dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We would like to thank  M. Diaz Muñoz  and  M. Flourakis  for insights. R. Meléndez García ,  D. Arredondo Zamarripa ,  E. Arnold ,  X. Ruiz-Herrera ,  G. Baeza Cruz , and  N. Adán  are Master's and Doctoral students from  Programa de Posgrado en Ciencias ,  Universidad Nacional Autónoma de México (UNAM)  and received fellowships from  CONACYT. We thank  F. López-Barrera ,  G. Nava ,  D. Mondragón ,  A. Prado ,  M. García , and  E. N. Hernández Ríos  for their technical assistance, and  D. D. Pless  for critically editing the manuscript. This study was supported by the  UNAM  grant  IN201814  (ST), the  National Council of Science and Technology of Mexico (CONACYT)  grant  176393  ( ST ), and the Shedid grant (ATM). The role of the three funders strictly consisted in providing funds to purchase all materials necessary in this study.
Guinea-Pig Isolated Urinary Bladder Guinea-pigs were sacrificed by cervical dislocation, to avoid the possible effect of anesthetics on bladder smooth muscle response and/or drugs tested in experiments. The whole urinary bladder was excised and the detrusor muscle was dissected free from connective tissue and urothelium and cut into two equal strips isolated from the posterior face. Strips were mounted in 5 mL organ baths containing a Krebs-Henseleit solution and 0. 3 µM GR159897, a selective NK 2 receptor antagonist  (Beresford et al. , 1995) , 1 µM propranolol and 1 µM indomethacin. A resting tension of 1 g was applied and contractile responses were measured using isometric tension transducers (EMKA Technologies, Paris, France) connected to amplifiers and to a data acquisition system (PowerLab 16s, ADInstruments, Sydney, NSW, Australia).
Cystometric Studies Guinea-pigs were anesthetized with urethane 1. 5 g/kg (i. p. ), a tracheotomy was performed and a PE cannula was inserted into the trachea. A polyethylene catheter (0. 3 and 0. 7 mm of internal and outer diameters, respectively) was implanted into the bladder through the dome. A catheter (0. 58 and 0. 96 mm of internal and outer diameters, respectively) was also introduced into a jugular vein for test substance administration. For isovolumetric recordings, the ureters were tied distally and cut to prevent the accumulation of urine in the bladder. Bladder catheters were connected via a T-tube to a strain gage (MX 860 Novatrans III Gold; Medex Médical Nantes-Carquefou, France) and to a single-syringe pump (70-2208 Model II Plus, Harvard Apparatus; Les Ulis, France). Vesical pressure was recorded continuously using a PowerLab interface (AD instruments) and the software Chart.
net). Alignment around indels was then improved using GATK ver. 3. 2 (refs 45,46). The average coverage per genome was about Â 17 and Â 30 for the parental light and dark lines, respectively, Â 44 and Â 80 for BC7 and NN introgression lines, respectively, and Â 21 for D. orena. Genome mapping. The PoPoolation2 ver. 1. 201 software package  47  was used to generate a synchronized mpileup file for the five genomes aligned to the D. erecta reference. The FLCD locus was identified by estimating the dark strain ancestry proportion in BC7 or NN individuals. For each diallelic single-nucleotide polymorphism (SNP) with a minimum count of ten in all lines, this quantity was calculated as the proportion of sequence reads carrying the allele that is fixed in the dark parental line and absent in the light parental line.
Dark strain ancestry proportion was averaged across SNPs within 100 kb windows. As a quality filter, windows with fewer than 1 fixed difference per 1,000 sites between the parental strains were excluded as potentially identical-by-descent between these strains. Genetic distances (D xy ) were then compared between the two parental lines of D. erecta at ten 100-kb windows that conformed to the expected average ancestry score of 75% and centred on tan, using a perl script (available upon request from the first author). For each diallelic SNP, with a minimum sequencing coverage of 2, D xy was estimated from the formula: D xy ¼ p D q L þ p L q D where p is the frequency of the allele similar to the allele in the reference D. erecta genome, and q is the frequency of the alternative allele in each line.
This tree was used to define the light and dark haplogroups. For each locus, DNA polymorphism was analysed using DnaSP ver. 5. 10. 1 (ref. 49). We estimated genetic differentiation (F ST ) within and between the two populations and the two haplogroups, as well as genetic divergence (D xy ) between the two haplogroups and between each haplogroup and D. orena genome. The HKA test  50  was conducted in R after counting the number of polymorphic and divergent SNPs at each locus. Phylogenetic analysis. Sequences of the 1-kb-long t_MSE-containing locus in the nine species of the melanogaster subgroup were obtained from GenBank or our sequenced genomes, and aligned using the Muscle algorithm  51  as implemented in the MEGA ver. 6. 06 software package  52. MEGA was also used to estimate the best substitution model, which was HKY with invariable sites.
The BEAST v. 1. 8 software package  53  was used to infer the phylogenetic relationships between the sequences. A run of 10,000,000 generations under the coalescence model was conducted and sampled every 1,000 generations. A burn-in period of 2,500 generations was used. Divergence times were estimated by assuming the most recent common ancestor of the melanogaster subgroup to have lived nearly 11 million years ago  27. Functional validation of the tan regulatory region. A B850-bp region including the t_MSE sequence (scaffold_4690:5995162. 5996017 of the D. erecta reference genome rel. 1. 3) was PCR amplified using forward (5 0 -TTCCGggcgcgccCCATG GAAGCCGAGCACCTGGTAGA-3 0 ) and reverse primers (5 0 -TTGCCcctgcaggC TACAACGTRGGTCATGTNCAGGG-3 0 ) with AscI and SbfI restriction sites given in small letters  54.
Acknowledgements We thank four anonymous reviewers for constructive comments,  S. B. Carroll  for discussion, the late  D. Lachaise  for collections of initial D. erecta lines, the late  N. Bangart  and  M. J. Monette  for laboratory assistance and  J. B. Lack  for bioinformatic assistance. Funding was provided by the  Richard Lounsbery Foundation  (to J. E. P. and J. R. D. ),  NIH  grant  R01 GM111797  (to J. E. P. ) and  ANR-IFORA  and  ANR-C3A  (to M. V. ).
In summary, we present preclinical evidence demonstrating that CLU-KD significantly augments the anti-tumor activity of cabazitaxel in a mCRPC model. These preclinical data support the current phase III study of OGX-011 in combination with cabazitaxel as a second-line treatment of mCRPC (NCT01578655; clinicaltrials. gov). We also define for the first time that resistance to taxanes may occur via Cdc25C-Wee1-MPF regulation and that co-targeting Wee1 induction caused by CLU silencing represents a new strategy to address adaptive survival pathway activation and treatment resistance.
Cell impedance assay (xCELLigence RTCA) PC3 cells were seeded overnight 24 h after CLU silencing at 10,000 cells/well in 96-well E-plates (Roche). Measurements were taken continuously for ~60 h at 37°C. The RTCA software was used for data analysis, with statistical analysis using GraphPad Prism 5. 0c (GraphPad Software Inc. , San Diego, CA).
Flow cytometry analysis Fixed synchronized cells were treated with 20 lg DNase-free RNase for 30 min and stained with propidium iodide (10 lg/ml) for 1 h. The percentage of cells in G1, S, G2, M, and sub-G1 phases was quantified using FACSCanto (Becton Dickinson) and analyzed with Cyflogic software. For phosphohistone H3 analysis, pellets were permeabilized in cold 0. 1% Triton X-100, washed in FACS buffer (PBS, 2% FCS, 0. 02% sodium azide, 0. 5 mM EDTA), stained with Alexa Fluor 647-conjugated phosphohistone H3 (Ser-10) antibody (no. 9716; Cell Signaling Technology) for 1 h at room temperature. Cells were washed and resuspended in PBS for FACS analysis.
Oligo microarray technology Total RNA quality was assessed with the Agilent 2100 bioanalyzer prior to microarray analysis. Samples with a RIN value of ≥ 8. 0 were deemed acceptable for microarray analysis. Samples were prepared following Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6. 0. An input of 100 ng of total RNA was used to generate cyanine-3-labeled cRNA. Samples were hybridized on custom Agilent SurePrint G3 Human GE 4 × 180K Microarray (Design ID 032034). Arrays were scanned with the Agilent DNA Microarray Scanner at a 3 lm scan resolution, and data were processed with Agilent Feature Extraction 10. 5. 1. 1. Processed signal was quantile normalized with Agilent GeneSpring 11. 5. 1. To find significantly regulated genes between treatment groups, fold change (1.
The images produced by each array were captured with a Perkin-Elmer ScanArray Reader laser array scanner (Waltham, MA). Signal quantification was performed with ImaGene 9. 0 from BioDiscovery (El Segundo, CA). The background-corrected raw intensity data were logarithmically transformed with base 2. Since Z normalization in general displays greater stability as a result of examining where each signal falls in the overall distribution of values within a given sample, as opposed to adjusting all of the signals in a sample by a single common value, Z scores were calculated by subtracting the overall average intensity of all spots within a sample from the raw intensity for each spot, and dividing it by the standard deviations (SD) of all of the measured intensities within each sample. Z ratios were further calculated by taking the difference between the averages of the observed protein Z scores and dividing by the SD of all of the differences for that particular comparison.
Statistical analysis The in vitro data were assessed using Student's t-test, ANCOVA, ANOVA and the Mann-Whitney test. The t-test was followed by Welch's correction when equal variance was not assumed. ANOVA was followed by a post hoc Bonferroni analysis. ANOVA followed by Dunnett's post hoc analysis was used to compare slopes of tumor growth for the in vivo experiment. GraphPad Prism software was used to calculate the statistical significance. The threshold of statistical significance was set at *P < 0. 05, **P < 0. 01, ***P < 0. 001, and ****P < 0. 0001. Exact P-values are indicated in the figure legends, when applicable. Expanded View for this article is available online.
and a 40% mean increase in population of G2/M cells (Fig 1B). To further investigate the role of CLU in cell cycle regulation, microarray transcriptome analysis was performed on PC3 cells transiently transfected with siRNA targeting clusterin mRNA (siCLU) or scramble RNA (siSCR). As shown in Fig EV1A, differential expression profiling identified many biologically related gene clusters involved in the regulation of apoptosis, cell cycle progression and cell growth/proliferation (GEO number: GSE67256). Among the cell cycle regulators, CLU knockdown resulted in increased mRNA expression of Cdc25C phosphatase, Cdk1 kinase (Cdk1) and Wee1 kinase (Fig 1C left panel). As expected, proteins levels of Cdc25C, Cdk1 and Wee1 were also up-regulated when CLU was silenced (Fig 1C right panel). These proteins regulate cell cycle progression both in to, and exit from, mitosis.
Acknowledgements This project was supported by a  Terry Fox New Frontiers Program  Project Grant  TFF116129 , a  Prostate Cancer Foundation of British Columbia (PCFBC)  Grant  2013 , and a  Prostate Cancer Canada Team  Grant  T2013-01. We would like to thank  Mr. Dulguun Battsogt  for his technical support and  Mr. Robert Bell  for his help with the statistical analysis.
5 nm). This implies a partial membrane protein coverage. To calculate the mass of protein deposited per unit surface, we calculate L, the number of moles per volume with the following equation: = × L 1/(N V ), A p rot where N A is the Avogrado number and Vprot is the volume of the protein (approximated to a cylinder of 4. 8 nm diameter and 7. 5 of length). The mass density of the protein can be calculated using the equation: = × d M L, where M is the molecular weight of the protein. Knowing the thickness of the protein layer, the incorporated mass of the protein is evaluated at 22 μ g/cm 2 that corresponds to a P/L ratio of 1/110 (about 50% of membrane coverage). This corresponds to about 1/6th of the added protein to the PWR cell sample, being reconstituted in the membrane. The addition of the same concentration of protein-free detergent to a similar membrane system had a very slight effect on resonance positions (+ 2 mdeg for the resonance observed with p-polarization, + 1 mdeg for the resonance observed with s-polarization, + 2 mdeg for TIR angle, data not shown), which faded upon washing with buffer (+ 1 mdeg for the resonance observed with p-polarization).
Then if all molecules added bind to the surface of the prism, the TIR will return to its initial position while p-and s-polarizations resonances will evolve according to the change of mass density and anisotropy induced by the binding. Upon saturation of the system with the molecular partner, the TIR starts to increase again, reflecting the excess of material in the bulk phase. The instrument is controlled via a program written with Labview (National Instruments) that is also used to streamline data analysis. Thus, aside from the spectra itself, properties that characterize a spectra as the resonance minimum position for p-and s-pol, the TIR angle, the spectral depth for both polarizations were recorded and monitored directly during the experiment. Additionally, the diagrams correlating the different parameters can also be obtained, which can aid in a first level data interpretation, for example a correlation of the resonance shifts obtained for p-and s-polarized light can directly provide information on the anisotropy of the response.
In terms of data analysis, quantitative information on the affinity (anywhere from pM to mM) or kinetics (msec) can be obtained (this is further described in sections 2. 4 and 2. 5). Another type of analysis is possible that consists in spectral simulation to obtain all optical parameters that characterize a PWR spectrum: refractive index and extinction coefficient for p-(n p and k p , respectively) and s-pol (n s and k s , respectively), thickness (t) of the deposited thin film. Fits of experimental spectra were performed with Winspall software which is based on the Fresnel equations and the matrix formalism (Worm J. , WINSPALL, version 3. 02; 2009; http:/www2. mpip-mainz. mpg. de/knoll/soft). Formation of a planar lipid membrane. The planar lipid bilayer is formed across a small hole (~3 mm diameter) in the Teflon PWR cell sample (total volume of the cell sample compartment is 280 μ L).
Cleared lysate samples were incubated at 4 °C for 3 hours with 300 nM 3 H-Cpd1 (an antagonist for the CCR5 receptor  57  ) in the presence of unlabelled competitors indicated (maraviroc and Cpd1) or a DMSO vehicle control. Unbound radioligand was then separated by size exclusion chromatography prior to reading bound radioactivity using a liquid scintillation and a Microbeta counter. Non-specific binding was determined using lysate from untransfected HEK293T cells. In the absence of competing ligand,  3  H-Cpd1 bound specifically to the CCR5 StaR, but this binding was ablated when either unlabelled Cpd1 or unlabelled Maraviroc were present. These data show that the CCR5 StaR retains the ability to bind structurally diverse small molecule antagonist ligands following detergent solubilisation (Fig.
For polarized ATR-FTIR experiments, the reconstitution process was performed in the same manner, the only difference being that the chamber is of about 200 μ L rather than 280 μ L. After incubating the protein with the lipid membrane during 1 h, the excess of detergent and non-inserted receptor is washed out with buffer. The kinetics data obtained by PWR was fitted by a two phase exponential association process using Graph Pad Prism software (version 5). An exponential equation models many chemical and biological processes. It is used whenever the rate of a reaction is proportional to the amount of one reactant. The two-phase model used postulates that receptor reconstitution is the result of the sum of a fast and slow exponential decay.
The first concentration point was chosen to be approximately 1 order of magnitude lower than the published dissociation constant (K D ) value for that ligand. Incremental amounts of ligand were then added in a cumulative fashion, and the PWR spectra were acquired for each point when equilibrium was reached (i. e. , when no further changes in the PWR spectra occurred). K D values were obtained from plotting the resonance minimum position for the PWR spectra (this reflects the R-L complex) as a function of total ligand concentration and fitting to the hyperbolic function that describes the 1:1 binding of a ligand to a receptor using GraphPad Prism (GraphPad Software). A control experiment is performed that consists in adding the same ligand concentrations to a lipid bilayer with no receptor reconstituted.
Acknowledgements M. De Maria  and  N. Tschammer  thank to Graduate Training School GRK1962 of  German Research Foundation (DFG)  for the financial support. N. T. participates in the European COST Action CM1207 (GLISTEN: GPCR-Ligand Interactions, Structures, and  Transmembrane Signalling : a  European Research Network). This study has received financial support from the  French State  in the framework of the  "Investiments for the future" Program ,  IdEx ,  Bordeaux , reference  ANR-10-IDEX-03-02. Pierre Calmet thanks the Graduate Training School GRK1962 of  German Research Foundation (DFG)  for financial support.
METHODS The European Group for Blood and Marrow Transplantation (EBMT) (www. ebmt. org) is a nonprofit organization established in 1974 to allow scientists and physicians involved in clinical SCT to share their experience and develop cooperative studies. The EBMT is divided into working parties, whose mission is the implementation of EBMT scientific and educational policy, the development and management of scientific proposals with the support of the Data Offices, the development and organization of educational activities with the support of the Executive Office, and assisting the development of definition of guidelines and policies. The Solid Tumor Working Party is dedicated to preclinical, translational, and clinical studies of cell therapy for solid tumors, including AHSCT and allogeneic HSCT, active and adoptive immunotherapy, and lymphoablative therapy with expanded T cells  [15, 16].
EBMT centers, which are homogenously distributed through European countries, are required to send patient data to the central EBMT database on a yearly basis. There are 2 levels of data: minimal essential data type A, which are compulsory and considered major items, such as demographic data, disease classification, type of transplantation, outcomes, and followup; and minimal essential data type B, referring to items sent on a volunteer basis (type of conditioning or mobilization regimens, complications, number of cells transplanted, etc. ).
DFS and OS rates were measured from the date of surgery to the date of last follow-up or death and the date of relapse, respectively. TRM was defined as mortality from any cause other than disease progression within 365 days of transplantation. NRM was defined as mortality from any cause other than disease progression or TRM, after the transplantation. Before starting the present analysis, EBMT centers were contacted for missing data. All P values were 2-sided, and a P <. 05 was considered statistically significant. Statistical calculations were carried out by using SAS software (version 9. 2; SAS Institute, Cary, NC).
RESULTS Among adjuvant patients with BC reported in the EBMT registry, 583 patients with 4 or more involved nodes at surgery were available for OS analysis and represent the body of this article. Informed consent to collect and register data to the EBMT record was obtained from participants. The baseline patient and treatment characteristics are summarized in Table  1. The median patient age was 47. 1 years (range, 22. 4 to 66. 5), and 57. 3% of women were premenopausal. Data on HR status and HER2 status were available in 84. 7% and 31. 4% of patients, respectively. Information for defining triple-negative (TN) BC (ie, tumors that lack estrogen receptor, progesterone receptor, and HER2 overexpression) was available in only 35 patients. Approximately 18% of patients had breast masses larger than 5 cm.
DISCUSSION The present study, reporting a retrospective data analysis on HDC and AHSCT for high-risk BC in Europe, includes 1 of the largest series in this field. Because it comes from a registry and derives from patients transplanted in many cases when only limited information on tumor biology was available, many parameters are lacking, making interpretation of results more difficult  [19, 20]. Patients included in the present analysis were selected if they had at least 4 positive lymph nodes. In the absence of other factors, mainly HER2 status, axillary node involvement was the major negative prognostic factor for recurrence  [11]  and was thus used to identify patients at high risk of recurrence to be selected for studies in the adjuvant setting. Our results showed that adjuvant HDC with AHSCT, in contrast with early studies  [21, 22] , is a safe procedure with a TRM that is, in more recent years, inferior to 1%.
HeLa cells were treated with BI2536 or with DMSO vehicle for 2 h before CLM treatment for 1 hour and were then incubated for different time periods in presence or absence of BI2536. As shown in Figure  2A , large BRCA1 foci were efficiently formed in control cells 2 h following CLM treatment. However, when cells were pre-treated with BI2536, BRCA1 foci were less efficiently formed and appeared smaller at the same time-point (Figure  2A ). To accurately assess BRCA1 foci formation, we counted the number of cells containing at least five large BRCA1 foci (BRCA1-positive cells) over a 24 h time-course. Our data showed that the number of BRCA1-positive cells was significantly reduced when cells were pre-treated with BI2536 before DNA damage (p-value < 0. 01; Figure  2C ). We confirmed these findings by examining BRCA1 foci formation following DSB when Plk1 was downregulated using siRNA.
Plk1-BRCA1 complex formation is dependent on CDK1 activity Since our data showed that Plk1 is necessary for efficient BRCA1 foci formation upon DNA damage, we next investigate whether BRCA1 can form a complex with Plk1. We assessed the co-immunoprecipitation of BRCA1 and Plk1 using antibodies against either protein in the cell lines used in this study. A constitutive complex formation was found in undamaged HeLa (Figure  3A ) and MCF-7 cells (Supplementary Figure  S3A ), as previously observed in U2OS cells  [33]. To bind Plk1, a substrate is usually primed by another kinase such as CDKs  [34]. CDK1 has been shown to participate in DNA damage response pathways  [35]  and phosphorylates BRCA1 at S1497 and S1189/S1191  [36]. To test whether CDK1 inhibition alters Plk1-BRCA1 complex formation, we performed co-immunoprecipitation experiments following treatment with RO-3306, a specific CDK1 inhibitor  [37].
As expected, a much higher level of 32 P incorporation was obtained onto recombinant BRCA1 using Plk1 immunoprecipitated from cells that were synchronized in mitosis using paclitaxel (PTX) (Figure  4D ) since the maximal activity and expression of Plk1 coincide with the G2/M cell cycle phases  [39]. Phosphorylation of BRCA1 following DNA damage results in a mobility shift in SDS-PAGE under adapted migration conditions  [20, 21]. We next tested whether Plk1 inhibition may affect the phosphorylation of BRCA1 in response to DSB in cellulo. Cells were incubated 2 h in the presence or absence of BI2536 before treatment with CLM. WCE were analyzed by high resolution SDS-PAGE and immunoblotting with anti-BRCA1 antibody. Data revealed that inhibition of Plk1 slightly reduced the mobility of BRCA1 in condition of DNA damage treatment (Figure  4E ).