dataesr/scientific-paragraphs-categorization huggingface dataset:
The expected evolution of ε DAQ with ∆ in Figure  12c  follows directly the measured trigger rates of Figure  12a , using as input the average DAQ dead-time per event and the post-RESET veto windows. Direct measurements with ratios of recorded events to number of randomtriggers issued to the DAQ system are superimposed, showing excellent agreement. At large ∆, ε DAQ is con- Basic filter selections, provided by (a) timing within a RESET period (∆t + and ∆t -of Figure  4b ), and (b) pedestal fluctuations. An additional selection is on the timing of SA6 maxima, displayed in Figure  9. "Reject" parameter spaces are shown as shaded regions. Data from pPCGe and nPCGe are used as illustrations in (a) and (b), respectively. stant and defined by the post-RESET veto time. Variations in the constant level among detectors can be attributed to differences in RESET time intervals.
Combined Background Spectra Data were taken with various Ge detectors at KSNL. Background events are identified and suppressed when they are (i) correlated with the AC and/or CR systems, (ii) induced by electronic noise with anomalous timing structures, or (iii) located at the surface of pPCGe. The various efficiency factors discussed in this article, namely ε Trig , ε DAQ , ε CR , ε AC , ε bf , ε BS and λ BS , and their uncertainties are applied. Their typical values are summarized in Table  III  and stated in the respective figures. The combined efficiency for nPCGe is 91% above its noise-edge of 373 eV ee , while that for pPCGe is depicted in Figure  13 , showing the values before and after BS-selection. The electronic noise-edge defines the lower reach of the extraction of physics signals for AC -⊗CR -events which are uncorrelated with other detector systems.
Relaxivity measurements To characterize the relaxation efficiency of the theranostic agent [DPP-ZnP-GdDOTA] À , nuclear magnetic relaxation dispersion (NMRD) profiles were recorded in water at two different temperatures in the field range of 10 kHz-600 MHz (Figure  3 ). Some relaxivity data were also obtained in an aqueous solution containing 1 % DMSO and were identical to those in water. Likewise, the relaxivities in the presence of 50 mm NaCl were very similar to those measured in H 2 O alone (Supporting Information, Figure  S14 ). The most important parameters that influence relaxivity are the number of water molecules directly coordinated to the Gd III (q), their exchange rate with the bulk water (k ex ), the rotational correlation time of the complex (t R ), and the parameters characterizing electron spin relaxation (t V and D 2 ).
The analysis of the luminescence decay profiles against time was accomplished with the DAS6 Decay Analysis Software provided by the manufacturer. Estimated errors are 10 % on exponential lifetimes, 20 % on quantum yields, 20 % on molar absorption coefficients and 3 nm on emission and absorption peaks. Singlet oxygen production quantum yields in DCM and D 2 O were measured with reference to Rose Bengal bis(triethylammonium)salt f D = 0. 48 in DCM),  [28]  and to 5,10,15,20-tetrakis(4-sulphonatophenyl)porphyrin (TPPS 4 ) (f D = 0. 64 in D 2 O),  [29]  respectively, by comparing the intensity of singlet oxygen phosphorescence spectra measured with a FLS920 spectrofluorimeter (Edinburgh) equipped with a Hamamatsu R5509-72 supercooled photomultiplier tube at 193 K and a TM300 emission monochromator with a grating blazed at 1000 nm.
Relaxometric measurements Proton NMRD profiles ([DPP-ZnP-GdDOTA] À = 1. 13 mm, pH 6. 6 in H 2 O, and [DPP-ZnP-GdDOTA] À = 0. 96 mm, pH 6. 85 in aqueous NaCl 50 mm) were recorded on a Stelar SMARTracer Fast Field Cycling relaxometer (0. 01-10 MHz) and a Bruker WP80 NMR electromagnet adapted to variable field measurements (20-80 MHz) and controlled by a SMARTracer PC NMR console. Higher field relaxivities were measured on Bruker AVANCE NMR spectrometers at 300 MHz, 400 MHz, and 600 MHz. The temperature was monitored by a VTC91 temperature control unit and maintained by a gas flow. The temperature was determined by previous calibration with a Pt resistance temperature probe. The longitudinal relaxation rates (1/ T 1 ) were determined in water and in aqueous NaCl 50 mm. The least-squares fit of the 1 H NMRD data was performed using Visualiseur/Optimiseur  [34]  running on a MATLAB 8.
Acknowledgements We thank  Agns Pallier  for performing relaxivity measurements. The icFRC (http://wwwicfrc. fr)and  Region Alsace  are gratefully acknowledged for a fellowship to J. S. , and the  Ligue contre le Cancer  for financial support. We thank warmly  E. Leize ,  C. Perret , and  H. Nierengarten  for the HR mass-spectrometry determination. The Italian CNR (Project  PM. P04. 010"MACOL" ),  MIUR  project  PRIN 2010CX2TLM , and  MIUR-CNR  project  Nanomax N-CHEM  are gratefully acknowledged. Keywords: diketopyrrolopyrrole • gadolinium • magnetic resonance imaging • photodynamic therapy • porphyrins • twophoton absorption.
Sequencing was carried out through 454 GS-FLX Titanium pyrosequencing (Roche Applied Science, Penzberg, Bavaria, Germany). Sequences were analyzed using the bioinformatics program QDD  (Meglécz et al. , 2010) , which detects microsatellite sequences and designs primers in flanking regions. We then selected 13 primer pairs among the microsatellite sequences (dinucleotide • Premise of the study: Polymorphic markers were required for a native tree of the Mascarene Islands, Foetidia mauritiana (Lecythidaceae), to investigate the effects of fragmentation of lowland tropical habitats on tree mating systems and on gene flow. • Methods and Results: Using microsatellite enrichment and next-generation sequencing, we identified 13 microsatellite loci (dinucleotide repeats). They were highly polymorphic in 121 trees sampled in the largest three populations on Réunion, revealing 2-17 different alleles per locus.
Allele sizes were estimated using the Microsatellite Plugin version 1. 4 implemented in Geneious version 8. 1. 7 (Biomatters, Auckland, New Zealand). The number of different alleles and observed and expected heterozygosity were calculated for each locus and population in GenAlEx  (Peakall and Smouse, 2006, 2012). Hardy-Weinberg exact tests (9999 iterations) and linkage disequilibrium were analyzed in GENEPOP version 4. 2  (Rousset, 2008). The presence of null alleles was estimated with  MICRO-CHECKER version 2. 2. 3 (van Oosterhout et al. , 2004). The minimum number of microsatellite loci necessary to discriminate repeats), because they had adequate flanking regions for designing primers (see Table  1  for locus information, primers, and GenBank accession numbers). Eight additional microsatellite loci are provided in this paper, although population testing was not conducted for these markers (Appendix 1).
5 μL 2× Type-it Multiplex PCR Master Mix (QIAGEN), 1. 5 μL individuals of F. mauritiana was assessed using the package poppr in R software  (Kamvar et al. , 2015). All microsatellite loci revealed polymorphisms in F. mauritiana populations on Réunion. The number of different alleles per locus ranged from two to 17 (Table  2 ). Four loci showed significant deviation from Hardy-Weinberg equilibrium: FmCIR27, FmCIR47, FmCIR16, and FmCIR3. No significant linkage disequilibrium was detected between pairs of loci. We found that the minimum number of loci necessary to discriminate individuals in the data set was eight (data not shown). Transferability of the microsatellite loci was tested on 28 individuals of F. mauritiana and 30 individuals of F. rodriguesiana F. Friedmann sampled across Mauritius and Rodrigues, respectively (sampling authorized by the National Parks and Conservation Service of Mauritius).
Half of the participants learning in the HMD and desktop systems were assigned a virtual body. Participants were then asked to place physical versions of the three objects in the physical laboratory in the same configuration. We tracked participant movement, measured object placement, and administered a questionnaire related to aspects of the experience. HMD learning resulted in statistically significant higher performance than desktop learning. Results indicate that, when learning in low detail VEs, there is no difference in performance between participants using HMD and desktop systems. Overall, providing the participant with a virtual body had a negative impact on performance. Preliminary inspection of navigation data indicates that spatial learning strategies are different in systems with varying levels of immersion.
The physical room contained a table and a computer that was not included in the model. Previous research has found no effect of presence and absence of rendered furniture on participant distance estimation  (Interrante et al. , 2008). Head tracking and object positional data were logged with a NaturalPoint OptiTrack motion capture system using twelve Flex 3 cameras and retroreflective markers, at a sampling rate of 60 Hz. The measured mean tracking error was 3 mm. A 27″ Dell U2713HM monitor and an Oculus Rift Development Kit 2 (DK2) were used as displays for the desktop and HMD learning conditions, respectively. High fidelity single point tracking virtual avatars, based on head tracking, were used in the corresponding desktop body and HMD body conditions. A female and male avatar model were obtained from the Rocketbox ® Library  (Havok, 2014).
The release of AMC from the synthetic substrates was determined spectrofluorimetrically using excitation and emission wavelengths of 370 ± 40 nm and 440 ± 40 nm, respectively (Synergy HT Microplate Reader, Winooski, VT, USA). The extent of release of AMC was calculated by reference to a standard curve relating AMC to fluorescence emission under the assay conditions. Activity was expressed as µmoles AMC/mL/min of sample. Data is presented as the mean of three replicate measurements of three replicate trials.
g. dead or permeabilised cells). As per manufacturing instructions, after labelling, cells were left to stand at room temperature in the dark for 15 min, after which they were transferred to BD TruCount TM tubes (Becton Dickinson, Oxford, UK) containing a known amount of fluorescent beads to enable actual population counts per sample. The fluorescence-labelled cells from each of the cheese juice samples and control panels were analysed in triplicate using a Becton Dickinson LSR II flow cytometer equipped with an Argon-ion laser at 488 nm. A total of 10,000 events were recorded for each sample. Forward Side Scatter (FSC) and Side Scatter (SSC), green fluorescence (515-545 nm) and red fluorescence ( > 670 nm) were also used to assess cell viability for each sample. Data acquisition and analysis were controlled using CellQuest software (Becton Dickinson, Oxford, UK).
Statistical analysis Analysis of variance (ANOVA) was carried out using a general linear model (GLM) procedure of SPSS (version 19, SPSS Inc. , Chicago, IL, USA). In this study, the effect of treatment and replicates were estimated for each response variable at each sampling point. Tukey's multiple comparison test was used as a guide for pair comparisons of the treatment means. Differences among treatments described subsequently as being significant were determined at P < 0. 05. Description of data was based on salt reduction and fat reduction for each salt and fat series of cheeses, respectively.
Raw data for Combing-Imaging by SIMS of bacterial DNA http://dx. doi. org/10. 5256/f1000research. 8361. d120278 Double-labeled (13C, 15N) chromosomal DNA from Bacillus subtilis was combed onto a silicon surface, analysed with a NanoSIMS 50 set to detect masses of 12, 13, 26, 27 and 28 for 12C-, 13C-, 12C14N-, 13C14N-and 13C15N-ions, respectively. The data were treated with Aphelion.
Dataset 1. 1 Raw data for Combing-Imaging by SIMS of bacterial DNA http://dx. doi. org/10. 5256/f1000research. 8361. d120278 Double-labeled (13C, 15N) chromosomal DNA from Bacillus subtilis was combed onto a silicon surface, analysed with a NanoSIMS 50 set to detect masses of 12, 13, 26, 27 and 28 for 12C-, 13C-, 12C14N-, 13C14N-and 13C15N-ions, respectively. The data were treated with Aphelion.
Data Extraction and Management The first author screened all titles and abstracts, and the full text was obtained for any potentially relevant articles. Full-text articles were reviewed to determine whether they met the inclusion criteria; where this was uncertain, articles were reviewed by a coauthor and disagreements were resolved by discussion. Data were initially extracted by the first author and double-checked by the coauthors. For each study we extracted data on the sample type used for the DPP-RDT and the reference treponemal and nontreponemal assay used. For each individual patient we recorded data on the presence and stage of clinical disease, the result of the reference treponemal and nontreponemal assays, and the result of the DPP-RDT. Sample types were classified as serum, plasma, whole blood, or finger-prick.
RESULTS A total of 192 studies met the search criteria, and 10 articles met the inclusion criteria  [10, [12] [13] [14] [15] [16] [17] [18]. Of these, 2 articles reported data on the same set of patients; 1 article evaluated the treponemal component of 4 RDTs including the DPP-RDT  [18] , the second study evaluated both the treponemal and nontreponemal component of the DPP-RDT and was included in this analysis  [13]. Two unpublished studies were identified by contacting groups known to have undertaken evaluations of the DPP-RDT (Figure  1 ). Overall, individual-level data from 9 studies involving 7267 test results were included in the metaanalysis. In all included studies the individual conducting the RDT was reported to be blinded to the results of the reference serological tests. The countries and characteristics of the included studies are shown in Table  1.
In 1 study  [10]  individual-level data were only available for 61. 8% of the full dataset. The performance of the DPP test did not differ between the full dataset and the individual-level data that were available (data not shown). Of patients included in the study, 5656 (77. 8%) underwent treponemal testing for suspected syphilis and 1611 for suspected yaws. Individual-level clinical data on the presence or absence of disease status were available for 2636 patients (36. 3%). Of patients for whom clinical data were available, 1417 (53. 8%) had clinical evidence of either active syphilis or active yaws at the time of testing and 1219 (46. 2%) had no clinical evidence of active disease. The reference treponemal test was positive in 4075 individuals (56. 1%) and the reference nontreponemal test was positive in 3112 (42.
8%). There was significant heterogeneity across the studies in the sensitivity of both the treponemal (I 2 95. 70%, P <. 01) and nontreponemal components (I 2 96. 70%, P <. 01) (Figure  2 ). When the results were restricted to high-titer samples, the heterogeneity was no longer statistically significant for either treponemal (I 2 26. 13%, P =. 21) or nontreponemal (I 2 26. 13%, P =. 79) components (Supplementary Figure  1 ). There was also heterogeneity in the specificity of the treponemal component (I 2 78. 98%, P <. 01) and the nontreponemal component (I 2 97. 59%, P <. 01; Figure  3 ). As there was significant heterogeneity between studies, an overall pooled summary estimate of the sensitivity and specificity of the RDT across the full dataset is not reported. Sensitivity was higher for specimens from patients with a high-titer RPR (≥1:16) (n = 1351) compared with specimens with a lower RPR titer (<1:16) for both the treponemal component (98.
DISCUSSION In this metaanalysis we combined data collected from more than 7200 patients to evaluate the performance of the combined treponemal-nontreponemal RDT for the diagnosis of syphilis and yaws. The use of individual patient data from a large number of samples allowed us to explore which factors are independently associated with test performance. We found that the DPP Syphilis Screen & Confirm RDT has good sensitivity and specificity compared with reference serology in cases of both suspected syphilis and yaws. As previously reported in one study, the sensitivity of the nontreponemal component of the RDT is related to the patient's RPR titer  [15] , with significantly higher sensitivity of the DPP kit for high-titer RPRs. We demonstrated that the sensitivity of the treponemal component is also related to the RPR titer.
This finding was explained predominantly by the lower sensitivity in yaws patients with low titers. Although lower titers are often found in patients with yaws compared with those with syphilis  [23] , it is unclear why the test performance should be worse in patients with yaws when controlling for antibody titer. These findings suggest that the DPP-RDT may be adequate in pre-mass treatment campaigns when there are many active cases with high-titer disease but that, as the number of active cases declines, it may be necessary to use a different testing strategy, either repeated testing or adoption of an alternative test with a higher sensitivity for low-titer disease. A limitation of our study was that the full individual clinical dataset was not available for 1 study  [10]. The missing data represent less than 10% of the total set included in this study, and the reported results from the full dataset do not differ significantly from the subset used in this metaanalysis.
Consequently, it seems unlikely that the missing data would substantially alter our findings. All data analyzed were collected as part of research studies and it is recognized that test performance may not be as  good in a real-world setting in the hands of the end users (healthcare workers) and that the use of test results may be influenced by factors other than simply the result  [24]. Training and support for healthcare workers has been shown to significantly improve use of RDTs in other areas  [25]  and should be a key component of the roll-out of RDTs for syphilis and yaws. This metaanalysis demonstrates that the DPP-RDT has high sensitivity and specificity for both treponemal and nontreponemal antibodies. Our analysis includes a large number of patients from many countries who were enrolled in studies and tested for syphilis or yaws.
Sample collections At the end of the experimental periods, the rats were sacrificed by intraperitoneal injection of Pentothal (Alcyon, Pau, France) with a suitable dosage (200 mg/1. 5 kg). The interested vertebrae were harvested. The samples were fixed in 5% formaldehyde solution in 4°C for 24 hours  [9]. implant three month after the surgical procedure. Reference plan was defined on the neck of the implant (Figure  3A ). After that, a ring was established around the reference area (Figure  3B  and 3D) bone implant contact is presented in Figure  3C. Bone implant contact was calculated from these data and they gray scale pixels to obtain the quantity and the percentage of bone implant contact. Bone implant contact (BIC), percentage of BIC along the threads of the implant surface; and bone volume fraction/density; percentage of the peri-implant bone volume to the total could be calculated.
Micro-CT analysis Vertebrae with osseointegrated implant were evaluated using an X-ray micro-CT instrument SKYSCAN 1176 X-ray Microtomograph (Bruker, Belgium). Implanted samples were scanned at 360° rotation at 0. 7 degree intervals. Measurements were made on the region of interest (ROI) × 1. 5 mm tissue volume (TV) on the computer-reconstructed 3D samples. The gray scale images were reconstructed from the software Nrecon (Bruker, Belgium) and visualize with FIJI 1. 5 software (NIH, USA). Then, these images were analyzed and aligned along the axis of the implant with DataViewer 1. 5.
1 ). The second survey was conducted at community level in the villages of Vapi District as a one-time point survey of pregnant women. Data were collected during the rainy season (i. e. , malaria transmission period) from July to October 2014. Both surveys were part of a larger programme (PALULAO, FEI n°13INI144), which aimed to assess the prevalence of asymptomatic and sub-microscopic malarial infections in the general population, including pregnant women, adults and children. This programme was led by the CMPE in Laos, in collaboration with the Salavan Provincial Department of Health, the Research Institute for Development (IRD) and the Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit (LOMWRU).
Study populations and designs At facility level, all women who delivered in one of the three participating maternity clinics between August and October 2014 were included after providing a written informed consent. Women were excluded from the study if they had abortion, complicated/at risk pregnancy requiring a pre-labour emergency or elective caesarean section. The following information was recorded on admission by specifically trained midwives: maternal characteristics (age, ethnicity, place of living, education level), obstetrical history (gravidity, number of spontaneous abortions, stillbirths, and live births), clinical data related to the current pregnancy (number and place of ANC visits, obstetrical complication, iron and folic acid supplementation, tobacco use, malaria history, and bed net use the night before admission), and working in the forest during the current pregnancy.
At delivery, gestational age, blood pressure, temperature, and delivery characteristics were recorded. Newborn anthropometric data (weight, height and head circumference), gender, Apgar score and congenital abnormalities were recorded. Newborn weight was measured within 1 h after birth using an electronic digital scale with an accuracy of 100 g (SECA Ltd). In addition, maternal peripheral, placental and umbilical cord blood samples were drawn for malaria diagnosis using rapid diagnostic tests (RDT), thick and thin blood smears (TBS) and real-time quantitative polymerase chain reactions (RT-qPCR). Haemoglobin (Hb) level, and proteinuria and glycosuria [using a urine dipstick test (Cybow 2GP ® )] were determined. At the community level, the cross-sectional survey was carried out in 30 randomly selected villages out of a total of 53 villages in Vapi District.
The day before the survey the head of the village made an announcement inviting all pregnant women to participate in the study. Moreover, women with suspicion of pregnancy were encouraged to visit the study team, which performed a urinary pregnancy test. Maternal characteristics, obstetrical history, clinical data related to the current pregnancy (including bed net use the night before the survey) and activities in the forest were collected. Women were screened for malaria using RDT, TBS and PCR whether or not they were symptomatic. Hb level and proteinuria and glycosuria were determined. In both surveys, data quality was monitored by study coordinators on a weekly basis. Women with positive RDTs for malaria as well as anaemic women were treated according to the national guidelines.
Association Between Vegetables With Plasma L and Z Dashes indicate variables not included in the model. * Model adjusted for age, sex, smoking status, BMI, lens status, retina status, supplementation, sun protection, and HDL-cholesterol. d'Avenir'' program with reference ANR-11-LABX-0021-01-LipSTIC Labex. Disclosure: S. Alassane, None; C. Binquet, None; V. Cottet, None; O. Fleck, None; N. Acar, None; S. Daniel, None; C. Delcourt, None; L. Bretillon, None; A. M. Bron, None; C. Creuzot-Garcher, None.
Acknowledgments Supported by an interregional grant (PHRC) and the  regional Council of Burgundy. This study was also funded by  INRA ,  CNRS ,  Université de Bourgogne, Regional Council of Burgundy France (PARI Agrale 1) ,  FEDER (European Funding for Regional Economic Development) , and a  French Government  grant managed by the  French National Research Agency (ANR)  under the ''Investisse-.