dataesr/scientific-paragraphs-categorization huggingface dataset:
Finally, FISH probes for transposable elements (TE) hAT-N145 and TC1-PP from amt intronic regions were designed from G. affinis aminomethyl transferaselike protein gene (partial coding sequence GenBank KP113677. 1): hAT_F: AAA AGG TAC AGT TCA GTA AAAC; hAT_R: ACT TGA GTG ACT TTT GGA TAA; TC1_F: TTT TGG GAC CAG AAC ACT; TC1_R: GGC GAT CCA CAG CTC AAG T. All PCR primers were synthesized by Eurofins MWG (Germany), PCR-cycles included initial denaturation at 95 °C for 3 min, 30 cycles (denaturation: 94 °C for 1 min; annealing 55 °C for 1. 5 min; extension 72 °C for 2 min) and final extension at 72 °C for 10 min. For each FISH experiment, all labeled PCR probes to be co-hybridized were combined (see the "Results" section), ethanol co-precipitated with 20 µg of salmon sperm DNA, and then resuspended in hybridization buffer at a final concentration of 500 ng/µl hybridization mix.
Sequence analysis of the G. affinis amt locus and primer design To characterize the repeat content of the amt locus, we scanned the 6498 bp amt sequence of G. affinis (Genbank KP113677;  [26] ) for simple repeats, TEs, long non-coding RNAs, and micro-RNAs in public databases (girinst. org, noncode. org, fishtedb. org, rnacentral. org, repeatmasker. org and dfam. org; accessed April 2019, February 2023). We used the BLAST (https:// blast. ncbi. nlm. nih. gov/ Blast) and EMBOSS (www. ebi. ac. uk/ Tools/ emboss) web tools for amt local sequence alignments; PCR primers were designed using primer 3 (www. ncbi. nlm. nih. gov/ tools/ primer-blast). Exonerate (https:// www. ebi. ac. uk/ about/ verte brate-genom ics/ softw are/ exone rate) was employed to align the protein sequence of amt from southern platyfish to the published female Gambusia assembly (  [24] ; chromosome W kept while Z removed).
Bioinformatic analyses of the assembled Wand Z-chromosomes DNA sequences of the W-and Z-chromosome were retrieved from a publicly available assembly of G. affinis  [24]. These sequences were aligned using minimap2 (https:// github. com/ lh3/ minim ap)  [40]  with the parameter "asm5. " The sequence difference was then calculated with minimap2 and an in-house perl script (https:// github. com/ dukec omeba ck/ maf2d iff. pl) as the percentage of mutations in 10-kb sliding windows. SNPs and Indels were counted as one change. To estimate and compare the extent of gene decay between the long (0-27. 5 Mbp) and short arm  of the W-chromosome, we collected 455,817 protein sequences from the vertebrate database of Swiss-Prot (https:// www. unipr ot. org/ stati stics/ Swiss-Prot), RefSeq database (proteins with ID starting with "NP" from "vertebrate_other"), and the NCBI genome annotation of human (GCF_000001405.
Microscopy and image analysis The microscopic evaluation of C-banding, Ag-NOR staining and of FISH experiments was carried out using an Axioplan 2 Imaging microscope (Zeiss, Germany), equipped with a brightfield/phase contrast unit and an epifluorescence setup, including fluorescence filter sets for DAPI, DEAC, FITC, Cy3, TexasRed, and Cy5. We analyzed at least ten male and female metaphases per experiment. Quantitative image densitometric analysis and chromosome arm length ratio measurements were performed using the Image J software (NIH, US) version 1. 48v color profiler and line analyzer tool, respectively, analyzing at least ten metaphases per experiment.
Acknowledgements DKL was supported by  ERASMUS+ (Bioinfomatics Centre Hradec Kralove , #  999869114 ), MS and KD were supported by the  Xiphophorus Genetic Stock Center of Texas State University ,  San Marcos , and MS has a grant from the  Deutsche Forschungsgemeinschaft  ( SCHA 408 13-1 ). We thank  Josef Wanzenböck  for the expert fish advise and fruitful discussions.
Oocytes deprived of TZPs reach a canonical size at the end of growth but are morphologically different from controls To determine the TZP-mediated contribution of follicular cells to oocyte development, we assessed whether Myo10 -/-full oocytes deprived of TZPs developed properly. We used our previously developed deep-learning approach to characterize in an automatic manner the morphology of Myo10 -/-full oocytes at the end of the growth phase with the software Oocytor  (21)  to assess their meiotic competence (defined as the ability of oocytes to resume meiosis at the end of growth and mature properly). First, Myo10 -/-full oocytes grew to normal sizes (Fig  2A  and B ) and were arrested in prophase. We then measured the thickness and the perimeter of the zona (A) Cumulus-oocyte complexes stained for myosin-X (MYO10, left images) and with phalloidin to label F-actin (right images).
Data are from four to 13 independent experiments. Statistical significance of differences was assessed by an ANOVA or a Kruskal-Wallis test depending on whether the data followed a Gaussian distribution, P < 0. 0001 (****, Ctrl full versus Myo10 -/-full), P = 0. 7183 (n. s, Ctrl full versus Ctrl oo), P = 0. 7291 (n. s, Ctrl full versus Myo10 -/-oo), P < 0. 0001 (****, Myo10 -/-full versus Ctrl oo), P < 0. 0001 (****, Myo10 -/-full versus Myo10 -/-oo), and P = 0. 9999 (n. s, Ctrl oo versus Myo10 -/-oo). n. s, not significant. (A) Volcano plot of differential gene expression between fully grown Myo10 +/-and Myo10 -/-full oocytes. Differential transcriptomic analysis was performed by RNA-Seq. Up-regulated transcripts are shown in red (up, 605 transcripts); down-regulated transcripts, in blue (down, 80 transcripts, including Myo10); and non-deregulated transcripts, in gray (not significant, 15,702 transcripts).
TZP-deprived oocytes are prone to stop development in meiosis I despite correct spindle morphogenesis and chromosome alignment We showed above that reduction in somatic contacts modulates the oocyte transcriptome. Importantly, oocytes depend on the transcripts synthesized during growth to develop until fertilization  (25, 26). We thus tested whether TZP-deprived oocytes successfully underwent the developmental step after growth, namely, meiotic divisions. After nuclear envelope breakdown (NEBD), the oocyte experiences an asymmetric division in size, leading to a large cell, the oocyte, and a tiny cell, the polar body. This size difference is essential to keep the nutrients stored during growth in the prospective fertilized oocyte for embryogenesis  (28). Importantly, we observed that Myo10 -/-full oocytes deprived of TZPs showed an increased frequency of developmental arrest at meiosis I, without extruding a polar body (Video 4 and Fig  4A  and B ; 38% of TZPdeprived oocytes do not extrude a polar body, compared with 15% in the controls), consistent with our morphological characterization using Oocytor (Fig  2C ).
Data are from three independent experiments. Statistical significance of differences was assessed by a two-sided Fisher exact test, P = 0. 0113. (C) Scatter plot of the timing in hours after NEBD of first polar body extrusion of control (dark gray) and Myo10 -/-(green) full oocytes. (n) is the number of oocytes analyzed. Data are the mean ± s. d. with individual data points plotted. Data are from six independent experiments. Statistical significance of differences was assessed by a two-tailed Mann-Whitney test, P = 0. 3194. n. s, not significant. Images are extracted from spinning disk videos from 30 min to 14 h 30 min after NEBD. The top images show a control oocyte; the middle ones, a Myo10 -/-full oocyte that extruded a polar body (PBE); and the bottom ones, a Myo10 -/-full oocyte that did not extrude a polar body (no PBE).
HPA024223; Sigma-Aldrich) as primary antibodies. The membrane was washed in TBST, blocked for 1 h in TBST containing 5% dried milk powder, rinsed in TBST, and incubated for 45 min in TBST containing 4% dried milk and donkey anti-rabbit IgG HRP-linked (1:10,000, Ref. NA934; Amersham) as secondary antibodies. The membrane was washed in TBST and incubated for 5 min in SuperSignal West Femto Maximum Sensitivity Substrate (Ref. 34095; Thermo Fisher Scientific). Protein expression was revealed using a chemiluminescence image analyzer (FUSION FX; Vilber, 20-s illumination). The membrane was then rinsed in TBST and stripped for 10 min in Restore Western Blot Stripping Buffer (Ref. 21059; Life Technologies). The membrane was washed in TBST and incubated for 45 min in TBST containing 4% dried milk and HRP mouse anti-betaactin AC-15 (1:25,000, Ref.
Ovaries were blocked and permeabilized in 1X PBS, 0. 2% gelatin, and 0. 5% Triton X-100 (PBSGT thereafter) for 4 d with rotation at room temperature. Antibody incubations were performed in PBSGT + 10X saponin (10 mg/ml) at 37°C with rotation at 70g for 1 wk for primary antibodies and overnight for secondary antibodies. Washes between antibody incubations and after secondary antibody incubation were done in PBSGT for 1 d with rotation at room temperature. We used rabbit anti-MYO10 (1:1,000, Ref. HPA024223; Sigma-Aldrich) and rat anti-MECA-32 (1:500, Ref. 550563; BD Pharmingen, data not shown) as primary antibodies and Cy3-conjugated donkey anti-rabbit IgG.
The spring constant was in a range of 0. 05-0. 015 N/m. Measurements were performed on a squared grid of 5 μm × 5 μm at the center of the oocyte. For each oocyte, 16 force-displacement curves were acquired, with a 1 μm/s approach velocity and a 0. 5 nN set point. The measurement takes no longer than 5 min for each oocyte. With JPK Data Processing software, the force-displacement curves were processed by correcting the piezo height with the deflection of the cantilever to get the vertical tip position. Finally, a Sneddon model was fitted on the approach force curves to obtain apparent Young's modulus  (52).
For spinning disk and OMX microscopy, follicles and complexes were mounted on slide wells filled with VECTASHIELD Antifade Mounting Medium with or without DAPI (Ref. H-1200 and H-1000; Vector Laboratories). We used rabbit anti-MYO10 (1:200, Ref. HPA024223; Sigma-Aldrich) as primary antibodies and Cy3-conjugated donkey anti-rabbit IgG.
Spinning disk microscopy Images were acquired with a PlanAPO 40×/1. 25 NA objective on a Leica DMI6000B microscope enclosed in a thermostatic chamber (Life Imaging Service) equipped with a Retiga 3 CCD camera (QImaging) coupled to a Sutter filter wheel (Roper Scientific) and a Yokogawa CSU-X1-M1 spinning disk. Data were collected with MetaMorph software (Universal Imaging).
Light-sheet fluorescence microscopy The cleared samples are acquired with the ultramicroscope I (LaVision BioTec-Miltenyi) assisted by ImSpector Pro software (LaVision BioTec-Miltenyi). The light sheet is created by two cylindrical lenses using the laser with three specific wavelengths: 561, 640, and 785 nm (Coherent Sapphire Laser, LaVision BioTec-Miltenyi). For all the acquisitions, we used a binocular stereomicroscope (MVX10, Olympus) with a 2× objective (MVPLAPO, Olympus) adding a protective dipping cap with corrective lens. For detection, we used a Zyla sCMOS camera (2,048 × 2,048 pixels) from Andor Oxford Instruments. The images were in 16-bit. We used for zoom magnification 3. 2X (pixel sizes x,y = 1. 02 μm). Samples were dived in a quartz tank (LaVision BioTec-Miltenyi) filled with DBE to maintain the clearing.
After thawing, RNA extraction was performed as described by the manufacturer. RNAs were eluted twice in 10 μl elution buffer and treated with DNaseI. RNA-seq and data analysis cDNA libraries and RNA-seq Library preparation and Illumina sequencing were performed at the Ecole normale sup érieure Genomics Core Facility. 5 ng of total RNA was amplified and reverse-transcribed to cDNA using SMART-Seq v4 Ultra Low Input RNA Kit (Ref. 634889; Clontech). Afterward, an average of 500 pg of amplified cDNA was used to prepare the libraries following the Nextera XT DNA Kit (Ref. FC-131-1096; Illumina). Libraries were multiplexed by 6 on high-output flow cells. A 75-bp read sequencing was performed on a NextSeq 500 device (Illumina). A mean of 26 ± 4 million passing Illumina quality filter reads was obtained for each of the six samples.
Bioinformatics analysis The analysis was performed using the Galaxy server of the ARTbio Bioinformatics Platform. Sequencing quality control was carried out with FastQC (Babraham Bioinformatics) (Galaxy version 0. 72+-galaxy1) and MultiQC tools (v1. 6). Alignment of reads to the genome of Mus musculus mm10 reference genome was done with Bowtie 2 (v2. 3. 4. 2) (54) with fast local option for soft clipping of the Nextera transposase adapter sequence. We used the mm10 GTF file (Ensembl GTF Mus_musculus. GRCm38. 94. chr) as annotation files. Counting of reads per gene and differential gene expression analysis were performed with featureCounts (v1. 6. 3+galaxy2) and DESeq2 (v2. 11. 40. 4), respectively. Transcripts were determined as differentially expressed based on a P-adj (adjusted P-value with false discovery rate correction) of less than 0.
Gene ontology (GO) enrichment analysis The analysis was performed with the PANTHER Classification System Overrepresentation Test (Released 20210224), with the annotation dataset GO biological process complete, using Fisher's exact test with a P-value with a false discovery rate correction threshold of 0. 05. For the GO biological process complete (Table  S1 ), the deregulated transcript list from the RNA-Seq analysis was used as the input list and the Mus musculus genome as the reference list. For the graph in Table  S1 , to provide an overview of the different enriched pathways, the enriched GO terms were selected as follows: for each term with a fold enrichment >10, we browsed their ancestor chart using QuickGO, and selected the highest ancestor term (only related by the type "A is a B") that is among the enriched terms with a fold enrichment >10, if any.
Machine-learning approach for oocyte morphological characterization We used our machine-learning pipeline presented in Reference 21 to automatically measure and compare the morphology of Myo10 -/- and control oocytes from brightfield images. Oocyte and zona pellucida contours were automatically determined with Oocytor neural networks. This segmentation allowed us to extract the value of 89 features for each oocyte-zona pellucida complex. These features characterize the size, shape, global intensity repartition, local texture, and spatial organization of the oocyte, perivitelline space, and zona pellucida. The complete list and description of the defined features are given in our GitHub repository (https:// github. com/gletort/Oocytor). As the features are not independent between themselves, we automatically selected a subset of uncorrelated features (with a threshold of 0.
75) as described in Reference 21. We next trained a Random Forest classifier  (55)  with these features to distinguish between fully grown Myo10 -/-and control oocytes cleared of follicular cells. Importantly for our study, the Random Forest algorithm scored each feature according to its importance for classification, based on the Gini index. We checked that the algorithm was able to recognize the oocyte type with a 10fold cross-validation on our dataset and obtained a classification accuracy of 82% (with a precision rate of 80. 9% and a recall rate of 83%). The most important features for classification concerned the composition of the zona pellucida with the presence of vertical linear structures in it (TZP-like structure), the texture of the cytoplasm, the heterogeneity in the thickness of the perivitelline space, and the circularity of both the oocyte and the internal limit of the zona pellucida.
The mean, minimum, maximum, SD (data not shown), and coefficient of variation were then calculated from the distribution of distances. Oocyte aspect ratio Aspect ratio was calculated as the ratio between the maximum Feret diameter (longest distance) of the oocyte shape and the minimum Feret diameter (distance in the perpendicular direction to the maximum Feret diameter). A circle has an aspect ratio of 1, whereas an elongated shape has a higher aspect ratio.
Statistical analysis We used GraphPad Prism 7. 0a software for statistical analysis of RT-qPCR, oocyte polar body extrusion rate, and image data. The Gaussian distribution of values was tested using a D'Agostino & Pearson normality test. Comparison of means was performed by a two-tailed unpaired t test (with Welch's correction for unequal variances) or by a two-tailed Mann-Whitney test (for a non-Gaussian distribution of values). For comparison of more than two conditions, a ANOVA test comparing the mean of each column with the mean of every other column when the data followed a Gaussian distribution, and a Kruskal-Wallis test comparing the mean rank of each column with the mean rank of every other column when the data did not were performed. We used two-sided Fisher's exact tests and a chisquared test for contingency table analysis.
(1:150, Ref. 711-165-152; Jackson ImmunoResearch) as secondary antibodies. Incubation with Alexa Fluor 488-conjugated phalloidin (10 U/ml, Ref. A12379; Thermo Fisher Scientific) was performed concurrently with secondary antibody incubation to stain F-actin. For STED microscopy, cumulus-oocyte complexes and oocytes freed from follicular cells were mounted on slide wells filled with Abberior Liquid Antifade Mounting Medium (Ref. MM-2009). We used rabbit anti-MYO10 (1:200, Ref. HPA024223; Sigma-Aldrich) as primary antibodies and Abberior STAR 580-conjugated anti-rabbit (1:200, Ref. ST580-1002) as secondary antibodies. Incubation of Abberior STAR RED-conjugated phalloidin (1:200, Ref. STRED-0100) was performed with secondary antibody to stain F-actin.
Acknowledgements We thank the  Verlhac/Terret laboratory  for comments on the article and discussion; and  C Antoniewski  and  N Naouar  from the  IBPS ARTbio Bioinformatics Platform  for their services and discussion. The STED microscopy was performed at the  Orion Platform  (member of  France-Bioimaging ANR-10-INBS-XX ) of the  Center for Interdisciplinary Research in Biology  ( UMR7241/U1050 ) of  Collège de France. The OMX microscopy was performed at the Cell and  Tissue Imaging Platform-PICT-IBiSA  (member of  France-Bioimaging   ANR-10-INBS-04 ) of the  Genetics and Developmental Biology Department  ( UMR3215/U934 ) of  Institut Curie , supported by the  European Research Council  ( ERC EPIGENETIX N°250367 ). The work at the  IBENS Genomics Platform  was supported by the France G énomique national infrastructure, funded as part of the  "Investissements d'Avenir" program  managed by the  Agence Nationale de la Recherche  (reference:  ANR-10-INBS-09 ).
This work was supported by the  Fondation pour la Recherche M édicale (FRM Label   EQU201903007796  to  M-H Verlhac ), by the  Agence Nationale de la Recherche  ( ANR-18-CE13  to  M-H Verlhac  and  Auguste Genovesio ,  IBENS/ENS ,  ANR-16-CE13  to  M-E Terret ), and by the  France Canada Research Fund  ( FCRF 2017  to  M-E Terret  and  Hugh J Clarke ,  McGill University ). F Crozet obtained a grant from the  Fondation pour la Recherche M édicale  for her fourth PhD year ( FDT202001010906 ). This work has received support from the  Fondation Bettencourt Schueller , and support under the program " Investissements d'Avenir " launched by the  French Government  and implemented by the  Agence Nationale de la Recherche , with the references:  ANR-10-LABX-54   MEMO LIFE  and  ANR-11-IDEX-0001-02 PSL* Research University.
Separation of disks, ellipticals and intermediates. As shown in Extended Data Fig. 1 , the GALFORM semi-analytical model results in a bimodal distribution of galaxy morphologies as characterized by the bulge-to-disk mass ratio B/D, or equivalently, bulge-to-total mass ratio B/T. We use B/D to classify SIBELIUS galaxies into disks, ellipticals and intermediates. By default, we designate galaxies with B/D < 1/4 as disks, those with 1/4 < B/D < 8 as intermediates and those with B/D > 8 as ellipticals  26. These two limits are indicated by dotted vertical lines in Extended Data Fig. 1. Using these values, 90% of disks have B/D < 0. 13, while 90% of ellipticals have B/D > 12. 6, indicative of a strongly bimodal distribution. It can also be seen that the morphology distribution depends on mass. In agreement with observations  53, 54  , the lower mass galaxy population contains a larger fraction of disks, while higher mass galaxies are more likely to be elliptical.
01 < z < 0. 02 is caused by the presence of the Local Supercluster in this region of the Local Universe. To compute the angular correlation functions ω(θ), we use the Landy-Szalay estimator  56. For each redshift range and each galaxy type, we use the full 2MRS sample, choosing matching numbers of most massive galaxies in SIBELIUS and of random points. We apply the same |b| > 10° mask for each data set and for the random samples. We use the jackknife method to account for the random nature of galaxy formation in every data set and also repeat the random sampling to estimate the statistical uncertainty.
We have no reason to believe that assembly bias does not also apply in the Local Universe, but it appears that the standard halo bias is the most significant effect in explaining the different distributions of the most massive disks and ellipticals with respect to the supergalactic plane. The blue curve shows galaxies in the stellar mass range 10 9 - 10 10 M ⊙ , the red curve shows galaxies above 10 10 M ⊙ , the grey dashed curve shows all galaxies above 10 9 M ⊙. There is a clear bimodality in the bulge fraction, and the fraction of The top row shows, from left to right, A = 3 and A = 4, while the bottom row shows A = 5 and A = 6. For reference, the 2MRS data is repeated on each panel. The greater abundance of ellipticals compared to disks at low supergalactic latitudes in Sibelius, and its dependence of N, is not sensitive to the particular choice of A.
Acknowledgements We sincerely thank  P. J. E. Peebles  for insightful discussions and guidance and T. S. thanks  S. Räsänen  for inspiring discussions. T. S. and P. H. J. acknowledge support from the  Academy of Finland  grant  339127. T. S. and C. S. F. are supported by the  European Research Council (ERC)   Advanced Investigator grant DMIDAS  ( GA 786910 ) and  STFC  Consolidated Grant  ST/T000244/1. P. H. J. also acknowledges support from the  European Research Council (ERC)   Consolidator Grant KETJU  (no. 818930 ). This work was also supported by the  Simons Collaboration on 'Learning the Universe '. This work used facilities hosted by the  CSC-IT Centre for Science, Finland  and the  DiRAC@Durham facility , managed by the  Institute for Computational Cosmology  on behalf of the  STFC DiRAC HPC Facility  (www.
Data availability All data used in this work is publicly available. The 2MRS catalogue is provided in ref. 28. The halo and galaxy catalogues of the SIBEL-IUS simulation can be accessed via SQL at: https://virgodb. dur. ac. uk. SQL scripts to obtain the data used in this work are provided with our analysis code. The data is also available at https://doi. org/10. 6084/ m9. figshare. 22250602.
Code availability The analysis in this paper was performed in python3 and makes extensive use of open-source libraries, including Matplotlib v. 3. 7. 0 (ref. 57), Scipy v. 1. 9. 3 (ref. 58), NumPy v. 1. 23. 5 (ref. 59), Astropy v. 5. 1. 1 (ref. 60) and Corrfunc v. 2. 5. 0 (ref. 61). A documented Juypter notebook containing the code to reproduce all figures in this paper is available at: https://github. com/TillSawala/supergalactic.
Study Design, Sites, and Population A quasi-experimental study design was used in this study wherein two groups were formed (control and intervention). The Department of Health (DOH)-Metro Manila Centers for Health Development data on the dengue incidence were obtained. The National Capital Region cities with high rates of dengue attacks were selected for the study. Parañaque City in the south of Manila, with an approximate population of 0. 5 million  [28] , was chosen. The criteria for choosing barangay sites in Parañaque City involved areas that constantly reported 10-50 dengue cases on a monthly basis and with repeated hotspots during the low transmission months. Barangays Sto. Niño (120°59'45" -120°59'54" East; 14°30'18" -14°30'32" North) and San Dionisio (120°59'11" -120°59'21" East; 14°29'1" -14°29'19" North) were selected as control and intervention groups, respectively.