dataesr/scientific-paragraphs-categorization huggingface dataset:
RSML Thesaurus The RSML format does not impose a restricted set of properties or functions. However, a thesaurus has been defined to promote the use of standardized terms. Any supporting software is not required to process these terms. So, unlike the main RSML definition, new terms may be added to this thesaurus without changing the format itself. Addition to the thesaurus follows a traditional open-source protocol as described on the RSML Web site (http://rootsystemml. github. io).
Open-Source Packages for RSML Analysis Five open-source application programming interfaces have been created to read and parse RSML data files from within C#, Excel (Fig. 3A ), R (Fig. 3B ), ImageJ (Fig. 3C ), and Python (Fig. 3D ). The aim of these packages is not to carry the analysis of the root system data but to provide end users with commonly used data structures within popular data-analysis pipelines. These packages have been released as open source to allow users to adapt them to their needs. They are available through the RSML Web site.
We believe that the existence of a standard format for root architecture will enable easier reproducibility among researchers and allow the comparison of multiple data sets, even those coming from different sources. In the second example, the image shown in Figure  6A  was analyzed using RhizoScan, RootSystemAnalyser, RootNav, and SmartRoot. The RSML files generated by the different tools were exported into a single data file and analyzed using R (  R Core Team, 2008). Supplemental Figure  S2  shows the comparison of the measured primary root length, lateral root length, lateral insertion angles, and lateral insertion positions for each software. This example illustrates how a shared format can streamline the validation of new algorithms and the creation of benchmark data sets with which to validate them.
In the third example, we illustrate the use of RSML for data storage and sharing between modeling tools. Figure  6A  shows the visual output of an Anagallis femina root system simulated by RootBox  (Leitner et al. , 2010). The simulated root architecture was stored as an RSML data file and converted into the MTG data structure  (Godin and Caraglio, 1998)  in the OpenAlea platform  (Pradal et al. , 2008). Taking advantage of the geometric modules of PlantGL  (Pradal et al. , 2009) , the 2D or 3D convex hull of the root system can easily be calculated (Fig. 6B ). The same RSML file was used in R-SWMS  (Javaux et al. , 2008)  to simulate water flow in the soil-root system, hence allowing the testing of the functional performance (in this case, water uptake) of the simulated root system. These three examples highlight the potential role of the RSML format as a cornerstone in analysis pipelines and show how it can hasten data (both simulated and experimental) exchange between researchers.
By storing root architecture in a common format, desired root traits can be calculated quickly over large data sets captured with a variety of software, regardless of the traits that were considered when that data set was first analyzed. We believe that the adoption of RSML will encourage the creation of central repositories for root architecture data, similar to those that exist in other domains. In molecular biology, it is even mandatory to upload gene expression data sets to a database such as EBI-ArrayExpress  (Rustici et al. , 2013)  prior to publication. Those publicly accessible repositories are frequently queried by the scientific community. The development of a similar public database for costly and valuable root architecture data would increase the pace and efficiency of root research.
This central repository also can be used as a benchmark to compare and evaluate computer programs used to reconstruct architectural data. New algorithms and software could be assessed to ensure that the data sets produced are scientifically valid. This benchmark will also greatly accelerate the impact and the adoption of new, independently developed algorithms for the automatic digital reconstruction of root system architecture. B, Screenshot of a root tracing done using RootNav. C, The RSML generated by RootNav was opened using SmartRoot, which computed the root diameter (which is not calculated by RootNav). D, R-generated graph showing lateral root length depending on the insertion position from the primary root base. These data were computed by RootNav. The dashed line represents the moving average across the data set.
CONCLUSION The RSML presented here facilitates the sharing of root architectures between software, experiments, and research groups. RSML accommodates a wide array of root architecture complexity (ranging from 2D projections of single roots to 3D representations of complete root systems) at varying levels of detail. The RSML format stores root topology (parent-child relationships), morphological properties (positions in space and time, length), and virtually any type of additional information used to describe root segments (e. g. diameter, color, and age) separately, linking them to form a coherent representation. The RSML format is currently implemented within five root image analysis software (RhizoScan, RootNav, RooTrak, RootSystemAnalyser, and SmartRoot), three functional-structural root models (RootBox, ArchiSimple, and R-SWMS), and is based on the MTG format used in the OpenAlea platform.
Five open-source packages were developed for the analysis and visualization of RSML data files (in C#, R, Excel, Java, and Python). We believe that the availability of RSML will encourage the creation of common analysis pipelines for root architecture information, enabling better data sharing between root researchers, and will facilitate the creation of a shared database of root architecture information. A complete description of the RSML, along with examples and application programming interface packages, are available at http://rootsystemml. github. io.
The analyzer was operated in constant pass energy of 40 eV using an analysis area of approximately 700 μm × 300 μm. Charge compensation was applied to minimize charging effects occurring during the analysis. The adventitious C 1s (285. 0 eV) binding energy (BE) was used as internal reference. Pressure was in the 10 -10 mbar range during the experiments. Quantification and simulation of the experimental photopeaks were carried out using CasaXPS and XPSPEAK41 software. Quantification is performed using nonlinear Shirley background subtraction. XPS spectra obtained from the orthorhombic phase are presented in the Supporting Information, Figures ESI. 14-ESI. 19. The XPS and LEIS instruments along with the atomic oxygen source are connected by a radial chamber at a pressure of 3 × 10 -9 mbar, which allowed the transfer of the samples from one instrument to the other without exposure to air.
When the IMFP values obtained from the database provided by NIST  32, 33  for La 4s and C 1s of 2. 9 nm are used, the calculated thickness after annealing is estimated to be 0. 53 nmroughly two monolayers of carbonate. In this case the experimental C 1s (carbonate)/La 4s intensities obtained after 10 and 20 min of exposure to atomic oxygen are also reproduced by the model when ∼50 and ∼20% of the surface is covered with carbonate. The differences arising from the two initial assumptions used in the model result mainly from the surface roughness of the sample and the actual atomic relative sensitivities of carbon compared to the value used due to the complexity of the carbon-oxide interface which includes C-Mn, C-La, and C-O bonds. However, in both cases the models predict ∼50 and ∼20% of the surface to be free after the application of oxygen when we assume that annealing results in a single atomic layer of carbonate on the surface.
This Frontiers Research topic on the promiscuous functions of the prion protein family incorporates contributions ranging from the field of developmental biology to that of structure-function, including aspects related to cell biology, signal transduction, and neuronal homeostasis. Starting from the embryo, the contribution by Halliez et al. provides a comprehensive review of the impact of PrP invalidation on embryonic development, compiling data from both mice and zebrafish and highlighting the key cellular pathways affected by PrP C deletion  (Halliez et al. , 2014). The review by Makzhami and colleagues is centered on the tissue with the second highest PrP C expression after the brain, i. e. , the placenta  (Makzhami et al. , 2014). It summarizes the recent data obtained with the help of PrP invalidated mice and discusses the pathophysiological implications stemming from the aberrant PrP C expression in human gestational diseases.
ACKNOWLEDGMENTS Stefanie A. G. Black  is supported by a  Postdoctoral Fellowship  from the  Multiple Sclerosis Society of Canada (MSSOC). Peter K. Stys  is supported by an  Alberta Innovates-Health Solutions  ( AI-HS) Scientist Award ; work in the lab of  Peter K. Stys  is supported by the  Canadian Institutes of Health Research (CIHR) ,  MSSOC , the  Alberta Prion Research Institute (APRI) ,  Canada Research Chairs. Gerald W. Zamponi  is a Canada Research Chair and an AI-HS Scientist; work in the  Gerald W. Zamponi lab  is supported by funds from  APRI  and  CIHR. Work in the lab of  Shigeki Tsutsui  is supported by  APRI/Alzheimer Society of Alberta and Northwest Territories (ASANT).
s. l). This monitoring program was designed to characterize and determine the thermal state of the permafrost and active layer, and to collect temperature data under variable snow-cover and structural conditions that could be used to calibrate and validate high-resolution numerical experiments on permafrost thermal processes. In this paper we describe the monitoring programme at the AdM, and present temperature data from nine surface miniloggers and three 10 m deep boreholes. Due to the morphology of the AdM, the monitoring network is concentrated in a very small area; however, the data obtained allowed us to address the following questions: -How much of the surface temperature variability over this small area is due to topography and snow cover? -How much of the variability in the active layer is due to the topography of the steep rock walls? -What are the thermal effects of snow and fractures on sub-surface temperatures at the AdM? We used 8 years of surface records and 4 years of borehole to analyse seasonal and annual variations in temperature patterns, in the active layer, and in the permafrost thermal regime.
g. electricity) at the summit station. Monitoring equipment was installed as part of the  PERMAdataROC (2006 PERMAdataROC ( -2008) )  and  PermaNET (2008 PermaNET ( -2011) )  projects, funded by the European Union and run jointly by EDYTEM Lab (France), ARPA VdA (Italy), and the Universities of Zurich (Switzerland), Bonn and Munich (Germany). As such, it complements other rock wall observation sites -for example, those within the Swiss Permafrost Monitoring Network (PERMOS). Data from the monitoring equipment on the AdM were completed by data from ARPA VdA's weather stations, which measured air temperature and relative humidity, incoming and outgoing shortwave and longwave solar radiation, wind speed, and wind direction on the south and north faces between 2006 and 2010. Electrical Resistivity Tomography (ERT) and Induced Polarization (IP) have been measured since 2008 in conjunction with the universities of Bonn and Munich.
High-resolution (cm scale) triangulated irregular networks (TIN) of rock walls and galleries of the AdM were obtained from terrestrial laser scanning. In July 2012, six crack-meters equipped with wireless sensors were installed in major fractures in the Piton Central and Piton Nord in order to complement existing studies of cleft dilatations and shearing movements in rock wall permafrost, to check the stability of the AdM and to test an early warning system. Finally, two GPR surveys were performed along vertical transects in 2013 and 2014. Not all of these data were used in the present study but they will contribute to future research.
Data set preparation The borehole time series were all continuous except for short periods for BH_S, as this logger was removed from September 2012 to January 2013 and from October 2013 to January 2014 to prevent it being damaged by engineering work close to the borehole. Gaps in the 0. 3 m temperature and AT time series were filled in so we could calculate seasonal and annual means (see Table  2 ). First, we calculated daily means from rock temperature time series for days with complete records. Then, we filled short gaps (< 5 days) by linear interpolation between the nearest available data points for the same depth. Longer gaps (up to 1. 5 month) were filled by replacing missing data with the average value for the 30 days before and 30 days after the gap (see  Hasler et al. , 2011a). To fill the longest gaps for E1, N1, S1, and W1 (from 4 December 2007 to 7 February 2008) we used a third approach that involved applying a linear regression equation, fitted using data from each pair of loggers (e.
, 2004a). However, our data did not conform to this prediction, as the change in ALT at BH_S was similar to the ALTs at the shadier BH_E and BH_N. Furthermore, BH_S experienced the smallest interannual changes at 10 m depth, and the shape of its T (z) profiles between 2010 and 2011 did not follow the trend of the MAAT signal at depths between 6 and 10 m. This may be due to the consumption of latent heat. In fact, previous studies have attributed the delaying and dampening effect of latent heat consumption to the thermal response of bedrock permafrost  (Kukkonen and  www. the-cryosphere. net/9/109/2015/ The Cryosphere, 9, 109-121, 2015 Safanda  , 2001; Wegmann et al. , 1998; Noetzli et al. , 2007). Field observations during drilling revealed the presence of wet-detritic materials in the fractures in BH_S, suggesting that latent heat may be consumed by phase changes between interstitial water and ice.
Acknowledgements. We would like to thank  S. Gruber ,  U. Morra di Cella ,  E. Cremonese  and  E. Malet , for their help with equipment installation and data acquisition at the  Aiguille du Midi. The  Chamonix Compagnie des Guides  provided invaluable assistance with the drilling operations. We would also like to thank the  Compagnie du Mont Blanc (especially E. Desvaux)  for allowing access to the site, and  Météo France  for providing air temperature data. We also thank  A. Hasler  and an anonymous reviewer for their useful comments and recommendations. The English text was corrected by  P. Henderson. This work was supported by the  Region Rhône-Alpes  ( CIBLE programme ). Edited by:  T. Zhang.
C. argentoratense strain CNM 463/05 was obtained in 2005 from a blood culture of a 3-year-old boy with upper respiratory tract infection, and strain CNM 601/08 was obtained in 2008 from a blood culture of an 85-year-old female with ischemic colitis. Both C. argentoratense isolates were routinely grown at 37°C on blood agar. Genomic DNA was purified by using the ChargeSwitch gDNA mini bacteria kit (Invitrogen). Genome data were obtained as previously described (11) using an Ion Torrent PGM platform. The reads were collected by the Torrent Suite software version 4. 0. The MIRA program version 3. 4. 0 (http://www. chevreux. org/projects_mira. html) was used for de novo assembly of the two genomes. Both genome sequences were annotated using the RAST genome annotation server  (12). Both C. argentoratense isolates showed similar genome sizes (approximately 2.
02 Mbp) and similar numbers of proteincoding regions (approximately 1,900), with a slightly higher num-ber (1. 3%) in the genome of CNM 463/05. The draft genome sequences of both isolates revealed a high grade of similarity between them (Ͼ99. 9%), as well as with the genome sequence of the type strain C. argentoratense DSM 44202 (Ͼ95. 0%). BLAST was used for the search for antibiotic resistance genes in the Antibiotic Resistance Genes Database  (13)  and in published genome information of Corynebacterium strains. The antibiotic resistance gene erm(X) coding for macrolide-lincosamide-streptogramin B resistance was detected in the genome of both isolates and was allocated to a specific genomic region with 100% similarity to the composite transposable element Tn5432, initially found on the R-plasmid pTP10 of Corynebacterium striatum M82B  (14, 15).
In contrast little is know on the link between hyperoxidation and HMW structures formation, which appears as a basic requirement for the chaperone function, and the few available data are very often controversial. The sulfenic acid then reacts with the resolving Cys (C R ) residue of the other subunit to form an intermolecular disulfide  [48]. This disulfide is then reduced by thioredoxin, which completes the catalytic cycle. Alternatively, when H2O2 levels raises, the C P -SOH can further react with H 2 O 2 , which leads to formation of a C P -sulfinic acid (CP-SO 2 H). The latter is reversed back to C P -SOH by ATP-dependent reduction by sulfiredoxin (Srx). To begin addressing the link between enzyme sulfinylation and HMW structures formation, we have tested whether the in vivo quaternary structure of 2-Cys Prxs could be evaluated by size exclusion chromatography on crude lysates.
Acknowledgement We are indebted to  Dr. Sue Goo Rhee ,  Sang Yeol Lee ,  Ho Hee Jang  and  Ho Zoon Chae  for the gifts of anti-Tsa1 and anti-SO 2/3 antibodies. This work was funded by grant from  ANR ERRed and InCA   PLBIO INCA_5869  to MBT, and supported by  COST Action BM1203 (EU-ROS ).
Collins and colleagues  [170]  highlighted that mismatch between species names applied to the specimens transiting in the international ornamental trade and taxonomic assignment based on DNA barcodes are due to either taxonomic uncertainty and/or conflict due to misidentifications. The authors hence caution the use of GenBank for identification purposes due to the potential absence of preserved voucher specimens and justified identifications and note that while BOLD data are generally better curated and with higher quality standards, they are also likely to suffer from misidentification to some degree. This case highlights the difficulties of establishing DNA barcode reference libraries when the taxonomic knowledge is rapidly evolving as exemplified with the Indonesian ichthyofauna. The freshwaters of Sulawesi are, due to the island's location east of Wallace's line, devoid of those freshwater fish lineages making up the vast species diversity of the islands formerly connected to Sundaland  [10].
They focused on cyprinids and included several popular aquarium fishes that are regularly exported from Indonesia, mostly Sumatra and Kalimantan. A total of 678 specimens, representing 45 genera and 172 cyprinid species were obtained by the authors from the aquarium trade. In addition, 562 barcode sequences from 238 species were obtained from reference libraries (GenBank/BOLD) increasing the total number of ornamental cyprinid species included in the study to 329. Many morphological similar species were well differentiated with DNA barcodes and identification success rates were generally high. The authors also observed, however, incongruence and inconsistencies in the DNA barcode data. For example, barcode sharing was observed in several groups, including taxa from Indonesia: between two Eirmotus species (E.
To further improve the quality of DNA barcode data, the BARCODE data standard as been implemented in GenBank for the records that are compliant with the following requirements: 1. Bi-directional sequences of at least 500 base-pairs from the approved barcode region of COI, containing no ambiguous sites 2. Links to electropherogram trace files available in the NCBI Trace Archive 3. Sequences for the forward and reverse PCR amplification primers 4. Species names that refer to documented names in a taxonomic publication or other documentation of the species concept used to increase the number of species descriptions based on such iterative procedures.
Here, authors defined a mini-barcode for the species-specific detection of Danio rerio with the use of a sliding window function from the DNA barcoding package Spider  [200]. In addition, short-length DNA barcodes have the advantage of better fitting the sequence length of most of the next-generation sequencing (NGS) platforms. NGS is indeed increasingly used to analyze the entire species composition either from pools of entire organisms or from environmental samples. This high-throughput multispecies identification approach was recently designated under the term "DNA metabarcoding"  [201]. Proofs of concept of this so-called DNA metabarcoding have been successfully achieved and have shown its overlaps that of sister taxa in nature, which can lead to incorrect identifications or species delineations  [22] , (2) DNA barcodes are effective whatever the life stages under scrutiny  [24, 184].
DNA barcoding has the potential to help increase rapidly this knowledge and to help promote more sustainable practices in taxonomy through the linkage between traditional and molecular taxonomy with online data systems and the development of new molecular tools for species identification. The main challenge at the moment is the development of comprehensive DNA barcodes reference libraries for the Indonesian ichthyofauna. Given the complex systematic and taxonomy of many freshwater fish lineages at the moment, this review and its associated database in Appendix is expected to help streamlining future campaigns of DNA barcoding in the country. great potential for deciphering the species richness and composition from a wide variety of samples  [191] [192] [193] 198, 202]. Addressing the potential of environmental DNA for monitoring rare and threatened freshwater species, Thomsen and colleagues  [203]  demonstrated that the diversity, and even the abundance, of such species could be monitored from DNA recovered from water samples of ponds, lakes and streams.
One of the rare studies focusing on this aspect highlighted the necessity to run replicates in order to reduce the risk of misestimating species diversity, particularly in regard to rare taxa  [199]. Finally, the accuracy of the DNA-based identifications is tightly dependent on the coverage of the DNA barcode reference libraries used to assign the sequences generated through NGS to known taxa [e. g. 17, 21, 28, 189, [205] [206] [207] [208] [209]. Whatever the type of sample used, the taxonomic identification of species relies on the ability to match sequences with the DNA barcodes reference librairies. While mini-barcodes are compatible with DNA barcodes data standard (i. e. voucher specimens deposited in formal collections, accessibility to collection metadata) and match the standardized DNA barcode system  [181, 182, 210] , yet another major limitation for the implementation of DNA metabarcoding in the management of the Indonesian ichthyodiversity is the necessity to expand the current coverage of those libraries for freshwater fishes beyond those currently available.
Acknowledgements: The authors wish to thank  Dr. Siti Nuramaliati Prijono ,  Dr. Tjak Witjaksono ,  Mohammad Irham ,  Dr. Marlina Adriyani ,  Dr. Rosichon Ubaidillah , at  Research Centre for Biology (RCB-LIPI ),  Dr. Jean-Paul Toutain ,  Dr. Jean-François Agnčse  and  Dr. Domenico Caruso  from the  'Institut de Recherche pour le Développement ', and  Dr. Bambang Suryobroto  at the  Bogor Agronomy University  for their support. We are thankful to  Dr. Daisy Wowor  at  RCB-LIPI, Sumanta and Bambang Dwisusilo at IRD Jakarta  for their help. The authors thank the anonymous referees for their helpful comments. This publication has ISEM number 2015-180 SUD.