dataesr/scientific-paragraphs-categorization huggingface dataset:
Central Valley spring-run streams temperature mapping To explore why Deer and Mill Creeks may exhibit multiple juvenile life histories and how life history expression may change with climate change, we compared current and future thermal conditions along every current and historical spring-run stream. Temperature was obtained from a mean monthly stream temperature model 60. In brief, FitzGerald et al. 60  employed a spatial stream temperature model to predict mean monthly stream temperature for nearly every river km in the western U. S. In the Central Valley, the test sample r 2 was 0. 813 and the mean absolute prediction error (MAPE) was 1. 024°C. We rst clipped this stream temperature dataset with the current and historical Central Valley spring-run distributions  61. In general, the distribution and stream networks matched, but a few reaches with spring-run did not have stream temperature.
Acknowledgements Funding for otoliths analysis was provided by  CA Sea Grant , award number:  82550-447552. Additional labor funding for the data analysis was contributed by the  US Bureau of Reclamation Central Valley spring-run life cycle modelling  project, agreement number:  R12PG20200  and  NOAA Investigations in Fisheries Ecology , award number:  NA150AR4320071. Metropolitan Water District provided matching funds through salary contribution of co-author  Corey Phillis. CDFW (Water Quality, Supply , and  Infrastructure Improvement Act of 2014  ( CWC §79707 [g])) provided matching funds through salary contribution of co-author Anna Sturrock. NOAA sheries provided matching funds through salary contribution of co-author  Rachel Johnson. We would like to thank  Matt Johnson ,  CDFW  for providing Mill and  Deer Creek  otoliths and rotary screw trap data used in this study.
(2019)  to quantify the similarity between the modelled biomes and the pollen data from the BIOME6000 database. This method uses the surrounding grid boxes of the studied grid cell (in each direction of the T31 grid) to compare with the pollen record. The agreement for each record is calculated with the distance weight of the best neighbour in each neighbourhood (using a Gaus-sian function) and varies between 1 if the modelled biomes in the grid box indicates the same biome as reconstructed and 0 if all grid cells in the neighbourhood disagree with the record. The BNS is the mean of all individual neighbourhood scores. The LGM modelled biomes in Fig. 4a  show an overall good agreement with the pollen data with a total BNS value of 0. 52. At high latitudes of the Northern Hemisphere, tundra and boreal forests are simulated in regions that are not covered by ice, which is consistent with the few pollen datasets available at these locations (BNS values of 0.
78 and 0. 19, respectively). Temperate forest is modelled over part of North America, grassland over Europe and temperate and warm forests over east Asia. This is in agreement with the pollen record even if some local discrepancies are observed like in central Asia. At low latitudes, the model mostly reproduces the tropical forest (over eastern South America, west Africa and Indonesia) as observed in the pollen data with a BNS value of 0. 38 (Fig. 4a ). Although the LGM conditions were different from those at 15 ka before MWP1a, in absence of other global reconstructions we also used the LGM BIOME6000 pollen record to compare to model results. According to our model, the biome distribution does not change much between 21 and 15 ka (Fig. 4a  and b ), so for many regions, the LGM pollen data show the same pattern as the simulated biomes at 15 ka.
Acknowledgements. We acknowledge support through the project  PalMod , funded by the  German Federal Ministry of Education and Research (BMBF). Simulations were performed at the  German Climate Computing Center (DKRZ). We thank  Thomas Riddick  for internal review of the manuscript. We also thank  Anne Dallmeyer  for her help with the biome reconstruction. We thank the editor and the two referees for their helpful comments. Financial support. This research has been supported by the  Bundesministerium für Bildung und Forschung  (grant no. FKZ 01LP1925C ). The article processing charges for this open-access publication were covered by the  Max Planck Society. Review statement. This paper was edited by  Luke Skinner  and reviewed by two anonymous referees.
Following Fisher-F-tests, all group wise comparisons were carried out by Fisher-protected LSD tests (three groups) or Tukey's (>3 groups). Following significant interactions, models were re-run keeping one of the factors in the interaction term constant in order to re-do all group-wise comparisons. Therefore, findings for pooled results (several conditions combined) are generally reported first, followed by individual comparisons. All analyses were carried out in SPSS (vs. 25, IBM statistics, Chicago, IL, USA).
Measurements of Chlorophyll a Fluorescence Chlorophyll a fluorescence parameters were monitored with an OS1p (Opti-Sciences, Inc. , Hudson, NH, United States). Measurements were made on three fully developed leaves for each scion/rootstock combination (n = 3) at between 7:00 and 11:00 am. Leaves were dark-adapted for 30 min using lightweight leaf clips to measure the minimal level of fluorescence (F o ) followed by the maximal fluorescence (F m ) after 1 s of a saturating flash (3,000 µmol photon•m -2 •s -1 ) by an array of three light-emitting diodes (650 nm). Maximum fluorescence [F v /F m = (F m -F o )/F m ] was calculated from these data according to  Maxwell and Johnson (2000). Leaves were exposed to actinic light to evaluate the current fluorescence yield (F s ) and the actual light-adapted fluorescence (F m ).
Statistical Analyses All statistical measurements were performed with R statistical software (v. 2. 12. 1) 1 and the Rcmdr package. The qualitative factors studied were sampling date (days) (D0 and D210 after nutrient deficiency, and 30DR of recovery for leaves and roots), the common clementine scion grafted onto rootstocks and subjected to nutrient deficiency (C/PMC, C/FL, C/CC, and C/CM, for leaves and roots) and the ploidy level of nutrient stressed rootstocks (C/PMC2x and C/PMC4x, C/FL4x, C/CM2x and C/CM4x, C/CC2x and C/CC4x for leaves and roots). The impact of these three factors was analyzed using a two-way ANOVA followed by LSD test at p < 0. 05. The data for gas exchange, chlorophyll fluorescence, antioxidant parameters and oxidative markers obtained at D210 of nutrient deficiency and after 30DR of recovery for clementine scions grafted onto the seven rootstocks were analyzed by hierarchical group analysis and heatmaps generated by Heatmap.
MD Simulations All MD simulations were performed with NAMD2. 14  [19] , on systems set up using AmberTools18  [20]. The ff14SB force field and the bsc1 corrections for DNA backbone parameters were employed  [21, 22] , and parameters for the 8-oxoG noncanonical nucleobase were taken from previous works  [23]. The systems were built from the experimental structure of OGG1 interacting with intrahelical 8-oxoG-bearing 9 bp DNA duplex PDB ID 6W13 [14]. To avoid edge effects, the DNA duplex was extended to 10 bp. The DNA sequence was modified to match the ones used by Sassa et al. to allow the direct comparison of the MD results with the experiments  [18] -see Figure  1C. The missing loop 79-83 was reconstructed using the SwissModel server  [24] , the Y207C and C253W mutations added for crystallization purposes were reversed, and crystallographic waters were kept as such.
Structural Analysis Structural parameters of the DNA duplex were computed using Curves+  [26]  on 1000 frames extracted from each replicate. The other descriptors monitoring and the clustering were carried out using the cpptraj module of AmberTools18  [20]. The clustering of the structures were performed based on RMSD deviations of the 5-bp centered on the 8-oxoG and the amino acids within 7 Å of the 8-oxoG. Plots, pictures, and figures were generated using the ggplot2 package of R3. 6. 3  [27, 28] , VMD  [29] , and Inkscape (https://inkscape. org/, accessed on 1 June 2021). The assessment of the protein flexibility was performed using a machine learning protocol proposed by Fleetwood and coworkers  [30] , which was in-house implemented and previously successfully used on the MutM bacterial analog of OGG1  [23].
Acknowledgments: The authors thank the regional Explor computing center for computational resources. E. B. thanks the  CNRS and French Ministry of Higher Education Research and Innovation (MESRI)  for her postdoc fellowship under the  "GAVO" program. ANR  and  CGI  are gratefully acknowledged for their financial support. The authors acknowledge the  SYSPROD  project and  AXELERA Pôle de Compétitivité  for financial support (PSMN Data Center).
The yield of Ξ 0,- b → e -Ξ -νe X is therefore computed using i) the  [62]  measured in e + e -collisions, and iii) the Ξ 0,- b → e -Ξ -νe X acceptance × efficiency (Acc×ε) from the simulations described below. The contribution to the WS pair yield from Ξ 0,- b baryon decays is estimated to be about 2%. The correction for the missing momentum of the neutrino is performed by using an unfolding technique with a response matrix which represents the correlation between the p T of the Ξ 0 c baryon and that of the reconstructed e + Ξ -pair. The response matrix is determined through a simulation with the PYTHIA 8. 243 event generator  [63]  and the GEANT 3 transport code  [64] , including a realistic description of the detector conditions and alignment during the data taking period. The response matrix needs to be determined using a realistic Ξ 0 c -baryon p T distribution which is not known a priori.
Intravital microscopy Intravital macroscopy was performed on anesthetized animals. The "Macrofluo" fluorescence microscope (Leica Microsystems SA, Rueil-Malmaison, France), equipped with a Cool Snap HQ2 Camera (Roper Scientific, Photometrics, Tucson, AZ, USA) was used as previously described  [15]. After i. v. injection of 100 μL of FDs, vessels were imaged by fluorescence using appropriate filters (excitation filter, BP: 480/40 nm, emission filter, BP 527/30 nm). Sequences of images were acquired covering a 30 min period; before, during and after signal exposure. The files were stored and analyzed off line after image acquisition (Metavue, Metamorph, Molecular devices, Sunnyvale, CA, USA and software ImageJ, National Institute of Mental Health, Bethesda, MD, USA). The fluorescence intensity outside the blood vessels was determined after image processing as previously described  [15, 19].
V. ; validation, R. V. and M-P. R. ; formal analysis, R. V. and M-P. R. ; investigation, J. K. T. , M. G. , E. B. , A. C. , T. C. , Q. S. , J. T. , and R. V. ; resources, M-P. R. ; data curation, M-P. R. ; writing-original draft preparation, J. K. T. , M. G. , R. V. and M-P. R. ; writing-review and editing, J. K. T. ; visualization, J. K. T. and M. G. ; supervision, R. V. and M-P. R. ; project administration, R. V. and M-P. R; funding acquisition, M-P. R. All authors have read and agreed to the published version of the manuscript. Funding: This research was funded by the French Ministry for Defense -Directorate General of Armaments (Direction Générale de l'Armement -DGA) and Agence Nationale de la Recherche as the Project ANR-ASTRID 12-ASTR-0039-02 PIERGEN. Institutional Review Board Statement: The study was conducted according to the guidelines of the Declaration of Helsinki, and approved by the National Ethics Committee (protocol code 2015032613444287; date of approval 24 Jul 2015).
, 2015). Histone extracts from wild-type REH cells and the two derived FASTKD1 KO cell lines were used in an unbiased approach to measure changes in histone butyrylation and propionylation. After trypsin digestion of histones, the resulting peptides were directly quantified using a label-free mass spectrometry method. These analyses were performed without prior enrichment of modified histone peptides (with anti-PTM antibodies) to detect and visualize the most abundant modified peptides. The results demonstrated that histone H4 K5, K8, and K12 butyrylation is the most responsive to FASTKD1 depletion (Figure  2A ; Tables  S1-S3 ). A detailed analysis of the mass spectrometry data also highlighted the occurrence of unique peptides with a combination of acetylation and butyrylation-propionylation (Data S1).
(legend continued on next page) 4 Cell Reports 36, 109460, July 27, 2021 samples from affected individuals (Table  S4 ). Using qRT-PCR in the same samples, we quantified carnitine palmitoyltransferase 1A (CPT1A) mRNA, encoding a protein involved in the transport of long-chain acyl groups into mitochondria and in controlling the fatty acids b-oxidation potential of the cells, as well as the mitochondrial gene ND2 mRNA as an indicator of mitochondrial activity. Figure  3A  shows that there is a tendency for coregulation between the expression of CPT1A mRNA as a measure of b-oxidation potential and the expression level of ND2 as a measure of mitochondrial activity (Spearman's rank [sr] correlation coefficient = 0. 531). From our functional data obtained in REH cells (Figures  1  and 2 ), we expected to find a relationship between the level of mitochondrial transcription (ND2 mRNA) and the intensity of H4K5 crotonylation and butyrylation.
Therefore, our prediction was that, in CobB-expressing cells, this increase in the H4K5acyl/acetyl ratio (B) Total extracts from wild-type and FASTKD1 KO cells were used to detect the indicated H4K5 and H4K8 modifications as well as actin using the corresponding specific antibodies as indicated. Antibody specificities were confirmed by dot blot analyses on peptides bearing the target H4K5 acylations as well as unrelated acylations (Data S2). (C) Wild-type and FASTKD1 KO cells were treated with rotenone (0. 5 mM) for 1 or 2 h. Protein extracts were prepared, and the corresponding immunoblots were probed as in (B). (D) Wild-type and FASTKD1 KO cells were treated with triascin (3 mM) for 16 h, and protein extracts were prepared and analyzed as in (B). (E) Wild-type and FASTKD1 KO cells were treated with ND-630 (100 nM) for 6 h, and extracts were prepared and analyzed as in (B).
1%HCl, twice with cold acetone and were dried completely in air. MS quantification of histone acylations 5 mg of each histone sample from REH wild-type, ko-1 and ko-2 cells were separated by SDS-PAGE and each spliced histone band was in-gel digested with trypsin. The tryptic peptides were analyzed by Orbitrap Fusion following an EASY-nLC 1000 HPLC system (Thermo Fisher Scientific, San Jose, CA). Mass spectrometry data were analyzed by Mascot software (version 2. 3. 01, Matrix Science Ltd. , London, UK) against an in-house human histone sequence database (83 sequences; 13,870 residues) generated from the Uni-Prot database (updated on 01/27/2015). All identified MS/MS spectra were manually verified. Peptides containing modifications were manually quantified using the Qual Browser (version 3.
Fluorescence recovery after photobleaching (FRAP) 2x10 5 COS-7 control and CobB expressing cells were seeded in 1-well Chambered Coverglass (LAB-TEK brand products, Thermo Fisher) respectively the day before being transfected with 1 mg BRD4-NUT-GFP plasmid using lipofectamine 2000 (Invitrogen). 24 hours after transfection, FRAP was performed on 8 independent cells of each group using fluorescent microscope (LSM710 NLO-LIVE7-Confocor3, Zeiss) equipped with a 488 nm laser and a LP505 filter. A circular region on GFP foci was bleached for 1. 592 s and the recovery of fluorescence was recorded each second for a duration of 75 s after photobleaching by software ZEN lite. Immunofluorescence photos of BRD4-NUT-GFP foci from control and CobB expressing cells were captured before FRAP. For the data analysis and plotting, fluorescence intensity was normalized and rescaled to a reference axis from 0 to 1.
The sequenced reads were aligned from raw sequence fastq data using STAR v2. 5. 2b software on UCSC hg19 reference genome. The aligned reads were normalized, and log transformed using the R bioconductor package DEseq2 (http://bioconductor. org/ packages/3. 12/bioc/html/DESeq2. html). The standardized and normalized read counts of mitochondrial genes were used to generate a heatmap in Figure  1A. Supervised transcriptomic analyses were performed to identify genes significantly up-and downregulated between two conditions using thresholds of Student t test p value < 0. 05 and fold change absolute value of 1. 5.
(E) COS-7 cells described in (D), expressing CobB-HA or not, were transfected with a GFP-BRD4-NUT expression vector. For each condition, 8 GFP-BRD4-NUT foci (one in each of 8 different cells) were bleached, and the recovery of GFP fluorescence (FRAP) was monitored as a function of time. The datasets corresponding to each FRAP experiment were individually fitted, allowing determination of the half-life (t1/2) of fluorescence recovery and the mobile fractions (values indicated below). The mean ± 2 SEM are shown for each time point. The scale bar represents 10 mm. See Figure S4A for the selective action of CobB on H4K5 acetylation compared with butyrylation and crotonylation in COS-7 cells. See Figure S4B for the effect of CobB expression in COS-7 cells on BRD4-chromatin interaction stability.
ACKNOWLEDGMENTS This program was supported by  Fondation ARC  program  RF20190208471 , the  ANR   Episperm4 program , the '' UniversiteGrenoble Alpes ''  ANR-15-IDEX-02 LIFE  and SYMER programs,  INCa  and  IreSP ,  Plan Cancer Pitcher , MSD Avenir ERICAN programs, as well as the  Cancer ITMO (Multi-Organisation Thematic Institute ) of the  French Alliance for Life Sciences and Health (AVIESAN) MIC program. J. M. 's lab is supported by the  National Natural Science Foundation of China  ( 81670147 ), the clinical research plan of the  Shanghai Hospital Development Center  ( 16CR3008A ), international cooperation projects of the  Shanghai Science and Technology Committee  ( 15410710200 ), and the innovation program of the  Shanghai Municipal Education Commission  ( 8201001096 ). M. G. follows a  Shanghai Jiao Tong University-Grenoble Alpes University joint PhD program of Cai Yuanpei-Campus de France  supported by the  China Scholarship Council.
This work was supported by the  University of Chicago , the  Nancy and Leonard Florsheim Family Fund  (to Y. Z. ), and  NIH  grants  GM135504  and  DK118266  (to Y. Z. ). M. T. 's group acknowledges funding from the  Natural Science Foundation of China  ( 91753203 ). The TGML Platform is supported by grants from  Inserm ,  GIS IBiSA, Aix-Marseille Universite , and  ANR-10-INBS-0009-10. N. H. and S. M. 's work was funded by the  Max Planck Institute of Molecular Physiology.
After washing, RCS complexes were flattened on a microscope slide with the RPE layer up. Retina sections or RCS complexes were then mounted with DAKO mounting medium (S3023, Agilent) and sealed with a coverslip. Images were acquired on a Zeiss LSM 710 confocal workstation. Microvilli height was measured by the length measurement tool available in ZEN software (Zeiss, Germany) based on the staining results. Other antibodies used for immunostaining: MCT3 (1:200, AMT013, Alomone Labs), Sodium Potassium ATPase, (1:200, ab76020, Abcam), and β-catenin (1:200, ab16051, Abcam). Transmission electron microscopy. Samples were prepared and transmission electron microscopy was performed as previously described  21. Briefly, mouse eyes were enucleated immediately after CO 2 euthanasia; a small slit was made at the limbus and then fixative (2.
The protein concentrations were determined by BCA assay. Phospho-RTK array. Mice were fasted for 36 h by withholding food without restriction on water availability, with or without a subsequent 3 h refeeding. All mice were sacrificed between 10 am and 12 pm. The RPE lysates were extracted as described above. Each RPE sample was pooled from four mice that had received the same treatment. An equal amount of each sample was used to quantify phospho-RTK proteins with a proteome profiler mouse phospho-RTK array kit (ARY014, R&D Systems). Quantification of the spot intensity in the arrays was conducted with Quantity One software (Bio-Rad). RPE flatmount culture and EGF stimulation. Eyeballs were enucleated from 2month-old mice immediately after euthanasia, and the anterior segments were removed thereafter.
For protein identification, MS files were analyzed using the Thermo Proteome Discoverer 1. 4. 1 platform (Thermo Scientific, Bremen, Germany) for peptide identification and protein assembly. A database search against public mouse proteins obtained from the NCBI website was performed based on the SEQUEST and percolator algorithms through the Proteome Discoverer 1. 4. 1 platform. The maximum false peptide discovery rate was specified as 0. 01. RFP pulldown experiment. To produce adenovirus constructs for the βA1 isoform, the first codon of Cryba1 was mutated and a silent mutation was also introduced to prevent the binding and re-cutting of the sequence by gRNA after homology-directed repair. To produce the longer (βA3) isoform, CCACC was inserted immediately before the first start site to strengthen the Kozak consensus sequence, thereby making the first start codon stronger.
Cells were infected with Ad-CMV-mCryba1-GFP and either Ad-CMV-mCherry-Pitpnb or Ad-CMV-mCherry control constructs for 24 h. Cells were then starved in FBSfree medium for 2 h and stimulated with or without 10 ng/mL EGF for 10 min. The colocalization analysis for dual-color observations was performed by using Fiji ImageJ software. Molecular modeling. The structures of βA3-crystallin, βA1-crystallin, and PITPβ were built by homology modeling using Yasara (http://www. yasara. org/). The molecules were docked and the complex structure was energy minimized in ucsf chimera (https://www. cgl. ucsf. edu/chimera). Phosphoinositide extraction and measurement. RPE-choroid complexes were isolated from 2-month-old Cryba1 cKO and age-matched control mice. Each sample was pooled from four mice from the same group.
Quantification of the band intensity was conducted with Quantity One software (Bio-Rad). Statistics and reproducibility. Statistical analysis was performed using GraphPad Prism v. 8 software. All graphs show mean ± SD. P values were obtained by either two-way ANOVA (multiple comparisons) or a two-tailed unpaired Student's t-test (comparison between two groups). The numbers of biological repeats (n) of each experiment are provided in the figure legends. All figures show the data from independent samples or otherwise are indicated in the figure legend as representative data from independent experiments. this manuscript are available upon request. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD026777.
Acknowledgements We thank  Dr. Alexander Sorkin , Chairman,  Department of Cell Biology, University of Pittsburgh , for critical reading and insightful discussions. This study was funded by the  National Eye Institute :  EY019037-S (D. S. )  and  EY00871  (R. V. S. R. ), University of Pittsburgh start-up funds (D. S. ),  Jennifer Salvitti Davis Chair  in Ophthalmology (D. S. ), and  Research to Prevent Blindness ,  NY  (D. S. and Ophthalmology, UPMC).
Introduction Physics event generators are one of the computational pillars of any High Energy Physics (HEP) experiment, and in particular of the Large Hadron Collider (LHC) experiments. In this paper, we review the main software and computing challenges for the physics event generators used by the ATLAS  [1]  and CMS  [2]  experiments, in view of the high-luminosity running phase of the LHC experimental programme (HL-LHC), which should be operational from the end of 2027  [3]. This document has been prepared by the Physics Event Generators Working Group (WG) [4] of the HEP Software Foundation (HSF), as an input to the review of the HL-LHC computing strategy by the LHC Experiments Committee (LHCC)  [5] , which has started in May 2020  [6] , as previously planned  [7] [8] [9] [10]. As is the case for the LHCC review, this paper focuses on ATLAS and CMS, but it also contains important considerations for AL-ICE  [11]  and LHCb  [12].