dataesr/scientific-paragraphs-categorization huggingface dataset:
PCL surface detection and geolocation There are two key challenges when working with data from a scanning PCL. First, properly georeferencing photons from up to 14°off nadir requires knowing the aircraft's orientation and the sensor's relative pointing biases with milliradian accuracy. Second, a PCL produces large volumes of data with a low signal-to-noise ratio. This demands computationally efficient approaches that use statistical inferences to determine the true surface within a spatial volume contaminated by solar photons (Fig. 8 ) and superposed electronic noise (Fig. 9 ). Our approach to addressing this challenge in postprocessing involves subsampling the photons into 'pseudobeams', chosen to mimic the planned ATLAS configuration, detecting a surface while still in the aircraft-relative frame, and finally georeferencing that surface point.
Data subsetting The objective of pseudobeam averaging is to generate a simple data product of manageable volume that can be used both to iteratively determine pointing biases and to accomplish first-order altimetry science goals. To do this we emulate the discrete beams found on the ATLAS system by filtering for photons within limited cones. For circular scan patterns, we selected six cones within the lidar reference frame (Fig. 7 ), sampling the edges, fore and aft, and at 45°. For linear scan patterns, we selected the edges of the scan pattern, the nadir point and two points in between. The typical cross-track spacing between the along-track and mid-cross-track pseudobeams is 70-100 m, similar to the 90 m separation of the planned ATLAS beams. Each pseudobeam consists of the photons within a single cone over 0.
25 s ($5 scans). At typical aircraft survey heights, this cone corresponds to a 10 m Â 25 m footprint for each pseudobeam. For each pseudobeam, a range to the surface is computed and the resulting vector is georeferenced. This approach greatly reduces the data volume, while preserving information content about the extrema of the scan pattern. A  version  (Blankenship and others, 2013b)  of this dataset (with geolocated photons) is available from NSIDC.
We then geolocate the surface range vector using the method used for the LAS system. Photon counts for the peak coarse and fine bins, the background noise rate, and information on the shape of the integrated surface return are also reported. These data are distributed by NSIDC as part of Operation IceBridge's ILSNP4 data  (Blankenship and others, 2013a). Locations of ILSNP4 PCL surface elevation data in the Wilkes Land region of East Antarctica are shown in Figure  1.
SURFACE-ELEVATION CHANGE DETERMINATION For this paper, we use the ILSNP4 slope and elevation data product to assess the linear, invariant component of surfaceelevation change over the ICESat record, as constrained by the ALAMO cross-track slope product. We also use the ILSNP4 data to investigate the surface-elevation change since the end of the ICESat record, for which ICECAP represents a unique record.
Slope derivation We derived surface slope using geolocated PCL beam surface detections within 200 m of each LAS point to determine a best-fit plane specified by zðx, yÞ ¼ ax þ by þ c ð3Þ where a, b and c are constants defining the slope, x and y are eastings and northings in the standard polar stereographic projection, and z is elevation in the WGS84 coordinate system. z at the location of the LAS coordinate is fixed to the LAS elevation. Solutions that are not constrained by at least ten points from a side-pointing pseudobeam are rejected, as are solutions where the centroid of the PCL points is >66 m from the LAS spot. We used a linear least-squares method to perform the fit, and output the standard deviation of the residuals, as well as the slope parameters. These combined surface-elevation and slope estimates are included in the ILSNP4 Hierarchical Data Format 5 (HDF5) data product available from NSIDC  (Blankenship and others, 2013a).
Totten Glacier is one of the largest glaciers on Earth and has exhibited consistent lowering across the satellite record  (Davis and others, 2005; Zwally and others, 2005; Flament and Rémy, 2012; Khazendar and others, 2013) , although rough terrain and pervasive cloud cover make it a difficult target for radar and optical systems, respectively. Denman Glacier represents another outlet of the Aurora Subglacial |Basin, and from satellite data has also exhibited lowering trends, associated with a dynamical ice shelf. However, due to its location in a pronounced valley in the ice sheet, and association with exposed nunataks and blueice regions, it has been hypothesized that the lowering may be due to enhanced wind erosion  (Flament and Rémy, 2012).
Results from Wilkes Land Our dz=dt analysis was extended to the two key glaciers further west in Wilkes Land, using data from the ICP3 and ICP5 seasons, where we find evidence for much more rapid change than at Cook Ice Shelf. The most prominent changes over the ICESat-ALAMO observation period are found over Denman and Totten Glaciers, along tracks 1335 (Fig. 11 ) and 0033 (Fig. 12 ), respectively. Each of these tracks was repeated in the ICP3 and ICP5 seasons. We find maximum rates of surface lowering for the ICESat epoch of À1 m a À1 on a fast-flowing interior bend of Denman Glacier, and À2 m a À1 near the grounding line of Totten Glacier (also identified by  Khazendar and others, 2013).
Totten Glacier In both the ICESat-only case (pink in Fig. 11  third panel) and the ALAMO-corrected datasets the hypothesis of no linear trend can be rejected, with confidence intervals of AE25 cm for most of the region. One region where the planar assumption used for both ICESat-only and ALAMO datasets appears to degrade is the south side and summit of Law Dome. This region of Law Dome is dominated by blue ice and steep ice slopes; increased residuals (and a corresponding increase in the size of the confidence interval) are apparent. For Totten Glacier, we find in general that the difference in ICESat and post-ICESat trends is within the 95% confidence interval, implying no significant changes in lowering. An exception is linked to a 5 km wide prominent spike of surface-elevation growth during the ICESat era at À67:8°, focused on a downstream stepping 200 m bed relief feature.
CONCLUSIONS During the course of NASA's Operation IceBridge, ICECAP collected 25 039 track kilometers of re-flights of ICESat lines over the margins of the East Antarctic ice sheet. The Airborne Laser Altimeter with Mapping Optics (ALAMO), a scanning photon-counting lidar registered to a nadir laser profiler, was deployed to extend the elevation record of ICESat. We find the ALAMO dataset meets IceBridge science requirements and can confirm and enhance the ICESat record in Antarctica. With our record along existing ICESat lines we find little evidence of broad surface-elevation change in the region feeding Cook Ice Shelf, indicating a relatively stable system there. Conversely, our observations show continued dramatic ice lowering at Denman and Totten Glaciers, likely driven by changes in the floating portions of the glaciers caused by enhanced ice-shelf melting.
ACKNOWLEDGEMENTS Funding for the fieldwork and data reduction was provided by  NASA  grants  NNX09AR52G ,  NNG10HP06C  and  NNX11AD33G ,  Program DACOTA  ( 06-VULN-016 ) of the  Agence Nationale pour la Recherche , and  UK Natural Environment Research Council  grant  NE/D003733/1. This work was supported by the  Australian Government's Cooperative Research Centres Programme  through the  Antarctic Climate and Ecosystems Cooperative Research Centre (ACE CRC). This work received funding from the  American Recovery and Reinvestment Act. Logistical support was provided by  Australian Antarctic Division  (through  Australian Antarctic Programme projects 3103  and  4077 ), the  US Antarctic Program  and the  French Polar Institute. We thank  DTU  for their loan of an  EGI  and thank  Gabriel Jodor  and  Christopher Field  of  Simga Space Corporation  for technical guidance with this system.
Patients receiving oxygen therapy and/or noninvasive ventilation (NIV) and/or with multiple stable comorbidities were able to be included in the rehabilitation program. All data were collected prospectively and were entered into our rehabilitation and TPE-computerized medical records. The Comité d'Evaluation des Protocoles de Recherche Observationnelle (CEPRO) (observational research protocol evaluation committee) of the Société de Pneumologie de Langue Française (French Language Society of Pulmonology) (CEPRO 2011-036) examined this project and approved analysis of the data collected from these patients.
statistical analysis Continuous variables were expressed as mean ± standard deviation. Qualitative variables were expressed as frequencies or percentages. The normal distribution of continuous variables was tested by the Shapiro-Wilk test. Analysis of variance with repeated measures or a paired Wilcoxon test was used to analyze the time course of the various parameters according to the normal or nonnormal distribution. Post hoc analyses using the Bonferroni procedure were performed. Statistical analysis was performed with SAS 9. 3 software (SAS Institute Inc. , Cary, NC, USA, NC 25513). A P-value ,0. 05 was considered statistically significant.
Acknowledgments The authors thank the rehabilitation team who managed these patients: GT, SD, FU, VW, and ML. The authors also thank Adair,  France Oxygène, Homeperf, LVL, Orkyn, Santélys, SOS Oxygène, Sysmed, VitalAire , and the  ARS Nord Pas De Calais  for their support of the home-based  PR program.
The number of GFP-LC3-positive puncta significantly increased in response to ethanolamine, both in the absence and presence of bafilomycin A1. Of note, the level of ethanolamine-mediated autophagy was equivalent to that observed upon nutrient deprivation (namely cultured in Earl's balanced salt solution), which was used as a positive control of autophagy stimulation. Autophagy induction by ethanolamine was neither associated with a decrease in mTORC1 activity, as measured by the phosphorylation of p70 s6k , nor with an activation of AMPK (Supplementary Figure  S4D ). All these experiments were repeated in a H4 neuroblastoma cell line stably expressing GFP-LCD, yielding similar results (data not shown). Hence, ethanolamine can stimulate autophagy in a variety of human cell lines. To assess cell survival, we finally performed a yeast-like chronological senescence assay, where highly confluent U2OS cells were left untreated or stimulated with 10 mM ethanolamine for 1 week.
). An anti-glyceraldehyde-3-phosphate dehydrogenase antibody (Chemicon International Inc. , Temecula, CA, USA) was used to control equal loading of lanes. Automated microscopy. U2OS or H4 cells stably expressing GFP-LC3 were seeded in 96-well imaging plates (BD Falcon, Sparks, USA) 24 h before stimulation. Cells were treated with the indicated agents for 4 h. Subsequently, cells were fixed with 4% PFA and counterstained with 10 μM Hoechst 33342. Images were acquired using a BD pathway 855 automated microscope (BD Imaging Systems, San José, USA) equipped with a 40X objective (Olympus, Center Valley, USA) coupled to a robotised Twister II plate handler (Caliper Life Sciences, Hopkinton, USA). Images were analyzed for the presence of GFP-LC3 puncta in the cytoplasm by means of the BD Attovision software (BD Imaging Systems).
Flies were collected at emergence and 20 females were kept per vial with an average of 87 flies per group and replicate. The food was changed twice a week and supplemented or not with ethanolamine hydrochloride (Sigma, E6133) at 1 mM or 10 mM final concentrations. The number of dead flies were recorded every weekday until all flies were dead. Five independent replicates were performed. The independent replicates, as well as the pooled data from all replicates were analysed by a Wilcoxon survival analysis test in R (script available on request). Statistical analysis. Statistical analyses were calculated in Origin8. For assessment of significance one-way ANOVA followed by Bonferroni post hoc test was performed, except for Figure  1b , Figures  2a  and b  and Figures  3b, c , g and h which were processed using a two-factor ANOVA with strain and time as independent factors.
Acknowledgements. This work was supported by the  Austrian Science Fund FWF  (grants LIPOTOX,  I1000-B20 ,  P23490-B12 , and  P24381-B20 ) to FM. We acknowledge support from  NAWI Graz. OK is a member of the  PhD program  ' Molecular Enzymology ', funded by the  FWF  (project  W901-B12 ). GK is supported by the  Ligue contre le Cancer  (équipe labelisée);  Agence National de la Recherche (ANR) ;  Association pour la recherche sur le cancer (ARC) ;  Cancéropôle Ile-de-France ;  Institut National du Cancer (INCa) ;  Fondation Bettencourt-Schueller ;  Fondation de France ;  Fondation pour la Recherche Médicale (FRM) ; the  European Commission (ArtForce) ; the  European Research Council (ERC) ; the  LabEx Immuno-Oncology ; the  SIRIC Stratified Oncology Cell DNA Repair and Tumour Immune Elimination (SOCRATE) ; the  SIRIC Cancer Research and Personalized Medicine (CARPEM) ; and the  Paris Alliance of Cancer Research Institutes (PACRI).
, 2006). The aim of this paper is to investigate the summertime evolution of snow SSA at Dome C, as well as to further understand its variability, from the daily to the interannual scale. To quantify this evolution, we use three data sets. Firstly, a large number of in situ SSA measurements were collected at Dome C during summer campaigns (Sect. 2. 1). These included vertical profiles between the surface and 10 cm, and snow samples from the surface, both measured manually during the summer campaigns 2012-2013 and 2013-2014 using the SSA profiler ASSSAP (a light version of POSSSUM;  Arnaud et al. , 2011). In addition, automatic measurements of snow spectral albedo were used to estimate the evolution of SSA close to the surface during daylight periods. Secondly, the evolution of SSA in the topmost centimetres was estimated from remote sensing observations of the snowpack in the microwave range over the period 2000-2014 based on Picard et al.
Acknowledgements. We are grateful to the anonymous reviewers and the editor for their valuable comments. LGGE is part of  LabEx OSUG@2020  ( ANR10 LABX56 ). This study was supported by the  ANR  program  1-JS56-005-01  MONISNOW. The authors acknowledge the  French Polar Institute (IPEV)  for the financial and logistic support at Concordia station in Antarctica through the  CALVA-Neige  and NIVO programs. We thank  Eric Brun  for insightful discussions about Crocus parameterizations. We are grateful to  Arnaud Mialon  for helping with the measurements at Dome C. The editor thanks the anonymous reviewers for their work. Edited by:  M. Schneebeli.
As shown by WB analysis (Fig. S1 ), Tau-5 IP allows the purification of full-length Tau (FL-Tau) as well as N-and C-terminally truncated Tau and aggregated species, which display lower and higher molecular weights, respectively. In order to improve detection sensitivity, Tau-5 IP products were then subjected to primary amine labeling using a covalently-linked biotin prior to enzymatic digestion with either trypsin or the endoproteinase Asp-N. Labeled peptides were then purified on streptavidin columns and identified using liquid chromatography-mass spectrometry (LC-MS/MS). This approach resulted in the identification of a number of Tau peptides (Table  S1 ; data compiled from all samples), including some semi-tryptic/ semi-Asp-N peptides. Indeed, 21 peptides displayed non-tryptic/ non-Asp-N residues at the N-terminus and constituted our set of candidates for N-truncated Tau species (Table  1 ).
We measured HDAC activity in cytoplasmic extracts, since HDAC6 is mainly cytoplasmic compared to other HDAC members. Our data (Fig. S4 ) show that there was no significant difference in HDAC activity between cells transfected with FL-Tau and those with N-terminally truncated species, indicating that the effect on tubulin acetylation is not related to differences in HDAC6 activity. Instead, this effect could be a consequence of improved microtubule polymerization and/or stabilization. In agreement with this possibility, the investigation of another posttranslational modification of tubulin, detyrosination, which is also representative of a stable population of microtubules  34  , revealed that it was significantly increased with Gln124-Tau when compared to FL-Tau (Fig. 3 ). Gln124-Tau binds more strongly to microtubules than FL-Tau and protects against depolymerization.
Methods Human tissue samples. Human brain autopsy samples were from the Lille NeuroBank collection (Centre de Ressources Biologiques du CHRU de Lille). Informed consent was obtained from all subjects. The Lille NeuroBank has been declared to the French Research Ministry by the Lille Regional Hospital (CHRU-Lille) on August 14, 2008 under the reference DC-2000-642 and fulfils the criteria defined by French Law regarding biological resources, including informed consent, ethics review committee approval and data protection. The study was approved by the ethics review committee of Lille NeuroBank. The Table  2  indicates the stage of Tau pathology, categorized on the basis of neuropathological characteristics according to Braak and Braak  11. Cell culture and transfection. N1E-115 mouse neuroblastoma cells were grown in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum without pyruvate, 2 mM L-glutamine and 50 units/ml penicillin/streptomycin (Invitrogen) in a 5% CO 2 humidified incubator at 37uC.
The raw data were processed using Xcalibur 2. 0. 7 software. The database search was done using the Mascot search engine (Matrix Science Mascot 2. 2. 04) on a homemade protein databank containing the 6 human Tau isoforms and some contaminants, or on the entire SwissProt protein databank. Proteome Discoverer 1. 3 (ThermoFisher Scientific) and Mascot were used to search data and filter the results. The following parameters were used: MS tolerance 5 ppm; MS/MS tolerance 0. 5 Da; semi-tryptic or semi-Asp-N peptides; one missed cleavage allowed; partial modifications: carbamidomethylation (C), oxidation (M), phosphorylation (ST), acetylation (N-term), thiopropionation (N-ter, K). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.
proteomexchange. org) via the PRIDE partner repository  56  with the dataset identifier PXD001353 and DOI 10. 6019/PXD001353. Western blotting (WB). Protein extraxts were standardized at 1 mg/mL with LDS 2X supplemented with a reducing agent (Invitrogen) and denatured at 100uC for 10 min. Proteins were then separated with SDS-PAGE using precast 4-12% Bis-Tris NuPage Novex gels (Invitrogen). Proteins were transferred to 0. 45 mM nitrocellulose membranes (Amersham TM Hybond ECL), which were saturated with 5% dry non-fat milk in TNT buffer; 140 mM NaCl, 0. 5% Tween20, 15 mM Tris, pH7. 4, or 5% bovine serum albumin in TNT (Sigma) depending on the primary antibody. Membranes were then incubated with the primary antibodies (Table  S2 ) overnight at 4uC, washed with TNT three times for ten minutes, incubated with the secondary antibodies (Vector) and washed again before development.
The gluco-and mineralocorticoids signaling comprises enzymes and receptors. (b) The cortico-and mineralocorticoid pathways components. Although the number of metabolites is high, the number of enzymes and receptors is rather limited. 39 potential contributors to any tissue extended RAAS taking into account kinin precursor and receptors and a complete gluco/mineralocorticoid pathways were considered. Adapted from KEGG database: http://genome. jp/kegg/pathway/map/map00140. html. suggesting a link between systemic risk factors and local activation of AGT expression in the arterial wall. We showed that this overexpression in type 2 diabetic patients could result from the imbalance in favor of the MAP kinase pathway over the PI3 kinase pathway seen in advanced atheroma stages and associated with insulin responses and insulin resistance  [32].
Extended RAAS in the human carotid atheroma. Boxes delineate investigated gene products, in black (similar levels), red (higher levels), and green (lower levels) in advanced stages of atheroma compared to low grade remodeling. Shaded parts are those which were at too low level for reliable quantification. Interrupted frames are those for which publicly available human carotid atheroma transcriptomic data indicated the presence of very low levels. Adapted from KEGG database: http://genome. jp/kegg/pathway/map/map04614. html.
Acknowledgments This work has been supported over time by the  CHU Grenoble, INSERM, Université Claude Bernard Lyon 1 ,  Région Rhône-Alpes ,  SFHTA ,  Fondation de France ,  Fondation pour la Recherche Médicale ,  Fondation de l' Athérothrombose, and Hôpital Nord-Ouest, Villefranche.
Extended RAAS in the human carotid atheroma. Boxes delineate investigated gene products, in black (similar levels), red (higher levels), and green (lower levels) in advanced stages of atheroma compared to low grade remodeling. Shaded parts are those which were at too low level for reliable quantification. Interrupted frames are those for which publicly available human carotid atheroma transcriptomic data indicated the presence of very low levels. Adapted from KEGG database: http://genome. jp/kegg/pathway/map/map04614. html. Angiotensin (1-5) Atherogenesis through Angiotensin (1-9) ACE MME ACE MAS1 proliferation, dedifferentiation, ATP6AP2 AGT KLK1 REN CTSD Angiotensin I CTSG ACE 2 CPA3 CTSA CTSG CMA1 ENPEP Angiotensin II MME NLN THOP1 PREP ACE 2 Angiotensin (1-7) AGTR1 AGTR2 HSD11B1 inflammation of VSMC transdifferentiation and CYP11B1 IGF2R Kallikrein-kinin system ACE Angiotensin III GR𝛼 Cortisol Complement and coagulation cascades DPP3 Inactive peptides ANPEP RNPEP Angiotensin IV DPP3 LNPEP MR ? Aldosterone CYP11B2 Figure 3: coordinated regulation during atherogenesis with synergistic variations toward the facilitation of Ang II and Ang IV formation and responses in the atherosclerotic arterial wall.
In human cultured VSMC from carotid artery, aminopep- tidase A and IRAP expression in human VSMC were both increased by low nanomolar concentrations of Ang II and both decreased by Ang IV (Hodroj unpublished results). Investigations into transcriptomic public databases of human carotid atheroma confirm the presence of high or very high levels of ANPEP, ENPEP, IRAP, and DPP3 mRNA in human carotid atheroma.
Severe restrictive aortic regurgitation due to aortic fibrous strand A transthoracic echocardiogram showed a tricuspid aortic valve with severe aortic regurgitation (Panel A). Aortic annulus and root were not dilated. Transoesophageal echocardiography showed a tricuspid aortic valve with normal opening movement and an adequate valve coaption between right coronary and non-coronary cusps (Panel B). A linear mobile echo like a chordae tendineae strand was connecting the left coronary sigmoid cusp to the sinotubular junction (Panel C), leading an important tenting and restriction of this cusp (Panel D and E, see Supplementary data online, Video S1). Colour flow displayed a severe aortic regurgitation (Panel F, see Supplementary data online, Video S2). Live three-dimensional echocardiography was performed, improving the assessment of the fibrous strand (Panel G, see Supplementary data online, Video S3).
The patient denied surgery The aortic chordae tendineae strand may be an embryonic remnant during the semilunar cusp formation process of the aortic valve. There are few reported cases, most of them from Asia, describing aortic regurgitation due to spontaneous rupture of chordeae tendineae. To our knowledge, there is only one case reported similar to ours, submitting an aortic valvular incompetence owing to this restrictive mechanism (fibrous strand) without another mechanism: annular dilatation, prolapse or any congenital heart defect. Supplementary data are available at European Heart Journal -Cardiovascular Imaging online. Published on behalf of the European Society of Cardiology. All rights reserved. & The Author 2015. For permissions please email: journals. permissions@oup. com.