dataesr/scientific-paragraphs-categorization huggingface dataset:
7%. This is dominated by the np modeling, which combines the systematic uncertainty on the np branching ratio for models in Sec. III. 2 and the efficiency of observing a n -n from Table  II. The total systematic uncertainty on the expected background from atmospheric-neutrino interactions (σ bkgd ) is a combination of the uncertainties on neutrino oscillation parameters (σ Φ atmo osc ), the uncertainties on detector efficiencies due to cut parameters and MRF reconstruction of through-going muons (σ ǫ atmo i ), and the uncertainties in the amplitude of different atmospheric-neutrino interac- ): σ bkgd = σ 2 Φ atmo osc + i T i σ Φ atmo i i T i 2 + i T i σ ǫ atmo i i T i 2 (12 ) and is 24. 5% for the 3-phase SNO data set. No calibration sources were available to calibrate events in the GeV scale.
Through-going muon events are used to characterize the fitter response between data and Monte Carlo. Since these events originated from outside the detector, there remain uncertainties in the response of the detector to contained events. A shift in likelihood space is observed for the multiple-ring fitter response between Monte Carlo and data of these through-going "calibration" events. Since we apply a cut on the likelihood space to determine whether there is a ring or not, there is a systematic uncertainty associated with this shift. This is referred to as the MRF reconstruction calibration uncertainty. In the case of atmospheric neutrino detection efficiency of contained events, the studies of the MRF calibration led to a systematic uncertainty of ∼15% in the observed number of rings. The effect of the MRF calibration is not noticeable as much for the n-n oscillation detection efficiency with an uncertainty due to the calibration of ∼7%, in part due to cleaner reconstruction of the individual rings.
ACKNOWLEDGMENTS This research was supported by:  Canada: Natural Sciences and Engineering Research Council, Industry Canada, National Research Council, Northern Ontario Heritage Fund ,  Atomic Energy of Canada, Ltd. , Ontario Power Generation, High Performance Computing Virtual Laboratory ,  Canada Foundation for Innovation ,  Canada  Research Chairs program; US:  Department of Energy, National Energy Research Scientific Computing Center, Alfred P. Sloan Foundation ; UK:  Science and Technology Facilities Council (formerly Particle Physics and Astronomy Research Council ); Portugal: Fundação para a Ciência e a Tecnologia. We thank the  SNO technical  staff for their strong contributions. We thank  INCO (now Vale, Ltd. )  for hosting this project in their Creighton mine.
An alternative method that incorporates prior knowledge into de-noising images is non-local means (NLM)  [20, 21]. In general, applying denoising methods correctly and accurately post-reconstruction is more difficult than within the reconstruction. This paper uses the maximum-likelihood expectation-maximization (MLEM) algorithm to reconstruct PET images  [22, 23]. Using MLEM for PET image reconstruction that has a noisy dataset results in a noisy image. Therefore, to improve the quality of the image, we propose a novel kernel-based image regularization technique. Of the various possible options of the kernel function, an exponentially-modified Gaussian kernel was used  [24] [25] [26] ; this is comparable to conventional MLEM reconstruction in terms of simplicity. Noise is modeled in the projection domain, where independent Poisson random variables effectively model the PET data.
Similarly, the recorded radionuclide projection data b i are represented as a matrix, in which each matrix element b i identifies both the angle and the location of the detector, where the data are recorded. We assume that we know the probability P ij of a photon emitted in voxel j being detected by detector i. The value of the detection probability P ij is directed by physical phenomena, such as the geometric efficiency of the collimator, the attenuation provided by the material surrounding the radioactive voxel j, and the detection efficiency of the imaging system. The behavior of the imaging system can be represented by using a matrix equation that couples the radionuclide concentration x j in the object to the complete set of detector measurements b i using the known value of the probability elements P ij :          b 1 b 2 • • • b i • • • b M          =          P 11 P 12 • • • P 1j • • • P 1N P 21 P 22 • • • P 2j • • • P 2N • • • • • • • • • • • • • • • • • • P i1 P i2 • • • P ij • • • P MN • • • • • • • • • • • • • • • • • • P M1 P M2 • • • P Mj • • • P MN          •          x 1 x 2 • • • x j • • • x N          (1) As the values of b i can be measured with the detector array and since the value of the probability elements P ij can be calculated from the physics of the imaging system, the matrix equation Equation (  1 ) can be mathematically inverted to solve for the radionuclide distribution x j.
The fraction of random and scatter was determined by counting them and dividing them by the total number of counts. Independent Poisson noise was then introduced to the projection data with the expected total number of events set to 300 k. All images were represented by 256 × 256 pixels with a pixel size of 3 × 3 mm 2. All of the codes in the following experiments are implemented in MATLAB R2013a and run on a desktop computer with i5-6600 @ 3. 30 GHz 3. 31 GHz Intel Core CPU and 8 GB memory.
Scientific articles The first investigator searched the databases and publication lists forwarded by the authors on request (see Additional file 1) and selected the potentially relevant full texts from titles and abstracts. As the authors were not familiar with FN, the selection of potentially relevant full texts was generous. ALM and CLY independently made the search in the journal Functional Neurology, Rehabilitation, and Ergonomics and selected the potential relevant full texts from titles and abstracts. All full texts were independently assessed in relation to the inclusion and exclusion criteria. In addition, the first investigator searched reference lists for relevant articles from the databases and the journal. Websites Once the first author had found the mention that the chiropractors were DACNB, the corresponding websites were screened (except for their blog section) sequentially, in the order by which they appeared in a Google search conducted in September 2016.
Descriptive checklists were created to collect systematic information from the scientific articles and from the websites, in relation to the research objectives (available in Additional file 2a and b). The format and contents were somewhat different, depending on the data source. For example, the websites were expected to provide information on expected outcome rather than reported outcome whereas the reverse was expected from the scientific literature. The search for relevant information in the scientific literature was done independently by two authors (ALM and CLY). The descriptive checklist for the websites was completed by the first author who blindly performed this procedure twice for each website.
Scientific articles The selection process is summarized in Fig. 1. Three case reports, one controlled trial, and one randomized controlled trial were found in our areas of inquiry in the selected databases. Six case reports were found through hand searching, including three in the journal Functional Neurology, Rehabilitation, and Ergonomics. Lists of publications obtained from known FN researchers and/or practitioners did not provide any additional relevant material. Nevertheless, the scientific literature provided information on diagnostic procedures, treatment modalities, treatment plans and clinical outcomes for various conditions. The controlled trial and the randomized controlled trial provided information only on diagnostic procedures and treatment modalities (see Additional file 3 for details).
ii) Scientific literature The usual strategy of searching for relevant articles by key words could not be used as it resulted in only one relevant article. The reason for this is that the term "functional neurology" is not usually used in such publications, maybe because FN covers many fields of clinical applications. Therefore, relevant keywords could not be predicted. Instead, we attempted a search by author, including at first all authors that appeared to publish in this area. However, this produced many irrelevant authors with the same surname and initials. Therefore, we stopped this strategy after the search for FR Carrick, RW Beck, G Leisman and R Melillo in the three selected databases. These four were selected because they appeared to be central to the FN movement. Thereafter, on the advice of a specialist librarian, we wrote directly to these four authors and authors known to have published with them, asking them for their lists of publications.
An upper bound on the flux of MMs in the galaxy (called the Parker bound  [15] ) has been obtained by requiring the rate of this energy loss to be small compared to the time scale on which the galactic field can be regenerated. With reasonable choices for the astrophysical parameters  [6] , the Parker bound corresponds to Φ M 10 -15 [cm -2 s -1 sr -1 ], M 10 17 GeV(c 2 10 -15 10 17 GeV M [cm -2 s -1 sr -1 ], M 10 17 GeV/c 2 (2) Search strategies are determined by the expected interactions of MMs as they pass through matter. These would give rise to a number of peculiar signatures. A complete description of the techniques used for the search of these particles is in  [7] , and a complete list of the results in  [6]. Several searches were carried out also using neutrino telescopes. The ANTARES neutrino telescope  [16]  was completed in 2008 and the collected data can be used to search for MMs with energies high enough to yield light emission.
The readout of OMs is performed in the storey's Local Control Module, which collects the data in packages of 104 ms. These packages are sent to an on-shore farm of computers for further data processing and filtering. Each detector storey has one local clock that is synchronized to the on-shore master clock  [19]. Furthermore, at the computer farm a system of triggers is applied on the data (see section 5), selecting signatures which may correspond to the passage of relativistic particles.
Magnetic monopole simulation Up-going MMs with one unit of Dirac charge, g = g D , have been simulated using nine equal width ranges of velocity in the region β = [0. 5945, 0. 9950]. The nine intervals of the velocity are defined in the first column of Table  1. MMs have been simulated using a Monte Carlo program based on GEANT3  [25]. The simulation is independent of the MM mass and the incoming direction of MMs was distributed isotropically over the lower hemisphere. The propagation and detection of emitted photons is processed inside a virtual cylindrical surface surrounding the instrumented volume around the detector. A radius of 480 m is chosen to take into account the large amount of light emitted by MMs.
Background simulation The main source of background comes from up-going muons induced by atmospheric neutrinos and down-going atmospheric muons wrongly reconstructed as up-going tracks. The simulation of atmospheric muons is carried out using the generator MUPAGE  [26]  based on the parametrisation of the angle and energy distributions of muons under-water as a function of the muon bundle multiplicity  [27]. MUPAGE produces muon events on the surface of the virtual cylinder. Up-going atmospheric neutrinos from the decay of pions and kaons are simulated using the package GENHEN  [28, 29]  assuming the model from the Bartol group  [30, 31]  which does not include the decay of charmed particles. The analysis presented in this paper is based on a run-by-run Monte Carlo simulation  [32] , which takes into consideration the real data taking conditions of the detector (e.
Results and discussion The unblinding was performed on the total set of data collected by the ANTARES telescope during five years, which corresponds to 1012 active days live time after subtracting the 10% burn sample. No significant excess of data events is observed over the expected background, and the upper limits on flux have been found using Eq. (  6 ). Table  1  summarizes, for each of the nine bins of β, the selection cuts, the number of expected background and observed events, and the 90% C. L. upper limits on the MM flux. The computation of the 90% C. L upper limits through Eq. (  6 ) includes the statistical uncertainties on the expected atmospheric muon events in column 3 of Table  1. These uncertainties are dominant over the uncertainties related to the detector response. The effects on the muon and neutrino rates due to the detector uncertainties are widely discussed elsewhere, particularly in  [34, 37, 38, 39].
Conclusion A search for relativistic MMs with the ANTARES neutrino telescope has been performed, using data collected during five years (from 2008 to 2012) and corresponding to a total live time of 1012 days. No signal has been observed above the atmospheric background expectation and new upper limits on the MM flux have been set. Above the threshold for direct Cherenkov radiation β ≥ 0. 74, the limits found are better than those of other neutrino experiments. Below Cherenkov threshold, direct comparison is not straightforward due to the model of cross section used. Neutrino telescopes are well suited for the search for MMs. The future detector KM3NeT  [44]  will improve the sensitivity to the detection of MMs due to its large volume and high detection performance. for the computing facilities.
Acknowledgments The authors acknowledge the financial support of the funding agencies:  Centre National de la Recherche Scientifique (CNRS) ,  Commissariat  à l'énergie atomique et aux énergies alternatives (CEA),  Commission Européenne (FEDER fund and Marie Curie Program) ,  Institut Universitaire de France (IUF) ,  IdEx program  and  UnivEarthS Labex program at Sorbonne Paris Cité  ( ANR-10-LABX-0023  and  ANR-11-IDEX-0005-02 ),  Labex OCEVU  ( ANR-11-LABX-0060 ) and the A* MIDEX  project ( ANR-11-IDEX-0001-02 ),  Région Île-de-France (DIM-ACAV) ,  Région Alsace  (contrat CPER),  Région Provence-Alpes-Côte d'Azur, Département du Var and Ville de La Seyne-sur-Mer, France ;  Bundesministerium für Bildung und Forschung (BMBF) ,  Germany ;  Istituto Nazionale di Fisica Nucleare (INFN), Italy ;  Stichting voor Fundamenteel Onderzoek der Materie (FOM) ,  Nederlandse organisatie voor Wetenschappelijk Onderzoek (NWO) , the  Netherlands; Council of the President of the Russian Federation  for young scientists and leading scientific schools supporting grants,  Russia ;  National Authority for Scientific Research (ANCS) ,  Romania ;  Ministerio de Economía y Competitividad (MINECO) :  Plan Estatal de Investigación  (refs.
data synthesis We extracted the following data: publication data (title of the article, first author, journal and publication date), study design (type of study, year(s) of inclusion, study quality score), population (total number of patients included, mean age and sex of patients), methodology of articles (the definition used for OA and dyslipidemia, OA location) and data needed for statistical analysis (number of patients with OA and/ or dyslipidemic patients; mean total cholesterol (TC), low-density lipoprotein (LDL), high-density lipoprotein (HDL) and triglyceride (TG) levels (mg/dL or mmol/L); and number of patients receiving statins, number with MetS and number with obesity or mean body mass index (BMI) in kg/cm 2 ). The quality of the study was estimated by using the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) scale, the score expressed in percentage of positive answers in relation to the number of items selected.
14 atistical analysis First, we performed a descriptive analysis of the prevalence of dyslipidemia in patients with and without OA and used the number of patients with dyslipidemia and total number with and without OA. To estimate this prevalence from cohort longitudinal prospective studies, we used baseline data. Prevalence was expressed as mean±SD Second, we calculated the mean TC, LDL, HDL and TG levels in patients with and without OA. Third, for studies examining an association between OA and dyslipidemia, we calculated the risk of dyslipidemia with OA by estimating the overall OR with 95% CIs. The data were extracted from studies examining the number of dyslipidemic patients with and without OA. We used Revman V. 5. 3 for the meta-analysis with a fixed-effects model. Heterogeneity was assessed by the I² index; with I²>50% (high heterogeneity), we used a random-effects model, and with I 2 <50% (low heterogeneity), we used a fixed-effects model.
Characteristics of studies included The selection of articles is reported in the flow chart (figure  1 ). We identified 605 publications; 48 articles (including 13 abstracts) from 43 studies were included (2 articles from the SEKOIA study, 4 from the FRAM-INGHAM study and 2 from the National Health and Nutrition Examination Survey III). One abstract  15  was obtained from the EMBASE database and not from screening congress abstracts. The 48 articles described 29 cross-sectional, 10 cohort and 9 case-control studies. Among them, 29 articles involved the OA population and 19 the general population (table  1 ). We did not find any studies based on a cohort of patients with dyslipidemia, which explains why the prevalence or relative risk of OA in patients with dyslipidemia was not calculated. Table  2  shows the definitions of OA and dyslipidemia in selected studies.
Acknowledgements laura Smales ( BioMed editing, Toronto, Canada ) Contributors PB, Kl, FB and JS were involved in conception and design. PB and Kl were involved in acquisition of data and statistical analysis. PB, Kl, CM, FB and JS were involved in analyses and interpretation of data, drafting of the manuscript, revision of the manuscript and final approval, had full access to all the data in the study and take responsibility for the integrity of the data and the accuracy of data analysis.
1A ). Furthermore, the trimodular CUB-EGF-CUB motif is found in all these proteinases, but nowhere else in mammalian protein databases. This motif plays key roles in the binding of complement proteases to defence collagens, and in the recognition of procollagen substrates by BTPs  7, 10, 11. In addition, there is increasing evidence for a link between complement and BTPs during inflammation and tissue repair, as found for example in myocardial infarction  12  and pulmonary fibrosis  13. Despite this, to date there have been no studies on possible interactions between BTPs and defence collagens. Here we describe interactions between C1q and MBL and the BTPs BMP-1 and mTLL-1 that provide further support for such a functional connection.
Soluble BMP-1 and mTLL-1 inhibit neither activation of the lectin pathway of human serum complement nor activation of the reconstituted C1 complex. (A,B) MBL-deficient (Δ-MBL) serum reconstituted with 2 µg/ml MBL, preincubated or not with BMP-1 or mTLL-1 at the indicated molar ratios (MR), was added to mannan-coated microtiter wells. The resulting MASP-2 cleaving activity was measured by a C4b deposition assay. Two independent experiments were performed and each data point is the mean of duplicate (A) and quadruplicate measurements (B). (C,D) Complexes (0. 25 μM) reconstituted from C1q, preincubated or not with BMP-1 or mTLL-1 at the indicated MR, and proenzyme C1s-C1r-C1r-C1s were incubated for 30 min at 30 °C. The extent of C1 self-activation was measured by SDS-PAGE, followed by Western blot analysis using an anti-C1s antibody.
Data were analyzed by global fitting to a 1:1 Langmuir binding model of both the association and dissociation phases for at least six analyte concentrations simultaneously, using the BIAevaluation 3. 2 software (GE Healthcare). Buffer blanks were subtracted from the datasets used for kinetic analysis (double referencing). The apparent equilibrium dissociation constants (K D ) were calculated from the ratio of the dissociation and association rate constants (k d /k a ). Chi2 values were below 7 in all cases. Complement activation assays. A C4 cleavage ELISA was used to measure human serum complement activation via the MBL-dependent lectin pathway. Activation was measured as described by Dumestre-Pérard et al. 19  , using mannan-coated plates and human MBL-deficient serum reconstituted with 2 µg/ml recombinant human MBL (pre-incubated or not with BMP-1 for 30 min at room temperature), except that plates were developed with tetramethylbenzidine (Sigma), the reaction was stopped by 1 N H 2 SO 4 and absorbance was read at 450 nm.
For the C1 complex activation assay, C1 (0. 25 μM) was first reconstituted from purified serum C1q and the proenzyme C1s-C1r-C1r-C1s tetramer  46. Self-activation was measured by incubating the resulting complexes at 30 °C for 30 min in 50 mM triethanolamine-HCl, 145 mM NaCl, 2. 5 mM CaCl 2 , pH 7. 4. The extent of C1 activation was determined from the amounts of the A and B chains of activated C1s generated, following Western blot analysis using an anti-C1s antibody and alkaline phosphatase immunodetection  46. Image acquisition and densitometric analysis were performed using the ChemiDoc MP imager with Image Lab software (Bio-Rad). Pre-incubation of C1q with BMP-1 or mTLL-1 prior to C1 reconstitution was performed at room temperature for 20 min.
Acknowledgements This work used the platforms of the  Grenoble Instruct-ERIC Centre (ISBG ;  UMS 3518 CNRS-CEA-UJF-EMBL ) with support from  FRISBI  ( ANR-10-INSB-05-02 ) and  GRAL  ( ANR-10-LABX-49-01 ) within the  Grenoble Partnership for Structural Biology  (PSB). We thank  Isabelle Bally  and  Jean-Baptiste Reiser  for assistance and access to the  SPR facility. This work was supported by grants from the  Rhône-Alpes Region (Cluster 10 "Infectiologie")  to N. M. T. and D. J. S. H. , the  French National Research Agency  ( ANR-09-PIRI-0021 ) to N. M. T. , and  DAAD (Deutscher Akademischer Austauschdienst)  to A. T.
, 2012). The supplement of the first ENIGMA paper  (Stein et al. , 2012)  contained 104 pages of ancillary tests supporting the validity and reliability of the data, including tests comparing different imaging software for brain volume quantification. On the genomic side, the ability to compare genomic data in a common reference frame depended on the availability of the HapMap3 (The International HapMap3 Consortium, 2010) and later the 1000 Genomes reference datasets  (Genomes Project C et al. , 2010). These reference panels are continually updated and refined, and allow genotyping data collected with one kind of genotyping array ("chip") to be imputed to match data collected using others, and pooled in the same overall study. A second issue is whether these findings could have been detected more efficiently using only some of the samples.
At the same time, many groups joined ENIGMA and provided only brain measures as their initial case-control analyses did not require genome-wide genotyping data on their cohorts. As such, truly vast samples began to be analyzed (N = 8,927, in the published ENIGMA-Depression study; N = 10,194 in the ENIGMA-Lifespan study; see Table  1 ). At the time of writing, ENIGMA's first studies of schizophrenia and major depression have been published; results are compared in Fig. 4. Some caveats are needed in showing these data side by side: the schizophrenia and major depression patients were not ascertained at the same sites, so site or geographic effects may be present. Among the subcortical structures so far assessed, the hippocampus shows the greatest differences in each disorder in terms of statistical effect sizes -but in major depression, it is the only structure showing differences, of those assessed so far  (Schmaal et al.