dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analyses Analyses were carried out using the R statistical package (v. 3. 0. 2). The prevalence of infected mosquitoes was analyzed on the whole dataset (n = 1156 mosquitoes) using GLM models with a binomial error structure, fitting mosquito sampling location (site), sampling time (month) and their interaction as fixed explanatory variables. The significant effect of month on mosquitoes infection prevalence was further confirmed by a mixed effect model approach in order to account for i) the nested structure of the dataset (month within site); and ii) potential temporal auto-correlations  [83]. Parasite prevalence (calculated for each site x month combination) was arcsine square root transformed  [83]  prior to fitting in a lme model (nlme package) using month as a fixed effect, site as a random term, and adding a temporal autocorrelation structure (month within site, corAR1 function) to our model as described in  [84].
Morphospecies or parasite genus, mosquito vectors, bird hosts order and sample regions are given according to the MalAvi database. For each lineage, we give the GenBank accession number used to build the phylogeny. Independently, we also give a non-exhaustive list of references in which the different lineages can be found, with emphasis on studies of vectors. enough individuals of each insecticide resistant category to warrant separate analyses for each of them, all insecticide resistant mosquitoes were grouped within a single insecticide resistant class (giving a binomial IR response variable with two levels: resistant and susceptible). Similarly, only two Wolbachia subgroups were found in mosquitoes giving a binomial response variable (Wolb). The effect of site and month on the probability of being insecticide resistant (IR) or belonging to a given Wolbachia subgroup (Wolb) were therefore analyzed using GLM models with a binomial error structure.
Three other lineages were found for the first time and could not be assigned to a given morphospecies, though two of them unambiguously fell within the Plasmodium genus and the third one within the Haemoproteus genus. The first one, which we named CXPIPS2 is close to several lineages within the P. relictum morphospecies (e. g. 97% identity at the nucleotide level with SGS1, GRW11 and COLL1; cf. Table  1  and Figure  3  for GenBank accession nos), while the second one, CXPIPS1, is closest to CXQUI01 (99% identity) and MANSON01 (99% identity) lineages which have been isolated in Japanese mosquitoes (Cx. quinquefasciatus and Mansonia sp. respectively  [72] ). Finally, the CXPIPS3 sequence matches that of several Haemoproteus lineages such as H. pallidulus lineage SYAT03 (97% identity), and H.
The two CO1 filiarial sequences were strictly identical and clearly match with sequences from members of the Onchocercidae family. The CO1 sequences obtained in this study [GenBank: KJ612514] were however not identical to sequences available in GenBank, preventing us from identifying the species infecting our Cx. pipiens samples. The most closely related sequence (90. 4% identity at the nucleotide level) found in GenBank is from the avian filarial nematode Chandlerella quiscali [GenBank: HM773029], which is naturally found in several species of Passeriformes.
Acknowledgments We are very grateful to  Karen McCoy  for her help with the site occupancy models, to  Muriel Dietrich  for her help with the phylogenetic analyses, to  Valérie Noel ,  Emilie Dumas  and the  Mylène Weill's group  for laboratory assistance and useful advice. This study was funded by the  French ANR program  ( ANR "IRMAL" ) to AR. AN and JV were funded by an  ERC   Starting Grant   243054  to SG, FZ was funded by a PhD grant from the  CNRS  and the  Languedoc-Roussillon Region. This is contribution ISEM 2014-127 of the  Institut des Sciences de l'Evolution de Montpellier  ( UMR 5554 CNRS -Université Montpellier 2 ).
Sera. A total of 20 samples from myositis patients positive for anti-HMGCR antibodies (see Table  1 ) using a research addressable laser bead assay (ALBIA, Rouen, France) identified in a previous study  [11]  and 20 negative controls (age and sex matched) were collected and tested using various methods. To verify the specificity of the QUANTA Lite HMGCR ELISA a total of 824 controls were tested (for details see Section 3). Diagnoses of the patients were established based on the respective disease classification criteria and as previously described  [12]. Collection of patient samples was carried out according to local ethics committee regulations. Patient data was anonymously used in keeping with the latest version of the Helsinki Declaration of human research ethics.
Epitope Mapping Studies. Autoantibodies to various peptides were studied using PEPperCHIP technology (PEPperPRINT GmbH, Heidelberg, Germany)  [15, 16]. Peptide arrays were blocked using blocking buffer (Rockland blocking buffer MB-070 (60 min before the first assay). Sera were diluted 1 : 1000 in incubation buffer (PBS, pH 7. 4 with 0. 05% Tween 20 and 10% Rockland blocking buffer) and incubated for 16 h at 4 ∘ C and shaking at 500 rpm. Arrays were then washed (2 × 1 min after each assay with Washing Buffer (PBS, pH 7. 4 with 0. 05% Tween 20). Secondary antibody (F(ab')2 goat anti-human IgG (H + L) DyLight680) diluted 1 : 5000 was added and incubated 30 min. Identified epitopes were synthesized as soluble peptides, coated to ELISA plates and tested with anti-HMGCR positive samples. By comparing the PEPperPRINT sequence reactivity data to public domain structures of HMGCR the reactive sequences that were likely to be accessible to antibodies were determined to be 531 GYMPIPVGVAGPL 543 , 748GYNAHAANIVTAI 760 , 554 MATTEGCLVASTN 566 , 689 TDKKPAAINWIEG 701 , 561 CLVASTNRGCRAI 573 , and 702 RGKSVVCEAVIPA 714.
Epitope Mapping. Several potential epitopes were identified using the solid phase peptide arrays (see Figure  5 ). A total of six sequences were selected based on surface exposure ( 531 GYMPIPVGVAGPL 543 , 748 GYNAHAANIVTAI 760 , 554 MATTEGCLVASTN 566 , 689 TDKKPAAINWIEG 701 , 561 CLVASTNRGCRAI 573 , and 702 RGKSVVCEAVIPA 714 ), synthesized as soluble peptides and tested with positive sera and controls by ELISA. Reactivity found by solid phase peptide arrays could not be confirmed (data not shown).
Background: This systematic literature review aimed to summarize evidence for the added value of drug sales data analysis for the surveillance of infectious diseases. Methods: A search for relevant publications was conducted in Pubmed, Embase, Scopus, Cochrane Library, African Index Medicus and Lilacs databases. Retrieved studies were evaluated in terms of objectives, diseases studied, data sources, methodologies and performance for real-time surveillance. Most studies compared drug sales data to reference surveillance data using correlation measurements or indicators of outbreak detection performance (sensitivity, specificity, timeliness of the detection). Results: We screened 3266 articles and included 27 in the review. Most studies focused on acute respiratory and gastroenteritis infections.
Methods We conducted a literature search from 1975 up to June 2012 to identify relevant peer-reviewed articles regarding surveillance of infectious diseases based on drug sales data. PRISMA guidelines were followed in the reporting of the review  [10]. Published articles were searched for on electronic databases (Pubmed, Embase, Scopus, LILACS, African Index Medicus, Cochrane Library), using combinations of the following key words: ("surveillance" OR outbreak detection OR warning system) AND (overthe-counter OR "prescription drugs" OR pharmacy OR (pharmaceutical OR drug OR medication) sales). The search was limited to articles in English or French. There were no limitations on study settings. To be included in the review, articles had to describe, test, or review an infectious disease surveillance based on drug sales data; and be original research that presented new data and results.
We excluded studies that monitored chronic diseases, as well as prevalence studies whose purpose was not epidemic detection. One reviewer screened and evaluated the titles and abstracts. Articles were widely included in a first stage. The full-text review and the final selection of the articles were made by two reviewers. We reviewed and described the articles in terms of objectives, diseases studied, data sources, methodologies, and performance for real time surveillance. To describe methods and results, we separated the articles into three groups based on their main objective: descriptive retrospective studies, drug selection studies, and prediction studies. Outcomes selected to compare drug sales data to reference surveillance data of the corresponding disease were correlation measurements (strength and timeliness of the correlation) and indicators of outbreak detection performance (sensitivity, i.
Drug sales data sources In most retrospective studies, data were collected specifically for the purpose of the study from a sample of pharmacies  [16, [24] [25] [26]  or from retailers  [13, 15, 17, 29]. For example, in a Canadian study  [17] , electronic data were provided by one major retailer for all of their 19 pharmacies in the study area. Automatically compiled data sources were used in all the drug selection and prediction studies and in some retrospective studies. Drug sales data were routinely collected in samples of a city's or country's pharmacies. Such routine data collection systems were mainly implemented by research or public health groups, such as the Johns Hopkins Applied Physics Laboratory  [20, 21, 35, 36] , the New York City Department of Health  [14] , the National Institute of Infectious Diseases in Japan  [27] , or the Real-Time Outbreak and Disease Surveillance Laboratory at the University of Pittsburg  [19].
Ten studies used cross-correlation function to measure the similarity of two curves and to determine the time lag at which the correlation between the datasets is maximized. Cross-correlation is a standard method to determine the time delay between two signals. In three studies, only correlation between the time series was examined without analyzing time-lagged relationship. Six studies used aberration detection methods to evaluate whether and by how long the date of signal detection by drug sales precedes the signal based on diagnostic data. The signal definition for aberration detection was based on either a simple threshold to define alerts  [15]  or more complex algorithms such as the Serfling method  [14] , ARIMA models  [19] , the simple moving average method (MA), the cumulative sum method (CUSUM)  [11, 16] , or the exponentially weighted moving average (EWMA)  [18].
Results from drug selection studies showed that it is possible to identify groups of products strongly associated with incidence data, which can then be used to predict future trends in clinical data and help public health authorities to prepare response planning. Such product selection procedures, however, depend on the existence of large clinical surveillance databases of the diseases concerned. Similarly, the validity of drug sales data analysis has been evaluated mainly for two disease groups, respiratory and gastrointestinal illness, for which clinical reference data, used as the gold standard, are readily available. Pertussis and syphilis have been evaluated in only one study each, and still require further confirmation. The concept of drug-based surveillance therefore needs to be validated for other infectious diseases.
Moreover, it should be noted that alternative sources of data for disease surveillance are currently under development. Healthcare management databases that can provide exhaustive information on drug consumption and diagnosis, as the Dossier Médical Personnel  [42]  in France, are promising tools for disease surveillance. Our review may be affected by a publication bias since studies unable to show correlations between drug sales and reference data may have been less published. In addition, selections bias may have occurred in the studies. Indeed, some studies in the review were based on a limited number of pharmacies and/or a limited study period (e. g. less than one year). Language bias may exist as we were not able to identify studies published in languages other than English and French.
Conclusion This review suggests that the analysis of drug sales data is a promising method for surveillance and outbreak detection of infectious diseases. It has the potential to trigger an outbreak alert earlier than most surveillance systems. However, the main challenges consist in the appropriate selection of indicator drug groups and the validation of this approach for diseases for which no or poor quality clinical surveillance data exists. The usefulness of the approach also depends on the available resources and the organization of the health care system. Drug sales databases with real-time or near real-time data transmission are available in several countries; future studies should be encouraged to expand their use on other infectious diseases.
[30] 2009 Dec 2006-April 2007 Sahai City, Osaka, Japan ILI Questionnaires mailed to 273 Prescribed Week pharmacies. 56% responding pharmacies. (456,000 people) Van den Wijngaard et al. 2001-2003 The Netherlands ILI Foundation for pharmaceutical Prescribed Week [28] 2008 statistics (85% of Dutch pharmacies) (13,8 million people) Edge et al. [17] 2006 Jan 2001-April 2004 Canada (one province) GI One major retailer with 19 OTC Week locations (12% of the pharmacies in the region) Das et al. [14] 2005 Aug 2002-March 2005 New York City ILI and GI New York City Department of OTC Day Health (248 NYC pharmacies, 30% of citywide sales) Okhusa et al. [22] 2005 Nov 2003-April 2004 Japan ILI Private marketing company (1100 OTC Day pharmacies, 2% of the pharmacies in Japan) Chen et al. [11] 2005 March 2003-July 2004 A rural county in New York State Pertussis Medicaid database Prescribed Day reimbursement Edge et al.
Anticandidal Activity of the NCR Peptides. Since cationic defensin-like NCR peptides have been shown to be active against a wide range of Gram-negative and Gram-positive bacteria, including animal and plant pathogens, 19 NCR peptides covering the isoelectric point (pI) spectrum of the peptide family (Table  1 ) were investigated for anticandidal activity in microdilution plate assays. In serum-free RPMI1640 (GIBCO), NCR peptides did not have any anticandidal activity (data not shown) which was not surprising as the concentration of NaCl (>100 mM) and the presence of Ca 2+ and Mg 2+ ions had been previously shown to inhibit their bactericidal effect  [12]  and are known to block AMP activities  [20, 21]. Hence, the NCR activity tests were performed in LSM medium that had been previously used successfully to measure antifungal activity of defensins.
Localization of NCR Peptides in C. albicans Cells. Although disruption of cell membranes is considered as a general action of cationic AMPs, they might exert other effects by entering the target cells and inhibiting DNA, RNA, or protein synthesis  [22]. Therefore, the cell penetration properties and the localization of the peptides in C. albicans cells were also investigated. For this purpose, FITC-conjugated NCR247 peptide was synthesized; the conjugated peptide  retained comparable anticandidal activity to the unconjugated form (data not shown). Similarly and as a control, the inactive NCR035 peptide was also labeled with FITC. C. albicans WO-1 cells were treated with the FITC-labeled peptides and the localization of fluorescence signals was observed with confocal microscopy. As expected, NCR035 did not show interaction with the negatively charged fungal membranes and did not label the C.
Determination of the Cytotoxicity of NCR Peptides on Human Cells. An antimicrobial agent cannot be a successful candidate for subsequent use in healthcare if it exhibits toxic activity against human cells. As a consequence, in order to determine whether NCR peptides are cytotoxic against human cells, two cell types, vaginal epithelial cells and keratinocytes (data not shown because of the similar results) that are the targets of Candida infections, were tested. The cytotoxicity was measured with cell viability/proliferation assays. The MTT assay provides information on the metabolic state of the cells by measuring the activity of mitochondrial dehydrogenases via the conversion of the tetrazolium dye MTT to formazan. The RTCA assay provides real-time, quantitative information about the number of the living, attached cells by measuring electrode impedance.
Acknowledgments The authors thank  Dr. Csaba Fekete  ( University of Pécs ) for providing primycin,  Katalin Vincze-Kontár  for technical assistance, and  Dr. Andrew McDowell  for critical reading of the paper. This study was supported by the  "SYM-BIOTICS" Advanced Grant  of the  European Research Council  (Grant no. 269067 ) and by the  Hungarian National Office for Research and Technology  ( NSPEPBAC: T ÉT 09-1-2010-0009 ). István Nagy was supported by the  János Bolyai Research Scholarship of the Hungarian Academy of Sciences.
Stump pain Body scheme a b s t r a c t Phantom phenomena are subject of various, often inconsistent, descriptions, and new concepts and treatment approaches emerge. The aim of the study is to describe contemporary terminology and developments in the field, and to share personal experience. A review of English and French language literature, published prior to 27th February, 2012, extracted from PubMed/MEDLINE, Google. fr, GoogleScholar databases, and by hand searching of selected full text papers and textbooks with correspondence to personal clinical experience was performed. The terminology and classification of phantom phenomena sensations, relations between intensity and character of phantom pain to the etiology and level of amputations, as well as the influence of presence and intensity of pre-operative limb pain and post-operative stump pain on phantom phenomena are described.
2 and an exponential cut-off at ǫ c = 200 keV in the IS. The data from INTEGRAL do not cover the energy range of the accretion disk emission. Therefore, we adopted kT max = 0. 3 keV, which is an intermediate value between the typical 0. 1 and 0. 6 keV in the LH and HS states, respectively  (Malzac et al. 2006 ). The disk inner radius was estimated according to  Vila et al. (2012) ; we considered a luminosity of the disk of L d = 4×10 37 erg s -1  (Poutanen 1998 ). The disk/corona ratio was taken as 0. 8, yielding R c ∼ 10r g. In the right panel of Fig. 2  we show the secondary-pair spectrum, which is softer at high energies than the corresponding spectrum in the LH state. In the IS there is no jet, and the accretion disk is much closer to the black hole. This suggests a small inclination angle for the field lines.
Acknowledgments This work was supported by the  Argentine Agencies CONICET  ( PIP 0078 ) and  ANPCyT  ( PICT 2012-00878 ), as well as by grant  AYA2010-21782-C03-01  (Spain). S. C. and G. E. R. acknowledge funding by the  Sorbonne Paris Cité (SPC) ,  Scientific Research Project -Argentina 2013. S. C. thanks the  Centre National d'Etudes Spatiales (CNES). This work is based on observations obtained with MINE: the  Multi-wavelength INTEGRAL NEtwork.
Data collection Data from cases, controls and case/control mothers (or relative) are collected through a standardized phone questionnaire administrated by professional interviewers (IPSOS company). Interviewers are unaware of the case or control status of study subjects. To ensure consistency in data collection, interviewers have been trained in the completion of the questionnaire and provided with a field guide. All data are entered directly on the specially designed online study platform used for registration and data collection (for items, see Table  1 ). Investigators, technicians and researchers have a personal login and password to access the platform. Accesses to sensitive data are restricted, based on the user profile. The coordinating center contact the clinicians in charge of cases to obtain the pathology report and serum markers (alpha feto-protein, beta-HCG).
Environmental exposure assessment Cases and controls residential history are gathered from 1 year prior to birth to date of the inclusion in the study. Semi-automatized fields in the study platform help to reduce misspellings when entering the questionnaire data. In case of inconsistency between subjects' and mothers' information, data provided by the mothers are used. Addresses are geocoded using the database "BD adresse" from the French National Geographic Institute (IGN), which contains coordinates of all addresses in France (unit: RGF Lambert 93). Since the coordinates of the database are centered on the postal address, a GIS technician moves manually the point to the center of the household. Using dedicated software (BD Adresse® for ArcGIS Locator), we identify all addresses geocoded with poor precision (at the street level or less) for manual verification or repositioning (when possible).
Specific additional questions are added to the questionnaire to help the GIS technician when no street number is available (closest crossing road or point of interest). The use of infra-red images, based on the greenness reflectance, has been used successfully in previous US studies to reconstruct land use data  [39, 40]. Satellites images are available from the Landsat® program from 1972 with an 80 m spatial resolution and from the SPOT® program from 1986 with a 20 m spatial resolution. Based on remote sensing of satellite images and/or photo interpretation of IGN aerial photography (available from 1920's), we determine the land use around each residence of interest. When data are not available or of poor quality, we assign land use data of the nearest available time period to the residence.
Samples were taken during the main period of pesticides use according to the representative cultures of the Rhône-Alpes region (orchards, wine, cereals), reflecting the main application modes used in France (rotary atomizer, inflatable ramps, pneumatic sprayer, and motorized mist blower mounted on straddle tractors). According to this study, our GIS methodology is based on 500 meter and 1000 meters buffers, the frequency of the wind direction (data from Meteo France®), the presence of topographic barriers (BD Alti, IGN), vegetative barriers (BD Topo®, aerial photography and/or remote sensing), and structural barriers (BD Topo®, aerial photography and/or remote sensing). The score we developed (Agricultural Exposure Index (AEI)) estimates the intensity of exposure to the different crop types for each address/year.
Acknowledgments The authors acknowledge the members of the  TESTIS Steering Committee  ( Dr. Béatrice Fervers ,  Dr. Joachim Schüz ,  Pr. Louis Bujan ,  Dr. Barbara Charbotel ,  Dr. David Cox ,  Dr. Virginie Chasles ,  Dr. Aude Flechon ,  Dr. Helen Boyle ,  Olivia Pérol ,  Rémi Béranger ,  Dr. Florence Brugnon ,  Dr. Florence Eustache ,  Dr. Isabelle Koscinski ,  Dr. Jeanne Perrin ,  Pr. Célia Ravel ,  Pr. Nathalie Rives ,  Dr. Sandrine Giscard d'Estaing ,  Dr Véronique Drouineaud ). The authors also thank  Gilles Clapisson  ( Centre Léon Bérard, Lyon ) and  Pr. John R. Nuckols  ( Colorado State University, CO, US ) for their support in the design of the study protocol. Rémi Béranger  received a doctoral grant from the  Rhône-Alpes region. This project is granted by the  French National Institute of Health and Medical Research (INSERM ,  N°ENV201306/CLB ) and the  French National Cancer Institute (INCa ,  N°2013-143 ).
Apoptosis detection Apoptosis of MDDC was detected by using the Annexin V-FITC Apoptosis Detection Kit (eBioscience, San Diego, CA)  [22]. Briefly, MDDC were treated with stimuli for either 24 or 48 h, as indicated, harvested and double-stained with FITC-conjugated annexin V and propidium iodide, according to the manufacturer's protocol. Cells were analyzed by flowcytometry in a FACScan (BD Biosciences, San Jose, CA) using CellQuest software. Data are expressed as % of positive cells.