dataesr/scientific-paragraphs-categorization huggingface dataset:
4a  and 4b ): Automation of beam delivery to the sample, including beamline alignment, monochromator optimization and mirror focusing; Automation of the data collection for fixed-and multiple-wavelength experiments with energy scans at the absorption edge as necessary; Information flow and book-keeping for the high-throughput experiments; Automatic analysis of data; Pipeline operation with the sample changer integrated with automatic sample mounting and centring, sample screening, multi-sample collection, online data analysis and database recording; Diagnostics in real time (for example, shutter synchronization data) or in a recording mode (historical database) that allows off-line analysis of events.
The absolute encoder, model IVO GM 400, has a resolution of 8192 points per rotation over 4096 rotations giving a unique position over a 163 range. The encoder therefore allows the monochromator Bragg angle to be driven close to the reference energy without difficulty. Once there, a diode and a platinum foil are inserted into the monochromatic X-ray beam in order to record an XANES spectrum of the platinum L-III absorption edge. After removing the platinum foil, a spectrum of the beam intensity across the same energy range but without platinum foil is recorded to allow normalization of the absorption-edge scan. The inflexion point is automatically calculated using a purpose-written programme in Python and used to set the monochromator energy with a typical error of less than 0. 1 eV. This automatic calibration procedure allows the inexperienced beamline operator to recalibrate the monochromator.
Beamline diagnostics Once all beamline elements are in their correct alignment it is essential that their positions are continually monitored, stored and compared with those corresponding to an optimum alignment of the beamline. On ID23, diagnostic data are recorded continuously using the ESRF storage-ring database, keeping track of machine performance parameters. This machine historical database (HDB) has been extended to allow the deposition of beamline data, which allows one to trace and correlate beamline events in time. All parameters, including the motor positions, temperature of optical components, beam positions and beam intensity, vacuum, machine intensity and state are archived centrally through a store server operating in the background. The configuration of the HDB allows different polling periods for each signal to be defined.
Typically the first method is the fastest and more reliable when users are present. The third method is planned to be used for multi-sample unattended screening and data collection. Recent crystal centring tests have been carried out on the beamline using a laser. This method is still under development but has shown exciting initial results. It will shortly be implemented on the beamline and be available to users. By placing a YAG screen at the sample position, the X-ray beam shape can be directly visualized and the centre of mass calculated. Knowing the centre of the beam and the calibration of the camera, it is simple to calculate the horizontal and vertical translations to apply to the experimental hutch table and slit systems for moving the beam centre onto the centre of rotation. This procedure has been fully implemented and it is accessible directly from the user software interface.
The quality of the rotation axis and the synchronization of the fast shutter with the rotation axis is important. The fast shutter is based on a piezo design (see http://www. emblgrenoble. fr/groups/instr) with a 400 mm horizontal aperture, an opening and closing time of less than 3 ms and fitted with strain gauges for status monitoring. These components have often been blamed for the poor quality of the data in the past and are amongst the beamline components undergoing the most cycles  (Flot et al. , 2006). It is, therefore, imperative that the quality of the synchronization (spindle position versus opening/closing of the shutter) is monitored continuously during the experiment. On ID23-1 several signals are recorded systematically during each image of the data collection: the encoder position of the rotation axis, the status of the command open/close shutter, the actual status of the shutter as read from the strain gauges and the X-ray beam intensity before and after the shutter.
These signals are entered into a multi-purpose unit for synchronization, sequencing and triggering (MUSST) card custom-built at the ESRF. The frequency of sampling by the card is adjustable and is calculated before each image as a function of the acquisition time of the image. This diagnostic is currently stored in a data file and saved automatically in the user directory where the diffraction images are written. In the future it is planned to store this information in the historical database. The beamline was originally equipped with a MAR 225 detector. This has been changed to a Quantum 315R from Area Detector Systems Corp during November 2005. The sample-to-detector distance can vary from 55 mm to a maximum 700 mm corresponding to a maximum detectable resolution of 0. 54 A ˚for the circle inscribed in the ADSC detector square face with 20.
Adjoining user environment and data back-up Beamline users occasionally bring unfrozen crystals to the beamlines; therefore a biochemical laboratory next to the control cabins and shared between ID23-1 and ID23-2 has been constructed as part of the beamline. It includes the standard equipment for the preparation of heavy-atom derivatives and also an Oxford Xenon cell for xenon derivatization. Space adjoining this laboratory has been dedicated to the ESRF MXpress industrial service in order to store cryogenically cooled samples. The beamline is currently able to produce up to 40 images a minute. In order to handle this data throughput, gigabit Ethernet links are provided between the ESRF central storage disks and the Linux and Windows CCD control and data backup computers at the beamline. These computers, which also have high-quality graphics cards for visualization of structures, are installed in the control cabin allowing the users to back up the data following the data collection but without disturbing the data processing.
Several Linux computers are also accessible to users in a dedicated back-up room near to the beamline. Even before the recent sample changer installation, the influence of which is not yet fully known, users have been able to collect huge numbers of images in a 24 h period. Over the last 12 months, just over half a million images have been taken, with the peak daily rate representing 8000 images, corresponding to 140 GB of data from the original MAR 225 detector made up of 28 data sets and 35 crystal diffraction tests.
User interface The existing graphical interface for users needed special attention. The final implementation choice is based on the Python programming language and Qt graphics library. The Python to Qt binding (PyQt) provides high-quality graphics and good performance. The Python programming language is the language of choice for this project owing to its flexibility and integrative capabilities. All these features allow optimal and modular programming where the final application is the result of joining together component 'bricks', each of which has a specific function. This approach should ease the evolution of the application to integrate new instruments or experimental methods. The software configuration of the hardware components corresponds to the modularity and flexibility of the application through the use of an XML-based configuration database.
Information tracking and book-keeping High-throughput experiments require a systematic approach to the handling of sample information. The ISPyB project is a two-fold development including a database design specific for MX experiments and an online web interface, both of which make use of data models for macromolecular crystallography experiments (see http://www. e-htpx. ac. uk). ISPyB obtains information from the ESRF user office database containing proposal information and safety authorization. Users can also introduce information in advance of the experiment about dewars and samples that can be later used to control the sample changer and help make decisions during data collection. The exes beamline control module records information (such as data collection parameters) to the ISPyB database produced during the experiment.
3 A ˚, c = 70. 4 A ˚with two molecules in the asymmetric unit. A data set of 720 images was collected using 7. 0 keV X-rays and integrated and reduced using MOSFLM  (Leslie, 1992)  and SCALA from the CCP4 program suite (Collaborative Computational Project, Number 4, 1994), giving the statistics summarized in Table  2. The sulfur substructure was determined using SHELXD  (Schneider & Sheldrick, 2002)  with data truncated to between 25 A ˚and 4 A ˚. A total of six major sites out of eight potential ones were clearly identified and used as input to SHARP (de la Fortelle & Bricogne, 1997) for phase refinement and density improvement giving the electron density map shown in Fig. 8. ARP/wARP  (Morris et al. , 2002)  was able to build 202 residues out of a total of 204 that are visible in the final model.
We note that the procedure of choice to characterize average source rock is specific to each Publisher: GSA Journal: GEOL: Geology DOI:10. 1130/G38671. 1 Page 7 of 17 large river basin. In the Amazon, Congo, and Ganges-Brahmaputra basins, sedimentary, igneous, and metamorphic rocks have distinct Nd isotope composition making it possible to quantify precisely the provenance of fine sediments using Nd isotopes (see the GSA Data Repository 1 ). For the Mackenzie River, we use trace elements (Cr, Ti, Cs) ratios (see the Data Repository). We emphasize that this calculation provides information on source rocks for fine sediments only, which can be different for other grain sizes  (Bouchez et al. , 2011a; Dellinger et al. , 2014; Garçon and Chauvel, 2014). However, in some cases like that of the Changjiang basin, neither Sr-Nd isotopes nor trace elements can be used to assess the provenance of sediments because the signatures of the main rock sources are under-constrained or not significantly different  (Chetelat et al.
3 ). Using the relationship between Li and the proportion of sediments derived from erosion of shales calibrated on rivers draining mountain ranges, we infer the proportion of shales Publisher: GSA Journal: GEOL: Geology DOI:10. 1130/G38671. 1 Page 8 of 17 contributing to the fine sediment load of the Changjiang basin river, which makes our set of 7 Lisource_material estimates complete (see Data Repository). Using the calculated proportion of shales and igneous rocks with the 7 Li of the rock end members, we estimate the Li isotope composition of the rock source ( 7 Lisource_material) for each fine river sediment sample (see the Data Repository). We note that the calibration of the Li provenance tracer in detrital sediments might also serve to determine the provenance and the 7 Lisource_material of ancient detrital sedimentary archives for which the potential bedrock sources are usually not constrained.
, (2013) , we can use these data along with the estimate of the Himalayan rock end-members  (Galy and France-Lanord, 2001; Singh et al. , 2008; Singh and France-Lanord, 2002)  to determine the provenance for this sample. We calculate that for this Brahmaputra sample, the proportion of LH, and therefore of shales-derived sediments, is 20±10%. Mackenzie River: The upper crust drained by the main Mackenzie tributaries is composed by a mixture between shales and igneous rocks having granodioritic to granitic composition  (Driver et al. , 2000; Reeder et al. , 1972). The Nd and Sr isotope composition has not been measured on sediments from the Mackenzie tributaries. However, a large dataset of shale chemical composition from the Liard River basin is available in  Ross and Bustin, (2009). Dellinger, (2013)  shows that some insoluble elements (Cr, Ti, Eu, Cs) have significantly distinct concentration between shales and granitic rocks.
, 2004; Pan et al. , 2006; James and Legras, 2009) , the filamentary structure in long-lived and short-lived species near the edge of the polar vortex  (Konopka et al. , 2003) , the transport of long-lived species and CO from the tropical troposphere to the stratosphere  (Pommrich et al. , 2014) , and the processes that control UTLS composition  (Riese et al. , 2012). The small-scale variability of CO 2 , its strong gradients across the tropopause, and the scarcity of suitable observations for validation purposes lead to a challenging task for CTMs and CCMs in reconstructing its distribution in the UTLS  (Hegglin et al. , 2008). In this paper, our goal is to build a database of the monthly zonal mean distribution of CO 2 on a global scale extending from the upper troposphere to the stratosphere using backward Lagrangian trajectories.
Acknowledgements. We particularly thank  Y. Sawa ,  H. Matsueda , and  T. Machida  for providing CO 2 measurements from CON-TRAIL, the  ECWMF  for providing reanalysis data, WDCGG (http://ds. data. jma. go. jp/gmd/wdcgg/) and its contributors for providing the ground station CO 2 data from 1989 to 1999, and the  CarbonTracker team  for providing the CO 2 data from 2000 to 2010. We thank  Harald Bönisch  and  Alain Chédin  for comments and helpful discussions. We acknowledge support from the  EU   7th Framework Programme  under grant  603557  (StratoClim). M. Diallo was mainly supported by a postdoctoral grant from the  ExCirEs Project  ( CGL2011-24826 ) funded by the  Government of Spain. Further thanks are due to the CICLAD cluster at the  Institut Pierre Simon Laplace in Paris , on which most parts of this work were carried out.
Data availability. The reconstructed CO 2 product will be published online at http://www. earth-system-science-data. net/ and made publicly available. The other data used in the manuscript are described in the manuscript and here: World Data Center for Greenhouse gases datasets are available at http://ds. data. jma. go. jp/gmd/wdcgg/, SOLVE datasets are from NASA  (Daube et al. , 2002)  and can be download from http://espoarchive. nasa. gov/archive, CarbonTracker datasets are available at ftp://aftp. cmdl. noaa. gov/products/carbontracker/co2/ CT2016/molefractions/co2_components/, and balloon CO 2 profiles are from  Engel et al. (2009)  and  Ray et al. (2014). These data are not publicly available but can be obtained by contacting Andreas Engel (an. engel@iau. uni-franfurt. de) or Eric Ray (eric.
on behalf of the ANTARES Collaboration We present a search for ANTARES neutrino events in spatial and temporal coincidence with IceCube High-Energy Starting Events (HESE). This analysis uses a maximum likelihood ratio approach based on track events due to muons induced by neutrino interactions observed with ANTARES. Each HESE is treated as the signature of a potential transient neutrino source while the neutrino burst duration, the source direction and the number of ANTARES signal events are obtained as those maximising the likelihood. Before applying the method to the unblinded ANTARES dataset, its sensitivity and discovery potential are computed through dedicated pseudo-experiments. This study provides an effective way to acquire information on the possible origin of the IceCube astrophysical signal from transient sources.
When dealing with transient emissions, the background of atmospheric neutrinos can be significantly reduced using a time-dependent approach that consists in searching for astrophysical neutrinos in smaller time windows around source flares (see e. g. [3] ). Here, we propose a model-independent approach based on the timing properties of both the ANTARES and IceCube data samples. In particular, we search for correlations in space and time between ANTARES muon neutrino candidates and thirteen muon track HESE previously published by the IceCube collaboration. The analysis uses a maximum likelihood ratio approach where each HESE is treated as the signature of a potential transient neutrino source while the neutrino burst duration, the number of ANTARES signal events and the source position are obtained as those maximising the likelihood.
Data Sample This analysis makes use of the thirteen HESE muon track candidates 1  detected by the IceCube neutrino telescope within the field-of-view of the ANTARES detector. They have been observed from September 2010 to April 2014 with a median angular error of ∼ 1. 3 • (see table  1 ). Data of the ANTARES neutrino telescope  [5]  collected from March 01, 2010 to October 31, 2014 are used in order to overlap the IceCube dataset and to search for flares lasting up to 6 months. Only events reconstructed as muon tracks are included in the dataset. These events are reconstructed by means of a multi-step procedure that estimates the direction and position of the muon using a maximum likelihood fit  [6]. Events are selected applying cuts on parameters provided by the reconstruction mechanism: the reconstructed zenith angle (cos θ > -0.
Estimated performances The detection power (at 50% confidence level) and sensitivity of the analysis are estimated through pseudo-experiments performed as described above. Figure  4  shows the preliminary discovery potential and sensitivity for the IceCube HESE with ID 3 as a function of the flare duration. The ANTARES data are currently blinded. They will be unblinded after having added ANTARES shower events. The 29 high-energy muon events observed by IceCube  [10]  will be added to the dataset as well before unblinding the analysis.
Conclusions A time-correlation analysis between the IceCube/HESE muon track sample and ANTARES muon neutrino candidates observed from 2010 to 2014 has been presented. Using a maximum likelihood ratio approach, it provides with a new way to constrain the origin of the IceCube astrophysical signal from possible transient sources. Limits can be set on the maximal amount of signal events in ANTARES related to a flare of a certain duration. Preliminary results show that sensitivity and discovery potential are better by at least a factor of two compared to time-integrated analyses. In the near future, ANTARES shower events will be included in the analysis and the 29 high-energy muon events observed by IceCube  [10]  will be added to the dataset as well. The analysis will be unblinded afterwards.
Subject area Renal Physiology More specific subject area Renal biomarkers serum creatinine (Scr) and serum cystatin C (ScysC) and their relation with directly measured glomerular filtration rate (mGFR) Type of data Assay results for serum creatinine, serum cystatin C and directly measured glomerular filtration rate from various reference methods, demographic data How data was acquired Diagnostic assays, accepted reference methods for GFR.
82 mg/L for subjects aged o 70 years and Q cysC ¼ 0. 95 mg/L for subjects aged Z 70 years  [2]. In this article, data and a new analysis are presented to further support these choices for the rescaling of ScysC. Only 'healthy' subjects were selected, that is, a subgroup is selected from the total collection of 8584 subjects, obtained from the normal population and from nephrology clinics. First, it was required that Scr/Q crea r 1. 33, or, only subjects with 'normal' Scr-values were selected. Q crea -values for Scr have been reported for children and adolescents  [3, 4]. For adults, Q crea ¼ 0. 70 mg/dL is used for females and Q crea ¼ 0. 90 mg/dL for males. This selection requirement reduces the total dataset from 8584 to 5352 patients. The additional requirement that mGFR Z 60 mL/min/1. 73 m² further reduces the dataset from 5352 to 4907.
Interchangeability between biomarkers and mGFR / FAS-eGFR Comparing (Scr/Q crea þ ScysC/Q cysC )/2 using the threshold of 1. 33 with mGFR using the fixed threshold of 60 mL/min/ 1. 73 m², for the complete n ¼ 8584 dataset, to detect renal impairment, we have ( Using the FAS combi equation to calculate eGFR from both Scr/Q crea and ScysC/Q cysC , the following table is obtained when comparing FAS-eGFR using the age-dependent threshold with the combined biomarker value (Scr/Q crea þScysC/Q cysC )/2 using the threshold of 1. 33 (Table  4 ): In Fig. 5a -b, the raw mGFR-values are plotted against age, for the subgroups defined by (Scr/Q crea þ ScysC/Q cysC )/2 below and above the threshold of 1. 33, together with the fixed threshold for mGFR ¼ 60 mL/min/1. 73 m² and the age-dependent threshold obtained from the FAS-equation with (Scr/Q crea þ ScysC/Q cysC )/2 ¼ 1.
Experimental design, materials and methods This is a retrospective study, where the data presented here were collected from 12 previously published cohorts (grand total of 8584 patients) and centralized for pooled data-analysis. Assay data for Scr and ScysC, together with measured GFR, age, sex were centralized for the data-analysis. The total number of patients was subdivided into subgroups corresponding with age-decades with the aim to perform a data-analysis of the diagnostic value (in terms of sensitivity and specificity) of the 1. 33, negative when 1. 33) and disease status defined by the fixed mGFR threshold of 60 mL/min/1. 73 m². Open circles correspond to the reversed situation, that is, mGFR as the test result (positive when mGFR o 60 and negative when mGFR Z 60) and disease status defined by the ScysC/Q cysC of 1.
ScysC/Q cysC )/2 using the threshold of 1. 33 with mGFR using an age-dependent threshold, for the complete n ¼ 8584 dataset, to detect renal impairment, we have (Table 3b): Exact McNemar's test: p ¼ 0. 1027. % agreement ¼ (5043 þ 2711) / 8584 ¼ 90. 3%.
Acknowledgements The  Chronic Renal Insufficiency Cohort Study (CRIC)  was conducted by the  CRIC Investigators  and supported by the  National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). The data from the CRIC Study reported here were supplied by the  NIDDK Central Repositories. This manuscript was not prepared in collaboration with Investigators of the CRIC study and does not necessarily reflect the opinions or views of the CRIC study, the  NIDDK Central Repositories , or the  NIDDK.
Materials and methods Strains and growth conditions P. aeruginosa strain PAK  (Takeya and Amako, 1966)  was grown in LB medium supplemented with 10 mM CaCl 2 at 37 °C unless stated otherwise. For RNA-seq experiments, cells were infected with bacteriophage PAK_P4  (Henry et al. , 2013)  using a multiplicity of infection (MOI) of 25 to ensure the synchronicity of the infection (95% of the bacterial population killed after 5 min phage-introduction). Bacteriophage PAK_P3 was isolated and described by  Morello et al. (2011). Updated phage genome sequences are available in Genbank and can be accessed via accession numbers NC_022970 (PAK_P3), NC_022986 (PAK_P4). Updated annotations of strain PAK genome are available via GenBank accession number CP020659. Adsorption assay and one-step growth experiment PAK_P4 adsorption assays (MOI 10 -3 ) and one-step growth experiments (MOI 10 -1 ) were performed as described in  Chevallereau et al.
5. 1 (QIAGEN Bioinformatics, Aarhus, Denmark) These alignments were then summarized into count tables of Total Gene Reads that map to phage or host gene features respectively. Each statistical comparison presented was performed using the DESeq2  (Love et al. , 2014 ) R/Bioconductor package to normalize host transcript populations to host transcript populations, or phage to phage, before testing for differential expression. RNA-seq data have been deposited in NCBI-GEO with accession no. GSE86022. RNA-seq coverage visualization is available through the COV2HTML software at https://mmonot. eu/ COV2HTML/visualisation. php?str_id = -36 for a comparison of the host (0 min/13 min) and https://mmonot. eu/COV2HTML/visualisation. php?str_id = -38 for a comparison of the phage (3. 5 min/13 min).