dataesr/scientific-paragraphs-categorization huggingface dataset:
Conclusion Lexicalized phrase structure parsing of morphologically rich languages used to be difficult since existing implementations targeting essentially English or Chinese do not allow a straightforward integration of morphology. Given multi-view treebanks, we achieve multilingual parsing with a language-agnostic head annotation procedure. Once this procedure has created the required data representation for lexicalized parsing, only modest and weakly language dependent feature engineering is required to achieve state-of-the-art accuracies on all languages considered: a minimal interface with morphology already contributes to improving accuracy, and this is specifically the case when heads are accurately identified. When heads are only approximatively identified, spanbased configurational modelling tends to correct the approximation.
For Basque, our problem comes from a recurrent inconsistency in the SPMRL data set. As annotated in the c-trees, the punctuation induces a modification of the d-structure: ctrees encode a different governor for punctuation marks than d-trees. This not only causes problem to our head annotation procedure but also for the parser to solving these attachments. A simple correction results in a significant improvement of these parsing results. However we decided to leave the data untouched in order to preserve fair comparisons with other systems.
Acknowledgements The  Sabah Parks Herbarium (SNP)  is gratefully acknowledged for the loan of the herbarium material. We would like to express our gratitude to  Sabah Parks  for the joint research project with  Rimi Repin  during which this species was discovered, and in particular to  Sukaibin Sumail  and  Rositti Karim  for their help and expertise in the field and in the herbarium. We would like to acknowledge the  Sabah Biodiversity Council  for granting permission for conducting research in Sabah. Finally, the  French National Research Agency  through the national " Investissements d'avenir" program  ( ANR-10-LABX-21-LABEX RESSOURCES21 ) is gratefully acknowledged for funding A. van der Ent's postdoctoral position in 2014-2015.
However, to date no data existed detailed enough to test these hypotheses. Here, we present a detailed investigation of cross-shelf transport during formation of a large mesoscale eddy in the eastern Indian Ocean. We argue that the eddy itself is the essential mixing crucible for the locally high production documented in warm core eddies off Western Australia, and that the eddy formation process represents the major driver of cross-shelf transport during the autumn. We use conductivity-temperature-depth (CTD) transects, SeaSoar transects, and Lagrangian surface drifters to investigate mixing water masses during eddy formation, and conclude that, while local phytoplankton sources provide significant chlorophyll a (Chl a) to the eddy during formation, particles from other sources are likely to be important.
Study area and data collection The formation of an anticyclonic eddy of the LC, located west of Rottnest Island off Western Australia, was investi-gated over a 25 d period during May 2006 on the RV Southern Surveyor. Eddies are a recurrent, but not permanent feature of the LC, so sampling was planned for the period of formation during the autumn intensification of the LC  (Cresswell 1991; Pearce 1991). The operational area was from 308S-348S and up to 370 km (1128E) offshore of the southwestern Australian coast  (Paterson et al. 2008; Fig. 1). The evolution of the anticyclonic eddy off the Perth Canyon was followed for the weeks prior to the cruise using remotely sensed sea surface temperature (SST) and sea surface height anomaly data  (Paterson et al. 2008 (Paterson et al. , 2013)). Along the ship track, continuous underway measurement of the horizontal current velocity field along the ships track was obtained using a vessel mounted RDI 70 kHz Ocean Surveyor Acoustic Doppler Current Profiler (ADCP) (Teledyne RD Instruments).
The instrument was set to record from just below the surface to a maximum water column depth of 300 m and data were averaged in 8 m depth bins. Between 02 May and 27 May, 120 CTD casts were performed across the eddy and in adjacent water masses using a Seabird SBE 911 Plus instrument with dual temperature and conductivity sensors and a Chelsea TGI fluorometer attached to a 24 3 10 L-bottle Niskin rosette. Maximum cast depth was to 500 m or to within 10 m of the bottom in shallower water. For some locations, CTD casts were performed to 1000 m. The rosette system carried a Wetlabs C-Star TM transmissometer, a Seabird dissolved oxygen sensor (SBE43) and transmissometer, used here as an indicator of fine particle concentration  (Karageorgis et al. 2008). Of the 120 CTD casts, 18 were primary production stations including measurements of particulate organic carbon (POC) and particulate nitrogen (PN), and 13 C carbon uptake (see below).
Underwater particles (>60 lm), which include phytoplankton chains and aggregates, detrital particles, and some zooplankton, were enumerated in situ using the Underwater Vision Profiler 4 (UVP4)  (Picheral et al. 2010). The UVP recorded images every 8 cm. To avoid light contamination, images deeper than 40 m were used for day profiles. Objects in each image were detected, sized, and enumerated on custom software  (Picheral et al. 2010)  based on the lateral scattering of light from a particle. Total number of pixels is converted to Equivalent Spherical Diameter. We present the data for small particles 60-550 lm. as volumetric particle concentrations (# L 21 ) or as biovolume/water volume (ppm). Particle biovolume was converted to C content of large particles using the equations in  Guidi et al.
CO 2 -fixation rates were calculated using a similar isotope mass balance approach as described by  Montoya et al. (1996)  and applied in similar field experiments by  Holl et al. (2007)  where the ambient concentration of dissolved inorganic carbon was based on the in situ salinity and temperature of the water collected and used in our experiments at each station  (Parsons et al. 1984). Vertically integrated CO 2 -fixation rates were estimated for each station, and were calculated via trapezoidal integration with depth. To determine regional correlates with oxygen concentrations, multiple linear regression on untransformed oxygen, transmission, salinity, temperature, latitude, and longitude, using the regression package associated with Sigmaplot V R v13.
(Period 1) for offshore flux calculations. We used an ADCP, UVP particle estimates, as well as POC and PN measurements from the Continental Shelf Water (CW) CTD cast and SS1 to estimate the offshore velocities and fluxes of nitrogen, carbon, and Chl a during Period 1. A weak LC instability is visible in SST data at 328S as early as mid-April, and the LC meander was fully visible by 29 April (Fig. 1A ), and shelf waters were flowing directly into the center of the meander (Fig. 1B ) thereafter. The meander then curled northward, almost closing shoreward gap (Fig. 1C, D ), but the opening toward the shelf persisted until 14 May, making this the end of Period 1. After 14 May, (Period 2) the meander was closed on the landward side (Fig. 1E ), and the northern arm of the meander flowing offshore had met the southern arm of the meander as it returned shoreward, closing the center of the eddy off from direct connection with the shelf.
Once closure of the meander isolated the eddy center, we used drifter tracks, and ADCP data to estimate the time and space scales of eddy rotation at three different distances from the eddy center. We made four separate estimates of oxygen depletion and nitrate release within the eddy based on (1) SeaSoar2 data, (2) CTD/UVP time series data along the drifter tracks (including particles, POC/PN, chlorophyll, dissolved nutrients, and oxygen) to estimate the rates of oxygen depletion and nitrate release within the eddy, (3) N-S CTD/UVP transect through the center of the eddy, and (4) pooled nitrate and oxygen data across the whole dataset.
7A ). Biogeochemical measurements indicated a spatial coherence of high nitrate and low oxygen signatures within the center of the eddy (Fig. 7B, C ), with oxygen depletion and nitrate release most extreme in the eddy center. Particle concentrations were highest in two layers, (1) within the mixed layer, and (2) in a clear maximum between the isopycnals q 5 25 and q 5 25. 5 between 200 m and 300 m depth, just above the nitrate maximum (Fig. 7D , see [NO 3 ] 5 2 lmol L 21 , Fig. 7B ). These were also concentrated toward the center of the eddy. Isopycnals within the eddy were deflected downward to at least 1000 m depth. Patterns in oxygen depletion emerging from complete dataset (Periods 1 and 2) Multiple regression analysis on untransformed oxygen electrode data throughout the dataset elucidated variables that independently contributed to the variation in oxygen, indicating that longitude, salinity, and transmission were independent predictors of equal statistical weight (all parameters significant (p <0.
Instead, we are exploring the nature of these relationships to understand whether distance from shore (longitude) is related to O 2 independently of particle concentration and salinity. Oxygen concentrations were lowest in waters of relatively low salinity (therefore possibly associated with intrusions of LC waters), close to shore, where there were high particle concentrations (i. e. , low transmission) (Table  2 ). The relationship was strongest between 150 m and 250 m depths, where salinity, transmission, and longitude together explained 67. 5% of the variation in oxygen concentrations. In this depth layer, the coefficient for transmission and salinity roughly doubled while that for longitude halved in comparison to the relationship within the entire water column (Table  2 ). Across all datasets, the relationship between nitrate and volumetric oxygen concentrations executed chemically from bottle casts revealed two separate relationships, one in the cooler waters (<188C) where oxygen concentrations rose to an asymptote of about 240 lmol L 21 at depth (Fig.
15 mol N/mol O 2 ). Between 50 m and 200 m, peak mixed layer nitrate concentrations (2 lmol L 21 ) occurred at the lowest oxygen concentrations, at about 208C (Fig. 8A ). Nitrate and phosphate concentrations were linearly correlated throughout the dataset, with a slight drop of the NO 2 3 : PO 23 4 ratio to 15. 1 in 4 points in deep waters (>30 lmol L 21 NO 2 3 ; data not shown). The lowest oxygen concentrations (below 193 lmol L 21 ) occurred at a water density of q 5 25. 4-25. 5, just below a significant particle peak at a density of q 5 24. 8 (Fig. 8B ) at temperatures of about 20-218C, collocated with, but slightly shallower than, the nitrate peak at about 208C, (Fig. 8A, B ). Overall, there was a striking physical coherence between low oxygen and high nitrate concentrations.
Calculations of biogeochemical impact of the forming eddy We use the multiple datasets presented here (SeaSoar transects, Drifters, and CTD stations and transects) to calculate the biogeochemical fluxes mediated by eddy activity: (1) offshore fluxes of carbon and Chl a in Period 1, and (2) oxygen depletion and nitrate release within the eddy from Period 2. Each dataset yields an estimate with different limitations and potential errors, but each is fully independent (Tables  1, 3 ).
The clearest and best-resolved time line of net oxygen depletion occurred along the track of Drifter 2a moving along the inner perimeter of the eddy (Fig. 10 ; Table  3 ). Examined with depth, there were oxygen minima at 120 m (ca. q 5 25. 3-25. 5), where higher oxygen depletion rates occurred (up to 3 mmol m 23 d 21 ), coinciding with net nitrate increases along the drifter track (0. 083 mmol m 23 d 21 and 0. 170 mmol m 23 d 21 ). In the euphotic zone there was a net oxygen production 7. 8 mmol m 23 over 1 week (very similar to those estimated via the SeaSoar2 data below, about 1 mmol m 23 d 21 above the q 5 25 density contour). Drifters 1 (LC) and 2b (Eddy Center) did not show significant oxygen depletion with time, but the difference between them points to a large net oxygen deficit in the eddy center, which is quantified further via the CTD transect data below.
The eddy center displayed no measurable changes with time in oxygen, nitrate, or physical structure, but its properties (see Fig. 10 ) suggested that oxygen depletion and associated nitrate release had occurred there since eddy formation. A layer of large particles was spatially contiguous with the coast in the early stages of eddy formation, and were later seen deep within the eddy, physically associated with the oxygen minimum and shallow nitrate peak along the q 5 25. 5 density interface; across all datasets the center of the eddy had the most profound oxygen deficit. Overall, then, we used the eddy center as an end point to our calculation of modifications in oxygen and nitrate in time and space. This was summarized further in Table  3  and below. Could local primary production account for carbon accumulation at the surface that could support the observed rate of oxygen depletion at depth? Our estimates of local carbon uptake rates suggest not.
Acknowledgements We thank  D. Krikke  for logistic and laboratory support, the captain and crew of the R. V. Southern Surveyor  for expert assistance at sea, and the  Australian National Marine Facility  for ship-time granted for this project. JPL is currently an  American Association for the Advancement of Science (AAAS)  Overseas Fellow serving at the  United States Agency for International Development. This article was a collaboration with JPL in his personal capacity, and is the result of the author's independent research. The opinions and views expressed in this article are the author's own and do not necessarily represent the views of  AAAS , or the  U. S. Agency for International Development  or the  United States Government.
ACKNOWLEDGMENTS This work was supported partially through  FUSTIPEN (French-U. S. Theory Institute for Physics with Exotic Nuclei)  under  DOE  grant number  DE-FG02-10ER41700  and by the  DOE  award number  DE-FG02-96ER40963  ( University of Tennessee ). One of the authors (M. P. ) wish to thank  COPIN  and  COPIGAL  for the support.
Ranked by bit score and discarding hits to hypothetical and unverified bacterial proteins, the top hits were capsid-and replication-associated proteins from viruses in the gemycircularvirus group  (7). We performed a MUSCLE (version 3. 8. 425) (8) alignment of our genome against the 32 gemycircularvirus group complete genomes in NCBI GenBank  (3, 6)  on 27 May 2015. The alignment resulted in 30 to 44. 5% identity with the genomes of the gemycircularvirus group at the amino acid level. Our genome sequence contributes to the resource of circular viral sequences isolated from vertebrate fecal samples  (9) (10) (11). Nucleotide sequence accession numbers. The genome has been deposited in GenBank under the accession no. KT309029. The version described in this paper is the first version, KT309029.
1. collection field work. This material is based upon work supported by theNational Science Foundation Graduate Research Fellowship under grantno. DGE 1106400 to Z. R. H. The funders had no role in the study design, data collection, and interpretation, or the decision to submit the work for publication. We thank Anna Sellas for assistance with lab work and Lisa Pajot for help with sample collection. We generated genetic data at the Center for Comparative Genomics, California Academy of Sciences. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the U.
NF-κB pathway activation is a shared characteristic of several pro-senescence kinases To see what the identified kinases might have in common, we first interrogated the STRING database to see if at least those displaying the greatest prosenescence effect, as judged from the level of SASP induction, might share a common protein association network. We built a network based on the seven kinases showing the strongest SASP-inducing effect (Fig. 3 ). In a KEGG pathway analysis of this network performed to identify overrepresented pathways, we detected strong enrichment in actors of the NF-κB signaling pathway (p=5. 8-16) (green circles, Fig. 3 ). Interestingly, SASP induction during replicative senescence or in response to senescence triggering by the RAS signaling pathway, through RAS or MEK activation, is reported to be mediated by the NF-κB transcription f actors  [11, 12].
The RT reaction mixture was diluted 1/20 and the cDNA template used for qPCR analysis. TaqMan quantitative PCR analysis was carried out in the CFX96 Connect Real-Time PCR Detection System (Bio-Rad). The FastStart Essential Probes Master (Roche) was used as PCR mix. The ACTB housekeeping gene was used for normalization. Real-time intron-spanning PCR assays were designed with the ProbeFinder software (Roche Applied Science). The following primers and UPL probes were used: ACTB-Forward ATTGGCAATGAGCGGTTC and ACTB-Reverse GGATGCCACAGGACTCCAT (UPL probe: 11), IL8-F agacagcagagcacacaagc and IL8-R atggttccttccggtggt (UPL probe: 72), IL6-F caggagcccagctatgaac and IL6-R gaaggcagcaggcaacac (UPL probe: 7), IL1A-F ggttgagtttaagccaatcca and IL1A-R tgctgacctaggcttgatga (UPL probe: 6), IL1B-F tacctgtcctgcgtgttgaa and IL1B-R tctttgggtaatttttgggatct (UPL probe: 78), p16-F gtggacctggctgaggag and p16-R ctttcaatcggggatgtctg (UPL probe: 34), IKBA-F gtcaaggagctgcaggagat and IKBA-R atggccaagtgcaggaac (UPL probe: 38), COX2-F gctttatgctgaagccctatga and COX2-R tccaactctgcagacatttcc (UPL probe: 2), SOD2-F aatcaggatccactgcaagg and SOD2-R taagcgtgctcccacacat (UPL probe: 3).
Graph II: Freight traffic on the Korean railway in tons(1910-1920)   Source: Chōsen Sōtokufu Tetsudō-kyoku, Chōsen tetsudō ronsan, op. cit. , p. 163. Graph III: Transport activities and profits index for the Korean railway NB: The source data for "passengers" are in number of people transported, "freight" in tonnes and "profits" in yen (less running costs and without deducting debt servicing). Source: Chōsen Sōtokufu Tetsudō-kyoku, Chōsen tetsudō ronsan, op. cit. , pp. 375-375, p. 171. The Beginnings of Japan's Economic Hold over Colonial Korea, 1900-1919 Cipango -French Journal of Japanese Studies, 4 | 2015Graph IV: Korean trade balance (1910-1920) (unit: thousand yen) Source: Yamamoto Yūzō, Shokuminchi keizai-shi kenkyū, op. cit. , p. 167. Graph V: Geography of Bank of Chōsen deposits (1910-1919) Source: Bank of Chosen, Economic History of Chosen, op.
NOTES 1. 1 Graph II: Freight traffic on the Korean railway in tons(1910-1920)   Source: Chōsen Sōtokufu Tetsudō-kyoku, Chōsen tetsudō ronsan, op. cit. , p. 163. Graph III: Transport activities and profits index for the Korean railway NB: The source data for "passengers" are in number of people transported, "freight" in tonnes and "profits" in yen (less running costs and without deducting debt servicing). Source: Chōsen Sōtokufu Tetsudō-kyoku, Chōsen tetsudō ronsan, op. cit. , pp. 375-375, p. 171. The Beginnings of Japan's Economic Hold over Colonial Korea, 1900-1919 Cipango -French Journal of Japanese Studies, 4 | 2015Graph IV: Korean trade balance (1910-1920) (unit: thousand yen) Source: Yamamoto Yūzō, Shokuminchi keizai-shi kenkyū, op. cit. , p. 167. Graph V: Geography of Bank of Chōsen deposits (1910-1919) Source: Bank of Chosen, Economic History of Chosen, op.
Bioturbation The vertical luminophores profile of each sediment column at final time of experimentation (30 days) was obtained from the percentages of the luminophores found in each layer with respect to the total amount in the core. The sediment retained on the 44 μm mesh was homogenized and subsampled to quantify luminophores using a microplate reader (Biotek Synergy Mx) at λex/λem: 565/602 and 460/500 nm for the green and pink luminophores, respectively. According to the respective time of deposition of the tracers at the surface of the cores, data from green particles reflected the reworking activity from the whole experimentation period (30 days), while pink particles indicate activity during the last 15 days. The quantification of sediment reworking was evaluated from the distributions of luminophores by the gallerydiffusor model  (François et al.
Statistical data analysis Data analyses were performed by corer using the software package PRIMER 5. 0 (Plymouth Marine Laboratory, UK). Specific richness (S), total abundance (expressed as densi-ty=number of individuals/m 2 ), the Shannon diversity index (H′), and Pielou's evenness index (J′) were calculated for each treatment. Differences in each biological variable were evaluated through one-way ANOVA considering conditions as fixed factors (n=12) (Statistica, version 7). The Tukey test for multiple mean comparisons was used to determine statistically significant differences between conditions. The ordination and sorting using the total abundance data was carried out with a non-metric multidimensional scaling (nMDS) and CLUSTER analysis (Bray-Curtis index; group average link; square root), respectively.
Acknowledgments This work was funded by the  Evaluationorientation de la Coopération Scientifique Sud -Ministerio de Ciencia, Tecnología e Innovación Productiva  ( ECOS Sud -MINCYT) collaboration program  ( Proyecto Caleta ; action no  A10U02 ) and the  French Agence Nationale de la Recherche  (project  DECAPAGE ;  ANR CESA-2011-006 01 ). We thank  Anthony Maire  for help in statistical analysis.
Linguistic validation and patient feedback To investigate the appropriateness of the item list developed in the previous steps, shoulder patients treated at the orthopedics department of the Kantonsspital St. Gallen (Switzerland) and the New Royal Infirmary of Edinburgh (Scotland, UK) provided feedback in the form of debriefing questionnaires after completing the item list. In this qualitative assessment we investigated whether the introductory text and the items were difficult to understand, whether items were intrusive, and whether patients found it difficult to report on their joint awareness. Additionally, patients were encouraged to raise further potentially relevant issues and to make general comments on the item list. Written informed consent was obtained from individual patients for their anonymized data to be used for research purposes.
g. , opening a tight jar is more difficult with an impaired hand than an impaired shoulder). This is likely to result in substantial DIF for a number of items when a general physical functioning item bank is employed. We found DIF for the forgotten joint concept in total hip and total knee arthroplasty patients in a previous study  [12]  in which, for example, the item on getting up from a low sitting position showed substantially different item difficulty in hip and knee patients. Therefore jointspecific CAT measures may result in better measurement precision, as they do not suffer from this problem. As limitations of our study we would like to note that our literature search did not include all available databases potentially relevant to shoulder outcome assessment, and we did not screen the references of the identified articles for further relevant articles or shoulder scores.
Acknowledgements The work of  Johannes M. Giesinger  has been funded by a grant from the  Austrian Science Fund  (FWF # J3353 ). The study was partly funded by a grant from the  European Society for Surgery of the Shoulder and the Elbow (ESSSE). We would like to thank  Lorraine Hollenstein  for her help with data collection at the  Kantonsspital St. Gallen. We would also like to thank  Prof. Colin Howie  and  Dr. Ian Brown  for their assistance in organizing data collection at the  New Royal Infirmary of Edinburgh.