dataesr/scientific-paragraphs-categorization huggingface dataset:
Type I collagen sequences of African wild bovids The LC-MS/MS data provided around 1000 acquired MS2 spectra per reference sample. One sample only, namely WALL_3 (of Litocranius walleri) gave no usable results. Database-assisted de novo sequencing from LC-MS/MS data permitted the reconstruction of the COL1A1 and COL1A2 sequences from the 19 species of interest (electronic supplementary material, table  S1 ), of which only nine are presented here (see Methods). All the other 10 species presented the same sequences as the ones available from Janzen et al. [39]. A total of 18 sequences with 100% sequence coverage were obtained for all nine species. Within the referenced species, we only observed 11 amino acid substitutions, with a predominance of alanine (A), threonine (T), valine (V), serine (S) and methionine (M) being the varying amino acids.
More systematic geoarchaeological work thus needs to be performed to refine the overall understanding of the site. As described by Sadr  [17] , three scenarios are currently proposed for the spread of domesticated caprines based on archaeological, linguistic and genetic data: the migration model, in which the caprine herds were brought south by mass movement of Khoe-speaking groups  [29, 94, 95] ; the demic model, in which livestock was traded from one group to a neighbouring one, without human migration  [96] ; and finally, a 'small-scale' model in which their diffusion was more sporadic, as royalsocietypublishing. org/journal/rsos R. Soc. Open Sci. 10: 231002 hunter-gatherer groups slowly became 'hunters with sheep'  [4, 97]. Although not intended to document the first occurrences of domesticated caprines in both eastern and southern Africa, our dataset, combined with the available zooarchaeological evidence in the same archaeological layers for each site, allows us to observe the associated presence of wild species of antelope and domesticated caprines at all studied sites.
These data suggest a mixed subsistence economy, with a continuity of hunting associated with the reliability of herding, something consistent with all three of the scenarios described by Sadr. Our conclusions on species attributions, coupled to the direct radiocarbon dating of molecularly identified remains of sheep and goat, indicate with certainty the presence of caprines from the Later Stone Age in both eastern and southern Africa (figure  4 ). Based on the data we present here, domesticated caprines are dated to 3143-2863 cal. BP at Prolonged Drift, their presence at Toteng is dated to 1346-1178 cal. BP, and they finally appear in the faunal assemblage of Leopard Cave around 919-743 cal. BP. Regardless of the scenario, the majority of southern African sites seem to support 'hunters with sheep', rather than the immigration of sheep-herding groups.
Finally, and even though we acknowledge the strong biases of our dataset (low number of sites, selection of faunal remains that may correspond to caprines, few assumed early occurrences), our palaeoproteomics analysis coupled with direct dating of domesticated caprines helps to refine the history of herding in eastern and southern Africa. We believe that this methodological approach offers 1000 km royalsocietypublishing. org/journal/rsos R. Soc. Open Sci. 10: 231002.
Acknowledgements. The authors would like to express their gratitude to all the people involved in fieldwork of the 17 archaeological sites included in this study, as well as to all the museum curators, head of fieldwork missions and workers who have made this work possible. The  National Museum of Kenya, Nairobi  is hereby acknowledged for permitting D. G. -G. access to the Prolonged Drift and Vaave Makonge faunal collections. The staff of the comparative anatomy collections of the MNHN is thanked for granting access and allowing sampling of the modern skeletons of all species used for generating the COL1 protein sequences. They are also grateful to  L. van der Sluis  for preparing the sample of Prolonged Drift for radiocarbon dating, to  N. Tisnerat-Laborde  and  F. Thil  ( LSCE, Saclay, Fr.
Funding. The work presented here is resulting from L. L. M. 's PhD project funded by the  DIM MAP Région Île de France ,  IBAAM  project and the  Muséum national d'Histoire naturelle  (2017-2021). Part of the analyses conducted here were funded through a  PEPS grant  from the  CNRS  awarded to A. Z. (D2CAP) and through the  Agence Nationale de la Recherche  under the  LabEx   ANR-10-LABX-0003 -BCDiv , in the program ' Investissement d'avenir '  ANR-11-IDEX-0004-02. During the re-analyses of the proteomics data and final drafting of this paper, L. L. M. was supported by a  Fyssen Foundation postdoctoral  fellowship for the project ' Looking for constraints ' (2021-2023) and a  Marie Skłodowska-Curie postdoctoral fellowship  under the  Horizon Europe programme  (grant agreement no. 101062449 ).
ANR-15-IDEX-01 ,  2018-2020 ). This work would not have been possible without the support of our partners in Ethiopia, namely the  Centre Français des Etudes Ethiopiennes (CFEE) , the  Afar Bureau of Tourism and Culture  and the  Ethiopian Heritage Authority in Ethiopia. Archaeological excavations in the Republic of Djibouti were enabled thanks to the  French Ministry of Europe and Foreign Affairs  and the  Institut de Recherches Archéologiques et Historiques (IRAH) of Djibouti  affiliated to the  Centre d'Etudes et de Recherches de Djibouti. Fieldwork conducted at Kurub was funded by the  VAPOR-Afar  project (PI: L. K. ).
Understanding Palaeolithic hominin subsistence strategies requires the comprehensive taxonomic identification of faunal remains. The high fragmentation of Late Pleistocene faunal assemblages often prevents proper taxonomic identification based on bone morphology. It has been assumed that the morphologically unidentifiable component of the faunal assemblage would reflect the taxonomic abundances of the morphologically identified portion. In this study, we analyse three faunal datasets covering the Middle to Upper Palaeolithic transition (MUPT) at Bacho Kiro Cave (Bulgaria) and Les Cottés and La Ferrassie (France) with the application of collagen type I peptide mass fingerprinting (ZooMS). Our results emphasise that the fragmented component of Palaeolithic bone assemblages can differ significantly from the morphologically identifiable component.
All faunal data were derived from recent excavation campaigns, and specimens from both the morphology and ZooMS components show similar spatial distributions over the excavated areas. As the fragment size cutoff of 20 mm was used for piece-proveniencing artefacts during the excavation of the sites and in order to permit eventual additional biomolecular analysis, fragmentary and morphologically unidentifiable piece-provenienced specimens generally > 20 mm in length were selected for proteomic analysis. Indeed, the zooarchaeological analysis of fragments smaller than 2 cm is commonly limited as taphonomic attributes are size dependent. Bone material resulting from sediment sieving during the excavation of the archaeological sites is not included in this study. All morphologically unidentifiable piece-provenienced specimens from the La Ferrassie layer 6 faunal assemblage were selected for ZooMS analysis.
0. (Strohalm et al. 2010 ) through manual peptide marker mass identification in comparison to a database of peptide marker series for all European Pleistocene mediumto large-sized mammals  (Welker et al. 2016 ). To assess any potential contamination by non-endogenous peptides, we performed laboratory blanks alongside the samples. These remained empty of collagenous peptides, excluding the possibility of modern laboratory or storage contamination. Peptide marker series can be similar for some closely related species, which is the case for the species belonging to the following taxonomic groups: Bos/Bison, Cervid/ Saiga, Equidae, and Ursidae. Cervid/Saiga can be attributed to either Cervus elaphus (red deer), Megaloceros giganteus (giant deer), Alces alces (elk), or Dama sp. (fallow deer). Equidae and Ursidae include, respectively, species from the genera Equus and Ursus, most likely Equus ferus and Equus hydruntinus or Ursus spelaeus and Ursus arctos.
Within all three datasets, teeth and antler were categorised separately from the cranial body part, as their inclusion might bias the comparison between components. Indeed, antlers and horn cores tend to be rare and are more easily identified morphologically, reducing their representation in the ZooMS component. Anatomically unidentifiable specimens (NID) were excluded from the assessment of skeletal element representation as they did not provide substantial information. Ecological diversity indices were calculated in order to investigate the effect of the addition of the ZooMS-identified specimens on the taxonomic diversity of the faunal community of each layer and site. We used the Shannon-Wiener index (H′)  (Shannon 1948 ) and R package vegan v. 2. 6-2  (Oksanen et al. 2019)  to quantify the taxonomic diversity of our three faunal assemblages between the ZooMS and morphology component and to assess any variation in faunal diversity between layers of each site, taking into account the taxonomic richness and the distribution of their abundance.
ZooMS analysis ZooMS analysis of all three datasets shows well-preserved collagen type I with a high success rate of taxonomic identification, up to the range of subfamily or genus, between 90 and 97% (SI Table  1 ). For 82% of the samples, the semi-destructive extraction protocol (AmBic) is sufficient to obtain a ZooMS identification. At Bacho Kiro Cave, collagen preservation is excellent (also noted by  Fewlass et al. (2020) ) resulting in a high proportion of discriminant taxonomic identities. All ZooMS samples could be extracted using only the AmBic protocol, while we extracted one specimen through acid demineralisation as well to verify its taxonomic identity (Castor fiber). At both Les Cottés and La Ferrassie, samples were processed using both AmBic and acid demineralisation protocols to improve and optimise taxonomic identifications (SI Table  2 ).
Deamidation between stratigraphic units and taxa Glutamine deamidation ratios are calculated in order to detect potential intrusive material between archaeological layers or differential collagen preservation between taxa. Because the data is not normally distributed (Shapiro-Wilk normality test, p-value < 0. 05), we used Wilcoxon-Mann-Whitney tests to compare the glutamine deamidation ratios between taxa and layers. The deamidation ratios presented here are derived from samples analysed using the acid-free protocol. At Bacho Kiro Cave, we observe that older samples from layer K show elevated levels of deamidation with values significantly different between layers (SI Table  5 , SI Fig. 2 ). In contrast, we note overlapping deamidation values between layers at Les Cottés (SI Fig. 3 ) with the exception of US06 which showed values significantly different from US04 lower and US08 (SI Table  5 ).
Bone length distribution As expected, larger bone fragments are generally more identifiable through comparative morphology as they often preserve more morphologically distinctive features. Smaller fragments tend to be identifiable only through ZooMS (Fig. 4 ). This pattern is particularly noticeable at Bacho Kiro Cave in layers I and K (SI Fig. 5 ). However, this is not the case for all taxa. We note a different specimen length distribution between both ZooMS and morphology components among dominant taxa. At Bacho Kiro Cave, Bos/Bison, Cervid/Saiga, and Equidae specimens show an opposite bipolar distribution of their specimen length whereas the two distributions are more similar for Capra sp. and Ursidae. Because the data is not normally distributed (Shapiro-Wilk normality test, p-value < 0.
Discussion This study combined palaeoproteomic and zooarchaeological analysis of faunal material from three datasets covering the Middle to Upper Palaeolithic transition. It aims to overcome methodological limits in taxonomic identification resulting from bone fragmentation and to address human subsistence and fauna processing behaviour during a period of possible interaction between Neanderthals and Late Pleistocene Homo sapiens groups in Europe. Together with a high success rate of taxonomic identification, the inclusion of ZooMS analysis of the fragmented, unidentifiable component of bone assemblages can identify species previously unrecognised through traditional morphological analysis and, furthermore, be integrated and correlated with traditional zooarchaeological, taphonomic, and ecological data  (Berto et al.
Acknowledgements We would like to thank  Harold Dibble  for codirecting the excavation at  La Ferrassie  and for his precious contribution during the early stages of this project. We would like to thank  Jean-Jacques Cleyet Merle ,  Catherine Cretin , and  Bernard Nicolas  for facilitating access to the La Ferrassie fauna stored at the  Musée National de Préhistoire (Les Eyzies, France). We thank  Prof. Nikolay Spassov , the  National Archaeological Institute  and the  National Museum of Natural History  from the  Bulgarian Academy of Sciences (Sofia, Bulgaria ), and the  Museum of History in Dryanovo  for supporting the  Bacho Kiro Cave  fieldwork and storage of the faunal collection from  Bacho Kiro Cave. Thanks are due to  Jakob Hansen  and  Lindsey Paskulin  for the technical assistance during sampling.
The animals were monitored twice daily and euthanized when moribund. During a 14-day drug treatment, we observed reduced morbidity and mortality of infected animals relative to vehicle controls (Figure  3, I  and J ). Whereas 100% of vehicle-treated mice succumbed to infection by day 10 after infection, lapatinib treatment protected 80% of the mice by day 10, and 40% of the mice by day 14. Since lapatinib's half-life is shorter in mice than in humans, we administered lapatinib twice daily (200 mg/kg) for 8 days in uninfected C57BL/6 mice, observing good tolerability and plasma concentrations exceeding the EC 50 deduced from our in vitro data by 6-to 43-fold (Supplemental Figure  4F ). Despite the earlier mortality of vehicle-treated mice observed in this independent experiment (100% succumbed to infection by day 8 after infection), treatment with 200 mg/kg lapatinib twice daily for 10 days in the VEEV (TC-83) murine model protected 60% of the mice (Figure  3, K  and L ).
Beyond ErbBs, lapatinib's kinome (HMS LINCS database ID: 20107; https://lincs. hms. harvard. edu/db/) reveals bind-both vaccine (TC-83) and wild-type (WT) (Trinidad donkey  [TrD] ) VEEV by plaque assays in human astrocyte (U-87 MG) cells (EC 50 = 1. 2 μM and 0. 9 μM, respectively, and CC 50 > 20 μM) (Figure  3, A  and B ). Similarly, lapatinib dose-dependently inhibited the replication of the flavivirus DENV2 (EC 50 = 2. 0 μM) via plaque assays, and the filoviruses EBOV (EC 50 = 2. 5 μM) and MARV (EC 50 = 2. 0 μM) via microneutralization assays, in human hepatoma (Huh7) cells, albeit lower CC 50 values were measured in infected Huh7 cells (10-11. 5 μM) than in other cell lines. Lapatinib dose-dependently inhibited the replication of 2 strains of monkeypox, a dsDNA virus, in A549 cells (EC 50 = 6.
ErbB inhibition suppresses virus-induced inflammation and tissue injury ex vivo in human ALO-derived monolayers and gNVUs. Data from animal and human models of non-infectious acute lung injury and acute respiratory distress syndrome indicate that ErbB1 and ErbB2 are key regulators of inflammation and tissue injury via activation of the p38 MAPK, AKT/mTOR, and Ras/RAF/MEK/ERK pathways  (20, (30) (31) (32) (33). To test the hypothesis that these pathways are activated in SARS-CoV-2 infection and suppressed by lapatinib's pan-ErbB inhibition, we measured their activation in Calu-3 cells upon SARS-CoV-2 infection and/or lapatinib treatment by Western blot analysis. At 1. 5 and 24 hpi, SARS-CoV-2 increased the ratio of phosphorylated to total protein level of AKT, ERK, and/or p38 MAPK more than 1.
MTT assay (Promega) was used to determine A549 cell viability according to the manufacturer's protocol at 570 nm using a microplate reader (BioTek Synergy). Combination drug treatment. Calu-3 cells were treated with lapatinib-DAA combinations and infected with rSARS-CoV-2/Nluc (USA-WA1/2020 strain) (MOI = 0. 05). At 24 hpi, the antiviral effect was measured via Nluc assay, and cellular viability was measured via ala-marBlue assay. The MacSynergy II program was used for data analysis, as described previously  (7, 12). Matrix data sets in 3 replicates were assessed at the 95% confidence interval for each experiment. siRNA transfection. siRNAs (10 pmol/well of a 96-well plate) were transfected into cells using Lipofectamine RNAiMAX transfection reagent (Invitrogen) 48 hours before viral infection.
eGFP signal was used as a marker for survival. Cells were excited at 485 to 20 nm, and emission was captured via a CCD camera and a BGRFRN_BGRFRN dichroic mirror and filter set (exposure time 0. 023 seconds). Imaging acquisition speed was optimized using a 2 × 2 binning on 1,104 × 1,104 pixel resolution and reducing the number of autofocus focal planes. Cellomics (Thermo Fisher Scientific) software was used for image analysis. A custom-made image analysis protocol was created using the Spot Detector bioapplication (Cellomics, Thermo Fisher Scientific). SpotTotalAreaCh2 (raw value of total amount of surface covered by fluorescent cells in image) was used for further data analysis. Human adult lung organoids. The adult lung organoid (ALO) model was generated from adult stem cells isolated from deep lung biopsy specimens  (11).
After 1-hour incubation, the temperature was shifted to 37°C to initiate infection. At 0. 5 and 1 hour after temperature shift, cells were washed with PBS and incubated for 15 minutes at room temperature with Zombie Aqua live/dead fixable dye (BioLegend) and FcR Blocking Reagent (Miltenyi Biotec). Cells were stained for 20 minutes at 4°C with anti-NRP1-BV421, anti-ACE2-APC, and anti-ErbB2-Alexa Fluor 488 antibodies, or with their corresponding isotype controls. Unbound antibody was washed, and cells were fixed with 4% PFA for 1 hour at room temperature. Cell acquisition was performed on an Aurora Cytek spectral flow cytometer, and data were analyzed using FlowJo software (Tree Star). Statistics. SuperScript IV First-Strand Synthesis kit (Invitrogen). The nsP2 region was amplified with Platinum Green Hot Start PCR Master Mix (2×) (Invitrogen) using primers AGGAAAATGTTAGAGGAGCACAAG (forward) and GTCAATATACAGGGTCTCTACGGGGTGT (reverse) and sequenced (Sequetech Corp.
). Signaling pathway analysis. After 2-hour starvation, Calu-3 cells or ALO-derived monolayers were treated with lapatinib or DMSO and, within an hour, infected with SARS-CoV-2 (MOI = 1). Cell lysates were obtained at 1. 5 and/or 24 hpi followed by Western blot analysis with antibodies targeting the phosphorylated and total protein forms (see Supplemental Methods). Phosphorylated to total protein ratios were quantified with ImageJ software (NIH). Cytokine measurements. Cytokine concentrations in ALO supernatants were quantified using a LEGENDplex Human Inflammation Panel 1 (BioLegend) kit and read on a Quanteon flow cytometer (Agilent). Data were analyzed using LEGENDplex v8. 0 software. Cytokine levels in gNVU perfused media were quantified using the MSD V-PLEX Proinflammatory Panel Human Kit (Meso Scale Discovery) and MESO QuickPlex SQ 120 (Meso Scale Discovery) reader.
Acknowledgments This work was supported by awards  W81XWH2210283  and  W81XWH-16-1-0691  from the  Department of Defense/Congressionally Directed Medical Research Programs  (to SE and SDJ), award  HDTRA11810039  from the  Defense Threat Reduction Agency/Fundamental Research to Counter Weapons of Mass Destruction  (to SE, SDJ, and AN), grants  1R01AI158569-01  (to SE and SDJ),  3R01DK107585-05S1  (to SD),  UCOP-R00RG2642  (to SD and PG),  UCOP-R01RG3780  (to PG and DS), and  3UH3TR002097-04S1  (to JPW and JAB) from the  National Insti-.
The box horizontal lines indicate the first, second (median), and third quartiles. Outliers above a cutoff of 15% were defined as positive hits. Dots represent individual compounds, and colors denote positive controls (purple), new hits (blue), and ErbB inhibitors (peach). (D) Heatmap of the EC 50 and CC 50 values of hits emerging in the HTS, color-coded based on the antiviral activity measured by plaque assays (green) and toxicity measured by alamarBlue assays (orange), 24 hours after infection of Vero cells with SARS-CoV-2 (USA-WA1/2020 strain, MOI = 0. 05). Selectivity indices (SI) greater than 5 are depicted in yellow. "#" indicates compounds from the 13-kinase set. (E) Dose-response curves of representative hits depicting SARS-CoV-2 infection (black) and cell viability (blue). Data are relative to DMSO.
2019)  was used for DNA sequencing. This kit targets a total of 469 Annonaceae wide exons. DNA extraction, DNA sequencing protocols, and the bioinformatic procedure are presented in  Couvreur et al. (2019)  and  Breé et al. (2020). Thus, after filtering our data for the genes covering 75% of each exon for 75% of the individuals, and eliminating suspected paralogues following HybPier approach (see  Couvreur et al. 2019; Breé et al. 2020) , we ended up with a total of 323 genes used for the phylogenetic analyses. Phylogenetic relationships among taxa were estimated using maximum likelihood (ML) methods performed with RAxML  (Stamatakis 2014). We also ran an ASTRAL-III (v5. 5. 11) analysis  (Zhang et al. 2017)  as performed by  Couvreur et al. (2019). The paired fastq sequences for individuals included in this study are available in Genbank SRA under Bioproject number PRJNA508895 (http:// www.
Notes on reproductive ecology Flower phenology was documented to determine the timing of the onset of stigmatic receptivity, its duration and the start and duration of the staminal phase (see  Ratnayake et al. 2007). Also, extensive observations on mature flowers of different individuals were made. Observations were made every hour from 8:00 a. m. to 6:00 p. m. on 10 different individuals. The identity of the visitor, visitor behavior and stage of sexual maturity of the flower (pistillate: colour change and stigma exudate; staminate: dehiscence in anthers or stigmas fall) were recorded. External visitors and visitors inside the flower were captured when possible. To determine potential pollinators, we used a poisson regression modelling approach for handling the visit frequency data  (Cameron and Trivedi 1998).
Acknowledgements We extend our sincere gratitude to  Héctor Gómez Dominguez , for his valuable support during the field trip and to  Paul J. M. Maas ,  Adriana Lobão  and  Michael Pirie  for their encouraging and constructive comments on the manuscript. Thanks to  Christopher Davidson  and  Sharon Christoph  for financing visits to the type locality through the project " KarstBio ". Also we thank  Leopoldo Hurtado  for his support during the preparation of Fig. 2, and  Berenit Mendoza-Garfias  at the  Laboratory of Electron Microscopy and Photography, Instituto de PhytoKeys 227 :  181-198 (2023 ), DOI: 10. 3897/phytokeys. 227. 102279María  Fernanda Martínez-Velarde  et al. :  Flagelliflorus new species Biología of Universidad Nacional Autónoma de México (IBUNAM)  for the SEM pictures. Finally, we are in debt to  Don Urbano Altamirano  from Poblado 11 who guided us to the locality of this species back in 2014, and has helped us ever since.
At the level of the Atlantic coast of Kribi, few research works have been carried out that have taken into account zooplankton in particular. To date, the only known work on zooplankton in the study area is that  [7]  on the zooplankton Dynamics of the Kienke Estuary (Kribi, South Region of Cameroon). To fill this gap, this work aims to assess the abiotic variables of the waters that influence the diversity and the dynamics of the zooplankton in order to contribute to the implementation of a reference database which would be used by the scientific community and the managers of these ecosystems.