dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analysis All statistical analyses were performed using SAS, version 9. 3, software (SAS Institute, Inc. , Cary, North Carolina). By cohort, adjusted means and standard errors of nutrient and food group intakes and HDI scores across alcoholic beverage preference categories were calculated using generalized linear models (analysis of covariance). Adjusted means were calculated by fitting a regression model using the variable of interest as the dependent variable and the covariates as independent variables. Combining all cohorts, inverse-variance weighted means were calculated. Based on a priori knowledge, factors that were associated with both alcoholic beverage preference and dietary habits were selected as potential confounders. Adjustments were made for age, gender (not applicable for Zutphen Elderly Study, since they included men only), education (primary or less (low), more than primary but less than college or university (middle), college or university (high)), employment status (not applicable for Zutphen Elderly Study and SENECA, where participants were all retirees, and not assessed in EPIC-Elderly Spain; full-time or part-time employment and not of pensionable age, self-employed, housewife and not of pensionable age, pensionable age and still working, pensionable age and not working, stopped work before retirement age due to poor health, unemployed and not of pensionable age), self-reported prevalent CHD (yes/no) or cancer (yes/no), smoking status (never, former, current), sports activity (hours per week; log-transformed; in the Rotterdam Study total physical activity measured at first follow-up was used; not available at time of analysis for EPIC-Elderly Sweden), moderate alcohol consumption (<0-12 gram/day; yes/no), and energy intake (kcal/day).
A strength of the CHANCES project is that it is a large-scale multi-national collaboration of cohort studies. Pooled analyses of the individual participant data from these different cohorts is a cost-efficient analytical approach and increases statistical power considerably. However, although a large effort has been made to harmonize the data across the cohorts, the study relies on secondary data collected according to different study objectives and protocols, which may be considered a weakness  [13]. The inconsistent results of the current as well as previous studies may indicate that (residual) confounding by in particular socio-economic status hampers the findings. Alcoholic beverage preference, diet, but also smoking behavior, physical activity are determined by age, sex, socio-economic status and cultural or religious norms.
The work of DS was supported by the  European Foundation for Alcohol Research (ERAB)  and the  Dutch Beer Institute. The sponsor did not have any role in the design and conduct of the study; collection, management, analysis and interpretation of the data; and preparation, review or approval of the manuscript. This analysis was part of the  Consortium on Health and Ageing (CHANCES)  project funded in the  FP7 framework programme  of the Directorate-General for Research & Innovation in the  European Commission  (grant  242244 ). The  CHANCES  project is coordinated by the  Hellenic Health Foundation, Greece. The  EPIC-Elderly Study  was partially supported by the  Health Research Fund (FIS)  of the  Spanish Ministry of Health (Spain) ; the  CIBER de Epidemiología y Salud Pública (CIBERESP) , and the  Spanish Regional Governments of Andalucia, Asturias ,  Basque Country ,  Murcia  (no.
A recent study of ten patients with wild-type RAS mCRC showed a strong correlation between 89 Zr-cetuximab tumour uptake and clinical response: four-out-of-six patients with 89 Zr-cetuximab uptake experienced meaningful clinical benefit, while progressive disease was observed in three-out-of-four patients without 89 Zr-cetuximab uptake  [40]. Trials are underway to further explore the relationship between 89 Zr-cetuximab uptake and treatment response (NCT01691391)  [41]  as a guide to dose escalation and, ultimately, to create a selection tool to predict cetuximab response (the IMPACT-CRC trial, NCT02117466)  [42].
Acknowledgments: Proceedings of a European Research Workshop in Digestive Oncology held in Barcelona, Spain, on Wednesday 5 July 2015. This workshop was endorsed by the  European Society of Digestive Oncology. The authors thank  ROCK Unlimited  for assistance with the preparation of this manuscript. Financial support for the European Research Workshop in Digestive Oncology and for this review article was provided by an educational grant from  Bayer Consumer Care AG.
Acknowledgements The authors thank  Omar Okasha ,  University of Tampere , for conducting the statistical analysis of an earlier version of the manuscript. Anna L. Funk  is a scholar in the  Pasteur-Paris University (PPU) International PhD program. We thank  Drs Hanaa Abu Elsood ,  Epidemiology and Surveillance Unit at Ministry of Health and Population, Egypt and Noha Salah at the Preventive Sector Technical Office  at  Ministry of Health and Population, Egypt  for facilitating the work. Disclaimer: The findings and conclusions in this report are those of the authors and do not necessarily reflect the official policy or position of the  Department of the Navy, Department of Defense, Egypt Ministry of Health and Population, US Centers for Disease Control and Pasteur Institute. Maha Talaat  is a contractor of the  U.
Image and data analysis Ring geometry was determined using cyanRing (for cytokinesis analysis of the contractile ring;  Dorn et al. , 2010; Bourdages et al. , 2014) , a semiautomated software tool written in Matlab (MathWorks, Natick, MA). cyanRing allows rectangular cropping with arbitrary orientation of the equatorial region of the embryo. This region is rotated and maximum projected to produce a view of the contractile ring along the spindle axis in the posterior direction. The user then defines the cell outline, as well as the outline of the contractile ring, by selecting at least three points, through which best-fit circles are drawn. Ring geometry is then calculated as shown in Supplemental Figure  2A. Not all depletions exhibited 100% penetrance. To characterize the depletion phenotype rather than the degree of penetrance, we did not include data for cells that were indistinguishable from controls.
Including these data with those of affected cells would have yielded a population average that does not reflect either the perturbation or the control. In addition, outlier data points were discarded, such as an apparent increase in the size of the contractile ring to more than the cell size, that are nonphysiological and most likely due to human error in annotating images. To avoid stylizing the data, the analysis pipeline does not allow reannotating the images. To average data, the time of anaphase onset was determined by visual inspection of the data and set to zero. This assignment has an error of up to 10 s (our sampling frequency). Owing to this error, averaging per time point would result in a population average for closure with an artifactually low slope. By contrast, ring size measurements are comparatively more reliable: the maximum speed of ring closure is very similar among cells within a condition.
ACKNOWLEDGMENTS We thank  Kerry Bloom ,  Julie Canman , and  Ewa Paluch  for critical reading of the manuscript. Carlos Patino Descovich  and all members of the Maddox labs provided discussion and support. Jean-Claude Labbé  provided feeding RNAs. James Fethiere  ( Institute for Research in Immunology and Cancer, Montreal, Canada ) provided purified protein fragments. We acknowledge the thoughtful and constructive input from the anonymous referees. J. F. D. was supported by a postdoctoral fellowship from the  Swiss National Science Foundation. This work was supported by  National Institutes of Health  Grant  GM102390  to A. S. M. J. L. is supported by the intramural research program of the  National Heart, Lung, and Blood Institute at the National Institutes of Health.
3A -D′,G-H′,I; P<0. 05), as well as a 26% significant increase of layer V Ctip2-positive neurons (Fig. 3A -B′, E-H′,J; P<0. 01) on rostral sections of the cortex. The cell density of the layers was evaluated and was unchanged (data not shown). These data support a role for RA in establishing the DL in the cortex. We analysed projection neurons of upper layers (UL) by using Cux1 (layers IV-II)  (Nieto et al. , 2004)  and Brn2 (layers II-III) Tamoxifen was administered at E10. 5. Scale bars: 250 μm. (Sugitani et al. , 2002)  as markers. Strikingly, the overall number of Cux1-positive cells was diminished by 15% (Fig. 4A -D′,K; P<0. 05) in Raldh2cKO mutants. In contrast, the overall numbers of Brn2-positive cells showed a 15% significant increase on rostral sections (Fig. 4A, B, E, F ,L; P<0.
05), and a tendency to an increase on more caudal sections (Fig. 4A′ ,B′,E′,F′,L), in the mutants. The cell density of the layers was evaluated and was unchanged (data not shown). These data further support a role for RA in proper establishment of projection neuron layers in the cortex. To refine this analysis, we counted the number of Cux1-positive, Brn2-negative cells, which identify layer IV neurons. Strikingly, this number was reduced by 30% (Fig. 4G, H ,M; P<0. 05) anteriorly and 45% caudally (Fig. 4G′ ,H′,M; P<0. 05). This observation led us to examine specifically layer IV neurons labelled by RORβ  (Jabaudon et al. , 2012). A loss by 20% of RORβ-expressing neurons was observed in mutants anteriorly (Fig. 4I, J ,N; P<0. 05) and by 30% posteriorly (Fig. 4I′ ,J′,N; P<0. 05). We assessed apoptotic cell death by performing immunolabelling for activated caspase 3 in Raldh2cKO mutants, and compared them with control littermates.
For morphology quantification, multipolar shaped cells (cells harboring at least three processes) and unipolar/bipolar shaped cells were counted in the IZ. For dual comparison, statistical analysis was performed using two-tailed Student's t-test between control and experimental conditions (Microsoft Excel), whereas statistics for multiple comparisons were generated using two-way ANOVA followed by appropriate post-hoc test (GraphPad Prism software version 7). All graphs plot mean±s. e. m. (*P<0. 05, **P<0. 01, ***P<0. 001 for all histograms in figures).
Acknowledgements We thank  Valeŕie Fraulob  for excellent technical assistance;  Meĺanie Schuh  for assistance during her undergraduate training;  Prof. Jamel Chelly  and  Dr Juliette Godin  ( IGBMC, Illkirch, France ) for sharing materials;  Dr Loic Broix  for advice on in utero electroporation;  Dr Juliette Godin  for critical comments on the manuscript.
Funding This work was supported by a grant from the  Agence Nationale de la Recherche  ( ANR grant ReSiNEs ,  ANR-11-BSV2-0003 ), and by an institutional grant from  Labx  ( ANR-10-LABX-0030-INRT ) under the frame programme  Investissements d'Avenir   ANR-10-IDEX-0002-02. P. D. was partly supported by the  Hôpitaux Universitaires de Strasbourg. C. H. was supported by PhD fellowships from the  Institut National de la Santéet de la Recherche Medicale ,  Reǵion Alsace , and  Association pour la Recherche sur le Cancer (ARC).
On the Nipkow disk microscope, standard dichroic and filter combinations for GFP and RFP (red fluorescent protein) fluorescence were used to acquire GFP comp (the fluorophore formed by complementation of non-fluorescent GFP1-10 and GFP11 fragments) and mCherry signals with excitation by 488 nm and 561 nm lasers, respectively. In all multicolor imaging, signals were acquired sequentially. Co-localization analysis was performed with ImageJ 1. 44c program (http://rsb. info. nih. gov/ij/); Pearson correlation coefficient was calculated; occurrence of false co-localization was excluded by calculating Pearson coefficient for "scrambled" images according to the Costes method using the Co-localization Test plug-in of ImageJ. Images were corrected for possible cross-talk between the channels; for presentation purpose, brightness and contrast of raw images were adjusted.
FCS Fluorescence correlation spectroscopy (FCS) measurements were performed with Confocor 3 system built on Zeiss AxioObserver Z1 inverted microscope equipped with 40x 1. 3NA water immersion objective and avalanche photodiode detectors (Carl Zeiss, Germany), as described in detail before  [40]. 488 nm and 561 nm diode lasers were used to excite GFP and mCherry fluorescence; the emission was separated with standard sets of filter cubes. The fluorescence fluctuation data were hardware-correlated, and the correlation curves were subsequently fitted with Zen software (Zeiss) to the single-component or two-component translational diffusion models.
FLIM-FRET Fluorescence lifetime imaging (FLIM) using two-photon excitation and time-correlated single photon counting was performed on Zeiss LSM 510 NLO META FLIM system (Carl Zeiss, Germany) equipped with a Tsunami Ti:Sapphire pulsed laser (Spectra Physics, USA) and on Zeiss LSM 710 NLO system equipped with a Cameleon, Vision II Ti:Sapphire pulsed laser, both with 40x oil immersion objectives. The two-photon excitation pulses at repetition rate of 80 MHz were tuned to 950 nm. The emission of GFP comp was collected at 505-550 nm. The single photon events were detected with a single photon counting photomultiplier H7422 (Hamamatsu, Japan) (LSM 510 NLO META FLIM) or GaAsP-APD hybride "photon counting" detector (LSM 710 NLO), and recorded on a SPC830 analyzer (Becker&Hickl, Germany); time-resolved fluorescence data were handled and analyzed by SPCImage software (Becker&Hickl, Germany).
From this, one can estimate brightness/particle ratio, which serves as a measure of the oligomerization status of the labeled species. Here, to obtain information on the mobility and the oligomerization status of NP-and PB2-containing species in the nuclei of infected cells, we acquired FCS data on HEK-293T cells transiently expressing GFP1-10. Two types of samples were characterized: 1) infected cells containing virus-encoded PB2-GFP11 and transiently expressing NP-mCherry, in which presumably most PB2 molecules were labeled by GFP comp , a small proportion of NP was labeled with mCherry, and all other components expressed by the virus were unlabeled; 2) mock-infected cells transiently expressing NP-mCherry and PB2-GFP11, mostly converted in PB2-GFP comp , in the absence of any other viral protein or RNA.
Acknowledgments The authors acknowledge  Yves Usson  and  Alexei Grichine  ( Institut Albert Bonniot, Grenoble ) for access to the  Microscopie Photonique-Imagerie Cellulaire facility  and for advice on FCS and FLIM experiments and data analysis;  Emmanuelle Perret  and  Jean-Yves Tinevez  for advice on instrumentation at the  Plateforme d'Imagerie Dynamique facility (Institut Pasteur, Paris) ;  Jan Ellenberg  and  Nathalie Daigle  ( EMBL, Heidelberg ) for advice, discussion and pmCherry-N1 vector;  Robert G. Webster  and  Scott Krauss  ( St Jude's Children Research Hospital, Memphis, TN ) for the NP monoclonal antibody clone 3/1.
S. A. was supported by a  Marie Curie Intra-European Fellowship  within the 7th  European Community Framework Programme  (Grant Agreement  PIEF-GA-2009-236959 ), and by an  EIPOD  fellowship (EMBL). This work was supported in part by the  EU   FP7  funded  FLUPHARM  project ( FP7-INFLUENZA-2010  grant  259751 , http:// flupharm. eu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Endurance capacity Endurance capacity was determined by using a closed treadmill (Columbus Instruments) with a 5°incline. Mice were acclimatized for 2 days. The endurance tests started at 8 m/min for 3 min, with increasing the speed by 2 m/min every 3 min until exhaustion. Data were collected before and during the running protocol and used for calculating maximal oxygen consumption (VO 2max ) and respiratory exchange ratio (RER) based on indirect calorimetry.
The data were analyzed using FlowJo v10. To isolate macrophages from uninjured muscles, TA, gastrocnemius, and quadriceps muscles of adult mice at the age of 20-26 weeks were pooled to obtain enough cells. The procedure was similar as described above, using collagenase B solution (Roche Diagnostics) to digest the muscles. Cell viability was verified by Propidium Iodide (BioLegend Cat#421301).
Image acquisition and quantification Images of immunostained muscle sections were acquired with a Zeiss LSM700 microscope using the Zen 2010 software and a 25x objective with 0. 5 zoom. H&E, NADH, and Masson's trichrome staining images were captured using an Olympus IX81 with a 4x objective. The entire area of the muscle sections was acquired and quantification was performed on the complete area using the ImageJ software. Intensity of NADH staining, area of macrophage staining (CD68 + area), and necrotic area were measured using the same software. Necrotic tissue assessment was based on the morphology and coloration of the fibers in H&E sections (swollen pink fibers as necrotic vs. small purple fibers as regenerating) as well as with the help of the CD68 + cells indicating the actively regenerating area.
Muscle contractility measurements in situ TA muscle regeneration was evaluated by measuring in situ isometric muscle contraction in response to nerve stimulation as previously described  [20]. Briefly, mice were anesthetized using a pentobarbital solution (ip, 60 mg/kg), and supplemental doses were given as required to maintain deep anesthesia during the experiments. Each hind paw was fixed with clamps to a platform, and the knees were immobilized using stainless steel pins. The distal tendons of the muscles were attached to an isometric transducer (Harvard Bioscience) using a silk ligature. The sciatic nerves were proximally crushed and distally stimulated with a bipolar silver electrode using supramaximal square wave pulses of 0. 1 ms duration. All data provided by the isometric transducer were recorded and analyzed using the PowerLab software (4SP, AD Instruments).
In contrast, a large proportion of the tissue resident macrophages are polarized towards an M2 phenotype (~40 % in WT and ~60 % in mTG). The higher proportion of polarized M2 macrophages in mTG animals suggests that the muscles of these animals might be preconditioned for faster repair and regeneration. This preconditioning is also partly supported by qPCR data showing higher expression levels of TGFβ and a substantial reduction of IL-12 expression in basal, non-injured state (Fig. 1c ). To investigate whether the preconditioning of these mice also alter the regeneration kinetics, CTX was injected into the TA muscles and abundance of pan-macrophages (F4/80 + ) as well as the relative numbers of M1 (F4/80 + CD80 + CD163 -) and M2 (F4/80 + CD80 - CD163 + ) macrophages were measured by FACS. At 1 and 3 days post-injection, a remarkable infiltration of macrophages was observed (Fig.
Funding This project was funded by the  ERC Consolidator  grant  616830-MUSCLE_NET , the  Swiss National Science Foundation ,  SystemsX. ch,the  Swiss Society for Research on Muscle Diseases (SSEM) , the  Neuromuscular Research Association Basel (NeRAB) , the  Gebert-Rüf Foundation "Rare Diseases" Program , the " Novartis Stiftung für medizinisch-biologische Forschung ", the  Biozentrum Basel International PhD Program "Fellowships for Excellence" , the  University of Basel , and the  Biozentrum. The funding bodies had no influence on the design of the study and collection, analysis, and interpretation of data and writing the manuscript.
The enhanced killing effect of the drug combination was associated with enhanced PERK-dependent ER stress signaling and autophagosome formation, as well as through death receptor activation  [6]. Congruent data were obtained using the parent drug of OSU-03012, celecoxib, and also with the multikinase inhibitors sorafenib, regorafenib and pazopanib  [7, 8]. These pre-clinical studies have resulted in two open clinical trials; in all solid tumor patients (NCT02466802) where patients are receiving increasing once daily dosing with regorafenib and sildenafil; in recurrent glioblastoma patients (NCT01817751) where they receive sorafenib, sildenafil and valproate twice daily. From the research of many laboratories it has been defined that multiple chaperone proteins interact to play key roles in preserving protein stability and signaling, most notably in tumor cells which very often express much higher levels of protein than non-transformed cells.
Acknowledgments Studies were supported by  PHS   R01 CA192614. PD is the holder of the  Universal Inc. Chair in Signal Transduction Research. Dr. Proniuk  and  Dr. Zukiwski  are paid officers of  Arno Therapeutics  which owns the license to  OSU-03012. Thanks to  Dr. H. F. Young  ( Neurosurgery, VCU ) and the Betts family fund for support in the purchase of the Hermes Wiscan instrument. Services in support of the research project were provided by the  VCU Massey Cancer Center Tissue  and Data Acquisition and Analysis Core, supported, in part, with funding from  NIH-NCI Cancer Center Support  Grant  P30 CA016059. The HIV viral replication studies were conducted in part [or in total] by  Southern Research Institute  using federal funds from the  Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health  under contract  HHSN272201400010I  entitled " In Vitro Testing Resources for HIV Therapeutics and Topical Microbicides ".
‚ AMD is an infrastructure-less data dissemination protocol supporting both highway and urban scenarios. A generalized time slot scheme is used to suppress broadcasting, which is based on directional sectors. The number of directional sector is adjusted adaptively between two or four according to the local road topology and the distribution of neighbors. A store-carry-forward mechanism resorts to a role transition, i. e. , from tail to non-tail, to trigger a new broadcast to uninformed vehicles. In the simulation of this paper, the time slot st is set to 5 ms and one time slot is assigned to one vehicle, i. e. , ts d " 1. Moreover, the additional delay AD ij is set to one DIFS, i. e. , 58 µs. The position list of intersections is preloaded in the system and is operated as the UV-CAST case.
‚ Data Dissemination Speed: This metric represents how fast the data can be disseminated among vehicles in the ROI. To record this metric, the source only sends data message once, and then the simulation computes the increase of data coverage with time. If the data coverage increases greatly in a short time, which means the protocol achieves a high dissemination performance. This metric is mainly used to estimate the impact of GPS drift on the performance of protocols. To comprehensively evaluate the performance of TrAD, various experiments were designed to analyze the impact of different urban maps, different traffic routes, network density and GPS drift. The geographic data were retrieved from OpenStreetMap (OSM) database. Traffic rules, e. g. , the speed limitation and the traffic light, were set according to the real world scenarios.
Different Urban Maps For urban scenarios, two maps were created. The first map is a fragment of Manhattan Island in New York City, USA (Figure  6a ), and the second map is the downtown area of the city of Clermont-Ferrand, France (Figure  6b ). The ROI size of both two maps is 1 × 1 km 2. The map statistics, as shown in Table  2 , indicate that the map of Clermont-Ferrand has more lanes, junctions and shorter street lengths than the Manhattan one, which means that the road traffic topology is more complex in Clermont-Ferrand than in Manhattan. The data messages are generated by a fixed source node located at an appropriate intersection and are collected by all vehicles moving in the ROI. Similar traffic routes were created for two maps, where vehicles are distributed uniformly in the scenarios.