dataesr/scientific-paragraphs-categorization huggingface dataset:
01) in the caudate nucleus of the human prodromal HD brain  (Agus et al. , 2019) , and (iv) HTT partner proteins identified from human, mouse, and rat libraries as listed in the HINT resource of the HdinHD database (https://www. hdinhd. org/). We performed these analyses for the genes implicated in the molecular responses defined at the cell type level (group I) and a larger group involving group I genes and the genes that modulate neuronal survival but for which cellular assignment is not available (group II). Orthologous genes were identified using the R package biomaRt (https://bioconductor. org/packages/release/bioc/html/biomaRt. html) and the DRSC integrative ortholog prediction tool  (Hu et al. , 2011) , followed by manual curation. To calculate statistical significance, we performed hypergeometric tests which the reference dataset for each comparison was the intersection between (i) all mouse genes with an ortholog and a cellular assignment (reference for group I), or all mouse genes with an ortholog and for which data on whole-striatum expression, cell-type-specific expression, and effect on striatal neuron survival are available in Hdh mice (reference for groupII) and (ii) all genes that were tested in the comparison dataset and that have a mouse ortholog.
Acknowledgements This work was supported by  Sorbonne Universite, CNRS  and  INSERM, Paris, France , and by the  CHDI Foundation  (grant number  A-14814 ), Princeton, USA (CN), and by  CNRS-Momentum 2017 award (BG)  and by grants from the  CDHI Foundation , the  JPB Foundation  and  NIH/NINDS  ( A-11582 , PIIF, 1  R01 NS100802 , and  1 R01 NS085880 ) (MH). We thank  Pascal Frey  and the  ISCD (Sorbonne Universite)  for access to high-performance computing facilities. JC was the recipient of a PhD fellowship from the  Systems Biology network (BioSys) of Sorbonne Universite.
Data availability Source data for RNA-seq analysis of whole striatum of Hdh mice  (Langfelder et al. 2016 ) and functional shRNA screen data (score) in the striatum of Hdh mice  (Wertz et al. 2020 ) have been previously reported. The visualization of whole-striatum RNA-seq data  (Langfelder et al. 2016) , cell typespecific gene expression data (LFC values)  (Lee et al. 2020 ) and data generated by Geomic analysis including the nomination of cell types associated with whole-striatum gene expression dysregulation, cell-type-specific gene-deregulation-surface clusters (centroids) and the type and temporal evolution of molecular responses in specific cell types and their corresponding networks and biological annotations are available at http://www. broca. inserm. fr/geomic/index. php (this database might take some time to load at first consultation).
Effect of APOD expression on sustained photoprotective energy dissipation Recently, it has been clearly demonstrated that LCNP contributed to qH, a NPQ component, which operates under stress conditions such as cold and high light and appeared to be photoprotective  (Malnoë et al. 2018). Whether APOD can replace LCNP in this function was investigated. Detached leaves of transgenic plants expressing APOD were exposed to high light at low temperature for 6 hours and maximal fluorescence Fm was recorded. The suppressor of quenching 1 mutant (soq1) with enhanced qH whose phenotype is reversed when LCNP is lacking was included in the experiment. Before the stress, wild-type plants (Col0) and the different mutant and transgenic lines displayed similar maximal fluorescence parameter (Fm, data not shown).
Acknowledgements We thank  Pr Eric Rassart  ( Université du Québec, Canada ) for the kind gift of APOD cDNA,  Dr. Olivier Batistic  ( Universität Münster, Germany ) for providing the mCherry. Calnexin1 (mCherry-CNX1), N-acetylglucosaminyl-transferase1. mCherry (GNT1-mCherry) and Two-pore-K + -channel1. mCherry(TPK1-mCherry) plasmids and Dr.
Procedure Stimuli were displayed using the Psychtoolbox  (Brainard, 1997; Pelli, 1997)  implemented in MATLAB R2016a (MathWorks, Natick, MA, USA) against a gray background (luminance of 0. 44) on a 23. 6-in. LCD monitor with a spatial resolution of 1,360 × 768 pixels, a refresh rate of 60 Hz, and a mean gray luminance of 51 cd/m 2. Participants were seated at a distance of 58 cm from the screen. Their head was maintained by a chin-and forehead rest. Eye movements were recorded using an Eyelink 1000 eye-tracker (SR Research) with a sampling rate of 1,000 Hz and a nominal spatial resolution of 0. 01°of visual angle. Only the right eye was recorded in each participant using the "pupil-corneal reflection" mode. The Eyelink software automatically detected saccades with the following thresholds: speed >30°/s, acceleration >8,000°/s2, and saccadic displacement >0.
Analyses were performed using MATLAB R2016 (MathWorks) and Statistica 10 software (Statsoft, Tulsa, OK, USA). Effect sizes were estimated by calculating partial eta-squared (η p 2 ). The significance level of tests was set at α = 0. 05, and p-values corrected for the number of tests are reported for pairwise comparisons. As done in previous studies using a saccadic choice task  (Crouzet et al. , 2010; Guyader et al. , 2017; Kirchner & Thorpe, 2006) , we also computed the minimum saccadic reaction times (minSRT) for each Target and Orientation condition. The minSRT corresponds to the minimum SRT for which there were significantly more correct than error saccades and was obtained as detailed below. The distributions of SRT were computed separately for correct and error saccades, taking all saccades of all participants.
Procedure Due to a change in the hosting institution of the experimenter, this experiment was not performed in the exact same conditions as Experiments 1 and 2. We, however, ensured that the viewing conditions remained comparable, namely in terms of visual angle of stimuli. Stimuli were displayed using the Psychtoolbox  (Brainard, 1997; Pelli, 1997)  implemented in MATLAB R2016a (MathWorks) against a gray background (luminance of 0. 44) on a 21-in. CRT monitor with a spatial resolution of 1,280 × 1,024 pixels, a refresh rate of 75 Hz, and a mean gray luminance of 51 cd/m 2. Participants were seated at a distance of 56 cm from the screen. Their head was maintained by a chin-and forehead rest. Eye movements were recorded with the same eye-tracker as in Experiments 1 and 2 using the same criteria to detect saccadic eye movements.
Conclusion Faces constitute a special class of stimuli that immediately attract the gaze and capture attention but also differ from other categories of visual stimuli in that they are processed holistically. The present study, however, revealed that a holistic processing is not a prerequisite to such ultra-rapid and involuntary orienting responses toward faces, which may rather be driven by the extraction of information available in isolated face parts, irrespective of their configurationalthough no specific face feature could be precisely identified. Our results, however, support the idea that when searching for a face, holistic representations and attributes such as color and shapes (e. g. , curved lines) would be used as a search template to facilitate its correct detection. Keywords: eye-tracking, saccadic choice task, face perception, holistic processing openly available but could not obtain the necessary information about the copyright of the image database used in previous studies.
Acknowledgments Supported by a funding from  NeuroCoG-IDEX of the University of Grenoble Alpes  obtained in the framework of the " Investissements d'avenir" program  of the  French National Research Agency  ( ANR-15-IDEX-02 ). Commercial relationships: none. Corresponding author: Louise Kauffmann. Email: louise. kauffmann@univ-grenoble-alpes. fr. Address:  LPNC -Laboratoire de Psychologie et NeuroCognition, CNRS UMR 5105 -UGA, Bâtiment Michel Dubois -1251 Av Centrale ,  CS40700 , 38058 Grenoble Cedex 9, France.
To evaluate whether the PAM2 motif was also required for SG targeting, we transiently co-infected tobacco leaves with AtATXN2-GFP and PAB2-RFP, which is the Arabidopsis ortholog of PABPC (Fig. 2E ). Identical to our observations in human cells, wildtype AtATXN2 partitioned with PABPC-positive SGs, whereas ΔPAM2 condensates did not mix with SGs. Together, these data indicate that the PAM2 switch modulates ATXN2 condensation across eukaryotes, providing evidence for the biological importance of this ancient regulatory element.
The results of our PopTag system provide evidence that RNA binding is required for PABPC's holdase activity. To test if these findings also applied to ATXN2, we first created a mutant where we replaced the PAM2 motif with the HA-tag. Similar to what we observed for ΔPAM2, this mutant spontaneously condensed under standard conditions and was unable to properly partition into SGs (Fig. 5H-I ). Coexpressing our engineered holdases revealed that RNA-binding by F-PABPC is also required to prevent spontaneous condensation and to drive SG partitioning of the HA-tag mutant ATXN2 (Fig. 5J-K ). Thus, our data indicate that PABPC is a holdase regulating ATXN2 protein phase separation by virtue of its interaction with RNA.
, 2021)  and Caenorhabditis  (Gnazzo et al. , 2016; Stubenvoll et al. , 2016) , with one study showing its enrichment on the mitotic spindle  (Gnazzo et al. , 2016). While it remains unknown if ATXN2 functions similarly in mammalian systems, it is noteworthy that ATXN2 and other SG proteins have been found in several mass spectrometry datasets of microtubule-binding proteins (Fig. S4 ). Moreover, since several of the implicated proteins carry both basic and aromatic IDRs, it will be interesting to see if such prion-like domains can more broadly act as quenchers of basic IDRs, thereby regulating their affinities for specific interaction partners. In this way, basic disordered peptides produced by abnormal translation of expanded repeats, have now been identified in three independent degenerative conditions  (Mizielinska et al.
Our data indicates that the precise balance between cis (i. e. , IDR2-IDR3) and trans (i. e. , RNA and PABPC) interactions tunes ATXN2's behavior. However, the dependence of this system on the client-holdase interaction may form its Achilles' heel in disease: polyQ expansion drives irreversible ATXN2 aggregation in patients and disease models  (Alves-Cruzeiro et al. , 2016). Despite chaperoning the C-terminal IDR against spontaneous condensation, PABPC is not able to counteract aggregation caused by the N-terminal polyQ domain. Pathology data from murine models has shown that PABPC colocalizes with the ATXN2 inclusion bodies  (Damrath et al. , 2012; Sen et al. , 2019). Since PABPC serves an important role in translational regulation, its sequestration into these irreversible aggregates could affect neuronal health via its loss of function.
FRAP measurements in human cells U2OS cells were cultured in glass bottom dishes (Ibidi) and transfected with GFP-ATXN2 constructs as described above. After 24 h, GFP-ATXN2 condensates were and fluorescence recovery after bleaching was monitored using ZEN software on a Zeiss LSM 710 confocal microscope with incubation chamber at 37 °C and 5 % CO2. Data were analyzed as described previously  (Boeynaems et al. , 2017b). In brief, raw data were background subtracted and normalized using Excel, and subsequently plotted using GraphPad Prism 8. 4. 1 software.
After washing five times with PBS-T, the immunoblots were visualized using Pierce ECL western blotting substrate according to the manufacturer's instructions. The tetracycline-induced trypanosomes were fixed with paraformaldehyde, adhered to poly-L-lysinecoated coverslips, permeabilized with Triton X-100, and blocked with BSA, as described previously  (Huang et al. , 2013). After blocking, trypanosomes were stained in 3% BSA/PBS with rabbit polyclonal antibody against GFP (1:250) for 1 h. After thoroughly washing with PBS containing 3% BSA, cells were incubated with Alexa 488-conjugated goat anti-rabbit antibody at 1:1,000 for 1 h. The cells were counterstained with 4′,6-diamidino-2-phenylindole (DAPI) before mounting with Gold ProLong Gold antifade reagent (Molecular Probes). Differential interference contrast (DIC) and fluorescent optical images were captured using an Olympus IX-71 inverted fluorescence microscope with a Photometrix CoolSnap HQ charge-coupled device camera driven by DeltaVision software (Applied Precision, Seattle, WA).
Plant microscopy Arabidopsis thaliana seedlings and tobacco leaves were imaged at room temperature on a LEICA TCS SP8 laser scanning confocal microscope in resonant scanning mode using the Leica Application Suite X software. Seedlings or tobacco samples were mounted in water and then imaged using the HC PL APO CS2 63X/1. 20 water objective. GFP and RFP fluorescence signals were detected by exciting with a white light laser at 488 nm and 555 nm, respectively, and by collecting emission from 500-550 nm and 565-615 nm, respectively, on a HyD SMD hybrid detector (Leica) with a lifetime gate filter of 1-6 ns to reduce background autofluorescence. Z-stacks (Arabidopsis) were collected with a bidirectional 64-line averaging while single-frame images (tobacco) were collected with a bidirectional 1024-line averaging.
Evolutionary analysis The cladogram depicted in Figure  3  and Figure  S2  was generated using phyloT v2 (https://phylot. biobyte. de/) and iTOL v6 (https://itol. embl. de/) (Letunic and Bork, 2021). species list for cladograms for amino acid composition and PAM2 (from top to bottom): Homo sapiens, Mus musculus, Bos taurus, Gallus gallus, Falco peregrinus, Alligator mississippiensis, Anolis carolinensis, Xenopus tropicalis, Latimeria chalumnae, Danio rerio, Apis mellifera, Drosophila melanogaster, Ustilago maydis, Aspergillus niger, Arabidopsis thaliana, Oryza sativa, Chlamydomonas reinhardtii, Naegleria gruberi, Toxoplasma gondii. Amino acid percentages were calculated via ProtParam (https://web. expasy. org/protparam/) (Wilkins et al. , 1999)  and plotted in heatmaps via Morpheus (https://software.
QUANTIFICATION AND STATISTICAL ANALYSIS All data was analyzed using GraphPad Prism 8. 5G ). This was done to correct for differences in expression between constructs. (Patel et al. , 2009). Performing GO enrichment on this dataset show an overrepresentation of terms associated with RNA granules and stress granules. Word cloud shows enriched terms with font size as a function of -log10(p-value). Several well-known stress granule proteins (colored ellipses) are found in this dataset. By overlapping the MAP dataset with mass spec datasets for spindle  (Sauer et al. , 2005)  and primary cilia proteins  (Narita et al. , 2012) , we find 188 proteins that were at least present in two out of three of these sets. This subgroup of proteins shares many physical interactions and shows a strong enrichment for stress granule proteins  (Jain et al.
By overlapping the MAP dataset with mass spec datasets for spindle (Sauer et al. , 2005)  and primary cilia proteins (Narita et al. , 2012) , we find 188 proteins that were at least present in two out of three of these sets. This subgroup of proteins shares many physical interactions and shows a strong enrichment for stress granule proteins (Jain et al. , 2016). Binomial test. (B) Possible interactions of ATXN2 with microtubules. (1) Direct interactions between acidic tubulin tails and the basic IDR2. (2) Indirect interactions of ATXN2 with disordered MAPs. (3) ATXN2 is found in RNA granules, which are tethered to the microtubules via molecular motors.
ACKNOWLEDGEMENTS: We thank all members of the  Gitler lab  as well as the  Carnegie-Stanford Intrinsically Disordered Protein Scientific Interest Group  (IDPSIG) for helpful discussion and suggestions. We thank the  Stanford Neuroscience Microscopy Service  for use of the core facility. We thank  Dr. Seung Y. Rhee  for resources and feedback,  G. Materassi-Shultz  for plant growth facilities management, and the  Carnegie Advanced Imaging facility. FUNDING: Work in the A. D. G. lab is supported by  NIH  (grant  R35NS097263 ). S. B. acknowledges an  EMBO Long Term Fellowship. Y. D. was supported by the  Stanford Graduate Fellowship in Science and Engineering, Carnegie Institution for Science, and Brigitte Berthelemot. G. K. is supported by a fellowship from the  Knight-Hennessy Scholars Program  at  Stanford University.
Several well-known stress granule proteins (colored ellipses) are found in this dataset. By overlapping the MAP dataset with mass spec datasets for spindle (Sauer et al. , 2005)  and primary cilia proteins (Narita et al. , 2012) , we find 188 proteins that were at least present in two out of three of these sets. This subgroup of proteins shares many physical interactions and shows a strong enrichment for stress granule proteins (Jain et al. , 2016). Binomial test. (B) Possible interactions of ATXN2 with microtubules. (1) Direct interactions between acidic tubulin tails and the basic IDR2. (2) Indirect interactions of ATXN2 with disordered MAPs. (3) ATXN2 is found in RNA granules, which are tethered to the microtubules via molecular motors.
29. 3. Physicochemical Parameters and Data Analysis. Concentrations of dissolved CO 2 in the lager beer were determined in two distinct steps: (1) in the bottle, immediately after uncapping but before pouring beer (denoted c bottle ) and (2) in the tasting glass, immediately after pouring the 250 mL of beer (denoted c 0 ). Dissolved CO 2 concentrations were determined according to the official method recommended by the International Office of Vine and Wine (OIV), based on the article by Caputi et al. 30  This method requires the use of carbonic anhydrase (labeled C2522 Carbonic Anhydrase Isozyme II from bovine erythrocytes and provided from Sigma-Aldrich). This titrimetric determination of dissolved CO 2 has been routinely used since the past decade in the science of champagne and sparkling wines and is reported in minute details by Liger-Belair et al.
| Histology Mouse heart tissue was fixed in PFA then embedded in paraffin and serially sectioned at 5 µm on a microtome. Tissue sections were stained with Sirius red to assess interstitial fibrosis. Briefly, paraffin-embedded sections were deparaffinized and washed in distilled water. Slides were then stained for 1 h with Sirius red (0. 1% of Sirius red in saturated aqueous picric acid) and washed twice in acetic acid solution (0. 5%). Slides were rinsed using absolute alcohol, dehydrated, cleared, and then mounted for observation. Images were acquired using axioscan (Zeiss, Göttingen, Germany, X20). Three mice per group were used and 10 to 12 images per mice were analyzed in left and right ventricles and septum by a blinded experimenter. Briefly, interstitial fibrosis was automatically segmented from these images, based on its specific reddish hue, with the help of a home-made ImageJ macro (https://github.
com/jbroc ardpl atim/Cardi ac-Fibrosis, code available in Supplementary data). Percentages of fibrosis were then calculated as the area of fibrosis divided by the area of the stained tissue. In order to determine cardiomyocytes cross-sectional area, tissue sections were stained with Wheat germ agglutinin (WGA) Oregon Green 488 conjugate (Molecular Probes). Staining was performed following standard procedures and images were acquired using the confocal microscopy (LSM5 10 Meta confocal microscope; Zeiss, Oberkochen, Germany). Cross-sectional area analysis (three mice per group, 10 to 15 images per mice and 50 cardiomyocytes per image) was performed by a blinded experimenter using Image J (Stochastic watershed plugin, adapted by Dr A. Fertin, TIMC-IMAG-UMR5525, France).
Behavior Motor behavior was assessed at 1 week and 1 day prior to injury, followed by acquisitions at 3 days, 5 days, and then once a week up to 6 weeks after injury (Figure  1A ). Habituation to the experimenter, novel environment, and apparatus was done to limit bias due to stress. Mice were placed on the CatWalk ® glass plate as well as in the open field arena for 10 min sessions without recording 7 days prior to the first motor assessment. An additional group of 3 uninjured mice were assessed similarly for 6 weeks. Gait analysis was done using CatWalk ® (Noldus, Wageningen, The Netherlands), and data were analyzed with CatMerge ® software (InnovationNet, Tiranges, France), as previously described  [10, [14] [15] [16] [17]. We used CatWalk ® version 7. 1. 9 for this study. Briefly, 6 runs per animal were recorded for each time-point with a minimum inclusion criterion of at least 3-full step sequence patterns per run and a minimum of 3 runs crossed at similar speed.
Several parameters were quantified including regularity index, base of support, and the "maximum contact at %" that represents the time of maximum contact relative to stand. Ipsilateral hind-paw were difficult to detect using CatWalk ® between day 3 to day 14 post-injury, therefore, representative graph bars obtained with CatWalk ® only show values from 2 to 6 weeks after SCI (Figure  1B-D ). Spontaneous motor activity was monitored using the open field test. Mice were placed in an empty test arena (50 × 50 cm), and their spontaneous locomotor activity was recorded by a camera located over the arena. Recording sessions lasted 8 min. Analyses were done using a video tracking software (EthoTrack ® , InnovationNet, Tiranges, France). We measured the total distance covered per mice during each recording session.
DW-MRI parameters: delta = 6. 88 ms, G = 10 G/cm -1 , separation = 15. 05 ms, TR = 1. 580 ms, TE = 30. 55 ms, AVG = 30, FOV=10 mm × 10 mm, slices = 36, thickness = 1 mm without gap, and acquisition matrix = 128 × 128. Segmentations were done using Myrian software (Intrasense, Montpellier, France) to quantify the lesion area (% of the total axial spinal surface), the extension of the lesion along the rostro-caudal axis, and the volume of the lesion (corresponding to the area under the curve). The longitudinal apparent diffusion coefficient (LADC) was measured on a 0. 8 cm segment rostral and caudal to the lesion, excluding the lesion site slice. After MRI acquisitions, spinal cords were immersed in 30% sucrose diluted with 0. 1 M PBS for cryoprotection, embedded with Tissue-Tek (Sakura, Alphenaanden Rijn, The Netherlands), frozen, and kept at -20 • C until processing.
Imaging and Quantifications All slides were scanned using NanoZoomer ® (NanoZoomer Digital Pathology System and NDP view software, Hamamatsu City, Japan). This apparatus uses constant exposure time as well as light intensity. Micrographs were exported at a constant magnification using NDPview ® software. Images were exported using the same parameters for a given staining. All quantifications were done blindly. Optical density (OD) was measured at different distances from the lesion site and at the epicenter using ImageJ software (National Institutes of Health, Bethesda, MD, USA), as described previously  [14, 19, 20]. OD quantifications included the grey matter, the white matter (excluding the dorsal funiculus), and the dorsal funiculus that is a notable zone presenting high rate of microglia/monocytes activation after SCI  [14, 19].
Statistics Two-way repeated-measure analysis of variance (ANOVA) with Bonferroni posthoc tests were used for Catwalk ® and open-field analysis. Unpaired t-tests were used for longitudinal diffusivity comparison and analysis of OD measurements in histology. Significance was accepted at p ≤ 0. 05. Data were analyzed using GraphPad Prism 5. 0 (GraphPad Software Inc. , San Diego, CA, USA) and expressed as the mean ± standard deviation of the mean (SEM).