dataesr/scientific-paragraphs-categorization huggingface dataset:
Intracellular Ca 2+ Measurement Cytosolic Ca 2+ was determined as previously described  [11]. Cortical neurons (DIV 7-12) were seeded on poly-L-lysine-coated glass coverslips (20 mm) and treated with either vehicle or G3 or G4 phosphorous dendrimers (10 µM; 1 h). Afterward, cells were incubated in Krebs-Henseleit (K-H) solution with the ionic composition (in mM) NaCl, 140; CaCl 2 , 2. 5; MgCl 2, 1; KCl, 5; Hepes, 5; and Glucose, 11 (pH, 7. 4) solution containing Fura-2 (5 µM) and 0. 005% (v/v) Pluronic (Thermo Fisher, Madrid, Spain) for 30 min at 37 • C in the dark. Coverslips were washed twice with K-H solution and mounted on the stage of a Nikon Eclipse TE2000-E fluorescence microscope (Nikkon, Tokyo, Japan). The cells were excited alternately at 340 nm and 380 nm and emitted fluorescence recorded at 510 nm using a CCD camera (Hamamatsu Photonics, Shizuoka, Japan), at 200 Hz sampling rate, using the NIS Elements AR software (Nikkon, Tokyo, Japan).
Mitochondrial Transmembrane Potential The mitochondrial transmembrane potential (Ψm) was determined as previously described  [58]. Briefly, cortical neurons (DIV 7-12) were treated with either vehicle or NMDA (150 µM) in the absence or presence of G3 or G4 phosphorous dendrimers at the indicated concentrations for different lengths of time. Afterward, the cells were incubated in K-H solution containing tetramethylrhodamine methyl ester (10 µM; TMRM) (Thermo Fisher, Madrid, Spain), washed with K-H solution, and mounted on the stage of a Nikon Eclipse TE2000-E fluorescence microscope (Nikon, Tokyo, Japan). The cells were excited at 535 nm wavelength and emitted fluorescence recorded at 590 nm using the NIS Elements AR software (Nikkon, Tokyo, Japan). Samples were recorded every 15 s for 5 min with a CCD camera (Hamamatsu Photonics, Shizuoka, Japan).
Afterward, the membranes were washed and incubated with the corresponding secondary antibody HRP anti-rabbit IgG (1:10,000) or HRP anti-mouse IgG (1:10,000). Immunoreactive bands were visualized using an enhanced chemiluminescence system (ECL, Amersham BiosciencesGE Healthcare, Upsala, Sweden). Densitometric analysis of immunoreactive bands was performed using ImageQuant 5. 2 software (GE Healthcare, Uppsala, Sweden).
9 g/mol) is strongly increased, allowing DiI to access and stain the hypodermis. To determine if the lipid composition of the cuticle was modified in gmap-1, we extracted lipids from the cuticle surface using lipodisq nanoparticles, previously reported to extract surface lipids of C. elegans without affecting worm survival  (Bada Juarez et al. , 2019). Next, lipids were extracted from lipodisq and characterised using LC-MS and LC-MS/MS. Multivariate analysis of the LC-MS chromatograms by Principal Component Analysis (PCA) determines 2 multivariate axis that represent together 72% of the variance observed in the full dataset made of 3 technical replicates for each strain: N2, gmap-1 and gmap-1 rescued in the hypodermis. A 2-dimensions PCA representation showed a clear segregation of N2 from gmap-1 mutants, while gmap-1 rescued in the hypodermis overlaid with N2 and gmap-1 (Fig.
As negative control, the [phsp-16::gmap-1-mCherry] strain was maintained at 15 o C, instead. One-way ANOVA followed by Kruskal-Wallis test and Dunn' correction for multiple comparisons. (N) Survival after 30 min of exposure to 1% SDS was measured for 60 dauers in 3 replicates. dauer survival was measured for N2, gmap-1(ulb13) mutants and gmap-1(ulb13) carrying Ex[agmo-1p::gmap-1SL2GFP]. One-way ANOVA followed by Kruskal-Wallis test and Dunn' correction for multiple comparisons. All data are represented as Mean +/-SEM.
(F) Analysis of the lipid composition of the epicuticle: PCA plot of the external cuticle layer extracted by lipodisq for N2 (black), gmap-1 mutants (red), and gmap-1 rescued in hypodermis (blue). (G) Contribution of each lipid family (indicated by their colour code on the right) on the total lipid extracted from the surface of the C. elegans cuticle from the N2, gmap-1 and gmap-1 rescued strains. (H) Survival to hypotonicity was measured for adult worms after 15 min exposure to deionized water (N=160 across 8 experimental replicates). Survival was measured for N2 controls, gmap-1(ulb13) and pld-1(ok2222) single mutants and gmap-1;pld-1 double mutants. One-way ANOVA followed by Kruskal-Wallis test. Data are represented as Mean +/-SEM. : Analysis of the lipid composition of the epicuticle.
ACKNOWLEDGEMENTS: LV and PL are respectively director of research and research associate of the Belgian National Fund for Scientific Research (FRS-FNRS). FNN received a stipend from "Les Amis de l'Institut Pasteur à Bruxelles". In vitro studies were funded by Instruct-ERIC through PID7256 and 20749 and to an internship to FNN at IGBMC, Strasbourg together with support from the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INSB-05. V. P and C. S. are supported by the DFG-grant GRK2581-P06, G. F. with grant FA1046/3-1 and CS with grant STI700/1-1. The Transmission Electron Microscope JEOL JEM-1400Flash was funded by the Deutsche Forschungsgemeinschaft (DFG,.
J o u r n a l P r e -p r o o f German Research Foundation) -426173797 (INST 93/1003-1 FUGG). We thank the Analytical Platform of the Faculty of Pharmacy (APFP) and the Imaging Facility of the Faculty of Medecine (LiMiF) which are ULB Platforms supported by the FRS-FNRS. We thank Jean-Marie Vanderwinden (LiMiF) for imaging advice; Nadia Messadeq (IGBMC Imaging Platform) for preliminary EM analysis and Fabien Alpy (IGBMC Functional Genomics and Cancer Dept) for fruitful discussions on protein/lipid interactions. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440).
elegans Genetics Centre (CGC). Transgenic animals were obtained by microinjection, the injection mix contained 10 or 30 ng/µl of the construct for transgenesis + 30 ng/µl of unc-122P::RFP as marker of transgenesis and 50 or 30 ng/µl DNA mass ladder. For all strains used, stable transgenic lines were J o u r n a l P r e -p r o o f selected based on the unc-122P::RFP marker, fluorescent in coelomocytes as visualized under the fluorescent stereoscope. Behavioural and morphological analysis: Behaviour was recorded on day 1 adults, on NGM plates in presence of OP50 using video recording unit. Videos extraction of behavioural features including was done using Tierpsy  (Javer et al. , 2018). Tierpsy is freely available at https://github. com/Tierpsy/tierpsytracker. Worms were placed in the new plates 30 min prior to video recording.
coli present in their body surface. Animals were then transferred into a 100 µl drop of freshly prepared 5 mM Sodium Azide (NaN3) (#S2002,Sigma-Aldrich, MO, USA) diluted with M9 buffer, or M9 buffer only for control groups. The 100 µl M9 or Sodium Azide drops were centered into 6 well plates (#734-2777 ,VWR, Leuven, BE) that were used to perform recordings with a 3 array camera connected to a computer equipped with Motif Software (Loopbio, Wien, Austria). Recordings were done for a 900 sec period at 15 fps (4024 × 3036 pixels) and the experiments were replicated 6 times for Sodium azide and 2 times for M9 control groups, the position of each group was randomized to avoid location-dependent effects. Recordings were cropped to only detect the drop area and later processed with a custom python script to generate a masked video based on a set threshold to detect the animal body surface.
Videos were analyzed with Tierpsy detection software as previously described  (Martineau et al. , 2020). We used the speed_midbody feature as a proxy to calculate the thrashing speed of a worm population over time. We then pooled the data for the different replicates and represented it as a time-course graph. Data analysis was done using GraphPad Prism, we plotted the curves and applied a no-linear one-phase exponential decay and from that we obtained the average half-lives representing the hypersensitivity to Sodium Azide for each genotype. Levamisole paralysis assay: Animals were synchronized by selecting L4 larva the day prior to the assay. The following day, 20 animals were transferred to region of the plate off-food to remove excess of remaining OP50 E. coli present in their body surface.
Hoechst 33342 Staining assay: Hoechst 33342 (membrane permeable but cuticle impermeable) was used to assess the integrity of the cuticular barrier as previously described. Briefly, worms were incubated in 1 µg/ml Hoechst 33342 in M9 buffer at room temperature for 15 min, followed by several washes with M9 buffer. Identical parameters (lens and magnifiers, filters, exposure time, resolution) were used. Fluorescence micrographs were processed using the ImageJ software for quantification of fluorescence intensity. DiI staining assay: Lipophilic dye DiI (1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine) staining was performed as in  (Schultz and Gumienny, 2012). (Briefly, 20-30 mid-to late-L4-stage larvae were washed once in 1 ml M9 buffer containing 0. 5% Triton X-100 (100ML; Sigma, St.
ProteoWizard MSConvert tools (Version 3. 03. 9393, 64-bit) was used to convert MS and MS/MS raw data to. mzXML file. Data pre-processing were performed with Mzmine 2. 53. The following parameter were applied. Range time of interest was set at 3-30 min being this part of the chromatograms the richest in the focused compounds. Mass detection was performed by fixing the noise level at 1000 for MS1 and 50 for MS2. ADAP Chromatogram Builder was employed to build chromatograms by setting the parameters as follows: minimum group size of three scans, group intensity = 50 and minimum intensity = 50. The m/z tolerance was fixed at 24 ppm. Baseline cut-off algorithm was used for deconvolution by fixing a minimum feature height at 200 and a peak duration range at 0 -5 min. The deconvolution was performed by fixing a value of 0.
1 Da as m/z range for MS2 scan pairing and 0. 2 min as RT range for MS2 scan pairing. Isotopic peak grouper was then performed with a m/z tolerance of 24 ppm, a RT tolerance of 0. 2 min and a maximum charge of 2. Join aligner for data alignment was used to generate a peak list. The parameters were set as follows: m/z tolerance = 24 ppm, weight for m/z = 75, RT tolerance = 0. 5 min, weight for RT = 25. Feature list filter was built by fixing m/z scan at 350 -2000, RT range at 1 -30, peak duration range at 0-5 min. Gap filled step was performed with 10 % of intensity tolerance, m/z tolerance = 24 ppm and RT tolerance = 0. 25. A filter to keep only peaks with MS2 scan (GNPS) was performed and data were then exported as. mgf files for spectra and. csv files as sample metadata. Molecular networks were built with MetGem 1.
3. 6 software (https://metgem. github. io/). Standard parameters were used to import Data ". mgf" and ". csv" : m/z tolerance was set at 0. 02 and minimum matched peaks were set at 4. A cosine score (CS) above 0. 4 has been applied to filter edges; maximum neighbour number (top K) of 10 and a max. connected component size of 1000 was set to build the networks. Annotation of each nodes/ each metabolite was performed according to a lipidomic database for identification (MS-DIAL)  (Olivon et al. , 2018). For each metabolite, the intensity of each replicate was summed. The surface of the node is coloured accordingly to the relative intensity of the metabolite in each genotype (S3 Figure A. ).
Bird data Birds were recorded in each orchard using the observation transect method. Transects were performed in the morning for 5 h after sunrise during birds' dawn peak activity on days without rain or wind  (Bibby et al. 2000; Bouvier et al. 2020). We identified and counted birds within orchards and their surrounding hedgerows by walking regularly on the periphery and then on the middle row of each orchard. We recorded all birds heard and seen except flyovers with the assistance of binoculars (Leica 10 × 42 BN). Because the orchards had a small area and an elongated shape, all recorded birds were within a 50 m distance from the observer. The length of the transects varied among the orchards with a mean ± standard error (SE) of 645 ± 30 m. This value was strongly correlated with the orchard area (Spearman r = 0.
Associated statistical tests were also performed with the DHARMa R package  (Hartig, 2019). Following analyses of residuals, a negative binomial distribution of data and a log link function were selected. Factors affecting the number of observed species and the improved Chao1 index estimations of species richness were investigated with models including the same independent variables. Following the same analysis of residuals as above, we assumed a Poisson distribution of data (log link function) for the number of observed species and a Gaussian distribution for the square-rooted Chao1 index. Variance inflation factors were also all below 2. Specific associations between the abundance of individual bird species and the same independent variables were assessed for frequent species (i. e. , species present in at least 10 orchards).
Overview We counted 705 birds belonging to 32 different species,that were all native species. Over the whole data set, the improved Chao1 index of species richness was very close to the total number of observed species (mean [95% confidence interval]: 32  [32, 34. 38] ). The coverage estimate for the entire dataset, i. e. , the estimated fraction of the entire population of individuals in the community that belonged to the species represented in the sample, was 1. This is consistent with the low estimated number of undetected species. Of these 32 species, 23 were observed in IPM orchards, 26 in ORG orchards, and 31 in ORGnet orchards (Table  1 ). Overall, 25 species (78% of the species) were songbirds. Fourteen of these are insectivorous, four are omnivorous, three are granivorous, and four feed on both arthropods and seeds or fruits at this time of year (Table  1 ).
Anthropogenic impacts on tropical and subtropical coastal environments are increasing at an alarming rate compromising ecosystem function, structure and services. Understanding the scale of marine population decline and diversity loss requires a long-term perspective that incorporates information from a range of sources. The Southern Atlantic Ocean, however, represents a major gap in our understanding of pre-industrial marine species composition. Here we contribute to ll this gap by performing an extensive review of the published data on Middle and Late Holocene marine sh composition along the southern coast of Brazil. This region preserves archaeological sites that are unique archives of past socio-ecological systems and of pre-European biological diversity. We assessed snapshots of species compositions and relative abundances spanning the last 5000 years, and modelled differences in species' functional traits between archaeological and modern sheries.
Material And Methods Literature survey and data compilation Faunal information was obtained from 70 reports produced between 1975 and 2022 on faunal assemblages recovered from Middle and Late Holocene sites along the southern coast of Brazil. We limited our review to coastal sites, using a maximum distance from the current shoreline of 100 km, following Small and Nicholls 108. This is also motivated by the fact that the high relative position of the sea level during the Middle Holocene (ca. +3 m,  41, 109  ) shifted the coastline further inland in areas with gentle slopes. Faunal reports included research articles (54. 3%), academic dissertations and theses (37. 1%), book Chaps. (7. 1%), and eld reports (1. 4%) available as physical and electronic copies in institutional repositories (universities, museums, public libraries) and publishers' websites.
The conservation status of species was compiled from the IUCN Red List of Threatened Species and the updated Red List of Threatened Species 101 of the Chico Mendes Institute for Biodiversity Conservation (Instituto Chico Mendes de Conservação da Biodiversidade -ICMBio). Comparing sh traits across time periods in Babitonga Bay Fish data were compiled for non-ceramic and ceramic assemblages, and for modern sheries catches in the region. A total of 124 species were documented as sheries targets for Babitonga Bay across the three studied periods. Of these, 62 species were recorded for the non-ceramic period, 34 for the ceramic period 39,100,111,117,121,122 , and 94 for modern catches (Projeto de Monitoramento da Atividade Pesqueira em Santa Catarina -PMAP/SC, available at: http://pmap-sc. acad.
univali. br/index. html) (SI6). Nonceramic sh assemblages were recovered from the sites of Cubatão, Espinheiros II, Ilha dos Espinheiros II, Forte Marechal Luz, Enseada I, Bupeva II, and Itacoara (dated between ~ 6000 and 1200 calibrated years before present, cal BP); ceramic assemblages included the sites of Forte Marechal Luz, Enseada I, Bupeva II, and Itacoara (dated between ~ 1200 and 600 cal BP) (Fig. 1B ). We also compiled data of modern sh assemblage composition (241 species) from surveys conducted in Babitonga Bay from 1994 to 2015 64,74 (SI6). For each species recorded, we compiled trophic level, trophic group, maximum body size (cm) and maximum body mass (g). Fish trophic level was taken from FishBase (see above) and ranged between 2. 0 to 4. 9. Trophic group categories were compiled from Quimbayo et al.
Chronological assessment of pre-European assemblages Radiocarbon dates for the analysed sites were obtained from the Brazilian Radiocarbon Database 149 , on dates generated from a range of archaeological materials (marine shells, human and faunal bones, charcoal). Conventional radiocarbon dates were calibrated and modelled using OxCal v. 4. 4 150. For sites with multiple dates (e. g. Forte Marechal Luz, Cubatão I, Jabuticabeira II, RS-PSG-07), the conventional dates were summed according to cultural attributes and/or chronology in order to estimate the median age of the assemblages. Terrestrial samples were calibrated using the 100% atmospheric calibration curve for the southern hemisphere, SHCal20 151. Marine organisms were calibrated using the 100% Marine20 curve 152 , applying an estimated average local marine radiocarbon reservoir correction value (ΔR) of -126 ± 29 for the coasts of São Paulo, Paraná, Santa Catarina and Rio Grande do Sul, generated from eight reference points between latitudes 32.
0 °S and 23. 7 °S  [153] [154] [155]  , according to the Marine Reservoir Correction database. Given the high contribution of marine carbon to bone collagen of human individuals in this region, the radiocarbon dates on human bone collagen were modelled using a mixed curve (SHCal20 and Local Marine curve) adopting the same ΔR value reported above. We considered the average relative contribution of marine carbon to collagen of 52 ± 9%, which is the average estimated contribution recently obtained from dozens of human individuals from archaeological sites in Babitonga Bay  38. Calibrated and modelled radiocarbon dates were rounded to 50 years (SI3).
Methods This study aims to identify industry's perceptions regarding UIC and its stimulating mechanisms for a low-income country in SSA. We posit that policy interventions to stimulate UIC at the country or industry level can be conceived as a mix of the mechanisms of trust-building, instilling company commitment and spanning boundaries between actors as presented in Table  1. We then assess firms' perceptions of the effectiveness of potential mixes of policy interventions for stimulating UIC. For this, we use the Discrete Choice Experiment (DCE) methodology on unique primary data collected in a cross-sectional survey of agro-processing companies operating in Rwanda. The DCE was originally developed in marketing research to analyze preferences for new products and is also referred to as the vignette methodology  (Wason et al.
The intention was to allow respondents to keep in mind the full meaning of each attribute level and its perceived importance while choosing scenarios. From the attributes and attributes levels, 16 choice sets were generated using orthogonal design in SPSS software. To meet the assumption of independence of the alternative choices  (Mangham et al. , 2008) , choice sets were randomly presented to the respondents in pairs, in the form of two scenarios of UIC-stimulating mechanisms. The task for respondents was then expressed as follows: "In the next set of questions, different scenarios of generic stimulating strategies are drawn by combinations of the aspects in the previous question. In total eight pairs of scenarios are proposed. For every pair of scenarios presented below, you are requested to choose the one you think would be more effective than the other in stimulating collaboration between agroprocessing companies and HEI.
" Table  3  showcases an example of a pair of scenarios as presented to respondents in the questionnaire. Eight pairs of scenarios were formed and, since the questionnaire was online, the "force response" option was set to ensure that respondents did not skip any pair presented without making a choice. Appendix C presents the 16 choice sets used in the questionnaire. The coding of choice sets and respondents' choices used a dummy coding approach  (Hauber et al. , 2016) , as indicated in Appendix B. Before using the DCE, we evaluated the current collaboration status by assessing the value obtained by companies from UIC activities, the extent to which existing challenges impeded collaboration and the perceived importance of each considered mechanism. This prior situation analysis had two purposes: for data collection, the questions on situation analysis served as warm-up questions needed to create contextual cues to reduce hypothetical bias in the stated preferences  (Schläpfer and Fischhoff, 2012)  and, for data analysis, data from the situation analysis provided the baseline information needed for interpretation of the companies' preferences.
Data collection Data were collected in December 2020, using a selfadministered online questionnaire with mainly closed questions in Likert scale format and a DCE section. The pool of companies used to select participants for the survey was constituted using the lists of agro-processing companies registered in the Rwanda Private Sector Federation (PSF) and RFDA. These are the two major organizing bodies of the agro-processing industry in Rwanda. To access the participants, an invitation was distributed to companies through their professional associations. The invitation indicated the date and venue of the meeting for data collection. In the meeting, participants were first given a brief introduction to the survey, its objectives and other practical information; then they were provided with a tablet connected to the Internet with a link to the questionnaire.
TALEN Plasmid Constructs Cep250 invalidation was performed by using the transcription activator-like effector nuclease (TALEN) genome editing technology. The end of exon 5 of mouse Cep250 gene was targeted at the site of the original mutation associated with Caprine-like Generalized Hypoplasia Syndrome (SHGC) phenotype in cattle (chromosome: GRCm38:2:155 958 456-155 998 900 (forward strand)). The target sequences were selected using the ZiFiT Targeter program (http://zifit. partners. org). A potential TALEN target sequence identified via this program was selected empirically, with a preference for an 18-16-18 combination (16 bases for the spacer). The chosen sequences were TAGTGAGGAAGGAGAGCC for the left TALEN and GGAGGTAGGAGAACAAGA for the right (localization 2: 165538094-165538145). No homology with the entire targeted sequence was identified (BLAST NCBI) at any other location in the genome, which might represent a potential off-target site.