dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistics The comparisons of both qualitative and quantitative criteria were performed using the Wilcoxon signed-rank test. The repeatability of the quantitative measurements was assessed using the intraclass correlation coefficient (ICC) with its 95% confidence interval, based on an absolute agreement, two-way mixed-effect model. P values <0. 05 were considered significant. All statistical analyzes were performed using GraphPad Prism 9. 0 (GraphPad Software, Inc. , San Diego, CA).
Despite the increasing number of studies on GS, comparative data for the JD and MV approach, i. e. measuring kg vs. kPa is not widely available hindering direct comparison between the two instruments. Correlation coefficients between both instruments ranged from r = 0. 63 to r = 0. 86 in a single-center study by Neumann et al. in 339 randomized patients (mean age 49 ± 18. 4 years) with symptom-free hands (excluding deformities, degenerative or inflammatory functional limitations of the upper extremities), indicating a moderate to high correlation  [22]. In addition, to our knowledge no validated equation has been published for a direct comparison of the two instruments or the units specified (kg vs. kPa). Therefore, our study aimed to examine sex-and agespecific GS cut-points in kPa using the Martin Vigorimeter for the dominant and non-dominant hand (DH; NDH) to identify clinically relevant weakness in generally healthy Swiss older adults, and to assess their convergent validity with additional markers of physical function.
Study design and participants We performed a cross-sectional analysis of baseline data of Swiss older adults included in DO-HEALTH, a three-year randomized controlled clinical trial in adults age 70 years and older from five European countries (NCT01745263)  [23]. Swiss participants were recruited in three study centers: Basel (n = 253), Geneva (n = 201), and Zurich (n = 552). Inclusion criteria were absence of major health events (i. e. cancer or myocardial infarction) in the five years prior to enrollment, sufficient mobility to come to the study centers without help, and good cognitive status (defined by a Mini-Mental State Examination (MMSE) score of at least 24 points). The DO-HEALTH trial protocol has been previously published  [23]. The Cantonal Ethics Committee of the Canton of Zurich approved our study (BASEC Nr.
Baseline characteristics of the study population Of the 1,006 Swiss DO-HEALTH trial participants, three and seven had missing baseline GS measurements at the DH and NDH, respectively. After excluding 27 outliers for GS at the DH and 22 outliers for GS at the NDH due to potential measurement or data-entry errors, data from 976 and 977 participants were used to derive GS cutpoints at the DH and NDH, respectively. The baseline characteristics of the 976 participants with available GS at the DH are presented in Table  1. Overall, the mean age was 75. 2 (4. 6) years and 61. 8% were women. The mean BMI was 25. 8 (4. 2) kg/m 2. Participants had good lower extremity function with a median Short Physical Performance Battery score of 12. 0 (11. 0-12. 0) and a mean gait speed of 1. 1 (0. 2) m/s. The prevalence of sarcopenia was 12.
Therefore, our findings remain to be confirmed in independent studies. At last, the potential for false positive results may exist since we did not adjust for multiple comparison testing. However, these limitations are balanced by several strengths. First, we report data from a meticulously executed clinical trial. Second, GS measurements in DO-HEALTH were performed according to a standardized protocol and accomplished at all participating sites by trained and certified study personnel. Third, by investigating GS in a group of generally healthy volunteers age 70 years and over without major health events within the last five years and intact cognitive function, our findings may serve as a reference for a comparable older population from Switzerland.
Results Our particle system, voxel engine, and simulation were implemented in Unity3D V5. 4. 0. Since our simulation produces a voxelized output, to obtain the images in this paper, and only for aesthetic reasons, we exported the simulation meshes at a given interval of time, and imported them into a dedicated modeling software (Blender v2. 78). Also, for illustrative purposes only, and to showcase the possibilities, we post-processed the model (with a smoothing algorithm) and rendered it to obtain the final results, see Fig. 11. Our standard scene, unless stated otherwise, contains 983k voxels of 0. 5 cm 3 , allowing a simulation volume of 0. 9 m × 0. 9 m × 0. 20 m similar to Fig. 2. It was also made of 20 bricks of approximately 30k voxels each (of size 0. 3 m×0. 15 m×0. 1 m) as well as an iron pipe (of about 15k voxels, with 0.
Electron identification Reconstructed tracks were selected based on the criteria listed in Table  3 , which are similar to those used in the analysis described in  [141, 142]. These requirements were applied depending on the data sample as well as the transverse momentum region of the analysis. The rapidity ranges used in the nominal-B field TPC-TOF analysis and the TPC-EMCal analysis were limited to |y| < 0. 8 and |y| < 0. 6, respectively, to avoid the edges of the detectors, where the systematic uncertainties related to the particle identification increase. In the low-B field TPC-TOF analyses for pp collisions, the rapidity interval was restricted to |y| < 0. 5, to ensure a stable estimation of the photonic electron background (Sec. 4. 2), which significantly increases in the low-B field sample for small p T and large rapidities, resulting in a small signal over background ratio.
For pp collisions, the π 0 spectrum was estimated as the average of the spectra of π + and π -  [148] , whereas the η spectrum was obtained using m T scaling, as in  [149] [150] [151]. For the p-Pb analysis, the measured transverse momentum spectra of π 0 and η were used  [152]. In the pp analysis, the tagging efficiency at low p T (p T < 1. 0 GeV/c) is 55-65% for the low-B field data set, whereas for the nominal-B field data set it is around 45-55% at low p T (p T < 1. 0 GeV/c) increasing to about 85% at high p T (p T > 15 GeV/c). In the p-Pb analysis, the tagging efficiency varies between 40% at low p T (p T < 3. 0 GeV/c) and 80% at high p T (p T > 7. 0 GeV/c). ≥ 2 ≥ 2 ≥ 2 ≥ 2 ≥ 2 χ 2 /N cls TPC < 4 < 4 < 4 < 4 < 4 |DCA xy | < 1 cm < 1 cm < 1 cm < 1 cm < 1 cm |DCA z | < 2 cm < 2 cm < 2 cm < 2 cm < 2 cm Due to the requirement of hits in the SPD layers, the contribution of electrons from K e3 decays was found to be negligible with respect to the heavy-flavour signal for p T > 0.
Therefore, a higher reconstruction efficiency is observed in the low-B field data compared to the nominal-B field sample. The TPC electron identification efficiency was determined using a data-driven approach based on the n TPC σ ,e distribution  [9]. It is about 88% at p T = 0. 2 GeV/c and increases to 89% for p T > 0. 5 GeV/c, for the low-B field data sample. In the nominal-B field data set, it was found to be around 86% at p T = 0. 5 GeV/c increasing to 88% for p T > 4 GeV/c. The electron identification efficiency with EMCal was estimated using MC simulations and was found to be about 60% at 3 GeV/c, increasing up to 80% for p T larger than 10 GeV/c for pp collisions. The total reconstruction efficiency (ε geo × ε reco × ε eID ) for different data sets and with different detectors is presented in Fig.
The uncertainty due to an imperfect description in the simulation of the TPC-TOF (and the TPC-ITS) track matching was estimated by calculating the difference between efficiencies of the TPC-TOF (and the TPC-ITS) track matching in data and MC. To obtain the matching efficiency, the abundances of primary and secondary particles in data were estimated via template fits to the track impact-parameter distributions, and the relative abundances in the simulation were weighted to match those in data  [160, 161]. For the low-B field sample in pp collisions, the uncertainty on the track matching between the ITS and TPC is 2% at p T = 0. 2 GeV/c increasing up to 4% at 4 GeV/c, whereas, the uncertainty on the track matching between the TPC and the TOF detector is 4% at p T = 0. 2 GeV/c and 2% at 4 GeV/c.
In case of the nominal-B field data set, the uncertainty is about 2% for the TPC-TOF track matching and about 3% for the TPC-ITS track matching in the whole p T range. In the p-Pb analysis, the uncertainty for the TPC-TOF track matching, as well as the TPC-ITS track matching, was found to be around 2% in the whole p T range. The systematic uncertainty on the SPD hit requirement was obtained by varying the condition on the minimum number of hits and the specific layer of the SPD on which a hit was required for both the TPC-TOF and the TPC-EMCal analyses. For the low-B field sample in pp collisions, the systematic uncertainty due to the SPD hit requirement was about 25% at p T = 0. 2 GeV/c decreasing to 15% at 0. 5 GeV/c, whereas for nominal-B field data sets in pp and p-Pb collisions, the uncertainty is about 10% at p T = 0.
5 T (0. 5 < p T < 4 GeV/c) data sets with the TPC and TOF detectors, as well as with the TPC and EMCal detectors (4 < p T < 35 GeV/c). The values presented as a range correspond to the lowest-and highest-p T intervals. 6, 7 , and 8. The assigned systematic uncertainties vary from 5% to 12% depending on the p T and the analysis method Additionally, the robustness of the fit procedure used to extract the hadron contamination in both electron identification strategies was checked. In the TPC-TOF analysis, different analytical functions were utilised to parameterise the TPC dE/dx, which had negligible effects on the estimated hadron contamination up to a p T of 3 GeV/c. In the TPC-EMCal analysis, the scaling region of the hadron E/p distribution was varied. The resulting uncertainties were found to be negligible at low p T and of the order of 5% at high p T.
Patients The RESSIF network was started in 2012 by the French National Reference Center for Invasive Mycoses and Antifungals (NRCMA, Institut Pasteur, Paris, France). 24  It is an active surveillance system involving 29 participating secondary and tertiary centres across metropolitan France and overseas French territories, with 21 centres who were active between 2013 and 2018 (and 13 centres in 2012). All IFDs occurring in these centres are prospectively and manually notified. These 21 university hospitals cover approximately 45% of hospitalisation days of all French university hospitals and cover 15/18 French regions, including overseas territories. Each collaborative centre aggregates several hospitals or wards, including adults and paediatric patients. A referent medical mycologist is responsible for the accuracy and completeness of the records based on local diagnosis in collaboration with clinicians and all data are monitored at National Reference Center by a senior physician.
Clinical and laboratory assessment Notification data include demographic, diagnostic and therapeutic information, details on underlying conditions and concomitant medications. We retrieved further data using local access to electronic health records, including the nature of the AID, year of diagnosis, dose of GCs at the time of IFD diagnosis and latest total lymphocyte and CD4+T cell counts (if measured within the previous 3 months) for patients with PCP. We described the population of patients with AID affected by IFD, by breaking down the population according to the main IFD categories (PCP, fungemia, Infections Infections Infections invasive aspergillosis) and reporting patients with several IFDs or another IFD in separate groups. For the analysis on how the treatment of the AID affected the mortality, the outcome was mortality at 30 days.
We also described separately the patients who did not have any other risk factor for IFD among malignancy, solid organ transplantation and recent surgery. We calculated the age-standardised and sex-standardised estimates for the main characteristics of the study population for the three main IFDs (PCP, fungemia, invasive aspergillosis) as well as across the 12 most frequent AIDs in the study, using the data on the French population (in 5-year age categories) provided by the World Bank for 2015. 27  Data were analysed using Stata/IC V. 15. 1 (College Station, Texas).
The detection range is from 175 nm to 3300 nm. The specular mode which includes diffuse reflection and specular reflection, has been considered. Infrared spectrometry analyses were carried out between 400 and 4000 cm -1 , using a Nicolet 6700 apparatus from Thermofisher Scientific. The specific surface area of the powders was measured by a Tristar 3020 of Micromeritics, using the Brunauer, Emmett and Teller model (BET). The adsorbed gas was nitrogen. The density of metal and ceramic manufactured parts was measured with an Archimedes balance. X-ray Computed tomography (CT) was carried out using a Phoenix V |tome| x M microfocus CT system from Baker Hughes. The scan was performed at 140 kV and the voxel size was 8 μm. The data was processed using Baker Hughes reconstruction software and VGSTUDIO MAX application suite (from Volume Graphics) was used for virtual cross-sections.
Acknowledgments The authors would like to thank  Marie-Claire Barthélémy ,  Vincent Baylac ,  Yann Borjon-Piron  at  Cirimat  for their help in surface area measurements, additive manufacturing support and logistic, and for the microscopy observations. They also thank  Patrick Nguyen  from  Elemca  for its technical support with the focused ion beam preparations. They are also grateful for the advice and experimental help provided by  Yohann Thimont  and  Diane Samelor  ( Cirimat ) for the optical measurements.
We acknowledge that our repeat surveys only cover 3. 5 years of the 14-year period from the 2004 earthquake to the SUBSAINTES cruise in 2017. It is possible that non-seismic processes trigger punctuated events that were The dot-dash lines represent optimal fits for different values of stress drop and widths of the seismogenic zone for increasing numbers of ruptured fault segments (F1-F4) from ref. 55  (MG07). Earthquake data is provided in Supplementary Data 6. not recorded in between the 2013 and 2017 surveys. However, we speculate that these long-term processes more likely act to weaken the bedrock and facilitate failure which occurs primarily when shaken during earthquakes. The suggestion that bedrock mass wasting on the uplifting footwall is triggered mainly by earthquakes is supported by on-land observations.
Methods Research cruises. We collected the main photographic, bathymetric, and video datasets analyzed for this study during the 2017 SUBSAINTES cruise onboard the research vessel L'Atalante  34. Data from the SUBSAINTES cruise was supplemented by further photographic, bathymetric, and video datasets from the 2013 ODEMAR cruise conducted onboard the research vessel Pourquoi pas?  33  and by ship-based multibeam bathymetry data obtained during the 2010 BATHYSAINTES cruise, also conducted onboard the research vessel Pourquoi pas?  68. A summary of the datasets used in this study is included in Supplementary Data 9. Bathymetry data. During the SUBSAINTES cruise, we collected near-bottom, high-resolution bathymetry data using the AUV Aster x (IFREMER, France), equipped with a Kongsberg Reson SMF EM2040.
The AUV surveyed at ~70 m above the seafloor, covering ~100 km 2 of seafloor between Les Saintes and Dominica (Fig. 1a ). The AUV data were processed using the CARAIBES (IFRE-MER) and gridded to produce digital terrain models (DTMs) with a 1-m cell size. AUV bathymetry was also acquired by AUV Abyss (GEOMAR) during the ODEMAR cruise and the resulting DTM was gridded with a 2-m cell size. Shipbased multibeam bathymetry data was obtained during the 2010 BATHYSAINTES cruise using a 0. 5°× 0. 5°beam width multibeam echosounder (Reson Seabat 7150 at 24 kHz). The resulting bathymetry provides continuous seafloor coverage across the study area and allows gridding of a DTM with a 10-m cell size (Fig. 1b ; see details in refs. 13, 69 ). ROV seafloor photomosaics. We collected still-camera images of the seafloor for each dive from the 2013 ODEMAR cruise and the 2017 SUBSAINTES cruise using vertically mounted cameras on the ROV Victor6000 (IFREMER, France).
For optimal laser measurements, we selected video frames that contained visible laser beams with imaging sub-perpendicular to the outcrop. From these frames, we digitized the top and bottom of coseismic features at several positions in each image to obtain an average value and an estimate of the associated error (Supplementary Fig. 4 ; Supplementary Data 3). At selected positions, we compared displacements evaluated from laser scaler imagery with those from 3D terrain models and the results are consistent and within the estimated errors. Seismicity data. For the M w 6. 3 2004 main shock and the six largest aftershocks, we used the relocated earthquake locations and magnitudes from ref. 3. For regional seismicity prior to the 2004 main shock, we used data from the Centre de Données Sismologiques des Antilles catalog, which represents an ongoing attempt to create an integrated database of the various earthquake catalogs from the Lesser Antilles  60.
For the period covering and following the 2004 Les Saintes earthquake, but not including the 2004 main shock and the six largest aftershocks, we assembled earthquake data from the seismic catalog generated by the Institut de Physique du Globe de Paris, which manages two volcanological and seismological observatories in Martinique and Guadeloupe. From this combined catalog, we excluded earthquakes deeper than 50 km and associated with the subducting plate interface, and those outside our study area (15. 95-15. 65°N and -61. 7 to -61. 4°W). The final combined dataset contained 7356 earthquakes recorded over ~9500 days up to November 2019 (Fig. 7 , Supplementary Fig. 3 ). Maps of peak ground accelerations. We calculated PGA using the ground motion predictive equation (GMPE) from for Les Saintes  71.
Acknowledgements We are indebted to the crew, officers, engineers, and science parties of the ODEMAR (2013) and SUBSAINTES (2017) cruises, whose tireless work allowed us to acquire the data used in this study. This work is supported by the  French Oceanographic Fleet , by  ANR  project  SERSURF  ( ANR-17-CE31-0020 ) and from  CNRS-INSU Syster  programs. GEOMAR supported AUV operations during the ODEMAR cruise.
Data availability A 25-m per cell version of the regional bathymetry data from the BATHYSAINTES cruise is available at https://doi. org/10. 17882/81174  72. The 1-m per cell AUV-bathymetry data from the SUBSAINTES cruise is available at https://doi. org/10. 17882/79895  73 and ROV-navigation files from the SUBSAINTES cruise are available at https://doi. org/10. 17882/82290  74. ROV dive footage from the SUBSAINTES cruise is available at https:// video. ifremer. fr/. Video-derived 3D terrain models along the Roseau fault are available from https://doi. org/10. 17882/84249  75. Photomosaics from the ODEMAR cruise are available at https://doi. org/10. 17882/95243  76 and photomosaics from the SUBSAINTES cruise are available at https://doi. org/10. 17882/95242  77. Full details of all datasets used in the study are summarized in Supplementary Data 9 which is available along with all other supplementary tables referenced in this work from https://doi.
In the present work, RNAseq data were used to search for and discover new TA systems. We first used our published RNAseq and TSS data  [5]  to identify potential TA system by screening for 2-genes long operons. This led to the discovery and characterization of a new type II TA system, which is carried in an integron cassette, like most type II TA system of V. cholerae. Moreover, since we had previously mapped all ncRNAs of N16961 strain  [5] , we systematically analyzed ncRNA presence inside the SI cassettes which carry a gene possessing its own promoter. This analysis allowed the identification of a new type I TA system candidate. In vivo assays were then performed to characterize their functionality.
RNAseq experiments RNAseq experiments were performed on RNA purified from V. cholerae N16961 grown at 37 C in Luria Broth with 332 mM NaCl until exponential (OD 600 ¼ 0. 4) and stationary growth phases. Directional libraries were prepared using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer's instructions (Illumina). The libraries were quantified and sequenced as previously described  [5]. Raw sequencing reads are treated, and count data analyzed as previously described  [5]. The RNAseq data have been deposited in NCBI's Gene Expression Omnibus  [23]  and are accessible through GEO Series accession number GSE214813 (https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi? acc¼GSE214813).
Functional characterization of the VCA0498 antitoxin We probed several protein structure databases with VCA0498 protein. This analysis revealed that the C-terminal part of the VCA0498 antitoxin matched with 3D structure of type II TA system antidote HipB, the antitoxin of the HipAB TA system, with 96. 2% confidence in the Phyre 2 model  [30]. HipB antitoxin acts by repressing the hipAB operon transcription, either alone or in protein complex with HipA, its cognate toxin  [31, 32]. Experiments were then performed to determine whether VCA0498 may similarly act as a repressor on its own operon promoter. To characterize a potential interaction between VCA0497 and VCA0498 proteins, a bacterial two-hybrid experiment was performed. VCA0497 was cloned in the low copy number plasmid pKT25 with N terminal fusion with T25 peptide, while VCA0498 was cloned in the high copy number plasmid pUT18C with N terminal fusion with T18 peptide of the BACTH system kit and transformed in BTH101 reporter strain.
Functional characterization of the VCA0495 toxin As for the toxin above, we probed protein databases using several domain and function prediction softwares. We found the domain of unknown function DUF3800, as well as DNA and RNA binding domains (with Predict Protein) inside VCA0495 toxin. Moreover, it matched with 3D structure of ribonuclease H with 60. 7% confidence, in the Phyre 2 modelization  [30]. We then performed experiment to explore this function using the RNase H deficient E. coli strain MIC2067  [29]. No complementation phenotype was observed with VCA0495 toxin. However, the complementation was based on the MIC2067 ability to grow at 42 C in the presence of RNase H gene; and the thermosensitive plasmid, that contained antitoxin ncRNA which represses VCA0495 toxin, was not lost from the beginning of 42 C incubation.
Acknowledgements We are grateful to  Olga Soutourina  and  Laurence Van Melderen  for helpful advice. We thank  Kenn Gerdes  and  Sidsel Henriksen  for the DssrA strain and pSC320 gift. We thank  Mitsuhiro Itaya  and  Joel Belasco  for the gift of strain MIC2067. We thank  Rachel Legendre  for her help in submitting the RNAseq data. This study was supported by the  Institut Pasteur , the  Centre National de la Recherche Scientifique  ( CNRS-UMR3525 ), the  French Government 's  Investissement d'Avenir program ,  Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases " (grant n  ANR-10-LABX-62-IBEID ) and the  Fondation pour la Recherche M edicale  grants  DBF20160635736  and  EQ U202103012569.