dataesr/scientific-paragraphs-categorization huggingface dataset:
Caribbean zooarchaeological quantitative and qualitative data The regional zooarchaeological dataset compiled for this study comprises counts of vertebrate bone remains from pre-Columbian deposits in the Lesser Antilles, Greater Antilles and the Bahamas royalsocietypublishing. org/journal/rsos R. Soc. Open Sci. 9: 220256 archipelago. Data from grey literature (i. e. unpublished archaeological reports) were excluded, and only limited bone counts data from Jamaica, Hispaniola and Cuba were included given difficulties in obtaining raw zooarchaeological data from these islands. The present review includes two datasets: (1) quantitative bone counts and (2) occurrence data for herpetofaunal taxa. The first dataset (electronic supplementary material, S1) comprises published bone counts for Caribbean zooarchaeological assemblages.
The number of identified skeletal parts (NISP) and the minimum number of individuals (NMI) of the main vertebrate taxa were used to calculate the proportion of herpetofaunal remains for each site (electronic supplementary material, S1). The different vertebrate categories included aquatic taxa (fish, marine mammals and marine turtles), birds, terrestrial mammals (including bats), squamates, amphibians and tortoises. Chronological sub-divisions of the assemblages were included when available. The first dataset comprises faunal data from a total of 95 assemblages (figure  1 ). Zooarchaeological data for samples that were not fully published were excluded, including several sites from Guadeloupe for which only reptile remains were published  [40]. The second dataset includes occurrence data for herpetofaunal taxa from 89 different deposits (electronic supplementary material, S2).
Statistical analyses All statistical analyses were conducted using the open-source R software  [45]  and the RStudio distribution  [46]. All statistical regressions were conducted using a 'standardized MNI value' obtained by dividing the MNI value of the taxa recovered from each site by the sum of the MNI for all taxa from the assemblage. This avoids giving more weight to large assemblages compared to smaller ones. To analyze proportion data, beta regressions were performed using the R 'betareg' package  [47]. In order to test compositional difference between the MNI data from several groups of faunal assemblages using χ 2 tests, the total MNI was calculated for the different sites in each group. χ 2 tests were performed using the R package 'rmngb'  [48]. Bonferroni corrections were applied to every pairwise χ 2 test using the same package.
The place of herpetofauna in indigenous archaeofaunal assemblages The analysis of deposits for which both MNI and NISP data were available shows the proportion of the taxa to differ depending on the quantification unit used (χ 2 -test; p < 0. 01). Consequently, proportions calculated from two quantification methods could not be combined in a single analysis. As most of the investigated assemblages (89/95) had MNI data and only half (48/95) had NISP data, all analyses using proportions of the different taxa in the faunal samples were based on MNI alone. In the end, five assemblages and five sites lacked published MNI data (El Gato Jíbaro cave, Sandy Hill, Golden Grove, Milford and Manzanilla) and were therefore excluded from the quantitative analysis. Most deposits are dominated by marine taxa, which represent more than 60% of identified individuals in 74 of the 89 assemblages, and more than 80% in 54 of them (electronic supplementary material, S1).
Amphibians are extremely rare and only appear in six deposits, primarily in the Greater Antilles (electronic supplementary material, S1). The proportion of squamates is positively correlated ( p > 0. 01) with the proportions of other terrestrial taxa. This correlation is stronger in the Lesser Antilles ( pseudo R 2 = 0. 33) compared to the overall dataset (pseudo R 2 = 0. 10). This would be consistent with the exploitation of squamates being partly linked to the general exploitation of terrestrial meat resources. This correlation is, however, far from absolute as the specific subsistence strategies of the inhabitants of each site cannot be reduced to a simple choice between terrestrial or marine resources.
These remains were identified as Trachemys decussata in Cuba, Trachemys stejnegeri in Puerto Rico, Trachemys sp. , Chelonoidis alburyorum keegani and Geochelone sp. in the Bahamas archipelago, Trachemys sp. and/or Geochelone sp. in St Thomas and Trinidad, and left unidentified in Nevis  [12, [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64]. The reports of crocodiles in the sample of sites for royalsocietypublishing. org/journal/rsos R. Soc. Open Sci. 9: 220256 Table  1. Herpetofaunal taxa identified in the insular Caribbean Indigenous archaeological record, with the percentages of the modern native and extinct taxa. ' Ã ' signals identifications that are inconsistent with biogeographic data or uncertain determinations. The number of native taxa currently present on the islands is from  [50]  for Trinidad and Tobago and from  [38]  for all the other islands.
Occurrence and zooarchaeological data regarding the different taxa In order to provide a more accurate and reliable vision of available zooarchaeological evidence for the past biodiversity in the insular Caribbean, I collated existing taxonomic data from archaeological deposits with their biogeographic contexts. Anurans: Anurans are very rarely identified in Caribbean archaeological deposits (see Results section) and nearly never attributed to genus or species. Anurans are nowadays mostly represented by Eleutherodactylid frogs  [38, 96]. These minute frogs with small, fragile bones can be very well represented in paleontological deposits in caves  [97]  but are difficult to collect, while tvin most archaeological assemblages. Larger anuran taxa are however currently present in the Caribbean islands, meaning that their absence is not due uniquely to taphonomic or recovery biases.
Data represent 253, 317, and 596 ULFs, respectively, collected from 9, 10, and 16 cells from three to four independent experiments. P value was calculated with a nested t test of the three repeats, ****P < 0. 0001. n. s. , not significant. (E and F) Top: Schematic of the Vimentin-Y117L-Spot-Tail protein (E) and Spot-Vimentin-Y117L protein (F). Bottom: Epifluorescence image (gray) and a higher magnification of the boxed region superimposed on the corresponding 2D dSTORM image (fire) of Spot-nanobodies-AF647 (Spot-nb-AF647) (fire). Inset: Magnifications of the boxed regions.
Filament pairwise distance analysis Analysis of the double length was performed using MATLAB (MathWorks) and Fiji and involved several steps depicted in Fig. 3C:  (1) isolating filaments, (2) detecting single vimentin peaks and linking them to their two nearest neighbors, (3) removing graph nodes that have four edges or more, (4) resolving triplets, (5) removing the connected components that have fewer than four nodes, and (6) measuring distances from the remaining edges. 1) Isolating filaments. The reconstructed super-resolution image of vimentin contains spurious signals away from filaments that we need to filter out. Because true vimentin peaks on filaments are spaced by a distance smaller than the filament persistence length, we can use filter operations to yield a broad mask that contains only the filaments.
Acknowledgments: We thank  R. Leube  and  R. Windoffer  from the  University of Aachen, P. Nassoy from University of Bordeaux ,  M. Lenz  from  University of Orsay , and  B. Boëda ,  V. Roca ,  B. Lelandais ,  C. Weber , and  T. Obadia  from  Institut Pasteur  for discussions; and  D. Pham-Dinh ,  J. Ries , and  H. Herrmann  for reagents. We thank  F. Eghiaian ,  J. Hanne , and  J. -G. Schloetel  from  Abberior Instruments GmbH  for imaging our samples. C. Leduc  thanks  H. Herrmann  and.
Trio analysis in negative cases identified ARHGAP35 as a candidate in two families and screening for variants in this gene specifically identified one more case. Sanger sequencing was used to confirm variants and for segregation analysis. An additional case was identified through clinical genome sequencing and Matchmaker Exchange Databases  [14]. Variants in ARHGAP35 were named based on reference sequence NM_004491. 4 and human Genome Build hg19 and evaluated according to ACMG/AMP guidelines  [15].
Amino Acid Sequence Determination The 5168. 3 Da peptide of peak 1 was sequenced by In Source Decay (ISD) MALDI mass spectrometry (Figure  2B ). We identified a fragment of 35 amino acids corresponding to the C-terminus of the peptide. The annotation showed 100% of local identity with the sequence of myotoxin-3 (UniProt database accession number: P63176), a 45-residue peptide belonging to the crotamine-like peptides found in crotalids. Peptides of the crotamine family are highly cationic at neutral pH and possess six cysteine residues that pair into three disulfide bonds. The remaining moiety of myotoxin-3, i. e. , the 10 N-terminus amino acids (YKRCHKKGGH), has a calculated monoisotopic mass (Peptide mass calculator) of 1212. 69 Da, quite similar to the mass of the last fragment from ISD fragmentation (1212.
Titration of 55 µM tubulin by 2. 2 mM of myotoxin-3 resulted in an exothermic binding curve, showing that this is an enthalpy-favorable interaction. Fitting experimental data with the "one-set-of-sites" model (Figure  10C ) revealed that tubulin is able to bind two myotoxin-3 molecules per tubulin heterodimer with low micromolar dissociation constant (Kd = 5. 3 µM) in the same range as other MTAs  [20]. We can thus hypothesize that each highly homologous a tubulin and b tubulin subunit binds one myotoxin-3 molecule. To obtain access to the parameters of binding of myotoxin-3 to ab-tubulin dimers, we used isothermal titration calorimetry (ITC). This biophysical technique needs amounts of myotoxin-3 that can hardly be obtained by purification. Even the yield of chemical synthesis is hindered by the presence and the formation of the three disulfide bonds in the right place.
Amino Acid Sequence Determination MALDI in-source decay was performed using an Ultraflextreme TOF/TOF mass spectrometer controlled by the FlexControl 3. 3 software (BrukerDaltonics). Spectra were acquired in positive reflectron ion mode with 2000 laser shots accumulated, and the laser power was set with an increase in 20% of fluensce to fragment protein in the source of the mass spectrometer using a 20 mg/mL solution of 1,8-diaminonaphtalen (DAN) matrix enabling the generation of hydrogen radicals that break the peptide backbone producing c-ions and z-ions from 1000 to 5000 Da. The generated fragment ions allowed the sequence annotation of the peptides. The mass spectrometer parameters were set according to the manufacturer's settings for optimal acquisition performance. Sequences were analyzed on Flex Analysis software, version 3.
0 (BrukerDaltonics). Mass spectrometer calibration was performed using the c-ions of 1 pmole of BSA spotted with the DAN matrix. N-terminal sequencing of the peptide present on the active fraction was performed by Edman degradation. Approximately 600 pmol of the sample was loaded on a glass fiber membrane pretreated with 10 µL of biobrene and then analyzed using an automatic sequencer model PPSQ 31B (Shimadzu, Kyoto, Japan). The sequence was compared with the Uniprot database and with the sequence obtained by MS.
4). Each image was recorded with the spectral mode of the CLSM selecting specific domains of the emission spectrum: the secondary AlexaFluor488-conjugated antibody was excited at 488 nm with an argon laser, and its fluorescence emission was collected between 496 nm and 535 nm, and the TRITC-coupled phalloidin was excited at 543 nm with a helium-neon laser and its fluorescence emission was collected at between 580 nm and 610 nm. The two fluorophores were excited sequentially. The public-domain ImageJ software was used for image analysis. 4. 9. Time-Lapse Microscopy and Analysis of Microtubule Dynamics MCF-7 cells were seeded at a density of 1. 5 × 10 4 per well in 8-well Nunc Lab-Tek II Chamber Slides™ (Thermo Fisher Scientific) coated with 10 µg/mL fibronectin. Adherent cells were then transfected with 0.
3 µg of tubulin-GFP DNA plasmid and incubated for 24 h. MCF-7 cells were treated with myotoxin-3 (0, 1, 5, or 25 µM) in observation media (phenol-free media, 1% FCS, 10 mM HEPES pH7. 4, penicillin/streptomycin) for 3 h at 37 • C under 5% CO 2 and 90% humidity. Time-lapse acquisitions for microtubule tracks were performed at 2-s intervals for 1 min by CLSM. For calculating dynamics, 50 to 80 individual microtubule trajectories were followed using manual tracking plugging from ImageJ software. Statistical differences were calculated using GraphPadPrism.
Sedimentation Velocity Experiments were carried out at 40,000 rpm and 20 • C in a Beckman Optima-XL-A analytical ultracentrifuge, using 3 mm double sector centerpieces in an AN50Ti rotor. Scans were acquired in continuous mode at 275 nm. At 20 • C, the partial specific volume of tubulin was 0. 736 mL. g -1. The buffer was composed of 20 mM NaPi, 10 µM GTP, pH 6. 5, and its density and viscosity were 1. 009 g/mL -1 and 0. 0147 poise, respectively. All these parameters were calculated with SEDNTERP designed by J Phylo  [43]. The data recorded from moving boundaries were analyzed in terms of continuous size distribution functions of sedimentation coefficient, C(S) using the program SEDFIT  [44] , and the apparent sedimentation coefficient at 20 • C in water (S 20,W ) determined by peak integration.
MATERIALS & METHODS Mouse. The Prkar1a fl/fl ::Sf1 cre/+ ::R26R mTmG/+ mouse line have been described previously  ((Muzumdar et al. 2007; Drelon et al. 2016). Mice were all maintained and bred on a mixed background. Throughout, WT refers Prkar1a fl/+ ::Sf1 cre/+ ::R26R mTmG/+ in which we did not observe any discernible phenotype. Littermate control animals were used in all experiments. Histology and immunostaining. For general morphology and melanin detection, sections were stained with hematoxylin and eosin and with Fontana Masson staining (MF-100-T ; Biognost), following the manufacturer's instructions. Immunohistological methods have been previously F o r R e v i e w O n l y described  (Drelon et al. 2016). Cell count was performed using the QuPath software  (Bankhead et al. 2017). See Table  S1  for conditions used.
Western blot. Twenty five (mouse WB) or twelve (human WB) micrograms of total proteins were loaded on 4/15% SDS-page gel, transfer on nitrocellulose and detected with primary antibodies (Table  S1 ). Signals were quantified with ChemiDoc MP Imaging System camera system (Bio-rad) and Image Lab software (Bio-rad). Expression of proteins were normalized to expression of the ACTIN or GAPDH protein. Real-time PCR analysis. Total RNAs were extracted from skin using the RNAII nucleotide extraction kit (Macherey Nagel), following the manufacturer's instructions. One microgram of total mRNAs was reverse transcribed for 1h at 37C with 5pmol of random hexamers primers, 200 units reverse transcriptase (M-MLV RT, M1701, Promega), 2mM dNTPs and 20 units RNAsin (N2615, Promega). One microlitre of a one-fourth dilution of cDNA was used in each qPCR.
funded through institutional support from Centre National de la Recherche Scientifique, INSERM, Université Clermont-Auvergne and by Agence Nationale pour la Recherche (ANR-18-CE14-0012-02). AUTHORS CONTRIBUTIONS ISB, AMLM, DD, JMB and AM designed experiments. ISB, AMLM, PV and AM prepared manuscript. ISB and AM supervised the project. CK, FRF and CAS provided human samples and clinical information. All authors edited the manuscript.
Statistical analysis. Qualitative data were expressed as percentages and quantitative data as means ± standard deviations. Univariate analysis was conducted using Student test (or Wilcoxon, as appropriate) for quantitative data and Chi 2 for qualitative data. Multivariable logistic regression was performed to study the characteristics associated with remission in 2015. Variables tested in association with remission were age at inclusion, csDMARDs, bDMARDs, sex, RF, ACPA, erosions, initial DAS 28 score. The association was presented as odds ratio (OR) with 95% confidence intervals (95% CI). A p value at 0. 05 was considered as significant. Statistical analysis was performed using SAS software, version 9. 1 (SAS Institute Inc. , Cary, NC, USA).
Using both methods each of the 21 P. vivax proteins had at least one identified P. knowlesi ortholog. When multiple orthologs were found, the top hit was selected by highest identity. The similarity and identity values for the hits on PlasmoDB were obtained by aligning the full-length protein sequences provided in the database using the EMBOSS Needle protein alignment tool;  35  the identity values for the NCBI BlastP hits were obtained from the BlastP search using only the protein construct sequence. The sequence identity of the full-length protein sequences (search strategy 1) ranged from 11% to 19% for MSP7F (A1H1 line or H strain, respectively) to 83. 4% for MSP8. A similar trend was found using the specific protein construct and NCBI BlastP (search strategy 2); however, the percent identity was often higher using this method (Table  1 ).
knowlesi infections were classified as recently exposed to P. vivax. The top eight P. vivax proteins used in the classification algorithm were: MSP1-19, MSP8, Pv-fam-a (PlasmoDB: PVX_096995), RAMA, RBP2b 161-1454 , Pv-fam-a (PlasmoDB: PVX_112670), MSP3a, and EBP. We utilized a balanced sensitivity and specificity target of 79%. The Random Forest classification algorithm was trained using existing datasets from prospective longitudinal cohorts in Brazil, Thailand, and the Solomon Islands. 9 In these studies, the prevalence of P. vivax infection was assessed monthly via qPCR for the year-long duration of the cohort, and antibody responses were measured at the final time point. This allowed a detailed characterization of the association between antibody responses and the time since previous P.
Article We re-trained the algorithm on our existing Thai, Brazilian, and Solomon Islands datasets  9  for these eight P. vivax proteins. Youden's J was used to determine the best trade-off balancing sensitivity and specificity, assuming equal importance of false positives and false negatives in the classification process. The algorithm trained with the modified panel of eight P. vivax proteins achieved 72. 4% sensitivity and 70. 8% specificity respectively, for classifying recent P. vivax infections within the prior 9 months using the existing Thai, Brazilian, and Solomon Islands datasets (Figure  S4A ). When applied to confirmed P. knowlesi clinical cases, we identified a reduced number of 210 of 462 (45%) samples being classed as recently exposed to P. vivax (Table  3 ) (compared with 281 of 462 (61%) using the original panel).
knowlesi samples at day 7 (fold change 2. 9 compared with the seropositivity cut-off), we replaced RBP2b 1986-2653 in the modified panel with RBP2b 161-1454. This improved classification of recent P. vivax infections in the Thai, Brazilian and Solomon Islands datasets to 78. 7% sensitivity and 76. 9% specificity (Figure  S4B ), which is more comparable with the original classifier. Applying this trained classification algorithm to the P. knowlesi sample sets resulted in 215 of 462 (47%) samples being misclassified (Table  3 ), lower than when the original algorithm (281) was used and similar to the 210 misclassified when RBP2b 1986-2653 was used in the modified panel (modified algorithm RBP2b 1986-2653 vs RBP2b 161-1454 , p = 0. 79, Fisher exact test). At day 7 post-P. knowlesi infection 68%-71% were classified as recently exposed to P.
When we applied our previously trained classification algorithm to the current P. knowlesi clinical datasets, 77%-82% of P. knowlesi patients at the peak antibody time point (day 7) in each cohort were classified as recently exposed to P. vivax blood-stage parasites in the past 9 months. This was reduced to 61%-69% at day 28 and 17% at day 365. As mentioned, at the time of the PACKNOW cohort (2016-2018), local P. vivax transmission in Sabah, Malaysia, had approached elimination, and nearly all malaria was from P. knowlesi. 39 Thus, in this cohort there is less risk that the anti-P. vivax antibody responses measured are due to past exposure to P. vivax, and a lower proportion of P. knowlesi patients were accordingly classified as recently exposed compared with the earlier ACTKNOW cohort. However, 77% of PACKNOW patients at day 7 were classified as recently exposed to P.
knowlesi clinical trials conducted in Sabah, Malaysia, denoted as ACTKNOW and PACKNOW, and four panels of malaria-naı ¨ve negative controls. The ACTKNOW study recruited patients over 2012-2014, with the aim of comparing artesunate-mefloquine versus chloroquine for the treatment of acute uncomplicated P. knowlesi malaria 36 (clinicaltrials. gov registration number NCT01708876). Patients were recruited from three hospitals (Kudat, Kota Marudu, Pitas) and were eligible for inclusion if they had microscopic diagnosis of P. knowlesi monoinfection, were more than 1 year of age, more than 10kg, had a negative P. falciparum rapid diagnostic test, and had a fever (%37. 5 C) or history of fever in the past 48 h. Patients who were not confirmed by PCR to have P. knowlesi monoinfection were retrospectively excluded.
36 Of those excluded, 14 were due to P. vivax infections detected upon PCR. The duration of self-reported history of fever (days) was recorded. Patients were treated as previously described,  36  with approximately half randomised to receive chloroquine and half to receive artemisinin-based combination therapy. Plasma samples were available for the current study from 99 patients at day 0 (time of enrollment), day 7 and day 28. Data is presented from 98 samples at day 0 for 20/21 P. vivax proteins due to one sample failing quality control of the antibody data, and the incorrect sample being repeated by mistake. See Table  2  for patient demographic details include age and gender. The PACKNOW study recruited patients over 2016-2018, with the aim of comparing regularly dosed paracetamol versus no paracetamol on renal function in P.
knowlesi malaria  37, 38  (clinicaltrials. gov registration number NCT03056391). All patients received antimalarial drug treatment with artemether-lumefantrine. Patients were recruited from four hospitals (Queen Elizabeth Hospital, Keningau, Ranau, Kota Marudu) and were eligible for inclusion if they had a microscopic diagnosis of P. knowlesi monoinfection, fever (R38 C) on admission or during the preceding 48 h, and were more than 5 years of age. Patients were enrolled within 18 h of commencing antimalarial treatment. 37, 38 Patients who were not confirmed by PCR to have P. knowlesi monoinfection were retrospectively excluded, using a validated PCR assay. 58 In contrast to the ACTKNOW study, only one participant was excluded due to P. vivax infection detected by PCR (unpublished data). Plasma samples were available for the current study from 41 patients at day 0 (time of enrollment), 7, 14, 28 and 365 (these exact time-points were not always available, exact days post-enrolment are stated in the results and relevant figure legends).