dataesr/scientific-paragraphs-categorization huggingface dataset:
This illustrates clearly that when analyzing longterm trends from CTD data, the CTD type has to be taken into account. Additionally, in situ onboard calibration, regular servicing and laboratory calibration, data processing procedures, and experienced operators are required for precise data. CTD data therefore are of the highest value only if they come with proper documentation. One ambitious project analyzing and describing the complete set of available Arctic CTD data in respect to quality is currently taking place and will hopefully be published soon  (Behrendt et al. , 2017).
To download several or all data sets at once, you can either use the Data Warehouse integrated into PANGAEA, or you can use a program especially designed for this purpose called PanGet. Data Warehouse: log in to PANGAEA (or create an account) at www. pangaea. de, then search for "PSctd" (or, for example, "PSctd + oxygen"). On the top right corner you can click on Data Warehouse (above the Google map). Here you can choose which parameters to download, followed by clicking on "Start Data Warehouse Query".
Background: This article provides a summary of the 2013 European Renal Association-European Dialysis and Transplant Association (ERA-EDTA) Registry Annual Report (available at http://www. era-edta-reg. org), with a focus on patients with diabetes mellitus (DM) as the cause of end-stage renal disease (ESRD). Methods: In 2015, the ERA-EDTA Registry received data on renal replacement therapy (RRT) for ESRD from 49 national or regional renal registries in 34 countries in Europe and bordering the Mediterranean Sea. Individual patient data were provided by 31 registries, while 18 registries provided aggregated data. The total population covered by the participating registries comprised 650 million people. Results: In total, 72 933 patients started RRT for ESRD within the countries and regions reporting to the ERA-EDTA Registry, resulting in an overall incidence of 112 per million population (pmp).
Methods In 2015, the ERA-EDTA Registry received 2013 data from 49 national and regional renal registries in 34 countries in Europe and those bordering the Mediterranean Sea. The majority of renal registries (31 of 49) contributed individual patient data, whereas the other 18 renal registries contributed aggregated data (Figure  1 ). While a standard Microsoft Excel template was used for the collection of aggregated data, the individual patient data were received in different formats, including SPSS, Microsoft Excel and SAS. Extensive data checking was performed and the data were converted to a standard format in order to be stored in a relational database. After data analysis, the results were checked by the participating renal registries. All registry-specific results in the ERA-EDTA Registry Annual Report were approved by the registries before publication.
Mid-year population data for the contributing countries/ regions were received from Eurostat (http://ec. europa. eu/eurostat), the national bureau of statistics or the renal registry. The incidence of RRT was defined as the number of patients starting RRT in one year (2013) and the prevalence of RRT as the number of patients alive and receiving RRT on 31 December 2013. Incidence and prevalence per million population ( pmp) were calculated by dividing the observed count by the mid-year population. Time trends of the incidence rates were analysed using Joinpoint regression, with the trends presented as annual percentage change (APC)  [2, 3]. Patient survival on RRT, on dialysis and following kidney transplantation was analysed using data from renal registries providing individual patient data for the period 2004-13.
Results For the majority of renal registries contributing data to the ERA-EDTA Registry, the coverage of the population was 100%, with the exception of Croatia (80%), Latvia (80%), Serbia (94%), Switzerland (94%), Spain (95%), Poland (95%), Georgia (96%), Bulgaria (97%), Czech Republic (98%) and Romania (99%). The total population covered by the participating registries comprised 650 million people. The proportion of the European population covered by the ERA-EDTA Registry in 2013 was 73. 6%. A list of the European countries with available data and those without is provided in the Appendix.
Patient survival Survival analyses included data from 22 registries in 11 countries, which provided individual patient data for the period of 2004-11. Table  5  shows the unadjusted and adjusted survival probabilities for patients starting RRT or dialysis or receiving their first kidney transplant between 2004 and 2008. In order to present more recent survival data, 1-and 2-year survival probabilities are also presented, for patients starting RRT/dialysis or receiving their first kidney transplant between 2007 and 2011. The survival of patients with DM as the cause of ESRD was worse when compared with the total group of patients starting RRT, dialysis or receiving a kidney transplant. Two-year survival probabilities were higher for patients starting RRT, dialysis or receiving a kidney transplant between 2007 and 2011 than between 2004 and 2008.
Discussion This summary of the 2013 ERA-EDTA Registry Annual Report includes data from 49 national and regional renal registries in 34 countries in Europe and bordering the Mediterranean Sea, with a special focus on patients receiving RRT for ESRD secondary to DM. Both the overall incidence of RRT for ESRD and the incidence of RRT for ESRD secondary to DM were substantially lower in Europe than in the USA  [4]. However, even in Europe and among countries bordering the Mediterranean Sea, there were notable differences in the incidence of RRT for ESRD secondary to DM. This variation may be explained in part by differences in the prevalence of DM within the general population [5], differences in preventive measures, such as lifestyle advice and the use of renoprotective medication, and differences in macroeconomic factors and nephrology services  [6].
Acknowledgements The ERA-EDTA Registry would like to thank the patients and staff of all the dialysis and transplant units who have contributed data via their national and regional renal registries. In addition, we would like to thank the persons and organizations listed in the 'Affiliated registries' for their contribution to the work of the ERA-EDTA Registry. The ERA-EDTA Registry is funded by the  ERA-EDTA. This article was written by  Anneke Kramer  et al. on behalf of the  ERA-EDTA Registry , which is an official body of the  ERA-EDTA , and it was approved by all co-authors.
If there was 70-90% of missing data for the DJFM period, data from a neighboring and representative buoy was used to fill in the data gaps (Bideford for Perranporth, Gascogne for Cap Ferret, and Bilbao for North Spain). This was achieved by adjusting for bias and offset after assessing the best fit with the supporting data set using all overlapping data available over the 6 year time series. The following DJFM wave statistics were computed: (1) average significant wave height; (2) maximum significant wave height; and (3) average wave energy flux computed using the energy period T e = 1. 32T m  [Cahill and Lewis, 2014] , where T m is the mean wave period which is the only wave period parameter that is consistently computed by all wave buoys. Additional parameters were derived based on a storm event analysis, where storms are identified as events during which the significant wave height is larger than the 1% exceedence significant wave height computed from the whole data record and where the 5% exceedence wave height is used to demarcate the start and end of storm events: (4) number of storms during DJFM period and (5) total storm duration.
, 2012]. Facing northnorthwest, the beach is partially sheltered from the direct impact of Atlantic swell, and MSR is 8. 5 m. Subaerial beach morphological data at all six sites have been collected rigorously for at least 6 years on a monthly basis using a variety of methods, including RTK-GPS and total station. At some sites single two-dimensional beach profiles are measured, while at other sites a three-dimensional morphological grid was collected that was alongshore averaged to obtain a mean beach profile. The response at Slapton Sands varied considerably along the beach; therefore, data from this site only were analyzed separately, corresponding to the middle (SP p10 ) and northern end (SP p18 ) of the embayment. The key parameter extracted from the profiles is the beach volume above MSL; for Vougot and Truc Vert the location of the dune foot has also been considered.
Measured Wave Conditions (2009-2015) Wave analysis was conducted for six European Atlantic wave buoys for which data are available since 2009, including the 2013/2014 winter season, to assist placing the longer-term modeled ocean wave climate within the context of the available measured inshore wave conditions. The results of this analysis are shown in Figure  3  and demonstrate that the 2013/2014 winter represents the most energetic period over the relatively short time series of observational wave data. Specifically, the number of storms and the total storm duration during the 2013/2014 winter is generally at least 100% larger than the second most energetic winter.
Acknowledgments This work was supported by  UK Natural Environment Research Council (NERC ;  NE/M004996/1 ),  French "Agence Nationale de la Recherche " through project  CHIPO  ( ANR-14-ASTR-0004-01 ), and the  "Laboratoire d'Excellence" LabexMER  ( ANR-10-LABX-19-01 ) program, and cofunded by a grant from the  French government  through the  "Investissements d'Avenir" program. G. D. is funded by the  French Directorate General of Armaments (DGA)  within the research program  PROTEVS  ( 12CR6 ) conducted by the  French Naval Oceanographic and Hydrographic Department (SHOM). The authors would like to thank the very many colleagues, postdocs, and PhD students involved with the beach profile data collection. The hindcasted 3-hourly WWIII wave data for the 1948-2015 period for the 1000 m isobaths model nodes, the coordinates of the wave model nodes and wave buoy locations, and time series of the beach volume are available as supporting information on the journal website.
The effects of MTEP pretreatment on depressive-like behaviors in the FST were assessed using 2-way ANOVA for factors "pretreatment" (ie, saline and MTEP) and "treatment" (ie, saline and morphine). For assessing the effects of MOPr gene deletion on mGlu 5 R binding, unpaired Student's t test was used in each individual region. For the regression analysis, Pearson correlation coefficient test was performed. ANOVAs were followed by a Bonferoni post-hoc test when significant interaction effect was reached (ie, P <. 05). All statistical analyses were performed using SigmaPlot v11. 0 (Systat Software, London, UK).
Results Recombinant CRX displays Ca 2 þ -dependent TRX activity. Recombinant CRX was isolated and purified via Ni 2 þ -NTA affinity chromatography. Binding of divalent cations to recombinant CRX was measured using Microscale Thermophoresis in the presence of calcium and magnesium. For calculation of Ca 2 þ and Mg 2 þ dissociation constants, the ratio between the fluorescence of the fluorescently labelled protein before and after the thermophoretic movement was determined at increasing cation concentrations (Fig. 1a ). An increase in Mg 2 þ concentration did not change the fluorescence ratio. On the other hand, an increase in Ca 2 þ concentration led to a clear decrease in the fluorescence ratio, indicating specific binding of Ca 2 þ but not Mg 2 þ to CRX. The Ca 2 þ response data were fitted, resulting in a dissociation constant (K d value) of 88.
A mammalian PRX4 existed as a ringshaped decameric form  46  , while the plant-type PRX forms a noncovalent homodimer  47. Although it is not clear yet which oligomeric state Chlamydomonas PRX1 has, the active site structure is conserved between these PRX structures. From the partial complex structure of TRX:PRX4-peptide, we can build the predicted CRX:PRX-peptide structure (Supplementary Fig. 8c ). The TRX domain of CRX has an open space for PRX binding. Additionally, the decameric PRX4 (PDB ID: 3VWU) can be modelled by fitting it's C-terminal peptide to the corresponding peptide in the CRX:PRX-peptide structure (Supplementary Fig. 8d ). Further the modelled structure shows a close fit to the open space formed by CRX that implies an additional interaction between CRX and PRX mediated by the CaM-like domain on binding of Ca 2 þ.
The eluates were pooled and further purified by gel filtration (Superdex-200). Crystallization and structure solution. WT CRX was crystallized at 20 °C using the hanging-drop vapour diffusion method. Protein concentration was adjusted to 10 mg ml À 1. Sample buffer contained 20 mM Tris-HCl pH 8. 0, 150 mM NaCl, 1 mM DTT and 150 mM CaCl 2. Precipitant solution was 1. 5 M LiSO 4 dissolved in 0. 1 M MES-NaOH buffer pH 6. To obtain the crystals, the drops contained 1 ml of the protein and 1 ml of precipitant solution. SeMet derivative crystals were grown with the same experimental setting. X-ray diffraction images were collected at 100 K using a synchrotron radiation source with 0. 90000 Å for native and 0. 97500 Å for SeMet. All data sets were collected at the SPring-8 using the BL44XU beamline.
The native and SeMet derivative data sets were processed using the HKL-2000 software. Phase problem was solved by the single-wavelength anomalous dispersion method using Phenix AutoSol in Phenix program suite at 2. 8 Å resolution. The SeMet derivative protein had 32 SeMet residues and 27 sites were found. The density modified resultant electron density map was clear enough for interpretation and the asymmetric unit contained two molecules of CRX. The model was build using COOT software along with the NCS-averaged electron density map calculated using DM in the CCP4 package. Crystallographic refinement was performed using REFMAC5. The final structure was validated using wwPDB validation server. The analysis showed that all residues were in the favoured region of Ramachandran plot, with no residues as outliers.
Crystallographic data and refinement statistics are shown in Table  1. Vector constructions. RNA isolation from Chlamydomonas reinhardtii was performed using TRI reagent solution (Sigma Aldrich) and 300 ng of DNase I treated RNA was used for cDNA synthesis (iScript cDNA Synthesis Kit, Biorad) according to the manufacturer's protocol. For in vitro experiments the crx and prx1 genes were amplified from cDNA lacking the transit peptide and the stop codon using the primers 5 0 -ggaattccatatgt gcagcgctcgctcc-3 0 and 5 0 -cgggatcctgcagggccgccagc-3 0 for CRX and 5 0 -ggtattc catatggcttcccacgccgag-3 0 and 5 0 -cgggatcctgcacggcagagaagtactcc-3 0 for PRX1. Each amplicon was digested with NdeI and BamHI (NEB) and cloned into the pET-22b( þ ) vector (Novagen). Based on the CRX plasmid, site-directed mutagenesis (QuickChange II Site-Directed Mutagenesis Kit, Agilent) was performed (C238S; C241S;C238S, C241S; Q154A; K242L and K263I) according to the manufacturer's protocol.
The super-library that included the IMcrx mutant was determined according to the sequencing data of a positive PCR product (Supplementary Fig. S5. The positive super-library was further separated into 15 small-libraries and each small-library DNA was checked individually by PCR with appropriate crx target primer. The single clone of the IMcrx mutant was picked from the small library after identification by colony PCR. Furthermore, insertion of the AphVIII fragment was confirmed with a primer pair binding adjacently to the insertion site (EX2-F, EX3-R, Supplementary Table  1 , Supplementary Fig. 5 ). Microscale thermophoresis binding analyses. Recombinant CRX (100 ml of 40 mM) was labelled with red fluorescent amine-reactive dye according to the instructions of the MO-L001 Monolith Protein Labeling Kit RED-NHS (amine reactive).
A constant concentration of labelled CRX (B115 nM) was mixed with defined concentrations of free Ca 2 þ or Mg 2 þ ions (up to 100 mM) in 30 mM MOPS (pH 7. 2), 100 mM KCl, 0. 05% Tween-20, 5 mM total EGTA or EDTA respectively. To prepare solutions with Ca 2 þ in the micromolar range we took advantage of available calcium buffer kits guidelines (ThermoScientific). Measurements were performed at 22 °C in standard treated glass capillaries (Monolith NT Capillaries, NanoTemper) and the thermophoresis analysis was performed on a NanoTemper Monolith NT. 115 instrument (20% LED; 20% infrared-laser power). The MST data were fitted with the law of mass action using the NanoTemper Analysis software to obtain K d values for binding between CRX and Ca 2 þ. Measurement of Ca 2 þ -dependent redox activity.
The redox activity of CRX was determined photometrically in a TRXR-dependent assay 62 (modified). E. coli (40 nM) TRXR were used to specifically reduce CRX (10 mM) by 10 min incubation in 30 mM MOPS, 100 mM KCl, pH 7. 2 with NADPH (200 mM) at RT. After addition of 200 mM DTNB, the formation of TNB À was followed at 412 nm (Ultrospec 3000, Amersham Biosciences). The reduction rate of DNTB was determined at defined free Ca 2 þ and Mg 2 þ concentrations and over a time course of 0-80 s after addition of DTNB. In Fig. 1b  the different activities were normalized on the highest activity measured for each batch of purified CRX, plotted against the free ion concentration and modelled according to Michaelis-Menten kinetics with GraphPad Prism 2. 01 software. Determination of redox potential. Oxidation-reduction titration was performed as follows.
Data were fitted with a two-electron Nernst curve using GraphPad Prism 2. 01 software to calculate the CRX E m value. Transient expression in Nicotiana benthamiana. Agrobacterium tumefaciens (GV3101 strain), containing the calredoxin-mCherry fusion construct (OD 600 0. 5), were coinfiltrated with the p19 strain (OD 600 0. 3) into 6-week-old N. benthamiana leaves as described previously  63. Microscopic analyses were conducted 3 days after infiltration on leaf discs (Ø 1. 2 cm) of the lower epidermis at room temperature with water as imaging medium. Microscopy. Protein fluorescence was detected by confocal laser-scanning microscopy using a Leica TCS-SP5 II setup consisting of an inverted confocal laserscanning microscope DMI6000 (Leica) equipped with an Â 63/1. 2 water immersion lens (HCX PL APO lambda blue 63.
0 Â 1. 20 Water UV). The following filters were used: mVenus, excitation 514 nm (Argon laser), scanning 525-550 nm; mCherry, excitation 561 nm (DPSS Laser), scanning 605-638 nm. Chlorophyll autofluorescence was detected at 690-740 nm (Supplementary Table  2 ). Image acquisition was performed using the Leica software (Leica Application Suite -Advanced Fluorescence 2. 6. 0. 7266; Leica Microsystems). Images are shown in RGB mode and brightness and contrast were adjusted using Adobe Photoshop CS3 software.
1% (v/v) formic acid in ultrapure water (A) and 80% acetonitrile/0. 08% formic acid in ultrapure water (B). Peptides were eluted at a flow rate of 300 nl min À 1 and employing the following gradient profile: 2. 5-35% B over 90 min, 35-60% B over 20 min, 60-99% B over 5 min and 99% B for 10 min. Afterwards the column was re-equilibrated with 97. 5% A for 25 min. The LC system was coupled via a nanospray source to a Q Exactive Plus mass spectrometer (Thermo Scientific) operating in positive ion mode. MS data were acquired in a data-dependent manner, dynamically choosing the 12 most abundant precursor ions from the survey scans (scan range m/z 400-1,600, resolution 70,000, AGC target value 1e6, maximum injection time 50 ms) for fragmentation (MS/MS) by higher-energy C-trap dissociation (27% normalized collision energy).
Spectra were searched against a database containing protein sequences of the Chlamydomonas v5. 5 gene models (Joint Genome Institute) merged with mitochondrial and chloroplast protein sequences from NCBI databases BK000554. 2 and NC_001638. 1. The database was further supplemented with commonly observed contaminants (http://www. thegpm. org/crap/). Cysteine carbamidomethylation was set as a fixed modification, the oxidation of methionine, protein N-terminal acetylation, and phosphorylation of serine, threonine and tyrosine were set as variable modifications. A false discovery rate of 1% was applied to peptide and protein identifications. False discovery rate calculation was performed by MaxQuant using a target-decoy approach. The 'match between runs' setting was activated. Correlation plots were produced using log2 transformed label-free quantification protein intensities.
Proteins were tryptically digested overnight on centrifugal ultrafiltration devices (cutoff: 30 kDa) according to the FASP method  42  with an enzyme-to-protein ratio of 1:100. LC-MS/MS analyses of WT IMcrx strains. Liquid chromatography and MS parameters were essentially the same as described above with the following modifications: Peptide chromatography was carried out on an Acclaim PepMap100 C18 capillary column (75 mm Â 50 cm, 2-mm particle size, 100-Å pore size; Thermo Scientific). The following gradient was applied: 2. 5-35% B over 195 min, 35-60% B over 40 min, 60-99% B over 5 min, 99% B for 15 min. MS data acquisition was performed using a data-dependent Top20 method (MS1: scan range m/z 375-1600, AGC target value 1e6, maximum injection time 30 ms. MS2 parameters: see above). The precursor isolation window was 1.
5 m/z. Full scan resolution was set to 70,000 (FWHM). Some samples were additionally analysed with an MS1 resolution of 140,000 (FWHM). Identification of peptide spectrum matches and statistical evaluation. MS2 Spectra were analysed using Ursgal  68. Post processing was performed using percolator (v. 2. 08)  69  and PSMs were filtered by 5% posterior error probability (PEP). Complete analysis pipeline was executed using the Python framework Ursgal (v 0. 3. 3) 68 using default profile 'QExactive þ '. Additionally, Methionine oxidation and N-terminal acetylation was included as post translational modification search parameter. Details on parameters can be inspected in the Ursgal log JSONs that have been uploaded with the raw result files. In total, 3,234,459 and 2,687,720 peptide spectrum matches for PEPsr5% and r1%, respectively, were observed.
This translates to 42,815 and 35,926 distinct peptides for PEPsr5% and r1%, respectively. Detailed listing of all identified peptides can be found in Supplementary Material 1. Metabolically labelled peptide quantification. All peptides (PEPr5%) were subjected to quantification using pyQms (refs 31,70) using default parameters. To quantify peptides irrespectively of their identification in a given LC-MS/MS run, retention time alignment was performed as described before  31, 70  All quantifications were grouped and processed using piqDB, an internal database structure based on Python, mongoDB and Hadoop. In total, all quantifications resulted in 1,462,589 matched isotope pattern chromatograms (MICs) containing at least one isotope pattern match with a mScore Z0. 7. However, to include a MIC further into the quantitative analysis a total of eight quantifications (MS1 hits) were required with a mScore Z0.
Acknowledgements M. H. acknowledges support from the  Deutsche Forschungsgemeinschaft (DFG ,  HI 739/9-1, FOR964 )). G. K. acknowledges support from the  Funding Program for Next Generation World-Leading Researchers  ( GS016 ) from the  Cabinet Office of Japan. This work was supported in part by an  International Joint Research Promotion Program and International Collaborative Research Program ,  Osaka University , (G. K. and M. H. ). G. F. acknowledges funding form the  Marie Curie ITN Accliphot , and the  HFSP  grants. K. H. acknowledges support from the  National Natural Science Foundation of China  ( 31171287 ). We are grateful to  Dr Jo ¨rg Kudla  for access to the NanoTemper station (J. K. acknowledges support from  DFG  ( FOR964 )) and to the staff at beamline BL44XU at SPring-8, Japan for their kind help during the data collection.