dataesr/scientific-paragraphs-categorization huggingface dataset:
Only probesets that mapped uniquely to one gene were used and for each gene, the probeset with the highest expression level was used. Cytometric bead assay. Splenocytes (1 × 10 6 ) were cultured overnight in 500 µl medium and supernatants were stored at -20 °C before analysis of IL2, IL17A and IFNγ levels using a cytometric bead assay (Bender MedSystems) with a FACS Canto-II (BD Biosciences) and FCAP Array software (BD Biosciences). Statistics. Statistical analyses were performed with GraphPad Prism. Student's t-test was used to compare two groups, while multiple groups were compared using analysis of variance or Student's t-tests with appropriate corrections as detailed in the legends. A p-value of 0. 05 was considered significant. Data availability. Microarray data that support the findings of this study have been deposited in National Center for Biotechnology Information Gene Expression Omnibus public database (http://www.
Acknowledgements We thank  Drs V. Cerovic  and  S. Milling  for critical reading of the manuscript,  Inge Brouwers-Haspels  for expert technical assistance and  Diane Vaughan  at the  Glasgow Flow Cytometry Facility  for help with sorting. Violaine Alunni  and  Christelle Thibault-Carpentier  ( Plateforme Biopuces et Séquençage de l'IGBMC, Strasbourg, France ) performed the microarray experiments (http://www-microarrays. u-strasbg. fr), with assistance from  Emeline Pollet  (CIML). This work was supported by  Wellcome Trust   UK Project Grant   094763  to C. C. B. and A. M. M. ,  Wellcome Trust  PhD Studentships 089892 (C. L. S. ) and  096988  (T. F. P. Z. -M. ), the  Medical Research Council UK  and grants from the  Netherlands Organization for Scientific Research (NWO ,  VIDI 917-76-365 ) to B.
To ensure observer blinding, the assessment of primary and secondary outcomes will be performed by medical doctors, which are not otherwise integrated in the conduct of the trial and blinded to the group allocation of participants. Observers will be surgeons of spatially separated participating study centers, specifically trained in the assessment of the CCI. The observer training has to be documented on a separate training log. The observers will receive the patient's surgical file only. Before sending the file, it has to be verified that this file contains data on the postoperative treatment only and no data that allow conclusions about the pre-surgical supportive treatment. All patient-related data and data concerning the study intervention have to be blanked out. The oncological file, in which the study specific treatment is documented, will not be available to the independent observers.
Data collection and management The applicable local regulations of data privacy protection will be followed. Before inclusion, patients will be informed that any patient-related data and materials will be appropriately pseudonymized (pursuant to GCP regulations  [16] ) and that these data may be used for analysis and publication purposes. All trial data will be recorded in eCRFs. After inclusion, baseline data (demographical data, medical history, anthropometric data) will be documented accordingly. A physical exam will be performed and a routinely taken blood sample analyzed (see Fig. 2  for included parameters). The EORTC QLQ-C30 questionnaire for the assessment of QoL will be documented and "nutrition diaries" will be handed out and explained to all participants. In case of women with childbearing potential, a pregnancy test will also be performed.
During NACT, three study visits will be performed where ECOG score, as well as AEs and SAEs will be assessed and documented in the eCRF. At visit 3 (pre-chemotherapy), data on the type, duration, and dosage of chemotherapy and any additional radiotherapy will be documented. In addition, parameters of the planned parenteral nutrition intervention, the planned application route (e. g. via intravenous port system) and the used product will be documented for patients in the experimental group. Furthermore, the IBW will be calculated as follows: - Subsequently the required daily calorie supply can be calculated as: -IBW * 30 kcal for men; and -IBW * 25 kcal for women. At visit 4 after the first half of chemotherapy, ECOG score, AEs, and SAEs will be assessed for all patients. In addition, anthropometric data will be reassessed and nutrition diaries will be collected and the enteral calorie intake documented.
If, however, the patient is unable to attend visit 9 due to postoperative treatment in a rehabilitation facility or for other medical reasons, a standardized protocol for evaluation and documentation will have to be filled out by the treating physician. At the end of the clinical study, all study-relevant data must be archived for at least ten years. Patient identification lists and patient files will be separately retained in the respective study sites. The infrastructure and the personnel for the data management will be provided by the Data Management Center at the MSZ, a member of the German Network of Coordinating Centers for Clinical Trials (Koordinierungszentren für Klinische Studien [KKS]). The eCRFs are checked for completeness, plausibility, and correctness at entry. The investigator is responsible for the accuracy and verifiability of each entry.
Access to data and dissemination of results Only the sponsor, personnel authorized by the sponsor, and the trial statistician will have access to the final dataset. Limited access for local investigators will be regulated in the Clinical Trial Agreement. After completion of the clinical study, the coordinating principal investigator will prepare a multicenter manuscript of the study results for publication in a reputable scientific journal. Authorship eligibility will be regulated in the Clinical Trial Agreement. The publication of the principal results from any single-center experience within the trial is not allowed until the preparation and publication of the multicenter results.
Monitoring Monitoring will be performed by the MSZ, an institution experienced in the monitoring of multicenter, surgical RCTs, in order to guarantee high quality of the study conduct and data retrieval. Monitoring will be carried out in accordance with ICH-GCP guidelines  [16]. Monitors will visit all participating centers on a regular basis, starting with an initiation visit at each site. Furthermore, close-out visits are planned for each center. A monitoring manual describing the scope of the monitoring activity in detail will be provided. The monitor is authorized to compare trial documents and original data in adherence to data protection rights. The investigator provides direct access of patient's documents/original source data to the monitor at any time. The monitor will also have regular contact to all participating centers and the sponsor.
Sample size calculation The sample size was calculated (nQuery Advisor software version 7. 0, Statistical Solutions Ltd. , Cork, Ireland) based on the primary endpoints of the study. Assuming that the nutrition intervention can reduce the CCI by 10 points (with a standard deviation of 20), 69 patients have to be recruited in each group to achieve a power of 80% with a two-sided significance level of 5% using the Wilcoxon signed-rank test. Expecting a drop-out rate of 8% (based on experience from previous similar trials) a total of 150 (75 per group) patients have to be included in the study.
Discussion The PERCOG trial has a pragmatic, two-armed study design (parenteral nutrition vs no parenteral nutrition during NACT) and shall be conducted in four centers within the German Surgical Trial network CHIR-Net. A multicenter approach was chosen to increase external validity. Internal validity and data quality assurance are established by adherence to the SPIRIT guideline and GCP regulations, regarding recruitment, training of study personnel, methods against bias, outcome reporting, and documentation. All patients suffering from non-metastatic gastric or esophago-gastric cancer, staged at least uT2N+ receiving NACT, will be screened within 27 months. Specialized oncological surgical centers were chosen and broad inclusion criteria were applied to ensure rapid and sufficient recruitment to achieve the target sample size.
Acknowledgements Silvia Egert  (MSZ) has served as scientific advisor. Petra Wagner  (MSZ),  Ursula Boecher , and  Jutta Wagner  ( Department of Surgery, Klinikum rechts der Isar, TUM ) have contributed as clinical trial assistants. Alfred Zollner (MSZ) has contributed as the main data manager of the PERCOG trial. We also thank all members of the  PERCOG Study Group  for their participation in the trial.
Methods 151 children with cerebral palsy, operated with at least a clinical gait analysis before and after surgery are studied. Gait analysis were performed pre and postoperatively from 2004 to 2007 with a SAGA 3RT Biogesta system and since 2008 with a Vicon system. Lower limb marker placements were identical and kinematic data were computed with the same software based on a modified Helen Hayes  (Davis III et al. , 1991; Kadaba et al. , 1990)  model with anatomical markers on the femoral condyles and the medial-malleolus. The lower limbs with a Goldberg index  (Goldberg et al. , 2006)  quoted 'Stiff ' or 'Borderline' are included. A RFT subgroup is matched to a No-RFT subgroup by Propensity Score Matching  (Ho et al. , 2007). The Propensity Score Matching is based on a logit model (caliper = 0.
Differential Scanning Calorimetry Differential scanning calorimetry (DSC) was performed on a Micro DSC III (SETARAM, Caluire, France). Proteins dispersions were heated in the calorimeter from 20 to 100 °C at 1 °C/ min, samples of ca. 800 mg were weighted into hermetically sealed in hastelloy pans and water was used as reference. The temperature of maximum heat absorption (Td, °C) and the enthalpy change of transition (ΔH, J/g dry protein), were obtained by analyzing the thermograms with the OriginPro 8 software (OriginLab Corporation, Northampton, MA, USA). The ΔH was estimated as the area between the DSC curve and a straight line extended from onset to final temperatures of each transition. The degree of protein denaturation (DD) was calculated according to the following equation: DD % ð Þ ¼ 100 À ΔH t =ΔH o x 100 Where ΔH o and ΔH t are the enthalpy changes corresponding to the unpressurized and HHP-treated samples, respectively.
Statistical Analysis Values were expressed as average ± standard error. Three dispersions were prepared and subjected to the corresponding pressure level for each condition. Factorial analysis of variance (ANOVA) was used to determine the influence of the different factors: pH of protein extraction during isolation, protein concentration, calcium concentration and/or HHP level. A Fisher LSD test with a confidence interval of 95% was used to compare the means of results. The statistical analysis was performed using the Infostat software developed by Di Rienzo et al. ,  [23].
Taken together, these data suggest that thermal properties of cowpea globulins are very sensitive to protein concentration and heating rate, and that their denaturation may involve a first step of dissociation of aggregates. To clarify this behavior, protein solubility was assessed on dispersions of CPI8 and CPI10 at 7. 5 and 10. 5% (w/w). The highest values of protein solubility were found for the lower protein concentration (Table  1 ). Moreover, in order to compare with the results of our previous work, we evaluated protein solubility at 15% (w/w) and the values were 63. 9 ± 0. 9 and 59. 2 ± 1. 6% for CPI8 and CPI10, respectively. Furthermore, in that work, protein solubility evaluated at 0. 1% (w/v) was higher than 90%. Taken together, these data show an inverse relationship between protein concentration and protein solubility in CPI, which would be explained by aggregation.
Ultrasound Image Analysis All ultrasound images were sent for qualitative review and quantitative analysis, with the demographic and clinical data masked. Deidentified images underwent initial screening for overall image quality. If image quality was considered inadequate to ascertain measurements, additional measurements were obtained from the same infant and, if adequate, were used for analysis. Linear measurements were then performed by a single reviewer (E. P. ) on all images of adequate quality for STMD and STBD as previously described. 17, 18 Intraobserver reproducibility of ultrasound measurements was assessed in approximately 10% of study participants' images using the intraclass correlation coefficient. 19 The intraobserver correlation coefficients were 0. 99 for STBD with and without compression and 0.
Primary Data Analysis Demographic and clinical characteristics, STBD, and STMD were summarized using descriptive statistics (mean [SD]) for continuous variables and number (percentage) for categorical variables. The STBD and STMD were analyzed within a mixed-effect model with fixed terms for axis (short and long axis), weight, and sex and a random term for participant. Axis and sex mean difference estimates and their associated 2-sided P values were provided within the mixed-model framework. Short-axis measurements were taken forward for further analyses because they are considered more accurate than long-axis measurements (due to potential off-axis measurements) and are the primary outcome of this study. The association between weight and STBD and STMD as measured by short axis was further explored using a linear regression model.
Weight slopes and associated 2-sided 95% confidence intervals were provided. Because of a significant weight effect, STBD and STMD were adjusted for weight for children weighing 7. 5, 11, and 15 kg. The percentage of children for whom a needle length would not strike the bone (estimated by 1-sided 95% tolerance intervals) and the percentage of children for whom a needle length would allow an intramuscular administration (estimated by 1-sided 95% tolerance intervals) were estimated for different needle lengths ranging from 6. 5 to 13 mm and for different weights ranging from 7. 5 to 15 kg. All analyses were performed using SAS statistical software, version 9. 2 (SAS Institute Inc, Cary, North Carolina).
Discussion To our knowledge, this is the first study to assess the STBD and STMD in children weighing 7. 5 to 15 kg with a modified ultrasound transducer designed to mimic real-life delivery of epinephrine using a specific EAI (Auvi-Q). Our findings suggest that the optimal needle length for an EAI for infants and toddlers weighing 7. 5 to 15 kg should be shorter than the needle length in current, commercially available pediatric EAIs to avoid inadvertent intraosseous injections. Current recommendations favor the intramuscular injection of epinephrine into the vastus lateralis muscle over subcutaneous injection based on data from small studies in adults and  children. 21, 22 In these studies, intramuscular injection led to epinephrine levels that were superior to subcutaneous injections. There is concern that the needle length of EAIs may be too short for some patients, resulting in subcutaneous rather than intramuscular injection.
Kim and colleagues  14  measured STBD and STMD in 100 children with food allergies weighing less than 15 kg. The investigators used a conventional ultrasound transducer to apply maximal pressure, which was estimated at 8 lb. They found that the maximum STBD was less than 12. 7 mm in 29% of children, suggesting that they were at risk of epinephrine injection into the bone. These findings are consistent with data from our study, which indicate that an EAI with a needle length of 12. 7 mm could strike the bone with a range of 21% to 55% of children weighing between 7. 5 and 15 kg. Our current study extends the methods and findings of prior investigations for several reasons. Apart from being a multicenter study, a modified ultrasound transducer closely resembling an actual EAI device was used to sonographically assess thigh distances.
In addition, we performed measurements at a standardized location on the midthigh based on the recommended injection site. Additional variability in measurements could have been introduced if measurements had been performed in more proximal or distal areas of the thigh. 17 Since our study cohort was predominantly white, our findings should be verified in ethnically and racially diverse populations. Finally, because of the age group in which this study was performed, we measured the distance to the bone noninvasively as a proxy for the risk of the autoinjector needle striking the bone, which may not account for real-world variations in needle angle or the risk of intraosseous infusion. Our data suggest that the optimal needle length for an EAI for infants and toddlers weighing 7. 5 to 15 kg should be shorter (measuring approximately 7e8 mm) than the needle length in current, commercially available pediatric EAIs to avoid unintentional intraosseous injections.
The reaction mixture containing the buffer, dNTPs and the polymerase (different concentrations of DnaE as indicated) was rsob. royalsocietypublishing. org Open Biol. 7: 170146 pre-incubated at 378C for 5 min before the addition of radiolabelled substrate (0. 66 nM) to initiate the reaction. The reaction proceeded for 15 min, as indicated, at 378C and terminated by the addition of 1/5th 5Â Urea-Stop buffer (5 mM Tris -HCl pH 7. 5, 20 mM EDTA, 7. 5 M urea). The mixture was then heated to 958C for 2 min and analysed by electrophoresis through 15% (v/v) polyacrylamideurea sequencing gels. Gels were dried under vacuum and imaged using a phosphorimager and associated software (Bio-Rad). Data were analysed and plotted using GraphPad PRISM 6. The activities of PolC, PolC pol-and PolC exo-were investigated as above with minor modifications: the titration assays were carried out for 15 min at 378C (the different protein concentrations were as indicated) while the time point assays were carried out with 80 nM PolC.
Alkaline agarose gels were dried overnight and imaged using a phosphorimager and associated software (Bio-Rad). Typically, the reaction buffer contained 20 mM HEPES pH 7. 5, 50 mM NaCl, 10 mM MgCl 2 , 1 mM DTT, 500 mM dNTPs, 2. 5 mM ATP and 2 nM radioactively labelled primed ssM13mp18 template. In all reactions with SSB-coated templates the reaction buffer was pre-incubated with SSB (1 mM), DnaN (80 nM), DnaX (120 nM), HolB (40 nM) and YqeN (40 nM) at 378C for 5 min before the addition of the polymerase DnaE (80 nM) to initiate the reactions. Quantification of percentage nascent DNA synthesized was carried out using a molecular imager and associated software (Bio-Rad) and bar graphs were prepared using GraphPad PRISM 4.
A and its effect on cell growth at 308C. Cells were grown exponentially in LB at 308C. At OD 600nm of approximately 0. 002, IPTG (0, 25, 200 and 1,000 mM) was added and cell growth was followed spectrophotometrically. The three DnaED. A mutated strains gave similar results ( presented data are with the dnaED382A allele). rsob. royalsocietypublishing. org Open Biol. 7: 170146 strains were viable at high temperature (the D382A data are presented in figure  2b ; similar results were obtained with the remaining D. A strains). Moreover, in contrast to native DnaE, a moderate accumulation of DnaED. A in the dnaETs context induced filament formation and eventually growth arrest at 308C (the D382A data are presented in figure  2c ; similar results were obtained with the remaining D. A strains). Collectively, these data indicate that the polymerasedeficient D.
When PolC and DnaEM7 were both overexpressed from the IPTG-inducible promoter (like DnaE, the PolC construction is expected to produce tens to one thousand of PolC molecules per cell, a range that covers the physiological concentration of PolC, approx. 100 molecules  [27, 34] ), the mutagenesis rate decreased compared with cells overexpressing DnaEM7 alone. These data show that the mutagenesis rate in the dnaEM7 background correlates proportionately with the DnaE/PolC ratio in vivo. To further test the interplay between the DnaE/PolC ratio and DnaEM7 mutagenesis, the DnaE/PolC ratio was increased by depleting PolC. To do this, we used strains encoding PolC from the Pspac promoter and DnaE or DnaEM7 from its natural locus. The rate of spontaneous mutagenesis after 15 generations at 6 and 250 mM IPTG was monitored using the Rif R assay (pre-cultures were carried out at 250 mM IPTG).
A protein was examined by Western blot, 2 h after IPTG addition (ii), and total proteins were visualized using Sypro red staining (i). (iii) IPTG dependent accumulation DnaED. A and its effect on cell growth at 308C. Cells were grown exponentially in LB at 308C. At OD 600nm of approximately 0. 002, IPTG (0, 25, 200 and 1,000 mM) was added and cell growth was followed spectrophotometrically. The three DnaED. A mutated strains gave similar results ( presented data are with the dnaED382A allele).
Acknowledgements. We thank  Prof. Bob Lloyd  for his critical comments on the manuscript,  James Berger ,  Richard Losick  and  Francois Lecointe  for the kind gift of plasmids p2BT, pDR111 and pFL6, respectively, and  Philippe Noirot ,  Jeff Errington  and  Etienne Dervyn  for the kind gift of strains ( JJS9 ,  PS1175 ,  EDV97 ,  EDJ148  and  HVS567 ).
Image acquisition and analysis Immunoreactive cells were quantified in the dorso-medial striatum (DM) and Nucleus Accumbens Shell (ShNAcc). Confocal images (SP5, Leica) were acquired bilaterally with a 40X oil immersion objective. Quantifications were performed using ImageJ software taking into account the cells with immunofluorescence above a fixed threshold Nucleus vs neuropil fluorescence intensity assessment: Images were acquired as described above. Image analyses were performed in ImageJ using custom-built procedures. Nuclei are segmented by a binarization of the Hoechst signal. The fluorescence was measured inside and outside the nuclei masks in order to discriminate proteins levels in neuropile or in the nucleus. The percent of positive nuclei represents the percent of nuclei upon a threshold defined by user relative to the total number of nuclei.
Arc and phospho-H3 colocalization within the nucleus: Confocal images were acquired in the DM bilaterally and images were taken with a 63X oil immersion objective, Zoom 4, pixel size: x = 0. 06µm, y = 0. 06µm, z = 0. 21 µm. A deconvolution step was performed using Maximum Likelihood Estimation algorithm with Huygens 3. 6 Software (Scientific Volume Imaging) as described in  (21). This treatment aims at limiting light diffraction, which increases the accuracy of colocalization analyzes. 3D segmentation of intra nuclear Arc and pH3 spots at high resolution has been computed thanks to the 3D ImageJ Suite plugins  (22)  as already described in  (23). The local maxima inside the nucleus are detected and defined as seeds of the spots. Then an adaptive threshold is automatically calculated for each object based on their intensity by measuring the signal in concentric spheres created around the seeds.
Unraveling the role of nuclear Arc in striatal neurons in vitro. Because our data indicated that cocaine-induced Arc accumulation in the nucleus preferentially occurred within active zones of transcription in striatal neurons, we hypothesized that Arc could be a regulator of chromatin remodeling. To test this, we used striatal cultured neurons treated with glutamate (10 µM), which induces increases in pH3 levels downstream from ERK-MSK1 activation  (29) (30). The impact of Arc expression on these cellular events, was studied after transfection of a cDNA encoding Arc fused to GFP, followed by live imaging. Under basal conditions, the GFP-Arc signal was detectable in all cellular compartments, with higher levels in the soma (Fig. 4A ; left panel). Incubation with glutamate triggered a progressive accumulation of GFP-Arc in the nucleus (Fig.