dataesr/scientific-paragraphs-categorization huggingface dataset:
However, these tissues are not completely flattened, their depth has only been reduced by about 3-fold. This still retains some valuable z-axis information as demonstrated by the three dimensional and depth coded datasets presented here. The entirety of adipose nerve fiber density is also maintained, which is important if the goal is comprehensive quantification of tissue innervation. If exact spatial organization is required as an imaging endpoint, optical clearing may be a preferred method; however, clearing methods also have their limitations and are well known to cause tissue structural changes such as tissue expansion, shrinkage, and stiffening which could also alter spatial organization. A final option is to obtain a block of tissue in order to assess innervation without ZDR (as we did to observe the neuro-adipose nexus), but this would not capture the heterogeneity of innervation across an intact tissue.
Widefield microscopy All widefield micrographs were captured on a Nikon E400 with either a DS-fi2 color camera (Nikon, Japan) It is also worth noting that the Python and MATLAB scripts developed for this study, provided above, allow the user to adjust the described parameters to account for batch differences due to variation in fluorescence intensity and autofluorescence. These adjustments can be made a priori or while looking at the skeletonized product of a single tile to quickly visualize how each adjustment changes the skeletonization. Fluorescent stains included: For vascular staining, tissues were incubated in isolectin IB 4 stain conjugated to either Alexa Fluor 594 (1ug/ml, ThermoFisher Scientific, Waltham, MA, USA; Cat. #I21413) or 647 (1ug/ml, ThermoFisher Scientific, Waltham, MA, USA; Cat.
QUANTIFICATION AND STATISTICAL ANALYSIS Cell size (N = 3-4) (Figure  2D ) and whole depot neurite density (N = 4-6) (Figure  7B ) was quantified using unpaired two-tailed t-tests with assumed Gaussian distribution and equal standard deviations in GraphPad Prism 9. Comparisons between Z-maximum projection, Z-slice averages, and Z-slice maximums (Figure  S5 ) were made using an F-test on linear regression fits and calculated using the R language, version 3. 4. 4.
ACKNOWLEDGMENTS Dr. Benjamin Harrison  of  UNE  for developing earlier iterations of whole depot innervation quantification method (published in Blaszkiewicz et al. , 2019a). Morganne Robinson ,  Thomas Szewczyk  and  James Miller  for technical assistance. Dr. Ian Meng  of The  University of New England  for gifting Na v 1. 8 reporter mice adipose tissues. Dr. DustinUpdike  of  MDI Biological Laboratory  for assistance with pilot imaging studies. This work was supported by  NIH   R01  ( 1R01DK114320-01A1 ) and  American Heart Association (AHA) Collaborative Sciences Award  ( 18CSA34090028 ).
II. RESULTS AND DISCUSSION The search for the optimal distribution of metal nanoparticles or nanostructures, able to maximize the heat generation, represents an open challenge. The basic idea is to shift the absorption cross section (σ abs ) so as to match the laser pump line, thus increasing the thermal variation. To this aim, several attempts have been made by optimizing the NPs distribution thus creating efficient hot-spots and square, diagonal, octagonal and circular patterns have been considered  [33] [34] [35] [36] [37]. As an approach to challenge the problem in a more systematic way, we implemented a Matlab code that considers main analytical curves as circles, parabolas and hyperbolas as traces along which Au spheres or disks can be positioned (Figure  1a ). For each obtained arrangement, COMSOL Multiphysics calculates the corresponding absorption cross section that is strongly dependent on the given design in the investigated spectral range (Figure  1b ).
ACKNOWLEDGEMENTS A. F. G. P and R. C thank the " Area della Ricerca di Roma 2" ,  Tor Vergata , for the access to the  ICT Services (ARToV-CNR)  for the use of the  COMSOL Multiphysics Platform and Origin Lab , and the  Infrastructure "BeyondNano"  ( PONa3-00362 ) of  CNR-Nanotec  for the access to research instruments. This work has been supported by the  Agence Nationale de la Recherche  and the  FEDER  ( INSOMNIA  project, contract " ANR-18-CE09-0003 "). Financial support of  NanoMat  ( www. nanomat. eu)by the  Ministre de lenseignement suprieur et de la recherche , the  Conseil rgional Champagne-Ardenne , the  Fonds Europen de Dveloppement Rgional (FEDER)  fund, and the  Conseil gnral de lAube  is also acknowledged by A. H and T. M.
At each station, 30 photoquadrats of 0. 25 m 2 (50 × 50 cm) were taken along three transects of 10 m length with an underwater camera (W300, Nikon, Tokyo, Japan). Percent cover was estimated using the Coral Point Count with Excel extension (CPCE 4. 1)  [41]  software. On each photo, 100 random points were used to quantify percent cover of major benthic categories: hard corals (scleractinian corals and the calcareous hydrocoral Millepora), dead corals (defined as recently dead coral with skeletons covered by thin layer of turf algae), soft corals (Alcyonacea, mainly represented by Xenia sp. and Sarcophyton sp. ), algae (coralline algae, macroalgae, turf), other living taxa (including sponges, hydroids, zoanthids, corallimorphs, tunicates and sea anemones), and abiotic substrates (rubble, and sand).
Acknowledgments: We thank  Jamal Mahafina , Director of the IH. SM, for facilitating this research, and all the staff of IH. SM for their logistical support. We also thank  Monja Theodore ,  Max Gasimandova ,  Noelson ,  Tovo  and all the volunteers who helped us during the sampling period. The authors gratefully acknowledge the critical comments and constructive remarks made by  Jane Ballard  and  Michel Pichon  on manuscript drafts.
This technique is an automated capillary size separation and nano-immunoassay system for performing a gel-free, blot-free, and hands-free capillary-based immunoassay that integrates and automates the entire protein separation and detection process with home-made antigens. To quantify the absolute response to viral proteins from samples, we followed the manufacturer's standard method for 12-230 kDa JessTM separation module (SM-W004). First, the poliovirus antigen (0. 24 µg/µL) was mixed with fluorescent 5× master mix (Protein Simple) to achieve a final concentration of 0. 20 µg/µL in the presence of fluorescent molecular weight markers and 400 mM dithiothreitol (DTT, Protein Simple). This preparation was then denatured at 95 • C for five minutes. The ladder (12-230 kDa) and viral proteins were separated in capillaries as they migrate through a separation matrix at 375 volts.
A protein simple proprietary photoactivated capture chemistry was used to immobilise separated viral proteins on the capillaries. Faecal samples were added and incubated for 30 min. After a wash step, goat HRP-conjugated anti-human IgG/IgA antibodies (Jackson ImmunoResearch, Ely, UK) diluted at 1:250 were added for 30 min. Finally, the chemiluminescent revelations of the ladder and samples were established with peroxide/luminol-S (Protein Simple). The digital image was analysed with Compass for SW software (v 4. 1. 0, Protein Simple), and quantified data of the detected proteins was reported, including the molecular weight, chemiluminescence intensity, and signal/noise ratio. Western blot analyses were performed according to this protocol, using (1) the polio vaccine and (2) the purified Ibou002 virus strain as antigens.
We then performed a western blot by Jess TM to characterise the specific antibodies. Western blot analysis of antibodies from gorilla faeces detected a single band of around 14 kDa using the antigens extracted from poliovirus vaccine. These data do not allow us to confirm the gorilla's immunisation from poliovirus due to the absence of antibodies against the main proteins of the poliovirus, namely VP1, VP2 and VP3. In addition, PCR testing for poliovirus RNA was negative  [23]. Based on the circulation of recombinant Enterovirus C  [23]  having at least three genes very close to the poliovirus in this geographical area, we then hypothesised that Sid the gorilla may have been suffering from the sequelae of a polio-like illness caused by this virus. Indeed, these polio-like diseases can be caused in humans by chimeric/recombinant.
We then performed a western blot by Jess TM to characterise the specific antibodies. Western blot analysis of antibodies from gorilla faeces detected a single band of around 14 kDa using the antigens extracted from poliovirus vaccine. These data do not allow us to confirm the gorilla's immunisation from poliovirus due to the absence of antibodies against the main proteins of the poliovirus, namely VP1, VP2 and VP3. In addition, PCR testing for poliovirus RNA was negative  [23]. Based on the circulation of recombinant Enterovirus C  [23]  having at least three genes very close to the poliovirus in this geographical area, we then hypothesised that Sid the gorilla may have been suffering from the sequelae of a polio-like illness caused by this virus. Indeed, these polio-like diseases can be caused in humans by chimeric/recombinant viruses  [20] [21] [22].
Acknowledgments: We thank  Lucile Pinault  and  Rita Jaafar  for their help and advice in the development of the experiments. This work was supported by the  French Government  under the " Investissements d'avenir" (Investments  for the future) programme managed by the  "Agence Nationale de la Recherche " (reference:  10-IAHU-03 ). Research and administrative authorisations for the collection of samples were granted by the  Congolese Ministry of Scientific Research and Technological Innovation  (n •  003/MRSIT/DGRST/DMAST ), the  Ministry of Forestry Economy and Sustainable Development , represented by the  Congolese Agency for Wildlife and Protected Areas  ( N • 0134/ACFAP-DTS ) and (N •  94/MEFDD/CAB/DGACFAP-DTS ), and the  Ministry of Health and Population  ( N • 000220/MSP-CAB-17  and  N • 208/MSP/CAB.
Omission of the primary antibody was used as a negative control. The chromatin was then counterstained with DAPI (diluted 1:1000 in PBS). The embryos were then observed using an inverted ZEISS AxioObserver Z1 microscope equipped with an ApoTome slider, a Colibri light source, and an Axiocam MRm camera controlled by Axiovision software (version 4. 8) (MIMA2 imaging platform, INRAE, Jouy-en-Josas, France 1 ). ICM cells were identified indirectly from the immunocytochemistry location of expression sites for prostaglandin G/H synthase 2 (PTGS2), a trophectoderm-specific protein seen during preimplantation development in ruminants  (Charpigny et al. , 1997; Sandra et al. , 2017). The total numbers of cells per trophectoderm and per ICM, and the numbers of OCT4labeled ICM cells, were all estimated using ImageJ software 2.
Using ImageJ software 2 , the area of the ICM was outlined manually on the image stack of the blastocyst, thus determining the region of interest (ROI) for each embryo. The ROI was then used to determine the total integrative density for the TUNEL signal and the ratio of TUNEL positive cells to total ICM cells. Three-dimensional (3D) projections of DAPI/TUNEL labeling were reconstructed using IMARIS 8. 3. 1 software (Bitplane, Switzerland).
Following PCR, a melting curve was performed on the amplified products to ensure that only specific PCR amplicons had been obtained and quantified. The expression of all target mRNAs was determined in each sample during independent assays. The PCR value was expressed as a ratio to ACTB mRNA for each sample. The primer sequences were designed using the Primer3Plus tool 4. Primer sequences, product sizes and accession numbers are provided in the Supplementary Table  SMM1.
Data Processing and Statistics Statistical analysis was performed under R software (v3. 6. 4). In experiments to evaluate (i) the cleavage rate, (ii) the blastocyst rate, and (iii) the post-thaw survival rate, data were analyzed using a generalized linear mixed-effects model (GLMM, glmer function, 'lme4-package' version 1. 1-21 and 'lmerTestpackage' version 3. 1-2 using a binomial distribution with logit link). The different embryo IVP sessions were considered as random variables. The different IVP conditions ("SC, " "SF" and "SF + PGE2") and days of post-thaw culture (day-1, day-2, and day-3) were fixed factors. Estimated marginal means (least-squares means) and post-hoc tests were performed using the 'emmeans' package, version 1. 4. 5, with emmeans and pairs functions. In the experiments on post-thawing embryo survival, the frequency of ICM cells expressing OCT4, the total number of trophoblastic cells and the quantification of signals from the TUNEL experiments analyzed using a linear mixed-effects model (GLMN, with the lmer function 'lme4-package, ' version 1.
1-21). The IVP condition was the fixed factor and the embryo production session the random effect. Contrasts were determined using the 'emmeans' package with emmeans and pairs functions. For the quantification of gene expression by RT-qPCR, the cDNA copy numbers were expressed relative to ACTB cDNA copy numbers. Analysis of variance with the lm function of R Stats Package (version 3. 6. 1) was used to test the significance of any differences in expression between groups. In the Figures, the results are shown as least-squares means with standard errors. Results were considered statistically significant at a P-value of less than 0. 05. A P-value lower than 0. 15 was considered as a tendency towards significance. For transcriptomic data derived from isolated ICM, the exploratory analysis and differential expression of gene levels were performed using RNAseq workflow, as previously described  (Love et al.
, 2015)  and the updated version 5. The Salmon method  (Patro et al. , 2017)  was used to quantify transcript abundance. The cDNA sequence database for Bos taurus was obtained from the Ensembl genome browser (release-98101; Bos_taurus. ARS-UCD1. 2. cdna. all. fa) and used to build a reference index for the bovine transcriptome  (Patro et al. , 2017). After quantifying the RNA-seq data, the tximport method  (Soneson et al. , 2015)  (R package version 1. 8. 0) was used to import Salmon's transcriptlevel quantifications into the downstream DESeq2 package (R package, version 1. 20. 0) to analyze differentially expressed genes (DEGs) using the statistical method proposed  (Love et al. , 2014). BioMart from Ensembl (release 101) 6  was used to extract gene names and gene descriptions via the Cow genes ARS-UCD1.
2 database. To explore the transcriptome of ICM from the three groups, between-class principal component analysis (bcPCA) was performed with ade4 (R package version 1. 7-15) using the variance stabilizing transformation output files from DESeq2. Differentially expressed genes were identified by DESeq2 through comparisons between IVP treatment groups ("SC, " "SF, " and "SF + PGE2") with an adjusted p-value of 0. 05.
DEGs in ICM under "SF" versus "SF + PGE2" ICM conditions Only eight genes are differentially expressed between the "SF" and "SF + PGE2" groups when the adjusted p-value was considered (P < 0. 05). Five were overexpressed in the "SF + PGE2" group (H4C7, ADAM22, GUCY2C, ANKRD13B, SYNJ2) and three in the "SF" group (CPA4, GPR50, RGS3). When account was taken of the unadjusted probability (P < 0. 05), 382 and 470 genes were overexpressed in "SF" and "SF + PGE2" groups, respectively (Supplementary Table  SR5 ). Genes overexpressed in the "SF + PGE2" group displayed enrichment in members of the C2 domain (BAIAP3 C2CD5, CC2D2A, CPNE8, DOCK1, DOCK4, DOCK5, PLA2G4A, PLCH1, SYTL4, UNC13B, WWC1, WWC3) (IPR035892), which is thought to be involved in calcium-dependent phospholipid binding.
e. that part of the blastocyst giving rise to the epiblast and then to all future intraembryonic tissues. Both the exploratory data and differential expression analysis enabled us to identify several biological processes occurring in the ICM whose levels of expression were influenced by IVP conditions. The biological processes we highlighted were determined by taking account of the cellular changes revealed during post-thawing embryo cultures. Our data showed that the expression of genes involved in several metabolic processes, including unsaturated fatty acid biosynthesis, membrane lipid biosynthesis, carbohydrate and organonitrogen metabolism, was markedly impacted when using the serum-containing IVP system. Our ICM transcriptome data reinforced previous reports of whole blastocyst transcriptome analyses that compared embryos produced in vivo versus in vitro under standard serumcontaining conditions  (Cagnone and Sirard, 2016).
Changes to gene expression related to lipid and carbohydrate metabolism were shown to be induced by the IVP procedure. Furthermore, we found that numerous genes related to catabolic activities were overexpressed in ICM derived under serum-supplemented conditions. The assumed increase in ICM catalytic activities induced by serum-supplemented conditions could partly account for the poorer embryo cryotolerance that was evidenced during the post-thawing period. Indeed, lower post-thawing survival and hatching rates were recorded when serum-containing IVP was applied. Overall, the previous and present data emphasize the impacts of both the IVP procedure itself and the composition of the culture medium on the adaptive metabolic response of the embryo to its surrogate environment. The weaker post-thawing performance associated with the serum-containing IVP system may reflect an inappropriate response of the embryo to the stress induced by these culture conditions.
ACKNOWLEDGMENTS We would like to thank  Luc Jouneau  and  Denis Laloe  ( INRAE, Research Center of Ile de France Jouy-en-Josas, Antony ) for their help with the RNAseq data analysis. We also thank the GenomEast platform, a member of the ' France Génomique' consortium  ( ANR-10-INBS-0009 ), for RNA Sequencing.
79 2. 85E-02 PIGN, ST6GALNAC4, process (GO:0046467) NAGA, PIGM, PGAP1, NEU1, GLA, DEGS1, Sphingolipid metabolic 6. 17 9. 90E-03 SGMS2, UGCG, SAMD8, process (GO:0006665) PIGM Ceramide metabolic 9. 26 2. 17E-03 process (GO:0006672) Phagocytosis (GO:0006909) 4. 55 3. 47E-02 BIN2, MET, MERTK, ANXA3, ENSBTAG00000001219, ANXA1, XKR8 Carbohydrate metabolic 3. 86 2. 96E-03 PIGN,ST6GALNAC4, process (GO:0005975) NAGA, PIGM, PGAP1, Glycolipid metabolic 7. 62 1. 69E-03 NEU1, GLA, UGCG, process (GO:0006664) PIGM Organic anion transport 3. 5 3. 04E-02 SLC16A7, (GO:0015711) ENSBTAG00000049434, CTNS, SLC38A9, SLC38A6, SLC36A2, Carboxylic acid transport 3. 51 1. 51E-03 SLC17A5, CLN3, (GO:0046942) SLC10A1, ANXA1.
4d  and Supplementary Fig. 6b ), suggests that knock-in efficiency at targeted locus mediated by Xential is dosedependent. We next investigated if the coedited cells are more prone to genomic translocation. To this end, we employed a droplet-digital PCR (ddPCR) assay designed to detect the monocentric translocation from the HIST1H2BC to the HBEGF locus. When only two sgRNAs were used, we observed an increase in genomic translocation in-between the loci. Interestingly, a combination of the two sgRNAs with corresponding DNA repair templates (Xential) vastly suppressed the translocations. This data suggests that the Xential co-selection reduces genomic rearrangements, therefore, provides a safety advantage over previous indels-based co-selection systems (Supplementary Fig. 6c ). To determine if Xential could be used to co-select for the insertion of small DNA fragments, such as oligonucleotides, we tested Xential co-selection for knock-in of a DNA oligo at the CD34 locus.
For comparing the puromycin selection with the DT selection, a self-cleavage puromycin resistant protein coding sequence was inserted between the HBEGF exon sequence and self-cleavage mCherry coding sequence (pHMEJ_PuroR, Supplementary Data 2). For the safety switch gene delivery, the mCherry gene was replaced with the HSV-TK gene (synthesized by GenScript, Supplementary Data 2). dsDNA templates were prepared by PCR amplification of the plasmid pHMEJ with primers listed in Supplementary Data 1, followed by purification with MAGBIO magnetic SPRI beads. PCR amplification was performed using Phusion Flash High-Fidelity PCR Master Mix (Life Technologies). ssDNA templates were prepared using the Guide-it™ Long ssDNA Production System (Takara Bio) with primers listed in Supplementary Data 1. Final products were purified by MAGBIO magnetic SPRI beads and analyzed by Fragment Analyzer (Agilent).
The oligo template used for CD34 locus was ordered from IDT as PAGE purified oligo (Supplementary Data 1). Cell culture. HEK293 (ATCC, CRL-1573), HCT116 (ATCC, CCL-247), and PC9-BFP  15  cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS). hiPSCs  75  were maintained in the Cellartis DEF-CS 500 Culture System (Takara Bio), according to manufacturer's instructions. All cell lines were cultured in 37 °C with 5% CO 2. Cell lines were authenticated by STR profiling and tested negative for mycoplasma. T-cell isolation, activation, and propagation. Healthy donors were recruited from AZ volunteers and all samples were taken following appropriate blood collection guidelines. All blood donor volunteers signed Informed Consent form and donation was approved by AstraZeneca's Institutional review board and local Ethic committee (033-10).
An extra purification step was performed on a HiLoad 26/600 Superdex 200 pg column (GE Healthcare) with a mobile phase consisting of 20 mM TrisCl pH 8. 0, 200 mM NaCl, 10% glycerol, and 1 mM TCEP. Purified CBE3 protein was concentrated to 5 mg/mL in a Vivaspin protein concentrator spin columns (28932363, GE Healthcare) at 4 °C, before flash freezing in small aliquots in liquid nitrogen. RNPs were prepared as follows; 20 μg CBE3 protein, 2 μg of target sgRNA and 2 μg of selection sgRNA (TrueGuide Synthetic gRNA, Life Technologies), and 2. 4 μg electroportation enhancer oligos (HPLCpurified, Sigma; Supplementary Data 1) were mixed and incubated for 15 min. Cells were washed with PBS and resuspended in buffer R at a concentration of 5 × 10 7 /mL. A total of 5 × 10 5 cells were electroporated with RNPs using the following settings: voltage: 1600 V, width: 10 ms, and pulse number: 3.
5 µM. Primer pair PCR1_fwd and PCR1_rev was used for PCR1 to detect knock-in junctions (annealing temp: 62 °C, elongation time: 1 min), and primer pair PCR2_fwd and PCR2_rev was used for PCR2 to detect the wild-type HBEGF intron (annealing temp: 64. 5 °C, elongation time: 5 s). Sequences of primer pairs are provided in Supplementary Data 1. For PCR2, the elongation time was set to 5 s to favor amplification of the wild-type HBEGF intron 3 PCR product (280 bp) over the integrant PCR product (2229 bp). PCR products were analyzed through agarose gel electrophoresis. For further analysis of the junction between inserted DNA and genomic DNA in Xential engineered cells, PCR was performed using the Left_F/ Left_R primer pair (forward insertion, PCR_L) or the Left_F/Right_F primer pair (reverse insertion, PCR_Lr).
Conditions for the PCR reactions and sequences of primers are provided in Supplementary Data 1. Flow cytometry analysis. The frequency of cells expressing mCherry and GFP was assessed with a BD Fortessa (BD Biosciences), and flow cytometry data were analyzed with the FlowJo software (Three Star). Genomic DNA extractions and next-generation Amplicon sequencing. Genomic DNA was extracted from cells 3 days after transfections or after completed DT selection using QuickExtract DNA extraction solution (Lucigen), according to the manual. Amplicons of interest were analyzed from genomic DNA samples on a NextSeq platform (Illumina). In brief, genomic sites of interest were amplified in a first round of PCR using primers that contained NGS forward and reverse adapters (Supplementary Data 1). The first PCR was setup using NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs) in 15 μL reactions, with 0.