dataesr/scientific-paragraphs-categorization huggingface dataset:
Scenario Databases The first initiatives to constitute databases of socio-economic and emission scenarios date back to the 90s, but the practice gained prominence in the late 2000s. Here again, the development of standardised, publicly available scenario databases can be traced to the AR5 process. A first database was elaborated to gather the RCPs and make them available to their users. A second IPCC-related database followed, to collect scenarios as part of the preparation of the report of WG III, which planned to use them to map "the solution space"  (Edenhofer, 2014). In 2012, WG III issued an open call for scenarios: IAM teams were invited to submit socioeconomic emission scenarios for consideration by WG III. To be included in the database, scenarios had to meet a series of criteria: being peer reviewed, providing a minimum set of mandatory variables, scenario documentation, or coming from "formal energy-economic or integrated assessment models" with a large coverage of energy sectors  (IAMC, 2012).
The data template (an excel file) gathered general instructions, the description of the scenarios, a model classification and data breakdown by models/regions/variables every ten years by 2100. These two databases are hosted on IIASA servers. IIASA has devoted human resources to the maintenance and operation of the databases in coordination with the IAMC (Interview 12a, Guivarch 2016, personal communication). A web-based infrastructure was built to enable modellers to upload their results and to allow outside users to access the data. It includes detailed information about the purpose of the database, the regions and sectors covered, the list of MIPs that contribute to the database, etc. (e. g. IPCC, 2014b) With such infrastructure available, most MIPs now gather scenarios in similar databases.
These are built according to similar templates and usually hosted on the same IIASA server, though not all of them are public. The evolution towards more standardised data management indicates an increasing professionalization of IAM-based scenario production, with a move from spreadsheets to big databases. While we previously, fifteen years ago, would run 3-4 scenarios and submit them via an Excel spreadsheet, and somebody would make -at hand -a PowerPoint presentation out of it, now we have these tools where we submit to a database, maybe 20 scenarios from each team, people have R scripts where they are able to pick up directly all kinds of analyses from these databases… So, we have become much more professional. (Interview 7) Databases shape IAM research in several ways. First, they are tools for scientific research: they serve to organise collaboration, allow for rapid checking of errors in reported data, and have become "standards to read data" that modellers "use for themselves" as "a way to learn the model" (Interview 13).
Second, they pool and order scenario data, making it available in usable forms. Some databases are public, anyone can access the data and work with it: modellers consider they "make a huge service to other scientific communities" by creating and maintaining them (Interview 10). Third, the increased reliance on standardised database encourages a degree of convergence in modelling approaches. Last, these databases pool together scenarios from a set of diverse models and organise them according to standardised templates, making them easily available. However, they do not stand-alone: to work with them meaningfully, one must have a sense of how scenarios were produced, to answer which questions, and by which models. This is mostly transmitted informally, via discussions and mutual understanding fostered by regular interactions (Interview 5).
Effects of the repertoire: professionalization and convergence The IAMC, MIPs and scenario database all emerged during the period of preparation of the IPCC, largely as tools to organise the contribution of IAM research to the AR5. They have perpetuated and they play a crucial role in the current configuration of IAM research, shaping day-to-day work within research groups, collective organisation, and communication with external audiences. Modellers argue that the field has become "more professional" owing to the consolidation of this repertoire (Interview 7). Interactions among teams are more sustained and institutionalised, leading to better cross-knowledge of the strengths and weaknesses of models and to less heated debates about basic modelling approaches (Interview 4, 7). The repertoire seems to allow for the articulation of common purposes.
In particular, it has enabled a coordinated reflexion on model evaluation to eventually take place  (Schwanitz, 2013 , Wilson et al. , 2017) , mostly within MIPs but also via the IAMC and its scientific working groups. This comes with added visibility -and scrutiny -for IAMs and their results, especially since some scenario databases are publically available. All the same, the consolidation of a repertoire for IAM research generates its own challenges and constraints. As  Leonelli and Ankeny (2015: 706)  noted: of convergence and "group thinking" (Interview 7) that some critics consider as insularity (Field notes 2015a, Interview 6). One widely acknowledged issue is that this organisation of research favours the investigation of common questions, the reproduction of scenarios, hence the development of similar features across models, to the expense of the improvement of models and the exploration of their core specificities (Interview 5, 13).
As for the EU, it funded several large IAM projects to inform and support its climate policy and to feed into the IPCC process; these enabled IAM research groups to capitalise on existing collective arrangements like the EMF, and to develop new methods and tools for cooperation, thereby equipping the definition of IAMs as a category of models. Last, we analysed three elements of the repertoire that emerged during this period of intense collaboration: the IAMC, Model Intercomparison Projects, and scenario databases. These are now central to the way integrated assessment modellers do research. They frame epistemic practices and demarcate the IAM community. This repertoire organises harmonisation and professionalization as well as increased interpersonal and informal exchanges. We showed how it seeks to articulate the technicity and diversity of IAMs, the ambition to combine the variety of perspectives they offer, and the need for transparency heightened by their ambition to inform policy.
All the same, and however difficult it is to maintain, the demarcation comes with constraints that partly shaped the repertoire of the IAM community. It led to the creation of an intermediary institution, the IAMC, to coordinate the preparation of RCPs. The peer-review criteria imposed a deadline for the publication of project results. Last, the choice by WG III to assess "the full breadth of baseline and mitigation scenarios in the literature"  (Edenhofer et al. , 2014:51)  spurred the creation of a scenario database, a practice which has now become a standard of multi-teams IAM projects. The joint construction of the IAM community and of the applications for IAM research also appears through the influence of the EU. Since the mid-2000s, most of the funding for European IAM teams came from MIPs funded by the DG Research Framework Programmes (FP6 and FP7).
These projects stimulated interactions among teams and heightened the need for common databases and protocols. The need for comparability and the expectations from the EU inevitably influenced IAM research priorities. By describing this process, we have shown how the IAM community worked its way to its current position in the academic landscape and with respect to climate change discussions. This position, we suggest, rests upon the articulation of epistemic practices with the pursuit of policy relevance. Emphasising this articulation as constitutive of certain scientific communities can inform a dynamic conception of epistemic communities as scientific communities that manage the balance and tensions between epistemic practices and policy relevance. In the case of IAMs, the vocation for policy-relevance does not necessarily curtail scientific dynamism.
, 2010; Moss et al. , 2010; van Vuuren et al. , 2012). vi New emissions scenarios for the IPCC process were discussed in workshops in Washington (January viii As is the case for the IPCC more broadly, IAM research mostly takes place in developed countries. While there are IAM teams and WG III authors from developing countries, they usually have strong links with institutions based in developed countries (e. g. having spent time there or using models based on those of developed countries teams)  (Corbera et al. , 2015; Vardy et al. , 2017)  ix However, those in charge of a specific Scientific Working Groups are often in charge of the same issue within projects. For instance, one of the co-chairs of the "data protocol and management working group" oversees the database infrastructure at IIASA; and two of the co-chairs of the "scenario working group" are representatives of the IAM Community in the "Scenario-MIP project".
The adoption of a repertoire unavoidably creates strong commitments to particular techniques, assumptions, values, institutions, funding sources, and methods, which although initially productive, can sometimes act as constraints to future integration and innovation. MIPs contributed to a proliferation of scenarios, to the extent that "[we might] reach a point where no two papers will use the same reference scenarios" (Field notes 2015b). More crucially, the shared protocols of intercomparison and the standardisation required for inclusion in databases lead to a form.
Isolation and growth conditions In 2017, as part of a study of the vaginal flora microbiome, the strain Marseille-P5643T was isolated from a swab sample from a woman living in Dielmo, a Senegalese village (West Africa). An attempt to identify this bacterium using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) did not provide a result. The identification process was performed on a Microflex LT spectrometer (Bruker, Daltonics, Bremen, Germany) as previously described  [15]. Spectra obtained were imported and analysed using the BIOTYPER 3. 0 software against the Bruker database, permanently improved with the local MEPHI database (Fig. 1 ). The vaginal swab was placed directly in liquid medium enriched with sheep's blood and rumen. Initial growth of bacterial cells was obtained after 15 days of pre-incubation in an anaerobic environment.
Strain identification To identify strain Marseille-P5643 T , the 16S rRNA gene was amplified using the primer pair fD1 and rP2 (Eurogentec, Angers, France) and sequenced using the Big Dye® Terminator v1. 1 Cycle Sequencing Kit and 3500xLGenetic Analyzer capillary sequencer (Thermofisher, Saint-Aubin, France), as previously reported  [16]. The 16S rRNA nucleotide sequences were assembled and corrected using CODONCODE ALIGNER software (http://www. codoncode. com). The 16S rRNA (accession number LT971014) gene sequence analyses showed 93. 7% similarity with Facklamia hominis strain ATCC 700628, confirming the status of strain Marseille-P5643 T as a new bacterium  [17, 18]. We accordingly proposed to classify Vaginisenegalia massiliensis as a new genus within the family Aerococcaceae belonging to the phylum Firmicutes (Fig.
Genome sequencing Using EZ1 biorobot with the EZ1 DNA tissue kit (Qiagen, Hilden, Germany), the genomic DNA of strain Marseille-P5643 T was extracted and then sequenced on a MiSeq sequencer (Illumina Inc, San Diego, CA, USA) with the Nextera  Mate Pair sample prep kit and Nextera XT Paired End (Illumina), following a previously described protocol  [19]. Genome assembly was carried out using a pipeline containing various softwares (VELVET  [20] , SPADES  [21] , and SOAP DENOVO  [22] ), and trimmed (MISEQ and TRIMMOMATIC  [23]  softwares) or untrimmed (only MISEQ software) data. GAPCLOSER was used to decrease assembly gaps. Scaffolds with a base pair number <800 bp and those with a depth value <25% at mean depth have been removed. Therefore, the best assembly was chosen by using different criteria (number of scaffolds, N50, number of N).
The genome size of Vaginisenegalia massiliensis strain Marseille-P5643 T is 1 754 973 bp with 39. 0 mol% G+C content. The GenBank accession number for the 16S rRNA gene sequence of strain Marseille-P5643 T is LT971014 and for the whole genome shotgun project is UWPC00000000. It was isolated from the vagina of a Senegalese woman living in a rural area.
SERS Measurements SERS measurements were carried out using a microRaman spectrometer (Xplora, Horiba) working at 532 nm or 785 nm laser wavelengths with a 1200 grooves/mm grating. The backscattered light was collected by a 10 × objective with 0. 25 NA, which generates a 7-μm large laser beam waist and provides an average SERS response, minimizing possible signal variability. Laser power values at the sample of 115 μW at 532 nm and 598 μW at 785 nm and an integration time of 10 s with two accumulations were used. SERS data are baseline corrected and represent an average of a minimum of 10 spectra collected by mapping experiments over.
Acknowledgements M. B. , C. D'A. , M. deA. , R. P. and P. M. acknowledge support from the  European Community  and the  Ministry of Education, University and Research of Italy (MIUR)  through the  ERANET EuroNanoMed III "Surface-enhanced Raman scattering with nanophotonic and biomedical amplifying systems for an early diagnosis of Alzheimer's disease pathology "  SPEEDY  project ( ID 221 ) and from the  Ministry of Foreign Affairs and International Cooperation of Italy (MAECI)  through the "Development of a cost-effective wearable metal nanowire-based chip sensor for optical monitoring of metabilites in sweat"  DESWEAT  project (n°KR19GR08) funded within the  frame of the Executive Programme of Scientific and Technological Cooperation between the Italian Republic  and the Korean Republic  2019-2021.
The construction of the grid and the calculation and extraction of the ecological variables were done in the R software (R Development Core Team, 2011) and in QGIS (Quantum GIS Development Team, 2013). Variable selection was done using a LASSO regularization path (Appendix 1). A model fitted with a LASSO penalty can shrink some parameter estimates to be exactly zero, effectively reducing the number of corresponding explanatory variables in the model. We fitted an entire regularization path of models with increasing penalties and chose the model which minimized BIC. We first assessed the effect of each covariate on the intensity of brown bears per square kilometre as estimated in the PPM. To visualise these effects, we produced scatterplots of the predicted intensities vs. standardised covariates, and then fitted a smoothed generalized additive model to produce a response curve.
Comparison of habitat suitability predictions with bear records and protected area distribution in Greece The Natura 2000 (N2K) network is a European network of protected areas for birds and habitats (http://ec. europa. eu/environment/nature/natura2000/db_gis/index_en. htm). Some of the sites in the N2K network (33 out of 419) comprise a dedicated network for the protection of bears in Greece [as reported in their Standard Data Forms (SDFs)]. To compare our habitat suitability predictions with the presence of bears and the distribution of protected areas in Greece, we mapped all the N2K sites in Greece (http://www. ekby. gr/ekby/en/Natura2000_main_en. html; last updated in 2012), identified the sites included in the dedicated network for the protection of bears in Greece and those which were not.
Discussion Understanding the processes associated with population recoveries and identifying areas that are suitable for recolonization by endangered species is essential to support effective conservation policies  (Cianfrani et al. , 2010). We used data from a citizen science project and habitat suitability modelling to understand the spatial aspects associated with the demographic and genetic recovery of an endangered brown bear population at the southern edge of its European distribution and to identify priority areas for conservation. Brown bear presence during the demographic and genetic recovery of the species in Greece was recorded in both the northeastern and northwestern nuclei of the species in the country. However, a significant percentage of the bear records of the study fell outside of the past distribution of the species in Greece, confirming previous circumstantial evidence  (Karamanlidis et al.
Overall, despite the fact that it was not possible to formally validate our correction for observer bias, studies that have had access to good validation datasets have already demonstrated the added value of correcting for observer bias using the approach we used here (e. g. Warton et al. , 2013). This is supported in our study also by the findings presented in Fig. 4  (i. e. comparison between our predictions and N2K sites with known bear presence), which indicate that most sites with known presence of bears are predicted as containing highly suitable habitat. Apart from being generally applicable to species that are rare and sampled by citizen science and for which there are only presence-only data, our use of  Warton et al. 's method (2013) , is of important, practical relevance for (endangered) species conservation in general and brown bear conservation in Greece in particular.
Our approach will help prioritize conservation actions in the country towards the areas that need it the most and serve as a model approach to other countries facing similar financial and logistic constraints in the monitoring of local biodiversity or facing similar challenges in managing the rapid recovery of a large carnivore. Acknowledging the previous, we propose the intensification of efforts in Greece to further develop the Hellenic Brown Bear Rescue and Information Network, by carrying out targeted awareness campaigns to the general public and selected stakeholders (e. g. Forestry and Veterinary Departments, Management Authorities of Protected areas) that will increase data input and ultimately the quality of the habitat suitability maps produced using this method. At the same time, it is clear that in the case of the brown bear the current setup of the protected areas network in Greece does not reflect the current conservation reality and that there is a clear need to reevaluate the existing network of protected areas in Greece so that it effectively supports the recovery of the species in the country.
On average, the eccentricity was 4°. position corresponding to the patients' PRL/non-PRL and to be sure that fixation was maintained. Calibration and recording procedures were as follows. Eye movements were recorded using a Mirametrix S2 eye tracker with  a sample rate of 60 Hz and an accuracy of 0. 5°. The calibration of the tracker and the gaze check were integrated into the main Matlab script using the Mirametrix Matlab Toolbox and API for Windows. Thanks to a custom calibration software, the calibration dot that normally sighted observers follow with the fovea was shifted by a constant so that, although MD patients could follow it with their PRL, the position of the eye relative to the calibration dot corresponded to that of a normally sighted observer. Due to the instability of fixation and the systematic error of the tracker, a tolerance window of ±1.
Apparatus and stimuli. Participants sat in a dark room 57 cm from the screen. Stimuli were displayed on an ASUS ML228H LCD LED 21. 5-inch monitor with a refresh rate of 60 Hz and a spatial resolution of 1920 × 1080 pixels, with a pixel pitch of 0. 248 mm. Stimuli were generated with Matlab Psychtoolbox  53, 54. Gamma correction for each color channel was applied through calibration with the Spyder 4 Elite colorimeter (DataColor). The calibration was further verified using a Minolta LS-100 photometer, which indicated that the mean luminance was 50 cd/m2. In that way, luminance was a linear function of the digital representation of the image. In order to represent 10. 7 bits of luminance (1786 gray levels) on an 8-bit display, we adopted a software solution called "Pseudo-Gray, " also known as "Bit-Stealing"  55  , implemented via a Psychtoolbox built-in function.
e. , 2λ, 3λ, 4λ, and 8λ). The patients were asked to maintain their gaze on the PRL, and stimuli were randomly presented over either the PRL or non-PRL position within a block. Controls had to fixate the center of the screen, and stimuli were randomly presented either left or right of fixation. Visual acuity and crowding stimuli. Visual acuity (eccentric VA) and crowding were measured at the same eccentricity as for the Gabor configuration. Stimuli were generated using Matlab Psychtoolbox  53, 54  and presented at 57 cm. The stimuli were 10 letters (D, N, S, C, K, R, Z, H, O, and V) with Sloan 57 character type, randomly presented for 133 ms. The target letter was presented randomly at the two eccentricities in the same block, either the PRL/non-PRL for MD patients or 4° left/right from fixation for controls.
Statistical analysis. Within-and between-group comparisons were carried out with ANOVAs on either contrast threshold or TE using, for pairwise comparisons, t-tests with Bonferroni correction. TE was also analyzed using one-sample, one-tail t-tests based on the hypothesis of TE as either >0 or <0 for suppressive and facilitatory effects, respectively. Visual acuity and crowding data were also analyzed with Tukey tests.
52 (correlation between raw and estimated data). Finally, we superimposed raw data and fit line over the model predictions from Zenger and Sagi (1996) at 0λ and 2λ. As the Fig. 7  shows, the regression line derived form our dataset approximate very vell the one predicted by the model, in particular the line that refers to the 0 λ, as expected by the fact that increasing eccentricity would shift the curve leftwards. Thus, the transition from inhibition to facilitation that most MD patients show at high contrast threshold suggests improved efficiency in integrating/grouping elements, possibly mediated by an integration between the flanker and target within the 2 nd order integrative field  31. Our results do not support the hypothesis that MD present cortical reorganization leading to a use-dependent increase of long-range connectivity.
ABSTRACT We analyze 7. 3 years of ANTARES high-energy neutrino and Fermi LAT γ-ray data in search of cosmic neutrino + γ-ray (ν+γ) transient sources or source populations. Our analysis has the potential to detect either individual ν+γ transient sources (durations δt ∼ < 1000 s), if they exhibit sufficient γ-ray or neutrino multiplicity, or a statistical excess of ν+γ transients of individually lower multiplicities. Individual high γ-ray-multiplicity events could be produced, for example, by a single ANTARES neutrino in coincidence with a LAT-detected γ-ray burst. Treating ANTARES track and cascade event types separately, we establish detection thresholds by Monte Carlo scrambling of the neutrino data, and determine our analysis sensitivity by signal injection against these scrambled datasets.
2005). Chief scientific results from ANTARES include searches for neutrino sources using track-and cascadelike events in data collected between  2007 and 2015 (Albert et al. 2017b)) ; dedicated studies along the Galactic Plane  (Albert et al. 2017c) , also in collaboration with the IceCube telescope  (Albert et al. 2018a) ; searches for an excess of high-energy cosmic neutrinos over the background of atmospheric events  (Albert et al. 2018b). No cosmic neutrinos have been positively identified in the ANTARES data. Despite this, by integrating the cosmic neutrino spectrum from IceCube Collaboration et al. (  2017 ) over the ANTARES effective area  (Albert et al. 2017b ), we estimate an expected 6. 8 neutrinos of cosmic origin are detected each year, though all but the most energetic will be indistinguishable from the atmospheric background.