dataesr/scientific-paragraphs-categorization huggingface dataset:
In terms of JPN data, two data sets were from center hospitals (university academic hospitals), and other two were submitted from several hospitals (the number of hospitals were not clear after anonymization). We evaluated only patients whose ethnicity was indicated in the database (350 patients for JPN, and 6025 for CAUC), and then we further selected these cases by age. JPN MDS patients were significantly younger than CAUC patients, with median ages of 62 years (range 16-90) and 71 years (16-106), respectively (P < 0. 001). Since patients of less than 40 years old comprised 14. 3% of the JPN group compared to 3. 1% of CAUC, to aid comparability, we restricted our analysis to patients older than 39 years in this study. Thus, the final number of JPN and CAUC patients for the analysis was 300 and 5838, respectively (6138 in total).
Background of the data selection Table  1  shows the demographic details of the 40 years and over JPN and CAUC patient cohorts within the IWG-PM database analyzed in this study. In these cohorts, median age of JPN and CAUC patients was 65. 5 and 71 years, and JPN patients were significantly younger (Table  1 , P < 0. 001). There was no difference in the distribution of gender.
Hematological and laboratory data Hematological and laboratory tests showed significantly lower values in white blood cells (WBC), absolute neutrophil count (ANC), hemoglobin (Hb), platelet (PLT), and ferritin in JPN than CAUC (Table  1 ). There was also significant difference in peripheral blood (PB) and bone marrow (BM) blast percentage between the two groups with less blasts in both PB and BM for JPN (P = 0. 003, and P = 0. 015, for PB and BM blast percentage, respectively).
Cytogenetic data and cytogenetic risk groups The frequency of IPSS-R cytogenetic groups was compared between two groups  [30]. The distribution in the cytogenetic risk groups (IPSS-R risk) was not different between JPN and CAUC (Table  1 , P = 0. 332). The percentage of normal karyotype was 65. 3% and 62. 7% in JPN (n = 300) and CAUC (n = 5838) groups, respectively, without significant difference (P = 0. 382). To compare the frequency of each aberration used in IPSS-R risk stratification, data which met ISCN criteria were selected and further analyzed (n = 5105)  [31]. Among 27 types of cytogenetic aberrations, we found significantly higher frequencies of +1/+1q, -1/del(1q), der(1;7), -9/del(9q), del(16q) and del (20q) in the JPN group (Table  2 ). Del(5q) was significantly lower among JPN (1.
Green lines showed JPN data with the adjustment for age and FAB subtypes to those of CAUC. Red lines were for CAUC. There were significant differences in survival between two groups with or without adjustment, although the difference was smaller after the adjustment for age and FAB subtypes. There was no difference in time to AML transformation. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article. ) Table  4  Impact of factors on OS and time to AML transformation. * 95% confidence interval. 25% AML trans, time to transform AML in 25% of the patients. NR, not reached. evaluated (Table  4 ). In the comparison between JPN and CAUC, Dxy values for cytopenias (i. e. , levels of Hb, PTL, and ANC) were smaller in JPN than CAUC, demonstrating smaller prognostic impact on survival and time to AML transformation.
Some P values for Dxy of cytopeniarelated factors showed no significant impact among JPN patients. On the other hand, Dxy of BM blast percentage was larger in JPN for both OS and time to AML transformation than CAUC. Dxy of cytogenetic risk group for JPN was larger for OS, but smaller for time to AML than CAUC. IPSS-R that combined these factors in JPN showed 0. 51 for OS and 0. 49 for time to AML, which were comparable to those of CAUC (0. 42 and 0. 53 for OS and time to AML, respectively). These data indicated a stronger impact of blast percentage and cytogenetics as compared to cytopenias on outcomes in the IPSS-R for JPN vs CAUC.
Acknowledgements This work was in part supported by the  Myelodysplastic Syndromes Foundation, Inc (U. S. A) , and the  National Research Group on Idiopathic Bone Marrow Failure Syndromes (Japan) , granted by the  Ministry of Health, Labor and Welfare, Japan  ( H26-Nanchi-Ippan-062 , and  H29-Nanchi-Ippan-026 ).
A tryptic digest of recombinant C9ORF72 long isoform was then used for selection of best responding peptides. Three peptides were selected based on signal intensity after digestion, size (i. e. , between 6 and 20 amino acids), and lack of cysteine, methionine and glutamine residues. Specificity of the selected peptides was assessed using Basic Local Alignment Search Tool (BLAST) against the UniprotKB/Swissprot human database. Among the three peptides selected for quantification (Figure  2 ), two are common to both the short and long isoforms and one is unique to the long isoform. The assay based on peptide 1 (TEIALSGK) and 2 (IILEGTER) quantify total  C9ORF72 whereas the assay based on peptide 3 (DSTGSFVLPFR) differentiates the long isoform. Internal standards AQUA peptides of the three selected peptides for quantification were synthesized by incorporating stable isotopes at the C-terminal amino acid residues ( 13 C 6 , 15 N 2 -labeled lysine and 13 C 6 , 15 N 4labeled arginine).
A PRM method was established targeting the three selected peptides for quantification, and the unique C9-S peptide for detection only. Ultra-high performance liquid chromatography was performed on a C18 column for peptide separation with a total runtime of 30 min. Shorter gradients resulted in interferences at the retention time of peptide DSTGSFVLPFR (SIL version) and a decrease of signal intensity up to a factor of 2 in brain samples (Supplementary Figure  S1  and Supplementary Table  S1 ). Data treatment increased sensitivity by summing the signals of up to six major and non-interfered fragment ions to provide one XIC for each targeted peptide  (Dupré et al. , 2015 ; Figure  3  and Supplementary Table  S2 ). Each endogenous peptide and their corresponding isotope-labeled form (AQUA peptides) must strictly co-elute with similar transition ratio across the different samples in comparison with a standard.
ACKNOWLEDGMENTS The authors thank the " NeuroCEB" Brain Bank  ( GIE Neuro-CEB BB-0033-00011 ); the brain donation program is funded by a consortium of patient associations: ARSEP (association for research on multiple sclerosis),  CSC  (association for research on cerebellar ataxias),  France Parkinson ,  France Alzheimer  and  LECMA-Vaincre Alzheimer. The  NeuroCEB Brain bank network includes :  Prof. Franck Letournel  ( CHU Angers ),  Prof. Anne Vital  ( CHU Bordeaux ),  Prof. Françoise Chapon  ( CHU Caen ),  Dr. Catherine Godfraind  ( CHU Clermont-Ferrand ),  Prof. Claude-Alain Maurage  ( CHU Lille ),  Dr. Vincent Deramecourt  ( CHU Lille ),  Dr. David Meyronnet  ( CHU Lyon ),  Dr. Nathalie Streichenberger  ( CHU Lyon ),  Dr. André Maues de Paula  ( CHU Marseille ),  Dr. Valérie Rigau  ( CHU Montpellier ),  Dr.
Objectives: Endovascular treatment of wide-neck intracranial aneurysms (IAs) is challenging, especially in bifurcation location. The intra-saccular flow-disruptor Woven EndoBridge (WEB) offers a new concept of endovascular therapy for wide-neck IAs. We performed an update of a systematic review aimed to report the feasibility, effectiveness and safety of WEB device therapy. Patients and Methods: A systematic review was conducted using several electronic databases (including PUBMED and EMBASE), and searching for studies published between October 2015 and December 2017 (those published between January 2010 and September 2015 were searched in our initial systematic review). Outcomes were: success of implantation, peri-procedural and procedure-related complications, mortality, and adequate occlusion (complete occlusion or neck remnant).
Search Strategy Studies were searched in several electronic databases (EMBASE, PUBMED, ClinicalTrials. gov, Database of Abstracts of Reviews of Effectiveness and Health Technology Assessment databases). In our first systematic review, we searched for studies published between January 2010 and September 2015  [8]. Here, our updated search period was October 2015 to December 2017. A combination of free-text and thesaurus terms relevant to 'WEB device' and 'Intracranial Aneurysms' were used to identify literature. Our search equations are available upon request. Reference lists of relevant studies were scanned to identify additional citations. One author (X. A. ) performed the literature search.
Data extraction and Quality Assessment Two reviewers (N. T. & U. S. G. ) independently extracted relevant data using an a priori defined pre-piloted extraction sheet. Data extracted included study author or study name, originating country, sample size, patient characteristics, IA characteristics, feasibility, effectiveness, and safety outcomes of interest. The data extracted were cross-checked and any disagreements were resolved by discussion or recourse to another reviewer (B. G. or X. A). Two reviewers (N. T. & U. S. G. ) independently assessed the quality of included studies. Since all included studies were uncontrolled case series, these were assessed using the "Quality Assessment Tool for Case Series Studies" published by the National Institutes of Health  [10]. Studies were rated as poor, fair, or good.
Data synthesis and analysis Study and population characteristics were summarised in tables and text. We built 95% confidence intervals (CIs) of the estimates using the Wilson method and calculated a pooled estimate for proportions with a random-effect model to account for the heterogeneity across studies using the metaprop command on STATA14 (Statacorp LP, College Station TX, USA)  [11]. In all analyses, we assessed heterogeneity of findings using the Cochran's Q test (P value threshold of 0. 05) and calculating the I 2 statistic. For clinical and angiographic outcomes, we attempted to detect bias using funnel plot and undertook the Egger's test  [12]. We considered exploratory analyses stratifying the outcomes according to study quality rating, presence of an adjudication committee, presence of an independent core laboratory, type of WEB device used.
Study Quality Assessment Overall, quality assessment was performed for 12 studies. All studies were uncontrolled case-series. The quality rating for five studies was considered "good", one study was rated as "poor" while the other six where considered "adequate". Owing to the small number of articles, we found irrelevant to undertake exploratory sub-group analyses according to study ratings. The main study quality limitations were the lack of clear description of the intervention method, no proper statistical analysis and no clear definition on the patient selection criteria. Most studies also did not include an adequate follow-up period. This resulted in large variability in data reporting, leading to a significant risk of bias in most studies. There was also a large heterogeneity in terms of methods for the assessment of outcomes in all studies.
In addition to being a phosphoablative protein, YfnI-T297A-FLAG is expected to be inactive since the LtaS-T297A protein has been shown to be inactivated by the same mutation  5. B. subtilis strains expressing WT or the mutant YfnI variants were grown in LB medium and proteins from the culture supernatant and the bacterial cell pellets analyzed. The fusion proteins were also produced in strains deleted for prkC or prpC and their localization compared to that in a WT strain. The extracellular domain of YfnI-FLAG proteins could only be detected in the culture supernatant in the three strains analyzed (Fig. 3A ). Furthermore, for all three YfnI variants tested (WT, phosphoablative or phosphomimetic), the extracellular domain was released in the culture medium (Fig. 3B ). These data suggest that the phosphorylation state of YfnI does not regulate its export or its release by the type I signal peptidases.
Thermal shift assay. In thin-walled 96-well PCR plates, each well (20 μl) contained 10 μM of eYfnI protein (or eYfnI mutated proteins) and 2 μl of the fluorescent SYPRO ® Orange dye solution (Molecular Probes, 5000x, diluted to 100x in water), in 40 mM NaCl, 1 mM MgCl 2 , 10 mM Tris/HCl, pH 8. 0 and increasing concentrations of GroP (from 0 to 20 mM) and was heated from 25 °C to 65 °C in 0. 5 °C steps. The fluorescence intensity (Ex/ Em = 470/570 nm) of SYPRO ® Orange was monitored using a real-time PCR apparatus CFX96 (Bio-Rad). The fluorescence of SYPRO ® Orange dye changes when it interacts with the protein undergoing thermal unfolding. The denaturation temperature (T m ) was analyzed from the melt peak using CFX Manager software (Bio-Rad). The shift of T m (ΔT m ) induced by the presence of ligand was plotted against the concentration of ligand.
Curve fitting was performed by using Microcal Origin 5. 0 software with the Hill equation. To test the affinity of GroP for the phosphorylated form of eYfnI, 400 µg of the protein was first incubated with 50 µg of PrkCc in 10 mM HEPES, pH 8. 0, 5 mM MgCl 2 and 5 mM ATP for 60 min at 37 °C. eYfnI-P was then used as described above. Growth tests. B. subtilis strains were grown in LB or CE minimal medium supplemented with 0. 5% gluconate as previously described in  21. Western Blot. For LTA detection, cells were grown at 37 °C in 30 ml of CE minimal medium supplemented with 0. 5% gluconate for 6 hours then treated as previously described  9. For YfnI-FLAG detection, cells were grown at 37 °C in 30 ml of LB medium containing 0. 5% xylose until OD 600 = 1. 2, then centrifuged for 10 min at 4000 rpm at 4 °C.
The membrane was blocked with PBS solution containing 5% milk powder (w/v), for 3 hours at room temperature with shaking, then incubated with anti-FLAG antibodies diluted to 1/1000 th overnight at 4 °C. After three washes, the secondary antibody, a peroxidase-conjugated Goat anti-Rabbit (Thermo scientific) antibody was used at 1/2000 th dilution for one hour. After three washes, the membrane was incubated with ECL reagents (PerkinElmer) and scanned for chemiluminescence with an ImageQuant LAS4000 (GE Healthcare). Microscopy. Strains were grown for 6 h in CE minimal medium supplemented with 0. 5% gluconate at 37 °C. Images were obtained by microscopy on a Zeiss Upright Axio Imager M2 microscope. Cell width was measured with the ObjectJ plugin of ImageJ software and a statistical analysis of these data was made using a Wilcoxon test in order to calculate p-values.
Acknowledgements This research was supported by the  CNRS , the  ANR (PiBaKi)  and  Aix Marseille Univ. We thank  Elodie Foulquier  for her help with the bacterial two-hybrid experiment and  Leon Espinosa  for his help with the statistical analysis used for Fig. 6. This research was supported by the  European Research Council  grant  260371 , the  Wellcome Trust  grant  100289  and the  Medical Research Council  grant  MR/P011071/1  to A. G. 2 J. R. 2 is supported by the  German Research Council (DFG)  Grant  RI 2920/1-1.
Benchmarking. A last element of comparison between the two methods that we looked at was the capability of the two methods to produce sequences of A-scans (B-scan) in real-time. For this purpose, the time to produce a B-scan was computed using a LabVIEW 2017 (National Instruments, Austin, Texas) program installed on a PC equipped with an Intel i7-7800X @ 3. 5 GHz (6 cores, 12 threads of execution) CPU and 16 GB RAM. A simplified flowchart detailing only the benchmarked mathematical operations performed after data acquisition is shown in Fig. 10. A detailed presentation of the mathematical operations performed before and after data acquisition can be found in the Methods section. When using PCDC, at the calibration step, a calibration vector k ˆ is produced. This vector is then used to resample the data using a cubic spline interpolation.
This may impact procedures of seeking reflectors positioned around a point, or producing topography of a single layer objects, or en-face OCT images. Despite the advantages that the CMS approach offer, some drawbacks of the method still exist: • At the calibration step, the mathematical complexity of inferring theoretical spectra to build matrix T is apparently higher as it involves the use of low level computational routines. When using the NUDFT, the construction of the Vandermonde matrix is a simpler task as it is provided by LabVIEW as a virtual instrument while MATLAB provides it as an inbuilt function, etc. However, through simple steps, clearly described in our papers  18, 19  a ready to use toolkit can potentially by developed. • After data acquisition, parallelisation of data processing is a must.
The spectrometer allows for an axial range of maximum 2 mm to be covered. The imaging instrument has been previously used in clinical studies (Mogensen et al. 33  ). The in-house developed OCT imaging instrument described above was used to collect data from optical phantoms as well as for in-vivo imaging of the healthy human thumb of one volunteer (co-author, Niels Møller Israelsen). Informed consent was obtained from the volunteer. This instrument was used for a larger clinical study including healthy volunteers from the Department of Dermatology at Bispebjerg Hospital, University of Copenhagen, study established in accordance with Helsinki II Declarations. All methods employed for imaging were performed in accordance with guidelines and regulations as described in the research protocol approved by the Ethics Committee of The Capital Region of Denmark, no.
Acknowledgements The authors would like to thank:  EPSRC grant REBOT  ( EP/N019229/1/) ,  ERC-POC ERC ADASMART 754695 ,  Marie-Curie Intra-European Fellowship for Career Development 625509, UBAPHODESA Marie Curie Industrial Doctorate  ( 607627 ),  NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust  and the  UCL Institute of Ophthalmology , the  Royal Society Wolfson  research merit award and the  Innovation Fund Denmark  through the project  ShapeOCT  (No. 4107-00011A ).
Magnetic and Electrical Property Measurements. A Quantum Design MPMS XL SQUID magnetometer was used to carry out magnetization measurements. Electrical resistivity measurements were carried out with a Quantum Design PPMS. Crystal and Magnetic Structures. HPHT reaction products were initially characterized by powder X-ray diffraction collected with a Bruker D2 diffractometer using Cu Kα radiation. High resolution powder synchrotron X-ray diffraction (PSXRD) data were collected at the ID22 beamline of the ESRF with incident wavelength 0. 39994 Å. A glass capillary with an outer diameter of 0. 3 mm was used to contain the polycrystalline sample of approximately 8 mg. Low temperature diffraction data were collected from 5 to 90 K using a liquid helium cryostat system and from 90 to 400 K with an Oxford Cryosystems nitrogen cryostream.
High resolution time-of-flight powder neutron diffraction (PND) data were collected at the WISH beamline of the ISIS facility, with 50 mg of powder from several highpressure syntheses packed into a vanadium can. Diffraction patterns were collected between 10 and 400 K using a closed cycle refrigerator (CCR) with a hot stage. The crystal and magnetic structures of CoFe3O5 were Rietveld-fitted using the Full-Prof Suite and General Structure Analysis System (GSAS),  15 , 16  and images were generated using VESTA. 17.
Experiments Data loggers, model EL-USB-2 (Lascar, Whiteparish, Wiltshire, Great Britain), were placed in one bag of each treatment to record temperature and relative humidity over the course of the experiments. Another data logger was placed outside to measure the ambient environmental conditions. Oxygen and carbon dioxide levels were monitored using a Mocon PAC Check Model 325 Headspace analyzer (Mocon, Minneapolis, MN, USA) fitted with a 20-gauge hypodermic needle for sampling through rubber septa or through the walls of the storage bags. We sealed punctures in bag walls with patches of electrician's tape. Oxygen and carbon dioxide data was collected from the second day of the experiment (November 27, 2015) until March 18, 2016 at which point some PICS bags had begun losing their airtightness.
The initial bruchid infestation level in the cowpea grain was assessed at the beginning of the experiment by randomly collecting 64 samples of 500 g each. Each 500 g sample was sieved to separate and count dead and live adults. Pupae were counted as adults. Three random samples of 100 seeds were picked from each 500 g sample and soaked in water for 15 min to soften the grains. The water-imbibed seeds were cracked and opened to count the number of living and dead or desiccated larvae, pupae, and adults. At the end of the experiment, 18 samples of 500 g and 54 samples of 100 grains per each treatment were evaluated for dead and live larvae, pupae, and adults. Data collected was recorded in Excel for calculating mean and standard errors. For temperatures and relative humidity, daily averages were determined as well as the correlations between the treatments and prevailing environmental conditions (temperature and relative humidity).
After thermal stabilization, the temperature was then slowly increased at 0. 3 K min -1 and the extreme of the δχMT /δT versus T plots gave the T(TIESST) values. Single crystal X-ray diffraction data for the structure determination of the three complexes were collected using a Bruker-Nonius diffractometer κ-CCD (λ = 0. 7170 Å) at 300 K and 120 K to mimic the data published for the iron analogue. 26d  The crystal structures were determined and refined using SHELX-97 and SHELX-2013  33  within the WinGX environment. 34. Cif files were deposited at CCDC under the numbers CCDC 1849970-1849974. All the crystal structures are of very good quality (table  SI2-SI4 ). The powder X-Ray diffraction were performed on a PANalytical X'Pert Pro diffractometer.
In consequence, the transition between HS and LS2/HS3 45 states can be hidden if we consider the samples with x  0. 892. For this reason, we have decided to investigate in more detail the hidden transition, i. e. to probe by thermal relaxation and/or light irradiation to study whether the predicted HS to LS2/HS3 transition may appear. The work is currently in progress. Nouvelle Aquitaine and by the LabEx AMADEus (ANR-10-LABX-42) within IdEx Bordeaux (ANR-10-IDEX-03-02), i. e. the Investissements d'Avenir programme of the French government managed by the Agence Nationale de la Recherche. The ANR is also warmly acknowledge (ANR femtomat n° 13-BS04-002). The UMS PLACAMAT is acknowledged for 65 the microprobe measurements.
Experimental Protocol and Data In the first set of experiments, C57BL/6 mice were intravenously infected with 10 6 infected red blood cells (iRBC) taken from mice infected either with wild-type PbGFP Luc con (P. berghei line 676m1c11) (WT), a GFP-luciferase transgenic derivative of P. berghei ANKA  (Franke-Fayard et al. , 2005) , or the mutant PbmaLS_05 (-) parasites (KO) generated in the wild-type PbGFP Luc con strain  (Fernandes et al. , submitted manuscript). An additional group of age-matched mice was left uninfected and treated as naïve controls. Daily blood samples of 10 µl were taken from all mice from the day of infection until day 4 post infection (p. i. ). The total red blood cell count and reticulocyte percentage were measured using a Coulter counter and FACS analysis of CD71 (CD71-PE, eBioscience, Clone R17217) labeled reticulocytes, respectively.