dataesr/scientific-paragraphs-categorization huggingface dataset:
As already described, clinical differences are observed between ART offspring that were exposed to different culture environments, highlighting the need to specifically examine the methylomes of these ART sub-groups. Here, we describe the saliva methylome of ART children (aged 9 or 10) that underwent embryo culture either in G3 (Vitrolife) or K-SICM (Cook) media. For this, we profiled DNA methylation on a genomewide scale, using the EPIC array, in the largest cohort of its kind to date. Comparison to naturally conceived children was attempted using data from the Flemish Environment Health Study (FLEHS) (Fig. 1A ).
Quality control and pre-processing Data were pre-processed using pre-processing functions contained within the RnBeads package  (Mu ¨ller et al. , 2019). Data were normalized using the subset-quantile within array normalization (SWAN) method  (Maksimovic et al. , 2012). Poor quality probes and samples were removed using the greedycut algorithm with a detection P-value threshold of 0. 05. Sites were further filtered out based on the following criteria: (i) if they were located on the sex chromosomes, (ii) if they were in close proximity to single-nucleotide polymorphisms, (iii) if more than 5% of the samples contained missing values and (iv) if they were not in a CpG context. Sites containing any missing values (between 0% and 5% missing values) were only used to aggregate sites into regions, they were excluded for all single site-based analyses.
Cellular deconvolution of saliva samples Cell composition of the samples was estimated using the reference-based Houseman algorithm  (Houseman et al. , 2014)  implemented using the ewastools package  (Heiss and Just, 2018). Probes for cell-type deconvolution were identified using DNA methylation signatures from sorted saliva samples collected from children  (Middleton et al. , 2022 ) (available at Gene Expression Omnibus GSE147318) yielding an estimate of the proportion of leucocytes and epithelial cells.
To identify differentially variable sites, the improved epigenetic variable outliers for risk prediction analysis (iEVORA) algorithm  (Teschendorff et al. , 2016)  was applied using the matrixTests package  (Koncevi cius, 2020). In brief, iEVORA applies Bartlett's test, a parametric test for differential variance, and a Student's t-test to each CpG site. Subsequently, sites reaching significance after multiple testing correction (false discovery rate (FDR) corrected P-value < 0. 05) of the Bartlett's test and reaching nominal significance (P-value < 0. 05 without multiple. testing correction) of the t-test are considered significant. This approach regularizes the result of the Bartlett's test which is usually overly sensitive to single outliers. The resulting differentially variable sites were used for Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses using functionality from the missMethyl package  (Phipson et al.
Funding This study was funded by  March of Dimes  ( 6-FY13-153 ). Additionally, it was further supported by  EVA (Erfelijkheid Voortplanting & Aanleg) specialty programme  (grant no. KP111513 ) from  Maastricht University Medical Centre (MUMCþ)  and the  Horizon 2020 innovation (ERIN)  (grant no. EU952516 ) from the  European Commission. The FLEHS dataset has been generated by the  Flemish Center of Expertise on Environment and Health  ( FLEHS 2016 ( FLEHS -2020 )), funded by the  Environment, Nature  and  Energy Department of the Flemish government. The views expressed in this manuscript are those of the author(s) and are not necessarily endorsed by the  Flemish government.
13  (Bradley et al. 2008; Watson et al. 2015; Knudsen et al. 2017). The high magnification (μ ∼ 9. 3) of this galaxy makes it an ideal target for a spatially resolved investigation of the ISM in the abundant population of sub-L * galaxies in the Epoch of Reionization, and indeed, recent high-resolution follow-up observations have successfully detected bright [C II] 158 μm and [O III] 88 μm emission lines (K. Knudsen et al. 2022, in preparation). Moreover, rich FIR continuum data have also been taken in bands 3, 6, 7, 8, and 9, providing valuable constraints on the FIR luminosity and dust temperature  (Bakx et al. 2021). The availability of deep, highresolution, multiwavelength ALMA data makes A1689-zD1 the ideal target to address the aforementioned issues and examine the extended [C II] emission around high-redshift galaxies.
The paper is structured as follows: In Section 2, we describe the data reduction steps for both ALMA and HST data. We report the results for the spatial extent of the [C II], [O III], UV, and FIR emission in Sections 3. 1 and 3. 2. In Section 3. 3, we spatially resolve the dust temperature, which we use in Section 3. 4 to derive the spatially resolved L [C II] -SFR and L [O III] -SFR relations for A1689-zD1. We present the line spectra of [C II] and [O III] in Section 3. 5. Finally, in Section 4 we discuss our results, including the interpretation of the extended emission as a "[C II] halo" versus an extended disk, and the physical origin of the emission. Throughout this work, we assume a ΛCDM cosmology with H 0 = 67. 4 km s -1 Mpc -1 , Ω M = 0. 315, Ω Λ = 0. 685 (Planck  Collaboration et al.
71 GHz. Similarly, bands 8 and 9 were tuned to the [O III] 88 μm, and [O III] 52 μm lines, respectively. Analysis of the [O III] 52 μm line will be presented in a separate, upcoming paper. Band 3 observations were tuned to cover the CO(7-6) and CO(6-5) lines. The Common Astronomy Software Applications package (CASA;  McMullin et al. 2007 ) was used for reduction, calibration, and imaging. The data were first processed via the standard ALMA pipeline reduction, which was sufficient for these observations. All images were produced with the tclean task in CASA, using natural weighting to maximize sensitivity. Cleaning was done using the "auto-multithresh" automasking algorithm  (Kepley et al. 2020) , initially down to the 3σ level but expanded to a lownoisethreshold of 1σ. In order to image both compact and extended emission, we apply the multiscale deconvolver  (Cornwell 2008)  with scales of zero (delta-function) one, and three times the beam size (i.
HST Data In addition to deep ALMA observations of FIR line and continuum emission, we use archival Hubble Space Telescope (HST) data to probe the rest-frame UV continuum of A1689-zD1  (Watson et al. 2015). We obtain images taken with Hubble WFC3/IR in the J (F125W) and H (F160W) bands. At z = 7. 13, these bands trace the UV continuum at 1350 Å < λ < 2050Å. These wavelengths are redder than the Lyman limit and unaffected by the Lyα forest, making this a good probe of the rest-frame UV continuum and the unobscured SFR. Recent works (e. g. ,  Rujopakarn et al. 2016; Dunlop et al. 2017; Fujimoto et al. 2019; Tamura et al. 2019; Herrera-Camus et al. 2021 ) have shown that there sometimes exist offsets of 0 1-0 3 between HST and ALMA astrometry, which can significantly impact results of comparisons between highresolution observations.
Source Plane Reconstruction To analyze the intrinsic ISM morphology of A1689-zD1, we reconstruct the ALMA and HST images into the source plane, correcting for the lens magnification and deflection. The magnification of A1689-zD1 is derived to be a factor of μ = 9. 3 ± 0. 5 based on the mass model originally published in  Limousin et al. (2007) , and refined to include spectroscopic information of multiple systems as described in  Bina et al. (2016). This parametric strong lensing model is constructed using the LENSTOOL  (Jullo et al. 2007)  software, which provides a set of models sampling the posterior distribution of each parameter of the mass distribution, allowing us to derive the statistical error on the magnification. The uncertainty of 0. 025 dex of the magnification at the location of the source was also confirmed independently as described in  Watson et al.
uv-plane Visibility Profiles We also analyze the spatial structures of the different emission in the uv-visibility plane using the Python package uvplot (Tazzari 2017). In the bottom panel of Figure  A2 , we show the real part of the visibility amplitude in bins of the uvdistance, which is inversely proportional to the observed angular scale θ. We apply a single and double Gaussian fits to the [O III], [C II], and dust continuum profiles (shown in blue and red, respectively). Based on the reduced chi-squared ( 2 c n ) statistic, the single Gaussian is a reasonably good model for the [O III] line and the dust continuum in both bands, with consistent FWHMs of ∼1 0; on the other hand, for the [C II] line, we find a significant offset from the best-fit single Gaussian at the shortest uv-distance regime far beyond the error scales.
Summary In this paper, we present deep ALMA observations of the strongly lensed, z = 7. 13 galaxy A1689-zD1, focusing on the [C II] 158 μm and [O III] 88 μm fine-structure lines as well as the FIR continuum. Utilizing archival HST data to probe the UV continuum, we compare the morphology and spatial extent of each wavelength of emission in order to examine the multiphase nature of the ISM. Our major findings are summarized below. Much remains uncertain about the ISM/CGM properties, kinematics, and evolutionary stage of A1689-zD1. As A1689-zD1 will be observed in JWST Cycle 1 (Prop. ID 1840, PI: Alvarez-Marquez), future work will be able to take full advantage of imaging from the rest-frame UV to the optical. The strongly gravitationally lensed nature of this galaxy makes it a prime target with which to constrain the processes of early galaxy evolution.
This work was supported by the  U. S. NSF  under grant  OISE-2005578  ( DAWN-IRES ). This project has recieved funding from the  European Union 's  Horizon 2020 research and innovation program  under the  Marie Sklodowska-Curie  grant agreement No. 847523  " INTERACTIONS. "H. B. A. acknowledges the support and collaboration of the mentors and fellow students involved in the  2021 DAWN-IRES program. S. F. and D. W. acknowledge support from the  European Research Council (ERC)   Consolidator Grant funding scheme  (project  ConTExt , grant No. 648179 ) and  Independent Research Fund Denmark  grant  DFF7014-00017. The Cosmic Dawn Center is funded by the  Danish National Research Foundation  under grant No. 140. K. K. acknowledges support from the  Knut and Alice Wallenberg Foundation. T. H. was supported by  Leading Initiative for Excellent Young Researchers, MEXT, Japan  ( HJH02007 ) and  KAKENHI  ( 20K22358 ).
A. K. I. is supported by  NAOJ ALMA   Scientific Research Grant Code   2020-16B. M. J. M. acknowledges the support of the  National Science Centre, Poland  through the  SONATA BIS  grant  2018/30/E/ST9/00208. Much of this work was conducted on the ancestral land of the  Meskwaki, Sauk , and  Ioway Peoples.
Main text 1) It was certainly not our intention to wilfully misrepresent Hall's data -which include excellent and incisive experiments and analyses. The impression that she has, merely reflects the fact that we have been consistently prudent and cautious in our interpretation of in vivo transposition data until such time as the intermediates in the process, in this case of conservative integration, have been identified. This can be seen in other IS family chapters of TnPedia We did not mean to imply that the entire IS6 family also possess the mechanistic variation proposed by Hall (i. e. , targeted conservative integration). That has clearly yet to be addressed. Consequently, to continue to provide a consistent structural framework for understanding the relationship between the nearly 6000 IS in the ISfinder database, we continue to adhere to these rules and include IS26 and close relatives as a sub-group within the IS6 family.
ACCEPTED MANUSCRIPT/ CLEAN COPY The movement of the champagne cork was controlled with a user-defined function (UDF) imported from the ANSYS Fluent software. In this function, the ejection speed of the cork stopper is fixed at 18. 6 m. s -1 (Fig. 2 ), as determined from a previous set of experimental observations conducted under the same flow conditions 6 (Fig. 3 ). These preliminary experiments proved to be essential to determine the speed of movement of the plug and thus to impose a realistic temporal evolution of the contour of the simulated flow field. It is noteworthy to mention that the elasticity of the cork stopper (visible on the experimental time sequence presented in Fig. 3 ) was not taken into account in the present simulations for the sake of simplicity. This is the reason why the base of the cork did not adopt the typical mushroom shape of a champagne popped cork but remained cylindrical once expelled from the bottleneck (as shown in Figs.
B. Calculation method. Our fluid dynamics calculation study was based on the commercial ANSYS Fluent software. More specifically, in the present study, Navier-Stokes axisymmetric equations and species transport equations (Eq. 1) were used in the finite volume formulation along with the mixing form for all the flow variables. where   is treated as a constant. In the current studies, flow is non-reacting hence the production rate of each species would be zero. This commercial solver accounts kinetic theory based ideal gas law for calculation of viscosity and thermal conductivity.
2014 , Lombard et al. 2015 , Sandoval-Denis et al. 2018 , 2019 , Crous et al. 2021b). The main goal of FUSA is to publish modern diagnoses of fusarioid taxa, based on multilocus phylogenies, ideally accompanied by genomic data, morphological descriptions, as well as physiological and ecological data. These data will subsequently be placed in an online database, www. fusarium. org, linked to the fusarioid-ID database, which aims to provide a stable, regularly updated, and user-friendly platform for the identification of Fusarium and other fusarioid genera and species through advanced BLASTn queries of well-curated DNA sequences. Contributors are encouraged to use FUSE as an instrument for typification events to stabilise the application of names by designating accurate lectotypes, epitypes and neotypes; proposing taxonomic novelties such as new combinations and replacement names; and publishing undescribed morphologies for known taxa (asexual/sexual-morph connections).
MATERIALS AND METHODS Methods, media, protocols and molecular analyses follow guidelines as outlined by  Crous et al. (2021b). Sequences derived in this study were deposited in GenBank (Table  1 ), alignments and phylogenetic trees in Figshare (www. figshare. com; doi identifier 10. 6084/m9. figshare. 20076044), and taxonomic novelties in MycoBank (www. MycoBank. org; Crous et al. 2004). Alignments composition and evolutionary models are summarized in Table  2.
Genome assembly DNA was extracted from mycelium grown on SAM  (Kruse et al. 2017 ) culture plates as described earlier  (Mishra et al. 2018). Library construction and short-read sequencing was done by a commercial sequencing provider (BGI, Hongkong, PRC). Pair-end reads (150 bp, 400 bp insert) were cleaned with Trimmomatic v. 0. 39  (Bolger et al. 2014)  with the following settings: remove leading and trailing low quality (< 3) or N bases; cutting when the average quality per base dropped below 15 in a 4-base sliding window; Illumina adaptor removal; removing reads shorter than 70 bp. Cleaned reads were used to assemble genomes with velvet v. 1. 2. 10 (Zerbino & Birney, 2008 ) using a k-mer value of 93. Assembly statistics were obtained using the stats. sh script of the BBTools package  (Bushnell 2021).
The assembly quality was evaluated with BUSCO v. 5. 2. 2 against the fungi_odb10 library  (Manni et al. 2021). Genome annotation was done with maker v. 3. 01. 03 (Cantarel et al. 2008)  for gene prediction using the protein sequences of Fusarium oxysporum from the UniProt database as reference. All genomes were submitted to GenBank (see Table  3  for details).
Phylogeny For this study, three multilocus analyses were carried out. The datasets were analysed using IQ-TREE v. 2. 1. 3 (Nguyen et al. 2015 , Minh et al. 2020 ) and MrBayes v. 3. 2. 7  (Ronquist & Huelsenbeck 2003)  as indicated in  Crous et al. (2021b). An overview of currently accepted taxa in Fusarium species complexes treated in this study is shown in a phylogeny constructed from combined rpb1, rpb2 and tef1 data of 62 strains, encompassing eight species complexes i. e. , Fusarium aywerte (FASC), F. buharicum (FBSC), F. burgessii (FBURSC), F. camptoceras (FCAMSC), F. chlamydosporum (FCSC), F. citricola (FCCSC), and F. concolor (FCOSC), including the outgroup taxa (F. lateritium NRRL 13622 and F. stilboides NRRL 20429, both species belonging to the F. lateritium species complex) (Fig.
2 ). IQ-TREE best tree (log-likelihood -15164. 779) was found after 117 iterations. Bayesian analysis lasted for 1 535 000 generations and recovered 3 072 trees from which 2 304 where sampled. Two strains obtained from soil in Zimbabwe  (MUCL 58143, 58144)  are formally described below as the novel species Fusicolla elongata. Sequence data from additional Fusicolla species known from culture  (Fu. gigas, Fu. hughesii, Fu. guangxiensis)  or sequenced from fungarium specimens (Fu. reyesiana) were initially included in the phylogenies and later removed from the final analyses due to their incomplete datasets (nrDNA or only ITS1 and ITS2 sequences available). Two species recently invalidly published i. e. , Fu. gigas and Fu. guangxiensis are re-validated here based on the original protologue  (Liu et al.
Genome announcements Other than providing illustrations, diagnoses and multilocus phylogenies of fusarioid taxa, a further aim of the FUSA series is to also provide access to genome data of newly sequenced species, the first of which are published here. The assemblies of Fusarium secorum (CBS 175. 32), Microcera coccophila (CBS 310. 34), Rectifusarium robinianum (CBS 430. 91), Rugonectria rugulosa (CBS 126565), and Thelonectria blattea (CBS 952. 68) are announced here. They were obtained from high coverage Illumina data (168-283×). Quality assessment done with BUSCO against 758 genes from the library for Fungi showed a high completeness (> 98 %) and a low duplication level (< 1 %) for the analysed genomes. The genome sizes varied from 34. 7 Mbp to 50. 5 Mbp. Assemblies of R. rugulosa, M. coccophila, R.
robinianum, and T. blattea showed similar number of scaffolds while in the F. secorum genome their amount was significantly increased due to a high number (> 10 k) of scaffolds with sizes smaller than < 1 kbp. The total number of annotated gene models varied from 24 411 in M. coccophila to 46 001 in F. secorum. All assemblies were deposited in GenBank, detailed statistics and BioProject numbers are shown in Table  3.
61 T NRRL 43631 2 acl1: partial ATP citrate lyase gene; ITS: internal transcribed spacer regions with intervening 5. 8S nrRNA gene; LSU: 28S large subunit of the nrDNA; rpb1: partial DNA-directed RNA polymerase II largest CBS 445. 67 T CBS 122438 T CBS 130394 CBS 145. 25 NT CBS 677. 77 NRRL 34013 NRRL 34019 CBS 511. 75 T subunit gene; rpb2: Fusarium chlamydosporum gene; tub2: Fusarium spinosum Fusarium sporodochiale Fusarium atrovinosum partial translation elongation factor 1-alpha NRRL 13338 99/1/33. 3 100/1/100 100/1/66. 7 100/1/50 100/1/100 100/1/100 -/0. 99/-99/1/33. 3 Fusarium peruvianum 100/1/50 Fusarium sp. (FCSC 9) partial DNA-directed RNA polymerase II second largest subunit gene, two accession numbers refer to two non-contiguous fragments; tef1: CBS 183. 34 T CBS 124. 73 T CBS 190.
Assembly size [Mbp] No. of scaffolds Scaff. N50 [kbp] Longest scaff. [kbp] Total no. of CDS Fusarium secorum CBS 175. 32 PRJNA826072 99. 1 % 50. 5 15 085 17. 3 156. 3 46 001 Microcera coccophila CBS 310. 34 PRJNA826070 98. 7 % 36. 7 2 725 27. 3 177. 9 24 411 Rectifusarium robinianum CBS 430. 91 T PRJNA826068 98. 7 % 34. 7 2 358 27. 4 219. 8 25 210 Rugonectria rugulosa CBS 126565 PRJNA826071 98. 8 % 46. 9 2 884 56. 0 353. 8 30 877 Thelonectria blattea CBS 952. 68 T PRJNA826075 98. 9 % 38. 9 3 001 34. 8 221. 9 26 348.
Primary Cultures (Figure 1C) Primary cultures of hippocampal neurons (Figure  1C ) were obtained from caspase reporter pregnant females on day E17 as previously described  (Beraldo et al. , 2010 (Beraldo et al. , , 2013))  (Data S1) was used to correct for a stable shading abnormality in our multiphoton system. Clarification was performed as previously described  (Hama et al. , 2011). Hippocampal Cultures (Figure  1C ) On DIV 7, hippocampal neurons were treated with either vehicle or staurosporine (100 nM). Cells were imaged at 3, 12 and 24 hours after treatment, and caspase-3 activity was measured using fluorescence from the mCerulean reporter. Fluorescence of neuronal cultures from 4 independent embryos of either sex was quantified using an FV1000 Olympus confocal microscope (excitation 405 nm and emission 470-485 nm).
Then the apex of the left ventricle was pierced with a 25-gauge needle attached to a 25-ml syringe containing 25 ml of 1:1 10% neutral buffered formalin : PBS plus 100 μl of 1000 U/ml heparin. Immediately, the solution was forced into the circulation at a moderate pace, and the right atrium was snipped as it expanded. All 25 ml of formalin/PBS/heparin was forced through the circulation at a steady pace within 1-2 minutes. Each mouse was assessed for paleness of liver and stiffness of body; 1 mouse out of the 42 used in the stress experiment was determined to have a poor perfusion based on these criteria and was later excluded from data analysis before the randomization was unblinded. Immediately after perfusion, the skin and mandible were carefully dissected from the skull, such that the skull was not compressed or dropped during the procedure.
5 SD greater than the mean for all 42 samples; this 1 poorly perfused sample was excluded from the analysis. For each round of the replication, the double-blind was broken only after the data analysis was complete. For the male-female comparison in Figure  4F , the protocol was the same as above except there was no stress intervention. For the cFos study in Figure  4A , B, the mice were unstressed and there was only 1 experimental group, so there was no blinding. Sections were stained overnight at 4 C with 1:500 c-Fos ((9F6) Rabbit mAb #2250, Cell Signaling Technology) primary antibody, and again overnight at 4 C with 1:500 Alexa Fluor 594 (Thermo Fisher Scientific) secondary antibody. The Imaris Spots function parameters were the same as for Figure  4G  and were applied to both channels. The Colocalize Spots function was used to remove repeated nuclei that met criteria for both channels, so that each nucleus was counted only once during the statistical analysis.
For the viral injections in Figure  4C-E , since mice were unstressed and constituted 1 experimental group, there was no blinding prior to data analysis. Mice were anesthetized with continuous 1. 5% isoflurane and injected stereotactically in the BLA at AP -1. 4, ML +/-3. 1, DV -3. 9 with 0. 5 μl of AAV10 containing 1:1 10,000-fold diluted CaMKII-Cre-ER : undiluted EF1a-CreDIO-FARN-mApple or 1:10 undiluted CaMKII-Cre-ER : undiluted EF1a-CreDIO-Actin- Chromobody®-mApple at a rate of 0. 25 μl/min. The needle was held in place for an additional 3 minutes. Two weeks later, mice were injected IP with 20 mg/kg tamoxifen. And 1-2 weeks after tamoxifen administration, mice were perfused as described above. Dendrite length was calculated with Imaris' Filaments function, while blind to caspase reporter intensity, which was subsequently measured using Imaris' Spots function.