dataesr/scientific-paragraphs-categorization huggingface dataset:
96 -l500 -s1000) for pre-assembly process. The FALCON pre-assembly resulted in 331 primary contigs of total length 125 Mb, contig N50 of 6 Mb and an additional 36 Mb of "associate contigs" that represent divergent haplotypes in the genome. FALCON-unzip was then used to phase the pre-assembly, producing contiguous leading contigs (named "primary") and associated contigs (i. e. phased, alternate haplotypes). The genome assembly was polished as part of the FALCON-Unzip pipeline using haplotype-phased reads. The haplotigs contain one of the two allelic copies of the heterozygous regions; in this respect, the haplotigs serve as phasing information for the haploid representation. The FALCON-Unzip assembly had 241 primary contigs and 999 haplotigs. FALCON-Phase (https://github. com/phasegenomics/FALCON-Phase) was developed to resolve haplotype switching in diploid genome assemblies.
The FALCON-Phase haplotig placement defines phased blocks in the FALCON-Unzip assembly. The Falcon-Phase Workflow steps 1 and 2 were used to place the haplotigs along primary contigs. Once the haplotig placement file and phase block pairings are done, the primary contigs are cut up into very small pieces at phase block boundaries with Falcon-phase workflow step 3. Scaffolding with instaGRAAL Hi-C contact maps were generated from paired-end reads using the hicstuff pipeline for processing generic 3C data, available at https://github. com/koszullab/hicstuff. The backend uses the bowtie2 aligner run in paired-end mode (with the following options: -{}-maxins 5 -{}-very-sensitive-local). We discarded alignments with mapping quality lower than 30. The remainder was converted to a sparse matrix representing contacts between each pair of DpnII restriction fragments.
The instaGRAAL program  16  was used in conjunction with the contact maps to scaffold the genomes. Prior to running it, restriction fragments are filtered based on their size and total coverage. Fragments shorter than fifty base pairs are discarded. Then, fragments whose coverage lesser than one standard deviation below the mean of the global coverage distribution are also removed from the initial contact map. These fragments were reintegrated later after the scaffolding step. The instaGRAAL scaffolder uses a Markov Chain Monte Carlo (MCMC) method: briefly, the contact data is fitted on a simple three-parameter polymer model. The 3D contacts are exploited and used by the program to infer the relative 1D positions of the sequences and thus the genome structure. To do so, the program attempts to perform a number of operations between each sequence and one of its neighbours (e.
g. flipping, swapping, merging or splitting contigs) and the operation is either accepted or rejected with a certain probability depending on the likelihood shift. The model parameters are then also updated and a new iteration begins. A set of computations whereby every sequence of the genome has been iterated over this way is called a cycle. The scaffolder was run for 100 cycles on each genome, after which convergence in both genome structure and model parameters was evidently apparent. The scaffolded assemblies were then refined using instaGRAAL's instaPolish module, with the aim of correcting the small artefactual inversions sometimes produced by instaGRAAL. Post-treatment of scaffolded assemblies Diploid assembly post-treatment (using FALCON): we used the repeat-aware finisherSC tool  55  to upgrade the de novo phased genome assembly of Adineta vaga.
Final round of polishing were performed with the Pilon corrector using Illumina data (sample ID GC047403, see Supplementary Table  1 ). Phased assembly post-treatment (using Bwise): to resolve a remaining fragmentation of one single chromosome (i. e. chromosome 5B) after scaffolding with instaGRAAL based on Hi-C data, we established a novel comparative approach that incorporates computational methods to transform fragmented contigs into near-chromosome fragments. First, Bwise contigs were aligned against themselves using NUCmer v4. 0  56. Ploidy pairing was evaluated using the online visualization tool, DOT (https:/dnanexus. github. io/dot/) and we were able to anchor fragmented contigs into a single chromosome using its homologous template (i. e. chromosome 5A). Ploidy, synteny and colinearity among the three A.
vaga genome assemblies Genome assembly tools rely on various assumptions including the ploidy level of the organism under study. In order to circumvent potential impact of such ploidy assumptions on genome structure, we compared our three new genome assemblies. First we evaluated the classical genome assembly statistics using in-house script (see Figure  1A ). We then used the illumina reads (i. e. GC047403, see Supplementary Table  1 , as input for the comp function of the KAT software  57  which uses k-mers distribution in order to explore ploidy levels of A. vaga genomes (see 1A). Genomes were aligned pairwise using nucmer 3. 1 (using -maxmatch option)  58  , the results of which were converted into paf format using minimap2 paftools script  59. We then used D-GENIES as a stand-alone  60  , modifying identity percentage thresholds to 1.
12/27 Genome size estimation The genome assemblies produced by all three methods (Bwise, Flye and Falcon) were markedly smaller than expected based on the generally admitted genome size of 0. 25 pg per (non-reduced) oocyte (http://www. genomesize. com/result_species. php?id=5369), equivalent to 244 Mbp for a diploid assembly or 122 Mbp for a haploid assembly. As there is considerable confusion in the literature considering the genome size of Adineta vaga (e. g. report of a nuclear DNA content of about 0. 7 pg 61 , nearly 3 times higher than in the Animal Genome Size database although the entry there refers to this article), we decide to perform an independent assessment of the genome size of Adineta vaga using flow cytometry, with Arabidopsis thaliana ecotype Colombia (for which a genome size of 157 Mbp was previously measured  62  as a genome-size standard for comparison.
The hybridization of the probes on embryos was adapted from previous protocols  63, 67. At least 100 embryos stored in methanol: acetic acid glacial were dropped onto an uncoated and clean microscope slide (VWR™, 631-1550) and let dry on a wet paper for 30 min. Then, a cover slip (VWR™, 631-1572) was placed over the embryos and they were squashed by gentle pressure on the slide. All following treatments of embryos on slides were conducted in Coplin jars. Embryos were permeabilized in 0. 1% saponin Investigating AV13 Palindromes Palindromes previously reported in the AV13 genome were investigated in the light of our new assembly. We first de novo determined the location of palindromes in AV13 by filtering ONT long reads, mapping them onto AV13 genome using NGMLR  89  with default parameters and subsequently detecting the palindromic breakpoints (PBR) using a in-house tool, huntPalindrome (available at https://github.
Funding This project received funding from the  Horizon 2020 research and innovation program  of the  European Union  under the  European Research Council (ERC)  grant agreement  725998  (RHEA) to KVD; under the  Marie Skłodowska-Curie  grant agreement  764840  to JFF (ITN IGNITE, www. itn-ignite. eu);from the  Fédération Wallonie-Bruxelles  via an ' Action de Recherche Concertée' (ARC)  grant to JFF; by funded by the  French Government  " Investissement d'Avenir" program FRANCE GENOMIQUE  ( ANR-10-INBS-09 ) and  Antoine Houtain  and  Alessandro Derzelle are Research Fellows of the Fonds de la Recherche Scientifique -FNRS. 16/27.
Data Processing A median filter (3 × 3-pixel radius) was applied to all images to reduce noise in the radiographs used to measure relative light output and detection efficiency. All radiographs were open-beam and dark-field corrected. Acquisition times were six seconds for the images taken in the unfiltered cold beam. For the epithermal (i. e. , cadmium-filtered) beam, a set of five 20-second images were taken for Once the radiograph measuring the light yield of the screens was captured, the borated screens were removed from the imaging system and a common 6 LiF/ZnS:Cu screen was mounted to the imaging system. An open beam image was acquired for the post-process correction of subsequent radiographs. The borated screens were then placed on the source-side of the 6 LiF/ZnS:Cu screen and a radiograph of the borated screens was acquired to measure the detection efficiency of each screen.
Data Processing A median filter (3 × 3-pixel radius) was applied to all images to reduce noise in the radiographs used to measure relative light output and detection efficiency. All radiographs were open-beam and dark-field corrected. Acquisition times were six seconds for the images taken in the unfiltered cold beam. For the epithermal (i. e. , cadmium-filtered) beam, a set of five 20-second images were taken for each measurement and summed together. Spatial resolution images were integrated over ten seconds. A python code was written to correlate data from both the light-yield and detectionefficiency measurements for each screen. Once correlated, relative light yield and detection efficiency as a function of scintillator layer thickness was calculated. A separate python script calculated the effective spatial resolution in terms of MTF.
Data Processing A median filter (3 × 3-pixel radius) was applied to all images to reduce noise in the radiographs used to measure relative light output and detection efficiency. All radiographs were open-beam and dark-field corrected. Acquisition times were six seconds for the images taken in the unfiltered cold beam. For the epithermal (i. e. , cadmium-filtered) beam, a set of five 20-second images were taken for each measurement and summed together. Spatial resolution images were integrated over ten seconds. A python code was written to correlate data from both the light-yield and detection-efficiency measurements for each screen. Once correlated, relative light yield and detection efficiency as a function of scintillator layer thickness was calculated. A separate python script calculated the effective spatial resolution in terms of MTF.
Acknowledgments: This work is based upon experiments performed at the ANTARES instrument operated by FRM II at  Heinz Maier-Leibnitz Zentrum  (MLZ), Garching,  Germany. The authors would like to thank the  FRM II  staff as well as  Amanda Smolinski  for their assistance during the measurement process. DMI/Reading Imaging fabricated and prepared the various materials (e. g. , the anhydrous 10 B converter compounds and scintillators) and the coating formulations, fabricated the sensors used in this study, and measured the Na  10 B5O8 density. Acknowledgments: This work is based upon experiments performed at the ANTARES instrument operated by FRM II at  Heinz Maier-Leibnitz Zentrum  (MLZ), Garching,  Germany. The authors would like to thank the  FRM II  staff as well as  Amanda Smolinski  for their assistance during the measurement process.
However, for 10% to 15% of these patients, the disease will become severe, which requires surveillance  [13, 14]. Various systems have been set up to carry out this surveillance, often involving general practitioners (GPs) and telephone-based and/or home visits, or the use of telehealth technologies for virtual consultations  [15, 16]. However, all these systems rely on the individual management of every patient by a single doctor (GP, infectious disease specialist, or any other specialist involved in COVID-19 management). In a pandemic situation, GPs and infectious disease specialists are scarce resources and should be mobilized wisely  [15, 17, 18]. To offer alternatives to patients while reserving medical resources for the situations that require it, the Greater Paris University Hospitals (Assistance Publique-Hôpitaux de Paris, [APHP]), in collaboration with regional GP organizations and a software company specializing in patient digital pathways, quickly developed a remote telesurveillance solution named Covidom for the home monitoring of patients with COVID-19.
Because of its simplicity and quick response, this solution could be easily adapted in other countries. Of course, the Covidom solution needs to be thoroughly evaluated; in particular, the efficiency and ability of the alerts to detect patients at high risk of deterioration and the medico-economic impact of such a solution need evaluation. To do this, we will link the Covidom database with hospitals and national social security databases to identify patients who directly contacted them or were self-referred to an emergency department. The Covidom system was sustainable during the lockdown due to the personnel availability that resulted from nonurgent elective procedures or appointments being rescheduled; most of the workforce comprised salaried employees (as opposed to a pay-per-service system).
We observed significant fluctuations in the availability of human resources. At first, and due to the lockdown, many volunteers offered their help. Since lockdown measures were lifted (May 11, 2020) and as control center cell physicians and RMRs progressively resumed their usual activities, finding enough personnel has become more of a challenge. Adapting the Covidom solution and offering alternatives to patients who had difficulty with the system (unfamiliar with these technologies or language issues) was done by connecting these patients to their GPs. However, additional options could have included translated versions of the questionnaires and the other available documents to help patients with language issues. Surveillance could also have been more flexible as it was found to be short for some patients with recurrent or persistent symptoms, while others would have preferred to stop the follow-up as soon as the symptoms disappeared.
Acknowledgments We thank  Falzon Alexandre ,  Fayolle Guillaume ,  Laporte Fanny ,  Amélie Tortel , and the  Nouveal-e Santé team  for their help with the web application and regional center surveillance interface development. We also thank  Debastard Laurent ,  Grenier Alexandre ,  Hody Julien ,  Penn Thomas , and the  Paris region URPS (Union régionale des professionnels de santé)  for their help in the development and dissemination of the Covidom solution. This study received funding from the  Programme Hospitalier de Recherche Clinique 2020 of the French Ministry of Health  and a research grant from the  APHP-Fondation de France. The Covidom platform received funding from the  EIT Health  for COVID-19 research. Members of the  AP-HP / Universities / Inserm  COVID-19 research collaboration are as follows: the Writing Committee ( Youri Yordanov ,  Agnes Dechartres ,  François-Xavier Lescure ,  Caroline Apra ,  Pascaline Villie ,  Jerôme Marchand-Arvier ,  Erwan Debuc ,  Aurélien Dinh , and  Patrick Jourdain ); the  Data-Sciences Committee  ( Caroline Apra ,  Charlotte Caucheteux ,  Luc Jaulmes ,  Alexandre Gramfort ,  Jenny Mansour , and  Arthur Mensch ); the  Scientific Committee (Amélie Aime-Eusebi ,  Caroline Apra ,  Alexandre Bleibtreu ,  Erwan Debuc ,  Agnes Dechartres ,  Laurène Deconinck ,  Aurélien Dinh ,  Patrick Jourdain ,  Christine Katlama ,  Josselin Lebel ,  François-Xavier Lescure , and  Youri Yordanov ); the  Covidom Regional Center Steering Commitee  ( Yves Artigou ,  Amélie Banzet ,  Elodie Boucheron ,  Christiane Boudier ,  Edouard Buzenac ,  Marie-Claire Chapron ,  Dalhia Chekaoui ,  Laurent De Bastard ,  Erwan Debuc ,  Aurélien Dinh ,  Alexandre Grenier ,  Pierre-Etienne Haas ,  Julien Hody ,  Michèle Jarraya ,  Patrick Jourdain ,  Louis Lacaille ,  Aurélie Le Guern ,  Jeremy Leclert ,  Fanny Male ,  Jerôme Marchand-Arvier ,  Emmanuel Martin-Blondet ,  Apolinne Nassour ,  Oussama Ourahou ,  Thomas Penn ,  Ambre Ribardiere ,  Nicolas Robin ,  Camille Rouge ,  Nicolas Schmidt , and  Pascaline Villie ); and the  Centre de Pharmaco-Epidémiologie de l'AP-HP (Sofia Zemouri ).
Intermediate voltage characterized by abnormal electrograms correspond to surviving myocardial fibers  [8]   [9]. The recent development of high-density mapping catheters enables the detection of late or fragmented potentials. The elimination of such electrograms has been assessed as a procedural endpoint  [10]. Unfortunately, a disadvantage of such a technique is that it induces larger tissue destruction than would be required if the actual VT circuits could be accurately identified. Pace-mapping data include surface electrocardiography (ECG) signals collected during pacing from many sites of the ventricle. They can be used to determine the VT circuit. Indeed, the exit site of the VT circuit is identified when the paced QRS morphology best matches that of the clinical VT  [11] , as assessed by a VT correlation map.
Therefore in this work we propose a specific and innovative method for catheter paced-ECG data, combining a waveletbased detection of stimulation spikes and a delineation of the subsequent QRS complex (peak and onset). The objective of the study is to evaluate the performance of the proposed paced-ECG detection and delineation and to demonstrate its potential for multi-parametric catheter mapping of VT in the clinical setting. The overall goal is to provide the interventional cardiologist with a software tool to rapidly visualize the relevant maps (voltage, correlation and sQRS) and identify the potential VT circuit(s) to be ablated.
A. PATIENT DATA ACQUISITION Thirteen patients (9 men, mean age = 59 ± 12 years) consecutively referred for post-infarct VT catheter ablation between March 2016 and October 2017 were included in this retrospective, non-interventional study. Inclusion criteria were: (i) spontaneous sustained monomorphic VT inducible during the electrophysiological study; (ii) identification of the VT isthmus by the pace-mapping technique and (iii) radiofrequency catheter ablation lesions along the isthmus prevented VT induction. The study complied with the declaration of Helsinki and all procedures complied with the CHRU-Nancy guidelines. All 18 procedures were performed with the CARTO3® (Biosense Webster, Inc. , Irvine, USA) and the Niobe® system (Stereotaxis Inc. , St. Louis, USA). Anonymized data were exported from the CARTO3® workstation and were then processed using an in-house software written in MATLAB language (The Mathworks, Natick, USA), version R2020a.
Electro-anatomic data were first loaded into the software, including: catheter positions and 2. 5 s of 12-lead ECG data acquired for each pace-mapping site; high-resolution vendor-generated 3D meshes of the ventricular cavity, as well as bipolar and unipolar voltage maps acquired in sinus rhythm. All other maps used in this study were generated offline with the MATLAB software, as described henceforth.
3. Determination of a paced-QRS flag by analysis of the previous QRS. A QRS was considered to be a paced QRS if similar to the previous one; similarity was defined by a distance-to-spike variation lower than 35 ms and a variation in the module of the vectorcardiogram below 33%. Overall 5176 QRS were present, of whom 2991 were paced. 4. Detection of the onset of a QRS by using the module of the vectorcardiogram. The QRS start was determined by backward search from the maximum of the VCG amplitude, until the module reached 5% of the maximum module. The time interval between pacing and the start of the resulting QRS complex, the sQRS interval, was finally determined. The dataset was split between a training set consisting of the first 5 patients and a test set with the data from the remaining 13 patients.
C. VALIDATION AGAINST EXPERT ANOTATIONS The software tool allowed visualization of all the automatically detected QRS signals. An experienced interventional cardiologist (N. H. ) was asked to review the ECG signals (pacing spike, whether a QRS was paced or not). The efficiency of the automated processing was assessed by common statistics for binary classifiers (using the cardiologist input as the ground truth), including the positive predictive value (PPV) and the sensitivity (Se). The position of the QRS onset varies slightly between cardiologists. To quantify this inter-observer variation, two experts were asked to mark the QRS onset: a clinical support specialist (P. H) defined as expert 1 and an interventional cardiologist (N. H. ) defined as expert 2. We also introduced a virtual delineation represented by the mean of both experts.
D. RECONSTRUCTION OF MULTI-PARAMETRIC MAPS Multiple 3D maps were generated to visualize the information. The bipolar voltage map was directly derived from the vendor's CARTO3® software. Additionally, a 3D surface mesh was generated from the pacemapping sites and used to create the following maps: (i) a sQRS interval map was generated by color-coding the sQRS interval induced by the pacing stimuli; (ii) a reference-less correlation gradient map was generated as described in  [12] The target for the clinician was to collect points with a distance of 10 mm in areas of low voltage. The distance between two points was higher in healthy areas. Correlation gradient values were considered to be defined only when the site-to-site distance was less than 20 mm. The rationale for computing these three maps is that sQRS maps are expected to highlight VT circuit entrance sites  [13]  and correlation gradient maps are expected to highlight VT circuit core zones  [12].
Finally, voltage maps are expected to help identify the exit of the VT circuit, which should be at the border between scar and healthy tissue. For better visualization purpose, the maps were finally projected from the coarse mesh formed by pacing sites onto the high-resolution anatomical mesh (distance between the vertices was 0. 8mm) provided by the vendor (using nearestneighbor interpolation). For final visualization of the 3D maps, the rendering engine (still within MATLAB in this study) was set to use interpolation of values defined at each vertex of the high resolution mesh, similarly to the vendor's CARTO3® software.
Bland-Altman plots (figure  4 ) show a good agreement between experts and the algorithm. The linear interpolation, which was used to reconstruct the final high resolution meshes, further decreased the impact of the difference between the algorithm and the experts' annotations. Figure  5  shows an example of multi-parametric mapping (3 maps) of the same patient. The sQRS interval map (A) and the correlation gradient map (B) were generated using the algorithm generated values. The bipolar voltage map (C) was derived from the CARTO3® software. The visualization of this multi-parametric mapping may help to determine the localization of the entrance, core and exit of the VT circuit. The objective of a VT ablation procedure is to identify the main components of all the fast reentrant circuits the patient is capable of sustaining.
The proposed software tool automatically creates voltage, correlation and sQRS maps. The creation of these multiparametric maps help determine the different characteristics of the VT isthmus. Previous articles have shown the importance of these parameters in identifying the isthmus. The isthmus is a complex structure and the visualization of a single parameter is not enough to be able to reconstruct the VT circuit. For each map, the global patterns with the highest and the lowest group of values are useful. Indeed it is important to know whether a sQRS is long (over 100 ms) or short (under 50 ms), thus the mean absolute error of 11. 1 ms is low enough for the automatic sQRS maps to be analyzed. It is important to have a global approach and take into account all the relevant information before establishing a diagnosis.