dataesr/scientific-paragraphs-categorization huggingface dataset:
After air-drying the chip, 2 μL of a 50% saturated solution of sinapinic acid was added and air-dried (twice). In addition, porcine dynorphin (2147. 5 m/z), human ACTH (1-24) (2933. 5 m/z), bovine insulin (β-chain) (3495. 9 m/z), human insulin (5807. 7 m/z), recombinant hirdin (6963. 5 m/z), hirdin BHVK (7033. 6 m/z), bovine cytochrome C (12,230. 9 m/z), equine myoglobin (16,951 m/z), bovine carbonic anhydrase (29,023 m/z), and S. cerevisiae enolase (46,671 m/z) were used as molecular weight calibration proteins. The protein chips were measured using the protein chip reader PCS4000 (Bio-Rad) and data was obtained through CiphergenEx-press™ Data Manager version 3. 0 (Bio-Rad). The measurement ranges were 0-100,000 m/z (Focus mass/SPA-Low; 6500) as the low molecular field data and 10,000-200,000 m/z (Focus mass/ SPA-High; 20,000) as the high molecular field data.
S. rheumatoid arthritis (ACR) diagnostic criteria, and we found that a class 2 patient and class 4 (severe) patient did not express CFMP. Therefore, we suggest that this CFMP peptide is specifically related to the mechanism of bone destruction in cancer metastasis and not to the bone destruction in rheumatoid arthritis (Figure  S1A  and Supplemental Mass Data). We also examined follow-up data in breast cancer patients. We also observed fluctuations in the levels of CEA, CA15-3, NCC-ST-439, ALP, and CFMP by ELISA in the serum (Figure  4D ) following the removal of breast cancer tissue; bone metastasis was not confirmed in the 3D-CT imaging performed in July 2005. As a result, we measured the serum CFMP levels in these patients. However, since the levels were already 0. 32 ± 0. 04 μM (P b. 05), we conducted a prospective study.
Acknowledgments We would like to acknowledge the individuals and families that participated in this research. We dedicate this article to the late emeritus professor  Akio Nomoto  ( Department of Microbiology, Graduate School of Medicine, University of Tokyo ). We thank  K. Fujii  ( Kurume General Hospital ),  R. Hachisu  ( Hokkaido System Science Co. ),  E. Majima  ( ProteNova Co. ),  H. Saito  ( Charles River Laboratories Japan, Inc. ),  K. Gondou , and  H. Rakumura  ( Kurume Research Park Co. ) for their helpful comments.
Reverse transcription polymerase chain reaction (RT-PCR) To determine whether deletions occurred at the eGFP locus, RNA was extracted from 100 mg homogenized infected tissue using the InviTrap Spin Plant RNA Mini Kit (Stratec Molecular). Reverse transcription (RT) was performed using MMuLV reverse transcriptase (Thermo Scientific) and reverse primer 5'-CGCACTACATAGGA-GAATTAG-3' located in the 3'UTR of the TEV-eGFP genome (GenBank accession; KC918545, positions 10235-10255). PCR was then performed with Taq DNA polymerase (Roche) and primers flanking the eGFP gene:.
Sequencing was performed at GenoScreen (Lille, France: www. genoscreen. com). Illumina HiSeq2500 2 × 100 bp paired-end libraries with dual-index adaptors were prepared along with an internal PhiX control. Libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina Inc. ). Sequencing quality control was performed by GenoScreen, based on PhiX error rate and Q30 values. Read artifact filtering and quality trimming (3' minimum Q28 and minimum read length of 50 bp) was done using FASTX-Toolkit v. 0. 0. 14  [25]. De-replication of the reads and 5' quality trimming requiring a minimum of Q28 was done using PRINSEQ-lite v. 0. 20. 4  [26]. Reads containing undefined nucleotides (N) were discarded. Initially, the ancestral TEV-eGFP sequence was mapped using Bowtie v. 2. 2. 6  [27]  against the reference TEV-eGFP sequence (GenBank accession: KC918545).
Virus accumulation and within-host competitive fitness assays Prior to performing assays, the genome equivalents per 100 mg of tissue of the ancestral virus stocks and all evolved lineages were determined for subsequent fitness assays. The InviTrap Spin Plant RNA Mini Kit (Stratec Molecular) was used to isolate total RNA of 100 mg homogenized infected tissue. Real-time quantitative RT-PCR (RT-qPCR) was performed using the One Step SYBR PrimeScript RT-PCR Kit II (Takara), in accordance with manufacturer instructions, in a StepOnePlus Real-Time PCR System (Applied Biosystems). Specific primers for the coat protein gene (CP) were used: forward 5'-TTGGTCTTGATGGCAACGTG-3' (positions 9968-9987) and reverse 5'-TGTGCCGTTCAGTGTCTTCCT-3' (positions 9998-10018). The StepOne Software v. 2. 2. 2 (Applied Biosystems) was used to analyze the data.
To measure within-host competitive fitness, we used TEV carrying a red fluorescent protein: TEV-mCherry as a common competitor. This virus has a similar insert size and within-host fitness compared with TEV-eGFP  [21]. All ancestral and evolved viral lineages were again normalized to the sample with the lowest concentration, and 1:1 mixtures of viral genome equivalents were made with TEV-mCherry  [23]. The mixture was mechanically inoculated on the same host plant on which it had been evolved, plus TEV and the ancestral TEV-eGFP virus on each of the hosts, using three independent plant replicates per viral lineage. The plant leaves were collected at 10 dpi, and stored at -80 °C. Total RNA was extracted from 100 mg homogenized tissue. RT-qPCR for the CP gene was used to determine total viral accumulation, and independent RT-qPCR reactions were also performed for the mCherry sequence (GenBank accession: AY678264) using specific primers: forward 5'-CGGCGAGTTCATC TACAAGG-3' (positions 360 to 379) and reverse 5'-TGG TCTTCTTCTGCATTACGG-3' (positions 416-436).
The ratio of the evolved and ancestral lineages to TEV-mCherry (R) is then R=(n CP -n mCherry )/(n mCherry ), where n CP and n mCherry are the RT-qPCR measured copy numbers of CP and mCherry, respectively. Then we can estimate the within-host competitive fitness as W ¼ ffiffiffiffiffiffiffiffiffiffiffi ffi R t =R o t p ; where R 0 is the ratio at the start of the experiment and R t the ratio after t days of competition  [24]. The statistical analyses comparing the fitness between lineages were performed using R v. 3. 2. 2  [30]  and IBM SPSS Statistics version 23.
stramonium, we observed a significant increase in competitive fitness compared to the ancestral TEV-eGFP (Fig. 5b , L8; t-test with Holm-Bonferroni correction: t 4 = -6. 890, P = 0. 002). Fig. 3  Genomes of the TEV-eGFP lineages evolved the three different hosts as compared to the ancestral lineage. Mutations were detected using NGS data of the evolved lineages (L1-L10), as compared to their ancestral population. The square symbols represent mutations that are fixed (>50%) and the circle symbols represent mutations that are not fixed (<50%). Filled symbols represent nonsynonymous substitutions and open symbols represent synonymous substitutions. The triangle symbols represent mutations that are present in either the 3'UTR or 5'UTR. Black substitutions occur only in one lineage, whereas color-coded substitutions are repeated in two or more lineages.
Note that the mutations are present at different frequencies as reported by VarScan 2. Grey boxes with continuous black lines indicate genomic deletions in the majority variant of the virus population. The grey transparent box with dotted black lines in L4 of N. benthamiana indicates a genomic deletion in a minority variant. The latter box was drawn to indicate the size of the deletion, assuming that the deletion starts at the first position of eGFP. The mutations discussed in the manuscript are highlighted on the top. For more information on the frequency of the mutations please see Additional file 2: Tables  S1-S3  This lineage is the only one to have a deletion in the eGFP insert. In N. benthamiana, 1/6 lineages had a significant increase in within-host fitness (Fig. 5a, L4 ; t-test with Holm-Bonferroni correction: t 4 = -5.
Such newly acquired voluntary right-hand movements were present but remained imprecise and fragile. Importantly, no obvious regain of motor function was observed for the left arm or hand (ipsilateral to the stimulation) neither any of the two legs. To confirm and eventually find an explanation for such an unexpected impact, the patient underwent a functional magnetic resonance imaging (fMRI) examination, performed 78 months after the stroke event, and 6 months following the last rTMS session over the left TPJ. During these recordings, previously regained right-hand motor improvement was still present. Neuroimaging data were acquired on a 3-T MRI scanner (Magnetom Verio TIM, Siemens, Erlangen, Germany) at the CENIR (ICM, Paris, France). Functional magnetic resonance imaging data were preprocessed and analyzed using SPM8 (Statistical Parameter Mapping, version 8, http://www.
No significant activations were detected when the left hand (always more impaired than the right hand) was used for grasping. Diffusion tensor imaging (DTI) was reconstructed using the Diffusion Toolkit to create 3D images of the white matter fiber tracts in the TrackVis software (Martinos Center for Biomedical Imaging, Massachusetts General Hospital)  (20). A FACT approach was performed to reconstruct fiber paths. For tractography, we used a streamline algorithm with an angular threshold of 35° and an FA threshold of 0. 2. The tensor was spectrally decomposed to obtain its eigenvalues and eigenvectors. The fiber direction is assumed to correspond to the principal eigenvector (i. e. , the eigenvector with the largest eigenvalue). This vector was color coded (green for anterior-posterior, blue for superior-inferior, and red for left-right) to generate a color FA map.
Functional and structural MRI recordings were carried out to objectively confirm and better understand the neural sources and mechanisms of right-hand function recovery following left TPJ rTMS. Diffusion data suggest that the modulation from the left TPJ of spared cortico-bulbar and cortico-spinal projections passing through the ipsilateral cerebral peduncle and reaching the pons and further down the pyramids in the medulla oblongata, could theoretically convey function and explain improvements of motor function. However, given the lack of neurophysiological evidence (for example, TMS-evoked motor potentials, MEP) prior and following the rTMS treatment for AHs, it is difficult to rule out if the few white matter fibers from the left TPJ reaching the brainstem might had driven meaningful motor output to the right-hand and forearm extensor muscles, hence subtend rTMS improvements of right-hand function.
aCKNoWLeDGMeNts The activities of the laboratory of Dr. Valero-Cabré are supported by research grants from IHU-A-ICM-Translationnel and ANR projet Générique OSCILOSCOPUS. JA was supported by a fellowship from the Fondation Fyssen. The authors also thank IFRAD Foundation and Naturalia and Biologia Foundation for logistical help and financial assistance for traveling and attendance to meetings.
Data acquisition and real-time alert reception in ANTARES The data acquisition system of the ANTARES detector is based on the "all-data-to shore" concept  [3]. The time and charge amplitude of all the photomultiplier (PMT) signals above a threshold of 0. 3 photoelectrons are sent to a computing farm onshore for processing. A filter is applied on shore to select the physics events among the raw dataset structured in time slices of 104. 85 ms and dominated by hits due to the optical background produced by bioluminescence and radioactive decay of 40 K. Two filtering algorithms look for a combination of local clusters of hits within a time winow of 2. 2 µs. The first one selects events made of five local causally connected clusters anywhere in the detector, while the second one requires at least two clusters on nearby PMT storeys.
The selected events are finally kept for online and offline reconstruction as described in  [4]. In particular, a fast and robust online algorithm reconstructs tracks in nearly real time  [5]. The remaining sample of events is then sent to a more accurate reconstruction algorithm  [6]  which improves the angular resolution of each event in less than 5 s. Both algorithms use an idealised geometry of the detector that does not take into account the dynamical positioning of the optical modules due to sea current variations. For high-energy tracks, this use limites the angular resolution by about 0. 1 •. These online data are routinely used to look for neutrino counterparts to various astrophysical transient events whose detection is notified directly to ANTARES through both VOEvents 1  and/or GCN socket and also to send alerts after the detection of interesting neutrino events (as presented in another proceedings  [7] ).
Follow-up of gravitational wave events The observation of two significant gravitational wave (GW) sources by Advanced LIGO on September 14 th and December 26 th , 2015  [9, 10]  represents an important step forward in the era of multi-messenger astrophysics. Since the beginning of the second observing run of Advanced LIGO interferometers on November 30, 2016, ANTARES is receiving gravitational wave alerts in real time. The angular resolution of ANTARES (∼0. 4 • at ∼10 TeV) compared to the size of the gravitational wave error box (a few hundreds of square degrees on the sky) offers the possibility to drastically reduce the size of the region of interest in case of a coincident neutrino detection. About 74 days of LIGO/Hanford and LIGO/Livingston simultaneous science data have been collected up to June 2017.
The average reach of the LIGO network for binary merger events is around 70 Mpc for 1. 4+1. 4 M , 300 Mpc for 10+10 M and 700 Mpc for 30+30 M mergers, with relative variations in time of the order of 10%. Prior to a commissioning break that occurred in May 2017, 7 triggers, identified by online analysis using a loose false-alarm-rate threshold of one per month, were identified and shared with partner collaborations who have signed memoranda of understanding with LIGO/Virgo for electromagnetic and neutrino follow-up. Each of the 7 alerts were followed by the ANTARES neutrino telescope by searching for a potential neutrino counterpart. A thorough investigation of the data via an offline GW analysis enabled to confirm a first significant detection which occurred on January 04 2017 and produced after the merger of two black holes with 31.
PoS(ICRC2017)984 Real-time transient analysis with ANTARES D. Dornic observe fast radio bursts (FRBs) and gamma-ray bursts (GRBs). While the latter are probably related to either the collapse of massive stars or the merger of two compact objects, the sources producing the former are still unknown. If hadrons are accelerated in relativistic outflows of both GRBs and FRBs, TeV-PeV neutrinos might be produced by photo-hadronic interactions. Dedicated offline analyses are performed by the ANTARES collaboration (see e. g. [21, 22, 23] ) and preliminary results of the more recent ones will be presented at this conference  [24, 25]. In particular, a stacked analysis based on the full ANTARES data sample from 2008 to 2016 enables to constrain the contribution of GRBs to the diffuse flux of cosmic neutrinos.
On the other hand, looking for individual GRBs and FRBs helps to constrain theoretical models of neutrino emission. ANTARES is able to react to external alerts sent through GCN after the detection of a GRB. More than 500 GRBs detected by Swift and Fermi have been followed by ANTARES in realtime so far (see Figure  3 ). Data analysis can be done in two alternative ways. A search for muontrack neutrino counterpart in the standard online dataset described in Section 2 is performed in real-time within 15 min around the detection and 2 • from the GRB position. To ensure the quality of the data at the alert time, the detector stability is checked over several hours before the alert. The result of the search is sent by email within 15 min after the release of the GCN. In case of a coincident neutrino detection, a dedicated offline analysis is run to confirm the result and compute its significance (expected to be higher than 3σ in most of the cases).
A dedicated algorithm searching for time and space correlations in a small region of interest around the GRB position is finally used as in standard offline analyses. An analysis based on this approach has recently been published by the ANTARES collaboration to test the photospheric model of neutrino emission in GRBs  [21]. As for FRBs, the Parkes radiotelescope, located in Australia, is the main discovery instrument so far and the SUrvey for Pulsars and Extragalactic Radio Bursts (SUPERB) is underway on this instrument  [28]. One of the main obstacles for constraining the nature of the FRBs is the latency between the detection of the burst and the starting of multi-wavelength and multimessenger follow-up observations aimed to identify a FRB counterpart. The SUPERB program was designed to drastically reduce the time needed to send a notification to the community.
Conclusion By simultaneously monitoring at least half of the sky, neutrino telescopes are well-suited to detect transient sources. In this context, multi-messenger approaches are destined for a bright future and will help to probe the physical processes at work in these objects. In addition to offline analyses, that search for time and space coincidences of ANTARES events with electromagnetic, gravitational wave or neutrino signals  [2, 30, 31] , ANTARES is also able to handle external alerts in real time (as described in this document) and to trigger electromagnetic follow-up of interesting neutrino candidates  [7, 8]. Furthermore, the capability of the ANTARES data acquisition system to store a few minutes of raw data coincident with a GCN alert extends the possibility of increasing offline sensitivity to transient astrophysical events.
Results and Discussion As the waveguide dimensions are smaller than the wavelength of the sensing IR radiation, a significant portion of the guided field extends outside the waveguide. This field, which decreases exponentially with the distance from the waveguide, is called evanescent field, and can be absorbed if the light frequency matches an absorption band of the surrounding medium. The decrease in intensity at the out-port of the waveguide can be determined by the Beer-Lambert law = • exp[- • • • ], (1) where is the absorption cross-section of the medium, its concentration, the optical path. The term is the evanescent-field ratio (EFR), a parameter that takes into account the fact that only a fraction of the total field undergoes interaction with the absorbing medium. In our case, was determined by FEM simulations performed with the COMSOL Multiphysics software.
Only peaks in the aliphatic region of the spectra were selected since the chemical shift assignment for this region is relatively complete. Examples are given in Supplementary Figs. 7  and 8. Also, intra-residue peaks were excluded to prevent the automatic chemical shiftmatching procedure from generating faulty ADRs based on unassigned intra-residue peaks, for which the correct assignment option is missing. Such intra-residue peaks were identified by comparison of the spectra recorded with short and long mixing times. Assignment possibilities for the ADRs were reduced via a CCPNMR analysis tool that explicitly considers labeling schemes and were limited to pairs of carbon spins for which the product of the labeling percentages exceeded 10%. About 128 φ/ψ torsion angles (256 in total) were predicted using the program TALOS+  22, 23.
As expected, the vast majority of assigned residues are predicted to be in a β-sheet conformation (Supplementary Fig. 9 ). These results are in good agreement with a prediction of the topology based solely on the amino-acid sequence by the program PRED-TMBB, which is specifically designed for the topology prediction of transmembrane β-barrels (Supplementary Fig. 9 , bottom row)  24. Structures were calculated without explicit, manual assignment of distance restraints by a modified ambiguous restraints for iterative assignment (ARIA) protocol  25, 26  , making a stepwise use of data from proton-and carbon-detected experiments. 1 Hdetected restraints between amide protons are very appropriate for constraining the backbone conformation of a protein that is almost entirely β-sheet. Therefore, in the first four iterations of the protocol, these were the only distance restraints employed (Supplementary Fig.
Amino acid-type selective labeling was applied to decrease spectral overlap and to provide complementary information for the sequential assignment process and restraint disambiguation. To be aware of effects of scrambling, metabolic and catabolic pathways were cross checked beforehand, using the ECOCYC database which includes most of the biochemical pathways of E. coli K12  41. The labeling patterns of all preparations were analyzed and verified by recording  13  C-  13  C proton-driven spin diffusion (PDSD) or DARR spectra. In the sections below, the preparation of individual samples is described, whereby the labeling pattern desired is given in amino acid one-letter code and accidentally labeled amino acids are given in brackets, or according to IUPAC in square brackets.
The carrier frequency was placed at 100 ppm. Data were recorded and processed using Topspin version 2. 1 (Bruker, Karlsruhe, Germany). The time domain data matrix of each experiment was 512 (t 1 ) × 2048 (t 2 ) points, with t 1 and t 2 increments of 10 and 16 μs, respectively. About 96 or 160 scans per point were recorded with a recycle delay of 3 s, resulting in total acquisition times of ~42 or 68 h, respectively. Data were processed with shifted-sinebell (in t 1 ) and Lorentzianto-Gaussian (in t 2 ) apodization functions and zero filling was applied to 4096 (t 1 ) × 8192 (t 2 ) points. The carbon chemical shifts were indirectly referenced to 2,2dimethyl-2-silapentane-5-sulfonic acid (DSS) by calibrating the downfield  13  C adamantane signal to 40. 48 ppm. 3D NCACX and NCOCX spectra were recorded on a wide-bore 400 MHz spectrometer equipped with a 3.
Torsion angle prediction for the structure calculations. The program TALOS+  22, 23  was used for prediction of torsion angles. Based on the chemical shift assignment, a reliable prediction was obtained for 128 φ and ψ torsion angles, yielding 256 torsion angle restraints in total. Distance restraints for the structure calculations. As input for the automated structure calculation using ARIA 2. 3. 2, lists with ambiguous distance restraints were produced by CCPN Analysis. The reason for using this rather than (unassigned) peak lists is that CCPN analysis supports the inclusion of complex isotopelabeling schemes as used in our studies into ARIA protocols. Still, the distance restraint lists were based on peak lists and produced using a CCPN macro script. This script is deposited in GitHub and can be downloaded under: https://github.
com/jorenretel/ompg_restraint_generation. The script is detailed in the next two sections. 1 H-1 H distance restraints. ADRs were generated from (H)N(HH)NH and (H) NHH spectra as well as from 2D  13  C-13 C DARR spectra. For the (H)N(HH)NH and (H)NHH spectra, a 2. 0 ms RFDR scheme was used for 1 H homonuclear mixing. Chemical shift-matching of the peaks in these spectra to a dedicated chemical shift list (taking care of sample deuteration) was performed with a tolerance of 0. 4 ppm in the 15 N dimension(s) and 0. 1 ppm in the indirectly detected 1 H-dimension. For the directly detected 1 H-dimension, a tolerance of 0. 7 ppm was employed for shift-matching. Furthermore, the four-fold redundancy present in these spectra was used to decrease the amount of assignment possibilities for each restraint.
Acknowledgements This work was supported from a  Joint Research Activity in the 7th Framework program  of the EC (BioNMR No. 261863 ), the  EU -project iNext (infrastructure for NMR, EM, and X-rays for Translational Research, GA  653706 ), and the  Deutsche Forschungsgemeinschaft  ( SFB 740  and  OS106/9 ). A. J. N. was supported by fellowships from the  Fulbright Program  and the  Alexander von Humboldt Foundation.