dataesr/scientific-paragraphs-categorization huggingface dataset:
Membranes were blocked for 1 h at room temperature with 5% milk in phosphate buffer (PBS), pH 7. 4, containing 0. 05% Tween 20, and incubated overnight at 4°C with the primary antibody in blocking buffer. Membranes were then rinsed in Tris-buffered saline, pH 7. 4, with 0. 05% Tween 20, incubated for 1 h at room temperature in horseradish peroxidase (HRP)-conjugated secondary antibodies (immunopure peroxidase conjugated; ThermoFisher Scientific), and visualized using SuperSignal West Pico Chemiluminescent Substrate (ThermoFisher Scientific). Chemiluminescent signals were acquired using films (Hyperfilm ECL, GE Healthcare) or an Image Quant LAS 4000 mini (GE Healthcare). Densitometric analysis was performed using the National Institutes of Health ImageJ program  (Schneider et al. , 2012). Equal loading was verified using MemCode (ThermoFisher Scientific) and levels of ␤I-tubulin or actin.
Protein levels were expressed as a ratio with ␤I-tubulin or actin. Phosphorylated proteins were normalized to the total amount of the respective protein. RNA isolation and quantitative real-time PCR. Retinas were removed and snap frozen in dry ice. RNA was isolated using the RNeasy mini kit (Qiagen) and cDNA was synthesized from 1 g of total RNA using the First-Strand cDNA Synthesis Kit (Qiagen). Quantitative real-time PCR was performed using the QuantiFast SYBR Green PCR Kit. (Qiagen) as previously described  (Ferrera et al. , 2014). Gene expression data were normalized to actin and GAPDH using the multiple internal control gene method with the GeNorm algorithm available in the qBasePlus software (Biogazelle). The following primers were used: TrkB, forward 5Ј-CCACG GCATGAGCGAGAC-3Ј, reverse 5Ј-CCTAAGCACAACGGACTCCC-3Ј; BDNF, forward 5Ј-AAGGTCTAGGATGGAGGTGG-3Ј, reverse 5Ј-CTA AGCAACTTGACACATCATTCC-3Ј; actin, forward 5Ј-AAGTGGTTA CAGGAAGTCC-3Ј, reverse 5Ј-ATAATTTACACAGAAGCAATGC-3Ј; GAPDH, forward 5Ј-GAACATCATCCCTGCATCCA-3Ј, reverse 5Ј-CC AGTGAGCTTCCCGTTCA-3Ј.
, 2004). Immunohistochemical analysis of brains from mice injected with brain extracts or PBS was performed on 30 m coronal sections collected 2. 80 -4. 60 mm behind bregma. Sections were immunolabeled with AT8 antibody and counterstained with the Congo red analog (E,E)-1-fluoro-2,5-bis(3-hydroxycarbonyl-4-hydroxy)styrylbenzene (FSB;  Sato et al. , 2004)  as previously described  (Gasparini et al. , 2011). Images were collected using an automated Olympus BX51 microscope, equipped with a MBF Optonic CX9000 camera and 10ϫ UPLFLN semi-apo fluorite 10ϫ numerical aperture 0. 3 objective and Neurolucida V11 software (MBF Bioscience) or by confocal microscopy, as described above. Sarkosyl extraction. Sarkosyl-insoluble tau was extracted from 200 mg of brain tissue of transgenic and WT age-matched mice as described previously  (Gasparini et al.
TrkB receptor is upregulated in RGCs of P301S transgenic mice To examine how tauopathy affects BDNF signaling in P301S RGCs, we next analyzed the expression of the BDNF receptor TrkB, and the related neurotrophin receptors P75NTR and TrkA. In the retina, TrkB is mainly expressed in RGC and inner plexiform layers  (Grishanin et al. , 2008; data not shown). In P301S mice, TrkB protein levels were significantly upregulated compared with WT mice (Fig. 3 A, B ), while P75NTR and TrkA were unchanged (Fig. 3 A, B ). To determine whether TrkB upregulation was mediated through an effect on gene expression, we evaluated TrkB mRNA levels by quantitative real-time PCR. mRNA levels were similar in P301S (1. 1 Ϯ 0. 1) and WT (1. 0 Ϯ 0. 1; p ϭ 0. 73, Student's t test) retinas, indicating unchanged TrkB gene transcription.
Statistical Analysis In order to test the hypothesis that immersion in seawater may change the chemical composition of driftwood, principal components analysis (PCA) was performed on the original data from the wood samples. This method is useful for revealing correlation patterns in complex databases (e. g. ,  Derrien et al. , 2012). The 14 ICP-MS element concentrations (variables) in 16 wood samples (individuals) were analyzed using multivariate analysis (PCA). The PCA was based on a correlation matrix, whereby the data set was standardized and normalized. The PCA and relative statistical tests were performed with XLSTAT (Addinsoft, v. 7. 5), using nonparametric tests for small samples of unknown distribution (Mann-Whitney).
, 2010; Juahir et al. , 2011; Derrien et al. , 2012) , but this method has also been applied to archaeological samples in order to identify the potential influence of geochemical processes in the geochemical signature of driftwood  (Caruso Fermé et al. , 2014). In the present study, PCA was used to assess the initial data set of wood samples and to represent the relationship among groups and individual samples on a graph using a linear combination of variables. After running the PCA on the 16 wet and dry samples, significant moderate low-dimensional structures were revealed (Fig. 3 , parts a and b). This model is considered to be well-suited for studying the correlations between the key variables of interest. The first principal component (PC1) explained 36% of the total variance, while the second principal component (PC2) explained 23% and the third principal component (PC3) explained 14% of the total variance.
Future research should apply PCA to additional samples in order to verify that there is no overlap between the different clusters. In particular, some of the variables in the PCA models seem to be orthogonal to each other and may indicate a correlation, such as the Ba/cations versus Zn/cations or the Mg/cations versus Mn/ cations (Fig. 3 , part a). The further comparison of these results with data obtained from archaeological wood samples would highlight the robustness of this PCA based on coniferous and deciduous samples. Moreover, archaeological wood samples would also provide information about the influence of burial in the soil. Indeed, possible chemical exchange between soil and wood may cause enrichment and depletion of some elements depending on meteorological and weathering conditions.
acknowledgMents This project was supported by grants from the Archaeosciences Laboratory and Observatory of Universe Sciences of the University of Rennes 1, the Social Sciences and Humanities Research Council of Canada (SSHRC), the Natural Sciences and Engineering Research Council of Canada (NSERC to Bhiry), the Avataq Cultural Institute, and the Centre d'études nordiques (Laval University). We thank A. Delwaide for assistance in collecting the coniferous samples, and we are indebted to the anonymous reviewers for their helpful comments on this manuscript.
METHODS The study was completed retrospectively between 1995 and 2013. We searched through the database of the Internal Medicine Department and the Neurophysiology Department of the Pitie-Salpetriere Hospital for the terms ''ganglionopathy,'' ''sensory neuronopathy,'' and ''Sjo ¨gren syndrome. '' Inclusion criteria were (1) Primary SS as defined by the American-European Consensus Group  22  (see Table  1 ). (  2 ) Probable SN defined by Camdessanchecriteria  23  (see Table  2 ). Exclusion criteria were   (4) Celiac disease (5) B12 insufficiency. Data were extracted from medical records. The following variables were studied: patients' signs and symptoms, neurological examinations, associated autoimmune diseases, biological profiles (antinuclear antibodies [ANA], precipitating antibodies to extractable nuclear antigens Ro/SSA and La/ SSB, rheumatoid factor, complement factors, immunoglobulins, monoclonal immunoglobulin component, and cryoglobulinemia).
As we collected the data retrospectively and anonymously, this study was not considered as a biomedical research. Electrophysiological studies were noted, including motor and sensory amplitudes and nerve conduction velocities, at the beginning and end of each treatment. All treatments given were noted. Handicap was evaluated using modified Rankin Scale (mRS) at the beginning and the end of each treatment. Side effects of the treatments were also recorded. Treatment response was classified as improvement, stability, or degradation for each treatment given for at least 6 months. Improvement was defined by a decrease of 1 or more points in the mRS or increase of 5 microVolts in at least 2 sensory nerve amplitudes. Worsening was defined by an increase of 1 or more points in the MRS or decrease of 5 microvolts in at least 2 sensory nerve amplitudes.
The direct association between the geographic stratification and malaria transmission has not been validated through field studies. As Mauritania attempts to move forward with an ambitious goal to reduce malaria-associated morbidity and mortality by 75 % before 2015 and eventually eliminate malaria from the country  [1] , there is an urgent need to establish an evidence-based malaria prevalence assessment in the general population living in different epidemiological strata that purportedly characterize malaria transmission pattern in the country. The present study was conducted with the aim to collect and analyse recent and reliable parasitological and entomological data from 12 study sites located in three different epidemiological strata during three time periods: during the 'cool' dry season after the rainy season (November-December 2011), during the 'hot' dry season (June 2012), and during the rainy season (October 2013).
Statistical analysis Aggregated parasite density by zones or years was expressed as the geometric mean and median. The comparisons of medians of parasite densities were performed with Mood's median test and illustrated with violin plot. Proportions were compared using the Chi square test or Fisher's exact test depending on the sample size. The level of statistical significance was set at P < 0. 05. Statistical tests were performed using SigmaStat 3. 5 (Systat Software, Inc. , Point Richmond, CA) and R statistical language (R Foundation for Statistical Computing, Vienna, Austria).
Acknowledgements We would like to express our gratitude to Deputy Regional Health Councillors, mayors, heads of household, and the medical staff of the health centres for facilitating the study. We thank  Professor Ali Ould Mohamed Salem Ould Boukhary  and  Mr Mohameden Ahmedou  for the map of study sites and  Dr Sidi Ould Zahaf  for his help. This work was supported by the  World Health Organization, Expertise France  ( 12INI215  grant), and  United Nations International Children's Emergency Fund  (UNICEF; now  United Nations Children's Fund).
5 nM by half serial dilution. The disssociation step was carried out over a 40 minute time period in Kinetics Buffer. The assay data were processed using Data Analysis (version 6. 3 -Forte Bio) to obtain kinetic values. Briefly, a buffer blank was used as a reference cell subtraction and the data series was evaluated using a global fit algorithm for 1:1 binding interaction. Fluorescent polarization assay was performed using the anti-canine CD20 monoclonal antibody onto FITC tagged human CD20 peptide, with the human-mouse chimeric monoclonal antibody Rituximab as the control antibody. Purified monoclonal antibody NCD1. 2 and Rituximab diluted in PBS were titrated against 30 nM fluorescein-labeled peptide corresponding to human CD20 (NCEPANPSEKNSPSTQYCYS) in assay buffer (PBS, 0. 05% Tween-20).
Transfection of human CD20 into H1299 cells Primers introducing BamHI and XhoI sites at the ends of reported sequence (Genbank accession number NP_068769. 2) of human CD20 were designed for its amplification and cloning into an EGFP-expression vector (N1). H1299 cells were grown as monolayers in RPMI 1640 supplemented with 10% fetal bovine serum (FBS). 1μg of DNA (GFP-CD20) was transfected in H1299 cells, along with GFP as a negative control using Attractene in order to measure the binding efficiency of the mouse anti-canine monoclonal antibody to its human CD20 counterpart. The binding was determined via Western blot as well as Immunofluorescence. Chemical fractionation into compartments was carried out using a fraction kit that separates into cytosolic, membrane/organelle, nuclear, and cytosolic/insoluble proteomes (Calbiochem).
Immunohistochemistry and FACS Canine samples were taken as part of normal diagnostic procedures from dogs treated by private veterinary practitioners for diagnostic and immunophenotyping analysis within veterinary schools (SC and LA) with newly diagnosed, previously untreated lymphoma. The samples are anonymized and unlinked and the authors have permission and authority to use the samples for research purposes. Biopsies were obtained from dogs with different types of B and T cell lymphomas, including Diffuse Large B-cell lymphoma (DLBCL), Marginal Zone Lymphoma (MZL), Follicular Lymphoma (FL), B-cell small lymphocytic (B-SLL), and Lymphoma and Peripheral T-cell Lymphoma (PTCL). All lymphoma samples were taken as part of normal diagnostic procedures from dogs with newly diagnosed, previously untreated lymphoma and the data are anonymized and unlinked  [40].
The acquisition parameters were kept constant for the duration of the study and the machine was routinely calibrated using calibration beads (CaliBRITE, Becton Dickinson, San Jose, CA, USA) to ensure comparable readings between different days. A minimum of 10,000 events was gated to exclude dead cells, and analysis was performed with Cell Quest software (Becton Dickinson, San Jose, CA, USA). Thus, the efficiency of anti-canine CD20 antibody was determined on different types of B and T cell lymphomas that are meant to be positive and negative for CD20, respectively using FACS. For the competition binding of unlabeled Rituximab or NCD1. 2 to the human SUDHL4 B-cell lymphoma cell line expressing CD20, incubations were with Rituximab conjugated by DyLight 488 and analzyed by FACS. The summary of the raw data is in Table  1.
A fluorescent (FITC) version of the human CD20 peptide sequence was used in fluorescence polarization to determine the relative affinity of the NCD1. 2 MAb compared to Rituximab (Fig  3A ). Purified monoclonal antibody NCD1. 2 and Rituximab diluted in PBS were titrated against 30 nM fluorescein-labeled peptide corresponding to human CD20 (ncepanpseknspstqycys) in assay buffer (PBS, 0. 05% Tween-20). These data confirm that the NCD1. 2 MAB binds to both the human and canine sequences. Rituximab was used as a control, however, there was no detectable binding in this assay relative to NCD1. 2, presumably as the Rituximab epitope differs form the canine sequence of CD20 and the MAB is reported to bind to a complex epitope on human CD20  [45, 46]. We also performed a converse competition assay on human cells expressing human CD20; we show that unlabeled Rituximab can compete with labeled Rituximab in binding to human cells; whereas the NCD1.
Reactivity of NCD1. 2 to canine CD20 protein from clinical samples The CD20 antibody was evaluated using lymph nodal fine needle aspirates and blood samples preserved in RPMI 1640 medium from dogs with different lymphoma subtypes using flow cytometry. On each sample complete immunophenotyping was performed according to previously published procedures  [41, 42]  in order to define cell origin and to identify the lymphoma subtype. These data reveal that NCD1. Together, this validation of the monoclonal antibody NCD1. 2, including its binding to canine and human CD20 protein and its binding to CD20 in the correct clinical tissue, prompted us to clone the antibody variable regions to determine whether it would be active as a recombinant antibody. Developing a scFv antibody phage library from hybridoma cell NCD1.
This instability of the purified scFv precluded its routine use (data not shown). As such, the scFv:NCD1. 2 phage library was next subjected to a biopanning screen in which the activity was tested when the scFv fusion to the gIII protein remained intact. A representative ELISA is shown where two high affinity scFv: gIII:phage fusions were identified and were very stable (Fig  8C ). The fusion to gIII protein may provide a stabilizing scaffold to the scFV much as a constant domain could in a full-length IgG. The DNA encoding scFv-3 and scFv-7 were sequenced to define areas of presumed similarity since they both bind to the CD20 peptide. Interestingly, the heavy chains had an identical sequence; however, the light chains were different but exhibited identity in CDR3 (Fig 9A  -9C ). The identity of CDR3 in the light chains (AQNLELPFT) means that we cannot rule out a contribution in antigen contact by the light chain.
Discussion Monoclonal antibody methodologies provide an approach to exploit the natural defense systems in mammals towards targeted or smart therapeutics. Perhaps the most successful example of this has been the wide application of the monoclonal antibody Rituximab towards a growing range of disease indications. Rituximab is a chimeric monoclonal antibody with humanized ELISA with peroxidase conjugated to protein A. The binding was quantified using TMB and was measured in optical density at 450nm. Five high affinity scFv were identified (highlighted 1-5). However, their instability precluded their routine use (data not shown). (C). Phage producing plaques from rounds 3 and 4 were grown overnight, the scFv-phage in the supernatant was PEG precipitated, and assayed in an ELISA using biotinylated CD20 peptide.
Acknowledgments This work was supported by the  BBSRC  ( BB/J00751X/1 ),  INSERM (Inserm Plan Cancer   A12112HS ; EM), partially supported by  Petplan , and was partially supported by the  project Ministry of Education Youth and Sports (MEYS) -NPS-I-LO1413. BV and PM were supported with  Czech Science Foundation (GACR)   P206/12/G151.
Blocks were subsequently trimmed for FIB-SEM or cut into 300-nm sections for correlative light and electron microscopy (CLEM) analysis using an ultramicrotome. For serial transmission electron microscopy (TEM), the resin-embedded embryos were trimmed and consecutive 100 nm distant sections were obtained with a section thickness of $80 nm. TEM imaging was carried out on a FEI Tecnai F30 equipped with Gatan US4000 CCD camera, operated at 300 kV or a FEI Biotwin equipped with an Olympus Keen View G2 camera operated at 120 kV, respectively. The fluorescence microscopy (FM) imaging was carried out as previously described  (Avinoam et al. , 2015; Kukulski et al. , 2011). Tomography was performed in 1 increments at 4,7003 magnification on a FEI Tecnai F30 electron microscope. FIB-SEM imaging was carried out on an Auriga 60 (Zeiss) using the Atlas3D software.
ACCESSION NUMBERS The accession number for the mass spectrometry proteomics data reported in this paper is ProteomeXchange Consortium: PXD004120. microscopy (EMCF), and proteomic (PCF) core facilities and Petra Riedinger for graphical design. We are grateful to Drs. P. Paul-Gilloteaux, X. Heiligenstein, and S. Mosalaganti for assistance and expertise in correlative light and electron microscopy analysis. B. H. was supported by the Agence Nationale de la Recherche (ANR) (Programme Blanc) NeMo (to T. L) and the European Molecular Biology Organisation (EMBO). K. H. B. was supported by postdoctoral fellowships from the Swiss National Science Foundation (SNF), EMBO, and Marie Curie Actions. M. B. acknowledges funding by EMBL and the European Research Council (309271-NPCAtlas).
ACKNOWLEDGMENTS We thank  Drs. Iain Mattaj  and  Peter Lenart  for critical reading of the manuscript and  Dr. Yannick Azou-Gros  for experimental assistance. We are grateful to our colleagues  Drs. V. Doye ,  N. Dostatni ,  A. Ephrussi ,  S. deRenzis ,  M. Mavrakis ,  A. Akhtar ,  G. Krohne ,  I. Mattaj , and  J. Ellenberg  for reagents. Stocks obtained from the  Bloomington Drosophila Stock Center  ( NIH P40OD018537 ) were used in this study. We gratefully acknowledge support by the  European Molecular Biology Laboratory  (EMBL) advanced light microscopy (ALMF), electron.
Methods Study Population Patients aged >18 years diagnosed with severe AS (AVA ≤1. 0 cm 2 ) and LVEF ≥50% at the echocardiography laboratories of 2 French tertiary centers (Amiens and Lille) between 2000 and 2012 were identified prospectively and included in an electronic database. We excluded patients (1) with more than mild aortic and/or mitral regurgitation; (2) with prosthetic valves, congenital heart disease (with the exception of bicuspid aortic valves), supravalvular or subvalvular AS, or dynamic left ventricular outflow tract (LVOT) obstruction; (3)  with symptoms by history or on exercise testing including angina, syncope, or dyspnea; (4) who denied authorization for research participation. A referent group of nonsevere AS was constituted including the patients with mild to moderate asymptomatic AS (AVA 1-1.
Statistical Analysis Continuous variables were expressed as meanAESD. The Shapiro-Wilk test was used to verify whether the residuals obtained on analysis of variance approximated a normal distribution. If this test failed, nonparametric analysis of variance (Kruskal-Wallis test) was used, and these variables were expressed as median (interquartile range). Post hoc comparisons were performed using either Scheffe's comparison or Mann-Whitney U tests with Bonferroni correction for multiple comparisons, as appropriate. Comparisons between 2 groups of patients were performed using the Student t test of the Mann-Whitney U test. Categorical data are expressed as a percentage and compared with a chi-square test. Followup time was quantified using the median of the Kaplan-Meier estimate of potential follow-up (also called the reverse Kaplan-Meier method).
Limitations Whereas echocardiographic data were prospectively collected, clinical and outcome data were obtained by review of medical records. Consequently, our study has the inherent limitations of retrospective analyses. 0] [31]  In routine practice, some patients are unable to perform an exercise test because of extracardiac conditions (eg, orthopedic, vascular, respiratory, obese). Plasma B-type natriuretic peptides were not available in the present study and may refine the predictive value of AVA. 32 Echo readings were not  specifically reviewed by a core laboratory; however, echocardiograms were performed by experienced echocardiographers with extensive experience in the field of valvular heart diseases. The calculation of the AVA by the continuity equation is prone to errors because of the notoriously difficult measure of the LVOT cross-sectional area owing to noncircular geometry of LVOT  33  or massive calcifications of the aortic annulus in some patients.
Modeling studies addressing daily to interannual coastal evolution typically relate shoreline change with waves, currents and sediment transport through complex processes and feedbacks. For wave-dominated environments, the main driver (waves) is controlled by the regional atmospheric circulation. Here a simple weather regime-driven shoreline model is developed for a 15-year shoreline dataset (2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014) collected at Truc Vert beach, Bay of Biscay, SW France. In all, 16 weather regimes (four per season) are considered. The centroids and occurrences are computed using the ERA-40 and ERA-Interim reanalyses, applying k-means and EOF methods to the anomalies of the 500-hPa geopotential height over the North Atlantic Basin.
Using this approach, the North Atlantic synoptic circulation can be accurately characterized, as atmospheric data located over the oceanic basin only are used for the weather regime computation  (Cassou et al. 2004; Barrier et al. 2013 Barrier et al. , 2014)). In this paper, a simple weather regime-driven shoreline model is implemented to investigate shoreline interannual variability at Truc Vert beach, Bay of Biscay, SW France. A set of 16 seasonal weather regimes (four per season) is computed for the North Atlantic Basin and the shoreline model is tested against a shoreline dataset covering a 15-year period from 2000 to 2014. The relation between weather regimes, waves and shoreline evolution, as well as the model skills are discussed.