dataesr/scientific-paragraphs-categorization huggingface dataset:
For this simulation, the actual number of components was provided to the algorithms in order to focus on modeling and classification abilities of both approaches. The left panel of Figure  7  shows the log-likelihood value of the whole dataset (training + test sets) divided by the number of observations for the inductive and transductive approaches according to the size of the unobserved class. In this figure, the information in which we are interested in is the relative behaviour of the inductive approach compared to the transductive one and not the the global behaviour of both curves. Indeed, for each situation, the approach with the highest log-likelihood value per point is the one which provides the best modeling of the data. On the one hand, it appears that the log-likelihood curve of the transductive approach is above the one of inductive approach for sizes of the unobserved class larger than 10.
We therefore recommend the use of AIC as model selection criterion in the context of unobserved class detection. Determination of the breakdown group size The two panels of Figure  9   recognition rate and the true positive rate should be close to 1 whereas the false positive rate should be close to 0. Both recognition rates were computed on a test dataset. Figure  9  shows that the three recognition rates are very good for sizes of the unobserved class larger than 10 in the case of inductive AMDA (left panel) and larger than 20 in the case of transductive AMDA (right panel). We observe as well that for sizes of the unobserved class smaller than 5-10 the true positive rate is very unstable and this means that the unobserved class is not well modeled. This confirms the observation made in the previous paragraph and the inductive approach seems more robust than transductive AMDA in the case of unobserved classes of small sizes.
To summarize, these Monte Carlo experiments have first demonstrated that the transductive version of AMDA should be used for modeling purpose on large dataset whereas inductive AMDA should be used for detecting and modeling small unobserved classes. They have also shown that AIC is the most efficient criterion for detecting unobserved classes and that the inductive version of AMDA is able to detect and model unobserved classes in the test set for unobserved classes as small as 5-10 observations.
The Add-Health dataset The social network studied here is from the National Longitudinal Study of Adolescent Health and it is a part of a big dataset, usually called the "Add-Health" dataset. The data were collected in 1994-95 within 80 high-schools and 52 middle schools in the USA. The whole study is detailed in  [20]  and  [42]. In addition to personal and social information, each student was asked to nominate his best friends. We consider here the social network based on the answers of 67 students from a single school, treating the grade of each student as the class variable. Two adolescents who nominated nobody were removed from the network. We therefore consider a whole dataset made of 65 students distributed into 5 classes: grade 7 to grade 11.
Detection of one unobserved community Among the 65 nodes of the network, we randomly selected a learning dataset of 55 nodes and a test dataset of 20 nodes among which all the 13 students in grade 11 (5th class). For facilitating the visualization of the results, the latent space dimension p has been fixed to 2 for this experiment and the following one. Once the supervised latent space learned and the test nodes projected into the latent space, QDA, QDA-ND, SVM-ND and AMDA have been applied within the latent space for classifying the test nodes and trying to detect unobserved classes. Figure  10  presents the classification results obtained in the latent space with the four considered methods. The panels of the first row respectively present the learning nodes organized into 4 (observed) groups and the 20 test nodes for which the class membership is assumed to be unknown.
The left panel of the second row provides the actual labels of  all the nodes. The three following panels show the classification results provided by QDA, QDA-ND and SVM-ND respectively. Finally, the last row presents the results of AMDA (inductive version). Table  4  provides the confusion tables for the four classification methods computed on the test dataset. First, it appears that the different classes of the network are quite homogeneous and that the network has a natural structure. Indeed, when considering the full network (left panel of 2nd row), only two nodes have latent positions which do not agree with the class membership of the nodes. Regarding the classification results, QDA classifies unsurprisingly all the test nodes between the known classes and does not detect the unobserved class (light blue diamonds).
Conclusion and further works This work has focused on the problem of learning a supervised classifier with unobserved classes. An adaptive model-based discriminant analysis method has been presented in this paper which is able to both detect unobserved groups of points in a new set of observations and to adapt the supervised classifier to the new situation. Two EM-based approaches have been proposed for parameter estimation: a transductive approach which considers all available observations for learning in a unique step and an inductive approach, which is made of a learning and a discovering phase. The detection of the number of unobserved classes is done using model selection criteria. Experiments on simulated and real datasets have shown that the proposed method is able to detect different kinds of unobserved classes (Gaussian, uniform noise,.
provides their confusion tables computed on the test dataset. As one can expect, QDA does not detect the unobserved classes (light blue diamonds and purple points) and assigns all nodes from these two classes to known classes. QDA-ND and SVM-ND both detect the presence of novelties but are unable to see the two new communities. QDA-ND and SVM-ND appear again too sensitive since they make several false novelty detection. Finally, AMDA both succeeds in detecting novelties and identifies two unobserved communities. As previously, AMDA fails in assigning the bottom-right node to its actual class but this is again understandable. This second experiment is particularly important since it demonstrates that AMDA is able to detect and model several unobserved classes in a real-world problem.
Data analysis A three-way ANOVA test was used to analyze the effects of temperature, relative humidity, rainfall and their interactions, on A. lucorum egg hatching. We also analyzed the effects and interactions of temperature, relative humidity, and sampling period on egg hatching rate and developmental duration. Oneway ANOVA was used to analyze the effects of temperature or relative humidity on developmental duration. Prior to analysis, egg hatching rates were transformed using the arcsine square root, and developmental duration data were transformed using log 10 (n+1) in order to satisfy the assumption of normality. Data on temperature, relative humidity and rainfall at the Langfang location between 2009 and 2013 were collected by the Chinese Meteorological Data Sharing Service (http://cdc.
© 2014 Falque et al. ; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons. org/licenses/by/2. 0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http:// creativecommons. org/publicdomain/zero/1. 0/) applies to the data made available in this article, unless otherwise stated.
Algal and viral abundance Samples to use for algal and viral enumeration were analysed using a benchtop BD FACSCalibur flow cytometer with a 488 nm argon laser (BD Biosciences, San Jose, USA). Algal abundances were determined without dilution by chlorophyll red autofluorescence and side scatter  (Marie et al. , 1999). Virus samples were, once thawed, diluted 100 to 10 000-fold in sterile TE buffer (pH = 8) according to  Brussaard (2004). In short, PgVs were stained with the nucleic acid-specific dye SYBR Green I to a final concentration of 0. 5 × 10 -4 of the commercial stock (Life technologies Ltd. Paisley, UK) for 10 min at 80 • C and discriminated by their green fluorescence and side scatter signal. All flow cytometry data were analysed using CYTOWIN 4. 31  (Vaulot, 1989).
, 2012). While the MS 2 and MS 3 spectra of both m/z 766 and 764 exhibited similar characteristics to those arising from the m/z 780 and 778 ions, full structural elucidation was not possible from ion-trap MS spectra. As all four glycosphingolipids were found equally present in both the infected and control cultures and were thus not affected by viral infection; further structural identification of the compounds fell outside of the scope of this study. Viral glycosphingolipids (vGSLs), with a dominant loss of 162 Da, as described by  Vardi (2009) , were not detected. The fatty acid moieties of the IPLs (IPL-FAs), determined using the fragment patterns observed in the MS 2 spectra of the [M+H] + ions exhibited only minor changes in composition due to the viral infection (data not shown). For example, the MGDG-FA distribution did not change significantly in the control cultures over the 48 h experiment.
Acknowledgements. We thank two anonymous reviewers for their constructive comments which improved the manuscript. We dedicate this paper to  Carlo Heip  ( † 15 February 2013). D. S. Maat was supported by a grant to  C. P. D. Brussaard  of the  Royal Netherlands Institute for Sea Research (NIOZ)  for funding of this project. NIOZ is an institute of the  Netherlands Organization for Scientific Research (NWO). N. J. Bale  was supported by a grant ( 839. 08. 331 ) to  J. S. Sinninghe Damsté  of  The National Ocean and Coastal Research Programme (ZKO)  supported by  NWO. Edited by:  G. Herndl.
10, 11 hole-exome sequencing (WES) of 790 individuals with suspected mitochondriopathy in five centers identified eight index case subjects (plus two affected siblings) with homozygous or two heterozygous rare variants (minor allele frequency < 0. 1%) in GTPBP3 (MIM 608536), with no such case being found in 11,295 control subjects. This presents a genome-wide significant enrichment in GTPBP3 (RefSeq accession number NM_032620. 3) mutation load in samples from individuals with the clinical diagnosis ''mitochondrial disease'' (p < 3. 2 3 10 À10 , Fisher exact test) in comparison to nonmitochondrial disorder samples. In addition, when filtering for genes coding for mitochondrial proteins,  12  in several individuals GTPBP3 was the only gene with two mutations. Further evidence for the pathogenic role of GTPBP3 mutations was derived from followup candidate gene sequencing of 18 individuals with similar phenotypes, which identified two more index cases.
Acknowledgments We thank  C. Terrile ,  M. Borzes , and  C. Fischer  for technical support and  F. Miyake  and  T. Wada  for referral of sample materials. This work was supported by the  Deutsche Forschungsgemeinschaft  within the framework of the  Munich Cluster for Systems Neurology (EXC 1010 SyNergy ), the  German Bundesministerium fu ¨r Bildung und Forschung (BMBF)  through funding of the  E-Rare  project  GENOMIT  ( 01GM1207  for T. M. and H. P. ,  2011-RARE-005-03  for A. R. and M. D. M. , J41J11000420001 for M. Z. , and  FWF I 920-B13  for J. A. M. ),  German Network  for Mitochondrial Disorders (mito- NET 01GM1113C  for T. M. , H. P. , and P. F. and  01GM1113A  for T. K. ), the  German Center for Heart Research  ( Z76010017300  and  Z56010015300  for T. M. ),  European Commission   7th Framework Program  (Project  N261123   GEUVADIS ),  Medical Research Council, UK  ( MC_U105697135  for T.
Objective To identify pharmaceutical policy changes during the economic recession in eight European countries and to determine whether policy measures resulted in lower sales of, and less expenditure on, pharmaceuticals. Methods Information on pharmaceutical policy changes between 2008 and 2011 in eight European countries was obtained from publications and pharmaceutical policy databases. Data on the volume and value of the quarterly sales of products between 2006 and 2011 in the 10 highest-selling therapeutic classes in each country were obtained from a pharmaceutical market research database. We compared these indicators in economically stable countries; Austria, Estonia and Finland, to those in economically less stable countries, Greece, Ireland, Portugal, Slovakia and Spain. Findings Economically stable countries implemented two to seven policy changes each, whereas less stable countries implemented 10 to 22 each.
Data sources For this longitudinal study, we used data from two sources to derive information on pharmaceutical policies: (i) the Pharmaceutical Pricing and Reimbursement Information Network (Austrian Health Institute, Vienna, Austria), which collects information from experts in national pharmaceutical pricing and from authorities responsible for reimbursement -the latter provide regular pharmaceutical policy updates; and (ii) the PharmaQuery database (IMS Health, Philadelphia, United States of America), which contains data on pharmaceutical policies. In addition, we included information on policy changes reported in the published literature. We grouped policy changes into 6-month implementation periods from January 2008 until December 2011 and we categorized policy as relating to one of three main areas: (i) pricing; (ii) reimbursement; and (iii) generic drugs.
Data analysis First, we described and analysed the number of policy measures implemented per year, per country group and per policy category. Next, we determined the volume and value of the sales of drugs in each therapeutic class between 2006 and 2011 in each country and, then, we calculated the combined volume and value of the sales of drugs for all 10 therapeutic classes for each country. Since our findings for individual therapeutic classes and for all therapeutic classes combined were similar, we present only the results for all therapeutic classes combined. For this analysis, we divided the volume and value of sales by the size of the country's population to control for population growth; annual population figures were obtained from the OECD. 22 e derived the annual and average growth rates over the study period using both the volume and value of pharmaceutical sales per capita: AGR y y = -         × - S S 1 1 100 (1) AAGR AGR = ∑ n ( 2 ) where AGR is the annual growth rate, S y is the per capital sales in a year, S y-1 is the per capital sales in the previous year, AAGR is the average annual growth rate and n is the number of years.
Les informations relatives aux changements de la politique pharmaceutique entre 2008 et 2011 dans huit pays européens ont été obtenues à partir des publications et des bases de données sur la politique pharmaceutique. Les données sur le volume et la valeur des ventes trimestrielles des produits entre 2006 et 2011 pour les 10 classes thérapeutiques les plus vendues dans chaque pays ont été obtenues à partir d'une base de données d' études de marché sur les médicaments. Nous avons comparé ces indicateurs dans des pays économiquement stables: Autriche, Estonie et Finlande, par rapport aux indicateurs mesurés dans des pays moins stables: Grèce, Irlande, Portugal, Slovaquie et Espagne. Résultats Les pays économiquement stables ont chacun mis en oeuvre 2 à 7 changements de politique, tandis que les pays moins stables en ont mis en oeuvre 10 à 22 chacun.
Acknowledgments We would like to thank  Vladimir Braun ,  Simon Caron-Huot ,  Juan Maldacena  and  Raymond Stora  for interesting discussions. We are indebted to  Juan Maldacena  for careful reading of the manuscript and useful comments. The work of A. B. was supported by the  U. S. National Science Foundation  under the grant No. PHY-1068286  and  CNRS. G. K. and E. S. acknowledge partial support by the  French National Agency for Research (ANR)  under contract StrongInt ( BLANC-SIMI-4-2011 ). A. Z. was supported in part by the  U. S. National Science Foundation  under Grant No. PHY-0756966. A. B. , S. H. and A. Z. are grateful to the  Institut de Physique Théorique (Saclay)  for the hospitality extended to them at various stages of the project.
Background. The incidence of paediatric nontraumatic clavicle lesions is unknown and there is limited literature regarding the management of such patients. Methods. A review of a prospectively complied radiological database held at the study was conducted for a defined 10-year period. The study centre is the only paediatric service available for a defined catchment population. The case notes of all patients with nontraumatic lesions were reviewed, and the mode of presentation, the diagnostic dilemmas, and the management were recorded. Results. A total of 2133 clavicle radiographs were performed during the study period, with only five having a nontraumatic history. The overall incidence of paediatric nontraumatic clavicle lesions was 0. 38 per 100,000 per year. Three patients were diagnosed with chronic recurrent osteomyelitis, one with chronic bifocal osteomyelitis, and one with Langerhans cell histiocytosis.
Methods Ethical approval was obtained for this study from the University of Edinburgh. Patients were identified retrospectively from a radiological database (MISYS Radiology) held at the study centre for a ten-year period (1998 to 2007), with a minimum of 6 years clinical follow up. All clavicle radiographs performed during this time were identified. Patients who were identified to have undergone a single radiograph during the study period and for subsequent 3 years after this period (until 2010) were excluded. The subsequent 3-year period was to ensure a patient that may have had an initial radiograph during the study period was not excluded due to a second radiograph being performed after the study period. Patients that had more than one clavicle radiograph were extracted for further investigation.
This makes the assumption that fractures were likely to have only one radiograph where as other lesions of the clavicle, especially nontraumatic lesion, would be more likely to undergo serial radiographic assessment. The radiological reports of the patients with more than one radiograph were then reviewed, which are recorded in the database. All those patients with fractures were excluded from the cohort leaving radiographs of clavicle swellings. Clinical case notes for these patients were then retrieved and the information regarding the presentation, diagnostic dilemmas, final diagnosis, and management issues relating to these patients were recorded. The study centre is the only hospital receiving paediatric trauma for a predominately urban population of 779,000, of which 132,465 (17%) were aged 14 years old or less during the study period.
This estimation was correct in 77% of cases, and was within one semitone of the actual pitch in 88% of cases (Fig. 5C , top). Most errors greater than one semitone correspond to octaves or fifths (octaves: 5. 5%, fifth: Ͻ2%), which also shows in the distribution of firing rate of pitch-tuned groups (Fig. 5C, bottom ). This performance was obtained with 400 frequency channels spanning 50 Hz to 8 kHz, and it degrades if the number of channels is reduced (e. g. , 35% score for N ϭ 100; Fig. 5D, top ), because the model relies on comparisons between neighboring channels. We then tested how performance was affected by constraints on the maximum delay (Fig. 5D, bottom ). We found no difference in performance when maximum delay ␦ max was varied between 2 and 15 ms. The highest f0 in our sound database was 440 Hz (A4), which corresponds to a period greater than 2 ms.
Grants  FP6-IST-027819  (ICEA);  FP6-IST-027140  (BACS)],  Fondation pour la Recherche Medicale  (Grant  SPF20110421459 , and Grant  FDT20110922969  to J. C. ),  French Agence National pour la Recherche  [Grant  ANR-10-BLAN-02  (Neurobot)],  Paris Neuroscience School  (to E. C. ), and  Fondation Fyssen  (to J. C. ). We thank  Alice Fruchart  for animal care and perfusions;  France Maloumian  for help with figures;  Suzette Doutremer  for histology;  Yves Dupraz  for mechanical engineering;  P. Leboucher  for developing the automated visual stimulation system;.
Secondary analysis The analyses for the secondary endpoints will be performed in a similar way to those previously described. The same applies to the secondary endpoint criteria: pain, functional status by WOMAC, maximal walking speed and performance, measurement of peak torques. The comparison of the qualitative parameters (for example the WOMAC scale categorized, for example, by median or quartiles) between the two groups will be made using the Chi-square test or Fisher's exact test (if appropriate). In order to measure the progression of the different parameters collected during the three visits (mobility, amyotrophy, deformation, effusion, and pain on palpation), we will conduct a longitudinal analysis of the data in two stages by ANOVA for repeated data followed by a post-hoc Tukey-Kramer test and using mixed models (or random effects models)  [19]  that will allow the measurement of the intrasubject correlation by taking into account the effects of the subject and time ('random intercept' and 'slope' effects).
ACKNOWLEDGMENTS We are grateful to  Elisa Izaurralde  for helpful comments on the manuscript and to  Elisa Izaurralde  and  Elena Conti  for sending preprints. Work in the authors' lab is supported by the  DFG  (Elmar The  CCR4-NOT complex in Drosophila Wahle ) and by the  CNRS UPR1142, ANR Blanche  ( ANR-2010-BLAN-1201 01 ),  FRM  ("Equipe  FRM 2013 DEQ20130326534 " and " Projets Innovants ING20101221078 ") and ARC Libre 2009 (N •  3192 ;  Martine Simonelig ).
Pandya et al. ; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons. org/licenses/by/2. 0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http:// creativecommons. org/publicdomain/zero/1. 0/) applies to the data made available in this article, unless otherwise stated.
Acknowledgments We are indebted to  Centre National de la Recherche Scientifique ,  Ecole Normale Supérieure de Lyon, Lyon Science Transfert  (projet  L659 ),  Région Rhône Alpes  ( CIBLE Program 2011 ),  INSERM  ( AAP Physique Cancer 2012 ), and the  French Agency for Research  ( ANR-AA-PPPP-005 , EMMA 2011) for their financial support. C. M. T. is very grateful to the  National Council of Science and Technology (CONACyT, Mexico)  for supporting her PhD scholarship. L. S. is very thankful to the  Association Française Contre les Myopathies, AFM-Téléthon , for supporting her PhD scholarship.
In contrast to other vehicle routing problems such as the PDP or VRPTW, in the DARP humans have to be transported instead of goods. Therefore, the aim besides minimizing the operating costs is to ensure patient convenience. This is done by introducing additional constraints such as the maximum user ride time or to specify tight time windows. There exist many variants of the DARP depending on the specific application. An excellent overview about considered problem variants and existing solution methods of this problem class can be found in  Cordeau and Laporte (2007)  and in  Parragh et al (2010a). In the classic DARP the objective function corresponds to minimizing the total routing costs. Cordeau and Laporte (2003)  proposed a Tabu Search algorithm to solve this variant of the problem. Ropke et al (2007)  present a Branch-and-Cut algorithm for solving the Pickup and Delivery Problems with time windows, as well as, exactly solving the easier instances of the benchmark data set for the DARP.