dataesr/scientific-paragraphs-categorization huggingface dataset:
Optical studies also report a twocomponent rise time (72 ps and 640 ps) at wavelengths characteristic of the photoisomerization product  23. Although a quantitative kinetic comparison of the two datasets is not particularly informative due to their different sensitivities (the optical absorption is attributed only to 1 G O formation and the S K-edge difference signal is attributed to formation of all Obonded excited and ground state species), they are consistent in reflecting the fast creation of O-bonded species. The slow rise in optical absorption was attributed to conformational relaxation of the isomerized complex; however the slow rise in S K-edge difference signal cannot be attributed to such structural changes as it is sensitive only to the Ru-S bond length which is not predicted to change significantly after formation of the  3  MC O species (Supplementary Table  1 , Supplementary Fig.
Methods Experimental procedures. X-ray absorption measurements were performed at the time-resolved beamline 6. 0. 1 of the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory. Synthesis of [Ru(bpy) 2 (pyESO)](PF 6 ) 2 followed published procedures  23. The sample was dissolved in propylene carbonate (15 mM), which was continuously refreshed using a sapphire nozzle liquid jet (50 um thickness) in a He atmosphere. The undulator beamline is equipped with a chopper running at 4 kHz, thus reducing the average X-ray flux and determining the data acquisition rate. A double crystal Si(111) monochromator produced monochromatic X-rays tunable around the Ru L 3 -edge (~2840 eV) and S K-edge (~2470 eV) with 0. 35 eV resolution. Two ALS filling modes were used: "multibunch" for the Ru L 3 -edge (276 electron bunches spaced by 2 ns and one so-called "camshaft" bunch separated by a 100 ns filling gap), and "two-bunch" mode for the S K-edge (two "camshaft" bunches separated by 328 ns).
Acknowledgements This work was supported by the  U. S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. This research used resources of the  Advanced Light Source ,  Lawrence Berkeley National Laboratory , which is a  DOE Office of Science User Facility. T. K. K. acknowledges funding from the  National Research Foundation (NRF)  grants, funded by the  Ministry of Science and ICT  (No. 2016K2A9A1A01945137 ,  2016R1E1A1A01941978 ,  2014R1A4A1001690 , and  2016K1A4A4A01922028 ). N. H. acknowledges funding from the  Max Planck Society , the  City of Hamburg , and the  German Science Foundation (DFG)  through the  SFB 925  " Light induced dynamics and control of correlated quantum systems ". J. J. R. and K. G. acknowledge funding from the  National Science Foundation  ( CHE 0947031 ,  CHE 1112250 , and  CHE 1602240 ).
Gel Permeation Chromatography/Size-Exclusion Chromatography (GPC/SEC) Characterization The analyses were made in an HPLC Waters chromatograph containing a Waters 515 isocratic pump and a Waters 2414 refractive index detector. In this apparatus, the oven was stabilized at 35 • C and the elution of samples was carried out through two PolyPore columns (Agilent, Santa Clara, CA, USA), protected by a PolyPore Guard column (Agilent). The software Empower ® performed the acquisition and data processing. THF was used as the eluent, at a flow rate of 1. 0 mL min -1. Before use, the solvent was filtered through 0. 45 µm of PTFE membranes Fluoropore (Merck Millipore, Burlington, MA, USA) and degassed in an ultrasound bath for 45 min. The oligomer/polymer samples were also filtered across 0. 20 µm PTFE filters Durapore (Merck Millipore).
The data are expressed as the mean and the respective standard deviation (mean ± SD) of 6 experiments. The statistical evaluation of data was performed using one-way analysis of variance (ANOVA). The Tukey-Kramer multiple comparison tests (GraphPad PRISM 5 software, GraphPad Software Inc. , La Jolla, CA, USA) were used to compare the significance of the difference between the groups; a p < 0. 05 was accepted as statistically significant.
Funding: The authors gratefully acknowledge the support of  CERENA  and CQE strategic projects ( FCT-UID/ ECI/04028/2013  and  UID/QUI/00100/2013 , respectively) funded by the  Fundação para Ciência e a Tecnologia (FCT) , Portugal. B. S. G. V. , R. G. S. and C. S. B. G. also acknowledge  FCT  for fellowships ( SFRH/BD/78962/2011 ,  SFRH/BPD/105662/2015  and  SFRH/BPD/107834/2015 , respectively).
Acknowledgments M. C. acknowledges the  University of Basilicata  for the hospitality during their research stages. A. G. M. thanks the  University of Rome "La Sapienza"  for financial support through the  Ateneo  Project  2015  ( C26A152T5M ). S. B. thanks the  University of Basilicata  for the funding through the RIL 2015 grant. ORCID Sergio Brutti https://orcid. org/ 0000-0001-8853-9710.
Zelda bypasses transcriptional memory. Our ability to track transcriptional activation in live embryos provided the opportunity to determine activity through multiple nuclear cycles. Using the sensitized snaE transgene, we recently documented the existence of a transcriptional mitotic memory, whereby the transcriptional status of mother nuclei at nc13 influences the timing of activation of the descendants in the following cycle  14. To address the challenge of following rapid movements during mitosis, we developed a semi-automatic mitotic nuclei tracking software (Fig. 2a ). By combining lineage information with transcriptional status, we quantified the timing of activation of hundreds of nuclei in nc14 in a spatially defined domain. This allowed us to distinguish those transcriptionally active nuclei that arose from an active mother nucleus (green curves, Fig.
The time of each jump from one state to another is provided by the parameter 'b'. Parameters of this model are predicted separately for nuclei coming from active and inactive mothers. The parameter fitting is based on Cdf of the random time to transcription in nc14 (t) (see also Supplementary Equation 1 Supplementary Methods). b Cdf of the random time to transcription in nc14. The origin of time is the end of mitosis nc13 to nc14, (determined by our automatic software, see "Methods" section) added to the time required to detect the first activation (proper to each genotype). Data (cross) are compared to predictions (solid curves) for nuclei, resulting from active (green) and inactive (red) mothers. c, d Mean 'a' parameter; error intervals correspond to the variation among optimal and best suboptimal fits (see Supplementary Methods and Supplementary Data 1).
Dostatni (Supplementary Fig. 7 ). Extra Zld-binding sites (consensus sequences CAGGTAG) were added to the wt snaE enhancer by PCR using the primers indicated in Supplementary Data 3. Insertion of an extra Zld-binding site in the middle of the snaE enhancer was done by directed mutagenesis using primers indicated in Supplementary Data 3. All transgenic MS2 flies were inserted in the same landing site (BL9750 line) using PhiC31 targeted insertion  39. Live imaging. Embryos were dechorionated with tape and mounted between a hydrophobic membrane and a coverslip as described in  14. All movies (except when specified) were acquired using a Zeiss LSM780 confocal microscope with the following settings: GFP and RFP proteins were excited using a 488 nm and a 561 nm laser respectively. A GaAsP detector was used to detect the GFP fluorescence; a 40x oil objective and a 2.
1 zoom on central ventral region of the embryo, 512 × 512 pixels, 16 bits/pixel, with monodirectional scanning and 21z stacks 0. 5μm apart. Under these conditions, the time resolution is in the range of 22-25 s per frame. Two and one movie respectively for snaE + 3Zld in white-RNAi and zld-RNAi background were acquired on a Zeiss LSM880, keeping the time resolution is in the range of 21-22 s per frame. Image processing of LSM780 and LSM880 movies of the MS2-MCP-GFP signal were performed in a semi-automatic way using custom made software, developed in Python TM. Live imaging of GFP-zld/ + ; His2Av-mRFP/ + and GFP-bcd/ + ; His2Av-mRFP/ + embryos were performed using a Zeiss LSM780 confocal microscope with the following settings: GFP and RFP proteins were excited using a 488 nm and a 561 nm laser respectively.
To minimize the effect of mobile fraction on C eq , M was kept between 0. 9 and 1. 1. Diffusion coefficients of the different molecules were determined according to D ¼ βw 2 4τ ð8Þ with w the value of the radius at 1/e 2 of the Gaussian beam (in our case, w = 0. 56 µm or 0. 4 µm) and β a discrete function of K tabulated in ref. 44. F exc (t) is defined as in ref. 29  , slightly modified with respect to the Gaussian illumination, leading to the following equation: F exc t ð Þ ¼ F 1 À ð 1 À e ÀK K À F 1 Þe Àk off t ð9Þ with K defined as previously. Fluorescence correlation spectroscopy. FCS experiments were performed on a Zeiss LSM780 microscope using a 40x/1. 2 water objective. GFP was excited using the 488 nm line of an Argon laser with a pinhole of 1 airy unit. Intensity fluctuation measured for 10 s were acquired and auto-correlation functions (ACFs) generated by Zen software were loaded in the PyCorrFit program  45.
Multiple measurements per nucleus, in multiple nuclei and embryos at 20 °C were used to generate multiple ACF, used to extract kinetic parameters. The FCS measurement volume was calibrated with a Rhodamine6G solution  46  using D f = 414 μm 2. s -. Each time series was fitted with the reaction dominant model  29  : G D τ ð Þ ¼ 1 2 3=2 N F eq 1 þ τ τ D f ! À1 1 þ τ ω 2 τ D f ! À1=2 þ 1 2 3=2 N C eq e Àk off τ þ G 1 ; ð10Þ where F eq = k off / (k off + k * on ), C eq = k * on / (k off + k * on ), τ Df = w 2 xy / 4 μ D f and ω = w z / w xy. For each correlogram the value of k* on , k off and D f (reaction constants and diffusion coefficient) were estimated using the PyCorrFit program implemented with Eq. 10. Photophysics of the dye was neglected and we introduced a G ∞ value to account for long time persistent correlation during the measurements.
Acknowledgements We are grateful to  T. Fukaya  for sharing the MCP-eGFP-His2Av-mRFP fly stock. We thank  L. Ringrose  for sharing Ash1-GFP fly stocks,  C. Rushlow  for  Zelda-RNAi  fly stocks and  N. Dostatni  for plasmids and eGFP-Bcd fly stocks. We thank  G. Cavalli  for providing the anti GAF antibody. We thank  M. Bellec ,  L. Ciandrini ,  E. Bertrand ,  R. Feil  and  T. Forné  for helpful discussions and critical reading of the manuscript. We acknowledge the imaging facility MRI, member of the national infrastructure  France-BioImaging  supported by the  French National Research Agency  ( ANR-10-INBS-04 ,  «Investments  for the future». A. T was a recipient of a  FRM fellowship  and is currently sponsored by the  SyncDev ERC  grant. Work in the lab of M. H. was supported by  NIH   R01GM111694.
Case Studies of the Republic of Côte d'Ivoire and the Democratic Republic of the Congo Purpose In most low-income countries, the diagnosis of retinoblastoma is delayed, resulting in a severe prognosis. The objectives of this study were to describe the access to diagnosis and care of children diagnosed with retinoblastoma and the challenges in two sub-Saharan African countries: the Republic of Côte d'Ivoire and the Democratic Republic of the Congo. Patients and Methods A descriptive cross-sectional study was conducted. Data were collected from the medical records of patients admitted during the period of January 1, 2013 to December 31, 2014. Data were entered and analyzed using Epi Info7. 1 software and SAS 9. 3. Results One hundred sixteen cases of retinoblastoma were collected, including 60 boys and 56 girls.
Collection and Analysis of Data Patients' medical records were reviewed by completing a similar form in all centers. Parents (one or both) or caregivers were interviewed in all cases to collect additional information. The pediatrician or ophthalmologist in each unit was responsible for the completion of the study. The main variables included and analyzed were: date of birth, sex, age at diagnosis, family history of retinoblastoma, laterality, place of diagnosis, date of diagnosis, form of retinoblastoma (intraocular or extraocular), first symptom and the date of its appearance, date of first health professional consultation and stage of the disease according to the International Retinoblastoma Staging System classification of retinoblastoma,  26  outcome, treatment achieved, average cost of treatment, parents' marital status, and level of education of the parents.
The time to diagnosis was defined as the time that had elapsed between the date of the first symptom/sign of retinoblastoma and the date when the diagnosis was confirmed by the ophthalmologist/pathologist. The time to treatment was defined as the time that had elapsed between the date of diagnosis and date of the treatment initiation. Entry and data analysis were conducted in the Epi Info 7. 1 and SAS 9. 3 (SAS Institute, Cary, NC) software.
ACKNOWLEDGMENT We thank the  Global Alliance Against Cancer  (http://www. cancer-amcc. org),the  Institute Curie  (https://www. institut-curie. org/),and the  Franco-African Group of Pediatric Oncology  (http://www. gfaop. org/)for the realization of a retinoblastoma project in sub-Saharan Africa. We also thank  Pierre Gilles de Genes Foundation  (http://www. fondation-pgg. fr/), which contributed to the development of this research project. In particular, we thank  Drs. Jean Michon ,  Brigitte Lacour , and  Alexia Savignoni , as well as the medical and paramedical staff of the  Institut Curie and Lubumbashi University Clinics  for their contribution to this study.
Tubes were vortexed and centrifuged as previously described and 1 µl was injected into the gas chromatograph. To quantify SCFAs, a calibration curve for the concentration range of 0. 015-1 mg/ml was constructed. SCFAs measurements were performed following a recently published protocol  41  : chromatographic analyses were performed using an Agilent 6850 system with ExChrom software, equipped with a 7683B automatic liquid sampler, a flame ionization detector (FID) (Agilent Technologies, USA), and a fused-silica capillary RTX-WAX (Restec Corporation, U. S. ) with dimensions of 60 m × 0. 25 mm internal diameter (i. d. ) coated with a 0. 15-µm thick layer of polyethylene glycol. The initial oven temperature was 100 °C (hold 2 min), which was increased to 200 °C at a rate of 15 °C/min (hold 5 min).
The Q-Exactive instrument was operated in the data-dependent acquisition (DDA) to automatically switch between full scan MS and MS/MS acquisition. Survey full scan MS spectra (from m/z 300-1150) were analyzed in the Orbitrap detector with resolution R = 60,000 at m/z 200. The 10 most intense peptides were sequentially isolated to a target value of 3 × 10 6 and fragmented by high-energy collisional dissociation (HCD) with a normalized collision energy setting of 27%. The maximum allowed ion accumulation times were 20 ms for full scans and 50 ms for MS/ MS and the target value for MS/MS was set to 1 × 10 6. Standard mass spectrometric conditions for all experiments were as follows: spray voltage, 2. 4 kV; no sheath and auxiliary gas flow. MS data analysis and relative abundance profiling. Acquired RAW data were analyzed by MaxQuant(MQ) software v1.
5. 2. 8, using the Andromeda search engine  46. Uniprot Mouse database (70,902 entries) was used for peptide identification. Enzyme specificity was set to Arg-C. Estimated false discovery rate of all peptide identifications was set at a maximum of 1% (Decoy database-based approach). Mass tolerance for searches was set to a maximum of 6 parts per million (ppm) for peptide masses and 20 ppm for HCD fragment ion masses. A maximum of three missed cleavages was allowed. In the search, we focused on lysine methylation and acylation, including as variable modifications: D3-acetylation (+45. 0294 Da), D3-acetylation (+45. 0294 Da) plus monomethylation (+14. 016 Da), to manual inspection and validation using the viewer. exe module integrated in MQ software  47. Extracted ion chromatograms were constructed for each precursor based on the m/z value, using a mass tolerance of 10 ppm with a mass precision up to four decimals.
For each histone-modified peptide, the relative abundance percentage (RA%) was estimated by dividing the area under the curve (AUC) of each modified peptide over the sum of the areas corresponding to all observed isoforms of that peptide, including the unmodified forms  48. Significant changes among crypt Incubation of crotonate, acetate, or butyrate with or without HDAC1 followed by western blotting analysis with anti-H3K18ac/bt/cr. Western blot of HDAC1 and crotonate assay is representative of two western blots and colon versus small intestine fraction have been calculated with a two-way ANOVA test using the Perseus software  49. p-Value < 0. 01 (1% FDR) were considered as significant. Antibodies and western blot analysis. Anti-lysine crotonyl antibody (PTM-501, 1:5000), anti-crotonyl-histone H3 lys18 (anti-H3K18cr, PTM-517, 1:5000), and anti-butyryl-histone H3 lys18 (anti-H3K18bt, PTM-306, 1:5000) were from PTM BIOLABS; anti-tri-methyl H3 lys4 antibody was from Active Motif (anti-H3K4me3, Cat.
) was applied for 1 h at RT in blocking solution supplemented with DAPI. After 4 × 5 min washes in 1× PBS, samples were mounted in Vectashield H-1000 and sealed. Controls without the primary antibody were processed accordingly. Imaging was performed with the Zeiss780 confocal microscope using 20× air and 63× oil immersion objectives at optimal resolution settings. Z-stacks of whole sections were imaged and further processed to maximum projections with ImageJ software. For optimal print results background correction and contrast enhancement with up to 3% pixel saturation were performed with ImageJ. Cell culture and cell cycle analysis. Human colon carcinoma cells (HCT116) were a gift from Simon Cook's lab (Babraham Institute) who obtained them from Bert Vogelstein, John Hopkins University, Baltimore.
This cell line is not in the database of commonly misidentified cell lines (ICLAC). They were grown in DMEM media containing glucose and pyruvate, 10% FBS, 2 mM L-glutamine, 100 units/ml penicillin, and 100 µg/ml streptomycin. For the cell cycle analysis, HCT116 cells were blocked at G1 with 15 nM of abemaciclib (LY2835219, Seleck Chemicals) for 48 h and released by washing 2× with PBS and adding fresh medium. Class I HDAC inhibition was with 5 μM MS275 for 48 h. Cells were washed 2× with PBS and fresh medium supplemented with 1 μM MS275 was added. Cells were harvested at indicated intervals after release and one half was analyzed by western blotting. The remainder were used to determine cell cycle profiles with propidium iodide staining using the BD Pharmingen PI/RNAse staining buffer on LSRII Flow Cytometer (BD Biosciences) and Cell Cycle tool on FlowJo 10.
Real time qPCR analysis was carried out on input and ChIP DNA samples using the SYBR® Green PCR Master Mix (Applied Biosystems) and run on a BioRad CFX96 qPCR system. Each experiment has been carried out two times (biological replicates) and each sample has been run in triplicate (technical replicate). One percent of starting chromatin was used as input and data were analyzed accordingly. Primers were used at a final concentration of 250 nM with 62 °C as annealing/ extension temperature and are listed in Table  2. RNA-seq. RNA was extracted from both HCT116 cells (four biological replicates) and mouse colon epithelium (three mice as biological replicates) using the RNeasy Plus Mini Kit (Qiagen), following the manufacturer's instructions. Extracted RNA was quantified with Nanodrop and the quality assessed on a Bioanalyzer (Agilent).
Library preparation was performed from 500 ng of RNA using the NEB Next® Ultra TM Directional RNA Library Prep Kit for Illumina® and the NEBNext® Poly (A) mRNA magnetic isolation module. Illumina Tru-Seq adaptors were used and library amplification was performed with the KAPA PCR Amplification kit (KAPA, Cat. KK2501) using 14 cycles. Libraries were sequenced on a HiSeq2500 sequencer (Illumina) according to the manufacturer's instructions. Bioinformatic analysis. RNA-seq: Sequencing reads were adaptor trimmed using Trim Galore! (version 0. 4. 2) and mapped to the mouse (GRCm38/mm10) reference genome with HiSat2 (version 2. 0. 5). Analysis of RNA-seq data was performed with SEQMONK version 1. 36. 0 on filtered reads with a MAPQ score of >60 for uniquely mapped reads. Read counts were quantified using the RNA-seq quantitation pipeline implemented in Seqmonk, quantifying only probes with at least one read.
Probe read values were corrected for transcript length and divided into percentile bins according to their average expression levels of three replicates. ChIP-seq analysis: For mouse colon and HCT116 H3K18cr, two replicates and for H3K4me3 three biological replicates were used. Sequencing reads were adaptor trimmed using Trim Galore! (version 0. 3. 8 and 0. 4. 2) and mapped to the mouse (GRCm38/mm10) or human (GRCh38) reference genomes with Bowtie2 (version 2. 0. 4. ). Analysis of ChIP-seq data was performed with SEQMONK version 1. 36. 0 on filtered reads with a MAPQ score of >42, duplicate reads were always removed. For Fig. 2b , the genome was segmented in 1000 bp non-overlapping 'probes' and read counts were quantified for each probe and normalized to the largest datastore. For Fig. 2c , H3K4me3 peaks were identified using the MACS peak finder embedded in the SEQMONK program with the ChIP-seq data of H3K4me3 from colon epithelial cells and INPUT as reference.
Selected fragment size was 300 bp and p-value significance threshold was 10 -5. Reads were quantitated in and ±5 kbp around the MACS peaks. For Fig. 2d , read counts were quantified over the TSS (using a window of ±1 kb upstream of genes) and probes that had more than 100 reads in input were removed in both input and ChIP. For Fig. 2e , read counts were quantified over the TSS (using a window of ±0. 5 kb upstream of transcripts) and were overlapped with RNA-seq data. KEGG pathway analysis was with DAVID 6. 8 with electronic annotations excluded. ChIP-qPCR data analysis. Prior to analysis, a logarithmic transformation of the data was carried out. Subsequently, we carried out a two-way ANOVA test followed by Holm-Sidak's multiple comparison test. Data were analyzed using the Graphpad Prism Software.
75 μM modified histones and 0. 12 μM HDAC1 (recombinant, human, Active Motif) or 0. 18 μM HDAC2 (recombinant, human, ABCAM) at 30 °C for 2 h. Recombinant HDAC3/Ncor1 complex was from ENZO Life Sciences. All HDACs were produced in insect cells and purified. After the reaction, the histone modifications were identified by western blot. The pixel intensities of the western blot bands were quantified with the Image J software. For the enzyme kinetic analysis, histone H3 was acetylated or crotonylated in vitro as described above. Dot blot western analysis with synthetic H3 peptides that were specifically crotonylated or acetylated at K18 indicated full crotonylation and acetylation of the histone H3 at K18 under these conditions, therefore, we assume that the histone had been fully crotonylated or acetylated.
Substrate concentration against time were plotted for each histone concentration and a linear regression was fitted for the first 30 s to 1 min of the reaction, as appropriate. The rate of each reaction set was plotted as replicates against substrate concentration. GraphPad Prism Version 7 software was used to calculate K m , V max , and K cat. Colorimetric deacetylation assay. Synthesis of BOC-Lys(acetyl)-AMC and BOC-Lys(crotonyl)-AMC and the colorimetric assay was essentially as in ref. 2  with some modifications: for the synthesis of crotonyl-N-hydroxysuccinimide, N-hydroxysuccinimide (149 mg, 6 equivalents, eq) was dissolved in 2. 5 ml anhydrous dichloromethane to which diisopropylethylamine (167 mg, 6 eq) was added. The solution was cooled in an ice bath and trans-crotonoyl chloride (135 mg, 6 eq) was added and the reaction stirred at 20 °C for 3 h.