dataesr/scientific-paragraphs-categorization huggingface dataset:
For each species, ohnologs were concatenated into two series of gene sequences. For the two-ratio model, we assumed one CF for the blind cavefish, S. anshuiensis, and one SF for the two eyed species, S. rhinocerous and S. grahami. For each dataset, likelihood ratio tests suggested that the two-ratio model was better than the one-ratio model (CF > SF) and the best model was the free-ratio model (supplementary table  S2 , Supplementary Material online). With the free-ratio model,  was higher in the blind S. anshuiensis (0. 36) than in the small-eyed S. rhinocerous (0. 32) and the eyed S. grahami (0. 23) with vision genes. With circadian clock genes,  was higher in the blind S. anshuiensis (0. 38) and the small-eyed S. rhinocerous (0. 37) than in the eyed S. grahami (0. 25). With pigmentation genes  was higher in the small eyed S.
RELAX detected relaxed purifying selection on L. dentata vision genes with an important shift toward  = 1 as k = 0. 2, and this was also true to a lesser extent in A. mexicanus cavefish (k = 0. 5). For pigmentation genes, the largest shift was also observed in L. dentata (k = 0. 48). No shift was observed with cavefish circadian clock genes, suggesting that most of these genes are under strong purifying selection in cavefishes Finally, with the aim of finding additional and independent evidence of relaxed purifying selection in cavefishes, in particular on A. mexicanus vision genes for which the number of mutations is particularly low and thus the estimate of  was not accurate, we developed a novel approach. First, nonsynonymous mutations in different lineages were inferred using the aaml program from the PAML package.
Genomic resources for two Cuban cave brotulas A draft genome and a transcriptome were obtained for a specimen belonging to Lucifuga dentata. The reads of a specimen belonging to a closely related species, L. gibarensis, were mapped onto the L. dentata genome. A detailed description of the materials, methods and results are given in supplementary Data S1, Supplementary Material online. In the present study, these genomic resources were used to retrieve exon sequences and intron splice sites. The transcriptome allowed us to assess the reliability of the LoF mutations found in the genome of L. dentata.
Vision, circadian clock and pigmentation gene sets The set of vision genes included all opsins, visual opsins that are expressed in eye photoreceptor cells (cone and rods) but also non-visual opsins that are expressed in various tissues. It also comprised eye specific crystallin genes that were selected using expression patterns reported in zebrafish from the ZFIN database (https://zfin. org/) and in A. mexicanus  (Hinaux, et al. 2015). However, crygm2 crystallin genes were excluded from the analyses. Indeed, many copies were found in fish genomes (more than 50 copies in A. mexicanus) and relaxed purifying selection on some copies could have occurred independently in response to any environmental shift. The set of vision genes also included genes coding for proteins involved in the phototransduction cascade and whose expression was restricted to the retina and/or the pineal complex: RPE65, Arrestins, Recoverins, Transducins, PDE6, CNGA3 and CNGB3, GCAPs, zGCs, and GRKs.
Construction of data sets The sequences of visual and non-visual opsins of zebrafish were retrieved from  (Davies, et al. 2015). Other vision genes, circadian clock and pigmentation genes of zebrafish were retrieved from GenBank. A series of blastn and tblastx  (Altschul, et al. 1990 ) with zebrafish sequences were performed against A. mexicanus surface and Pachón cave genomes (GCF_000372685. 2 and GCF_000372685. 1 respectively), S. grahami, S. rhinocerous, S. anshuiensis, P. nattereri, B. barbata, C. acus and L. exutus genomes (GCF_001515645. 1, GCF_001515625. 1, GCF_001515605. 1, GCF_001682695. 1, GCA_900303265. 1, GCA_900312935. 1 and GCA_900312555. 1 respectively), and L. dentata and L. gibarensis genomes (this study). Matching regions were extracted using samtools  (Li 2011 ) and CDS were predicted using EXONERATE with protein sequences of zebrafish  (Slater and Birney 2005).
Other analyses of the relaxation of purifying selection in cavefishes For each diploid species, gene sequences belonging to the same gene set (vision, circadian clock or pigmentation) were concatenated. In order to analyze gene sequences of the tetraploid Sinocyclocheilus species, another alignment was produced. For each species and each gene set, gene sequences were concatenated after having taken at random one gene from each pair of ohnologs. This sampling process produced for each gene set two concatenated gene sequences for each species. With these six alignments of concatenated sequences, maximum likelihood estimates of  were obtained using the program codeml from the PAML package Version 4. 9h  (Yang 2007). We considered three nested branch models: a 'one-ratio' model assuming the same  for all branches in the phylogeny; a 'two-ratio' model assuming one  for blind cavefishes (CF) and one  for the other fishes (SF); a free-ratio model allowing a different  for each branch.
Likelihood ratio tests were performed to compare the likelihood values of the different models. Each likelihood ratio (LR) was calculated as twice the difference of log likelihood between the two models compared. The significance of the LR was determined by using the χ2 distribution with the number of degrees of freedom equal to the difference between the number of estimated parameters in the two models. A further approach for detecting relaxed selection was carried out using the program RELAX  (Wertheim, et al. 2015) , assigning the surface fishes as the reference. Each cavefish was independently assigned as the test branch. A value of the parameter k significantly different from one (k < 1 if selection is relaxed and k > 1 if selection is intensified) suggests a change in the selective regime in the cavefish lineage.
Inferring the deleterious impact of amino acid variants with MutPred2 Maximum likelihood inference of amino acids substitutions were performed using the program aaml from the PAML package Version 4. 9h  (Yang 2007). For each amino acid substitution, MutPred2 scores  (Pejaver, et al. 2017 ) and Grantham's distances  (Grantham 1974)  were computed to estimate its deleterious impact. In order to compare the distribution of scores (or distances) for a set of genes within a branch with the distribution expected under completely relaxed purifying selection, simulations of random mutations of nucleotides were generated, taking into account the length of the coding sequence of each gene and the transition/transversion ratio (https://github. com/MaximePolicarpo/Molecular-decay-of-light-processing-genes-incavefishes/blob/master/Neutral_evolution_for_mutpred.
For assessing the effect of the variation of LoF among genes on dating, a program was written to simulate gene decay through accumulation of LoF mutations, taking into account the length and the number of introns to compute a LoF for each gene (more details are given in supplementary Data S3, Supplementary Material online. Other methods for dating relaxation of purifying selection on vision genes in L. dentata Vision genes from the two Cuban cave brotulas (L. dentata and L. gibarensis) and an outgroup (Brotula barbata) were concatenated and aligned. We assumed that vision genes have been under purifying selection along the branches of the phylogenetic tree, except in the lineage leading to L. dentata which is a mixed branch (with a period under purifying selection followed by a period under completely relaxed selection).
Acknowledgments ScholarOne, 375  Greenbrier Drive , Charlottesville, VA, 22901 Support: (434) 964-4100 This work was supported by a collaborative grant from  Agence Nationale de la Recherche (BLINDTEST  to S. R. and D. C. ) and from  Institut Diversité Ecologie et Evolution du Vivant  (to S. R. and D. C). We thank  Yan Jaszczyszyn ,  Jean Mainguy ,  Nina Paffoni  and  Isabelle Germon  for their help in sequencing and analyzing the genomes of L. dentata and L. gibarensis,  Patrick Laurenti  for animal drawings,  Cushla Metcalfe  and a reviewer for improving the English. We also thank  Carlsbergfondet  for financial support (grant no. 2013_01_0501 ) for sampling Lucifuga gibarensis.
All stations are maintained by the US Geological Survey's Hawaiian Volcano Observatory and their data were available in real time from the Incorporated Research Institutions for Seismology (IRIS). We should note, the LERZ station PHOD was destroyed by a lava-induced forest fire on August 1, ~90 days after the start of the eruption. Additionally, during the eruption, a large crack opened directly beneath station KLUD. Three summit stations were also temporarily or permanently lost between May 25 and June 1 from caldera collapse (NPT) and power fluctuations (NAHU and PUHI). Although not used in this analysis, six additional seismic stations were established in the LERZ during the eruption (ERZ1-4, P07, 2816 and KIND), and were critical in realtime hazard analysis and earthquake relocation.
Relative seismic velocity change (dv/v) measurement Noise cross-correlation functions (NCFs) were computed using two independent processing workflows, both implemented using the MSNoise software package  (Lecocq et al. 2014 ). In the first workflow, NCFs were computed for 3 years of continuous data prior to May 2018 using a dataprocessing scheme similar to  Brenguier et al. (2008b) ,  Taira et al. (2015)  and  Taira and Brenguier (2016). (  1 ) First, instrument responses were removed from 1-day-long records, bandpassed between 0. 025 and 2 Hz, down-sampled to 20 Hz, split into 30-min-long segments clipped to 3 rms, and spectrally whitened in the frequency range of 0. 0666-1 Hz (i. e. , 1-15 s). (2) NCFs were computed for these 30-min-long segments for all possible station pairs and varying channel combinations, for a lapse time between ± 120 s.
3 software  (Toda et al. 2011 ) at five locations: two in the SWRZ (DESD, HLPD), one in the upper ERZ/ERZ connector (PAUD), at Pu'u 'Ō'ō, and one in the LERZ (PHOD). In both Coulomb 3. 3 and to convert the computed strain to stress, we used a shear modulus (G) of 25. 6 GPa and a Poisson's ratio of 0. 15, based on the temperature dependence of  Ryan (1987)  assuming T = 140 °C, i. e. , the temperature at 1-km depth in the Scientific Observation Hole 4 (SOH-4) borehole  (Olson and Deymonaz 1993). The earthquake origin and focal mechanism were taken from the US Geological Survey Hawaiian Volcano Observatory (event ID: hv61792931) and National Earthquake Information Center (NEIC; event ID: us20009lc3) catalogs. The fault length and width were computed with an empirical relationship between earthquake magnitude and faulting style  (Wells and Coppersmith 1994).
Acknowledgments This work was possible only through the dedication and support of the  Hawaiian Volcano Observatory 's instrumentation/ technical staff and seismic-network monitoring group. The study benefited greatly from an eruption chronology by  S. Ogburn  and interferograms supplied by  M. Poland  and  M. McLay. Conversations  with  K. Anderson ,  P. Dawson , and  N. Nakata  were crucial to the understanding of geophysical processes involved. Insightful peer reviews by  A. Hotovec-Ellis ,  M. Patrick ,  G. Olivier ,  D. Swanson ,  A. Harris  and  G. Waite  improved both the science and story. C. F. Boomer  provided critical last-minute support. C. Caudron  acknowledges a  F. R. S-FNRS Chargé de Recherches fellowship. T. Taira acknowledges a France-Berkeley Fund  ( 2014-0051 ) and a  NSF   Geophysics program  ( 1053211 ).
Methods We selected our participants according to the 1991 NIH criteria (patients with a body mass index (BMI) of 40 kg/m 2 or BMI of 35 kg/m 2 due to at least one comorbid condition such as arterial hypertension, type 2 diabetes, obstructive sleep apnea (OSA), and dyslipidemia ). Their surgeries and histopathological examinations were performed at a university hospital setting. The ethics committee approved this study. We retrospectively and systematically analyzed the demographic, clinical, and histopathological data obtained from the medical records of all patients who underwent LSG for morbid obesity. Between June 2018 and December 2019, the resected gastric samples of 170 patients with LSG underwent histopathological examination. Samples were obtained after vertical resection of the stomach during an LSG.
Resection was tailored by using 38 Fr bougie. These samples were permanently sectioned in formalin and examined in general. Representative cross-section blocks of 2 mm thickness were fixed by formalin and paraffin, stained with hematoxylin and eosin, and examined by pathologists in the form of 2-mm thick-sliced slides. All patients with LSG received a routine Helicobacter pylori test. Slides were also stained with Giemsa to control the microorganisms. Additional pathological findings were examined with additional slides. The inclusion criteria were all patients undergoing LSG. All patients had undergone preoperative endoscopy. We also extracted the pre-operative clinical findings and postsurgical course of the patients. Then, data were entered and analyzed. Ethical Statement: All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.
Statistical Analysis Extracted data were analyzed using the Statistical Package (SPSS) version 22. 0 (SPSS Inc. , Chicago, IL). Differences were considered statistically significant when p < 0. 05. The participants' demographic, clinical, and histopathological characteristics were summarized by descriptive statistics (frequency, percentage, and mean ± SD or median and range). We also calculated the means and standard errors and 95% confidence intervals for continuous variables. Any association between two or more categorical variables was assessed by Chi-square/Fisher exact test as appropriate. In addition, any association between the two independent groups of quantitative variables was examined by unpaired ttest or Mann-Whitney U test as applicable.
Viscoelastic properties were introduced considering Prony series: G t ð Þ ¼ a � m 2 þ X n k¼1 G k exp À t=t k Where G is the shear modulus, μ and α the Ogden material constants, τ k are the relaxation times and G k the shear moduli associated with them. Three different data sets were used to model WM and GM properties as observed in the literature. First, 1 st order Ogden laws were fitted to Ichihara et al. [22]  experimental data. These data were derived from tensile tests on bovine WM and GM distinctly and present a gray matter twice stiffer than white matter. Secondly, the laws developed by Maikos et al. [11]  for describing the rat spinal cord mechanical behavior were used. In this study, the spinal cord was described as a uniform structure and white and gray matters had the same stiffness.
Accordingly, the impactor was translated laterally and cranio-caudally of ±0. 1mm from its initial position and rotated in the transverse plane (± 3˚) and in the sagittal plane (± 3˚). The different data sets for WM and GM material properties described in Model Generation were tested as a three-level mechanical factor: one with WM stiffer than GM, one with GM stiffer than WM and one with homogeneous WM and GM. To summarize, the effects of 7 three-level factors were investigated: material properties, SC curvature, SC diameter, impactor transverse tilt, impactor sagittal tilt, impactor lateral positioning and impactor cranio-caudal positioning. Each factor was individually tested and 11 interactions of interest were also tested (listed in Table  2 ) This investigation resulted in a total of 98 runs.
Statistical Analysis Data are presented as means and either standard deviation or standard error on the mean. Statistical significance was evaluated using GraphPad Instat 3. 10 software (GraphPad Sofware, San Diego, CA, USA). For all the comparisons between two conditions, we used the non-parametric Wilcoxon-Mann-Whitney two sample rank test (two-tailed p value provided), while for the comparison between more than three conditions we applied a Kruskal-Wallis test, followed by Dunn's Multiple Comparisons Test. One star (*) corresponds to p < 0. 05, ** to p < 0. 01 and *** to p < 10 -3.
Loading Capacity of Nanodiamonds for siRNA Binding We quantified the loading capacity of H-DND for siRNA binding. To this aim, we measured by fluorescence (see Materials and Methods), for a fixed amount of siRNA, the remaining free unbound siRNA for increasing amounts of hydrogenated nanodiamonds. The results are presented in Figure  1  for two conditions: one in which H-DND and siRNA were simply mixed, the other in which the mixing was done under sonication, both for the same duration. For these two conditions, the complete fixation of siRNA occurred at the same mass ratio m H-DND /m siRNA of 10:1. These data suggest the sonication assistance leads to a faster adsorption of siRNA onto H-DND, resulting from the larger thermal agitation brought by ultrasound waves. Nanomaterials 2020, 10, x FOR PEER REVIEW 6 of 14.
Loading Capacity of Nanodiamonds for siRNA Binding We quantified the loading capacity of H-DND for siRNA binding. To this aim, we measured by fluorescence (see Materials and Methods), for a fixed amount of siRNA, the remaining free unbound siRNA for increasing amounts of hydrogenated nanodiamonds. The results are presented in Figure  1  for two conditions: one in which H-DND and siRNA were simply mixed, the other in which the mixing was done under sonication, both for the same duration. For these two conditions, the complete fixation of siRNA occurred at the same mass ratio mH-DND/msiRNA of 10:1. These data suggest the sonication assistance leads to a faster adsorption of siRNA onto H-DND, resulting from the larger thermal agitation brought by ultrasound waves.
In order to confirm these data with our specific conjugate, we formed a solution of H-DND:siRNA at the same mass ratio of 5:1 used in the in vivo experiment, and measured its hydrodynamic diameter in DMEM culture medium supplemented with 10% Fetal Bovine Serum. We found a diameter of 35 nm, a value even smaller than the diameter of 90 nm of the same conjugate in pure water (see Table  S2 ), which is a strong indication that injecting intravenously an aqueous suspension of H-DND:siRNA (mass ratio 5:1), will rather induce a small deagglomeration than an aggregation in the blood circulation.
However, it is well established (see for example S. Hamelaar et al. [25] ) that the serum favors the dispersion of electrostatically-charged nanoparticles when they are dispersed in a culture medium. In order to confirm these data with our specific conjugate, we formed a solution of H-DND:siRNA at the same mass ratio of 5:1 used in the in vivo experiment, and measured its hydrodynamic diameter in DMEM culture medium supplemented with 10% Fetal Bovine Serum. We found a diameter of 35 nm, a value even smaller than the diameter of 90 nm of the same conjugate in pure water (see Table  S2 ), which is a strong indication that injecting intravenously an aqueous suspension of H-DND:siRNA (mass ratio 5:1), will rather induce a small deagglomeration than an aggregation in the blood circulation.
Indeed, since the majority of DND are captured by liver cells, their transfer to the intestine lumen by the bile may be the main way for T-DND elimination. Feces were collected for all the animals simultaneously in the same metabolism cage, but the total amount, including non-expelled feces is not known which is why we could not include feces data in B. ND + siAS: DND complexed with siRNA sequence antisense for EWS-FLI1 oncogene. The differences between error bars for the different conditions are due to (i) the variability between animal groups, and (ii) to the fact that the T-DND quantifications were done only on portions of ≈100 mg of each organ, and that we cannot exclude an inhomogeneous distribution of T-DND within the organs. One of the major questions for the use of mineral origin nanoparticles for biomedical applications is how they may be eliminated after injection in animals.
Discussion In a previous work, we had demonstrated that cationic hydrogenated detonation nanodiamonds can deliver active siRNA to Ewing Sarcoma cell in culture  [16]. Here, we wanted to establish if small hydrogenated DND are able to deliver active siRNA in vivo to mice model of Ewing sarcoma. In order to investigate simultaneously their biodistribution, we produced hydrogenated and tritiated Feces were collected for all the animals simultaneously in the same metabolism cage, but the total amount, including non-expelled feces is not known which is why we could not include feces data in B. ND + siAS: DND complexed with siRNA sequence antisense for EWS-FLI1 oncogene. The differences between error bars for the different conditions are due to (i) the variability between animal groups, and (ii) to the fact that the T-DND quantifications were done only on portions of ≈100 mg of each organ, and that we cannot exclude an inhomogeneous distribution of T-DND within the organs.
Nanomaterials 2020 , 14 Figure 5. 2020145 Figure 5. Mouse organ distribution of uncomplexed T-DND or complexed with siRNA at mass ratio 5:1 of T-DND:siRNA. The total radioactivity of each tissue is measured after 4 h and 24 h for 3 animals per series. Error bars: standard deviations. (a) Radioactivity presented as count per minutes (cpm) per gram of tissue or feces. The latter corresponds only to the fraction collected in the rectum of each animal. (b) Radioactivity from each full organ, presented as the percentage of the total injected dose. Feces were collected for all the animals simultaneously in the same metabolism cage, but the total amount, including non-expelled feces is not known which is why we could not include feces data in B. ND + siAS: DND complexed with siRNA sequence antisense for EWS-FLI1 oncogene.
Theoretical calculations of the Ξ ++ cc mass  [18] [19] [20] [21]  after the LHCb observation fall into a ±20 MeV/c 2 window around the experimental value measured by LHCb. At present, the experimental uncertainty on the Ξ ++ cc mass is still large compared to that of the singly charmed baryons. This paper presents an updated measurement of the Ξ ++ cc mass using the decay modes Ξ ++ cc → Λ + c (→ pK -π + )K -π + π + and Ξ ++ cc → Ξ + c (→ pK -π + )π +. The analysis uses a data sample corresponding to an integrated luminosity of 5. 6 fb -1 , collected by the LHCb experiment during 2016-2018 in pp collisions at a centre-of-mass energy of 13 TeV. This measurement supersedes the results reported on the Ξ ++ cc mass in Refs. [3, 4] , which only use pp collision data at  13  TeV taken in 2016, corresponding to an integrated luminosity of 1.
In between the two software stages, an alignment and calibration of the detector is performed in near real-time  [32]. This process allows the reconstruction of the Ξ ++ cc decays to be performed entirely in the software trigger, whose output is used as input to the present analysis. Simulated samples are used to model the effects of the detector acceptance, optimise selections and verify the validity of the methods used in the measurement. In the simulation, pp collisions are generated using Pythia 8  [33]  with a LHCb specific configuration  [34]. The production of doubly charmed Ξ ++ cc baryons is simulated using the dedicated generator GenXicc2. 0 [35]. Decays of hadrons are described by EvtGen  [36] , in which final-state radiation is generated using Photos  [37]. The interaction of the generated particles with the detector, and its response, are implemented using the Geant4 toolkit  [38]  as described in Ref.