dataesr/scientific-paragraphs-categorization huggingface dataset:
With larger samples it will further be possible to quantify the co-evolving fraction of AGNs within clusters as a function of redshift. Overall, the class of AC clusters is rich for both astrophysical and cosmological uses, with a potentially significant impact on future X-ray studies. Larger and deeper datasets will allow for a more precise determination of the properties of these objects to maximise the cosmological potential of clusters. Cluster candidate XLSSU J232936. 7-555349 showing two galaxies at the centre of the X-ray emission at z = 0. 31 and a QSO at z = 2. 03. Both galaxies host an AGN. Some additional galaxies nearby are possibly at the same redshift. This is a line-of-sight projection of AGN or a small group. A92, page 20 of 24        A92, page 24 of 24.
Acknowledgements. XXL is an international project based around an XMM Very Large Programme surveying two 25 deg 2 extragalactic fields at a depth of ∼6 × 10 -15 erg cm -2 s -1 in the [0. 5-2] keV band for point-like sources. The XXL website is http://irfu. cea. fr/xxl. The authors would like to thank the anonymous referee for instructive comments that helped improve the manuscript considerably. The Saclay team (S. B. , M. P. , N. C. ) acknowledges long term support from the  Centre National d'Etudes Spatiales (CNES). S. B. acknowledges a  CNES  postdoc and support from  CNRS , support from the  ESA Archival Research Visitor Programme , and would like to thank  P. A. Giles ,  A. Pellissier ,  J. B. Melin , and  R. T. Duffy  for fruitful comments. This work was supported by the  Programme National Cosmology et Galaxies (PNCG) of CNRS/INSU  with INP and  IN2P3 , co-funded by  CEA  and  CNES.
B. J. M. acknowledges support from  STFC  grant  ST/V000454/1. This work was based in part on observations made at  Observatoire de Haute Provence (CNRS), France , with the MISTRAL instrument. This research has made use of the MISTRAL database, based on observations made at  Observatoire de Haute Provence (CNRS), France , with the MISTRAL spectro-imager, and operated at  CeSAM (LAM), Marseille, France. This research made use of astropy (http://www. astropy. org), a community-developed core Python package for astronomy (Astropy Collaboration 2013, 2018). This work also made use of the pyproffit package (Eckert et al. 2020), as well as numpy, scipy and matplotlib. The data underlying this study are available in the article.
Then, we conducted comparisons of the coverage between all possible windows across species using Mann-Whitney U tests. Due to the disparity on mtDNA length across species, we only analysed the first 320 windows representing 16,000 bp in mtDNA (1 st ~ 16,000 th bp), starting with the gene tRNA-Phe. To further confirm our results, we simulated a null distribution of mtDNA coverage by randomly reshuffling mitogenome coordinates of NUMTs for each species, performed pairwise comparisons of the coverage between all windows as mentioned above, and repeated these analyses 1,000 times. For the coordinates, we only randomly picked a start position for each NUMT (between 1 ~ 16,000) and used the length of observed NUMTs to calculate the end coordinates. Hence, the length distribution of NUMTs was identical between the observed and simulated datasets.
In order to take mtDNA circularity into account, coordinates greater than  16,000 (e. g. 16,200 ~ 16,450)  were subtracted 16,000 (e. g. leading to 200 ~ 450). Finally, the number of significant tests obtained from the observed dataset was compared to the distribution obtained from the 1,000 simulated datasets (i. e. null distribution if coverage was homogenous).
It is noted that TE content may be underestimated because the TE database is currently biased for only a few model species such as human and mouse  (Smit 2013 (Smit -2015)). Because TE were compared across windows of NUMT flanking regions within species, this bias is unlikely to affect our conclusions. To further explore if newly-inserted NUMTs are located in proximity to TE, for each species we performed correlation analyses between NUMT/mtDNA sequence identity and the distance of NUMTs to their closest TE (averaged by both ends) using Spearman's correlation tests. Owing to the heterogeneity in sequence identity of individual NUMTs, NUMT blocks were excluded from this analysis. Next, we investigated if NUMTs are prone to insert into intronic or intergenic regions. To achieve this we obtained the high-quality genome annotation files published along with the genomes from the National Center for Biotechnology Information (NCBI).
Acknowledgements We thank  Emmanuel Douzery  from  University of Montpellier  for discussions on phylogenetic analyses. We also acknowledge the  UCD Sonic High Performance Computing  for the provision of computational facilities and support. This study is supported by the  Irish Research Council   Laureate Bursary Grant  (No. 74725 ) and the  UCD  seed funding (No. 68674 ) to Z. H. , the  Irish Research Council Laureate  Award  IRCLA/2017/58  and  Science Foundation Ireland Future Frontiers   19/FFP/6790  awarded to E. C. T. , and the  Junior Chair  from  Institut Universitaire de France  awarded to S. J. P.
| Effect of ITPP treatment on the activation of endothelial PTEN Frozen sections of murine melanoma tumours treated as previously described  19  were labelled by anti-PTEN (rabbit IgG) (Cell Signalling) and mouse anti-CD31 (rat monoclonal IgG2a) (eBiosciences) before detection by tetramethylrhodamine isothiocyanate and fluorescein isothiocyanate secondary antibodies, respectively. Nuclei were stained with bis-Benzimide H 33258 (Sigma-Aldrich). Fluorescent microscopy visualization was performed on a Zeiss 200 M inverted fluorescence microscope (Le Pecq, France), a video microscopy station with a controlled temperature, hygrometry and gas composition. Analyses were carried out using the Axiovision software.
The same samples were passed over a control chip surface without an immobilized ligand. Three replicates of each analyte concentration were injected. The resulting sensorgrams were obtained by first subtracting the buffer blank from the curves recorded for the interactions of PIP3 with PTEN. Then, the curves recorded when PIP3 was passed over the blank surface were subtracted from such sensorgram. The equilibrium constants were determined using BIAevaluation 3. 1 software. For global fitting, a 1:1 Langmuir binding model with an included mass transport step was applied based on the criteria provided by the BIAevaluation handbook.
Acknowledgements We gratefully acknowledge support from  Agence Nationale de la Recherche  ( ANR-19-CE09-0013  APMJ). acknowledges  NSF  funding through the  REU Modern Optics in the City of Light  (award number  1757523 ). We thank  Dr Pascal Berto ,  Prof. J. C. Lacroix  and  Dr Sarra G. Derrouich  for their helpful discussions.
Added value of this study There are two novel elements of this study: first, we collected longitudinal data and estimated the survival rate in patients with hepatocellular carcinoma and in patients with cirrhosis without hepatocellular carcinoma, and second, we assessed the effectiveness of TDF on survival in HBV-positive patients with cirrhosis in a real-life African setting. We analysed the clinical characteristics of patients with hepatocellular carcinoma and cirrhosis in a prospective cohort using high-quality diagnostic tests (including liver histology in a subgroup of patients) in The Gambia, west Africa. As previously shown in African countries, our study found that viral hepatitis, especially HBV infection, remains the main cause of these two disorders, and that patients present at very advanced disease stages in The Gambia.
Results Between June, 2012, and July, 2015, 529 consecutive patients aged 15 years or older with suspected cirrhosis or hepatocellular carcinoma were enrolled in the study. Of these, 193 were excluded from this analysis because of incomplete baseline data (n=119; including 69 of 119 patients with elevated AFP but no focal lesion on ultrasound and no evidence of cirrhosis) or diagnosis other than cirrhosis or hepatocellular carcinoma (n=74). Among the 336 patients included in this analysis, 252 had hepatocellular carcinoma and 84 had cirrhosis without hepatocellular carcinoma (figure  1 ). The study population was predominantly male (n=253/336, 75%), with a median age of 42 years (IQR 33-55) and median BMI of 19•6 kg/m² (IQR 17•6-22•0; table 1). About half of the patients (172/312, 55%) had a WHO performance status of 2 or higher at diagnosis.
In patients with decompensated cirrhosis (n=49), the median survival was 11•3 months (95% CI 4•7-24•0), and survival rates at 3, 6, 12, and 24 months were 72%, 57%, 48%, and 38%, respectively. Survival rates significantly differed between patients with compensated cirrhosis, decompensated cirrhosis, and hepatocellular carcinoma (p<0•0001; figure  2 ). Among 84 patients with cirrhosis and without hepatocellular carcinoma, 63 (75%) were positive for HBsAg and naive for antiviral therapy. Of these 63 patients with HBV-related cirrhosis, seven (11%) were excluded (did not come back to the clinic and could not be contacted by telephone calls) and 56 were included in survival analysis. Characteristics of patients without survival data and patients with survival data were similar except a higher proportion of patients who did not attend school suggesting a lower education level in patients without survival data than in patients with survival data (data not shown).
Acknowledgments We thank the  Gambian Ministry of Health  and the  Medical Research Council (MRC) Unit The Gambia at London School of Hygiene & Tropical Medicine  for hosting and supporting the study,  Gilead Sciences  for providing treatment, and the  European Commission 's  Seventh Framework Program  (grant  265994 ) and the  MRC UK  ( New Investigator Research Grant ; reference  MR/R011117/1 ) for funding our research programme. We thank the entire  PROLIFICA  team and the patients and their families, and  Nuredin Mohammed  for his statistical advice. We are grateful to our missed colleague,  Harr F Njai.
Raman spectroscopy measurements A LabRam HR microRaman spectrometer (Jobin Yvon Horiba Group) was used for the measurements at room temperature. Raman scattering was excited by a 785 nm solid-state laser and recorded in the 50-850 cm À1 spectral range. The laser power was 0. 75 mW. Two to three spectra were registered for each sample at different positions to verify the sample homogeneity and the absence of photoinduced phenomena. Raman spectra over the temperature range 293 r T r 873 K were measured using a Senterra Raman spectrometer (Bruker) equipped with a microscope and a Linkam TS1000 hot stage. The spectra were excited by a 785 nm laser diode with a power of 1 mW and recorded in the 75-1500 cm À1 spectral range (reliable data above 100 cm À1 ). Glassy Sb 2 S 3 was placed in a silica tube (2 mm ID/3 mm OD, length 25 mm) and sealed under vacuum.
High-energy X-ray diffraction The 6-ID-D beamline at the Advanced Photon Source (Argonne National Laboratory, Chicago) was used for high-energy X-ray diffraction measurements under ambient conditions and as a function of temperature. The photon energy was 99. 9593 keV, and the wavelength was 0. 124035 Å. A two-dimensional (2D) setup was used for data collection with a Varex area detector, 2880 Â 2880 pixels, and a pixel size of 150 Â 150 mm 2. The sample-to-detector distance was 287. 7 mm for a roomtemperature setup, and 334. 9 mm for furnace measurements over the 673 r T r 1143 K temperature range on cooling. Cerium dioxide was used as a calibrant. The exposure time was 0. 2 s Â 1500 frames, using one dark-field image file followed by five light files. Glass samples were fixed on a Kapton tape for the room temperature measurements.
A Sb 2 S 3 sample in evacuated silica tube (2 mm ID/3 mm OD) was used for the furnace experiments. The 2D diffraction patterns were reduced using the Fit2D software. 38 The measured background intensity (either the Kapton tape or the empty silica at various temperatures) was subtracted, and corrections were made for the different detector geometries and efficiencies, sample selfattenuation, and Compton scattering using standard procedures,  39  providing the X-ray structure factor S X (Q). S X (Q) = w SbSb (Q)S SbSb (Q) + w SbS (Q)S SbS (Q) + w SS (Q)S SS (Q), (1) where w ij (Q) are Q-dependent X-ray weighting coefficients and S ij (Q) the Faber-Ziman partial structure factors. Typical raw diffraction data for nanocrystalline and glassy Sb 2 S 3 are shown in Fig. S1  (ESI †). Canonical As 2 S 3 glass and liquid were also additionally measured at the BL04B2 beamline of the SPring-8 facility (Hyogo Prefecture, Japan) using a dedicated two-axis diffractometer equipped with four CdTe detectors at low angles and three Ge diodes at high diffraction angles.
40 The temperature measurements were carried out from 300 to 1223 K in a furnace. The 7-detector setup and incident X-ray energy of 112. 6386 keV allows the diffraction pattern to be collected up to Q = 30 Å À1 with a high signal-to-noise ratio and sufficient energy resolution to discriminate both fluorescence from the sample and higher harmonic reflections from the monochromator crystal. The empty silica tube at different temperatures was also measured and used for background intensity subtraction. Further data analysis included absorption, Compton scattering, and polarization corrections using standard procedures  41  giving the total X-ray structure factor of S X (Q). 42, 43.
First-principles simulations The DFT calculations of vibrational spectra were carried out using Gaussian 16 software. 44 The structural optimization and harmonic vibrational frequency calculations were performed for size-limited clusters: SbSb 3 H   45  and the Lee-Yang-Parr correlation functional (B3LYP)  46  were used for these simulations. The smallcore relativistic pseudopotential basis set (cc-pVTZ-PP)  47  and the effective core potentials  48  were applied for cluster geometry optimization and Raman intensity calculations. Most of the structures were optimized using the tight convergence option ensuring adequate convergence and reliability of computed wavenumbers. An extra quadratically convergent self-consistent field procedure  49  was used for difficult convergence cases. ] [52]  Modeling of the diffraction data was carried out using Born-Oppenheimer molecular dynamics implemented within the CP2K package.
Acknowledgements This work was supported by the  Region Hauts de France and the Ministere de l'Enseignement Superieur et de la Recherche (CPER Climibio) , as well as by the  European Fund for Regional Economic Development. Work at the  Advanced Photon Source, Argonne National Laboratory , was supported in part by the  Office of Basic Energy Sciences, US Department of Energy , under Contract No. DE-AC02-06CH1135. The experiments at SPring-8 were approved by the  Japan Synchrotron Radiation Research Institute  (proposal No. 2017B1771  and  2022B1471 ) and supported by the  Centre for Advanced Science and Technology (Japan ) as well as by  JSPS KAKENHI, Japan  (Grant Number  20H02430 ). MKh work at  ILIT RAS was supported by state assignment FSRC ''Crystallography and Photonics '',  Russian Academy of Sciences.
Landscape data The composition of the landscapes surrounding each cave sampled was initially accessed within a circular 12km-radius buffer, centered around the main cave entrance, using photo-interpreted data from Sentinel 2 images with 10 meters of spatial resolution. We initially discriminated six habitat types as landscape categories (Forest, canga, mining land, pasture, exposed bare land and water covered land) and quantified their availability within each buffer. Our experimental design was then composed of three categories of landscape dominance (treatments): landscapes dominated by conserved natural habitats (forests, savannah-like "canga"), landscapes dominated by mining land use (mine) and landscapes dominated by pastures (pasture) (Fig  1 ). All imagery analyses were conducted using QGIS 3.
The weight of each transmitter was 0. 31 to 0. 41 g corresponding to roughly 8% of the smaller bat's weight. Radio-tagged bats were then released inside the caves in which they were captured, and radiotelemetry data begin to be recorded departing from the next night, to avoid bias resulting from the capture and handling of individuals. Only healthy adult and non-reproductive females, as diagnosed by physical examination was selected to receive radio transmitters. We complied with the guidelines from the American Society of Mammalogists  [40]  for the use of wildlife in research, and this study was authorized by the Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (IBAMA) (ABIO Nº 1000/2018).
Home range estimates We used Best Bi-angulation Estimators to determine locations, after correcting for magnetic declination in all compass bearings, using LOAS™ (Ecological Software Solutions, Inc. ). Location datasets determined for each individual were incorporated into QGIS 3. 14 software and subsequently, range areas were estimated using the HRT 2 extension, Home Range Tools  [43]. We generated range area estimates for each individual following Kernohan et al. [44], as the ''extent of area with a defined probability of occurrence of an animal during a specified time period''. We used fixed normal kernel density estimations (KF) with 95% (KF 95%) and 50% (KF 50%) kernel isopleths to delineate the range areas  [45] , using least-squares cross-validation (LSCV) to estimate the smoothing parameter (H)  [46].
Habitat use/selection To evaluate habitat selection patterns, we estimated individual-based habitat uses by contrasting the proportional use of habitats by each individual with our quantified amounts of habitat availability. Since "habitat" is a scale-dependent concept we organize our data following Johnson's  [47]  hierarchical orders of habitat selection. In our framework, the second-order selection represents the proportional habitat use considering 95% kernel density estimations (KF 95%), and the third-order selection is the proportional habitat use considering KF 50% kernel density estimations (KF), both within the MPC estimated for each individual. We used the non-parametric analytics as proposed by Fattorini et al. [48]  based on the combination of sign tests. Within that framework, each habitat is individually tested, and an overall statistic value for the simultaneous assessment of habitat selection in all habitat types can be obtained by combining P values from each test through permutation.
2014)  were released in 2014, followed by two improved versions of the CSS (v2 and v3). The virtual gene order map generated for the CSS, the POPSEQ data were used to order sequence contigs on chromosomes  (Mascher et al. 2013) , and mapped marker sets were associated with these assemblies. The reference sequence of the bread wheat genome released in 2018 (IWGSC RefSeq v1. 0, 2018) included the whole genome, pseudomolecules of individual chromosomes or chromosome arms, scaffolds with the structural and functional annotation of genes, transposable elements (TEs) and non-coding RNAs. In addition, mapped markers as well as annotations supported with alignments of nucleic acid and protein evidence were made available. Manual annotations for specific gene families or regions of specific chromosomes (ca.
The corresponding IWGSC v2. 1 annotation accompanying the IWGSC RefSeq v2. 1 assembly was also completed. The transposable elements (TEs) in the resulting assembly IWGSC RefSeq v2. 1 were heterogeneous datasets. The greatest value of these data lies in their integration to generate new knowledge as a result of effective sharing to allow transparency and openness. The wheat data landscape relies on repositories centred on (i) one or multiple data types (such as genomics, genetics or phenomics) that are highly curated and integrated with a common reference genome (e. g. the accession CHINESE SPRING developed by the IWGSC, 2018), (ii) projects or community of users with dedicated tools to mine the data. To improve the FAIRness (Findable, Interoperable, Accessible, and Reusable,  Wilkinson et al.
IWGSC Data Repository The International Wheat Genome Sequencing Consortium (IWGSC) has developed a variety of resources for bread wheat (Triticum aestivum L. ) through its long-term efforts to achieve a high quality and functionally annotated reference wheat genome sequence (accession CHINESE SPRING). These data are available in a dedicated IWGSC data repository (https://wheat-urgi. versailles. inrae. fr/Seq-Repository,  Alaux et al. 2018)  categorised by data type as shown in Fig. 2. 1.
Sequence Assemblies and Annotations IWGSC wheat genome sequence assemblies are available for download, BLAST  (Altschul et al. 1990) , and display in genome browsers. The assembly dataset includes the draft and the reference sequences, along with their annotations. reannotated, and gene annotations were updated by transferring the known gene models from previous annotations using a fine-tuned, dedicated strategy implemented in the Marker-Assisted Gene Annotation Transfer for Triticeae pipeline (https://forgemia. inra. fr/umr-gdec/magatt). The released IWGSC Annotation v2. 1 contains 266,753 genes comprising 106,913 high-confidence genes and 159,840 low-confidence genes  (Zhu et al. 2021 ). In addition to the bread wheat reference sequence, the IWGSC also sequenced the genome of the Turkish bread wheat elite cultivar SONMEZ  (Nelson et al.
Variation Data These datasets consist of the 1000 wheat exome project  (He et al. 2019) , whole exome capture and genotyping-by-sequencing approaches of 62 diverse wheat lines  (Jordan et al. 2015)  Fig. 2. 2 Summary of IWGSC activities and varietal and intervarietal SNPs  (Rimbert et al. 2018). VCF data files are downloadable, and the variant calls can be displayed in the browser (https://wheat-urgi. versailles. inrae. fr/ Seq-Repository/Variations).
Wheat@URGI The Wheat@URGI portal, developed by INRAE (French National Research Institute for Agriculture, Food and Environment) URGI unit, hosts the IWGSC data repository and GnpIS, a dedicated information system following the Findable Accessible Interoperable Reusable (FAIR) principles: https://wheat-urgi. versailles. inrae. fr/  (Alaux et al. 2018; Pommier et al. 2019 ). GnpIS encompasses a set of integrated databases to manage genomic data using well-known tools such as BLAST, JBrowse, GBrowse and InterMine. An in-house database called GnpIS-coreDB developed by URGI to manage genetic and phenomic plant data, especially wheat, has been produced from French, European and international projects since 2000. A significant amount of this data is available as open access, and some project-restricted data can be obtained through a material transfer agreement.
Data managed by GnpIS-coreDB include: genetic information (markers, quantitative trait loci (QTLs), germplasm, genome-wide association studies (GWAS), genomic information (SNP discovery experiments, genotyping and synteny) and phenomic data. The phenomic data are available as whole trials including phenotypic and environmental observations on wellidentified plant material provided by reference sources such as European genebanks. Detailed descriptions of these datasets are available in  Alaux et al. (2018)  and  Pommier et al. (2019) , and Table  2. 1 presents a data summary. The genetic and phenomic data have been produced from large collaborative projects such as BreedWheat  (Paux et al. 2022)  and Whealbi  (Pont et al. 2019). These different types of data are linked within the GnpIS information system.