dataesr/scientific-paragraphs-categorization huggingface dataset:
The KORA F4 studies were financed by  Helmholtz Zentrum München, German Research Center for Environmental Health, BMBF, German National Genome Research Network , and the  Munich Center of Health Sciences. The Heinz Nixdorf Recall cohort was funded by the  Heinz Nixdorf Foundation  ( Dr jur. G. Schmidt , Chairman) and  BMBF. Coriell Cell Repositories is supported by  NINDS  and the  Intramural Research Program  of the  National Institute on Aging. The authors acknowledge the use of genotype data from the 1958 Birth Cohort collection, funded by the  MRC  and the  Wellcome Trust  which was genotyped by the  Wellcome Trust Case Control Consortium  and the  Type-1 Diabetes Genetics Consortium , sponsored by the  National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Allergy and Infectious Diseases, National Human Genome Research Institute, National Institute of Child Health and Human Development , and  Juvenile Diabetes Research Foundation International.
The samples that exceed the threshold DM (5. 5σ -a standard deviation, calculated for each integrated time series with corresponding trial DM), are put down to the database, indicating their DM, S/N ratio of the event and the time elapsed from the beginning of the file. They are marked on the "time -dispersion measure" plane by circles, with radii proportional to the S/N value of the event. To check for false-positive detections, the pre-processed data are examined in different ways, introducing different input parameter values (e. g. checking in different frequency bands) and also are checked visually. Fig. 1  shows the example of false-positive detection. The dynamic spectrum (after the dispersion delay compensation) shows the frequency sweep of the signal, different from the dispersion relation (1).
Methodology of Pulsar and Transient Search By the beginning of 2014, the initial observations, which began in April 2010, were almost completed. We have obtained the records of more than 90 % of the Northern sky. For the remaining areas (gaps between the strips, which were recorded with a sixmonth shift, and the circumpolar regions), one more short-term observational session is required. Fig. 2  shows the map of surveyed sky regions. The survey database includes: -raw data, -normalized data after RFI mitigation, -intermediate files with compensated dispersion delay, -outputs of repetitive and transient search routines. Preprocessing (steps 1 and 2 of the pipeline) is now completed for a half of the raw data. Using the aforesaid search routines, we have processed the survey data that contain recordings of radio emission of known pulsars, such as PSR В0809+74, В0834+06, В0950+08.
Acknowledgements This work has been supported by Projects "Development of the  UTR-2 radio telescope cluster  for the  UTR and GURT data processing " in the  framework of   NASU Program  " Informatization for 2014 ", and " Coordinated simultaneous studies of the solar system  objects by means of the  methods of ground-and space-based low-frequency radio astronomy " within the  NASU Program "Scientific Space Research for 2012-2016 ".
Second, the detector readout used multiplexing SQUID amplifiers to reduce the number of wires and therefore the heat load on the focal plane. We have continued to apply the BICEP1 methods to achieve low systematics and remaining noise-limited, and in addition we have developed new analysis techniques to purify the data of instrumental signals. These methods and the application to the BICEP2 beams and instrument will be described in the Systematics Paper and Beams Paper. As the first experiment to deploy the Caltech-JPL antennacoupled TES detectors, BICEP2 has opened a path to larger arrays that will continue to increase in sensitivity and cover multiple frequencies for possible foreground removal. The ongoing development of the arrays is described in the Detector Paper. The Keck Array (2010-present;  Sheehy et al.
Observing site The South Pole is an excellent site for millimeter-wave observation from the ground, with a record of successful polarimetry experiments including DASI, BICEP1, QUAD and the South Pole Telescope. Situated on the Antarctic Plateau, it has exceptionally low precipitable water vapor  (Chamberlin et al. 1997) , reducing atmospheric noise due to the absorption and emission of water near the 150 GHz observing band. The South Pole site also has very stable weather, especially during the dark winter months, so that the majority of the data are taken under clear-sky conditions of very low atmospheric 1/ f noise and low loading  (Stark 2002). The consistently low atmospheric loading is crucially important because the sensitivity of the experiment is limited by photon noise, so that low atmospheric emission is a key to high CMB mapping speed.
3% of the antenna response in the experiment as deployed. 7. 5. Device yield Initial electrical testing of detector arrays checked for continuity across the devices, with correct room-temperature resistance and no shorts. This fabrication yield was extremely high, 99% for the four tiles in BICEP2. When the detectors were integrated into the focal plane and telescope there were additional losses from open lines in the readout, further reducing the overall yield to 82%. The remaining 412 "good light detectors" are those that were optically coupled and had stable bias and working SQUID readout. A detector has been included in this count only if both it and its polarization partner satisfy the same criteria. The number is reduced somewhat in analysis by data quality cuts on beam shape and noise properties as described in §13.
The filter effectively isolated the focal plane from thermal fluctuations on time scales shorter than about 1300 s. With no additional heating, the focal plane achieved a base temperature of ∼250 mK. Temperature control modules (TCMs) consisting of two NTD thermometers and one resistive heater were employed in a feedback loop to control the temperature of the focal plane and the fridge side of the thermal filter (as shown in Fig. 5 ) to 280 and 272 mK respectively, well below the 500 mK titanium TES transition temperature. Temperature stability of the tile substrates was monitored using NTD thermometers mounted on each detector tile and by dark TESs on the detector tiles. The tile NTD data have been used to demonstrate that the achieved thermal stability met the requirements of the experiment ( §11.
DATA ACQUISITION SYSTEM BICEP2 used a multiplexed SQUID readout that allowed it to operate a large number of detectors with low readout noise and acceptably low heat load from the wiring. We describe the NIST SQUIDs and other cold hardware, the roomtemperature Multi-Channel-Electronics (MCE) system, and the custom control software that were used for data acquisition. 9. 1. Multiplexed SQUID readout BICEP2 used the "MUX07a" model of cryogenic SQUID readout electronics provided by  NIST (de Korte et al. 2003 ). These were designed for time-domain multiplexing  (Chervenak et al. 1999; Irwin et al. 2002) , in which groups of 33 channels are read out in succession through a common amplifier chain. This scheme supports large channel counts with a small number of physical wires so that the heat load on the cold stages remains low.
BICEP2 was supported by the US National Science Foundation under grants ANT-0742818 and ANT-1044978 (Caltech/Harvard) and ANT-0742592 and ANT-1110087 (Chicago/Minnesota). The development of antenna-coupled detector technology was supported by the JPL Research and Technology Development Fund and grants 06-ARPA206-0040 and 10-SAT10-0017 from the NASA APRA and SAT programs. The development and testing of focal planes were supported by the Gordon and Betty Moore Foundation at Caltech. Readout electronics were supported by a Canada Foundation for Innovation grant to UBC. The receiver development was supported in part by a grant from the W. M. Keck Foundation. The computations in this paper were run on the Odyssey cluster supported by the FAS Science Division Research Computing Group at Harvard University.
Background: In Africa, relapsing fever borreliae are neglected vector-borne pathogens that cause mild to deadly septicemia and miscarriage. Screening vectors for the presence of borreliae currently requires technically demanding, time-and resource-consuming molecular methods. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has recently emerged as a tool for the rapid identification of vectors and the identification of cultured borreliae. We investigated whether MALDI-TOF-MS could detect relapsing fever borreliae directly in ticks. Methodology/Principal Findings: As a first step, a Borrelia MALDI-TOF-MS database was created to house the newly determined Mean Spectrum Projections for four Lyme disease group and ten relapsing fever group reference borreliae.
MALDI-TOF-MS yielded a unique protein profile for each of the 14 tested Borrelia species, with 100% reproducibility over 12 repeats. In a second proof-of-concept step, the Borrelia database and a custom software program that subtracts the uninfected O. sonrai profile were used to detect Borrelia crocidurae in 20 Ornithodoros sonrai ticks, including eight ticks that tested positive for B. crocidurae by PCR-sequencing. A B. crocidurae-specific pattern consisting of 3405, 5071, 5898, 7041, 8580 and 9757-m/z peaks was found in all B. crocidurae-infected ticks and not found in any of the un-infected ticks. In a final blind validation step, MALDI-TOF-MS exhibited 88. 9% sensitivity and 93. 75% specificity for the detection of B. crocidurae in 50 O. sonrai ticks, including 18 that tested positive for B.
crocidurae by PCR-sequencing. MALDI-TOF-MS took 45 minutes to be completed. Conclusions/Significance: After the development of an appropriate database, MALDI-TOF-MS can be used to identify tick species and the presence of relapsing fever borreliae in a single assay. This work paves the way for the use of MALDI-TOF-MS for the dual identification of vectors and vectorized pathogens.
In particular, MALDI-TOF-MS has been used to identify spirochetes of the genus Leptospira  [13]  and Brachyspira  [14] , and recently cultured Borrelia spp. [15]. Also, MALDI-TOF-MS has recently been used to identify vectors  [16] [17] [18]. In this study, we investigated whether MALDI-TOF-MS could further detect relapsing fever borreliae directly in their tick vectors. More specifically, we developed a step-by-step approach, first creating a Borrelia MALDI-TOF-MS database, then performing a proof-of-concept B. crocidurae detection in Ornithodoros sonrai ticks, and finally, blindly testing the MALDI-TOF-MS approach to detect B. crocidurae in O. sonrai ticks.
Borreliae MALDI-TOF-MS database A 1 mL aliquot of the suspension was deposited onto a spot on an MSP 96 target polished steel micro Scout target plate (Bruker Daltonics, Wissembourg, France). After air-drying, 1. 5 mL of matrix solution (a saturated solution of alpha-cyanohydroxycinnaminic acid in 50% aqueous acetonitrile containing 2. 5% trifluoroacetic acid) was added, and the plate was air-dried for 15 min before being processed in the mass spectrometer. A total of 12 spots were deposited for each Borrelia strain, and this manipulation was repeated in two independent runs. On each plate, Escherichia coli DH5 alpha (Bruker Daltonics) was used as a positive control, and non-inoculated BSK-H medium and noninoculated-matrix solution were used as negative controls. The analysis was conducted using a Microflex LT spectrometer (Bruker Daltonics), and the spectra were recorded in a linear, positive ion mode with an acceleration voltage of 20 kV.
The spectra were collected as a sum of 240 shots across a spot. The preprocessing and identification steps were performed using the manufacturer's parameters. For each of the 14 Borrelia species, a consensus pattern referred to as the Mean Spectrum Projection (MSP) was obtained by the Biotyper MSP Creation Standard Method (Bruker Daltonics). To assess the reproducibility of the MALDI-TOF-MS profiling, the 14 Borrelia strains included in the database were further blindly analyzed by MALDI-TOF-MS as described above. For each strain, 12 spots were analyzed, and the 12 spectra obtained were compared with the Borrelia MSP database. The results of the pattern-matching process were expressed as an Table  1. Borrelia species used to establish a MALDI-TOF-MS reference database. identifying score varying from 0 to 3.
A score of between 3 and 1. 9 indicated a species level identification; a score of 1. 9-1. 7 indicated a genus level identification; and a score of ,1. 7 was regarded as an unreliable identification  [22]. The MSP spectra from Borrelia spp. were used to generate a dendogram with the MALDI Biotyper 2. 0 software (Bruker Daltonics).
MALDI-TOF-MS Borrelia database Negative controls yielded no identifiable patterns while the positive controls yielded E. coli with identification scores from 1. 9-2. 3. Each of the 14 Borrelia reference isolates yielded a unique reproducible protein profile combining 25 to 123 peaks (Table  S1 ). Each profile differed from the ones in the Bruker Daltonics database (V3. 1. 2. 0) and each profile was specific for each species of Borrelia (Table  S1 ). Further blind test correctly identified all of the 14 Borrelia strains, with identification scores from 2. 15-2. 67 after incorporation of the reference spectra (Table  1 ).
MALDI-TOF-MS detection of B. crocidurae in O. sonrai ticks The 12 un-infected O. sonrai ticks yielded no matches, as the database we used did not contain a reference spectrum for this soft tick species; we therefore added this new reference MSP in the ticks' database being constructed in our laboratory  [17]. The eight infected O. sonrai ticks consistently yielded a specific pattern of six peaks of 3405, 5071, 5898, 7041, 8580 and 9757 m/z. After subtraction of the O. sonrai MSP, none of the 12 un-infected ticks yielded such a pattern. This 6-peak pattern was found in the B. crocidurae MALDI-TOF-MS pattern (Figures  1, 2 ). Using this 6peak pattern, B. crocidurae was detected in 100% of infected ticks and 0% of non-infected ticks.
Blind detection of B. crocidurae in O. sonrai During the blind test, 100% of the 50 tested ticks were identified as O. sonrai (after the corresponding MSP had been added to the database). Furthermore, the 6-peak B. crocidurae pattern was blindly detected in 16/18 (sensitivity, 88. 9%) infected ticks and in 2/32 (6. 25%) non-infected ticks (specificity of 93. 75%) (Table  2 ). Re-testing these four ticks with both glpQ-qPCR and MALDI-TOF-MS yielded the same results as in previous experiment.
Discussion For ten years, MALDI-TOF-MS has revolutionized the routine identification of bacteria  [11, 22, 24]  and archaea  [12] , but few studies have examined its application to spirochetes, including Leptospira spp. [13]  Brachyspira spp. [14]  and Borreliae spp. [15]. Here, using a simple protocol consisting of only one centrifugation step, 14 Borrelia isolates yielded an interpretable, identifying protein pattern. Identification was achieved starting from only 10 4   Borrelia/mL, in the same range as the 10 5 Leptospira/mL previously reported  [13]. These data completely confirm a recently published study showing that cultured Borreliae are identifiable by MALDI-TOF-MS  [15]. The MSP for the 14 Borrelia isolates described herein have been deposited into our freely available Mediterranee Infection Institute website database (http:// www.
mediterranee-infection. com/article. php?laref = 256&titre = urmsdatabase) to assist other scientists with their identification work. As the reliability of MALDI-TOF-MS bacterial identifications depends on the quality of the database  [22] , we carefully validated the reproducibility of the Borrelia spectra. No misidentifications were discovered when all of the Borrelia strains analyzed in this study were matched with non-borreliae spirochetes (Leptospira and Brachyspira). Further enrichments of the database and the creation of additional super spectra using several genetically/morphologically different strains of the same species will likely increase the power of MALDI-TOF-MS for the identification of borreliae. We also added an MSP for O. sonrai to the tick MALDI-TOF-MS database that we are building  [17].
Using this extended database and a piece of subtraction software, MALDI-TOF-MS allowed for the blindly identification of O. sonrai ticks and detection of B. crocidurae in these ticks within 45 minutes. Interestingly, infection by B. crocidurae did not hamper the MALDI-TOF-MS identification of the infected O. sonrai. Moreover, the 6-peak signature found in B. crocidurae infected ticks is comprised of six proteins that are specifically found in B. crocidurae. Therefore, this 6-peak signature is not an unspecific pattern due to any ticks' infection or inflammatory response to Borrelia, but indeed a signature specific to B. crocidurae. Using a 96-spot plate, a total of 23 ticks could be screened in the same experiment, including controls and quadruplicate spots per tick. These data indicate that MALDI-TOF-MS can be used for the rapid, one-shot identification of ticks and tick-borne borreliae.
On completion of this programme, the park aims to study one or several lakes in each valley that will be representative of the park's lakes in terms of altitude, surface area and trophic level. At the same time, major efforts have been made to collect, validate and format all available biological, but also mesological and socio-economic data for each lake. This work has been planned to enable coordinated management between stakeholders and users (fishermen, shepherds, hikers, etc. ) and their federation or representatives. Inventory results, which still need to be completed, have already given the park authorities an idea of the specific richness and composition of the living community with the registration of several patrimonial species (Somatochlora alpestris, Alytes obstetricans and others).
YGRKKRRQRRR was used as the TAT sequence, which is responsible for cell penetration of the peptides. 38 The sequence PEP-1 was TAT-DPYHATSGALSPAKDCGSQKYAYFNGCSSPTAPLSPMSP, the sequence PEP-2 was TAT-AYFNGCSSPTAPLSPMSP and the sequence for PEP-3 was TAT-PTAPLSPMSP. Peptides were used at different concentrations (25, 50, 75  or 100 mM) in culture medium at 37 1C for the indicated time. Plasmid constructs and cell transfection. The pIres-Cx43 construct was generated by ligating a PCR-amplified fragment encoding the human Cx43 sequence (accession number: NM_000165) into the AgeI-BamHI sites of the bicistronic pIres-puro2 vector that encodes the puromycin resistance gene. The fragment encoding the human Cx43 sequence was obtained by RT-PCR performed on a template of total RNA isolated from GliNS2 cells using the following primers: 5 0 -TATATACCGGTATGGGTGACTGGAGCGCCTT-3 0 and 5 0 -CGGGATCCCGCTAGATCTCCAGGTCATCAG-3 0.
, Heidelberg, Germany; sc-488; 1 : 500), Sox2 (Abcam, Cambridge, UK; ab97959; 1 : 1000), E-cadherin (Santa Cruz; sc-7870; 1 : 100), N-cadherin (Santa Cruz; sc-7939; 1 : 500). Antibody against glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (Applied Biosystems, Madrid, Spain; AM4300; 1 : 5000) or a-actinin (Millipore, Billerica, MA, USA; MAB1682; 1 : 1000) were used as a loading control. After extensive washing, membranes were incubated with HRP-conjugated anti-rabbit or anti-mouse antibodies in TTBS. Proteins were developed with a chemiluminiscent substrate. Densitometry analysis of the bands was performed using Image J program (Wayne Rasband; NIH, Bethesda, MD, USA). The amounts of GAPDH or a-actinin recovered in each sample served as loading control and the values for each protein were normalized to their corresponding GAPDH or a-actinin level.
Acknowledgements. This work was supported by the  Ministerio de Economı ´a y Competitividad ,  FEDER BFU2011-27602  (AT). E Gangoso (ref. AP2008-03515 ) was recipient of a fellowship from the  Ministerio de Educacion, Cultura y Deporte. We are grateful for the technical assistance of  T del Rey  and we thank  Dr. M Morales  for his help in peptide design,  Dr. F de Castro  for O4 antibody and  Elizabeth Nestor  for her linguistic assistance.
Genomic and phylogenetic analysis MLST analysis was performed by sequencing four housekeeping genes: cts (encoding citrate synthase), gapA (glyceraldehyde-3phosphate dehydrogenase A), rpoD (RNA polymerase sigma 70 factor) and gyrB (gyrase B), using the Morris MLST schema of the Plant Associated and Environmental Microbes Database (PAMDB, http://genome. ppws. vt. edu/cgi-bin/MLST/home. pl) in combination with gapA and gyrB of the Hwang PAMDB schema  [16, 20]. For each locus, sequences were extracted from GenBank and PAMDB, aligned with the P. syringae sequences by using DAMBE software version 5  [21]  and were cut to the same size (1859 bp for the concatenated sequences). In order to clarify the phylogenetic position of strain LzW4 isolated from Antarctica and misclassified as P. syringae  [22] , housekeeping gene sequences were obtained from its genome.
The concatenated sequences were used to construct the phylogeny with maximum likelihood and Bayesian methods by using the PHYLIP package version 3. 6 (http://evolution. genetics. washington. edu/phylip. html) and Mr. Bayes version 3. 1. 2, respectively  [23]. For maximum likelihood analysis, consensus trees were created from 100 independent phylogenies. Bayesian trees were constructed by using 500,000 generations with a burn-in period of 250,000. All sequences and critical metadata of strains were deposited in the PAMDB data base  [24]. Genetic distances among the strains were determined with the Kimura 2-parameter model, with a gamma correction of 1, by using the PHYLIP package. For delimitation of phylogroups, the distance used as a criterion was chosen to allow delineation of the seven previously-described phylogroups of P.
Phylogenetic analysis of partial core genomes (sequences of 107 genes) was also performed. Core genomes were extracted from 29 P. syringae genomes (Table  S1 ) as described previously  [25]. Alignment of the core genome was made by using DAMBE version 5 as described above and a Bayesian tree was built with Mr. Bayes. Accession numbers of all sequences are reported in Table  S1.
Rarefaction curves Rarefaction curves were constructed by randomly sampling a set of 830 individuals representing 13 different phylogroups or 23 different clades in the same proportions as delimited by their assignment to clades and phylogroups as described above. Random samples were drawn 830 times from the set of individuals and the average cumulative numbers of clades or phylogroups observed for each draw were calculated with R software version 2. 9. 1 with an in-house program (The R Development Core Team, 2009) after 1,000 iterations of the succession of draws.
2 , Fig. 3 ), but also with only its partial sequence (409 bp) (Table  S6 ). For routine phylogenetic analysis, only partial cts sequences (409 bp) could be used. We propose a list of reference strains labelled with their phylogenetic affiliation, together with their partial cts sequences in a table (Table  S11 ) as well as in a FASTA file (File S1). These strains represent all phylogroups and clades identified in this study. For each clade and each phylogroup the most distant strains from the set of 216 P. syringae characterized by MLST were selected for cts sequence analysis. These sequences have also been deposited in GenBank (accession numbers indicated in Table  S11 ). The procedure of classification consists of the following steps: 1) alignment of the partial cts gene sequence of the strain to be identified with those in Table  S11 ; 2) analysis of tree branches and of the matrix of pairwise distances to find the phylogroup and clade with which it is most similar and 3) assignment to the phylogroup or clade if the following criteria are met: ,4% difference in the sequences for assignment to a phylogroup, and ,1.