dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements EH benefited from a joint grant from the  European Commission and Cobb-Vantress Inc. within the framework of the  Erasmus-Mundus joint doctorate "EGS-ABG ". BB was supported by the  "Development of genetic selection technology for polyvalent resistance to infectious diseases" (POLY-REID)  (Grant Number  10-093534 ) project granted by the  Danish Council for Strategic Research , the  Danish Poultry Council, The Hatchery Hellevad, and Cobb-Vantress Inc.
, 2006). Salt blocks and water were available ad libitum. To characterise starch sources and to estimate the potential starch dumping in the hindgut, starch gelatinisation and pre-caecal starch digestibility estimated by starch mobile bag disappearance between the oesophagus and the caecum had been measured on these four barley forms in this experiment (Philippeau et al. , 2014) (Table  1 ). Total tract apparent digestibility measurements Each data collection period began with the measurement of in vivo total tract apparent digestibility using a 3-day total collection of faeces  (Goachet et al. , 2009). Faeces samples were collected using a collection harness to which horses had been previously adapted to wearing. They were emptied three times a day. For each horse, the amount of feed All barley forms came from the same batch of cereal.
Colonic abiotic and biotic parameters determination On day 9 of data collection, 4 h after the morning meal, colonic contents were collected using gravity via the cannula, and the pH was immediately measured using an electronic pH-meter (MP 120; Mettler, Toledo, Spain). Subsequently, aliquots of colonic contents were filtered through a 100-µm sieve nylon filter (Bluetex; SAATI, Sailly-Saillisel, France) and frozen (-20°C) for further biochemical measurements. Total volatile fatty acid (VFA) concentrations were determined by GLC (Clarus 500 PPC; PerkinElmer, Courtaboeuf, France), following the procedure described by  Jouany (1982). For microbial analyses, one aliquot of colonic contents was held in CO 2 -saturated flasks at 38°C before inoculation. Microbial analyses were carried out as described by  Julliand et al.
Statistical analysis The variance homogeneity of variables was assessed using the Shapiro-Wilk test in Minitab (Minitab Inc. , State College, PA, USA). All the variables were analysed using the MIXED procedure of SAS v9 (SAS Institute Inc. , Cary, NC, USA). Daily nutrient intakes, digestibility coefficients, pH values, organic acid concentrations and microbial counts were analysed in a model, including period and barley form as fixed effects and horse as the random effect. Least square means were calculated for each variable and separated using pair-wise t-tests when significant effect due to barley form was found (PDIFF option of SAS). Significance was declared at P ⩽ 0. 05 and a trend towards significance at P ⩽ 0. 10.
Acknowledgments M. K. and R. M. are supported by the  Centre National de la Recherche Scientifique (CNRS)  and the  Agence Nationale de la Recherche  ( ANR-12-BS08-0013-02 ). We would like to thank the reviewers for very thoughtful suggestions. Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http://creativecommons. org/licenses/by/4. 0/),which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Searching An extensive database search (PubMed, GoogleScholar, Cabdirect) was undertaken using broad search terms in English and French (Brucel* AND Morocco or Brucel* AND Maroc) for 1910 to 30 June 2015. The library database of the Institut Agronomique et Veterinaire Hassan II (IAVHII)  [109]  was searched in February 2015 using the same search terms to identify veterinary and PhD theses on brucellosis in Morocco. Searches through the references of retrieved articles/ theses were also conducted. Additional data sources were identified through a nonsystematic, targeted search of in-country authoritative texts, conference proceedings, personal contacts with experts and unpublished primary research. Data from local seminars, workshops and country reports on brucellosis with limited distribution from 1980 to 2015 were available through Moroccan co-authors.
Category 1 studies were further subdivided into serological studies, bacteriological studies and official or clinical case reports. General inclusion criteria applicable to both categories included publication date between 1910 and June 2015 and data derived from Moroccan animal or human populations. For serological studies (Category 1), only articles providing some information on the serological test(s) used were included. Secondary sources cited in veterinary theses and local journals for which the original reference was not obtainable were included only when the sampling, population and diagnostic tests were described in sufficient detail.
Acknowledgements This research has received funding from the  European Union 's  Seventh Framework Program  ( FP7/2007-2013)  under grant agreement n°221948, ICONZ (Integrated control of Neglected Zoonoses). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the  European Commission. Special thanks to  Ian Maudlin  for his thorough edit of the review.
Data analysis Raw data was carefully recorded and stored in Microsoft Excel database system used for data management. Statistical software package called SPSS for windows version 17. 0 was used for data analysis. Descriptive statistics, percentages and 95 % confidence intervals were used to summarize the proportion of infested and non-infested animals. The effects of different environmental and host risk factors were analyzed by regression and χ2 test. Statistical significance was set at p ≤ 0. 05.
Thin sections were prepared from 0. 3 cm thick wafers of bone removed transversely from either side of the minimum diaphyseal circumference of Maiasaura tibiae. Thin section slides were processed using a Buehler Ecomet 4 variable speed grinder, using the following sequence of grit papers: 60, 180, 320, 600, and 800. Completed slides were analysed using a Nikon Optiphot-Pol polarizing microscope at either 10 X or 40 X total magnification, and photomicrographs were taken incrementally using a Nikon DS-Fi1 digital sight camera. The software package NIS-Elements BR 3. 0 was used to create a single image from multiple photographs, so that composite images of the tibia thin sections have a mosaic appearance. Minimum age of Maiasaura individuals was determined by counting the number of annually deposited lines of arrested growth (see  [10] [11] [12]  for descriptions of skeletochronology methods).
Statistical analysis Correlations between UPC, storage duration, SDS-AGE and quantitative urinary marker results were assessed with Spearman's correlation coefficients and their corresponding significance. Potential differences between UPC subgroups for urinary marker results were assessed by a Kruskal-Wallis test. All calculations were performed using computer software (Systat 13, SPSS Inc. , Chicago, IL, USA). For all analyses, p-value <0. 05 was considered significant. Urinary markers RI were determined according to international human and veterinary guidelines  [34, 35]. Possible outliers were detected by visual inspection of histograms and Tukey's criterion and excluded from the calculation of reference limits. Normality of distribution of the native or transformed values was tested with the Anderson-Darling test.
Data analysis The first two parameters were snail survival on day 30 p. e. and the prevalence of F. hepatica infection calculated using the ratio: number of cercariae-shedding (CS) snails/number of surviving snails on day 30 p. e. A v 2 test was used to compare the differences between snail survival and prevalence rates. The shell height of CS snails at their death, the lengths of the prepatent and patent periods, and the total number of metacercariae were also considered. Individual values recorded for the last four parameters were averaged and standard deviations were established for each snail group. Normality of these last values was analysed using Shapiro-Wilk test  [25]. According to results given by this test, one-way analysis of variance (ANOVA), Student's t test or Kruskal-Wallis test was used to establish levels of significance.
All the statistical analyses were performed using Statview 5. 0 software (SAS Institute Inc. , Cary, NC, USA). As the aim of the present study was to determine the better lymnaeid species for metacercarial production of F. hepatica, the statistical tests were only used to compare the differences between values noted for both lymnaeid species or for miracidial doses used at exposure (two or five miracidia/snail). The differences between values recorded for the two snail populations of each lymnaeid were not considered here. As the cost price of F. hepatica metacercariae was dependent on the method used for breeding the snail host  [17] , it was interesting to determine whether the method using pre-adult P. columella resulted in a decrease in this price. The maintenance cost for 100 snails took into account (i) the time spent by a technician for snail exposure to miracidia, the surveillance of breeding recipients, the count of metacercariae and their transfer to Eppendorf tubes, and (ii) the purchase price of consumables and lettuce.
Mosquito survival Kaplan-Meier survival estimates were calculated to investigate whether females' longevities were affected by a blood meal taken on cattle at different DAI of a therapeutic dose of ivermectin. Uncensored data were used, as all mosquitoes were dead by the end of the experiment. The effects of the ivermectin treatment, the time after injection and their interaction were further tested using Cox proportional hazards model. Because the blood from different cattle may represent different nutritive values, the effect of cattle on female survival was evaluated for each DAI and within each treatment status (i. e. , ivermectin-treated or control). This cattle effect on mosquito survival was also assessed for the four cattle before the ivermectin was injected (0 DAI) in order to ensure that any difference in mosquito survival was due, at least in part, to the ivermectin treatment.
At 2 DAI, 100 % of the mosquitoes would die in 2. 87 ± 0. 35 days, in 4 ± 0. 53, 5. 5 ± 3. 07, 17 ± 4. 24 and in 19. 5 ± 11. 61 days at seven, 15, 21 and 28 DAI, respectively. By comparison, 100 % mortality for the control treatment was achieved in 32. 12 ± 5. 74, 24. 37 ± 3. 99, 24 ± 4. 45, 27. 87 ± 5. 59 and 27. 12 ± 5. 40 at two, seven, 15, 21 and 28 DAI, respectively. For the 15 DAI time point, values from supplemental data were taken (see Additional files 1 and 2). The effect of an additional blood meal taken on treated cattle was further investigated for its impact on the survival of vector mosquitoes (Additional files 1, 2 and 3). The significant treatment × DAI × number of blood meals is due to the fact that the impact of a second blood meal varies with the time elapsed since ivermectin injection: while it had no effect at one, seven and 15 DAI, it further decreased mosquito survival at 21 DAI and was beneficial (i.
Acknowledgements We thank  MERIAL  for providing free of charge veterinarian ivermectin doses (IVOMEC D). We are grateful to the staff of LAMIVECT,  PATTEC-Burkina, IRD ,  IRSS, CIRDES  for the financial and technical supports. We are grateful to the dedicated technicians of these organizations for their precious contributions, and in particular, we thank  Boly Saïdou ,  Bazié Bali J, Hien Dombagniro R ,  Nikiema Boubakar ,  Tapsoba Salif ,  Tapsoba Janvier B ,  Toé Ange I, and Zoungrana Sebastien. We also thank two anonymous reviewers for their constructive comments, which improved our manuscript.
This does not distinguish accurately between M. abscessus subspecies but does offer the data for which the subspeciation is generally performed-whether or not there is inducible macrolide resistance. Should DST be performed on NTM isolates from individuals with CF? Recommendation 17: The CF Foundation and the ECFS recommend that for MAC, clarithromycin susceptibility testing should be performed on an isolate recovered prior to initiation of treatment. Clarithromycin susceptibility testing should also be performed on subsequent isolates if the patient (a) fails to culture convert after 6 months of NTM treatment; (b) recultures MAC after initial culture conversion while on NTM treatment or (c) recultures MAC after completion of NTM treatment. Recommendation 18: The CF Foundation and the ECFS recommend that for MABSC, susceptibility testing should include at least clarithromycin, cefoxitin and amikacin (and preferably also tigecycline, imipenem, minocycline, moxifloxacin and linezolid).
Treatment: adjuvant therapy and surgery In the context of infectious disease, adjuvants have been defined as 'therapies that act by rendering the organism more susceptible to attack by antibiotics or the host immune system, by rendering the organism less virulent or killing it by other means'. 172  number of approaches have been proposed as candidates for adjuvant therapy in NTM infection in CF, including interferon γ (IFNγ; or agents that promote IFNγ release) and vitamin D. Drug delivery vehicles, such as liposomes, may be considered adjuvants. Liposomes have been studied as a mode of delivering amikacin for infection with P. aeruginosa in CF,  173  and this approach is also being evaluated (clinicaltrials. gov/show/ NCT01315236) for NTM.
037). The greater response rate with IFNγ was sustained at 12 months after completion of treatment. However, the small study size, the use of composite end points and the lack of microbiological response after 6 months treatment mean that these data need to be interpreted with caution. Furthermore three large trials (ClinicalTrials. gov Identifiers NCT00001318, NCT00111397 and NCT00043355) examining IFNγ therapy for pulmonary NTM disease remain unpublished or have been terminated (potentially due to lack of efficacy), again questioning the role of IFNγ adjuvant therapy.
Data collection Location data were collected using the global positioning system (GPS) monitoring technique. Five wild asses (four males: individuals 594, 595, 596, and 597; one female: individual 598) were captured near the artificial water point between July 2012 and early August 2013. The individuals were shot from a shelter located above the water point, using a dart gun (J-M 25 Special by Dan-inject). They were immobilised by a mixture of Etorphine Hydrochloride (Cap-tivon™ 98 by Wildlife Pharmaceuticals) and Butorphanol (Butomidor 1 10mg/ml). The five animals were equipped with GPS collars (African Wildlife Tracking company) that were scheduled to attempt a location every hour. After the procedure of collaring, Naltrexone (Trexonil™ 20 50 mg/ml by Wildlife Pharmaceuticals) was injected IV to antagonise the Etorphine.
A permit to capture and collar the wild asses was given by the Israel Nature and Park Authority, so that all necessary permits were obtained for the described study, which complied with all relevant regulations. In addition to GPS location data, we collected data on the species activity rhythm. Visual observations were made in summer, using the scan sampling method  [62] : for any group encountered while driving around in the study area, we chose an individual at random (among the collared members, if any), and recorded its activity every five minutes. The individual was considered as resting when lying or standing motionless; otherwise, it was considered as active. A total of 274 hours of observation was performed.
Data analysis Two 50-day periods that provided almost complete sequences of the GPS locations for the five equipped animals were used for the present study: 12 Aug. -30 Sep. 2013 for summer, and 12 Dec. 2013-30 Jan. 2014 for winter. Fifty-day home ranges. The monitored individuals' 95% and 50% fifty-day home ranges (here and after defined as home range-HR) were estimated for each season, using the Movement-based Kernel Density Estimator (MKDE;  [63, 64] ). In contrast to the classical kernel estimators, MKDE takes into account the correlation between successive locations. Estimation was performed with the following parameter values: T max = 2. 5 hour, τ = 0. 1 hour, L min = 50 m, h min = 100 m, b = 0 (see  [64, 65]  for details). Displacement. We computed the distances between successive locations for each monitored animal within a given season.
As the hydrological network was encoded in the form of lines in ArcGIS (http://mapi. gov. il/en/Pages/default. aspx), thalweg areas were identified, applying a 25-m buffer to this network; the corresponding variable took value 1 inside the buffer and 0 outside. NDVI scores were derived from Landsat 8 data (30 x 30 m resolution) taken on 6 Sep. 2013 for summer and on 12 Jan. 2014 for winter. The NDVI does not provide any information on vegetation type, but the wild ass is considered as very flexible with respect to plant community  [26, 28, 66]. Elevation above sea level and slope (in degrees) were derived from a 25 x 25 m resolution digital elevation model (DEM) of the Negev Desert. Aspect (i. e. , slope azimuth, measured clockwise in degrees from the northern baseline) was extracted from the same model and converted into the variable 'northern exposure': E N ¼ sinycosa; where θ is the slope, and α, the slope azimuth.
The smallest AIC value was obtained with model M5-k for summer and model M4-k for winter, in both cases for k = 3, implying that the envisaged models that best fit the data exhibited maximums every 24 h minus 3 h. well as the time of the day at which the locations were recorded. We might a priori have chosen any threshold between 10% and 50% to define the main recursion sites. With our dataset, however, mapping 20% of the locations appeared as the best compromise: using a higher percentage resulted in the inclusion of sites with very low recursion levels in winter, whereas using a lower percentage generated sites composed of too few locations to be characterized.
Models Software and descriptive statistics. Ecological characteristics of the GPS locations and home ranges were obtained using ArcGIS10 (ESRI, Environmental Systems Research Institute, Inc. , Redlands, California, USA). Statistical calculations were performed using the R software (R Core Team 2014) and, more specifically, the 'adehabitatHR' package  [65]  for the MKDE method, the 'nlme' package  [69]  for the linear mixed-effect models, and the 'survival' package  [70]  for the Kaplan-Meier method. In the Results section, unless otherwise specified, means are given ± SE. In the case of repeated measures per individual, this refers to the mean ± SE of the individual means.
Acknowledgments We would like to thank  Yishay Hofman ,  Gili Greenbaum ,  Tamar Ben Nun ,  Haim Berger ,  Alexander Auer ,  Sharon Renan ,  Tomer Gueta ,  Alan R. Templeton ,  Jean Joachim ,  Ben Yana  and  Boris Josasha  for their valuable contributions to this study. We acknowledge  Roni King ,  Nimrod Ben-Aharon  and the rangers of  INPA  for collaring the animals. We are grateful to  Ron.
Chromosome preparations and banding procedures For chromosome preparations, testes were removed from freshly killed adults, and fixed in an ethanol-glacial acetic acid mixture (3:1,v:v). Subsequently, we performed C-banding to establish the diploid chromosome number (2n) and the C-heterochromatin distribution  [21]. We also applied FISH analyses to determine the location of 45S ribosomal clusters  [17]. For each specimen, at least 20 cells were analyzed. Chromosome preparations were examined under a Nikon Eclipse 80i microscope and the images were obtained with a DS-5Mc-U2 digital camera using Nikon Nis Element s3. 1 Advanced Research software and processed with Adobe Photoshop® software.
Molecular datasets, sequence alignments and phylogenetic analyses Fourteen T. sordida, T. garciabesi and T. guasayana partial COI gene sequences deposited in GenBank were employed for phylogenetic analyses, plus two T. rubrovaria sequences used as outgroup. Other sequences of this subcomplex available in GenBank were excluded from this study since their geographical origin was unknown. All sequence accession numbers are specified in Fig. 3. Maximum likelihood (ML) phylogenetic analyses were implemented in MEGA 6  [22]  with statistical support for the nodes evaluated with 1000 bootstrap replicates. The best fitted substitution model was also determined using MEGA 6 software  [22]. The alignment included 522 bp including 113 variable sites (21. 6 %), 101 of which were informative for parsimony  (19.
Below, we discuss our results for each chromosomal taxon here identified, in comparison with previously published determinations. T. guasayana: The morphological differentiation of T. guasayana with T. sordida is very difficult, especially in   Genetic markers (isoenzymes, chromosomal and mitochondrial sequences) clearly differentiated T. guasayana from the other species of sordida subcomplex  [7, 9, 10, [23] [24] [25]. However, probably due to their morphological similarity, COI sequences deposited in GenBank reveal at least one mistaken identification: a specimen from Santa Cruz, Bolivia (Chaco, Tita) (KC249342) originally identified as T. guasayana, should be recognized as T. sordida (Fig. 3 ). At phylogenetic level, genetic distances between T. guasayana and the other sordida taxa are the most extreme, between 14 and 14.
3 ). This paper establishes the chromosomal identity between T. garciabesi and the T. sordida group 2 from Bolivia defined by isoenzymes  [9, 10]. Despite the genetic and phenotypic differentiation, taxonomic problems still persist in terms of distinguishing T. garciabesi from other species of the subcomplex. Individuals from established laboratory colonies (Salta, La Rioja, Santiago del Estero, Formosa and Chaco) which were originally identified as T. sordida, presented the chromosomal characteristics of T. garciabesi (Table  2 ). Hence, incorrect identification of this species is also seen in the sequences deposited in GenBank. The two individuals from the Bolivian Chaco (Romerillo) probably belong to T. garciabesi rather than T. sordida (Fig. 3 ). Recently, comparative analyses of T. sordida populations from Western (Chaco) and Eastern regions of Paraguay reveal striking differences in the feeding patterns, random amplified polymorphic DNA profiles (RAPD), and head and wing morphometrics  [14].
Acknowledgements This paper is part of Sebastian Pita Doctoral Thesis at  PEDECIBA and Udelar (Comision Sectorial de Investigación Cientifica) from Uruguay. We also thank the following researchers for supplying triatomine material:  Delmi Canale  ( CRV-Centro de Referencia de Vectores, Córdoba, Argentina ) and  María E. Bar  ( Cátedra de Artrópodos, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina ). We thank to  Chris John Schofield (LSHTM, UK)  for their technical review and suggestions.
Financial support This work has been supported by project grants from the  "Comisión Sectorial de Investigación Científica" (CSIC-Udelar-Uruguay) ,  Programa de Desarrollo de las Ciencias Básicas (PEDECIBA Uruguay)  and  Agencia Nacional de Investigación e Innovación (ANII, Uruguay). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
To ensure optimal separation of the fluorochromes, blue & red signals were acquired simultaneously in one track and green & far-red signals in a second track. The electronic zoom factor and stack depth were adjusted to the region of interest while keeping image scaling constant (x-y: 0. 066 micron, z: 0. 287 micron). A line average of 8 was used and datasets were stored as 8-bit proprietary Ã. czi files. The images were displayed using Zen2012 software (Zeiss) with linear manual contrast adjustment and exported as 8-bit uncompressed Ã. TIF images. The figures were prepared with the Canvas program.