dataesr/scientific-paragraphs-categorization huggingface dataset:
CtBP2 is required for the proliferation of NSPCs during cortical development and for proper migration into the cortical plate To study the role of CtBP2 during cortical development, we performed in utero electroporation of CtBP2 siRNA and GFP vector in E14. 5 mouse embryos, and the brains were fixed 3 days later, at E17. 5, for analysis. To compare with the CtBP2 knockdown group (SiCtBP2), we used control siRNA and GFP vector for a control group (SiControl). The efficiency of siRNA mediated knockdown of CtBP2 was assessed in vitro in rat E15 NSPCs, as mouse NSPCs at corresponding age and cultured in the presence of FGF2 showed very low survival rate after passaging and siRNA delivery (data not shown). Both immunoblotting and gene expression analysis showed successful gene silencing with approximately 50% reduction of protein level and over 60% reduction of CtBP2 mRNA (Supplementary Fig.
Patients This ancillary study of the S-TRAC trial (ClinicalTrials. gov number, NCT00375674) included patients from six centers. Eligible patients were at least 18 years old and had a locoregional RCC (tumor stage III or higher, regional lymphnode metastasis, or both) on the basis of modified University of California Los Angeles Integrated Staging System (UISS) criteria  (10). Other eligibility criteria included histologic confirmation of clear-cell RCC (ccRCC) and no previous systemic treatment.
Patients and Treatment The French cohort of STRAC included 44 cases of ccRCC that were collected from six centers. Overall, 40 patients met the study criteria were exploitable and frozen tissue was available from 25 patients. Baseline clinical and pathological findings were similar in both groups and are summarized in Table  1. Seventeen patients were included in the sunitinib arm (43%), of whom 10 patients had a dose reduction (25%). At the time of data collection, 11 (52. 3%) and 10 (47. 7%) patients had progressed in the placebo and sunitinib arms, respectively. Overall, eight had lung metastases, four lymph node invasion, and eight had various metastatic locations. Progression was similar in both arms.
General design The experiment was performed in Dijon, Burgundy, France from February to June 2018. The general design is presented in Fig. 1  and summarized below. In total, 187 mother-child dyads participated in the present study. Mothers were included in the study because, as indicated previously, they are still mostly in charge of food purchases in French households  (Mathé & Hébel, 2013). Data were collected during two sessions conducted in the laboratory at T1 (February) and T2 (April). During these two sessions, participants were invited to choose two out of ten food items for their own midafternoon snacks. Then, they were asked to choose two food items among the same set of ten food items for the midafternoon snack of the other dyad member. The participants also rated their liking and perceived healthiness of the ten food items.
Participants Participants were recruited from the population registered in the ChemoSens Platform database. This database has been declared to the relevant authority (Commission Nationale Informatique et Libertés -CNIL -n°1148039). Participants were also recruited with the help of a consumer recruitment company. For children, the inclusion criterion was a grade level of 3 rd , 4 th or 5 th grade. An information sheet was sent to mothers and their child in which they were told that the study will aim to better understand the food choices of children and mothers. They were informed that they will have to participate in two laboratory sessions, that they will receive 3 boxes at home and that they will have to fill in different questionnaires in the laboratory and at home and give some feedback about the box content.
Mothers and their children provided written consent to participate in this experiment, and the study was reviewed and approved by the ethics evaluation committee of Inserm (IRB00003888). One hundred and eighty-nine dyads were recruited, but data from two dyads were excluded because they participated only in the first session. Thus, data from 187 mother-child dyads were included in the present paper. The mothers were compensated for their participation with a €40 gift voucher distributed at the end of the second session. After T1, all dyads participating in sessions on the same day were randomly assigned to either the experimental or control group by an experimenter who was not present during the sessions. The experimental group was composed of 94 dyads, and the control group was composed of 93 dyads.
Only quadrats with densities of 20-30 individuals were sampled. After sampling, the coast intervals where animals were collected were marked to avoid re-sampling it again. Environmental variables (i. e. water temperature, salinity, and dissolved oxygen) were monthly monitored. One single measurement was taken for each parameter (one-off values), and these were taken once a month at the same time of the day using a multiparameter sensor (Xylem -WTW 3320). Data on climatic variables such as air temperature, hours of insolation and rainfall were provided by the National Institute of Meteorology of Tunisia. At the same time, fecundity of S. pectinata was estimated by counting individuals and egg-ribbons contained in 10 quadrats (1 m 2 each) placed at 20 m intervals and at the same shore level.
The data from the northern Adriatic (GSA 17) were analysed separately for the west (GSA 17a) and east (GSA 17b) side to account for differences due to fishing pressure and/or differences in the environmental characteristics between these two areas. The proportional rate of change in BI y was calculated between the first and the last 3 years  (i. e. 1994-96 and 2013-15)  in  GSAs 1, 6, 7, 8, 9, 10, 11, 16, 17a, 17b, 18, 19, 20, 22 and 23. In the case of GSAs 5 15 and 25, where the MEDITS time series is shorter, the change in BI y was estimated between 2007-09 and  2013 -15 (GSA 5), and 2005 -07 and 2013-15 (GSAs 15 and 25). The non-parametric LOESS smoother was used to find a curve of best fit of species BI y in each GSA and ecoregion over time without assuming that the data must fit to a specific distribution shape  (Cleveland et al.
Randomisation Patients were centrally randomised using a computer generated randomisation list (1:1 ratio) and allocated to either meropenem or one of the two SOC regimens (ampicillin + gentamicin or cefotaxime + gentamicin) chosen by each site prior to the start of the study. The randomization list was prepared by the trial statistician before the beginning of the trial, with the SAS 1 software (version 9. 3), using computerized random numbers. Randomization was blocked and stratified by SOC regimen and use of systemic antibiotics for LOS within 24 hours prior to randomisation. The randomization list was kept confidential to trial team and sites received automated treatment assignment centrally via the e-CRF. No masking was used.
Short-term follow-up visit was performed on Day 28 by on-site visit or telephone call for all surviving patients. To avoid bias of the open label study, the components of the primary endpoint were assessed by the investigator as described below in outcomes section. Investigators assessed resolution or improvement of the clinical and/or laboratory parameters based on predefined algorithms. Investigators assessement was cross-checked againts data on clinical examination, laboratory parameters, microbiological assessments, etc. to verify correctness of all components of the primary endpoint. Microbiological samples from normally sterile sites were taken at baseline, Day 3, on appearance of any new signs suggestive of LOS and repeated until the relevant microorganisms were no longer detected. All samples were processed at local laboratories according to their own laboratory procedures.
The NeoMero1 study differed from previous studies in LOS in many ways. First, it was a multicentre study including countries with low to moderate antibiotic resistance rates (http:// ecdc. europa. eu/en/healthtopics/antimicrobial_resistance/database/) in contrast to previous single center and/or national studies  [5, 19]. Second, the demanding inclusion criteria resulted in recruitment of a very sick patient population (e. g. 55% mechanically ventilated, 35% with BW of <1000g) compared to previous studies  [5]. Third, only 2% of patients were ineligible (did not have LOS) and altogether 52% had culture proven LOS as opposed to 15% in a recent study of complicated intra-abdominal infections  [19]. Fourth, NeoMero1 had an ambitious primary endpoint that in addition to resolution or significant improvement of clinical and laboratory criteria, did not allow any changes of allocated therapy such as deviations from fixed treatment duration, dosing and/or addition of another antibiotic, in contrast to more liberal or less specific endpoints in previous studies  [5, 19].
Acknowledgments We would like to thank all patients and their parents participating in this study. Data safety monitoring board:  Hugo Devlieger  (chair),  Jim Gray ,  John Van den Anker  and  Pollyanna Hardy. NeoMero Consortium:  Oguz Akbas ,  Antonella Allegro ,  Davide Bilardi ,  Giulia Bonatti ,  Nijole Drazdienė ,  Silvia Faggion ,  Eva Germovsek ,  Genny Gottardi ,  Tiziana Grossele ,  Cristina Haass ,  Tatiana Munera Huertas ,  Valentina Ierardi ,  Sandrine Kahi ,  Paraskevi Karagianni ,  Aspasia Katragkou ,  Eve Kaur ,  Birgit Kiilaspa  ¨a ¨,  Karin Kipper ,  Aggeliki Kontou ,  Victoria Kougia ,  Hayriye Go  ¨zde,  Kanmaz Kutman ,  Elisabetta Lolli ,  Valentina Montinaro ,  Makis Mylonas ,  Kader Ben Abdelkader Emmanuelle Netzer ,  Clarissa Oeser ,  Felix Omenaca ,  Maria Luisa Paoloni ,  Simona Perniciaro ,  Laura Picault ,  Carlo Pietrasanta ,  Andrea Ronchi ,  Suzan Şahin ,  Yacine Saidi ,  Marina Spinelli ,  Joseph Standing ,  Claudia Tagliabue ,  Tuuli Tammekunn ,  Nina Tiburzi.
Lower Limb MRI Bilateral magnetic resonance imaging (MRI) scans of both lower limbs were performed using a 3. 0 Tesla MRI scanner (Siemens Trio, Berlin, Germany) with the participant in supine lying, with knees and hips fully extended. Scanning parameters included: repetition time=723 ms; echo time=10 ms; α=140°; field of view=400x400 mm; pixel size=0. 714 mm; width=560 pixels; Height=448 pixels; slice thickness=5 mm; slice increment 5 mm; number of slices=162. Data were transferred in DICOM format. For both legs, the triceps surae, tibialis anterior, quadriceps and other thigh muscles (OTM, including knee flexor and adductor muscles, and sartorius) were manually outlined for all the slices of the MRI images using 3D image analysis software (Mimics, Materialise, Belgium). Examples of muscle area determination are presented in Fig.
1A  for the thigh muscles, and in Fig. 1B  for the calf muscles. The volume of each muscle or muscle group was calculated from 3D reconstruction (selected option on the mimic software: Optimal). A view of the 3D reconstruction is presented in Fig. 1C. Bone mineral density (BMD) BMD was assessed from dual energy X-ray absorptiometry scan (DXA) (Hologic Bone Densitometer system n°83752A, model Discovery A, Hologic Company, Marlborough, MA 01752, United States) for the left proximal femur region including the femoral neck, intertrochanteric region, greater trochanter.
Statistical analysis While chronological age is determined by date of birth, physiological age can vary according to numerous health metrics. In this study, we chose to compare some physiological characteristics (HRmax, VO2max, MVCISO, and MVC60) of DL by providing her estimated physiological age based on equations previously established in large samples. For HRmax, we used the equation (1) of Tanaka et al. 15  , obtained from a meta-analysis including 351 studies and 18,712 individuals. For VO2max, we used the equation (2) of Myers et al. 16  , obtained from a database including the VO2max (recorded during a maximal treadmill test) of 3,158 healthy females aged 20-79 years. For MVCISO, we used the equation (3) of Harbo et al. 17  , obtained from a database including the MVCISO of 85 females aged 21-75 years.
For MVC60, we used the equation (4) of Neder et al. 18  , obtained from a database including the MVC60 of 51 females aged 20-80 years. For the total thigh, quadriceps and other thigh muscle volumes, data was normalized using Zscores with individual data expressed as the number of standard deviations from the mean of the 'healthy older females' group in the study by Maden-Wilkinson et al. ,  19.
The samples were loaded in polycarbonate cuvettes with a path length of 5 or 10 mm depending on the sample. The Viper soware was used for isolating the EXAFS function (c), using standard procedures for pre-edge subtraction, data normalization and subtraction of the atomic background with a smoothing spline. 44 The ab initio code FEFF 7. 0 was used to calculate the theoretical phase and amplitude functions that were subsequently used in the non-linear leastsquares renement of the experimental data by tting in R + D ( Å) space. 45 The samples or the more polar phase were tted with two shells consisting of the In-O and In-Cl single scattering paths, whereas the samples of the less polar phase were tted with one In-Cl single scattering path. The amplitude reduction factor S 0 was xed to 0.
Results and discussion The work done is based on the modeling and simulation of the refrigeration machine using the Aspen-Hysys software which is an advanced flow-sheeting tool for process simulation. It has a rich library of model calculations of thermodynamic properties. Stated below in table 1 are the characteristics of the generator's inlet in 1. In this work we modeled and simulated all three types of absorption cycles. However only the combined ejectorflash tank absorption is represented with Aspen-Hysys. Figure  5  illustrates the combined ejector-flash tank absorption cycle model in Aspen-Hysys. Figure  5  illustrates the combined ejector-flash tank absorption cycle model in Aspen-Hysys. We can conclude that the combined ejector flash absorption cycle provides potentially a COP of around of 76% higher than that of the single effect absorption cycle (COP= 64%) and that of ejector-absorption cycle (COP= 73%).
RNAi Transformed Wheat Lines Show Silencing of ATI Genes During the Kernel Development Stages In total, 1669 immature embryos of Triticum aestivum L. cv. Bobwhite were co-transformed using three RNAi constructs (pRDPT-CM3, pRDPT-CM16 and pRDPT-0. 28) and the plasmid pUBI::BAR. Eight T 0 independent transgenic lines resistant to Bialaphos were obtained which represents 0. 44% transformation efficiency. The presence of the transgenes was verified by PCR analysis on genomic DNA from regenerated plants (data not shown). No significant differences in morphology or growth were observed between the "null" genotype that had lost the transgene by segregation (null-segregant), and the untransformed plants (data not shown), thus we have used the untransformed plant (indicated as either BW or WT) for the experiments.
Data Analysis All the raw MS data were analyzed using ProteinPilotTM software versions 5. 0 (AB Sciex) for protein identification and quantification. ProteinPilot applies a hybrid approach to integrate de novo sequencing with a traditional database searching approach in identifying proteins. Firstly, high-confidence small peptide sequence segments are identified, called taglets; taglets are then used to improve the downstream database searching procedure  [27]. ProteinPilot is a well-established protein identification algorithm in the proteomics community. Spectral data were analyzed against the database "UniProt Taxonomy: Viridiplantae (Green plants), Version: August 2019". The number of the sequences in the database was 8,344,090. iTRAQ impurity was automatically corrected following the protocol provided by ABI Sciex for ProteinPilot.
After three washes with PBS-0. 05% Tween 20, the plate was incubated for 1h at 37 • C with the secondary antibody (anti-rabbit IgG labelled with the enzyme HRP). After three additional washes with PBS-0. 05% Tween 20, the colorimetric substrate for HRP OPD (o-Phenylenediamine) in 0. 05M citrate buffer plus H 2 O 2 were introduced to have a yellow-orange product detectable at 490 nm. The OPD reaction was stopped after 30 min with H 2 SO 4 4N. Three biological and three technical replicates were used. All data were subjected to ANOVA analysis by using SYSTAT12 software (Systat Software Incorporated, San Jose, CA, USA). When significant F values were observed, a pairwise analysis was carried out by the Tukey Honestly Significant Difference test (Tukey test).
[32]. Three replicates were performed for each serum. Data are presented as mean values with their standard errors. Statistical analyses were performed using GraphPad Prism 5. 02 software (GraphPad Software, La Jolla, CA, USA), and p values below 0. 05 were considered significant. Analyses of variance (Two-way ANOVA) with subsequent Bonferroni's multiple-comparisons tests between means of the Bobwhite vs. RNAi lines were performed.
7 was applied. MALDI TOF MS of salt-water extracts was performed according Call et al. [20]  after purification with C18 ZipTips (Millipore, Merck, Germany). Thousand kernel weight (TKW) was used as a yield indicator. It was calculated by weighing and counting the kernels. Besides, coleoptile length was used as a parameter to measure seedling vigor and growth. It was measured at 5 and 7 days after imbibition (DPI) by using a scale. For both parameters, two independent experiments were performed. Data were subjected to ANOVA analysis. The percentage of unextractable polymeric proteins (%UPP) was determined according to Gupta et al. [2]. Soluble glutenin polymers were extracted from 10 mg of flour by using 50% ACN 0. 05% TFA in a 1:10 (w/v) ratio. The samples were left under stirring for 30 min at room temperature and subsequently centrifuged for 15 min at 10,000 g.
6 mm. The samples were injected using 100-µL loop connected to a six-way valve, elution occurred under isocratic conditions using 50% ACN 0. 05% TFA eluent, at a flow rate of 1 mL/min for a duration of the stroke chromatography of 10 min. The column was kept at the temperature of 30 • C. Three biological and three technical replicates were used. All data were subjected to ANOVA analysis by using SYSTAT12 software (Systat Software Incorporated, San Jose, CA, USA). When significant F values were observed, a pairwise analysis was carried out by the Tukey Honestly Significant Difference test (Tukey test).
Bioinformatic Comparison of HMW-GS Gene Sequences The NCBI (National Centre for Biotechnology Information https://www. ncbi. nlm. nih. gov. ) data bank was used to compare 0. 28 (accession number AJ223492. 1), CM3 and CM16 (accession numbers AY436554. 1 and X17573. 1, respectively), with the following HMW-GS genes: Dx5 (accession number DQ907161. 1), Dy10 (accession number X12929. 2), Ax2* (accession number M22208. 2), Bx7 (accession number BK006773. 1) e By9 (accession number X61026. 1). Alignment was performed with the software ClustalOmega (https://www. ebi. ac. uk/Tools/msa/ clustalo/r). Supplementary Materials: Supplementary Materials can be found at http://www. mdpi. com/1422-0067/21/16/ 5817/s1.
Simulations We simulated a dairy cattle breeding scheme with partially overlapping generations, progeny testing, and selection. Only females were phenotyped, with only 1 record each, because of limitations of the simulation software. Two heritabilities (h 2 = 0. 10 and 0. 30) were simulated. We used the QMSim v. 1. 10 software program  (Sargolzaei and Schenkel, 2009) , and the main parameters of the simulation are shown in Table  1  and the parameter file in Appendix 1. In each generation, 8% of born males and 45% of born females were selected to join the pool of reproducers, provided their EBV was high enough. Accordingly, animals with the lowest EBV in the pool were discarded. The pool of reproducers contains, potentially, animals of all previous generations, and therefore parents of a given generation may came from any of the preceding generations.
For instance, in Figure  1 , we show an example of the generation of origin of parents of individuals in generation 7. It can be observed that, of 45,000 animals born in generation 7, 1,800 sires were born in generation 6, 1,192 were born in generation 5, and so on. All born females have a single performance. The mating system seeks to minimize inbreeding (mating design = minf in QMSim parameter file;  Sonesson and Meuwissen, 2000) , achieving an average inbreeding, for all generations, close to zero. Instead of using QMSim internal BLUP evaluations, genetic evaluations were performed at the end of each generation, using as external software blupf90  (Misztal et al. , 2002). Then QMSim selects individuals with higher external EBV to be parents for the next generation. This scheme allowed us the flexibility required to explore competing scenarios.
Thus, 1 ˆ, ρ p w is the relative increase of accuracy from partial to whole information. For instance, if ˆ, ρ p w is equal to 0. 5, the addition of information doubled the accuracy. Accuracy of EBV from the Partial Data Set. The formula for accuracy in the partial data set is acc cov u u p w p g i 2 2 = ( ) ˆ, , , σ where σ g i , 2 is the genetic variance of the individuals of interest. The original  Legarra and Reverter (2018)  paper suggests the formula acc cov u u F f p w p g 2 2 1 2 = ( ) + - ( ) ˆ, , , σ ∞ where F is the average inbreeding coefficient, 2f is the average relationship between individuals, and σ ∞ g, 2 is the genetic variance at equilibrium in a population under selection. However, this formula applies if animals of interest are representative samples of their generation-in other words, they are not yet selected.
ACKNOWLEDGMENTS The authors thank projects ARDI funded by  IN-TERREG POCTEFA  ( Programa INTERREG V-A España-Francia-Andorra, Jaca, Spain ),  Metaprogram SELGEN of INRA , the  Department of Animal Genetics of INRA  and  La Région Occitanie , which financed this research. In addition, we are grateful to the  Genotoul Bioinformatics Platform Toulouse Midi-Pyrenees  ( Bioinfo Genotoul; Toulouse, France ) for providing computing and storage resources. This work has also received funding from the  European Union   Horizon 2020 Research and Innovation program  under grant agreement  N°772787 , SMARTER. We further thank  Vincent Ducrocq  ( INRA, Jouy-en-Josas, France ),  Alain Charcosset  ( INRA, Gif-sur-Yvette, France ),  Catherine Larzul  ( INRA, Toulouse, France ),  Anne Ricard  ( Institut Français du Cheval et de l'Equitation, Toulouse ), and  Leopoldo Sanchez-Rodriguez  ( INRA, Orleans, France ), and the two anonymous reviewers for their helpful advice.
Results Characteristics of CAD patients according to vital status. The present cohort was constituted of 214 CAD male patients. After inclusion, the vital patients' status was yearly assessed. The median follow-up period was 12. 5 years (mean: 10. 7 years). During follow-up, 78 deaths had been recorded giving a death rate of 36. 4% and a mean annual rate of 3. 4%. Cardiovascular mortality accounted for the majority of deaths recorded (64. 1%, n = 50) and cancers accounted for 16. 7% (n = 13). Comparison of patients' data when they were included in the cohort is given in Table  1. Results are presented distinguishing two groups: the "alive group" (patients living at the end of the follow-up) and the "deceased group" (patients who died during follow-up). Hypertension was diagnosed or treated in 65.