  project  BioMarKs  ( 2008-6530 ,  ERA-net Biodiversa, EU)  to BE and LB, and by the  MINOS  project funded by  EU-ERC  (project no. 250254 ) funding salary for AL. We thank  Rita Amundsen , captain  Sindre Holm  and the crew onboard  R/V Trygve Braarud  for assistance during sampling,  Sissel Brubak  and  Berit Kaasa  for analysing Chlorophyll a and nutrient samples,  Colomban de Vargas  for valuable input on haptophyte ecology,  Thijs C. van Son  for valuable discussions on ordination analysis and  Lars Nersveen  for the R scripts for the contour plots.
g. , formamidopyrimidine DNA glycosylase, Endonuclease III, thereby originating specific breaks. However, despite their strong interest and their early introduction in plant studies  (Menke et al. , 2000) , these enzymes are still not much used in plants. Comets may then be visualized by microscopy, by using a suitable DNA-binding dye, e. g. , fluorescent dyes or silver staining. Data can be analyzed by visual scoring, ranging from 0 to 4 according to the damage class, or using computer-based image analysis (e. g. , the software http://casplab. com/) that allows the quantification of several comet parameters, including the tail DNA %, tail length, tail extension moment or Olive tail movement  (Azqueta et al. , 2011b). Criteria for the best scoring approaches are however debatable (e. g. ,  Azqueta et al.
Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers' questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients.
2 Atypical cases deemed "clinically probable" by the referring physician were also included in this analysis and included subjects with onset of first symptoms > 18 months of age but whose phenotype fulfilled all other diagnostic criteria for AHC. One hundred sixty-nine patients were simplex cases, and DNAs of both parents were available for 70 (41%). The cohort included two sets of monozygotic twins who were concordantly affected. Fourteen subjects in 5 multiplex pedigrees, 2 with dominant inheritance, were also included in the present analysis. Patients and their parents gave informed written consent for clinical data and DNA storage and analysis. Ethics approval was obtained from the Institutional Review Board at the University of Utah. Among the 187 patients, 13 have been included in the genetic study published by Heinzen et al in 2012  [12].
Methods DNA was extracted from peripheral venous blood using QIAmp DNA minikit (Qiagen, Hilden, Germany). ATP1A3 sequencing was performed on DNA from AHC probands and family members using the Sanger method after PCR amplification of the 23 coding exons and their flanking regions with intronic primers as defined by Heinzen et al (reference sequence ENSG00000105409/NCBI:NM_001256214. 1)  [12]. PCR products were purified with ExoSA-P-IT (Affymetrix, Santa Clara, CA) and sequenced using the BigDye3. 1 terminator method on an ABI PRISM 3730xl Genetic Analyzer (Applied Biosystems, Foster City, CA). Sequences were analyzed with Sequencher 4. 9 Software (Genes Codes Corporation, Ann Harbor, MI) and DNA variants were described using ALAMUT Software (Interactive-Biosoftware, France). Evaluation of pathogenicity of the DNA variants was made using the Polymorphism Phenotyping (Polyphen) program (http://genetics.
bwh. harvard. edu/pph/), the Provean program (http:// provean. jcvi. org/index. php) and the Human Splicing Finder tool (http://www. umd. be/HSF/). Detection of the proband's mutation in the DNA of the parents was performed by Sanger sequencing of the mutated exon. DNA from an additional 30 probands was examined via whole genome sequencing on the CGI platform (Complete Genomics Inc. , Mountain View, CA), including 25 parent-child trios and an additional 5 multiplex AHC pedigrees. Sequences were aligned to the GRCh37 (hg19) human reference genome. Variants were evaluated using QIA-GEN's Ingenuity Variant Analysis software. We tested for presence and frequency of identified variants in the Kaviar database (version 141029), which integrates data from 1000 genomes, the Personal Genome Project, ESP6500, dbSNP and several other public resources, and thousands of private genome sequences  [40].
For the clinical phenotype portion of the study, information was collected using standardized questionnaires completed by the parent or caregiver first, and then validated by the physician. For some patients, follow-up information was available from medical records, subsequent in-person evaluations at one of several national family meetings sponsored by the AHCF, or via follow-up telephone interviews. Main characteristics of the subset of AHC patients with complete clinical data are summarized in Table  1. Clinical characteristics were compared among a cohort of 164 subjects with and without ATP1A3 mutations. We also compared clinical data between individual patient cohorts with the two most frequent mutations, D801N and E815K, and to those with other ATP1A3 mutations.
We tested for their presence and frequency in the Kaviar database and concluded that these variants have never been observed other than in AHC patients. No mutation was detected in the exonic sequence of ATP1A3 in 33 AHC patients. The predominant mutation, D801N, was found in 40% of the simplex patients (58/143) and the mutation E815K in 26% (38/145); neither of these mutations were observed in multiplex cases (see S1 Table ). In the 70 simplex cases for which DNA was available from both parents, all were confirmed to be de novo mutations. One dominant family with 4 affected family members was previously reported  [3]. In another family, a heterozygous mutation (R756H) segregates with the disease phenotype in an affected mother and her two affected children. No ATP1A3 mutation was found in 3 other multiplex families.
Phenotype analysis and correlations Data were extracted from standardized medical questionnaires that had been previously entered into a RedCAP database associated with the registry. Data for the current analysis were selected according to the reliability of documentation, their availability in most patients, and their perceived importance as indicated by emphasis in other recent publications. The variables include: 1) the age of the first paroxysmal symptom or sign (i. e. , ocular movements, dyskinesia, or unilateral or bilateral paralysis or seizure-like episode); 2) the age at which the child achieved unsupported sitting; 3) the age at which the child achieved independent walking, and 4) a history of status epilepticus and/or sudden unexplained death during the time of follow up. All patients with the D801N or E815K mutation had onset of their first paroxysmal symptoms by 18 months of age.
Conclusion Further progress in our understanding of the pathophysiology of AHC and the broader spectrum of ATP1A3 related phenotypes will require that a number of initiatives proceed in parallel, including 1) close collaboration among patients, physicians and researchers to facilitate early diagnosis via molecular studies; 2) early enrollment of the majority of patients in registries and prospective longitudinal studies; 3) a strong international collaboration to ensure uniform collection of data to better understand disease pathogenesis and outcome; and 4) the identification and implementation of valid, reliable, and sensitive outcome measures for future use in clinical trials to assess promising therapies. Such outcomes measures should include (a) caregiver questionnaires and patient or caregiver reported outcomes, (b) standardized patient assessments of motor and cognitive function over a wide range of age and disease severity, and (c) tools for tracking AHC episode characteristics such as duration, frequency, and severity.
Acknowledgments We are grateful to the patients and families who have participated in these studies over nearly two decades. We are especially grateful to  Sharon Ciccodicola  and  Lynn Egan  of the  US Alternating Hemiplegia of Childhood Foundation ,  Dominique Poncelin  of the  Association Française de l'Hémiplégie Alternante and Rosaria Vavassori of the Associazione Italiana per la Sindrome di Emiplegia Alternante  for their leadership and support of this work. We gratefully acknowledge the.
Acknowledgements We thank  Drs P. Maire  ( Institut Cochin, Paris ) and  F. Relaix  ( Paris Est-Creteil University, Creteil ) for Six1, Six4 and Pax3 expression vectors and  Dr R. Maxson  ( University of Southern California, Los Angeles ) for the Msx1 flox mouse strain. Drs J. F Ouimette  and  C. Rougeulle  are acknowledged for their advice on ChIP experiments. C. Bodin  provided tissue cryostat sectioning. Dr P. Maire  is acknowledged for his constant support.
The remaining 112 million paired reads were assembled with IDBA-UD (3) and the scaffolding tool from the Platanus assembler (4). Ends and gaps within scaffolds were tentatively closed using GapFiller  (5). Extended scaffolds were assembled using CAP3  (6). Read pairs were mapped onto scaffolds using Bowtie  (7)  and sequencing coverage levels were estimated for each scaffold using SAMtools  (8). All 16S sequences were retrieved and taxonomically annotated following homology searches run on the SILVA database  (9). A typical 16S Rhodobacteraceae-like sequence was determined at a high coverage rate (1,005ϫ), approximately corresponding to 20 bacterial cells per sponge cell. We propose "Candidatus Rhodobacter lobularis" as a name for this new species based on its 16S taxonomic classification and its association with the sponge.
The two large scaffolds corresponding to this species were pointed out by their high sequencing coverage (Ͼ1,070ϫ in average) and further characterized through a similarity search of their predicted genes (using MetaGeneMark  [10] ) on the NR database (best BLASTp hits, E Ͻ 10 Ϫ5 ). The resulting 5,034,992-bp draft genome sequence is GϩC rich (63. 5%). The genome assembly was annotated with the Rapid Annotation using Subsystems Technology (RAST) server  (11). Annotations of protein encoding genes were validated using homology searches on GenBank, eventually improved using Artemis  (12). A total of 47 tRNA genes and 4,787 proteins were predicted, corresponding to 85. 75% of the assembled sequence. We identified all Alphaproteobacteria core genes  (13) , suggesting that the present sequence is nearly complete.
Of the predicted proteins, 3,523 (73%) were assigned to gene families using OrthoMCL algorithm and database (14) and 2,416 (50. 5%) were assigned to biological KEGG pathways using the KAAS server  (15). As expected, "Ca. Rhodobacter lobularis" harbors the core metabolic pathways such as glycolysis, gluconeogenesis, the tricarboxylic acid cycle (TCA), and the pentose phosphate pathway. The genome also exhibits a tandem cluster of gene transfer agents, the bacteriophage-like elements that mediate horizontal gene transfer found in nearly all Rhodobacterales  (16). Comparison with genome sequences available in RAST showed that Phaeobacter gallaeciensis (score, 518), Sagittula stellata (score, 509), Roseobacter sp. AzwK-3b (score, 503), Rhodobacterales bacterium Y4I (score, 489), Roseobacter sp.
SK209-2-6 (score, 482), Silicibacter pomeroyi (score, 452), and Ruegeria pomeroyi DSS-3 (score, 438), all Rhodobacterales, were the closest neighbors of this new species. Nucleotide sequence accession numbers. The whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LFTY00000000. The version described in this paper is the first version, LFTY01000000, and consists of the two sequences LFTY01000001 and LFTY01000002.
ACKNOWLEDGMENTS This work has been carried out thanks to the support of the A* MIDEX  project ( ANR-11-IDEX-0001-02 ) funded by the " Investissements d'avenir" French Government program , managed by the  French National Research Agency (ANR). This work was supported by the  Aix-Marseille University  and the Centre national de la recherche scientifique. We thank the ProfileXpert platform (http://www. profilexpert. fr/) for genome sequencing and the IMBE services of scientific diving and molecular biology for sponge sampling and DNA extraction. We thank the  OSU Institute  and  Spongex  project partners for their help, especially Carole crossmark Genome Announcements September/October 2015 Volume 3 Issue 5 e00977-15 genomea. asm. org 1 Borchiellini,  Jean Vacelet ,  Alexander Ereskovsky ,  Emmanuelle Renard ,  Guillaume Blanc ,  Laurent Kodjabachian , and  Hassiba Belahbib.