dataesr/scientific-paragraphs-categorization huggingface dataset:
5 days, separated by a bad weather event. The repetition rate of the signals was set to 15 min during the first period and 5 min in the second period to attain a higher time resolution. The signals were transmitted in three different frequency bands: low frequency band (400-800 Hz), medium frequency band (1500-3500 Hz), and frequency band (6500-8500 Hz). The instantaneous energy of the received signals and its half-hour running average was computed (Figure  6 ). We used the optode data from a mooring that has been deployed since August 2006  (Champenois and Borges, 2012). The mooring is located over the P. oceanica meadow at 10 m depth (8. 733 E 42. 567 N) close to the STARESO research station. Aanderaa O 2 optodes (3835) mounted on Alec Instruments loggers were deployed at 4. 5, 7. 0, and 9.
5 m depth. Oxygen saturation level and temperature were measured and logged at hourly intervals, to accommodate the typical duration of deployments (∼3 months) and lithium battery life at that sampling rate (∼5 months). Mooring data are interpreted in conjunction with other data, among which wind speed measured with an anemometer (Thies Clima) deployed on top of one of buildings of the STARESO station (at 11. 8 m height) at a distance of about 100 m from the mooring. The temporal variations of the instantaneous energy of the accoustic signals and of the optodes was similar (Figure  6 ). The time evolution of the received energy show high correlation with the photosynthesis activity: during the night the received energy is higher and its variability is low, during the daylight period the signal is highly attenuated with a remarkable fast fall of energy at sunrise.
ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron the cyanide-resistant oxidation of ubiquinol and the reduction of molecular oxygen to water. Increases respiration when the cytochrome respiratory protein (IP) subunit of succinate dehydrogenase (SDH), involved in complex II of the mitochondrial electron transport chain and responsible for transferring electrons from succinate to ubiquinone (coenzyme Q) Tricarboxylic acid cycle CMDH Malate dehydrogenase Catalytic activity: (S)-malate + NAD + = oxaloacetate + NADH Both photosynthetic and respiratory genes are shown. Gene names based on best scoring hits obtained blasting sequences against the Swiss-Prot database.
ACKNOWLEDGMENTS We thank the  ESF COST Action  ( ES 0906 ) Seagrass Productivity:  From Genes  to  Ecosystem Management  for the funds provided and all the participants to the October  2011 WG1  and  WG2  Workshop: linking seagrass productivity, community metabolism, and ecosystem carbon fluxes, for their fruitful contribution during the workshop. We thank  Alexandre Volpon  for his willingness to solve hitches.
Ethics Medical records: Patients all sought medical treatment for CL and were not enrolled in a study. We received geographical data on where patients live and anonymous diagnostic data were collected in the lab to be correlated with the geographical data. Private medical records were not accessed in this study nor were names or other identifying aspects provided. The Helsinki Committee on Research Involving Human Subjects of The Hebrew University -Hadassah Medical School of Jerusalem, Israel approved the study on ''Emergence of Cutaneous Leishmaniasis in the Middle East: An Investigation of Leishmania tropica'' under which medical data were obtained (permit No. 362-7. 09. 07). Trapping of wild sand flies and rodents and experimentation on rodents was approved by the Israel Nature and Parks Authority (INPA permit No.
Human cases of Cutaneous Leishmaniasis The diagnostic data of all CL cases from Sde Eliyahu that were registered in either the local clinic or regional hospital (HaEmek Hospital, Afula), were used to associate between the season and locality of morbidity. This list included the year of birth, date of positive diagnosis, diagnostic test conducted and diagnosing facility. Personal details were withheld, and locations of their residences were mapped anonymously on a blank map of the site (Fig. 1 ).
An average of 7. 9% of the females was positive for Leishmania ITS1 DNA. The infection rate increased from 5. 2% in August, peaking at 11. 76% by late October (Table  4 ). Sand fly numbers decreased significantly in November as the sand fly season ended. A sample of ten ITS1 PCR products from wild caught sand flies was analyzed by reverse line blotting (RLB) and DNA sequencing to identify the Leishmania species. All samples were shown to be L. major (data not shown).
Acknowledgments We thank  E. Klement  for help with statistical analyses,  M. Freund ,  O. Kirstein ,  H. Guetta  and  A. Moncaz  for assisting with the field work and manuscript preparation,  Alex Shtern  for the sand fly colony and  Svetlana Vaisman  who reared the wild-caught rodents. We also wish to thank residents of  Kibbutz Sde Eliyahu , and  Kibbutz Tirat Tzvi. C. L. J. holds the Michael and Penny Feiwel Chair in Dermatology.
This research was supported by a grant from the  Deployed War-Fighter Protection (DWFP) Research Program , funded by the  U. S. Department of Defense  through the  Armed Forces Pest Management Board  (AFPMB) and grant No. SCHO 448/8-2  from the  Deutsche Forschungsgemeinschaft (DFG): ''Emergence of Cutaneous Leishmaniasis due  to Leishmania tropica and L. major in The  Palestinian Authority and Israel ''. Additional funding was provided by  The Israel Science Foundation  (grant No. 135/08 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
MATERIALS AND METHODS Study design The RAPID 1 OLE was conducted in 22 countries between June 2005 and September 2011. Study designs for the RAPID 1 RCT (NCT00152386)  5  and OLE (NCT00175877)  6  have been reported. In the RCT, patients were randomised 2:2:1 to receive either CZP 400 mg or CZP 200 mg Q2W (induction dosing: CZP 400 mg at weeks 0, 2 and 4), or placebo, with concomitant MTX. At OLE entry, patients were treated with CZP 400 mg Q2W +MTX. However, while this OLE was underway, data from two Phase III studies (RAPID 1,  5  RAPID 2  7  ) demonstrated no additional benefit with CZP 400 mg Q2W versus 200 mg Q2W. Consequently, following a protocol amendment, the CZP dosage in the OLE was reduced from 400 mg to 200 mg Q2W. Changes in MTX dose were permitted in OLE (if clinically indicated) but MTX discontinuation was not.
Safety The primary objective of the OLE was to assess the safety of CZP+MTX treatment. Combined safety data from RCT and OLE are presented. The safety population includes all patients who received ≥1 dose of CZP in either study. Data are presented from time of first CZP exposure until last visit, or patient withdrawal plus 12-week follow-up. Adverse events (AE) and serious AEs (SAE) were assessed at every visit and classified by system organ class (SOC) and preferred term (PT) according to the MedDRA dictionary (V. 9. 0). Exposure-adjusted event rates (ER) and incidence rates (IR) per 100 patient-years ( pt-yr) are reported. IRs are presented for AEs typically occurring in individual patients only once (eg, malignancy) with data, including exposure, censored after the first occurrence of a particular event in a patient.
Efficacy analyses Secondary objectives of the OLE were assessment of the continued tolerability, efficacy and effect on physical function and health outcomes of CZP+MTX. Efficacy data is reported for two populations: (1) Patients randomised to CZP 400 mg or 200 mg+MTX in the RAPID 1 RCT who completed the 52-week RCT and enrolled into the OLE (week 52 CZP completers), (2) All patients randomised to CZP in the RCT (CZP intent-to-treat (ITT) population). Efficacy data are presented from baseline of the RAPID 1 RCT to 5 years CZP treatment (eg, for completers, 52 weeks of treatment in RCT followed by 204 weeks in OLE). Efficacy data beyond week 256 are not presented due to a sharp decline in patient numbers, occurring due to site closure as CZP became commercially available. Patient-reported outcomes (PRO) are presented for the week 52 CZP completer population only.
Statistical analyses Dichotomous data were imputed by modified non-responder imputation (mNRI), whereby missing data due to patient withdrawal secondary to an AE, lack of efficacy or use of rescue medication were imputed by NRI; if dichotomous data were missing for reasons other than these, last observation carried forward (LOCF) imputation was applied. If no suitable LOCF value existed, NRI was used. Missing continuous data were imputed by LOCF. Observed ACR20/50/70 data are also presented. Kaplan-Meier analysis was used to estimate patient retention in CZP ITT patients who withdrew for any reason, and who withdrew due to AE or lack of efficacy. Patients withdrawing for other reasons were censored at time of withdrawal. Patients who did not withdraw were censored at their last scheduled visit.
Here, we describe the genome sequence of R. gravesii strain BWI-1 T. R. gravesii (deposited in the Collection de Souches de l'Unite des Rickettsies [CSUR] under reference R172) was grown in XTC and L929 cells, and its genomic DNA was extracted using a phenol-chloroform protocol. Sequencing was performed using the MiSeq platform (Illumina, San Diego, CA) with a 2 ϫ 250-bp paired-end run after library preparation with the Nextera XT sample preparation kit (Illumina). De novo genome assembly was done using the CLC Genomics Workbench 4. 9 (CLC bio, Aarhus, Denmark). The resulting contigs were reordered in Mauve 2. 3. 1 (7) using the genome sequence from R. massiliae strain MTU5 (GenBank accession no. CP000683) (8) as a reference. Open reading frame (ORF) prediction and gene annotation were carried out using RAST 4.
EF564599). The chromosome contains 1,675 protein-encoding genes and, like other Rickettsia species, 3 noncontiguous rRNAs (5S, 16S, and 23S rRNA), 33 tRNAs, and 3 other RNAs. In addition, the pRgr plasmid contains 24 proteinencoding genes, including a split sca12 gene and a proline-betaine transporter gene, but no RNAs. Compared to that of R. massiliae MTU5, the R. gravesii chromosome exhibits a high level of synteny with the exception of four inversions of 37,978 bp, 4,791 bp, 2,782 bp, and 1,339 bp. Moreover, several genes are lacking in the R. gravesii genome, including paaJ (acetyl-coenzyme A [CoA] acetyltransferase), def3 (polypeptide deformylase), and genes for several transposases and inactivated derivatives. Nucleotide sequence accession number. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no.
For the localization of CpG sites in PMDs or outside PMDs, we downloaded data published for fetal lung fibroblasts (IMR90)  [14]. The genes were considered to be located in PMDs if their promoters were located within PMDs. The graphs were prepared using GraphPad Prism 5. 0 for Windows, GraphPad Software, San Diego California USA. For the graph of the distribution of CpG sites detected by DREAM, we average 25 to 50 neighbor points according to their distance to TSS, and the data were then smoothed using GraphPad Prism 5. 0. For gene body methylation, the average of CpG sites located +1000 bp from the start of transcription to the transcription end site was calculated. For GSEA, gene sets were downloaded from the Broad Institute's MSigDB website  [29]. Gene set permutations were used to determine statistical enrichment of the gene sets using the difference of methylation between Twist1-transduced cells (monolayer) and vector cells.
Acknowledgements This work was supported in part by an  MD   Anderson Research Trust Fellow Award , funded by the  George and Barbara Bush Endowment for Innovative Cancer Research (SAM)  and  DOD Breast Cancer Research Postdoctoral Fellowship (JHT ). GGM was also funded by the following non-for-profit organizations:  Fondation Nadine Midy, Foundation Nelia et Amadeo Barletta (FNAB)  and the  Association pour l'Aide à'la Recherche et l'Enseignement en Cancérologie (AAREC).
Time scale and gain thus vary together, with small gains associated with short time scales and large gains associated with long time scales. (B) The K z filter is broader than the K y filter and, hence, can capture memory effects and mimic feedback. The parameter set is based upon the salamander data (see Methods and Table  2 ). doi:10. 1371/journal. pcbi. 1003289. g001 [13] ). Parameters were chosen so as to minimize the root-mean-squared error in the voltage traces, and result in faster peaks at high intensities; alternative fitting criteria could better fit the peak timing. (E) The model predicts that responses to paired flashes add non-linearly. A conditioning flash (10 ms, 560 photons/mm 2 /s) is presented at t~0 ms. A test flash of identical intensity to the conditioning flash is presented either before or after the conditioning flash, and the response is measured.
(For a discussion of the relation of the DA model with molecular mechanisms, see below. ) We note that the form of the flash response in the case of bright backgrounds, expressed analytically in Eq. (  8 ), exhibits precisely the Weber-Fechner form. Response dynamics also vary with background light intensity: brighter backgrounds speed up responses. Both data and model predictions exhibit a reduction of the peak delay for increasing background intensities, followed by a characteristic saturation at high background intensities (Fig. 5G ). In the DA model, this For data from Baylor's papers, for instance, all theoretical curves used the 'BHL' parameter set, with only the parameter a varying to match amplitudes. The parameters for each author's data set were chosen by fitting routines as described in the Methods section.
Specifically, throughout we used the form K z t ð Þ~c t ny n y !t nyz1 y e {t=ty h t ð Þz 1{c ð Þ t nz n z !t nzz1 z e {t=tz h t ð Þ, ð13Þ according to which z(t) involves a fast component that responds on the time scales of the linear response, t y , and a slow component that responds on a somewhat longer time scale, t z. The prefactors, c and 1{c, weigh the relative importance of the two components and ensure normalization to unity. Throughout, we integrated the DA model with standard techniques in Matlab (Mathworks, Natick, MA). We fit our model parameters separately to each of the three data sets we used, from the experiments of Baylor, Hodgkin, and Lamb  [13] [14] [15] , the experiments of Burkhardt  [18] , and the experiments of Daly and Normann  [16]. We used a gradient descent method in Matlab to find the parameter sets that yielded the least squared error from the experimental results.
Salamander Experiments and Analyses with LN and DA Models Salamander retinae were exposed to whole-field flicker of timevarying intensity while a sharp electrode voltage recording was made of cone cells, following the protocol of Ref. [8]. Flicker was presented with a CRT at 67 Hz, with a mean light intensity of , 10mW/m 2. Intensities were updated every 2 frames and chosen from a Gaussian distribution with standard deviation equal to 35% of the mean. All data integration and analysis were performed with custom-written routines in Matlab. (We provide some of these codes as online supplementary material. ) LN model analysis. Best-fit linear filters were found using crosscorrelation methods, as described in Ref. [8]. A 500 ms filter was used to produce the linear portion of the LN model output, followed by a third degree polynomial fit of that output to the experimental response.
6I. Peak correlation time, for each average of cross-correlations, was defined as the average of the 10 times of maximum correlation. In Fig. 6I , we selected the time points with lowest, middle, and highest instantaneous gains, and plotted the filters corresponding to each of the three subsets of data. DA model analysis. Model parameters were fit to the salamander data (Fig. 6B ) with a least squares minimization routine in Matlab and Eq. (  2 ) was integrated with the use of standard methods in Matlab, with the functional forms described above. All parameters (a, b, c, n y , n z , t r , t y , and t z ) were varied, but n y and n z were imposed to take integer values. The parameters used to fit salamander data are recorded in Table  2. Analysis of statistical significance. To assess the significance of the difference in slopes, we applied a Monte Carlo shuffle analysis, in which we ran the slope fitting routine 3000 times, each time offsetting the stimulus and response by a random temporal delay, using circular boundary conditions.
Material and methods The specimen is included in a completely opaque piece of amber from the Lower Cretaceous of France. Due to the impossibility of surveying the interior of the piece due to the opacity, propagation phase contrast X-ray synchrotron microtomography (afterwards PPC-SRμCT) was used to recognize any possible inclusion inside the amber. The specimen was scanned following the protocols described in  Lak et al. (2008)  with a set energy of 30 keV (using a double Si 111 Bragg monochromator) and 960 mm of distance between the camera and the sample. Scan acquisition consisted of 1999 images over 180º, with 0. 7 s of exposure time, and 5. 06 μ of voxel size. After the scan, the slices were reconstructed using a filtered back-projection algorithm adapted for local tomography applications (PyHST software, ESRF).
The later three-dimensional processing was made using VGStudioMax 2. 1 software (Volume Graphics, Heidelberg, Germany). By using this method it is possible not only to examine the habitus of the fossil under all desirable angles, but also to see internal structures which are usually not available in fossil insects (structure of the head, thorax, abdomen and hidden hind wings). This method is especially interesting for future studies of the inclusions in Mesozoic amber which is very frequently opaque. More than 80% of the amber of French Late Albian is opaque and cannot be studied using conventional methods. All the data regarding the scan adquisition parameters, including original reconstruction of the scan, parameters of acquisition, VGStudioMax segmentation file, stereolithographic surface file for 3D printing, plates and animations are available online in the ESRF Paleontological Database (http://paleo.
Acknowledgements The authors would like to express their gratitude for their support and help to the staff of ID19 beamline, especially to  Jose Baruchel  and  Elodie Boller  ( ESRF, France ). We are grateful to  Malvina Lak  and  Simon Defortis  for their assistance in the original scanning and segmentation of this specimen. Rich Leschen  ( New Zealand Arthopod Collection, Auckland New Zealand ) and  Dan Young  ( University of Wisconsin-Madison, USA ) provided useful comments on an earlier version of this paper. DAP thanks especially  Jaroslaw Stolarski  for his patience during the publication of this manuscript. Partial support for this work was provided by the  AMBRACE  Project of the  French National Research Agency  ( ANR-BLAN07-1-184190 ), and by the  ESRF  through attribution of in-house beam-time on the beamline ID19.
Calibration The ECM signal is temperature dependent and was calibrated to a standard temperature of -14 • C by using an Arrhenius law with an activation energy of 0. 23 eV  (Neftel et al. , 1985). The exact conversion between ECM and ice acidity is ambiguous. Even for a specific set of electrodes, the data display a large amount of scatter, and several calibration curves have been suggested based on measured H + ion concentrations. The initial calibration curve suggested by  Hammer (1980)  uses a square-law relationship, but the appropriate parameters in this calibration seem to be ice-core dependent  (Moore et al. , 1992). This is partly a result of different ambient conditions and operational differences (e. g. pressure applied to the electrodes) during measurements. Also, the exact procedures concerning storage and cleaning of the ice core surface may play a role.
Data quality The quality of the ECM measurements is generally higher in ice than in the firn, where the lower density makes it difficult to maintain constant contact area between ice crystals and electrodes. This leads to generally lower currents and enhanced scatter in data from the uppermost part of the ice core. To ensure the quality of the ECM data, the ECM profile was measured twice for each core section and the two profiles were subsequently checked for agreement. In case of major dissimilarities, measurements were repeated until reproducible results were obtained and a representative run could be selected. In this way, the reproducibility of the ECM data was continuously checked. The manually operated ECM device is fast and simple, and it allows the scientific investigator to take advantage of the best-preserved section of the ice core surface by manoeuvring the electrodes around cracks or other areas of poorquality ice.
Breaks across the entire core diameter cannot be avoided, and can be recognized as abrupt dips in the ECM profile. The location of breaks was logged as part of the ECM measurements, and data from these sections have subsequently been removed from the resulting ECM data sets. A disadvantage of the handheld electrode approach is that the depth assignment is only accurate to 1-2 cm, which is a consequence of the flexibility in the electrode set-up together with the uncertainty of the registration of the move-ment of the electrodes along the length of the core. The depth uncertainty of 1-2 cm of the ECM data makes a detailed comparison with, for example, high-resolution chemistry measurements of the ice core challenging. Data have subsequently been interpolated to a depth resolution of 1 cm for NGRIP1 and NEEM data and 1 mm for NGRIP2 data, with the different resolution reflecting changes in the data post-measurement treatment.
Dielectrical profiling (DEP) The dielectrical stratigraphy of the NEEM and NGRIP cores were recorded in the field with the dielectric profiling (DEP) technique  (Wilhelms et al. , 1998). Comparisons with highresolution chemistry measurements suggest that the DEP signal in Greenland mainly reflects the acidity of the ice and the core's content of ammonium and salts  (Moore et al. , 1994). Ice core sections of 1. 65-2. 2 m were usually analysed no more than one day after drilling. The brittle zone ice could not be handled directly after drilling and was stored and processed during the subsequent season, but all the data used here comes from below the brittle zone. At NEEM, approximately every day a free air measurement was recorded for data calibration. For each measurement the cable stray capacitance and conductance -as determined in the corresponding daily free air measurements -are subtracted from the respective capacitance and conductance records.
These measurements are not available for NGRIP, and the missing correction for cable stray conductance means that the NGRIP data set still contains a periodic variation with amplitude of up to 2 % of the baseline conductivity and a wavelength of 1. 65 m. After multiplying the conductance with the vacuum permittivity, permittivity and conductivity are calculated by division with the free air capacitance. The relative permittivity increases during the initial densification in the upper part of the core and remains just above three in deeper core sections. Therefore, permittivity values significantly below this threshold are good indicators of sections with bad core quality influenced, for example, by breaks or missing pieces. Data from these sections are not trustworthy, and corrected data sets are created by removing sections where the permittivity drops below a chosen threshold (see Fig.