dataesr/scientific-paragraphs-categorization huggingface dataset:
The data were recorded using the "Living Image" software version 4. 4 (IVIS Imaging Systems) yielding, after calibration, the total radiance efficiency ([photons/s/cm²/sr] / [µW/ cm²]) thus accounting for the incident power density. The data treatment required to subtract the fluorescence background. It was estimated thanks to the measurement performed on a region of interest (ROI) delimited in a site without fluorescent implant. An averaged background level was calculated and the background level was then subtracted to each fluorescence value. The data were normalized to the fluorescence at D00 (t = 0) following Equation  2 : ( ) ( ) ( ) bck c,n bck F t F F t F t 0 F - = = - (2) where Fc,n(t) is the background-corrected normalized fluorescence, F(t) is the raw fluorescence integrated over the ROI at time t, Fbck is the background fluorescence, and F(t = 0) is the raw fluorescence integrated in the ROI at day 0.
Acknowledgements The authors would like to thank the funders of this work,  BPI ,  Grand Lyon  and  Region Auvergne-Rhône-Alpes  ( Fonds Unique Interministeriel ColoMatrix  project  ET2014-003 ). We also would like to thank the  CTµ, plateforme de microscopie multidisciplinaire , from  Université Claude Bernard Lyon 1 , for the support to realise the Scanning Electron Microscope (SEM) analysis.
Statistical analysis All analysis were performed using R© version 3. 2. 3 software (R foundation for Statistical Computing). The significance threshold was set at p ≤ 0. 05. All measures are given as the mean and variability as the standard deviation. Survival rate between size of host oysters and between mabé, keshi and/or pearl graft oyster were tested using proportions test and if significant the pairwise test associated with Bonferroni correction. Quantitative parameters of mabé, keshi and pearls were tested with ttests when conditions of normality and homoscedasticity were respected, otherwise Mann-Whitney test were performed. Normality and homoscedasticity were verified with Shapiro and Bartlett tests, respectively.
study population People were selected from the Public Health England London TB register, a routine surveillance system used throughout London. Patient information is entered in the database by TB clinic staff. People diagnosed with pulmonary TB (with or without extrapulmonary sites), notified from 2012 to 2018 and 18 years of age or over at the start of treatment were included in this study. People with TB identified through contact tracing or TB screening programme were excluded. We analysed presentation delay and healthcare delay separately. All people with a negative or missing delay were excluded from the analysis of the respective delay. To analyse treatment outcome, we excluded cases with central nervous system, miliary or spinal extrapulmonary TB sites, multidrug-resistant TB and rifampicin-resistant TB and people who started their treatment after the 31 December 2017.
22 Sensitivity analyses were performed by changing the point of positive delay, for Open access   16 ) 834 (  18 ) 1048 (  20 ) 891 (  16 ) presentation delay we used the 21-day WHO recommendation, and for both presentation and healthcare delay we used the median. Another sensitivity analysis was to change the missing data for social risk factors to the 'No' group. Statistical significance of the variables was set for two-sided p values <0. 05. All analysis and data cleaning were performed in R V. 3. 5. 2.
Data for presentation delay and healthcare delay were missing in 37% and 28% of cases, respectively. We believe that the subsets of the population were representative of the whole study population but due to complete case analysis, our findings may be under or over-estimated. Also, when considering the missing values for social risk factors as 'no', our results were the same as those found in our initial analysis. When analysing outcome, we included isoniazid-resistant TB as their treatment should be completed within 12 months. We used treatment completion which is a broad outcome since this does not assess the actual health outcomes of people after they have completed their treatment regimen. Finally, extrapolation of these results must be done with caution, as the London population of people with TB is likely to differ from other parts of the UK or abroad, as will access to local healthcare services.
Acknowledgements We wish to acknowledge the contribution of all nurses and clinicians from all tuberculosis clinics in London for the data they collect without which these studies would not be possible. Also, we wish to thank  Jacqui Carless  and  Neil Billingham  for data extraction from the LTBR. All authors have contributed to the writing of this paper. contributors PE, SB and  CSA  designed the study. PE performed all statistical analysis with advice from SB and  CSA. AR and BK provided input from their respective fields to the paper written by PE under guidance from SB and  CSA. All authors approved the final manuscript. Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.
Study population and therapies TRANSITION (NCT02661217) was a randomised, multicentre, open-label study performed in 19 countries and 156 hospitals worldwide. The study design and rationale have been previously published. 9 he study included male or female patients aged ≥ 18 years who were hospitalised for an episode of ADHF (de novo HF or due to exacerbation of chronic HF), with New York Heart Association (NYHA) class II-IV, blood pressure ≥ 100 mmHg and left-ventricular ejection fraction (LVEF) ≤ 40%. The study was conducted in accordance with the ICH Harmonised Tripartite Guidelines for Good Clinical Practice and with the ethical principles of the Declaration of Helsinki. 10 Trial protocol was approved by ethics committees at participating centres. All patients provided written informed consent 24 h after haemodynamic stabilisation [no need for intravenous diuretics in the 24 h prior to signing informed consent, and systolic blood pressure (SBP) ≥ 110 mmHg for ≥ 6 h prior to randomisation].
Chlorophyll was imaged with excitation laser 561 nm and with emission filter BP629/62. Final figures showing representative images from two independent experiments were created from 25 Z-stacks (total thickness 93. 36 µm) flatten to one image with Orthogonal Projection function of ZEN 2010 (blue edition) software. Average of mean intensity values for YFP channels from two measurements were normalized according to chlorophyll while unspecific background signal of empty vectors was subtracted. Co-localization of mCherry-Tagged MPK3 With PLDα1-YFP MPK3:mCherry and mCherry:MPK3 constructs driven by 1485 bp long native promoter sequence and complete coding region of MPK3 were prepared by MultiSite Gateway R technology. This constructs were cloned in to the pB7m34GW binary vector. YEB medium (5 ml) including appropriate selection antibiotics was individually inoculated with A.
5 h. After five washing steps in TBS-T, proteins were detected by incubating the membranes in Clarity Western ECL substrate (Bio-Rad, Hercules, CA, United States). Luminescence was detected using ChemiDoc MP documentation system (Bio-Rad). The band intensities were quantified using Image Lab Software (Bio-Rad) and the data were statistically evaluated using Student's t-test. Immunoblot analyses were performed in three biological replicates.
Setting This monocentric prospective study was conducted in Strasbourg University Hospital from 2012 to 2018. The study protocol was approved by the local Ethics Comity of the University Hospital of Strasbourg (PRI -HUS n°4683) and was performed according to the revised version of the Declaration of Helsinki. All subjects provided written informed consent prior the entry into the study. This study was also registered at clinicaltrial. gov under number NCT01306825.
Chromatographic conditions Twenty μl of the supernatant (serum or bone) was injected into a Prominence HPLC system (Shimadzu USA Manufacturing Inc. , Canby, OR) comprising an LP-20AT pump and a SPD-20A UV-visible detector. A Rheodyne model 7725i manual sample injector (Rheodyne, Rohnert Park, CA) was used with a 20-μl loop. Chromatographic separation was achieved on a reversed-phase C18, 150 x 4. 6-mm, 3-μm Uptisphère column (Interchim, Montluçon, France) with a mobile phase consisting of an isocratic mixture of 20 mM phosphate buffer and 40% acetonitrile. The pH was adjusted to 3. 5 with phosphoric acid. A 1. 0ml/min flow rate was used, and the detection wavelength was set at 224 nm. Under these conditions, the retention time for daptomycin was 7. 5 min. The LC solution Shimadzu software (Shimadzu France, Champs sur Marne, France) was used for acquiring and processing the data.
Virus and Cell Lines We used the Homo sapiens/Haiti-1/2015 MAYV strain (Genotype L; GenBank accession number KX496990)  [22] , a low-passaged strain isolated in 2015 from the plasma of an 8-year-old Haitian child who had fever and abdominal pain. This strain derived from a reverse genetics system based on its GenBank sequence. The infectious subgenomic amplicons (ISA) method was used to rescue infectious viral particles as previously described  [23, 24]. Briefly, the whole viral genome was de novo synthesized in three double-stranded overlapping DNA fragments. First and last DNA fragments were flanked respectively at the 5 and 3 termini by the human cytomegalovirus immediate early enhancer/promoter and the hepatitis delta ribozyme followed by the simian virus 40 polyadenylation signal. These synthetic DNA fragments were used as template to generate subgenomic amplicons by polymerase chain reaction (PCR).
Acknowledgments: This work was supported by grants from the  Agence Nationale de la Recherche  ( ANR-15-CE15-00029 ). Michèle Bengue  was supported by a fellowship from the  Méditerranée Infection foundation. This work was also publicly funded through the  French National Research Agency  under the " Investissements d'avenir " programme with the reference  ANR-16-IDEX-0006.
Funding information FEDER (European Funding of Regional Development) and Conseil Régional Auvergne, Grant/Award Number: convention n 36760 (2013); Conseil Régional Auvergne; FEDER (European Funding of Regional Development) In a previous article we reported that mutations favoring cancer at adulthood seemed to improve fertility and limit miscarriages. Because spontaneous abortion may result from anomalies in embryo, we questioned if an increased frequency of congenital malformation could be evidenced among cancer-prone families. Oncogenetics database (≈193 000 members) of the comprehensive cancer center Jean Perrin was crossed with regional registry of congenital malformations (≈10 000). Among children born between 1986 and 2011, 176 children with malformation matched in both databases. In breast/ovaries cancer-prone families, the risk for malformations was multiplied by 2.
| INTRODUCTION Predisposition to cancer in early adulthood exerts selective pressure on predisposed individuals by reducing life expectancy and consequently the length of the reproductive period. Mutations in one of the BRCA genes, with an associated risk of cancer starting as early as age 30, are relatively frequent in spite of this selective pressure. 2] [3]  In a large retrospective survey of our oncogenetic database, we found that in families predisposed to breast/ovarian cancer, women from BRCA mutated families had a 36% lower miscarriage frequency (P = 0. 015) than those from families with no known deleterious mutation; among individuals of both genders tested for a BRCA mutation, childless individuals were 22% less frequent for carriers (P = 0. 0022) and the interval between first and last child was 16% longer (P = 0.
Sources of data on both conditions were available in the Auvergne region of France and were extensive enough to enable research regarding this issue. We crossed the information available in two large databases, the first used by the oncogenetic service of Centre Jean Perrin Comprehensive Cancer Center containing pedigrees of cancer-prone families and the second from the regional register of congenital malformations that includes all children born with a congenital malformation. The study period corresponded to 26 years, from January 1986 to December 2011.
| Centre Jean Perrin Oncogenetics database Created in 1988, the oncogenetics department of the regional comprehensive anticancer Centre Jean Perrin is the only center in the region offering evaluation of hereditary cancer risk. A large majority of local individuals belonging to high-risk families seeking oncogenetics advice address this department. At the time of this study, the database included about 190 000 family members from 6600 families. Based on the population size of Auvergne and the expected prevalence of women with BRCA mutations in France, about 45% of women with familial breast/ovarian cancer risk in the region are included in the database. Types of cancer risk were grouped by geneticists into several categories. It was based on their expertise in the early days and later on the calculation of scores like Eisinger  12  or Manchester  13  for hereditary breast and ovarian syndrome or, for hereditary colon cancer syndrome (HNPCC), using Amsterdam 14 and/or Bethesda criteria.
| Database matching A temporary mixed database was constituted to evaluate the frequencies of congenital abnormalities: children born alive between 1986 and 2011, regardless of parental mutation status and type of cancer predisposition were extracted from our oncogenetic database. A computer "robot" was developed to match its records with those of the malformations register, based on similar/close children names, date of birth, mother's names, and age of parents; a visual control list permitted to validated manually each proposed match. To limit bias, that is, artificially increase the risk for malformation in particular subgroups of cancer-prone families because of a syndrome combining both cancers and malformations, four cases of microcephaly were excluded from the analysis: these cases were referred for genetic analysis on the basis of specific congenital abnormalities suggestive of Nijmegen breakage syndrome (NBS), a syndrome that includes strong predisposition to lymphoid malignancy.
16 Their corresponding families were thus excluded from the data-matching diagram (Figure  1 ). Fanconi anemia was considered for exclusion, but none of our cancer-prone families presenting with this syndrome had children born after 1985. One hundred and seventy-seven children with congenital anomalies corresponded to children in our oncogenetic database. The  Because the risk for congenital malformation increases in cases of multiple births,  [17] [18] [19] [20] [21]  the frequency of these events was computed per subgroup. These frequencies were compared to frequencies of congenital anomaly both to verify that our statistics were not biased because of this, and also to control that these frequencies were in accordance with national figures. To compare proportions of children with abnormalities between subsets, χ 2 test were used, or Fisher's exact test if needed.
| RESULTS In the oncogenetic database, 16 798 children with a known date of birth were born between 1986 and 2011, of whom 2292 belonged to families with a BRCA mutation and 390 to families with an MMR mutation. The registry contained 11 234 cases diagnosed during the same period, with 10 026 corresponding to the selection criteria. Considering about 364 000 children were born in Auvergne during the 26-year study period, this corresponds to a malformation rate of 2. 8%, a rate compatible to the nation-wide estimation equal to 2. 4% in 2011 to 2012. 11 Overall, 176 children with congenital anomalies corresponded to children in our oncogenetic database (the matching process is described in the material and methods section).
33 abnormalities found for the 3244 children belonging to families with cancer predispositions other than Lynch and HBOC were excluded from the analysis because of the wide heterogeneity of this population. NB. A public repository has been created in order to make data available. It contains several Excel sheets with first, an explanation on how are organized other sheets, second the results sheets and finally detailed information by subgroup. The address of the repository is: http://www. cjp. fr/fichiers/Anoccan_data. zip 2. 4 | Ethics CEMC-Auvergne is certified by the National Committee of Registries (2012-2015) and the database was authorized by the French Authority for personal data protection (CNIL no 1387396). The consent signed by parents to enter this registry, allows the use of clinical data for research purpose.
Centre Jean Perrin Database was declared by the CNIL correspondent under the number 1621407V0 on January first 2001. This certificate was renewed by CNIL on May 17th 2017 (no 2030983V 1). Counselees signed an informed consent that enables the use of data for research purpose. Another special authorization was requested because of the French regulation regarding the merge of databases coming from different entities (here CCC Jean Perrin and CEMC belonging to the Regional University Hospital). This authorization was granted by CEERES (national expertize committee for research, studies and evaluation regarding health) on March 15th 2018 (no TPS 37636) and then by CNIL on May 18th 2018 (DR 2018-108) which permitted us to perform our study without any special information to families members about it.
ACKNOWLEDGMENTS This work was supported by  FEDER  (European Funding of Regional Development) and Conseil Régional Auvergne: convention n 36 760 (2013). These public funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors thank  Laurence, Mélanie ,  Sandra , and Sandrine, secretaries of oncogenetics department, for their constant attention and care with pedigree constitution. They also thank  Claire Laquet , genetic counselor nowadays retired, that collected clinical information of family members during decades.
MRI data acquisition For all MRI examinations, a 1. 5-T clinical system (Magnetom AERA ® , Siemens Healthineers) was used with an 18-channel body phased-array coil. MRE acquisition was performed after intravenous administration of a gadolinium-based contrast agent per clinical protocol (gadoterate meglumine, Dotarem ® , Guerbet or gadobenate dimeglumine, Multihance ® , Bracco)  [17]. Patients were asked to fast for 4 hours prior to liver MRI to eliminate post-prandial effects on portal venous blood flow  [18]. For MRE acquisition, 60-Hz shear waves were generated by using a 19-cm-diameter, 1. 5-cm-thick, passive acoustic driver, which was placed against the right anterior chest wall at the level of the xiphoid process overlying the liver. Wave imaging was performed by using a modified two-dimensional phase-contrast GRE pulse sequence with motion-encoding gradients along the z-axis.
Statistical analysis Quantitative data were expressed as mean ± standard deviation (SD) and range. Qualitative data were expressed as raw numbers, proportions and percentages. First, the heterogeneity of the measurements between the 3 and the 9-elliptical ROIs was assessed for observer 1. Second, the inter-observer reproducibility for the elliptical ROI methods, using only the values from the 3 ROIs of the center slice (called "3-elliptical ROIs method) or using the values from the 9 ROIs (called "9-elliptical ROIs method), was assessed. In a third part, the reproducibility between the 3 approaches was analyzed, using the measurement of observer 1 (based on the results of the first part of the analysis). The heterogeneity between the 3 and the 9-elliptical ROIs was assessed using the coefficient of variation of the values in the ROIs.
Both inter-observer and inter-method reproducibility were assessed using intra-class coefficient correlation (ICC) and Bland-Altman analysis. The analyses were performed by comparing the methods 2-by-2 and globally. For ICC, the 95% confident intervals (CI) were computed. ICC values of 0-0. 2, 0. 2-0. 4, 0. 4-0. 6, 0. 6-0. 8 and 0. 8-1 are representative of slight, fair, moderate, substantial and almost perfect reliability. The Bland-Altman analysis included the computation of the bias, the 95% limits of agreement (BALA) as well as the coefficient of reproducibility (CR = 1. 96 × standard deviation of bias). All analyses were performed using MATLAB (version R2015a, MathWorks).
5 min, and increased again to 98% B after 12. 5 min, kept at 98% B during 13 min at the end. After passing through the diode array absorbance detector, the eluent was directed to the connected ion trap mass spectrometer with a standard electrospray source. The ionization method used was ESI in the positive ion mode (heated capillary temperature 340°C, gas flow 8 L/min, nebulizer gas 30 psi). Full scan mass spectra were acquired in the profile mode scanning m/z 50 to 1000. For the ESI-MS/MS studies, the mass spectrometer was equipped with the ESI source used for ESI-MS studies described above and with the same source parameter settings. The ionization mode was ESI in the positive ion mode. The isolation width was 4 m/z. Data were processed using Agilent MassHunter Qualitative Analysis software.
EPR studies EPR spectra were recorded on an EPR X-band spectrometer (ESP300E, Bruker Biospin GmbH, Germany) equipped with a high sensitivity resonator (4119HS-W1, Bruker Biospin GmbH, Germany). The g calibration was performed using Bruker standard (strong pitch) with known isotropic g factor of 2. 0028. The principal experimental parameters values were: microwave power of circa 5 mW, modulation amplitude 1 G, and conversion time of circa 160 ms with 1024 points per spectrum resulting in a sweep time of circa 3 min per scan. Several spectra were accumulated to ensure a good signal-to-noise ratio (S/N). Spectra were recorded at room temperature (295K±1K). All experimental EPR spectra were analyzed by means of computer simulation using labmade scripts based on Easyspin toolbox under Matlab (Mathworks) environment  (Stoll and Schweiger 2006).
Acknowledgements This work was part of the  DEFCHEMSKALL Franco-German Collaborative International Research Project  financially supported by the  ANR (Agence Nationale de la Recherche ; project no. ANR-15-CE15-0023-01 ) and the  DFG (Deutsche Forschungsgemeinschaft ; project no. DFG ,  BL340/6-1 ). The  Reseau NAtional de Rpe interDisciplinaire (RENARD, Fédération IR-RPE CNRS  # 3443 ) is also acknowledged. Fig. 3 -24- Fig. 4.
The Sub-Hourly Power System Operation The sub-hourly power system operation was formulated using the MATLAB programming along with MATPOWER  [23]  tool. The MATPOWER tool was used to solve the Optimal Power Flow (OPF) problem using Newton-Raphson (N-R) method in a dynamic system setup. Evaluation of the OPF involves several iterations on the system network parameters to arrive at the final optimal values. The initial angle of the reference bus (slack) is assumed to be zero. The wind generation and the PHG are added to the base thermal power system operation, and assigned the required specifications and constraints. Consistent internal structure of the MATPOWER is accomplished by using the case struct data conversion. A modified IEEE24-RTS bus system shown in Figure  8  with wind generation as in the work by the authors of  [24] , and PHG (added on bus 24) was used for running the simulations.