dataesr/scientific-paragraphs-categorization huggingface dataset:
The sea state monitoring system was calibrated with benchmark sea state records, which were reconstructed from the ship motion. Measurements were also compared against available observations from satellite-borne sensors to verify the robustness of the database. The data set includes observations around the Southern Ocean from latitude 34 to 74 • south. This comprises records in the open ocean across the Antarctic Circumpolar Current and in the Antarctic marginal ice zone. Due to its exposure to strong westerly winds, the Southern Ocean is subjected to harsh sea state conditions all year round. Although the expedition took place during the Austral summer, the data set contains records of severe sea states, in excess of the 90th percentile expected for the season. The expedition was conceived to bring together a broad range of Earth Science disciplines with the aim of exploring the interplay of processes in the lower atmosphere, ocean surface, subsurface, and land with simultaneous observations.
Additional data sets of atmospheric and oceanic variables that relate to sea state can be found in  Schmale et al. (2019 ), Rodríguez-Ros et al. (2020 ), Smart et al. (2020 ), Thurnherr et al. (2020 ), and Suaria et al. (2020). These include, but are not limited to, air-sea fluxes (mass, gas, heat, and momentum), aerosol concentrations, stable water isotopologues, and micro-fibres. Collocated observations have been the foundation for research on moist diabatic processes  (Thurnherr et al. , 2020)  and sea spray aerosols dynamics  (Landwehr et al. , 2021) , demonstrating capacities for surface waves to modulate water isotopologue concentrations and marine aerosols emissions, settling velocity and lifetime in the ma-rine boundary layer up to the cloud condensation height. The presented database has further potentials to support research enhancing wave model performances in the Southern Ocean, wave dynamics, including occurrence of rogue waves, wave dissipation mechanisms as well as other coupled processes, including those interconnecting waves with the upper ocean and sea ice in the Antarctic marginal ice zone.
Acknowledgements. This work was part of the  Antarctic Circumnavigation Expedition (ACE). MHD was partially supported by a PhD top-up scholarship from the  Australian Bureau of Meteorology. MHD, AA, FN and AT acknowledge technical support form the  Air-Sea-Ice Lab initiative. Financial support. This research has been supported by the  ACE Foundation and Ferring Pharmaceuticals  (Project 17), the  CRC-P initiative of the Australian Government  (grant no. CRC-P53991 ), and the  Australian Antarctic Program  (grant no. AAS 4434 ). Review statement. This paper was edited by  Giuseppe M. R. Manzella  and reviewed by three anonymous referees.
For microhomology analysis, junctions that contain insertions were not included. To evaluate insertions at the nickase site, the extracted sequences were filtered for unique sequences longer than the expected wild type sequence (≥376nt). These sequences were transformed to fasta format and a search for sequence homologies was performed using NCBI blast+ (v2. 10. 0) (21) , the hg19 human genomic database was completed by adding sequences of used plasmids and the del11q junction sequence. Sequence homologies to the nickase site at chr11 (chr11:106892584-107762754) were excluded. Furthermore, homologies that map to nickase site or del11q junction were selected to define intervals of homologies (alignment ≥87%). All other homologies (alignment ≥ 99%) were checked for overlaps with these intervals.
Moreover, genomic positions of detected homologies were compared to the list of aphidicolin-sensitive genes generated by Crosetto et al. (22) , which was downloaded from the BLESS supporting website http://breakome. utmb. edu/ Home. html. For statistical analysis of insertions, the numbers of reads containing homologies versus reads without homologies were evaluated by Fisher's exact test. All analyses were performed on a Linux Redhat system using custom bash or R (v3. 6. 1) scripting. The following R-packages were used: BiocManager, BSgenome, BSgenome. Hsapiens. UCSC. hg19, dplyr, IRanges, GenomeRanges, stringr, openxlsx, spgs, Biostrings, ggplot2, EasyGgplot2, devtools, circlize  (23).
Statistics and data availability No explicit power analysis was used for sample size estimation. N-values indicate biological replicates, which were independent experiments (cells handled separately) but sequenced on the Illumina platform as pooled (indexed) samples. All indices are provided together with sequencing data, which have been deposited in the ArrayExpress database at EMBL-EBI (www. ebi. ac. uk/arrayexpress) under accession number E-MTAB-8382.
Finally, we wanted to examine all sequences for presence of insertions that mapped to distant genomic regions or to transfected plasmids. To systematically detect insertions mapping to distant DNA sites at del11q junctions from our amplicon-sequencing dataset, we developed automated blast searches on all unique sequences longer than 376nt, corresponding to repair joints descending from refilled overhangs. Thereby, we found a significantly higher percentage of junctions with insertions mapping to distant sites in samples lacking SAMHD1 or expressing K312A variant compared to SAMHD1 proficient cells or cells expressing the catalytically active SAMHD1 K11A or K484T mutant (Supplementary Figure  S8 ; Supplementary table  S4 ). Corroboratively, increased dNTP levels upon dN addition in HEK293 and HeLa cells also yielded a higher percentage of junctions with insertions mapping to distant genomic regions or to transfected plasmids (Supplementary Figure  S5E  and F; Supplementary table  S4 ).
Acknowledgements J. Y. , J. C. , and Z. W. contributed equally to this work. This work was supported by the  Singapore Ministry of Education Academic Research Fund Tier 2  ( MOE2019-T2-2-127  and  MOE-T2EP50120-0002 ),  A*STAR  under  AME IRG (A2083c0062 ),  A*STAR  under  IAF-ICP (I2001E0067 (IAF-ICP)-P2. 1 )and I2001E0067 (Schaeffler)  P2. 1 , the  Singapore Ministry of Education Academic Research Fund Tier 1  ( RG90/19  and  RG73/19 ), and the  Singapore National Research Foundation Competitive Research Program  ( NRF-CRP18-2017-02 ). This work was also supported by  Nanyang Technological University.
The samples were coated with a 10 nm layer of gold before SEM observation. An INCAx-act detector was used to measure local chemical composition. Three measurements were carried out in the fusion zone and the first layer of deposited material of each sample. To evaluate the dimension and mechanical properties of the HAZ, hardness measurements were performed in the transverse cross-sectional plane 1 mm below the substrate top surface, as shown by the path A in Figure  2. These measurements were performed on one sample per alloy combination using a Vickers micro hardness testing machine (Auto-C. A. M. S. of Zwick Roell) with a load of 100 g and a duration of 15 s. In the PMZ, the peak temperature reached was above the melting point of the solute atoms on and along the grain boundaries. This zone was characterised by the presence of liquations, and its width was measured on SEM images using the Axiovision software.
Therefore, new improved anti-TB vaccines are needed. MTBVAC is a promising TB-vaccine candidate based on a live-attenuated Mycobacterium tuberculosis strain that contains major antigens absent in BCG, such as ESAT6 and CFP10  [15, 16]. MTBVAC was attenuated by two independent unmarked deletions in the phoP and fadD26 virulence genes, and protection against TB challenge was demonstrated in mice, guinea pigs, and rhesus macaques  [15, 17]. It has completed Phase I clinical trials for safety and immunogenicity in healthy adults in Switzerland  [18]  and new-borns in South Africa  [19]. MTBVAC is now in Phase IIa dose-finding trials in both adolescents and new-borns in South Africa (NCT02933281 and NCT03536117). As MTBVAC targets TB prevention in new-borns  [20] , it is important to demonstrate that the non-specific beneficial effects of BCG vaccination are maintained by MTBVAC  [21].
The current vaccines against Bordetella pertussis infection have shown limitations in the protection of infants  [22]. Whole-cell pertussis vaccines (wP) are reactogenic, limiting their acceptability and use beyond childhood  [23]. Acellular vaccines (aP) have an improved safety profile but provide only relatively short-term protection, likely because of skewing of the immune response towards a Th2 profile  [24] , whereas wP vaccines favor Th1 immune responses, similar to natural infection  [25]. A pertussis vaccination approach that combines the safety profile of aP with immunity induced by natural infection would thus be desirable. One approach would be the use of liveattenuated pertussis vaccines, such as BPZE1, currently in clinical development (NCT03541499)  [26]. An alternative or complementary approach could make use of the non-specific effects of BCG  [7, 8]  or in the future MTBVAC, to enhance the desired immune responses to pertussis vaccines.
Ecological epidemiologic studies To examine whether prior immunization with BCG is associated with improved pertussis control, an ecological epidemiologic study comparing pertussis incidence between countries that include BCG vaccination at birth in their national immunization programs (NIP) with those that do not, was performed. The ecological epidemiologic study from 192 countries worldwide used epidemiological data from 2012 to 2017 obtained from the WHO (https://www. who. int/es), with population and socioeconomic data from the World Development Indicators webpage (https://dataca talog. worldbank. org/dataset/world-development-indicators) and BCG vaccination policies from the BCG Atlas website (http://www. bcgatlas. org). DTwP/DTaP information were extracted from the WHO (https://www. who.
int/es) [27]. From these countries, 131 were analyzed after exclusion of those without BCG vaccine status  [18] , countries with missing data  [10] , with no pertussis incidence data  [33] , and those without information about DTwP/DTaP vaccination  [4]. Yearly incidence rates of pertussis were calculated for each country considering the average rates for the studied period to obtain robust estimations. Income levels were taken into account and used to categorize countries in "low or lower-middle-income" (LIC) and "uppermiddle or high income" (UIC) as a possible confounding variable. We also took into account the timing of the first BCG dose and the BCG vaccination coverage for countries with available data (http://www. bcgatlas. org). Mumps and measles incidence rates were considered as control pathologies.
Statistical analysis In all experimental studies, GraphPad Prism 5. 0 software was used for representation and statistical analyses. Statistical significances are indicated in the Figures (Fig. 1 , Fig. S1  and Fig. 2 ) by asterisks as follows *P-value < 0¢05, **P-value < 0¢01 or ***P-value < 0¢001. Outliers in experimental data were detected by the application of Grubbs' test with a significance level of 0¢05 and then excluded from the analysis. The normality of experimental data was evaluated by the Shapiro-Wilk test. The unpaired t-test was used to compare levels of total IgG in mouse serum between groups vaccinated with DTaP/DTwP alone and groups vaccinated also with MTBVAC/BCG (Fig. 1e , Fig. 1f , and Fig. 2b ). Cytokine levels did not pass the normality test. Therefore, the Mann-Whitney U test was used to analyze them.
S5 , Table  S1 ). The unpaired t-test was used to compare the three-dose DTaP vaccination coverage in a particular year between European countries that use or not BCG (Fig. S3 ) To avoid underestimation of incidence rates for the different analyses, countries with zero incidence data for the different pathologies were excluded from the analyses, since this can potentially be associated with small population sizes (for instance, Barbados, Seychelles, or the Solomon Islands), or lack of data (for instance, Egypt, Mali, Mongolia), or even ineffective health reporting systems. We considered 0¢05 as the significance level. The statistical results and Figures related to the epidemiologic study have been obtained using R 3. 4. 2 for MAC OS X,  [32] , and specifically, maps were created using the R package maptools.
Acknowledgments The authors acknowledge the Controle Imunobiol ogico section of  Instituto Butantan and Direcci on General de Salud P ublica, Gobierno de Arag on (Zaragoza, Spain)  for kindly providing DTwP and DTaP vaccines, respectively, and  Scientific and Technical Services from Instituto Aragon es de Ciencias de la Salud  and  Universidad de Zaragoza  for their assistance. FM-T research activities received support from the  Instituto de Salud Carlos III (Proyecto de Investigaci on en Salud ,  Acci on Estrat egica en Salud ,  GePEM ISCIII/PI16/01478 / Cofinanciado FEDER  and project  ReSVinext ISCIII/PI16/01569 /Cofinanciado FEDER;  Consellería de Sanidade ,  Xunta de Galicia  ( RHI07/2 -intensificaci on actividad investigadora,  PS09749  and  10PXIB918184PR ),  Instituto de Salud Carlos III  (Intensificaci on de la actividad investigadora  2007À2012 ,  PI16/01569 ),  Fondo de Investigaci on Sanitaria  (FIS;  PI070069 ,  PI1000540 ,  PI1901090 ) del plan nacional de I + D + I and 'fondos FEDER', and  2016-PG071  Consolidaci on e Estructuraci on REDES  2016GI-1344 G3VIP  ( Grupo Gallego de Gen etica Vacunas Infecciones y Pediatría ,  ED341D R2016/021 ).
E. B, N. A, J. G. A and C. M activities were supported by the  Spanish Ministry of "Economía y Competitividad " [Grant Nos  BFU2015-72190-EXP  and  BES-2012-052937  to E. B. ]; the  Spanish Ministry of "Ciencia, Innovaci on y Universidades"  [Grant No. RTI2018-097625-B-I00 ];  European Commission   H2020  program  European Union European & Developing Countries Clinical Trials Partnership (EDCTP)   RIA2016V-1637  and  "Gobierno de Arag on-Fondo Europeo de Desarrollo Regional (FEDER)   2014À2020 :  Construyendo Europa Desde Arag  on". L. C. C. L and A. I. K research received support from " Fundação Butantan ".
A mutation library with more than 10 7 clones was created from the 13 in silico predicted mutations using the transfer-polymerase chain reaction (TP-PCR) technique  41  and a set of mutagenic primers with predicted mutations. Cells associated with stronger fluorescence intensities were isolated by three rounds of FACS sorting. Stronger fluorescence was verified for the isolated single clones. The brightest isolated clone eUnaG1 showed a significantly higher fluorescent signal when using FACS than the parental variant (Figure  1g , engineering step 1). eUnaG1 was further improved by incorporating additional four mutations found in other selected colonies (Figure  1g , engineering step 2). Finally, our inspection of the crystal structure PDB ID 4i3b showed a solvent-exposed hydrophobic patch formed between residues V89, V93, V98, V100, and V111.
The dockerin proteins (Clostridium cellulolyticum, sequence ID: M93096. 1; Bacteroides cellulosolvens, AF224509. 3; Clostridium thermocellum, L06942. 1), the receptor IL-20RB, and the angiotensin-converting enzyme ACE2 are preferentially expressed as N-terminal fusions, in contrast to kanamycin resistance protein  48  and biotin ligase ID2 from Aquifex aeolicus  49  which best express as C-terminal fusions. Our inspection of 3D structures for all tested proteins explained only the lack of expression for the kanamycin resistance protein PDB ID 4H05. The strictly conserved C-terminus of this protein was found buried deep inside the structure, not allowing for C-terminus modifications. Therefore, we suggest experimental expression testing for every construct and its expression optimization to achieve good separation between nonexpressing and expressing populations (Figure  2g ).
The fitting of the standard noncooperative Hill equation was performed via nonlinear least-squares regression using Python 3. 7. The total concentration of yeast exposed protein was fitted together with two additional parameters describing the given titration curve similarly to. 74 rotein-Protein Docking Computations. The structures of PDB ID 1sso (Sso7d) and PDB ID 1swu (Streptavidin-APC) were used for initial structure manipulations before the docking. All nonstandard residues were manually deleted from the PDB files. The mutant residues were introduced (most probable rotamers) and minimized in UCSF Chimera. 75 The docking models were computed using the ClusPro server. 76 onfocal Fluorescence Microscopy. Yeast cells were imaged with an Olympus FluoView FV1000 IX81 Spectral/ SIM Scanner confocal laser-scanning microscope (Olympus GmbH, Hamburg, Germany), using 60 X phase-contrast oilimmersion objective, numerical aperture 1.
* sı Supporting Information The Supporting Information is available free of charge at https://pubs. acs. org/doi/10. 1021/acssynbio. 1c00395. pJYD plasmid sequence segment with cytoplasmic and cell surface expression of UnaG wild type, step-by-step protocol, secretory leader and linker optimization, scaffold sequences, randomized positions, library constructs, and stringent selection sequences, eUnaG2 properties and tailoring ALFA-tag binding nanobody for effective yeast display exposure by protein engineering, stability in growth media of the mNeonGreen fluorescence signal over time, secretory leader and linker optimization. pJYDC expression analysis, ALFA-tagged fluorescent proteins and fusions with DnbALFA for yeast display, multiple-sequence alignment of variants of the WD40 domain of ATG16L1, sequence design and testing of the Kan-Nfr scaffold, FoldEX and MSA comparison for mutation site identification in PDB: 4H05, and FACS gating strategy (PDF).
■ ACKNOWLEDGMENTS This research was funded by a grant from the  Israel Science Foundation  (ISF) number  1268/18 , a grant from the  Pasteur-Weizmann Collaborative Research Funds  and by the  United States-Israel Binational Science Foundation0  number  2015376. We thank  Dr. Shira Albeck ,  Dr. Tamar Unger , and  Dr. Yoav Peleg  from the structural proteomics unit (ISPC) of the  Weizmann Institute of Science  for their invaluable help in cloning and protein production and CB2 group for valuable discussion and support.
Methods The code and materials employed to conduct the experiment and analyses presented here can be found at: https://doi. org/10. 17605/OSF. IO/JSEU8. Due to data protection regulations, data cannot be publicly shared, but can be made privately available upon reasonable request. For the review process exclusively, data can be accessed here: https://osf. io/mkvez/?view_only=3cdfc3e68f1c442b8f20ca6edcef4998.
EEG recording and preprocessing Scalp potentials were recorded with a 64-channel Biosemi system with active electrodes and a sampling rate of 1024 Hz. Additional electrodes were used to track horizontal and vertical eye movements. Data analyses were conducted with MNE-Python  (Gramfort et al. , 2014). EEG signals were first cleaned from eyeblink artifacts using independent component analysis with a semiautomatic routine (fastICA algorithm). Visual inspection was used as a quality check. After removing ICA components, the raw signals were filtered with a pass band of 0. 5-35 Hz and re-referenced to the mastoids. Epochs -100 to 400 ms from tone onsets were extracted and baseline corrected with a prestimulus baseline of 100 ms. Epochs with an amplitude exceeding 150 μV were rejected to further clean the data from remaining artefacts.
Funding information This work was conducted in the framework of the  LabEx CeLyA (''Centre Lyonnais d'Acoustique ",  ANR-10-LABX-0060 ) and of the  LabEx Cortex (''Construction ,  Cognitive Function and Rehabilitation of the Cortex ",  ANR-11-LABX-0042 ) of  Université de Lyon , within the  program ''Investissements d'avenir"  ( ANR-16-IDEX-0005 ) operated by the  French National Research Agency (ANR). DQ, EB, and PV are supported by the  Danish National Research Foundation  ( DNRF 117 ).
B. SNR evaluation Thanks to the methodology presented in II, it is possible to evaluate the SNR ratio. Table  1  shows results obtained for fresh UO2 test rod for the three detectors beyond the collimator. The second case study concerns the simulated signal over noise ratio for a non-fissile material. In this theoretical case the value should be 0, because no neutrons (or at least very few) come from the test rod. The SNR is contained in the interval [-2. 0% ; 1. 5%]. As shown from this results, in the case of the aluminum test rod, the computed SNR is close to 0, as expected. This was considered as promising results for this preliminary modelling, and further analysis has to be realized with irradiated fuel pins, in order to increase the validation database of the model.
Histograms of masses that are built require the knowledge of the scattering coefficient  [6]. For the previous experiments (sodium loop configuration), this parameter has been determined thanks to a specific experimental campaign. For the Pressurized Water Loop configuration, the parameter introduced in the analysis will be the calculated one. Hence this work shows the possibility to access to such kind of information with acceptable uncertainties and reasonable calculation time. Results presented in Table  4  show the quite good consistency between these preliminary simulated values and the measured ones. A more complete analysis of the discrepancy between measures and calculation has now to be done, by performing sensitivity studies and increasing the experimental validation database. Counting rate of the i th column (r=right, c=center, and l=left)   ,  The value into bin j th : -1=test rod signal, -2= test rod (n,xn) or (n,n'), -3=elastic scattered neutrons, -4= all other contributions of the i th column (r=right, c=center, and l=left) evaluated with TAG option (TAG1 or TAG3).
The LHCb experiment at CERN is undergoing an upgrade in preparation for the Run 3 data taking period of the LHC. As part of this upgrade the trigger is moving to a fully software implementation operating at the LHC bunch crossing rate. We present an evaluation of a CPU-based and a GPU-based implementation of the first stage of the High Level Trigger. After a detailed comparison both options are found to be viable. This document summarizes the performance and implementation details of these options, the outcome of which has led to the choice of the GPU-based implementation as the baseline.
Introduction The LHCb experiment is a general purpose spectrometer instrumented in the forward direction based at the LHC. [1]  Although optimized for the study of hadrons containing beauty and charm quarks, LHCb's physics programme gradually expanded over the course of its first datataking period  1  , taking in Kaon physics, prompt spectroscopy, Electroweak physics, and searches for putative heavy and long-lived exotic particles beyond the Standard Model. The LHC provides a non-empty bunch crossing rate of up to 30 MHz, with a variable number of inelastic proton-proton interactions per bunch crossing (µ) which can be adjusted to suit the physics programme of each experiment. During Runs 1 and 2 LHCb took data with a µ of between 1. 1 and 2. 5, corresponding to an instantaneous luminosity of around 4 • 10 32 cm -2 s -1.
A fixed-latency hardware trigger (L0), based on calorimeter and muon system information, reduced the 30 MHz LHCb bunch crossing rate to ∼1 MHz at which the detector readout operated. These events were then passed to a two stage asynchronous High Level Trigger (HLT) system entirely implemented in software. In the first stage, HLT1, a partial event reconstruction selected events based on inclusive signatures, reducing the event rate by an order of magnitude. Accepted events were stored using a 11 PB disk buffer in order to align and calibrate the detector. After this procedure, events were passed to the second stage, HLT2, which had sufficient computing resources to run the full offline-quality detector reconstruction. A multitude of dedicated selections deployed in HLT2 reduced the data to an output rate of 12.