dataesr/scientific-paragraphs-categorization huggingface dataset:
Dataset: For the evaluation of the classifiers, retrospective data from 90 patients are utilised. The data were provided by the second Department of Cardiology, University Hospital of Ioannina. Patients: (i) who have been diagnosed with HF (Framingham criteria) with continuous symptoms and frequent recurrence, (ii) who have HF in the functional NYHA II-IV classes with optimal treatment (angiotensin converting enzyme inhibitors, sartanes, beta-blockers, furosemide, spironolactone and/or digoxin), (iii) with a recent hospitalisation, emergency admission or specialised consultation (at least one in the last six months) for decompensated HF, disregarding the fraction of ejection and any etiology, (iv) who, at least, have undergone in the last 12 months one electrocardiogram and HF compatible symptoms, are included in the Letter.
2. 1. 1 Dataset: For the evaluation of the classifiers, retrospective data from 90 patients are utilised. The data were provided by the second Department of Cardiology, University Hospital of Ioannina. Patients: (i) who have been diagnosed with HF (Framingham criteria) with continuous symptoms and frequent recurrence, (ii) who have HF in the functional NYHA II-IV classes with optimal treatment (angiotensin converting enzyme inhibitors, sartanes, beta-blockers, furosemide, spironolactone and/or digoxin), (iii) with a recent hospitalisation, emergency admission or specialised consultation (at least one in the last six months) for decompensated HF, disregarding the fraction of ejection and any etiology, (iv) who, at least, have undergone in the last 12 months one electrocardiogram and HF compatible symptoms, are included in the Letter.
Similar findings were obtained in at least another recent study performed in MSM-PWIDs in San Francisco  17. In that study, it was suggested that an independent association with sex work had emerged as a result of an "unmasking" effect, with the prevalence of needle-sharing declining. This may also be a plausible hypothesis in the present situation as needle/syringe-sharing in the SurvUDI network significantly decreased from 1995 to 2014 (data not shown), with large-scale implementation of harm reduction programs on the whole territory during that period. In some studies, authors suggested that the association frequently observed between HIV transmission and crack use may be explained by higher-risk sexual behaviours in crack users  28, 31. This is consistent with the present data where participants of both sexes who reported sex work were also significantly more likely to use non injected crack.
ACKNOWLEDGEMENTS All authors contributed to the study. K. B. , C. B. and M. A. undertook the analysis and K. B. drafted the article. É. R. , C. M. , P. L. , R. P. , B. S. and M. A. contributed to the design of the study. All authors provided feedback on drafts and approved the final version. This study was supported by the  Public Health Agency of Canada (PHAC)  and the "  Ministère de la santé et des services sociaux du Québec  ". The authors wish to thank the invaluable contribution of interviewers. The contribution of  Lise Leblanc  and  Éric Demers  is also gratefully acknowledged for technical assistance and statistical analyses, respectively. The authors also wish to thank all participants for their excellent collaboration and all members of the SurvUDI Working Group :  Nathalie Deshaies ,  Marie-Michèle Grenier ,  Geneviève Pouliot-Gagné ,  Marcel Gauthier ,  Marie-Andrée Roy ,  Lynne Leonard ,  Lina Noël ,  Nathanaëlle Thériault ,  Andrée Côté ,  Andrée Perreault ,  Julie Levesque  and  Marie Hortas.
Off-Line Data Analysis Eye movement data were analyzed off-line using laboratory made software developed with Matlab v. 7. 10 (Mathworks, MA, USA). The position and time of the beginning and end of each primary saccade were detected using a velocity threshold of 50 • /s. The following parameters were calculated: horizontal saccade duration (difference between offset time and onset time of saccade), peak velocity (maximum velocity), saccade amplitude (difference between final and initial eye positions measured 50 ms after saccade termination and 50 ms before saccade onset, respectively), retinal eccentricity (difference between target position and saccade starting position) and saccadic gain (ratio between horizontal saccade amplitude and retinal eccentricity). The mean gain, peak velocity and duration of saccades were calculated, separately for the different conditions, for rightward and leftward saccades, in the pre-and post-exposure blocks as well as in the two exposure blocks (expo1 and expo2).
ACKNOWLEDGMENTS The authors thank  Christian Urquizar  for his help with the eye-movement and stimuli software. This work was performed within the framework of the  LABEX CORTEX  ( ANR-11-LABX-0042 ) of  Université de Lyon , within the  program ''Investissements d'Avenir''  ( ANR-11-IDEX-0007 ), operated by the  French National Research Agency (ANR).
These authors conclude that the increase anticipated by prices set in futures markets, exacerbated by speculators, was transmitted to the spot market. On the other hand, in 2015 futures prices were above the spot price, reflecting a situation of contango in the market. Table  3  reports the descriptive statistics for spot and futures prices obtained as the longest maturities and estimated by a stochastic model, Jarque-Bera test for normality (Jarque and Bera  [19] ) as implemented in the R package tseries (Trapletti and Hornik  [20] ) as well as the Augmented Dickey-Fuller (ADF) unit-root test (Dickey and Fuller  [21] ) as implemented in the R package tseries (Trapletti and Hornik  [20] ) with structural breaks. A first glance, the skewness shows that in all cases the data sets have a slight asymmetric probability distribution.
In order to analyze the relationship between spot and long-term futures prices from the crude oil market time series at different time/period horizons, we compute the wavelet cross-correlation (WCC). We follow the methodology for computing the wavelet transform (MODWT) and WCC given by Gencay et al. [13] , as implemented in the R package Waveslim  [30]. To obtain a graphical interpretation of wavelet correlation and cross-correlation analysis, we use the R package W2CWM2C  [17, 31]. The MODWT unbiased estimator of the wavelet correlation for scale λ j between two time series X and Y can be expressed as follows  [13] : ρ XY = cov( W X,j,t , W Y,j,t ) var{ W X,j,t }var{ W Y,j,t } = γ XY λ j σ X λ j σ Y λ j ( 6 ) where γ XY λ j is the unbiased estimator of the wavelet covariance between wavelet coefficients W X,j,t and W Y,j,t , and σ X λ j and σ Y λ j are the unbiased estimators of the wavelet variances for X and Y respectively, associated with scale λ j.
However, it tends to over-reject the null hypothesis if it is true (Diks and Panchenko  [16, 38] ). For this reason, Diks and Panchenko  [16]  proposed a new nonparametric and nonlinear Granger causality test to avoid the over-rejection. In our work, we use the causality test of Diks and Panchenko  [16] , as implemented in the C program GCTtest, which is freely available on the Internet  [39]. In addition, we use the test of Toda and Yamamoto  [40]  only to analyze potential causal relationships in raw data. This test is implemented in the R language and it is available freely on the web  [41].
Acknowledgments:  Josué M. Polanco-Martínez  was funded by a  Basque Government post-doctoral fellowship  (Reference No. POS_2015_1_006 ). Luis M. Abadie  gratefully acknowledges financial support from the  Basque Government   IT799-13  and from the  Spanish Ministry of Science and Innovation  ( ECO2015-68023 ). This funding has covered the cost of publishing in open access. We would like to show our gratitude to the anonymous reviewers whose comments and suggestions have been very helpful in improving this paper. We thank  J. Feuchwanger  for improving English of this paper.
Bacteria and growth conditions Staphylococcus aureus strain Newman wild type (wt) was obtained from Professor T. Foster, Trinity College, Dublin. Bacteria were routinely grown on Horse Blood Agar (HBA) plates (Oxoid, UK) or in tryptic soy broth (TSB, Oxoid, UK). Long-term storage of bacteria was at -80°C. Strain identity was checked by colony morphology, Gram stain, mannitol fermentation, coagulase production, DNAse activity, and sequencing of PCR products obtained across the SpA locus (data not shown). For infection of mice, 3-4 colonies of S. aureus were picked from HBA plates and transferred to TSB and grown overnight at 37°C, 130 rpm. This overnight culture was subcultured 1:100 into fresh TSB and grown statically for 2. 5 h at 37°C. The culture was washed and resuspended in Phosphate Buffered Saline (PBS, Sigma Aldrich, UK) at approximately 1×10 8 CFU/ml.
Assessment of Vaccine Immunity: Luciferase ImmunoPrecipitation System (LIPS) A Luciferase ImmunoPrecipitation System (LIPS) assay was used to detect specific serum anti-S. aureus Sortase A antibodies as described  [23]. Briefly, serially diluted serum was incubated with Renilla luciferase-Sortase A fusion protein. The mix was added to filter plates loaded with A/G beads (Thermo Fisher). After incubation and subsequent washings, chemoluminescence was measured in a Luminometer (VarioSkan Flash, Thermo Fisher) after adding substrate (Renilla luciferase assay system, Promega UK Ltd. ). Log transformation was applied to luminescence data prior to statistical analysis. Specific luminescence was generated by subtracting the assay background, which was considered to be the luminescence observed in the absence of any sera.
In particular, allowing for the data to be acquired in unattended overnight runs greatly maximises the usage of an (expensive) preclinical MR-system. While it was not specifically optimized for the detection of abscess in kidneys, the first test experiments yielded excellent resolution and contrast, demonstrating the applicability of our MRI technique to successfully differentiate between healthy kidney tissues and abscess. Imaging experiments were carried out on a 9. 4 T (400 MHz) MR system (Varian Inc. , Palo Alto, USA) comprising a horizontal magnet (bore size 210 mm), a VNMRS Direct DriveTM console and an actively shielded gradient system (1000 mT/m, rise time 130 msec, od 115 mm, id 60 mm). A quadrature-driven birdcage RF-coil (Rapid Biomedical, Rimpar, Germany) was used for transmitting / receiving the MR signals.
Image analysis Images were analysed using Amira software version 5. 6 (FEI Visualisation Sciences Group). This software reconstructs 2D images from the 3D MRI in any plane, allowing the comparison with histological analysis conducted on the same tissue. Abscesses were identified visually by operators reviewing the MRI images simultaneously in three views (xy, xz, yz) by scrolling through 'movie' style, and then reviewing suspect areas. Criteria used to identify suspect areas include (i) loss of normal renal architecture around the lesion (ii) an area of altered density identified by histological comparison to reflect an abscess (iii) areas of segmental abnormality, suggestive of vascular infarction. These latter were noted, but were not considered to be part of abscess formation. A supplementary protocol provides additional details.
Amira image analysis software was used to assist with detection and marking of lesion margins, and to compute their sizes. Two observers with no previous background in imaging were trained. Subsequently, a 16 kidney test data set (S1-S3 Videos), consisting of 4 kidneys from each of four time points (uninfected, 3, 7, 10 days post infection), was assembled and scored independently, blind to group membership, by the two independent observers. Importantly, when the infected kidneys were analysed and compared blindly by two observers, there was a strong positive correlation in the abscess volumes as calculated by each observer (Pearson's correlation coefficient = 0. 915, p<0. 005), Fig 2. We concluded the process of reading MRI scans was reproducible. Validation of MRI technique by subsequent histology.
Acknowledgments Disclaimer: The views expressed are those of the author(s) and not necessarily those of the  NHS , the  NIHR  or the Department of Health. The research leading to these results has received funding from the  European Union 's  Seventh Framework Programme  under the grant agreement  n°601783  ( BELLEROPHON  project, to DW) and  316655  (VACTRAIN) (CL). The research was supported in part by the  National Institute for Health Research (NIHR) Oxford Biomedical Research Centre based at Oxford University Hospitals NHS Trust  and  University of Oxford  (to DW). JES is a  BHF Senior Basic Science Research Fellow  ( FS/11/50/29038 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. CR is a Jenner Institute Investigator and an  Oxford Martin  fellow.
The research leading to these results has received funding from the  European Union 's  Seventh Framework Programme  under the grant agreement n  °601783  ( BELLEROPHON  project, to DW) and  316655  (VACTRAIN) (CL). The research was supported in part by the  National Institute for Health Research (NIHR) Oxford Biomedical Research Centre based at Oxford University Hospitals NHS Trust  and  University of Oxford  (to DW). JES is a  BHF Senior Basic Science Research Fellow  ( FS/11/50/ 29038 ). The views expressed are those of the author (s) and not necessarily those of the  NHS , the  NIHR  or the  Department of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. CR is a Jenner Institute Investigator and an  Oxford Martin  fellow.
For our analysis, we used 1 min data from the horizontal component of the geomagnetic field (H ) and the eastward component (D) measured at L'Aquila (AQU: λ g = 42. 38 • N and φ g = 13. 32 • E; λ g and φ g are the geographic latitude and longitude, respectively) permanent geomagnetic observatory to study the time variations of the geomagnetic field. Moreover, we used 1 min geosynchronous satellite observations at 6. 6 R E from Geostationary Operational Environmental Satellites (GOES) (GOES10: LT = UT-9; GOES12: LT = UT-5; both in the Geocentric Solar Ecliptic -GSE -coordinate system) for the magnetospheric field (http: //cdaweb. gsfc. nasa. gov/). More specifically, we used the B Z, GSE magnetospheric component and the H ground component. At high and middle latitudes, their behavior should be comparable because of the 90 • rotation of the polarization axes through the ionosphere  (Hughes and Southwood, 1974; Sciffer et al.
Data availability The GOES magnetic field data were provided by H. Singer (National Oceanic and Atmospheric Administration Space Environment Center, Asheville, NC, USA) through the NASA's cdaweb site (http://cdaweb. gsfc. nasa. gov. ) (Singer, 2016). The results presented in this paper rely on public data collected at AQU permanent geomagnetic observatory which are available through INTERMAGNET (2016) (www. intermagnet. org). The full data for this paper are available by contacting the corresponding author.
Acknowledgements. The authors thank the reviewer for his/her useful comments and suggestions and  G. Consolini  ( Istituto di Astrofisica e Planetologia Spaziali ) for his helpful cooperation. We thank the  INGV  that supports INTERMAGNET to promote high standards of magnetic observatory practice. This work is supported by the  Italian Ministry for Education and Research MIUR PRIN  Grant No. 2012P2HRCR  on "The active  Sun  and its effects on Space and Earth climate". The topical editor,  G. Balasis , thanks two anonymous referees for help in evaluating this paper.
Acknowledgments This work was funded with support for AP from the  National Science Center in Poland  (Grant Project No. 2012/07/B/ ST10/04186 ), for RM from the  Regione Autonoma della Sardegna  ( RAS2012-LR7/2007-CRP60215 ), for PAS from the  U. S. National Science Foundation  ( DEB-0716606  and  DEB-1144098 ), and for APW from the  Natural Sciences and Engineering Research Council of Canada. We are indebted to  Aleksandra Hołda-Michalska  ( Institute of Paleobiology, Warsaw ) for her help with figure preparation. We thank two anonymous reviewers for improving the paper. Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http://crea tivecommons. org/licenses/by/4. 0/),which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Devices were assembled on glass slide coated with poly-D-Lysine according the manufacturer's instructions. Human neurons were seeded into the central chamber (2. 0 × 10 4 cells) in neuronal medium. When pulp fibroblasts were seeded in the AXIS's peripheral chambers (Fig. 5Aa ), the same number of neurites was detected inside microgrooves over 48 hour period toward the two sides (Fig. 5Ba ), and the total neurite lengths toward both sides were equal (Fig. 5Ca ). These data were not affected when the pulp fibroblasts of one of   d, f, h ). For each condition, negative controls, performed by replacement of the FSP and C5aR primary antibodies with isotype controls, showed no labeling (i,j). Secondary antibody used to detect FSP was Alexa-594 (red), C5aR detection was done with Alexa-488 (green); Nuclei were counter-stained with DAPI (blue).
0 × 10 5 cells) ± LTA (10 μg/ml). Simultaneously, human pulp cells were incubated either with or without W54011 (10 nmol/L). After 48 hours at 37 °C and 5% CO2, cells were fixed with 4% paraformaldehyde during 10 minutes. Then cells were permeabilized with 0. 3% Tween-20/0. 3% glycine in PBS for 30 minutes and saturated for 1 hour with 3% BSA in PBS. Cells were incubated overnight at 4 °C with rabbit anti-beta II tubulin (1 μg/mL), or their respective isotypes. Finally, cells were incubated for 45 minutes with Alexa Fluor-488 mouse anti-rabbit IgG (2 μg/mL) and DAPI (1 μg/mL). Photographs were took using a Leica DMI6000 B fluorescent microscope, and neurite outgrowth inside microgrooves from the central chamber toward peripheral chambers was analyzed using ImageJ 1. 43 software (NIH, Bethesda, MD).
Acknowledgements We thank  Dr. Jean-Charles Gardon  for providing the third molars and  Dr. David A. Reed  from  the department of Oral Biology, University of Illinois at Chicago , for kindly providing the microscope (Leica  DM2000 ) used for generated histologic pictures. This study was supported by start-up funds from  University of Illinois at Chicago College of Dentistry  (to S. -H. Chung).
Most of these studies have been, however, performed in settings of emergency departments  [10] [11] [12] [13] , and data from intensive care units (ICUs) are scarce. Also, few studies have focused on community-acquired pneumonia  [14] [15] [16]. In addition, plasma concentrations of Presepsin in most of previous reports were determined by ELISA method, which is time-consuming and not suitable for emergency. Yet, the new development of a fully automated point of care assay for rapid whole-blood Presepsin measurement updated its clinical use in emergency and ICUs  [8, 11, 17]. Therefore, this study aimed to evaluate the diagnostic and prognostic utility of Presepsin measurements using the new fast method in severe sepsis and septic shock intensive care unit (ICU) patients. We also aimed to evaluate the diagnostic and prognostic utility of Presepsin measurements for severe community-acquired pneumonia (sCAP) in the subgroup of patients admitted to the ICU with acute respiratory failure.
Study population During the study period, a total of 222 critically ill patients were admitted in ICUs. After the exclusion of 78 patients, 144 were included: 88 males and 56 females. One hundred patients conformed to the criteria of bacterial sepsis: 44 with SS and 56 with SSh. Among the 44 non-septic patients, 19 were assigned for non-SIRS and 25 for SIRS. The screening process is shown in Fig. 1. The two study physicians were on total agreement on reviewing patient's data (kappa = 1). Patient's baseline characteristics are summarized in Table  1. Non-septic and septic patients did not differ in age, sex, SAPS II score and current clinical and biological parameters, except for SOFA scores that were significantly higher in septic group. Forty of 100 septic patients experienced positive blood cultures.
Clinical tumor staging (cTNM) will be based on data obtained from CT scan, EUS and PET-CT, and established using the 7 th UICC classification  [7]. Quality of life questionnaires QLQC30 and OES18 module will be performed at baseline. Before each cycle of chemotherapy, a physical examination, with documentation of adverse events will be performed, as well as standard laboratory tests. After the completion of nCRT tumor re-staging will be mandatory and will include at least an esophagoscopy with a minimum of four biopsies at the initial site of the tumor and a CT-scan of the neck, thorax, abdomen and pelvis.
Data collection and follow-up The data management team of the Methodology and Biostatistics Unit of the Oscar Lambret Cancer Centre will undertake data Management. A trial-specific database will be created, tested and validated before the start of data capture. This database will be developed using Clinsight (ENNOV). The essential data necessary for monitoring the primary and secondary endpoints will be identified and managed at regular intervals throughout the trial in collaboration with the coordinator and the Oscar Lambret Cancer Centre Sponsorship Unit. The electronic case report forms will be completed at each investigator site. Treatment will continue unless one or more of the following occur i) disease progression during preoperative treatment (according to Response Evaluation Criteria in Solid Tumors, version 1.
If only one treatment arm satisfies the decision rules, then continuation of the trial with 1 or 2 arms will depend on the recommendations of the Data Monitoring Committee. During a second stage, each treatment will be evaluated after a total of 48 patients in each arm can be evaluated. Either arm will be considered of insufficient value if there are ≤ 39 R0 resections or ≥ 18 patients with severe post operative toxicity (≤30 patients without severe toxicity). Results at the end of the trial will allow a go/no go decision to be made for continuing to a phase III trial.
Re-scale of the wood density data The approximate date wood formation (re-scale) may be inferred when the radial growth of the trunk is measured through dendrometric bands of trees from which samples were made to determine the wood density. The thicknesses of the barks of the radial samples cut to determine the wood density were measured and used to determine the linear regression equation (R²=0. 99) (eq. 1) which enabled the correction of radial growth data, removing bark thickness from the measurements. The re-scale of the average wood density enables obtaining values every 14 days, or according to the dendrometer reading date. Therefore, the values obtained may be related with the growth and climatic values, also every14 days.