dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS The authors would like to thank  Jan Hrbacek  ( Paul Scherrer Institute, Villigen, Switzerland ) for fruitful discussions,  Johannes Schmidt  ( Varian Medical Systems, Inc. , Palo Alto ) for supplying needed information and  Kees Spruijt  ( Hol-landPTC, Delft, The Netherlands ) for providing beam commissioning preliminary data. Petra Trnkov a currently works at the  Department of Radiation Oncology at Medical University of Vienna. This research was co-founded by the research program  PROTONS4Vision  (Grant  NWO 14654 ), which is financed by the  Netherlands Organization for Scientific Research (NWO) ,  Technology Foundation STW , the  Top consortium for Knowledge & Innovation (TKI-HTSM)  and  Varian Medical Systems, Inc. ,  Palo Alto.
Climate and ice sheet models iLOVECLIM (here in version 1. 1) is a code fork of the LOVECLIM 1. 2 model  (Goosse et al. , 2010). The core of the model is a combination of a quasi-geostrophic atmospheric model solved on a T21 (∼ 5. 6 • × 5. 6 • ) spectral grid (EC-Bilt,  Haarsma et al. , 1997; Opsteegh et al. , 1998) ; a free surface oceanic general circulation model on a 3 • × 3 • spherical grid which includes a thermodynamic sea ice model (CLIO,  Goosse and Fichefet, 1999) ; and a dynamic vegetation and carbon allocation model  (VECODE, Brovkin et al. , 1997). iLOVECLIM has been extensively used to study millennial climate change during the Quaternary. For example, it has proven able to reproduce the glacial-interglacial variability of the hydrological cycle in the tropics  (Caley et al. , 2014).
Acknowledgements. We would like to thank the two referees,  Evan Gowan  and  Javier Blasco , for their insightful comments. Catherine Ritz  is warmly thanked for her dedication to the GRISLI ice sheet model. We acknowledge the  Institut Pierre Simon Laplace  for hosting the iLOVECLIM model code under the LUDUS framework project (https://forge. ipsl. jussieu. fr/ludus, last access: 8 October 2021). Financial support. The research leading to these results has received funding from the  SCOR foundation  project  COASTRISK.
The fact that the tank located in a very dark place enables the tests under an optically controlled environment. Using the Mini-EUSO data taken since 2019 onboard the ISS, we will report on the comparison between TurLab and ISS measurements in view of future experiments at TurLab. Moreover, in the forthcoming months we will start testing the trigger logic of the EUSO-SPB2 mission. We report also on the plans and status for this purpose.
By means of the rotating tank with the capabilities mentioned above, we have been testing the EUSO electronics such as its basic performance and the first level trigger (L1) for cosmic-rays, in view of various and even changing background conditions as well as atmospheric phenomena such as meteors and lightning that EUSO telescopes will observe. Mini-EUSO  [3]  is a scientific mission within the JEM-EUSO program  [4]. The telescope has been launched in August 2019 and currently in operation onboard the ISS. The main goal of Mini-EUSO is to measure the UV emissions from the ground and atmosphere, using an orbital platform. These observations will provide interesting data for the scientific study of a variety of UV phenomena such as transient luminous events (TLEs)  [7] , space debris  [8] , meteors and hypothetical strange quark matter (SQM)  [9]  and bioluminescence  [5].
PoS(ICRC2021)318 for EECR detection. Mini-EUSO observes the atmosphere from a nadir-facing window inside the Zvezda module of the ISS. It is based on one EUSO detection unit, referred to as the Photo Detector Module (PDM). The PDM consists of 36 multi-anode photomultiplier tubes (MAPMTs), each one having 64 pixels, for a total of 2304 pixels. The MAPMTs are provided by Hamamatsu Photonics, model R11265-M64, and are covered with a 2 mm thickness of BG3 UV filter with anti-reflective coating. The full Mini-EUSO telescope consists of 3 main systems: the optical system, the PDM and the data acquisition system  [6]. The optical system of 2 Fresnel lenses is used to focus light onto the PDM in order to achieve a large FoV (44 • × 44 • ) with a relatively light and compact design, well-suited for space application  [10].
EUSO@TurLab project The EUSO@TurLab project  [2]  is a series of measurement campaign, in which we have tested several kinds of prototypes and pathfinders of the fluorescence telescopes equipped with the "EUSO electronics". Those telescopes are designed to observe the Earth's atmosphere from the stratosphere or space from the orbit of the ISS. By means of the rotating tank, we have been testing the EUSO electronics such as its basic performance and the first level trigger (L1) for cosmic-rays, in view of various and even changing background conditions as well as atmospheric phenomena such as meteors and lightning that EUSO telescopes will observe. The Fig. 3  shows the light curve in summed D3 data of a full tank rotation taken by one EC-unit with a Mini-EUSO type electronics. During the year 2018 and 2019, Mini-EUSO Engineering Model (Mini-EUSO EM)  [14]  and Torino EC telescope assembled with Mini-EUSO electronics are tested at TurLab  [15].
Comparison with Mini-EUSO data Fig. 4  shows a comparison between an example of meteor event reproduced in TurLab measurement by Lissajous (left) and the meteor events detected by Mini-EUSO (middle and right). In Mini-EUSO data, there are meteors with different brightness and time duration. The meteor we simulated at TurLab has characteristics that have been found among such meteors. To see the performance of the telescope against a city, we made a scaled size of city of Turin. The scale factor is arbitrary due to the restriction of the size, also it is not our main purpose to reproduce exact image of a particular city but to see the performance against general cities as well as to investigate parameters such as light intensity or density to reproduce the city view in Mini-EUSO. Top part of Fig.
Acknowledgements This work was supported by  State Space Corporation ROSCOSMOS , by the  Italian Space Agency  through the  ASI INFN  agreement n. 2020-26-HH. 0  and contract n. 2016-1-U. 0,by the  French Space agency CNES, National Science Centre in Poland  grant  2017/27/B/ST9/02162. This research has been supported by the  Interdisciplinary Scientific and Educational School of Moscow University "Fundamental and Applied Space Research". The article has been prepared based on research materials carried out in the space experiment "UV atmosphere". The authors express their deep and collegial thanks to the entire  JEM-EUSO program  and all its individual members.
PCR products were purified with ExoSap-IT (USB Corporation, Cleveland, OH, USA) and sequenced in both directions. Sequencing reactions were performed at the Centre for Biodiversity Genomics, University of Guelph, Canada, using the BigDye Terminator v3. 1 Cycle Sequencing Ready Reaction kit following standard protocols described in  [38]. Sequencing was performed on an ABI 3730xl capillary sequencer (Applied Biosystems). Sequences and collateral information were deposited on BOLD  [39]  and are available as a public data set (dx. doi. org/10. 5883/DS-BARBONYM, accessed on 15 January 2021, Table  S1 ).
2. 3  [43, 49] , and (4) General Mixed Yule-Coalescent (GMYC) in its single (sGMYC) and multiple threshold version (mGMYC) as implemented in the R package Splits 1. 0-19  [50]. Both the mPTP algorithm and the GYMC use phylogenetic trees as input files. We reconstructed a maximum likelihood (ML) tree for the former using RAxML  [51]  based on a GTR + I + Γ substitution model. For the GYMC algorithm, we calculated an ultrametric, fully resolved tree using the Bayesian approach implemented in BEAST 2. 6. 2  [52]. Sequences were collapsed into haplotypes prior to reconstructing the ultrametric tree using RAxML, and Bayesian reconstruction was based on a strict-clock prior of 1. 2% per million year  [53]. Two Markov chains of 20 million each were run independently using Yule pure birth and GTR + I + Γ substitution models.
Trees were sampled every 5000 states, after an initial burn-in period of 5 million. Both runs were combined with trees resampled every 20,000 states using LogCombiner 2. 6. 2, and the maximum credibility tree was constructed using TreeAnnotator 2. 6. 2  [52]. A final COI gene tree was reconstructed using the SpeciesTreeUCLN algorithm of the StarBEAST2 package  [54]. This approach implements a mixed-model including a coalescent component within species and a diversification component between species that allows accounting for variations of substitution rates within and between species  [55]. SpeciesTreeUCLN jointly reconstructs gene trees and species trees and therefore requires the designation of species, which were determined using the consensus of our species delimitation analyses. The SpeciesTreeUCLN analysis was performed with the same parameters as mentioned above.
Results The total of 173 DNA barcodes used for this study comprised 154 sequences mined from BOLD and 19 sequences generated for Barbonymus specimens originating from Sumatra and Borneo. The newly generated sequences represent the first DNA barcode records of Barbonymus for Borneo. All the sequences were above 500 bp in length and no stop codons were detected, suggesting that the sequences collected represent functional coding regions. DNA-based species delimitation methods resulted in congruent delimitation schemes with 6 MOTUs for mPTP, sPTP, ABGD, RESL, and sGMYC (Figure  2 ; Table  S1 ). However, mGMYC resulted in the delimitation of 31 highly incongruent MOTUs. Therefore, the mGMYC partitioning scheme was discarded. The final consensus scheme consisted of six MOTUs (Figure  2 ; Table  2 ) showing a distinct barcoding gap, which is defined as the lack of overlap between maximum intraspecific and minimum interspecific genetic distance.
Discussion The present study provides an update of the Barbonymus diversity in Sundaland through the aggregation of newly generated and recently published DNA barcode records, resulting in a reference library consisting of 173 sequences largely distributed across mainland Asia and Sundaland (the haplotype MK978151 was observed in five individuals in  [16] , resulting in a dataset in BOLD consisting of 169 sequences). DNA-based species delimitation methods largely agreed on the delineation of six MOTUs, except mGMYC with a much higher estimate, a fact that was already reported in other studies  [22, 27, 46, 48, 60]. Aside from this noticeable exception, methods were concordant in their delimitations, and a barcoding gap was observed between all six MOTUs, with maximum K2P distances mostly <1% within MOTUs, thereby falling into previously observed ranges for Cypriniformes in Sundaland  [9, 16, 21, 22].
A single case of unrecognized diversity is detected within B. altus, with two MOTUs detected including BOLD:AAE2136 and BOLD:AEB4313. The MOTU BOLD:AEB4313 corresponds to a singleton mined from GenBank and originating from a specimen sampled in the Mekong River (Vietnam), which is consistent with the identification as B. altus considering its type locality is the neighboring Chao Phraya River in Thailand. Raw electropherograms are not available for this sequence, which makes its quality assessment impossible; however, its placement within B. altus seems to confirm that this singleton does not result from poor sequence quality.
Acknowledgments: We wish to thank  Siti Nuramaliati Prijono ,  Witjaksono ,  Mohammad Irham ,  Marlina Adriyani ,  Ruliyana Susanti ,  Hari Sutrisno ,  Yuli Fitriana ,  Muhamad Syamsul Arifin Zein , late  Sri Sulandari , and late  Renny K. Hadiaty , at  Research Centre for Biology (RCB-LIPI) , as well as  Joel Le Bail  and  Nicolas Gascoin  at the  French embassy in Jakarta  for their continuous support. We are thankful to  Daisy Wowor  and  Ujang Nurhaman  at  RCB-LIPI , and  Sumanta  and  Bambang Dwisusilo  at  IRD Jakarta  for their help during the field sampling. Finally, we acknowledge the reviewers who helped to improve this manuscript. A permit to collect fish was awarded to  Nicolas Hubert  ( 7/TKPIPA/FRP/SM/VII/2012 ,  68/EXT/SIP/FRP/SM/VIII/2013 ,  41/EXT/SIP/FRP/SM/VIII/2014 ,  361/SIP/FRP/E5/Dit.
Funding: This research was funded by the  CFREF  to the  University of Guelph 's  Food from Thought program , by the  "Institut de Recherche pour le Développement"  through annual funding and " Fonds d'Amorçage " ( 226F2ABIOS ), by the  French Embassy in Indonesia through the program  " Science et Impact ", by  Campus France  through a  Bio-Asia grant  ( BIOSHOT  project) and by  ANR  ( ANR-17-ASIE-0006 ).
Results: We introduce the use of the straightforward Fisher's exact test as a post processing of the results provided by the popular CODEML sequence comparison software. The respective rates of nucleotide changes at the non-synonymous vs. synonymous position (as determined by CODEML), are turned into entries into a 2x2 contingency table, the probability of which is computed under the Null hypothesis that they should not behave differently if the ORFs do not encode actual proteins. Using the genome sequences of two recently isolated giant viruses, we show that strong negative selection pressures do not always provide a solid argument in favor of the existence of proteins.
Introduction Since the first two bacterial genomes were sequenced 25 years ago  (Fleischmann et al. , 1995; Fraser et al. , 1995) , partial and whole genome sequencing have become the method of choice in identifying and characterizing new microorganisms (bacteria, archaea, unicellular eukaryotes, viruses), revealing the stupendous extent of their diversity. By their simplicity of use and low cost, the most recent 3rd generation sequencing platforms  (Goodwin et al. , 2016)  have made microbial genomics accessible to non-specialists  (MacLean et al. , 2009; Gwinn et al. , 2019) , while a few large centers are fully taking advantage of their huge throughput to run biodiversity exploration projects of ever increasing dimensions  (Lewin et al. 2018; Sunagawa et al. , 2020; Chen et al. 2021). The most recurring (and unexpected) lesson emerging from the analyses of these enormous datasets is that overall morphological and phylogenetic similarities, as well as similar metabolisms and lifestyles, could hide large differences in gene contents and encoded proteomes.
Given the A+T richness of STOP codons (TAA, TAG, TGA), random ORFs are also statistically expected to occur at higher frequency in high G+C content genomes, increasing the risk of protein overprediction  (Legendre et al. , 2019). The uncertainty further increases when the predicted proteins are short (typically less than 100 residues), or do not exhibit neither a functional motif nor a significant sequence similarity in the reference databases  (Sayers et al. , 2021). Such cases, referred to as "ORFans" represent a large proportion of predicted microbial proteomes  (Entwistle et al. , 2019)  in particular for large viruses  (Philippe et al. , 2013; Gallot-Lavallée et al. , 2017; Legendre et al. , 2018; Abergel & Claverie, 2020; Boratto et al. , 2020). The validation of ORFans is important to document the intriguing evolutionary process of de novo gene creations from noncoding regions in prokaryotes, eukaryotes, and their viruses  (Legendre et al.
To overcome this difficulty it has become customary to compute the selection pressure, i. e. the ratio of the synonymous vs. nonsynonymous mutation rates as a way to validate bioinformatic protein predictions (e. g. :  Doutre et al. , 2014 : González et al. , 2016) ;  Prabh & Rödelsperger, 2016); Christo-Foroux et al. , 2020). The concept/calculation of the selection pressure is based on the fact that proteins are made for a purpose and that their functions, directly derived from their amino-acid sequences, tend to be conserved throughout evolution. Accordingly, we expect that the non-synonymous positions of their coding regions will vary much less rapidly than the synonymous ones, the changes of which have lesser consequence on the organism's fitness. The concept of selection pressure, was most widely disseminated via the CODEML program of the PAML package for phylogenetic analysis  (Yang, 2007; Yang, 2014; Jeffares, 2015).
N NS and d S. N S , respectively. These values are directly read from the standard CODEML output, then rounded to the nearest integers to be compatible with Fisher's test. The probability (p-value) that both position types (synonymous and non-synonymous) behave differently (hence that the ORFS prediction are dubious) can be calculated by any available implementation of Fisher's test (online or in R, for instance). The pairwise sequence alignments were analyzed using the PAML 4. 9j package version for UNIX/Linux with the following relevant options: noisy=0; verbose=0; runmode=-2 (pairwise); seqtype = 1 (codons); CodonFreq=2; model=1; NSsites=0; icode=0 (universal code); fix_kappa=1; kappa=1; fix_omega=0 (omega to be estimated); omega=0. 5. We apply the above procedure to the evaluation of the whole predicted proteomes of two virus sequenced in our laboratory, constituting the only two known members of the proposed Molliviridae giant virus family.
We started this work by noting that ω is defined as the ratio of two small quantities (d N /d S ) themselves computed from a limited number of substitution events (n s , n NS ) imposed by the necessity of flawless pairwise sequence alignments. Values of ω are thus highly sensitive to random fluctuations making them unreliable to assess the validity of protein prediction. We showed here that applying the Fischer's exact test to the standard CODEML output, provides a simple way to improve the reliability and predictive power of pressure selection computations. This procedure might thus constitute a useful addition to the standard genome annotation pipe-line and previously proposed software tools to help identify spurious ORFs  (Eberhardt et al. , 2012; Höps et al. , 2018)  side benefit, the use of Fisher's test automatically filters out pairwise alignments that do not exhibit enough substitutions because they are too similar, or their alignments too short.
Software and Data Availability The PAML 4. 9j package used to run CODML is freely available at: http://abacus. gene. ucl. ac. uk/software/paml. html. The sequence data used here are available at https://www. ncbi. nlm. nih. gov/nuccore/ under accession#: NC_027867 and MN812837 for Mollivirus sibericum and Mollivirus kamchatka, respectively.
The tool, EASI-AV, is presented in section 4. 3. In Section 4. 4, we exemplify its application with empirical data from a pilot site, next on section 4. 5 the implications of the method as well as the limitations of our proposition are discussed. Section 4. 6 concludes on the study. This chapter is a parallel study alongside the AVENUE project. The Autonomous Vehicles to Evolve to a New Urban Experience project (AVENUE), is an EU funded project which aims to design and carry out full-scale demonstrations of urban transport automation by deploying, for the first time worldwide, fleets of AVCTs on mixed-traffic conditions. Providing innovative services, like door-to-door and multimodal transportations, in low to medium demand areas of 4 European demonstrator cities: Geneva, Lyon, Copenhagen, and Luxembourg (AVENUE, 2018).
EASY-AV design methodology The Economic Assessment of Services with Intelligent Autonomous Vehicles (EASI-AV) tool was developed as a support tool to assist decision makers in cities, as well as transport operators, and other organizations to estimate the economic assessment of implementing a service with AVCTs. EASI-AV has been developed within the European project AVENUE. We worked with the transport operators in charge of the collective transport network and responsible for the demonstrators in the four cities in the project (Copenhagen, Geneva, Lyon, and Luxembourg). We collected their data on the autonomous service as well as on traditional services to test the tool and check the reliability of its algorithms. The EASI-AV tool was firstly designed using a spreadsheet software and manual data entry with automated calculation.
These ratios will be used afterwards for a detailed comparison between other transport modes. To help the user, we created a list of the most relevant Capex and Opex cost sources that are explained on a specific side-document and via drop-down menus for the web application. In order to integrate economies of scale, the user can choose if the cost applies to a single vehicle or to the entire fleet (for example feasibility study is not a cost per vehicle whereas acquisition costs is a cost per unit). In some cases, it is possible that the people who are filling out the tool do not know the exact cost values for the autonomous shuttle, being a new (and until now scarcely implemented technology), data about costs and financial values may not be easily accessible and foreseeable for everyone. For these cases, we provide the option of using the standard costs (determined based on the average results obtained in the AVENUE project).
Part 1 -Service contextualization The Pfaffenthal area of 0. 38 km2 has a total population of 1. 284 inhabitants, and is not served by the city's traditional public transport network. In June 2018, as part of the European Commission funded project AVENUE (AVENUE, 2018), the local transport operator (Sales-Lentz) implemented in the area a 1. 2 km fixed-looped route (with 4 stops) serviced by two Navya ARMA shuttles to run free of charge to passengers every Tuesday, Thursday from 12h00 to 20h00 and every weekend and public holidays from 10h00 to 21h00. Regarding the data entry, it is worth emphasizing that data characterizing the context can be filled in manually by the users on the spreadsheet, while for the web application, extraction algorithms can collect data concerning surface and population when the user enters identification geographic points.
Part 5 -Global impact evaluation and scenarios The four previous parts conduct a picture of a global impact assessment for decision making concerning the implementation of autonomous mobility. In Luxembourg, Figure  4. 6 shows that the revenue model is not diversified yet but the tool is ready to let decision makers re-imagine the business model future of their autonomous fleet. Revenue data are used to calculate financial ratios like the breakeven point or the net present value; those ratios quantify the cost-benefit analysis and contribute to the decision making process for investors as well as for policy makers (if different). Since investors or policy makers need to choose how to implement multimodality, EASI-AV systematically gives tables and indicators to compare the impact of autonomous services with other collective transport modes options.
It is dedicated to allow a continuous monitoring of data quality and consistency, in line with the French Health Data Hub. Results: Depending on cohorts, the objectives are to describe the natural history of the studied RD(s), identify the underlying disease genes, establish phenotype-genotype correlations, decipher their pathophysiology, assess their societal and medico-economic impact, and/or identify patients eligible for new therapeutic approaches. Inclusion of prevalent and incident cases started at the end of 2016. As of April 2021, 5558 patients have been included within 13 RD e-cohorts covering 67 diseases integrated in 10 European Reference Networks and contributing to the European Joint Program on RDs. Several original results have been obtained in relation with the secondary objectives of the RaDiCo cohorts.