dataesr/scientific-paragraphs-categorization huggingface dataset:
25% paraformaldehyde for 30 minutes at 4°C. The fi xed cells were permeabilized after washing with PBS containing 0. 05% Tween 20 and 1% FBS for 15 minutes at 37°C. Cells were then washed twice by centrifugation with PBS-1% FBS and labeled with a PE-conjugated antibody recognizing the active form of caspase-3 (clone C92-605, BD Bioscience) or a FITC-conjugated antibody recognizing a degradation product of PARP (clone 214/216, Biosource, Camarillo. CA, USA) for 30 minutes at 4°C. Flow cytometry was carried out on a FACSCalibur (BD Bioscience) and data analysis was carried out using CELLQuest software.
Patient Recruitment and Screening Evaluations Preliminary data on the safety and effi cacy of MCWF instilled in the bladder after dilution in saline was performed at a single veterinary site in Brazil (Estima Veterinary Hospital, Taubaté, Brazil). An experimental study protocol (protocol # BNC01-082011-CCAU) was developed in accordance with the Canadian Council on Animal Care (CCAC), and was reviewed and approved by the research ethics committee at the participating site. Signed informed consent was obtained from the owners whose dogs were recruited for the study. Dogs with histologically confi rmed TCC were completely staged using 3 view thoracic radiographs and abdominal ultrasound. Inclusion criteria allowed enrolment of the dogs with tumor recurrence following surgery and/ or chemotherapy or when owners declined standard treatment.
Patient selection Patients who presented to the Oncology Center from Hospital Sírio-Libanês (HSL) and Instituto do Câncer do Estado de Sao Paulo (ICESP) after definitive breast surgery from March 2000 through June 2013 and were treated with adjuvant TC regimen were included in our analysis. A retrospective review of the medical records charts from these patients was performed. Data abstracted included age at diagnosis; race; BMI (body mass index); performance status (ECOG); associated comorbidities; tumor pathological staging; tumor grade and histology, neutropenia and FN rates, use of granulocyte colony stimulating factor (G-CSF), either before (primary prophylaxis) or after a documented FN event (secondary prophylaxis). Data on other previous chemotherapy for the current BC diagnosis as well as cytotoxic chemotherapy treatment for other previous malignancies were also collected.
Statistical analysis Patient characteristics were summarized using frequency distributions and percentages. All statistical analyses were carried out using SPSS for Windows Version 13. 0. Chi square test was used to correlate a FN episode with the categorical variables. Binomial test was used to compare proportions in one sample. Student's t-test was elected to equate a FN episode in relation to numerical categories. We considered a p-value less than 0. 05 to be statically significant.
FN episode and G-CSF use Among the 95 patients included in our analysis, data on G-CSF administration was available in 85 of them. G-CSF was used as primary prophylaxis in 31 (70. 5%) patients and in 13 patients as secondary prophylaxis, following a prior diagnosis of febrile neutropenia. Overall, fifteen women (15. 8%) had a documented FN episode. Among women who received G-CSF as primary prophylaxis, the rate of FN was 6. 45% (2 patients). In contrast, among patients who did not receive primary prophylaxis with G-CSF, the FN rate was considerably higher, namely 24. 07% (13 patients). Patients who received primary prophylaxis with G-CSF had a statistically significant lower risk of experiencing a FN episode (p=0. 049). Table  2  demonstrates this finding.
Sperm Characteristics Measured by Flow Cytometry. Flow cytometric analyses were performed on a Guava Easy-Cyte 5 (Merck KGaA, Darmstadt, Germany) cytometer. The fluorescent probes used in the experiment were excited by an Argon ion 488 nm laser. Acquisitions were done using the GuavaSoft6 3. 1. 1 software (Merck KGaA, Darmstadt, Germany). The nonsperm events were gated out based on scatter properties and not analyzed. A total of 10,000 events were analyzed for each sample. (1) Plasma Membrane Integrity. Sperm membrane integrity was assessed by Live/Dead Sperm Viability Kit: SYBR-14, propidium iodide (PI) (Life Technologies Ltd. , Grand Island, NY, USA), according to the protocol described by Partyka et al. [33]. The diluted samples (300 L) were stained with 5 L of SYBR-14 and 5 L of PI. Sperm SYBR-14 positive showing green fluorescence and PI negative were considered as plasma membrane intact (PMI) live sperm.
02°2Ɵ step and an angular range from 5 to 100°. Crystalline phase determination was carried out using International Center for Diffraction Data database (ICDD)  24  and the Xpert High Score plus software (PANalytical, Almelo, the Netherlands) for phase matching. 25  Determination of lattice parameters was carried out using a full-pattern matching method (Le Bail function) with the help of the Fullprof suite program. 25  Finally, phase ratios were determined by Rietveld refinement using Xpert High Score software. Sample observations on polished cross sections with 1 lm surface finish, were carried out in a scanning electron microscope (SEM) Auriga (Zeiss, Oberkochen, Germany), under back-scattering electron (BSE) and secondary electron (SE) imaging modes, equipped with an energy-dispersive spectroscopy (EDS) detector with ultra-thin polymer window (Oxford Instruments, Oxford, UK).
| Theoretical method The plane wave DFT code CASTEP,  26  was used with exchange and correlation interactions being formulated by employing the corrected density functional of Perdew, Burke and Ernzerhof (PBE)  27  in the generalized gradient approximation (GGA) and in conjunction with ultrasoft pseudopotentials. 28 The virtual crystal approximation (VCA) was used initially to model disorder in these cells; this is an effective medium method that can be used to model disordered alloys. 29 In VCA disorder is introduced by assigning partial occupancies to each atomic site of the disordered sublattice. A disadvantage of the technique is the assumption of a homogeneous distribution of atoms on the disordered sublattice and this does not consider the possibility of clustering. For all the VCA calculations, the unit cell was relaxed to a stress of less than 50 MPa using the algorithm of Pfrommer et al.
| Population analysis and theoretical hardness The population analysis in density functional theory using the CASTEP module is performed with a projection of the plane wave states onto a localized basis by means of a method developed by Sanchez-Portal et al. 43  Population analysis of the resulting projected states is executed via the Mulliken formalism. 44 This method is extensively used in the analysis of electronic structure computations with the Linear Combination of Atomic Orbitals (LCAO) basis sets. In addition to providing a relevant condition in favor of bonding between atoms, the overlap population can be used to judge the covalent or ionic character of a bond. The bond population with a high value is a sign of a covalent bond, while a low value signifies an ionic interaction. The bonding and antibonding states are due to positive and negative bond overlap populations respectively.
ACKNOWLEDGMENTS E. Z. S, A. T. , and W. E. L. work was funded as part of the  EPSRC Carbides for Future Fission Environments (CAFFE)  consortium ( EP/M018563/1 ;  EP/M018768/1 ). A. C. and D. C. P. are grateful for funding from the  Lloyd's Register Foundation , a charitable foundation helping to protect life and property by supporting engineering-related education, public engagement, and the application of research.
Independent Validation Cohort Patients for the independent cohort were taken from a database maintained at the Dana-Farber Cancer Institute (DFCI) in Boston, Massachusetts. This overall cohort has been described elsewhere. 16, 17 None of these patients was part of the development cohort. Briefly, beginning in 2006, adult patients with biopsy-confirmed MDS presenting for initial evaluation at DFCI (hereafter denoted as "baseline" for the DFCI cohort) were eligible for enrollment into the Dana-Farber/Harvard Cancer Center MDS Clinical Research Information System database; 85% of eligible patients consented to enrollment. Starting in 2011, an ongoing effort was made to enrich the database for patients with higher risk disease. 18 Patients enrolled through October 2016 were included in this analysis.
The Clinical Research Information System database includes clinical, pathologic, and laboratory data from the initial evaluation at DFCI, which was used to determine the original IPSS score for each patient. For this analysis, only those patients classified with IPSS intermediate-2 risk and high-risk disease were included. At baseline, enrolled patients also completed a series of HRQOL questionnaires. It is important to note that although their HRQOL assessment was performed concurrently with their assessment of having intermediate-2 or high-risk disease, patients could have been treated with agents other than supportive care before their presentation to DFCI, unlike the international cohort above.
Internal and external validation Discrimination and calibration were evaluated for both the development (internal validation) and independent application (external validation) data sets. Calibration was evaluated by estimating the standardized incidence ratio (SIR) and performing a goodness-of-fit chi-square test for the effect of risk group, using a Poisson regression modelbased approach. 24 SIR is the percentage of observed out of expected events from the prognostic index, with a value equal to 1 indicating the best performance. For external validation, calibration was evaluated by comparing the risk-stratified Kaplan-Meier survival estimates between data sets. All analyses were performed using SAS statistical software (version 9. 4; SAS Institute Inc, Cary, North Carolina).
The current study also has notable strengths. We developed a prognostic tool that can be implemented easily and inexpensively in clinical practice and that also possibly could enhance a more patient-centered approach during the initial diagnostic workup. In addition, unlike many other studies in this area that used secondary data analyses, the current study was specifically designed and adequately powered to test the prognostic value of fatigue severity for survival. Patients also were recruited in a multicenter and international observational setting, lending further credit to the generalizability of the current study findings to patients typically seen in clinical practice. Finally, the FA-IPSS(h) index outperformed the original IPSS index both in the development and independent cohorts, and validation data were independently collected and analyzed.
1 μm) sends light to each of the focal planes. MVIC has seven separate detectors, six time-delay integration (TDI) CCDs, and one frame transfer CCD. Four of the TDI CCDs are used for color observations; the other focal planes provide panchromatic imaging capabilities. When a color observation is executed, New Horizons data are recorded from all four color TDI arrays simultaneously. Each TDI array has 32 × 5000 optically active pixels  (Reuter et al. 2008). There are three broadband channels: blue, red, near-infrared, and a narrow band methane channel (Table  1 ). The narrow band channel is called the methane channel because it is sensitive to methane ice absorptions at 890 nm. The responsivity of each of the MVIC channels is described in  Howett et al. (2017).
Reduction The raw images from the spacecraft were processed using the following steps. 1. The raw images have a bias level subtracted from the raw counts. The bias level is a fixed number that depends on the focal plane array and electronics side used for the observation and is given in Table  3. 2. Each row of the image is divided by a one-dimensional flat-field array (5000 elements long) to remove flat-field effects. The bias subtracted and flat-fielded images are archived on the Planetary Data Systems Small Bodies Node. 3. Model and remove the low-level (approximately 2 DN) pattern noise. The noise has a striped pattern that aligns with the row direction of the detector locally, but it is not consistent across the whole field of view. Using the pixels adjacent to the Pluto image, a model for the pattern noise can be determined and removed.
The finite scan rate combines with spacecraft and target motion so that each of the MVIC colors images a point on the target from a slightly different point of view, so the geometry is a little different. Thus, each color channel is treated as an independent instrument and registered to the relevant Pluto and Charon base maps separately  (Schenk et al. 2016 ). After they are all registered to the base map, they can be reprojected to a common geometry. To perform this task, we used version 3. 5. 0. 7383 of the Integrated Software for Images and Spectrometers (ISIS3) package from the United States Geological Survey and selected the geometry for the BLUE filter as our target geometry for each scan. As this involves resampling, we sub-sampled to a finer grid approximately a factor of two finer than the original pixel scale to minimize loss of spatial information.
Transcriptome Assembly and SNP Calling A set of predicted cDNA was obtained following the workflow of  Cahais et al. (2012). Contigs shorter than 200 base pairs were discarded. Open reading frames (ORFs) were predicted using the script transcripts_to_best_scoring_ORFs. pl, which is part of the Trinity package (see a summary of the contig assembly in table 2). The reads were mapped to the predicted cDNA using BWA  (Li and Durbin, 2009). More specifically, we used BWA ALN for read mapping with the command line bwa aln -n 0. 04 -o 1 -e -1 -d 16 -i 5 -k 1 -t 4 -M 10 -O 11 -E 4. For each position of each contig and each individual, genotypes were called using the reads2snps method developed by  Tsagkogeorga et al. (2012)  and  Gayral et al. (2013). This method includes a module for detecting hidden paralogy, which in the case of RNA-seq data manifests via an excess of heterozygous genotypes and positive across-individual correlation in read counts  (Gayral et al.
Contig Annotation We used a homology search to identify the contigs located in cytoplasmic genomes (i. e. , chloroplast or mitochondrial genomes). We used two reference sequences from close relatives to thyme: the Origanum vulgare chloroplast genome (114 genes, NCBI accession number JX880022,  Lukas and Novak, 2013)  and Salvia miltiorrhiza mitochondrial genome (167 genes including 138 protein coding genes, NCBI accession number NC_023209. 1, Qian et al. , 2013). A blastn with default parameters and an identity threshold set to 95% was applied to the ORF-containing subset of our de novo assembled contigs using the two reference sequences as search databases. Contigs matching any of these reference sequences were annotated as cytoplasmic contigs and analyzed separately for SNP calling. This was done by using the reads2snps program  (Gayral et al.
We then used custom-made scripts to merge the cytoplasmic contigs into a concatenated sequence, with an option to filter out contigs with traces of heterozygosity. We also examined whether any contigs in our transcriptome displayed homology to the pentatricopeptide repeat gene family that contains known nuclear restorers  (Kotchoni et al. , 2010; Touzet and Meyer, 2014)  but no such contigs were found (data not shown). Blastn and blast2go  (Conesa et al. , 2005; Bethesda, 2008)  were used on the fasta sequences of the identified candidate contigs to determine their putative functions, along with web searches on the returned results in Genbank.
3 ), which is incompatible with the positive TD predicted by Reciprocal homology searches using mitochondrial or chloroplast sequences as Query/Database were performed to assess the amount of genes that shared exhibited shared homology between these two genomes. FIG. 3 -Genome-wide distribution of Tajima's D statistic in the nuclear (blue histogram) genome versus cytoplasmic contigs (red: mitochondrial genome; green: cytoplasmic genome; orange: supercontig). Tajima's D for the chloroplasts lies in the 0. 0089th quantile of most negative values observed in the nuclear genome. Tajima's D for the mitochondria lies in the 0. 0027th quantile of most negative values. scenario B (maintenance of CMS alleles via balancing selection), but consistent with scenario A, in which a new CMS lineage has recently swept to fixation.
Hypnic headache Comments Reports of hypnic headache in children are scarce. The hallmark of the headache is the intensity which rouses from sleep, often at the same time, on a nightly basis. The ICHD-2 age requirement of onset after age 50 years was eliminated in the ICHD-3. A recent literature review of six children with hypnic headache (HH), was used to evaluate the validity of the ICHD-3 criteria in children. There are important differences in children with HH compared to adults which required more data without any limitation of ICHD-3  [3, 73, 74].
Limitations of this paper In pediatric medicine, the age of the patient and the education of the parents may affect the reliability and validity of the diagnosis. There may also be differences in diagnostic accuracy by language and culture. This paper is based on the data reported in the literature and the personal experience of pediatric headache specialists. The use of interviews, standardized questionnaires and diaries is another important source of variation in the assessment of headache in children and adolescents. We did not use a common database to calculate the validity, sensitivity, or specificity of the ICHD-3 beta criteria. We are planning to organize a prospective, language-adapted study supported by clinical assessments of video-taped interviews. Furthermore, some of our comments were restricted by a sparsity of data or absence of knowledge on the applicability of specific aspects/points to the pediatric population.
Microarray Analysis Based on monoterpene accumulation during berry development in 2006 (Figure  2 ), five time points were chosen along this season (Figure  1  and Table  1 ). Total RNA was extracted from grape skins using the Spectrum TM Plant Total RNA Kit (Sigma-Aldrich, St. Louis, Missouri, USA). RNA quantity and quality were evaluated with a NanoDrop ND-8000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, Ontario, Canada). Microarray experiments were carried out with a 70-mer oligoarray containing all 14,562 probes from the Array-Ready Oligo Set TM (AROS) for the Grape (Vitis vinifera) Genome version 1. 0 (Operon Biotechnologies, Huntsville, Alabama, USA). At the time this platform represented a good compromise between genome coverage, cost and computational effort required for data analysis.
The metabolites were quantified by using solid SPE-HRGC-MS and referring to the internal standard 1-heptanol. The lines connecting data points were smoothed through the specific option provided by Excel. hybridization and scanning are described in Supplementary Data1: Method S2. Spot intensities were quantified with the software MAIA 2. 75  (Novikov and Barillot, 2007). After excluding poor quality spots due to bad spotting (e. g. , spots with irregular shapes or highly unequal intensity distributions), median intensity gene expression data without background subtraction were normalized by a global lowess method followed by a print-tip median method with a modified version of the Goulphar script version 1. 1. 2 (Lemoine et al. , 2006). Differentially expressed probes (DEPs) with a false discovery rate (FDR) < 1% and a cutoff of 2-fold change (FC) were identified with the R/Bioconductor Limma package using linear models  (Smyth, 2004)  and taking into account biological and technical replicates by doing a twofactor analysis.
Probe Functional Annotation The 70-mer probes spotted on the Grape AROS V1. 0 array represent 14,562 transcripts from The Institute for Genomic Research (TIGR) Grape Gene Index (VvGI), release 3  (August 13, 2003). The corresponding annotation is based upon a match between each oligo and the gene set of the 12X version of the grape genome at CRIBI (http://genomes. cribi. unipd. it/grape/) and is publicly available at GEO (http://www. ncbi. nlm. nih. gov/geo/) under the accession number GPL15453. Since this annotation provides every oligo with a text description but doesn't associate it to any gene prediction identifier, we independently achieved this information by blastN alignment against the grape gene sets at CRIBI (http://genomes. cribi. unipd. it/grape/, 12X version of the genome, V1 gene prediction, annotation from  Grimplet et al.
Microarray Validation via Real-Time PCR Real-time quantitative reverse transcription-PCR (qRT-PCR) was used to validate the microarray results. Since RNA from berries collected in 2006 was no more available, new samples (with three biological replicates from pooled berries) as closest as possible to those analyzed in 2006 were obtained in 2016 by adopting the same sampling procedure and the same protocol for RNA extraction. Primers for the amplification of unique PCR products from 70 to 250 bp were designed on 15 Vitis vinifera gene predictions perfectly matching with the microarray 70-mers by using Primer3  (Untergasser et al. , 2012) , as reported in Supplementary Table  S3. Details for the amplification reaction and expression analysis are described in Supplementary Data1: Method S3. The relationship between microarray and qRT-PCR data was established through Pearson correlation.
Integration of 2006 Transcriptomic and Metabolic Data Different approaches were tested in order to discover transcripts linked with the accumulation of one or more metabolites. In a first identification step of candidates, the most stable expression changes were preferred to the biggest ones, hence the microarray probes with adjusted p-values < 0. 05 in all comparisons were considered, irrespective of their fold change  (4, 450). Working at probe level instead of gene level was chosen for two main reasons: (1) different probes supposedly matching to the same gene (especially long genes) often show different expression values, which might be an indicator of alternative transcription and (2) the sequence specificity to CRIBI 12X gene predictions is not optimal for a number of probes spotted on the AROS array (this is especially true for probes related to secondary metabolism); for a detailed assessment of probe specificity, Moscato Bianco genome and transcriptome assembly would be required, which is out of the scope of this work.
Soft clustering Soft clustering of the metabolite and transcript differentials was performed by using the R/Bioconductor Mfuzz package  (Kumar and Futschik, 2007)  with the default value 1. 25 for the fuzzy parameter m. A membership value in the range of 0-1 was assigned to each metabolite and probe. Soft clustering offers several advantages with respect to hard clustering; in particular, it has been suggested to be more suitable for time course microarray data in which expression patterns are often not well separated  (Futschik and Carlisle, 2005; Kumar and Futschik, 2007). The biological significance of the clusters was analyzed by enrichment analysis of the MapMan functional categories assigned to the probes in each cluster. Specifically, Chi square and Fisher statistical tests were employed to search for significant differences (p-value < 0.
Microarray Validation via Real-Time PCR Specific primers were designed for 15 candidate genes and the change in their expression during berry development was analyzed in skin tissues by qRT-PCR to validate the microarray dataset (Figure  4 ). A strong relationship was found between the microarray and qPCR fold changes in the expression levels of the 15 genes (overall Pearson correlation coefficient r = 0. 84, with individual values ranging from 0. 47 to 1), indicating the reliability of the whole transcriptome assay (Figure  4  and Supplementary Table  S3 ).