dataesr/scientific-paragraphs-categorization huggingface dataset:
Migration Goals The main objective of the migration goals is to establish in a formal and shareable manner the main constraints exposed from the application (or its owner) for the migration. The requirements for the migration that cannot be extracted from the legacy software itself will be established by the migration goals and circulated over the other ARTIST tool to be accessible in all migration phases. These migration goals are worked out through a questionnaire and finally determined by the end-user and are circulated over other migration phases with the purpose of having information about the nonfunctional requirements required for the migration (quality metrics required, infrastructure information, etc. ). These user specified migration goals will be validated in combination with the functional requirements in the validation phase c.
First, we adapt the migration techniques of ARTIST in order to migrate not only the software itself but also potentially existing test cases. If no test cases are available or if their test coverage of is insufficient, we follow a second approach to assess the functional correctness. In particular, we provide techniques to generate test cases automatically from the PIM, corresponding to the overall spirit in ARTIST to apply techniques from model-driven engineering. Therefore, not only structural but also behavioural models are reverse-engineered from the legacy software and represented in the PIM. These behavioural models are then used in a model-based test generator tool developed in the course of ARTIST to derive test inputs until the execution of the software with these test inputs leads to a certain test coverage.
Certification Model One of the shortcomings for the final implantation of SaaS and cloud computing in the software industry is the reluctance of the users to this new service offering. The purpose of the certification phase in ARTIST is to obtain an independent and impartial judgment of SaaS providers, focusing on businesses, processes and technology aspects  (ARTIST D11. 4. 1, 2013)  in order to create consumer confidence in software applications offered as services considering reliability parameters (categories) that will be evaluated. The certification model proposed by ARTIST, Service based Software Provider (SbSp) focus on organisations that develop and offer software based services using methodologies and business models that are connected to the Future Internet and cloud computing schemes.
CONCLUSIONS In this paper we present a novel cloudification approach, supporting software vendors paving the path to a smoother transition to the cloud computing paradigm. The presented ARTIST methodology and framework considers both technical and business aspects of the legacy applications and covers not only the core migration phase but also the premigration phase, where based on the assessment of the initial and target situations added to the results of a technical and business feasibility analysis, the various steps and tasks of the methodology are customized, as well as the post-migration phase where the outcomes are validated and certified. ARTIST proposes a set of tools supporting each methodology phase based on model-driven engineering approaches, allowing when possible the reuse of artefacts.
Data set and selection This analysis uses the data set collected by LHCb corresponding to an integrated luminosity of 3 fb -1. The data in 2011 (1 fb -1 ) were taken at a centre-of-mass energy of 7 TeV and the data in 2012 (2 fb -1 ) were taken at a centre-of-mass energy of 8 TeV. The fraction of data collected with up (down) polarity of the magnetic field is 40% (60%) in 2011 and 52% (48%) in 2012. Charge-dependent detection asymmetries originating from any left-right asymmetry in the detector change sign when the field polarity is reversed. By design, the analysis method does not rely on any cancellation due to the regular field reversals, since all detection asymmetries are already removed in the determination of the CP asymmetries. This assumption is tested by performing the analysis separately for the two polarities.
CP asymmetry measurements The raw asymmetries are determined with likelihood fits to the binned D 0 and D + mass distributions using the mass models and event weights as described in Sects. 5. 1 and 5. 2. The fits are done separately for the 2011 and 2012 data sets and for the two magnet polarities. For each data set the mean value of the raw asymmetry is the arithmetic average of the fit results for the two magnet polarities. The final raw asymmetry is then the statistically weighted average over the full data set. The derivation of the K -π + detection asymmetry using prompt D + → K -π + π + and D + → K 0 π + decays is shown in Table  3. The measured asymmetry, A D (K -π + ) = (-1. 17 ± 0. 12)%, is dominated by the different interaction cross sections of K -and K + mesons in matter. Figure  3  shows Table  3 : Asymmetries (in %) entering the calculation of the K -π + detection asymmetry for the two magnet polarities, and for the mean value.
Incomplete adherence to treatment was evaluated by the recall of missed treatment in the preceding 4 days and the preceding 30 days, with both measures dichotomized as 100% vs. <100% adherent. Data relating to the child's HIV status, disease history and treatment was retrieved from hospital records after the interview. The child's health status was confirmed by the physician on duty. The evolution of the child's health since the onset of treatment was reported by the parents/ guardians (improved, deteriorated, stable).
Data management and analysis Data were entered in Epidata freeware (www. epidata. dk, Odense, Denmark) and cross-checked against original data sheets. We used open-ended questions to determine occupations, reasons for missed appointments, difficulties in treatment, etc. All responses were recorded and eventually categorized by common themes. A new variable was created for each common theme using a 0-1 classification and tested in univariate analysis. Analyses were carried out with Stata software, Version 8 (Stata Corporation, College Station, TX, USA). Chi 2 or Fisher's exact test were used to assess associations between categorical variables as appropriate, and Student's t-test for two normally distributed continuous variables. P ≤ 0. 05 was considered significant. Associations between perceived stigma and children's characteristics were initially measured using bivariate analyses (age over 7 and 10 years, sex, socio-economic conditions, death of one or both parents, schooling, time since diagnosis and ART, tolerance to ART, and adherence to treatment).
Ethics statement The study was authorized by the National Pediatric hospital authorities. Ethical approval was granted by the Lao Medical Ethics Committee. The study complied with the Cambodian law on personal protection of PLWHA. Children and parents/guardians were informed about the study in Khmer language and given an information sheet describing the study. Children were included if they consented to participate and if their parents/guardians had given written informed consent. Confidentiality was guaranteed and interviews were conducted in a private room. Data was recorded anonymously.
Statistical Analysis. Means and standard deviations or medians and interquartile ranges were calculated for continuous data (for normally and not normally distributed variables, resp. ) and percentages for categorical data. Differences in frequency distribution of categorical variables were evaluated by Chi-square test. One-way analysis of variance and Kruskal-Wallis tests were used for comparison of normal and not normal variables, respectively, among subgroups. Normality of variable distributions was evaluated by Kolmogorov-Smirnov test. All computations were performed by StatView statistical software package (SAS Institute, Cary, NC, USA). A  value <0. 05 was considered statistically significant.
For the tensile tests carried out on the V-shaped sample, it is necessary to calculate the local strain field to know the load path on the interest area. These calculations are performed using Cast3m finite element code  [5]. The finite element model is based on an elastic plastic isotropic constitutive law which has been identified thanks to standard tensile test (10 -4 s -1 ). For each V-shaped sample, dimensions of the simulated V-shaped geometry are adjusted on real specimen dimensions measured after the polishing step. Calculations take into account the symmetry of the specimen and are carried out in 2D using plane strain hypothesis. Two boundary conditions are defined. The X displacement of symmetry axis in the V apex equals zero. A load is imposed on the head of V sample. Thanks to that, the strain in the apex of the V can be calculated as well as the displacement of the extremity of the sample.
Actually, a gradient of strain is imposed on the area of interest. This calculated plastic strain gradient, shown on Fig. 3 , is between 8% and 2%. Calculations at 650 • C are performed with the same method. After mechanical tests, SEM observations are performed to visualized damage. These observations are focus on the intrados of the V, which is the preferential area of damage for V-shaped specimen. Each crack initiation, or crack propagation out of a precipitate is localized and measured. We record if these crack initiations are or are not linked to a carbide/carbonitride (cf. Fig. 4 ). Thanks to this method, for each test, two data are obtained: the number of cracks and the fraction of cracks linked to a precipitate.
9 mM sodium pyrophosphate pH 8. 8 reaction buffer containing 10 mM NAD + and 1. 13 M ethanol. The absorption time course of NADH at 340 nm was recorded for 1 min with a computer using Spectra Manager software (JASCO Corporation, Hachioji, Japan) that gave directly the activity (U/mL) of ADH. The extinction coefficient of NADH used was 6. 31 × 10 3 L mol -1 cm -1. The retention of ADH activity was calculated by dividing the activity of ADH in spray-dried powder by the activity of ADH in the feed solution. Spray drying was carried out once or twice for each operational condition (inlet temperature and MD addition). For every sample of spray-dried powder, two samples were collected and the ADH activity was measured in triplicate or quadruplicate for every sample.
01% DMSO. Divalent cations, verapamil and mibefradil were freshly diluted in external solution just prior all experiments. The internal solution contained (in mM): 150 Cs + , 120 methanesulfate, 10 NaCl, 10 EGTA, 4 CaCl 2 , 0. 3 Na 2 -GTP, 2 Mg-ATP, and 10 HEPES pH 7. 4 with CsOH (,300 mOsm/L). HEK-293T cells were recorded by the whole-cell patch clamp method using an AxoPatch 200B or MultiClamp 700B amplifier from Molecular Devices, combined with their Digidata 1440A Data Acquisition System and pCLAMP 10 Software. Recordings were carried out at room temperature, with patch pipettes bearing resistances between 2 to 5 MV. HEK-293T cells were perfused in a constant stream of solutions with a ValveLink8 pinch valve perfusion system (Automate Scientific). Perfusion solutions contained NMDG + or low 0.
Materials characterization SEM images were obtained by using a field emission gun scanning electron microscope (FEG-SEM Zeiss Sigma HD microscope) equipped with an in-lens detector working at 1 kV and at a short working distance (WD) equal to 3. 3 mm for the TiO 2 thin film images and equipped with a secondary electron detector (SE) working at 1 kV and at a short working distance (WD) equal to 3. 8 mm for the TiO 2 /PBA nanocomposite images. Tapping mode topography and phase imaging was [Fe(CN accomplished by using an Innova AFM (Bruker) with NanoDrive v8. 02 software. Tapping mode images were acquired by using silicon tips from Nanosensors (PPP NCSTR) with a resonance frequency ranging between 76 and 263 kHz. Images were processed by using WsXM software. Fourier transform-infrared (FTIR) spectra were collected in the attenuated total reflection (ATR) mode by using a Vertex 70 spectrometer with a germanium crystal.
Quantitative analysis of transcript abundance Real time RT-qPCR was performed using a MX3000P detection system (Stratagene), as previously described  [52] , and the SensiMix Plus SYBR commercial kit (Quantace) was utilized, according to the manufacturer's instructions. A fragment of the grapevine VvGPDH gene (VvGLYCERALDEHYDE-3-PHOSPHATE DEHYDRO-GENASE, GI: 359491598)  [53]  and a fragment of the grapevine VvUBI1 gene (VvUbiquitin1, TC53702, TIGR database)  [54]  were utilized as housekeepings genes. In order to estimate relative transcript abundance values, a ratio between the expression of the gene of interest (GOI) and the geometric mean of the expression of the housekeeping genes, VvGPDH and VvUBI1, was generated according to the equation 4: Table  3. RT-qPCR primers.
Funding provided by  ECOS-CONICYT , project number  C11B01 , http://www. conicyt. cl/pci/category/lineas-del-programa/movilidad-lineas-delprograma/?anio = 2011,  Millennium Nucleus Center for Plant Functional Genomics   P10-062 ,  FONDECYT 1100709 , http://w1. conicyt. cl/bases/fondecyt/proyectos/01/2010/1100709. html, CONICYT Fellowships, http://www. conicyt. cl/becas-conicyt/sobre-becas-conicyt/que-es-becas-conicyt/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data analysis We compared men to women for first values obtained in each calendar year. Demographic, clinical and immuno-virological characteristics including age, region of origin, HIV transmission group, AIDS stage, CD4 count, HIV-1 RNA level, use and type of cART, hepatitis B and C status, presence of dyslipidemia (hypercholesterolemia, hyper triglyceridemia), diabetes mellitus, high blood pressure and tobacco use were described. We compared patients' characteristics between men and women at hospitalization, by statistical tests for independent samples using nonparametric methods when appropriate. Descriptive analyses of detailed severe morbidities in each category, according to sex were performed. Yearly rates of patients hospitalized and hospitalizations were calculated by dividing the number of patients hospitalized and hospitalizations by the total number of patients actively followed in each year.
GEE models have been extensively used in data in which the responses are correlated  [19, 20]. Variables included in the model were calendar year, sex, transmission group, age, HIV RNA, CD4 cell count, cART use, AIDS stage, dyslipidemia, diabetes, high blood pressure, hepatitis B and C, and tobacco use. Sensitivity analyses taking into account interactions between sex and different determinants of severe morbidity were also performed. All analyses were performed with SAS software, version 9,2 (SAS Institute, Cary, North Carolina, USA).
Recent studies have noted a higher relative risk of myocardial infarction (MI) among HIV-infected women in comparison with men and higher standardized mortality ratio (SMR) in comparison with the general population  [29] [30] [31]. In the French hospital Database on HIV (FHDH), MI SMRs of 1. 4 and 2. 7 have been reported respectivley for men and women in comparison with the general population  [29]. In our study, cardiovascular events are in 2007 and 2008 more frequent in women whereas the frequency of risk factors are higher in men. This is probably due to an unequal treatment of these risk factors between men and women. In the Aquitaine Cohort, the cardiovascular risk factors are equally measured for men and women. Traditionally, men are more often addressed to cardiovascular specialists for screening of CV disease, because the male sex has always been counted like one CV risk factor achieving 50 years of age.
Finally, the calendar period of our study was limited to 2008. This paper follows a previous work on the Aquitaine Cohort covering the period 2000-2004  [21]. Validation of severe morbid events is very time-consuming with return to files needed on a vast territory of health care centers in the Aquitaine region (South-Western France). So it was not possible to include completely validated data on the most recent period. We believe however that the main messages would remain true until the most recent years. In the Aquitaine Cohort, sizeable efforts are allocated for the collection, documentation and uniform classification and coding of morbid events. There is a lack of published studies on the longterm causes of severe morbidity leading to hospitalization in HIVinfected patients, although such information is highly valuable in identifying priorities for case management and improvement of the quality of life of patients with a chronic disease requiring lifelong treatment.
Compression tests were then performed at a strain rate of 0. 001 s -1 until failure. During testing, force was measured using a 1 kN load cell, and specimen deformation was imaged using a digital camera (Canon EOS, Canon Inc. , Japan). After testing, successive images were processed to derive compressive axial strain using custom-written digital image correlation post-processing software  [13]. Using the apparent stress vs. strain data thus derived, the apparent level Young's modulus was identified by least-squares fitting of the middle third of the linear region of the apparent stress vs. strain curve. The ultimate stress was identified as the maximal nominal stress obtained during each test. Note that when reporting mechanical test results, we use the terms 'apparent' elastic modulus and 'apparent' ultimate strength, to refer to the fact that the scale being tested is above that of the tissue level (as would be interrogated by nanoindentation), therefore the apparent properties are a function of both tissue material properties and microstructure.
A full wave retarder plate was used to enhance interference color generation on the unstained specimens. All images were saved in TIFF format, and, with the exception of background thresholding to change the first order red background induced by the waveplate to a black background, no post-processing or color modification was performed on any of the images. Following image acquisition, the ImageJ software (version 1. 48, National Institutes of Health, USA) was used in order to measure areal intra-cortical porosity on the polarized light microscopic images. Total specimen surface area was measured first using the ImageJ area measuring tool, then the outline of each pore in the bone was manually traced and its area measured. Note that using either 4× or 10× microscope objectives limits the optical resolution of the microscope to approximately 3 μm, therefore the porosity measure did not include pores smaller than several tens of microns in diameter, as these cannot be adequately segmented at the magnifications used.
Functional annotation was performed using (i) sequence similarity searches against public databases as well as the main available predicted insect proteomes and (ii) automated open reading frame (ORF) prediction, followed by search for signal peptide and InterPro domains on the translated sequences (Additional file 1: Figure  S1 ). As already evidenced in previous venom analyses  [18, 22, 25] , more than 60% of unisequences had no significant similarity in databases and could not be assigned an InterPro annotation (Additional file 2: Table  S1  and Additional file 4: Table  S2 ). The proteomic analysis was performed on the A. ervi FR strain, on venom gland and reservoir samples separately. On a 6-16% SDS-PAGE, the protein content of each compartment was resolved in bands from less than 15 kDa to more than 250 kDa (apparent molecular mass, Figure  1 ).
This raises the questions whether it is a fully active γ-GT and which role it may play in A. ervi parasitism success. A # indicates that a SP was predicted for some but not all unisequences. Using Hymenopteran databases, we were able to identify three distinct types of non-venomous γ-GTs forming three distinct phylogenetic clades (Figure  4 ). Interestingly, the three A. ervi venomous γ-GTs group with clade A, while the two γ-GTs recently identified in N. vitripennis venom, which function is yet unknown  [22] , group with clade B (Figure  4 ). The venomous γ-GTs of these parasitoid species may thus originate from distinct duplication events of two different genes coding for γ-GT "classical" proteins. Interestingly, γ-GTs can be used by bacteria as virulence determinants. For instance, a γ-GT contributes to Helicobacter pylori tolerizing effects on murine dendritic cells and suppressive activity on T cells, mainly via the depletion of glutamine  [30].
The combined analysis of two datasets corresponding to different A. ervi strains (French and Italian) confirmed that the major venom proteins are shared by different parasitoid populations. However, it also identified striking differences in the abundance of transcripts for some of the main unisequences such as the γ-GTs, suggesting variations in allele frequency and/ or gene expression level among populations that remain to be explored. Our study confirmed the identification of Ae-γ-GT as the most abundant protein by far in A. ervi venom, thus supporting its role as a key player in parasitism success  [13]. In addition to an allelic form of Ae-γ-GT, we identified a divergent, possibly non-functional, γ-GT, whose biological function, if any, remains to be explored. Interestingly, we recently identified a multigenic family for a venom protein of a parasitoid of Drosophila, with all members except one mutated in one or more essential amino acids  [18].
Sequencing, EST processing and assembly A general overview of the sequence data processing is given in Additional file 1: Figure  S1. Sanger sequencing was done on an ABI sequencer using the standard M13 forward primer and BigDye terminator cycle sequencing kit (Applied Biosystems, Foster City, CA, USA). Following a primary step of analysis of 384 clones to check the quality of each library and confirm the presence of venom protein-related sequences, a total of 6,000 clones were sequenced, 5,000 for A. ervi FR and 1,000 for A. ervi IT. FR ESTs were processed using SURF analysis pipeline tools (SURF: SeqUence Repository and Feature detection) as previously described  [18]. IT ESTs were trimmed using TIGR SeqClean software. High quality trimmed ESTs longer than 100 bp from FT and IT libraries were then pooled and assembled into contigs using the TIGR-TGICL tool with different parameters.
Sequence annotation and analysis To identify similarities with known proteins, the sequences of contigs and singletons were compared using the blastx algorithm against local non-redundant NR (NCBI, 2012-10-25), UniProtKB/Swiss-Prot (SIB, 2012-10-21), and insect predicted protein/proteome databases (Acromyrmex echinatior v3. 8, Acyrthosiphon pisum v2. 1, Aedes aegypti v1. 3, Anopheles gambiae v3. 6, Apis mellifera v4. 5, Bombyx mori, Drosophila melanogaster v5. 46, Drosophila pseudoobscura v2. 28, Nasonia vitripennis v1. 2 and Tribolium castaneum v20051011) with a cut-off E-value of 1e-7. ORF prediction and translation were performed using FrameDP software  [56]  (available at http://iant. toulouse. inra. fr/FrameDP/). Signal peptide prediction was obtained using TargetP (available at http://www.
cbs. dtu. dk/ services/). Search for protein domains was performed using InterProScan. Gene functions and GO terms were automatically assigned to the predicted proteins based on the identification of InterPro domains with InterProScan. Only the root domain of the hierarchical domain organization available from EBI was conserved. Comparison of GO terms between FR and IT contigs and homogenization of the annotation level were performed using the GO slim. Multiple amino acid sequence alignments were performed using MUSCLE  [57]. For phylogeny, search for Hymenopteran γ-GT sequences was performed using BLASTP at NCBI (http://www. ncbi. nlm. nih. gov/blast/). Identification of N. vitripennis NV24088-PA sequence was performed using HMMsearch from the HMMER package  [58]  with the G_glu_transpept (PF01019) HMM profile on N.