dataesr/scientific-paragraphs-categorization huggingface dataset:
However, such a measurement does not provide information on the time structure of the background and could be affected by other effects at low neutron energies. In this paper, the neutron sensitivity of the whole capture setup used at n TOF has been studied by means of Monte Carlo simulations performed with the GEANT4 tool. A complete and detailed software replica of experimental hall and apparatus has been implemented in the simulations, and the results have been analyzed with the same procedure applied to the experimental data. All relevant physical processes were taken into account in the simulations, for neutrons generated in the full energy range of the n TOF facility, i. e. from thermal up to 10 GeV. The lack of correlations between γ-rays in a cascade, typical of most Monte Carlo simulations, has been proven to bear no effect on the results, provided that the weighting function technique is correctly applied to the simulations.
Acknowledgements We are indebted to the  members of Laboratory for Advanced Computing at Faculty of Science, University of Zagreb , for granting us access to the computer cluster we have used for running the simulations. The authors are indebted to the national and international funding agencies that have supported the n TOF Collaboration. The research leading to these results has received funding from the  European Atomic Energy Community 's ( Euratom) Seventh Framework Programme   FP7/2007-2011  under the  Project "ANDES" (Grant Agreement n   249671 ) and  CHANDA  (GA n. 605203).
Materials and Methods A qualitative approach was chosen because this type of research would enable us to explore the meanings of diagnostic signs and symptoms used in the diagnostic reasoning process of FPs  [12]. Individual face-to-face semi-structured interviews were carried out with FPs. Interviews were chosen because we wanted to access to the personal experience of each FP, and not that of the group of FPs as a whole. We aimed to reveal issues which had not been documented previously  [13]. It was conducted within a grounded theory perspective in order to describe from the data the way FPs perform the diagnostic process  [14].
Participant selection Two groups of participants were selected. The first group consisted of 14 FPs who had referred a patient to the emergency unit of the local hospital in the area of Brest, Brittany and where a pulmonary embolism was ultimately diagnosed. Data of all the cases of pulmonary embolism from June to November 2011 were collected. The patient's FP was identified where he/she had been the physician who had sent the patient to the emergency unit. We had no information on the reason why the physician referred the patient to the emergency unit when we interviewed him/her. We undertook the FPs' interviews a few days after the positive diagnosis of PE. The first consecutive 14 FPs who agreed to participate made up the first group. A second group of FPs was chosen using a purposeful sampling method.
Data Collection The research team developed the interview form with a topic guide, drawn up to answer the research question (see table  1 ). It was composed of open-ended questions for exploration and closed questions to refine the participants' answers. The first question focused on the case report of a hospitalized patient for the first group and a recollected consultation about a positive diagnosis of PE for the second group. In order to match what emerged from the interviews, we added new questions to the interview guide when participants raised aspects which had not previously been mentioned  [15]. All the interviews were audio-recorded. The recordings were transcribed and checked. All the interviews took place at the FP's office. In order to improve validity and credibility, all transcripts were returned to participants for member checking.
Characteristics of study participants The current analysis includes 1,275 prostate cancer cases [1,131 (88. 7 %) localized, 141 (11. 1 %) locally advanced, 3 (0. 24 %) missing stage; 887 (69. 6 %) low grade, 385 (30. 2 %) high grade, 3 (0. 24 %) missing grade], and 2,062 controls that have at least one available SNP. 39. 3 % of participants had data available on all SNPs, and 43 % were missing data on three or fewer SNPs. No man was missing more than 10 SNPs. Of these, 926 cases and 872 controls had an available 25(OH)D measurement and 779 cases and 737 controls had an available 1,25(OH) 2 D measurement (Fig. 2 ). The mean age of cases was 62. 6 years and of controls was 61. 7 years. As expected, the mean PSA level in cases was higher than in controls (9. 5 vs 1. 0 ng/mL). There were no substantial differences in baseline characteristics between cases and controls, except that more cases had a family history of prostate cancer versus controls (8.
Acknowledgments Ethics approvals for ProtecT and ProMPT: All men provided written informed consent prior to inclusion in the study. Trent Multicentre Research Ethics Committee (MREC)  approved the ProtecT study ( MREC/01/4/025 ) and the associated ProMPT study which collected biological material ( MREC/01/4/061 ). The authors would like to acknowledge the provision of additional epidemiological data by the  NHS R&D Directorate  supported Prodigal study. Also the  ProMPT (Prostate Mechanisms of Progression and Treatment , Grant Code  G0500966/75466 ) collaboration which has funded tissue and urine collections and is supported by the  National Cancer Research Institute (NCRI)  formed by the  Department of Health , the  Medical Research Council and Cancer Research UK. These collaborations are supported by the  University of Cambridge Cancer Research UK , and the  National Institute for Health Research funded Cambridge Bio-medical Research Center, Cambridge, UK.
This work was supported by the  World Cancer Research Fund UK  (Grant Number  2006/15 ). RG is recipient of a  Cancer Research   UK Graduate Training Fellowship  ( C31211/A10095 ) and a  Cancer Research UK   Population Research Postdoctoral Fellowship  ( C31211/A15194 ). The  UK Department of Health  funded the ProtecT study through the  NIHR Health Technology Assessment programme. JPK is funded by a  Wellcome Trust  4 years PhD studentship in molecular, genetic, and life course epidemiology ( WT083431MA ). The Integrative Epidemiology Unit is supported by the  Medical Research Council  and the  University of Bristol. The  NIHR Bristol Nutrition Biomedical Research Unit  is funded by the  National Institute for Health Research (NIHR)  and is a partnership between  University Hospitals Bristol NHS Foundation Trust  and the  University of Bristol.
background An exaggerated morning blood pressure surge (MBPS) may be associated with stroke and other cardiovascular events, but the threshold at which an MBPS becomes pathological is unclear. This study aimed to systematically review the existing literature and establish the most appropriate definition of pathological MBPS. methods A MEDLINE search strategy was adapted for a range of literature databases to identify all prospective studies relating an exaggerated MBPS to cardiovascular endpoints. Hazard ratios (HRs) were extracted and synthesized using random-effects meta-analysis.
Search strategy A search strategy (see Supplementary Table  S1 ) designed to capture all studies relating definitions of the MBPS to cardiovascular disease endpoints was developed for use with MEDLINE, and this was adapted to be run across the following additional databases: Cochrane (Wiley) CENTRAL Register of Controlled Trials, MEDLINE In Process (Ovid), EMBASE (Ovid), CINAHL (EBSCO), Cochrane Database of Systematic Reviews (CDSR), Database of Abstracts of Reviews of Effects (DARE), and Health Technology Assessment Database (HTA). The ZETOC (Mimas) database and Conference Proceedings Citation Index (ISI Web of Knowledge) were searched for conference proceedings and abstracts. In addition, the Current Controlled Trials metaRegister, NIHR Clinical Research Network Portfolio, ClinicalTrials.
Selection of studies and inclusion criteria Two reviewers (J. S. and J. H. ) independently reviewed the titles and abstracts of potentially relevant articles for inclusion. Studies were selected for full document screening and data extraction provided they fulfilled the following inclusion criteria: (i) they were a prospective study; (ii) they defined and measured the MBPS; and (iii) they examined the relationship between MBPS and subsequent cardiovascular disease endpoints. All selected studies had to include at least 1 measurement of the MBPS in each study participant (at baseline, calculated from blood pressure measurements made using ambulatory or home blood pressure monitoring). No restrictions were made on the populations studied or the context in which MBPS was measured.
Data collection Data were independently extracted from each included article by J. S. and J. H. Differences were resolved by consensus. Extracted data included any information about the sample population (e. g. , patient demographics, mean blood pressure, dipping status, diagnosis of white coat or masked hypertension, prescribed medication, and history of cardiovascular disease and risk factors), the threshold value (if used), and definition of MBPS. Because the outcome was onset of cardiovascular disease subsequent to the measurement of MBPS, the suitable effect measure to quantify the association was a hazard ratio (HR). 15 This compares the relative rate of cardiovascular disease in those with higher compared with lower MBPS values across the entire follow-up period. Where HRs were not reported directly, we used the methods of Parmar et al.
RESULTS The search strategy identified 4,200 articles, of which 1,236 were duplicates. Of the remaining 2,964 articles, 133 (4. 5%) were eligible for full-text screening, from which 17 (0. 6%) were suitable for data extraction and included in the analysis (Figure  2 ). Included studies were conducted in 14 different countries and examined a total of 33,154 patients with a mean age of 60 years (Table  1 ). Studies differed according to sample size (42-11,291 patients), mean age (49-72 years), sex (32%-64% women), and the proportion of patients on blood pressure-lowering treatment (0%-76%) (Table  1 ). All studies recorded MBPS at baseline, and the majority (n = 11 studies) examined hypertensive patients in a secondary care setting. Patients were followed up for 37-137 months. ] [10] [11] 19, 21, 22, 24  Reporting of outcome measures was generally good (n = 14 of 17 studies),  4, 11, 19, [21] [22] [23] [24] [25]  but reporting of prognostic factor measurement and account of confounding was less satisfactory overall (n = 11 of 17  4, 5, [7] [8] [9] [10] [11] [19] [20] [21] [22]  and 10 of 17 studies,  4, [6] [7] [8] [9] [10] [11] 19, 24, 27  respectively).
28, 29 However, given the paucity and quality of studies examining the MBPS in this way, further work is needed, perhaps through reanalysis of existing data, before definitive recommendations for clinical practice can be made. This study used a thorough and extensive search strategy in a large number of research literature databases to capture existing prospective studies relating MBPS to cardiovascular disease endpoints. Despite screening a large number of potentially relevant studies (n = 2,964), only 17 articles fulfilled the study inclusion criteria, and only 6 of these could be pooled in a meta-analysis. This limited the extent to which different definitions and thresholds of MBPS could be compared as originally planned. This was particularly evident in the assessment of the MBPS as a continuous variable, where only the association between the prewaking surge and all stroke events was examined by >1 study and the 2 largest, highest quality studies  4, 9  could not be included.
In our pooled analyses, HRs comparing those with an exaggerated MBPS against those with a minimal MBPS (lowest quartile of MBPS) were used. Thus the estimates of association between MBPS and cardiovascular endpoints from this study are likely to be more pronounced compared with that seen in other studies. It should also be noted that there were differences in the adjustment for other prognostic factors (confounders) used across studies (Supplementary Table  S2 ). Despite this, it is a strength that studies adjusted for multiple variables, thus allowing the independent prognostic association for MBPS and outcome to be summarized. One study included in our pooled analyses was that of Li et al. ,  4  which examined data from the International Database of Ambulatory Blood Pressure in Relation to Cardiovascular Outcome.
30 This database includes patients from studies conducted around the world, including those from the Ohasama Study  31  and the Allied Irish Bank study. 32 It is possible that these same patients may have been included in other studies identified by this review,  6, 8  although it was not possible to confirm this from the data available. This potential overlap only affected analyses of the association between sleep-trough prewaking surge and stroke events (examined using a threshold to define exaggerated MBPS) (Figure  3 ), neither of which showed significant results, and thus the impact on the overall findings of this study are likely to be minimal. Our study did not explicitly set out to consider the influence of nocturnal dipping status on cardiovascular disease risk, although some studies included in the meta-analysis did adjust their findings for dipping status in the sample population (Supplementary Table  S2 ).
ACKNOwLEDgMENTS We would like to thank David Moore for his advice in the design of this work and Jeremy Nagle and Paul Terry at the British Library for their assistance in sourcing the fulltext articles screened for inclusion in this work. Forest plot of adjusted hazard ratios depicting the risk of cardiovascular morbidity and/or mortality with an exaggerated morning blood pressure surge. Data were analyzed as continuous variables and presented here per 10 mm Hg increase in morning blood pressure surge. *Unit of increase relating to this hazard ratio was not reported. Other hazard ratios reported in this article referred to a single standard deviation increase in prewaking surge equivalent to 13. 8 mm Hg. 8  Abbreviation: NA, not available. on the PROSPERO International prospective register of systematic reviews (registration No.
Identification Using Mass Spectrometry The isolated colonies were deposited on a MALDI-TOF target microflex (Bruker Daltonik, Wissembourg, France) and overlaid with matrix solution, a saturated solution of acyano-4hydroxycinnamic acid in 50% acetonitrile and 2. 5% trifluoroacetic acid, after air-drying at room temperature for 5 minutes. Each colony was picked from an Eppendorf tube containing the Trypticase-Casein-Soy (AES) culture medium stored at 37uC. Broth culture-specific thioglycollate (BD Diagnostics) was used for anaerobes. Two spots were examined for each colony. Each deposit was covered with 2 ml of the matrix solution. The Biotyper software was used to compare the protein profile of the bacteria obtained from a database (Bruker and the base of the Timone hospital) of protein profiles regularly updated based on the results of clinical diagnosis.
16S rRNA Amplification and Sequencing Identification Thirty-two isolates out of the 2,750 (1. 2%) were not identified by MALDI-TOF mass spectrometry. Among these isolates, 11 were identified using 16S rRNA sequencing: Bacteroides nordii, Bacillus clausii, Bacillus thuringiensis, Clostridium cadaveris, Clostridium neonatale, Paenibacillus polymyxa, Staphylococcus sciuri, Shigella boydii, Shigella sonnei, and two new species were identified: a new clostridial species that was called Clostridium dakarense sp. nov. (GenBank accession number KC517358) and a new Bacillus species, Bacillus casamencensis sp. nov. (GenBank accession number AF519462. 1). The 16S rRNA sequence of this Bacillus species has been already detected in rice soils in Senegal but no description of the bacterium has been yet reported.
2%) Acinetobacter baumannii isolates. When the spectra of the aforementioned isolates were added to the Bruker database, further identifications of these organisms by MALDI-TOF were accurate. Common bacteria. Seven bacterial species (3. 7%) were identified more than 100 times in fecal samples (261 Escherichia coli isolates, 256 Enterococcus faecium isolates, 159 Clostridium bifermentans isolates, 153 Enterococcus faecalis isolates, 152 Clostridium perfringens isolates, 137 Bacillus cereus isolates, and 106 Enterococcus hirae isolates). Surprisingly, several bacteria were more common in patients without diarrhea including E. coli than those without (P# 10 23 ), E. faecium (P#10 23 ), C. bifermentans (P = 0. 002), and C. perfringens (P#10 23 ), see Table  4  and Figure  2. Thirty-nine bacterial species (20.
In contrast, several species of the genera Bacteroides (4) and Enterococcus (2) were detected only among patients without diarrhea. Bacterial identification depending of the age range. The isolates obtained from people with and without diarrhea depending of the age range (less than 5 years, from 5 to 20 years, and more than 20 years) were compared. Only significant differences are presented (Table  S1 ). For children from 0 to 5 year-old, 2 species of the genera Clostridium were significantly more frequent among those without diarrhea, including 1 species C. glycolycum, for which the data were not significant when the entire population was analyzed. For adult of more than 20 year-old, 6 species (E. coli, E. faecium, B. uniformis, B. vulgatus, C. orbiscindens, and E. lenta), as previously observed in the entire population, were significantly more observed in people without diarrhea.
Discussion MALDI-TOF mass spectrometry coupled with culturomics has allowed for the identification of a large collection of bacterial species from specimens from Senegal and a preliminary comparison between the bacterial microbiota of people with and without diarrhea. This technique has allowed for the accurate identification of a large panel of anaerobes that are usually poorly identified by current phenotypic methods, which lack specificity and result in ambiguous or even erroneous identification  [21, 22]. For several bacterial species, their identification by MALDI-TOF failed because either the corresponding species missed in the database or either the number of spectra of the species was insufficient. Indeed, the continuous increases of the entries in database with the addition of our new spectra solved these problems and improved bacterial identification.
In addition, the use of MALDI-TOF mass spectrometry detects the presence of previously rare bacteria that were difficult to identify using phenotypic methods  [6, [23] [24] [25] [26] [27]. Overall, the percentage of isolates from Senegal that were correctly identified at the genus and species level by mass spectrometry (98. 2%) is nearly the same than the percentage (95. 4%) observed in the first large scale experiment that used mass spectrometry in Marseille, France  [1]. Both studies were performed using the same database. This study has allowed us to test a large collection of isolated strains from Senegalese people. Only 3 bacterial species, Clostridium senegalense, Bacillus casamancensis, and Clostridium dakarense, have been currently identified in Senegal. This confirms the high potential for culturomics approaches to result in the detection of new bacterial species associated with humans  [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39].
The increases in the database by the addition of more bacteria have allowed for improved bacterial identification by MALDI-TOF mass spectrometry. Thus, the current database seems accurate for the identification of bacteria in Senegal. This work allowed for the identification of 166 bacterial species already found in the human gut, 11 species previously detected in humans but not in the gut, 10 species detected in humans for the first time, and 2 unknown species. The composition of the gut microbiota is complex  [40]. A recent culturomics experiment using many culture conditions was performed on fecal samples from 2 healthy Senegalese individuals, 1 obese person, 1 person with resistant tuberculosis, and a patient with anorexia nervosa. This allowed the identification of 99, 219, 192, 39, and 133 different bacterial species per fecal sample, respectively  [12] [13] [14].
Introduction This paper, one of a set associated with the 2013 release of data from the Planck † mission (Planck Collaboration I 2014), presents a study of Doppler boosting effects using the small-"And yet it moves," the phrase popularly attributed to Galileo Galilei after being forced to recant his view that the Earth goes around the Sun. Corresponding author: Douglas Scott, dscott@phas. ubc. ca. ca † Planck (http://www. esa. int/Planck) is a project of the European Space Agency (ESA) with instruments provided by two scientific consortia funded by ESA member states (in particular the lead countries France and Italy), with contributions from NASA (USA) and telescope reflectors provided by a collaboration between ESA and a scientific consortium led and funded by Denmark. scale temperature fluctuations of the Planck cosmic microwave background (CMB) maps.
Data and simulations Given the frequency-dependent nature of the velocity effects we are searching for (at least for the τ component), we will focus for the most part on estimates of β obtained from individual frequency maps, although in Sect. 6 we will also discuss the analysis of component-separated maps obtained from combinations of the entire Planck frequency range. Our analysis procedure is essentially identical to that of Planck Collaboration XVII (  2014 ), and so we only provide a brief review of it here. We use the 143 and 217 GHz Planck maps, which contain the majority of the available CMB signal probed by Planck at the high multipoles required to observe the velocity effects. The 143 GHz map has a noise level that is reasonably well approximated by 45 µK arcmin white noise, while the 217 GHz map has approximately twice as much noise power, with a level of 60 µK arcmin.
Acknowledgements. The development of Planck has been supported by:  ESA ;  CNES  and  CNRS/INSU-IN2P3-INP (France) ;  ASI ,  CNR , and  INAF (Italy) ;  NASA and DoE (USA) ;  STFC  and  UKSA (UK) ;  CSIC ,  MICINN , JA, and  RES (Spain) ;  Tekes, AoF , and  CSC (Finland) ;  DLR  and  MPG (Germany) ;  CSA (Canada) ;  DTU Space (Denmark) ;  SER/SSO (Switzerland) ;  RCN (Norway) ;  SFI (Ireland) ;  FCT/MCTES (Portugal) ; and  PRACE (EU). A description of the Planck Collaboration and a list of its members, including the technical or scientific activities in which they have been involved, can be found at http://www. sciops. esa. int/index. php?project=planck&page=Planck_Collaboration. Some of the results in this paper have been derived using the HEALPix package. This research used resources of the  National Energy Research Scientific Computing Center , which is supported by the  Office of Science of the U.
Objective: The best combination of questions to define asthma in epidemiological asthma studies is not known. We summarized the operational definitions of asthma used in prevalence studies and empirically assess how asthma prevalence estimates vary depending on the definition used. Methods: We searched the Thomson Reuters ISI Web of knowledge and included (1) cross-sectional studies (2) on asthma prevalence (3) conducted in the general population and (  4 ) containing an explicit definition of asthma. The search was limited to the 100 most-cited papers or published since January 2010. For each paper, we recorded the asthma definition used and other variables. Then we applied the definitions to the data of the Portuguese National Asthma survey (INAsma) and of the 2005-2006 National Health and Nutrition Examination Survey (NHANES) computing asthma prevalence estimates for the different definitions.