dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analysis In-hospital maternal mortality was the outcome of interest. Accordingly, all deaths that occurred during the hospital stay (before hospital discharge) among women who had delivered in the selected centers during the study period were counted as the outcomes. In this study, because of the very low prevalence of the outcome (maternal in-hospital death) in the large data base of the study resulting in highly unbalanced distribution of the dependent variable, standard prediction methods based on logistic regression or classification trees are not appropriate  [20, 21]. The method extracts specific multivariate 'risk patterns', which identify subgroups of patients for whom the prevalence of the outcome (here: risk of maternal death) is higher than in the entire study population.
We describe the method elsewhere  [22]. Briefly, the first step on the analysis is a training step which use the Apriori algorithm developed by Agrawal and Coll  [23] , one of the most widely used algorithms in the data mining literature, to discover frequent 'risk patterns'. Since the Apriori algorithm results in a very large number of 'risk patterns', the second step is a pruning step that aims to produce a smaller set of non redundant 'risk patterns'. In the third step, we validate and combine the 'non redundant risk patterns' in a classification rule. In the last step, we assess the performance of the classification rule by computing its sensibility and specificity (with 95% confidence interval). This process requires to split the database randomly into three subsets, each comprising 33% of all the patients.
The first and second steps are run using the 'training' dataset. The first step results in 929 frequent rules and the second step results in 575 no redundant rules. The third step is run using the 'validation' dataset. After this validation step the number of remaining rules is 20. The fourth step is run using the 'test' dataset. Descriptive analyses were carried out with Epi-Info software (version 3. 5. 3). All analyses related to the proposed classification method were performed using the packages ''arules'' in the version 2. 15. 1 (2012-06-22) of the programming environment R  [24].
Results Among the 89,847 enrolled patients, 329 were excluded (175 women who died before delivery and 154 women transferred to another health facility), leaving 89,518 women for the analyses, 29,840 for the 'training' dataset, 29,839 for the 'validation' data set and 29,839 for the 'test' dataset. Table  1  presents in-hospital maternal mortality rates, according to the type of institution and the country, and some indicators of the risk of the pregnant population served by each type of institution. The proportions of high risk women were higher in hospitals outside the capital that in hospitals located in Dakar or Bamako. In each category of health care facility, the mean length of hospital stay was higher for women with a cesarean section than for women who deliver by vaginal way. Hospital-based mortality rates in district hospitals, regional hospitals and in hospitals in the capitals (Dakar or Bamako) varied between centers, ranging from 0.
These results are in accordance with other studies in Latin America, Asia and Africa  [7, 8, 9, 10, 17, 18, 19]. This study is one of the largest one on hospital-based maternal mortality in Sub-Saharan Africa. The participant hospitals were representative of the existing health system in both countries, taking into account the full variety of contexts and levels of care. The large database and the system of data control we implemented in all participating hospitals allowed us to obtain reliable information on maternal outcomes  [16]. Our findings may be generalized to other countries with similar health care systems and other referral hospitals with similar population. Potential limitations of this study should be taken into account in interpreting our results. First, data are restricted to in-hospital critical events; therefore maternal mortality and late complications  as puerperal infection that occurred after hospital discharge may be underestimated.
Molecular techniques. All DNA manipulations were carried out by using standard procedures. Sequencing was done by cycle sequencing performed with a BigDye kit (Applied Biosystems) in a 3130 Genetic Analyzer (Applied Biosystems). Sequence data of B. suis were obtained from The Institute for Genomic Research (TIGR) website (http://www. tigr. org). PCR primers containing added restriction enzyme sites were designed to amplify the flanking regions of btaE. Primers F1 (5=-CGGGA TCCATCGAGTGAGGCAAGAGTC-3=) and R1 (5=-GGCTGCAGCATG AGATATAATCTCTTAT-3=) amplified a region of 463 bp upstream of btaE, and primers F2 (5=-CGCTGCAGTGGAGCATAATCCGACCGCA GC-3=) and R2 (5=-GCGCATGCGTCACACACCAATGTCCAGT-3=) amplified a region of 332 bp downstream of the gene. New restriction sites are underlined. The generated PCR fragments were purified, cleaved with the corresponding enzymes, ligated together, and cloned into the pK18mobsacB mobilizable suicide vector (Km resistant)  (21) , obtaining pKmobsac⌬btaE plasmid.
vet. unicen. edu. ar). BALB/c mice (10 per group) were inoculated by intragastric delivery of wild-type B. suis 1330 (1. 3 ϫ 10 8 CFU/mouse), its isogenic ⌬btaE mutant (1. 3 ϫ 10 8 CFU/mouse), or the complemented mutant (1. 48 ϫ 10 8 CFU/ mouse) suspended in 300 l of 10% sodium bicarbonate by use of a plastic feeding tube introduced through the mouth. Five mice from each group were sacrificed at 7 and 30 days postinfection (p. i. ), and spleens were removed. Dilutions of spleen homogenates were plated in duplicate on TSA. After 4 days of incubation, CFU were counted and expressed as the log 10 value per spleen. The CFU data were normalized by log transformation and evaluated by analysis of variance (ANOVA) followed by Dunnett's post hoc test (Prism 5. 0; GraphPad Software, Inc. ). The experiment was repeated twice with similar results.
RESULTS BtaE: a putative adhesin from the trimeric autotransporter family. Database searches within the NCBI genomic BLAST search engine showed the presence in the B. suis 1330 genome of 11 predicted ORFs that exhibit one or more conserved domains associated with adhesion, including BmaC  (15). One of these candidates (BR0072) is annotated in the B. suis 1330 genome (32) as an "outer membrane protein" and has a predicted molecular mass of 75. 45 kDa (740 amino acids). In silico analysis indicated that BR0072 displays an N-terminal signal peptide  (26) , a YadA-like C-terminal region  (23) , and a sequence of 642 amino acids between the two regions. The YadA-like and N-terminal regions (together with a central region or "passenger domain") are the characteristic precursor domains of type II trimeric autotransporter (TA) proteins  (17, 33, 34) ; therefore, we named BR0072 BtaE (for Brucella trimeric autotransporter).
Three regions corresponding to the head (amino acids 154 to 222, 254 to 335, and 434 to 529) and four corresponding to the neck (amino acids 223 to 244, 336 to 357, 530 to 551, and 600 to 618) were identified. Interestingly, in silico analysis using the Pfam protein database  (23)  showed that two of the three regions predicted to be part of the head contain three Hep_Hag repeats, and the neck portions overlap four noncontiguous HIM repeat motifs (Fig. 1 ), which represent potential adhesion motifs. In addition, an anchor domain and connectors were also identified. As expected, the anchor domain matches the YadA-like C-terminal region (Fig. 1 ). In vitro binding activities: BtaE is involved in adhesion to hyaluronic acid. It has been shown that Brucella spp. bind to components of the ECM, such as fibronectin and collagen.
To further investigate the in vivo adhesive phenotype of the btaE mutant, the A549 epithelial cell line from human lung was used as an alternative cellular model in the binding assay  (39). B. suis ⌬btaE showed a significant reduction in the ability to adhere to (by 50% Ϯ 8%) and invade (by 51% Ϯ 13%) A549 cells compared with the wild type (considered 100%) (Fig. 4A  and B ). As predicted, the pBBRbtaE plasmid restored adhesion and invasion capacity to wild-type levels in the B. suis ⌬btaE mutant. Similar to the phenotypes in HeLa cells, our data indicate that the decrease in the invasion capacity of B. suis ⌬btaE was a consequence of a lower adhesion to A549 cells (Fig. 4C ). To test the possibility that BtaE could participate in later steps of host cell infection, such as intracellular survival, a classical intracellular proliferation assay was carried out, using murine J774 macrophages and HeLa cells.
We also evaluated the BtaE localization in the E. coli heterologous host, carrying the pBBRbtaE plasmid. Western blot analysis indicated the presence of the 75-kDa protein corresponding to BtaE in the total membrane fraction of E. coli pBBRbtaE, which was absent in the control strain (Fig. 6C ). Interestingly, immunofluorescence analysis of GFP-tagged E. coli carrying pBBRbtaE showed BtaE foci at one bacterial pole in 5% of bacteria examined (Fig. 6D ), while no signal was observed in the control strain (data not shown). This observation suggests that the mechanism involved in polar targeting of the BtaE trimeric autotransporter is conserved in E. coli. Brucella's new pole is functionally differentiated for adhesion. Brucellae are proposed to be polarized bacteria, exhibiting asymmetric division  (44)  and unipolar growth, as seen with sev-eral other Rhizobiales  (45).
Features and Functionalities OptiMAS main algorithms (described in documentation available as Supplementary Material) have been deployed to trace parental alleles along generations, using information given by markers located in the vicinity of the estimated QTL/gene positions. Probabilities of allele transmission are computed in different MAS schemes and mating designs (intercrossing, selfing, backcrossing, double haploids, recombinant inbred lines) with the possibility of considering generations without genotypic information. Then, strategies are proposed to select the best plants considering estimated molecular scores and to efficiently intermate them based on the expected value of their progenies. These functionalities have been defined in connection with a panel of users working on different species and tested on two reference datasets provided with the tool.
Implementation Two versions of the tool have been developed. The first one, managing computationally intensive processes for step 1, is written in C-ANSI and runs in command line, which provides a convenient integration with custom analysis pipelines and databases. The second version integrates the C program and additional functionalities within a GUI coded in C++ using Qt, Qwt, and Graphviz libraries. Installable versions are distributed to run under most modern GNU/Linux, Windows (XP/7), and Mac OS X (10. 5 or later with Intel processor) systems. Although completely standalone, with data imported via simple plain-text formats, OptiMAS is part of the Integrated Breeding Platform (IBP), a web-based workflow system providing analytical tools and services to help breeders to improve crops for greater food security in the developing world (https://www.
These three signals were recorded with the same acquisition system and with the same parameters as the ones used during the cutting experiments. Modal analysis and calculus of frequency response functions were performed with a special software developed with Mathematica. FRFs between the reference force sensor and the two sensitive parts of the experimental set-up (strain gauge and piezoelectric force sensor) were obtained between 0 to 8 kHz with a LBF width of 400 Hz. The coherence function associated with the correction function of the strain gauge signal (not presented here) showed that the FRF quality was not good enough to ensure an accurate correction of the signal recorded by the strain gauge. In a lesser scale and for low frequencies, the FRF of the strain gauge obtained thanks to the pulse tests (Fig.
This could have compromised the results, identifying persons as depressed who do not meet the criteria for a clinical diagnosis and failing to identify persons with a depressive disorder. No data on sick leave, disability, or other social benefits were collected. The use of such data would have yielded a more complete and realistic cost-effectiveness estimate. However, these benefits would only have increased the estimated savings and present Internet-based interventions in an even more attractive way. Finally, the Rosser Index is just one way to estimate health gains, and other methods could have produced different results  [79]. However, this method has been employed previously, and the Rosser Index has its strengths at a policy level often used on existing datasets to foretell health care demands  [57].
Data were collected and analyzed using pCLAMP 9. 2 (Molecular Devices) and fitted using KaleidaGraph (Synergy Software). All recordings were performed at a holding potential of Ϫ60 mV and at room temperature. Expression and Purification of NMDA Receptors-NMDA receptors were expressed in HEK293T (tsA201) cells. Cells were grown in Dulbecco's modified Eagle's medium (Sigma) supplemented with 10% (v/v) fetal bovine serum, 100 units/ml penicillin, and 100 g/ml streptomycin in an atmosphere of 5% CO 2 /air. Transfection was carried out using either Effectene transfection reagent (Qiagen) or calcium phosphate precipitation. After transfection, cells were incubated for 24 -48 h at 37 °C to allow expression of receptors. All purification steps were carried out at 4 °C. For receptors to be imaged in air, transfected cells were solubilized in 1% Triton X-100 for 1 h before centrifugation at 61,740 ϫ g to remove insoluble material.
This equation assumes that the particle image has the form of a spherical cap. The theoretical volume of the extracellular region of an intact NMDA receptor tetramer was estimated assuming that it has an overall structure similar to that of the AMPA receptor (3). After removal of the transmembrane domains (amino acids 523-620 and 790 -817 of each subunit) from the AMPA receptor crystal structure (Protein Data Bank code 3KG2) using Swiss-PdbViewer (version 4. 1), a volume of 369 nm 3 was calcu-lated. This volume, which includes enclosed cavities, is based on the space-filling/Corey-Pauling-Koltun model with a fixed radius for each atom. The structure was smoothed with a probe size of 1. 4 Å. To determine the degree of overestimation of particle volumes as a result of convolution caused by the geometry of the scanning tip, gold particles of known diameter (and hence volume) were imaged under the same conditions as used for the proteolipid bilayers.
" Informally, a view is an architectural design of a stakeholder's viewpoint that covers delicately all its interests and required functionalities, and represents them formally in a structured architecture. An abstraction level represents a level of details defined in order to treat the extra complexities retained after decomposing our system into multiple viewpoints, by relegating some viewpoints' details which appear to be irrelevant in the first stages of the modeling process to lower abstraction levels, so we can zoom into a specific viewpoint to the desired level of details. In this paper, a survey is presented dealing with the evolution of role and usage of two major concepts in software engineering, which are the views and abstraction levels. Also an overview of our architectural modeling approach called MoVAL (Model, View and abstraction level) is suggested.
In MoVal, both views and abstraction levels concepts are integrated allowing the architect to build robustly a multi-views and multi-granularities software architectures. This paper is further structured as follows: In sections 2 and 3, studies and proposed solutions related to the views and abstraction levels fields are presented. Section 5 and 6 presents our comparative analysis and the deducted limitations of current solutions, respectively, in order to motivate the contribution of our approach presented in section 4, where we will suggest the beginning of theory and practice of views and abstraction levels suitable for software system architectures. Finally section 7 concludes the paper. Viewpoints are the perspectives of different people or stakeholders towards an information system  (Finkelstein and Sommerville, 1996).
Those links actually will hold the consistency rules that will be defined later in our approach, and that will ensure the consistency of the resulting software architectural description. Each column of the matrix represents a distinct view of the model, and each line represents an abstraction level defined for this model. In reality, a view of the model does not have necessarily representations in all of the defined abstraction levels due to the absence of the isomorphism between model's views. So, each view could have one or more rep-resentations respectively in one or more abstraction levels defined by the architect, depending on the system's requirements. Note that the system decomposition to views and abstraction levels should be done, for now, manually based on the architects' expertise in the system's application domain, and there is no defined mechanisms offered in MoVAL helping architects to determine the architectural views and abstraction levels.
RELATED WORKS LIMITATIONS As mentioned in  (Rozanski and Woods, 2011) , using views and viewpoints to describe the architecture of a system benefits the architecture definition process in a number of ways that are : Separation of concerns, Communication with stakeholder groups, Management of complexity and Improved developer focus. However, some limitations remain when using existing view-based approaches. We can summarize some of these limitations, which were solved in MoVAL, as follows: • Needs to move between different abstraction levels : Despite software architecture is defined as the high-level system structure, we assume that a software architect should define views at different levels of details. In fact, some stakeholders may settle for an overview information, while others require detailed information and those whose needs are between (i.
• Lack of an Architectural Description Process: In almost all the studied approaches, except in  (Clements et al. , 2002) , it is unclear what the software architect has to do to define the suitable architectural description. This task is based mainly • Views Inconsistency: Using a number of Views to describe a system inevitably brings inconsistencies problems. So we need to achieve a crossview consistency within an architectural description, which is not offered by the majority of the studied related works, but MoVAL has defined the links (section 4. 4) which hold the needed coher-ence rules in order to solve those inconsistencies problems.
CONCLUSION This paper has presented a preliminary approach for documenting intensive software systems architecture based on views and abstraction levels. This approach complies with the view-based approach of IEEE-1471 and aims at extending it in three different ways that are : (1) providing the software architect means to define views at different levels of detail and to move between them; (2) defining relationships that solve the inconsistencies between the architectural views; (3) the specification of an architectural description process which guides the architect while selecting pertinent views, documenting them and refining them at different abstraction levels. Actually, we are validating MoVAL's methodology or development process that will allow system architects to build a rough and coherent multi-views/multiabstraction levels software architecture.
Interestingly, this co-treatment fully suppressed U118 and U87-MG cell growth (up to 99%) as measured by the MTT assay, showing that fluvastatin potentiated the cytotoxic effects of celecoxib in GBM human cells (Figure  2b ). GBM cell shrinkage and cell-adhesion-loss observed by microscopy also confirmed the efficacy of such a combination (data not shown). To further investigate the combination of celecoxib and fluvastatin, growth inhibition assays were performed on the two GBM cell lines after incubation with a range of drug concentrations. Combination index (CI) values were determined on the basis of the Chou and Talalay method for all tested concentrations of chemotherapeutic drugs, using Calcusyn® software (Table  1 ). In U87-MG cells, the interaction between celecoxib and fluvastatin was synergistic at all concentrations tested (CI<1), except for the highest concentrations that resulted in additive effects (CI=1).
After 24 hours, cells were collected and analyzed for fluorescein annexin-V and propidium iodide (PI) labelling by FACS in order to distinguish and quantitatively analyze non-apoptotic cells (Annexin-V negative/ PI negative, lower-left), early apoptotic cells (Annexin -V positive/PI negative, lower-right), late apoptotic/necrotic cells (Annexin-V positive/PI positive, upper-right) and dead cells (Annexin V negative/PI positive, upper-left). This double-labelling was performed on untreated cells and treated cells with the drug combination (100 μM of celecoxib/240 μM of fluvastatin). data confirms these findings as celecoxib demonstrates anti-tumor activity in 2 GBM cell lines and 3 PA explants cultures. Fluvastatin was also identified as a drug that could target genes of interest and therefore we hypothesized that it could be another potential agent for the treatment of H/C PA.
The IC 50 values of both drugs for the 2 GBM cell lines were determined. Then, synergistic interaction between fluvastatin and celecoxib was analysed using the combination index (CI) values that were calculated with the Calcusyn software based on the Chou and Talalay method  [50]. The CI theorem provides quantitative definition for additive effects (CI=1), synergisms (CI<1) and antagonisms (CI>1) in drug combinations.
KI67 staining Quantification of cell proliferation was performed by KI67 staining. After permeabilization, cells were incubated with KI67 antibody (1/25) (Dako, Glostrup) for 30 min at 4°C. Then, cells were incubated with the secondary antibody (anti-mouse IgG FITC, 1/100) (Jackson immunoresearch, West Grove, USA). Cells were analysed by flow cytometry (FACS Calibur; BD Biosciences) and data were analyzed using CellQuest Pro analysis software.
Annexin V/PI double staining Apoptotic cells were quantified by Annexin V/PI double staining assay using the FITC Annexin V Apoptosis Detection Kit (BD Biosciences, Le Pont de Claix, France) as recommended by the manufacturer. The cells were analysed by flow cytometry using a FACS Calibur flow cytometer (BD Biosciences) within 1 hour and data were analyzed by CellQuest Pro analysis software.
Acknowledgments This work was supported by  Institut National Contre le Cancer  (grant  INCa -DGOS-Inserm 6038 ),  PACA Canceropole ,  Institutional grants  ( INSERM, Aix-Marseille University ),  Amélie la Vie ,  Ln13 la Vie  and  The Brain Tumour Charity (S. Lambert's funding, UK). We thank the  Societé Française de Lutte contre les Cancers et les Leucémies de l'Enfant et de l'Adolescent (SFCE)  and the  Association pour la Recherche sur les Tumeurs Cérébrales (ARTC-Sud)  for their financial support. Frozen samples were provided by the  AP-HM Tumor Bank  (Authorization Number  2008-70 ) and we are grateful to  Peter Collins  ( Department of Pathology, University of Cambridge, Cambridge, England ) for providing 7 tumor samples. We are grateful to  Anderson Loundou  ( Epidemiology Unit, DRRC, Marseille ) for his help in statistical analyses and to Charles Prévot (INSERM,  U911 ,  Marseille)  for his help in flow cytometry experiments.