dataesr/scientific-paragraphs-categorization huggingface dataset:
Because climate variation was significantly associated with the first PC genomic (absolute Spearman's correlation coefficients ranging from 0. 148 to 0. 316; Supplementary Table  S2 ), we evaluated to which extent the level of correlation of the analyzed covariables with this axis can have affected the performance of GEA analyses. We analyzed 250 data sets simulated under the inference model and each data set consisted of 10,000 SNPs including 100 SNPs associated with a given environmental covariable out of 10 simulated ones (25 data sets per covariable) that displayed different levels of correlation with the first PC genomic (ranging from 0 to 0. 9 with an increasing step of 0. 1). The simulation model was calibrated to obtain data sets closely mimicking our observed climate data, both in terms of the sample design (number of populations, haploid sample size of the pools, read coverage, across population allele frequencies) and population structure (summarized by the matrix ).
Numerical calculations Boundary element method (BEM) calculations were used to simulate the electrostatic potential of a real device, with 100 V applied between the rectangular biprism and the counterelectrodes, using the program Coulomb from the company IES (Integrated Engineering Software; https://www. integratedsoft. com/ product/coulomb/ ). A mesh was generated with a higher density of elements only where needed and a coarser mesh was used where the element density was not as critical. The geometry used in the calculation included the contacts to the biprism and the counterelectrodes, which produce fringing fields. Fig. 4  a shows a projection of the transverse electric field in the electron beam direction. The integrated transverse electric field is homogeneous along the length of the biprism, e xcept near its ends.
After that, the microstructures of all the samples (QC, AC and tempering samples) were examined by using electron back-scattered diffraction (EBSD) (Oxford Instruments, Oxford, UK) with step sizes of 50-200 nm conducted on a Zeiss-∑IGMA500 scanning electron microscope (Carl Zeiss AG, Oberkochen, Germany). It should be pointed out that because of the slight tetragonality (c/a ≈ 1. 02) of the γ lattice, it is quite difficult identify by EBSD  [12] ; in the present study it was treated as normal face-centered cubic (FCC) lattice instead. The EBSD data was analyzed by using the HKL Channel 5 software (Oxford Instruments, Oxford, UK). Before that, noise reduction was preformed so that the "wild spikes" were removed. An energy dispersive spectrometer (EDS) (Oxford Instruments, Oxford, UK) was also performed to reveal the compositional deviation among various constituent phases.
Study design Data and sera used were collected from 41 French pig farms involved in a study on the course of PCV2 infection (western France 2014-2015). The study was carried out in subclinically PCV2-infected herds without piglet vaccination against this virus. The herds were provided by the veterinarians at 'Univet santé élevage' and 'Cybelvet' veterinary clinics. Blood was sampled from 20 pigs selected at random from two batches in each herd (10 pigs 10-12 weeks old and 10 pigs at least 22 weeks old). Data on management, biosecurity and farm practices were collected via a questionnaire that was filled out with the farmer. The questionnaire is available upon request (in French,  26.
The FactoMineR package for R was used  [32]. The effects of the explanatory factors on the level of technical performances were then quantified by performing a logistic-regression analysis. All selected explanatory variables were checked for multicolinearity (χ 2 -test, p < 0. 05), and those most strongly associated with the outcome variable and having biological relevance were selected. The logistic regression was performed according to the method described in Hosmer and Lemeshow  [33]  (PROC LOGISTIC, SAS 9. 1, SAS Inst. , Cary, NC, USA). A backward stepwise procedure was used to select the variables that were significantly (p < 0. 05) associated with the outcome variable. At each step, the variable with the highest p-value was removed from the model. This procedure was continued until all variables were significant (p < 0.
These factors can be further investigated in prospective observational studies to assess the time sequence of events. In cross-sectional studies, the outcome and potential risk factors are measured at one particular time point, making the temporality and the separation of cause and effects difficult to ascertain. In the present study, data on the technical performance as well as non-infectious factors were collected in the year prior to data collection on the infectious variables, all assayed at one time point. This study design is wellsuited for examining invariable characteristics (factors that are consistent in time and not influenced by the presence or absence of the disease)  [35, 36] , and, accordingly, our data were mainly related to herd management, hygiene and biosecurity measures, which are believed to be relatively constant over time  [37].
All data were collected by the veterinarians in charge of the herd health management plan, against which the farmer's answers to the questionnaire could be compared. The infectious status of the herds regarding several respiratory or digestive pathogens was established by laboratory analysis performed on the samples collected during the study. The results were compared with the veterinarians' knowledge of the herd health status and discrepancies were checked and corrected when needed if recent infections had occurred. Misclassification bias of infectious status was thus reduced. Serology is an efficient tool widely used to describe exposure to pathogens in swine field studies  [3, [38] [39] [40] [41]. Most of the assays being generally imperfects, association of different tests such as serological and molecular techniques is recommended to increase diagnostic accuracy  [3].
closed or semi-closed questions). The main technical performance values of the growingfinishing steps (average daily weight gain from 8 to 115 kg [ADG], feed conversion ratio from 8 to 115 kg [FCR], mortality from 8 to 115 kg [MORT] and carcass slaughter weight [CSW] in 2014) were obtained from the technical-economic database managed by the French Pork and Pig Institute (IFIP).
Methods and findings Registry based 2/1 cluster randomized controlled trial, a cluster gathering the enlisted patients of 75 GPs aged over 16 years. The trial, run during the 2014-2015 influenza vaccination campaign, compared patient's awareness from being in 50 GPs' standard waiting rooms (control group) versus that of waiting in 25 rooms from GPs who had received and exposed pamphlets and one poster on influenza vaccine (intervention group), in addition to standard mandatory information. The main outcome was the number of vaccination units delivered in pharmacies. Data were extracted from the SIAM-ERASME claim database of the Health Insurance Fund of Lille-Douai (France). The association between the intervention (yes/no) and the main outcome was assessed through a generalized estimating equation.
Baseline was defined as the 2013-2014 seasonal influenza vaccination campaign. Data were extracted between October 15, 2014 and February 28, 2015 from the SIAM-ERASME claim database of the Lille-Douai district Health Insurance Fund on patient level. The study was lengthened by one month (February 2015) following the extension of the vaccination campaign duration by health authorities. The protocol had therefore been amended. The prescription of the seasonal influenza vaccine units was delivered by an individual GP depending on the skills, training and motivation of the latter. This may lead to a potential clustering of the outcome for patients treated by the same GP. To provide valid results, considering the cluster allocation by GP of patients, a correction has to be introduced in computing the number of GPs needed for the trial, called intra-cluster correlation coefficient (ICC).
Target population The GPs participating in the study had previously been contacted by telephone and had given their written consent. GPs without waiting room, or sharing one single waiting room with several other GPs, or participating in another ongoing study, were not eligible to participate in this study. Language barriers in patients were not considered. The study population existed of patients over the age of 16, who were registered by the Health Insurance on the participating GPs' patients lists. The target population were patients over the age of 65 or having a chronic disease requiring seasonal influenza immunization (like COPD or diabetes). Patients were informed about the anonymous use of their data and could refuse to participate at any time.
[1] However, the number of delivered and not injected vaccines is probably comparable in both arms of the trial. As patients under the age of 16 were not enlisted with a GP by the health insurance before 2017, no data were collected in patients under the age of 16 with a chronic disease (like asthma). Encounters with a different GP than the one by whom patients were enlisted was not taken into account. The influenza immunization rate increased in both arms of the study compared to the prior year. Contemporarily, at regional and national level, the number of vaccinated people decreased. The Hawthorne effect, i. e. the trend of people to change their behaviour when they know that they are under observation, might have masked the effect of posters and pamphlets. [29]  The study group carries out a new study to compare the control group in this study with a new control group enrolled a posteriori and measure the Hawthorne effect (Zelen Design  [30] ).
The ensemble learning has the advantage to reduce the sensitivity due to the limited size of the training data and is performed based on random subspace sampling over 2D-PCA space while keeping the image inherent structure and information. In order to obtain discriminative dictionaries satisfying SRC assumption, a new space is learned by minimizing and maximizing the intra-class and inter-class variations using 2D-LDA. Extensive experiments are conducted on two publicly available palmprint data sets: multispectral and PolyU. Obtained results showed very promising results compared with both state-of-the-art holistic and coding methods. Besides these findings, we provide an empirical analysis of the parameters involved in the proposed technique to guide the neophyte.
Unlike in the case of existing methods, the dictionaries are generated by random sampling procedure over 2D-PCA which has the advantage to keep inherent images information. To satisfy SRC assumption and ensure the discrimination of dictionaries, projected training data in each subspace from different classes are further separated by minimizing and maximizing the intra and inter class variation through 2D-LDA. To the best of our knowledge no such method has previously been proposed for palmprint identification. The effectiveness and the efficiency of the proposed method have been corroborated by extensive experiments conducted on two publicly palmparint dataset: multispectral  [48]  and PolyU  [19]. Experimental results showed very promising results when compared to both holistic  [4] ,  [5] ,  [7] ,  [8] ,  [36] ,  [37]  and structural methods  [19] -  [26].
IV. EXPERIMENTS AND RESULTS We performed a series of experiments to evaluate the proposed approach on two publicly available palmprint datasets: multi spectral  [48]  and PolyU  [19]. The obtained results are compared with seven state-of-art holistic methods including PCA  [4] , 2D-PCA  [7] , LDA  [5] , 2D-LDA  [8] , 2D-LPP  [9] , SRC  [36]  and LRC  [37]. In addition to eight structural coding-based techniques including Palm Code  [19] , Competitive Code  [20] , Ordinal Code  [21] , Fusion Code  [22] , Binary Orientation Co-occurrence Vector (BOCV)  [23] , E-BOCV  [24] , Robust Line Orientation Code (RLOC)  [25]  and Half Orientation Code (HOC)  [26]. For fair comparisons, we have followed the protocols and data splits proposed by Fei et al. [26].
A. PALMPRINT DATABASES The multispectral palmprint dataset 1 contains four independent datasets including Red, Green, Blue and Near Infrared (NIR) spectrums. 12 images per each hand and illumination from 250 subjects were captured. In the following we refer to this dataset by multispectral. In the left and right palmprint dataset 2 , 187 subjects were asked to provide 10 palmprint images per each hand. In the following this dataset is referred to as the PolyU. The content of datasets is summarized in Table  3. Note that the two palms of the same subject are considered as two distinct classes.
B. EXPERIMENTAL SETTING In our experiments we have used the provided palmprint region of interest of fixed size 32 × 32 (Figure  2 ) extracted by the algorithm described in  [19]. Since we are interested to the identification, the accuracy is measured by the Correct Classification Rate (CCR) corresponding to the ratio of correct classified images to overall images. For sake of comparison, we have used the same number of training samples in the literature following the proposed protocols and data splits. We perform our experiments with 2 and 4 training samples and the remaining ones as test. Each experiment is repeated 10 times to average out the effect of random subspace sampling and we report the mean accuracy and standard deviation. In the proposed method there are four parameters to tune including N , m, L and λ.
E. COMPUTATIONAL COST ANALYSIS Experiments were performed in Matlab on Dell Precision Tower 5810. The execution time increases linearly with the increasing dimensionality for either N and m as shown in Figure  6. For N = 10, for L = 500 and m = 10 our algorithm takes approximately 0. 60 seconds to process one palmprint image. Table  6  compares the execution time of our method to other state-of-the-art terhniqques. It can be seen that the speed of our algorithm is good compared to other techniques, the speed can further be increased by parallel processing.
Identification of the eps orthologous clusters Proteins orthologous to V. diabolicus HE800 biosynthetic cluster were searched in the downloaded genomes by blastp comparisons using the standalone BLAST+2. 2. 30 package  [10]. A local database gathering the 103 genomes was formatted with the makeblastdb program; a multifasta file containing the 16 V. diabolicus eps genes was used as the blastp query. Alignment length ratios were calculated as follows: MinLrap = Lmatch/min(Lprot1, Lprot2) and MaxLrap = Lmatch/max(Lprot1, Lprot2) where Lmatch = match length, Lprot1 (or Lprot2) = protein 1 (or 2) length and min (or max) = minimum (or maximum) of the two values  [11]. These values indicate, when both are equal to 1, that both whole proteins align. Alignment length ratios (close to 1), similar protein sizes, low expectation value (< 10 -25 ) and identity percentage (above 40%) were taken into account to identify the first protein (usually A); genomic context was further inspected to evaluate if neighboring genes encode proteins which also share homology with V.
In silico analyses of the protein coding sequence sets Proteins encoded by the genes inserted between D and F were identified by Blast search against the NCBI database  [12]. A phylogenetic tree was constructed using a concatenate of proteins; sequences were aligned with COBALT (https://www. ncbi. nlm. nih. gov/tools/cobalt/) and phylogenetic analyses were conducted with MEGA software v7 using the Neighbor-Joining method  [13, 14].
V. nigripulchritudo is also the sole Vibrio to have E protein which is also found in Fischeri, Enterovibrio and Phosphoreum species. V. vulnificus and V. mimicus are the only representatives of the Vulnificus and Cholerae clades, respectively, sharing the eps cluster. Nevertheless, V. mimicus seems to be an atypical species of Cholerae clade  [36, 37]. All the 11 Splendidus clade species possess the eps cluster. Moreover, all studied species of seven clades examined (Coralliilyticus, Enterovibrio, Fischeri, Mediterranei, Nigripulchritudo, Scophthalmi, Splendidus) share the eps cluster. On the other hand, betaine ABC transporter genes were found only in the Splendidus clade with the exception of V. kanaloae and V. toranzoniae. Blast search on the NCBI genome sequence database  [12]  excluding all Vibrionaceae species was used to infer the overall occurrence of the eps cluster.
Methods Plasmids. TALE nucleases were produced starting with plasmids for TALE repeats kindly provided by Dr. Bo Zhang  5. TALEN DNA-binding domains targeted the Fig. 5  HDR stimulation by the HE domain takes place at different target genes and can depend on the guide RNA used. a Relative frequencies of HDR induced by Cas9-HE were compared to those induced by Cas9 at five different target genes in HEK293 cells using previously published guide RNAs and donor plasmids  36. Targeted integration of the donor plasmid results in in-frame insertion of E2A-neoR cDNA  36. G418 (neomycin)-resistant colonies were counted after Cresyl violet staining to measure HDR-mediated events and normalized by the number of colonies obtained with Cas9 to give the relative HDR frequencies indicated. Data represented are from three independent experiments for TGIF2, RAD21, and CREB genes and from four experiments for ATF4 and GABP genes and are provided in Supplementary Fig.
Each sample was assigned to a primer set with a unique barcode to enable multiplex sequencing. PCR products were purified on a 2% agarose gel and treated by the MNHN genomics center and sequences on Ion Torrent PGM. A custom python pipeline was used to count and characterize indels as detailed in ref. 31. All sequence data from Immunohistochemistry. Briefly, cells were fixed with PBS containing 8% paraformaldehyde for 20 min at 4 °C. After washing with PBS, cells were permeabilized and blocked with PBS containing 0. 1% Triton-X-100 for 15 min at 4 °C. After washing with PBS, the cells were blocked with PBS containing 1% BSA and 10% horse serum for 1 h at room temperature. Then, the cells were incubated, with mouse anti-α-actinin antibody (dilution: 1/800; A7811; Sigma) and with rabbit anti-MYL2 antibody (dilution:1/600; 10906-1-AP; Proteintech), overnight at 4 °C.
For each sample, the events were captured on the MACSQuant VYB flow cytometer and analyzed with MACSQuantify Software. RPA foci formation assay. Twenty-four hours after plating, RG37 fibroblast cells were transfected with siRNA using Interferin (Polyplus, Ozyme). siNT(control): AUGAACGUGAAUUGCUCAA(dTdT). siCtIP: GCUAAAACAGGAACGAAUC. Three days after plating, cells were transfected with expression plasmids for Cas9, Cas9-HE, and Cas9-CtIP using JetPei (Polyplus, Ozyme). Five days after plating, cells were irradiated with X-rays at 6 Gy (XRAD 320, 1. 03 Gy/min). At 0, 1, 2, 4, 6, and 8 h after irradiation, cells on coverslips were pre-permeabilized with PBS-Triton 0. 25% for 3 min on ice, and then fixed in paraformaldehyde 2% for 15 min. The cells were then incubated with PBS containing 0. 5% Triton-X-100 for 5 min at RT for permeabilization.
After blocking in PBS containing 3% BSA and 0. 05% Tween-20 solution for 30 min at RT, immunostaining was performed using the following primary antibody: mouse anti-RPA (1:300, ANA19L, Millipore). Incubation was performed for 1 h 30 min at 37 °C with antibodies diluted in PBS containing 3% BSA and 0. 05% Tween-20. Next, the coverslips were incubated for 45 min with Alexa-488conjugated anti-mouse secondary antibody (Life Technologies) at 37 °C and mounted in mounting medium (Dako) supplemented with 40,60-diamidino-2phenylindole (DAPI) (Sigma). Images were captured using a Zeiss Axio Imager Z1 microscope with a ×63 objective equipped with a Hamamatsu camera. Acquisition was performed using AxioVision (4. 7. 2). Images were imported, processed, and merged in the ImageJ software.
35ble1are available from NCBI BioPRoject with the accession number PRJNA433647. Rosa26 locus, the CAG promoter controlling GFP expression flanked by homology arms of 800 bp of Rosa26 contiguous to the site of cleavage directed by guide RNA with the following target sequence GTGTATGAAACTAATCTGTC TGG 34 or (ii) when targeting the IL22BP locus, E2A-GFP cDNA flanked by 2-kbp homology arms to the following guide RNA target site TGTGTGCAGATTCCATAAAC TGG. The Cas9-HE or Cas9 mRNAs, sgRNA, and donor DNA were mixed (50, 10, and 2 ng/μl, respectively) and microinjected into the pronucleus and cytoplasm of zygotes. Zygotes surviving microinjection were implanted into pseudopregnant females. At day 14, females were sacrificed, and DNA was extracted from embryos for genotyping. Genotyping was performed using the primers and PCR conditions described in Supplementary Fig.
Acknowledgements Work reported here was supported by grants  ANR-II-INSB-0014 ,  ANR-16-CE18-0012-01 , AFM no. 18566 , from  Region Pays de la Loire  through  Biogenouest , and  ANR-14-LAB5-0008 ,  ANR-11-LABX-0016-01  ( LABEX IGO ),  ANR-10-IBHU-005  ( IHU-CESTI ). A. K. was partially supported by  ANRT. Plasmids were kindly sent by the  Wu lab  and made available from the  Joung, Church, Mendenhall, and Zhang labs through Addgene as  indicated in the Methods section. We are grateful to  Régis Debruyne  at the  MNHN genomics center  for deep sequencing of PCR products and to  Jean-Baptiste Renaud  for help with preliminary experiments.
To answer our first question, that is to find out 'Who is there?', a biomolecular analysis of microbial community composition was performed. PCR-amplified fragments of microbial 16S ribosomal RNA (rRNA) genes of all three samples were analysed using MiSeq Illumina sequencing to explore the archaeal and bacterial content of the samples  (Ramiro-Garcia et al. , 2016). Similarity of the observed microbial communities was plotted using principal component analysis (PCA) (Fig. 1A ). Furthermore, microbial communities were visualized in their original habitat, being on human skin, cat skin and plant leaves using electron microscopy. The electron microscopy also answered the question 'Where are they from?' (Fig. 2 ). Next to an understanding of 'Who is there?', data answering 'What are they communicating?' was gathered.
When case was hospitalised in a ward other than ICU, his/her C1 had to be hospitalised in a ward of the same type as that of case (medicine, surgery, paediatric, rehabilitation). The second control (C2) was the first inpatient with culture-negative sample(s), and without known carriage of CRE in the digestive tract since admission and until 3 days after the pre-case detection. C2 could be hospitalised in any ward. Written informed consent was obtained from all adult cases and controls and from parents for child cases and controls. Each pre-case was included (case) as soon as the standardised questionnaire was filled out for him/herself and his/her controls. This study was registered on ClinicalTrials. gov (Identifier: NCT02127450).
Acknowledgements We thank  Estelle Marcault  of the  Unité de Recherche Clinique Paris Nord Val de Seine (AP-HP)  for her help in the management of the administrative exchanges and financial aspects with the different hospitals, and  Marion Schneider , belonging to the same unit, for checking the patient files and preparing the data base for statistical analyses. We also thank all of the technicians of the different  Unités de Recherche Clinique  who visited the patients to file in the standard questionnaire and  Christel Pallu  for her secretarial assistance.