dataesr/scientific-paragraphs-categorization huggingface dataset:
Immunoblotting-Cells were lysed using RIPA lysis buffer containing proteases and phosphatases inhibitors. Cell lysates were centrifuged at 15 000rpm for 30 min at 4°C, and supernatants were used for immunoblotting using standard protocol. RNA Extraction, Reverse Transcription, qPCR and transcriptomic analyses-Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific, Waltham, USA) and RNeasy Kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions. Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, USA). RNA was reverse-transcribed with the iScript Reverse Transcription Supermix (Biorad, Hercules, USA). Real-time qPCR analysis was performed using iTaq Universal SybrGreen Supermix (Biorad, Hercules, USA) on Biorad CFX96.
The MouseWG-6 v2. 0 BeadChip profiles more than 45,200 transcripts derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36, Release 22), the Mouse Exonic Evidence Based Oligonucleotide (MEEBO) set as well as from exemplar protein-coding sequences described in the RIKEN FANTOM2 database. The Illumina I-Scan system was used to scan all Expression BeadChips, according to Illumina recommendations. Using the Gene Expression Module 1. 9. 0 of GenomeStudio V2011. 1 software (Illumina -USA), the Quantile normalization method was applied to the primary probe data. Processed probe data were then filtered according to the following criteria: minimal signal intensity fold change of 1. 50 across all samples, minimal probe signal intensity absolute change of 150 across all samples.
Filtered data were then log2transformed, and the expression values compared between the   cells and wild-type  f/f samples using Omics Explorer 3. 2(42) (Qlucore, Sweden). Genes were considered differentially expressed when their expression level satisfied two criteria: the adjusted p-value (q-value) was < 0. 01(which corresponded to a |R|> 0. 96 ii) the absolute fold change between the mean expression value in the samples from mutant cells compared to that in controls was > 1. 5. Two-dimension hierarchical clustering analysis was performed using Omics Explorer 3. 2  (42)  software on normalized data (mean=0, variance=1) with the average linkage option. Cell Proliferation Assay-Cells were treated with BrdU or alternatively with EdU (10µM, Sigma) during 1 hour or 30 min for osteoblasts and MEFs respectively.
Quantification of YAP nuclear localization-Cells were immuno-stained with an anti YAP and immuno-microscopy was carried out with a confocal laser scanning microscope (Zeiss LSM510) equipped with a 63X planapo oil immersion objective (n. a. 1. 4) and a pinhole set to one Airy. On each cell image a ROI was defined positioned either within the nuclei, or in the cytoplasmic area next to the nuclei envelope. Since the thickness of the two ROI positions were likely identical, the average fluorescence intensity is likely proportional to YAP concentration and was estimated using Image J public software. Within the same cell, the ratio of both fluorescence intensities reflects YAP concentration ratio in both compartments. This ratio was represented under a logarithmic scale in order to have an identical range for positive and negative ratios.
Measurements were performed with n ≥ 50 and statistical significance was estimated with Student test. Boxplots were performed using R public software. Colocalization microscopy-Confocal images were taken using LSM510 Zeiss microscope. Visualization and quantification of colocalized pixels were carries out using Wright cell imaging (55) facility plugins of Image J. (http://wwwfacilities. uhnresearch. ca/wcif/imagej /colour_analysis. htm). FIGURE LEGENDS.
Accepted Article This article is protected by copyright. All rights reserved. Mexico, Morocco, Peru, Spain, Tunisia, USA and Venezuela). These sites include the 224 sites used in  Maestre et al. (2012)  plus 12 additional sites in Botswana, Ghana and Burkina Faso surveyed in 2012 and 2013 (Supplementary Figure  1 ). Sites were chosen to cover a wide spectrum of abiotic (climatic, soil type, slope) and biotic (type of vegetation, total cover, species richness) features characterizing drylands worldwide. In order to test for the consequences of increasing aridity levels (arid, semiarid and dry-subhumid) on the magnitude of fertile islands, we calculated the Aridity Index (AI, defined as precipitation/potential evapotranspiration) of each site as described in  Zomer et al. (2008) , who used data interpolation obtained from WorldClim  (Hijmans et al.
VEGETATION SURVEY All study sites were sampled following the same protocol. At each site, we surveyed 80 1. 5 m × 1. 5 m quadrats within one 30 m × 30 m plot. Quadrats were located along four 30-m long transects separated eight meters from each other. In each quadrat, we estimated the cover of all perennial plant species and used these data to estimate plant diversity (Shannon-Wiener index). In parallel, we calculated the relative coverage of woody plants along the transects using the line-intercept method (see Maestre et al. 2012 for methodological details).
2015  for details). To avoid problems associated with the use of multiple laboratories when analysing soils from different sites, and to facilitate the comparison of results between them, dried and frozen soil samples from all locations were shipped to Spain for laboratory analyses. We compiled a dataset of the functional traits of the dominant plant species beneath which soil samples had been collected from. These functional traits included: functional type (grass, shrub or tree), ability to fix atmospheric N (fixers vs. non-fixers), canopy in contact with the soil (a surrogate for canopy architecture, influencing, among others, the ability of plants to capture aeolian and water-transported sediments and their suitability for animal resting; yes, no), maximum height at maturity (hereafter referred to as height), and specific leaf area (SLA).
2012 ) and the 341F/805R (bacteria) and FITS7/ITS4 (fungi) primer sets  (Herlemann et al. 2011; Ihrmark et al. 2012)  as described in Appendix A. Sequencing was done at the Next Generation Genome Sequencing Facility of the Western Sydney University (Australia). These data were used to calculate Shannon diversity indices there is a fertile island effect for a given variable). By using this index, we removed betweensite variation in uncontrolled factors that could affect soil fertility in the sampled patches but that are not related to the magnitude of the fertile island effect. We used a multiple threshold approach  (Byrnes et al. 2014)  to calculate an overall fertile island effect using fourteen soil biogeochemical variables (i. e. , all variables measured except total soil P, for which we had missing values at some locations).
Accepted Article This article is protected by copyright. All rights reserved. more active and abundant fungal community, as supported by our SEM. In contrast, the direct effects of SLA appeared to be consistently positive, particularly for C-degrading extracellular enzymes and aromatic compounds, suggesting that, in agreement with the recent literature  (Cotrufo et al. 2015) , labile C sources can be equally stabilised in the long-term organic matter pool. The direct and indirect effects of SLA on the fertile island effect cancelled each other out in our SEMs, supporting the lack of relationship between SLA and the fertile island effect at any given threshold in the reduced dataset. However, the negative association between SLA and the fertile island effect for thresholds between 11-42% when the analysis was carried out using the complete dataset suggests that the indirect negative effects of greater SLA through fungal abundance might be more important than the direct positive effects.
ACKNOWLEDGEMENTS We thank  M. D. Puche ,  V. Ochoa ,  B. Gozalo  and  D. Encinar  for their help with the laboratory analyses and data management. This research is supported by the  European Research Council (ERC)  under the European Community's  Seventh Framework Programme  (FP7/2007-2013)/ ERC  Grant agreement n° 242658 (BIOCOM), by the  Spanish Ministry of Economy and Competitiveness  ( BIOMOD , project  CGL2013-44661-R ) and by the  Australian Research Council  (project  DP13010484 ). FTM also acknowledges support from the  ERC  Grant Agreement 647038 (BIODESERT). JRG thanks  CONICYT/FONDECYT 1160026. YLBP was supported by a  Marie Sklodowska-Curie   Actions Individual Fellowship (MSCA-IF ) within the  European Program Horizon 2020  ( DRYFUN  Project  656035 ). NG was supported by the  AgreenSkills+  fellowship programme which has received funding from the  EU's Seventh Framework Programme  under grant agreement  N° FP7-609398  (AgreenSkills+ contract).
The most severe biotic crisis on Earth history occurred during the Permian-Triassic (PT) transition around 252 Ma. Whereas in the marine realm such extinction event is well-constrained, in terrestrial settings it is still poorly known, mainly due to the lack of suitable complete sections. This is utterly the case along the Western Tethys region, located at Pangaea's equator, where terrestrial successions are typically build-up of red beds often characterised by a significant erosive gap at the base of the Triassic strata. Henceforth, documenting potentially complete terrestrial successions along the PT transition becomes fundamental. Here, we document the exceptional Coll de Terrers area from the Catalan Pyrenees (NE Iberian Peninsula), for which a multidisciplinary research is conducted along the PT transition.
Introduction The Permian and Triassic periods are characterised by large continental landmasses resulting from the formation of Pangaea, which enhanced global aridity and red-beds deposits  (Gibbs et al. , 2002; Chumakov and Zharkov, 2003; Roscher and Schneider, 2006; Schneider et al. , 2006; Looy et al. , 2016; Kustatscher et al. , 2017). The Permian-Triassic record has been largely studied, mostly with the aim of unravelling the events that triggered the major biological crisis of Earth's history, i. e. , the end-Permian mass extinction  (Erwin, 1994). Such event is now well-documented in the marine realm  (Payne and Clapham, 2012) , but questions still remain open in the case of the continental record  (Gastaldo et al. , 2015; Chu et al. , 2016; Zhang et al. , 2016). Benton and Newell (2014)  have recently considered several key zones to study both the Permian-Triassic continental record and the Permian-Triassic boundary (PTB), including Western and Central Europe, Russia and Siberia, central India, South China, central-eastern South America, South Africa, Australia and Antarctica.
, 2011; Kustatscher et al. , 2017). In the present work we introduce and characterise a new section from the Catalan Pyrenees spanning from the uppermost Permian to the lowermost Triassic record. The multidisciplinary study performed on this section includes lithostratigraphy, sedimentology, cyclostratigraphy, mineralogy (X-ray diffraction, XRD), geochemistry (X-ray fluorescence, XRF) and palaeontology (tetrapod and invertebrate ichnology), as well as palaeomagnetism (magnetostratigraphy). Based on our analyses, this section is free from the Triassic erosive gap, so it is a prospective area to identify the PTB in a continental succession of the Western peri-Tethyan domain, in equatorial Pangaea (Fig. 1A ).
Geological setting During the late Palaeozoic and early Mesozoic, the Iberian microplate was located in the equatorial latitudes of Pangaea, in the Western peri-Tethyan region, at the confluence of Gondwana and Laurasia landmasses  (Dercourt et al. , 2000 ; Fig. 1A ). The microplate rotation at that time generated the extensional (rifting) Iberian, Catalan and Pyrenean basins  (De la Horra et al. , 2012). The present-day Pyrenean range (located at the NE Iberian Peninsula and originated during the Alpine orogeny; Fig. 1B ) was formerly composed of continental sedimentary basins controlled by a transtensional tectonic activity  (Speksnijder, 1985; Saura and Teixell, 2006; Gretter et al. , 2015). Pyrenean basins accumulated sediments from the late Carboniferous to the Middle Triassic because of the erosion of the Variscan orogen and the associated volcanic episodes  (Gisbert, 1981; Martí, 1983; Gisbert et al.
, 1985; Pereira et al. , 2014) , related to the breakup of Pangaea  (Torsvik and Cocks, 2013). The lithostratigraphic record was defined by  Mey et al. (1968)  and  Nagtegaal (1969) , while  Gisbert (1981)  established the depositional units here used (Fig. 1C ). These units are, from base to top: Grey Unit (GU), Transition Unit (TU), Lower Red Unit (LRU), Upper Red Unit (URU) and Buntsandstein facies unit. The present work is focused in the red-beds of the URU and its transition to the Buntsandstein facies unit, corresponding to the uppermost Permian and the lowermost Triassic Pyrenean record, respectively  (Mujal et al. , 2016a). Whereas the Buntsandstein facies is found along the entire Catalan Pyrenees, the URU is only recorded in the eastern part, in the Cadí sub-basin  (Gisbert, 1981; Speksnijder, 1985).
The lithologic succession of the upper URU and lowermost Buntsandstein has been codified to make it amenable to spectral analysis in order to explore its cyclic nature (Fig. 2C ). Two approaches have been applied. The first one (code 1) assigns either 1 or -1 to the respective red mudstones or thin-bedded sandstone layers constituting the basic sequences. The second approach (code 2) assigns the stratigraphic thickness of the sequence throughout the encompassed interval of such sequence. The codified series at 2 cm resolution were used for spectral analysis. The Blackman-Tuckey method implemented in the AnalySeries v. 2 software package  (Paillard et al. , 1996)  and the REDFIT program  (Schulz and Mudelsee, 2002)  were employed. AnalySeries was further used for filtering the time series. After preliminary prospective mineralogical and elemental analysis by XRD and XRF, sampling was mainly focused on the transition between the three units in order to identify any mineralogical variation.
Sampling of lower and upper URU and Buntsandstein accounted for 15, 44 and 15 samples, respectively (Fig. 2B ). For the XRD measurements the samples were pulverised and homogenised to produce randomly-oriented powders. XRD scans were acquired between 4°and 65°in 2θ (0. 02 o per step) by using a Bruker D8-A25 diffractometer equipped with a Cu X-ray source (CuKα radiation) and a LynxEye position sensitive detector. Phase identification was performed by using the DIFFRAC. EVA software together with the Fig. 3. Coll de Terrers section. A. Overview of the studied units with partial labelling of the orbital cycles (numbers). B. Thin-bedded and fine-grained sandstone interval of cycle 22; note the thickest basal layer and the common load structures in most of sandstone layers. C-E. Thin sections of sandstone layers including: parallel and cross laminae; fining upwards of the laminae; mud drapes with load structures (white vertical arrows in C, D); long exposure levels (black arrow in C); small pedogenic nodules at the sandstone/mudstone interface (D); and section of a tetrapod footprint in lower laminae (white arrows in E).
F. Fine-grained sandstone channel at the topmost part of the upper URU (cycle 49). G, H. Upper URU/Buntsandstein boundary (white dashed line), represented by a quartz microbreccia. I. Thin section of the basal Buntsandstein mircrobreccia, with most of the pebbles of quarts, but also including feldspars. J. Grey mudstone interval at the base of the Buntsandstein facies and overlying red mudstones. Powder Diffraction File PDF-2 and the Crystallography Open Database (COD). Semi-quantitative phase analyses (SQPA) were carried out by using Reference Intensity Ratio (RIR) values for each of the identified phases. The elemental composition of the samples was investigated by XRF measurements. For this purpose, a Bruker Tracer IV-Geo energy-dispersive XRF analyser equipped with a large area (30 mm 2 ) silicon drift detector and a 40 kV Rh X-ray tube was employed.
1 Megapixel and processed using open access software following the methods of  Mujal et al. (2016b) : Visual SFM v. 0. 5. 24 (http://www. ccwu. me/vsfm/; to obtain the point cloud), MeshLab v. 1. 3. 2 (http://meshlab. sourceforge. net; to create, scale and orientate the 3D mesh), and ParaView v. 4. 1. 0 (http:// www. paraview. org; to create the colour depth maps and contour lines). An ex situ slab bearing small tetrapod footprints was collected and is stored at Institut Català de Paleontologia Miquel Crusafont (Sabadell, Catalonia, Spain) and labelled as IPS-99097.
3E ). Invertebrate trace fossils with tiny, well-defined features (see Section 4. 4. 2 below) are also found in the fine-grained sandstone layers, usually preserved as casts. The whole set of sedimentary structures suggests a relatively dry setting if compared with the lower URU. The upper URU is here interpreted as a distal alluvial plain system (fan fringe/playa-lake, or ephemeral lacustrine). The muddy portions of the succession would indicate conditions of low or absent stagnant water in the depositional environment. In contrast, the relatively coarser intervals (i. e. , the 54 intervals of thin-bedded and fine-grained sandstone layers) would represent conditions of more persistent stable water within a complexivelly arid climate. Such duality of environments has been recorded as a monsoonal system related to the formation of Pangaea  (Parrish and Peterson, 1988; Kutzbach and Ziegler, 1993; Roscher and Schneider, 2006; Roscher et al.
Recently,  Xu et al. (2017)  documented the appearance of chlorite (i. e. , from the clinochlore group) across the Permian-Triassic transition in South China, being indicative of an accelerated aridification. The clinochlore increase across the upper URU/Buntsandstein transition may also indicate an intensified aridification. Thus, we conclude that most probably semiarid conditions persisted (and increased) across the upper URU and lowermost Buntsandstein, also supporting continuity in sedimentation throughout these units. Trends of calcite are not considered here, as this mineral infills postdepositional fractures crosscutting the succession (Fig. 3C-E ). Thus, part of the measured calcite is not from the rock composition but of diagenetic origin instead. The mineralogical data was complemented with XRF measurements, which allowed us to monitor XRF signals for a range of major and trace elements (Al, Si, K, Fe, Cu, Rb and Sr in Fig.
8 ). This climatic shift is possibly related to that of the upper portion of the Alcotas formation in the Iberian Basin  (De la Horra et al. , 2012)  and also to the climatic shift documented in the early late Permian of northern Pangaea  (Retallack et al. , 2006; Roscher and Schneider, 2006; Słowakiewicz et al. , 2009). This may imply that the lower/upper URU boundary could be correlated with the middle-late Capitanian (around the middle Permian extinction event)  (Retallack et al. , 2006; Sheldon et al. , 2014; Day et al. , 2015). Nevertheless, the lower/upper URU boundary possibly represents a paraconformity or sedimentary hiatus (i. e. , long periods of exposition and development of levels with large nodules; Fig. 8, S2 ); no evidences of the middle Permian extinction have been identified in the Pyrenees so far.
The upper URU records a cyclic alternation of facies, from mudstones to fine-grained sandstones, related to a monsoon system of orbital recurrence (Figs. 2, 3A, B ). Such duality of facies would represent the seasonality proposed in the late Permian palaeoclimatic model of  Roscher et al. (2011). Similarly, late Permian seasonality has also been documented in the Central Pangaean Moradi formation of Niger  (Looy et al. , 2016)  and the Southern Pangaean Karoo Basin of South Africa  (Gastaldo et al. , 2015). The tetrapod footprint morphotypes I and II recovered in Coll de Terrers were potentially produced by similar (or the same) trackmakers as those corresponding to Dicynodontipus and Pachypes (i. e. , dicynodonts and pareiasaurs, respectively), being present at the Karoo Basin (de Klerk, 2002) and at the Moradi formation  (Smith et al.
, 2015) , respectively. In fact, the upper URU mudstones are barren of fossils, but the thin-bedded sandstone layers preserve tetrapod footprints, possibly indicative of periods of more favourable conditions for life development. The presence of burrows and notostracan ichnites may indicate that the fine-grained sandstone layers acted as a source of food. These ichnites were impressed in a submerged substrate, as their trackmakers are unable to move out of water  (Gand et al. , 2008) , further denoting different conditions than those of the muddy intervals. Noteworthy, the thin-bedded sandstone layers record periods of subaerial exposure (Figs. 6A, 8 ) that, together with the notostractan ichnites, indicate recurrent dry and wet periods. This is indicative of a similar seasonality to that of Central Pangaea  (Looy et al.
Conclusions The Catalan Pyrenees, together with other regions from the Western peri-Tethyan domain, are a key target to decipher the late Palaeozoic-early Mesozoic events. Here we have provided new data on the continental Permian-Triassic transition of a recently identified area, Coll de Terrers. The sedimentary succession of the uppermost Permian units records different environments that, supported by the XRD analyses, point towards a transition from humid to semiarid climate that correlates with the late Permian aridification. The tetrapod ichnoassemblage also suggests a late Permian age for the uppermost Permian. The late Permian succession was deposited under a monsoonal regime (already documented in equatorial Pangaea) in a low-energy setting (i. e. , a distal alluvial plain), and orbital forcing imprint recurrence conditions (i.
e. , potential eccentricity and long-term obliquity cycles, hitherto unknown in the Permian-Triassic record of the Iberian Peninsula). The continuous sedimentary succession and the lack of any major erosion across the uppermost Permian and lowermost Triassic deposits imply the potential record of the Permian-Triassic boundary. This is supported by a sudden increase of the system energy and an intensified aridification close to the Permian-Triassic transition (documented in both northern and southern Pangaea), the possible anoxic interval in the lowermost Triassic deposits, and also by the lack of any major erosion and sedimentary hiatus as indicated by the preliminary cyclostratigraphic results. In summary, Coll de Terrers records events and features globally recognized in Permian-Triassic terrestrial successions.
This area, located in a narrow rift system at the Gondwana and Laurasia confluence, emerges as a reference zone to investigate the Permian-Triassic transition in terrestrial settings often characterised by scarcity of stratigraphic record. Further ongoing works will clarify whether the Permian-Triassic boundary is recorded in this Pyrenean terrestrial succession and in equivalent areas as well. This is the first contribution to improve correlations between northern and southern Pangaean regions, shedding new light on the terrestrial Permian extinction events. Supplementary data to this article can be found online at https:// doi. org/10. 1016/j. gloplacha. 2017. 10. 004.