dataesr/scientific-paragraphs-categorization huggingface dataset:
Analysis of diversity of NAT genes in the genus Pan and comparison with humans and other great apes Frequency distributions of NAT haplotypes in the Pan and human population samples were used to test for possible deviations from Hardy Weinberg equilibrium, to estimate expected heterozygosity, (h, equivalent to Nei's gene diversity,  (Nei 1987) ) and nucleotide diversity (p), to estimate levels of population differentiation (F ST statistics), and to test for possible departure from selective neutrality and demographic equilibrium (Ewens-Watterson homozygosity test, Tajima's D test and Fu's F S test,), with the program Arlequin ver. 3. 5  (Excoffier and Lischer 2010). Each of these three latter tests relies on different summaries of diversity (homozygosity for the Ewens-Watterson test, number of polymorphic sites and nucleotide diversity for Tajima's D, and number of different haplotypes and nucleotide diversity for Fu's F s ), and only Tajima's D and Fu's F s tests explicitly account for the mutational events distinguishing haplotypes.
05 for NATP) and the transition to transversion ratio (2. 67, 2. 0 and 2. 5 for NAT1, NAT2 and NATP, respectively). The program Network ver. 5. 0  (Bandelt et al. 1999 ) was used to construct median-joining networks of NAT haplotypes in Pan. Prediction of functional impact of specific mutations in Pan haplotypes at the NAT1 and NAT2 loci Phenotypic predictions of the functional impact of specific mutations in Pan NAT1 and NAT2 haplotypes were performed with three online software tools (analysis done in May 2017): PolyPhen  (Adzhubei et al. 2010) , SIFT  (Sim et al. 2012 ) and the PANTHER cSNP Scoring tool  (Tang and Thomas 2016). These three tools are able to predict the effect of a single nonsynonymous substitution on a protein sequence (Supplementary File S1). To investigate and compare the results returned by these methods, we first applied the three tools on human haplotypes of known phenotypes (Supplementary File S1).
Data availability File S1 contains detailed descriptions of the protocols used for DNA amplification, PCR product purification and sequencing of great ape samples, retrieval of unphased NAT polymorphic positions from the Great Ape Genome Project (GAGP), inference of Pan NAT haplotypes, and retrieval of phased human NAT haplotypes from the 1000 Genomes Project. Table  S1  lists the PCR and sequencing primers used for Sanger sequencing of NAT genes in non-human great ape DNA samples, and available information on these samples is provided in Table  S2. Hominid polymorphic positions detected in NAT1, NAT2, and NATP are listed in Tables  S3, S4 , and S5, respectively. Table  S6  reports estimates of differentiation levels between Pan (sub-)species. Table  S7  lists the human population samples included in the modern human dataset, with associated diversity estimates and results of Hardy-Weinberg equilibrium tests.
RESULTS In this study, we Sanger sequenced approximately 1 Kb of homologous sequence in each of the three members of the arylamine N-acetyltransferase (NAT) gene family, NAT1, NAT2 and the NATP pseudogene, in 84 great ape samples, of which 68 are chimpanzees of the Pan troglodytes verus sub-species. Out of the 84 DNA samples of great apes available, we obtained 248 NAT genotypes (83, 81 and 83 NAT1, NAT2 and NATP genotypes, respectively, Supplementary File S1). We extended our dataset with 231 NAT genotypes from 79 individuals belonging to six great ape (sub-)species retrieved from the GAGP  (Prado-Martinez et al. 2013). As reported in Tables  1  and 2 , the total dataset assembled for analysis thus included 93 genotypes from four Pan troglodytes (common chimpanzee) sub-species for NAT1 and NAT2 (96 for NATP), 14 genotypes from Pan paniscus (bonobo) for each of the 3 NAT genes, 35 genotypes from two Gorilla species for NAT2 and NATP (36 for NAT1), and 17 genotypes from two Pongo (orangutan) species for NAT1 and NAT2 (18 for NATP).
For comparative analysis purposes, we also assembled a human NAT dataset totalizing 1'159 to 1'240 unrelated individuals from 18 to 20 populations distributed on four continents. In spite of the high level of known homology between the three NAT genes, approximately 8% nucleotide positions in NAT1 (76 out of 903 bp), 10% in NAT2 (117 out of 1'115 bp), and 15% in NATP (151 out of 1'002 bp) are segregating positions in hominids, that were found to either be divergent between species, polymorphic within a species, or both (Supplementary Tables  S3, S4 , and S5). Among them, 21 (28%) substitutions in NAT1, 38 (32%) in NAT2, and 77 (51%) in NATP correspond to inter-species divergence. NAT polymorphisms in hominids and polymorphism sharing among species Despite the high numbers of segregating sites detected at the three NAT genes in hominids, little polymorphism was found to be shared between humans, gorillas, orangutans and Pan: two SNPs at NAT1, four at NAT2 and six at the NATP pseudogene (Table  1 ).
We also note that an A/G polymorphism is reported in Denisova (at position 18'228'182) which, according to our dataset, has not been detected in any other hominid species. Within the Pan genus, the largest group of genotyped samples in this study (and in particular the Western chimpanzee sub-species, Pan troglodytes verus), 40 segregating sites were observed in total for the three NAT genes. Among these 40 sites, only 15 were found in Western chimpanzees (Table  2 ; see also Supplementary File S1, and Supplementary Tables  S3, S4  and S5 ). We detected 32 polymorphic positions in common chimpanzees (P. troglodytes), but only five are shared by all Pan troglodytes sub-species (Table  2 ). None of the polymorphic positions shared between all common chimpanzees is observed in bonobos (P. paniscus).
Predicted functional differences among NAT1 and NAT2 haplotypes in Pan We chose Pan NAT1 Ã 1 and Pan NAT2 Ã 4, the basal haplotypes in the median-joining networks of NAT1 and NAT2 haplotypes, respectively (Supplementary Figures  S2  and S3 ), as reference sequences to predict the functional impact of NAT mutations in Pan using PolyPhen, SIFT and PANTHER cSNP Scoring, three online software tools. Four of the 11 Pan NAT1 haplotypes derived from NAT1 Ã 1 were predicted to be damaging with more or less confidence (Table  5 ): NAT1 Ã 4 and NAT1 Ã 7, each predicted by two tools, and NAT1 Ã 3 and NAT1 Ã 8 by one tool only. The other seven haplotypes were either predicted as not damaging or only differ from the others by synonymous mutations. The cumulated frequencies of potentially damaging haplotypes could thus reach the values of 10-13% in Western (P.
Comparison of NAT genetic diversity between Pan and humans The total number of human haplotypes represented in the dataset of human populations analyzed here (Supplementary Table  S7 ) is 21 for NAT1 (3. 5 per sample, on average), 44 for NAT2 (10. 7), and 58 for NATP (10. 6). No deviation from Hardy-Weinberg equilibrium was found for any of the human samples at any of the NAT genes, after correction for multiple testing (Supplementary Table  S7 ). When compared to chimpanzees and bonobos, humans appear to have about five times less diversity than Pan at the homologous NAT1 gene, while four to nine times more diversity than Pan at NAT2 (Figure  2 , Table  6  and Supplementary Table  S7 ). In Figure  2 , the documented high level of diversity of human NAT2 is clearly illustrated by its similarity to NATP  (Sabbagh et al.
2018). Indeed, a marked geographic structure characterizes human NATP diversity, with less diversity in populations from Europe, Asia and the Americas than in African populations (as illustrated in Supplementary Figure  S6  for the human dataset assembled in this study). For NAT2, the observations are of an excess of non-synonymous relative to synonymous SNPs, a lack of correlation of genetic and geographic distances at the worldwide scale, and an unusual pattern of population structure that differentiates Asian populations from Africans and Europeans more than expected on neutral grounds. Finally, NAT1 is much less polymorphic in humans, and is associated with a significant excess of homozygotes in many populations. In Pan, the frequency distributions of inferred haplotypes suggest that NAT genes have evolved under different selective regimes in these species too.
Finally, we acknowledge that our analyses are based on only a few segregating sites, which is expected given the short length of the NATs open-reading frames. Hence larger sample sizes than the ones available in this study are required to make robust assertions on the prevalence of distinct acetylator profiles, and to confirm the patterns of molecular diversity of NAT genes found in chimpanzees and bonobos. Divergent selective pressures acting on the evolution of NAT genes in humans and chimpanzees The results of the three tests of selective neutrality used on the human dataset analyzed here support the current view that human NAT1 diversity is constrained by purifying selection (Table  6  and Supplementary Table  S12 ). On the other hand, the finding of higher frequencies of human NAT2 slow acetylator phenotypes in food-producing populations compared to hunter-gatherers supports the idea that the gene was impacted by selective pressures induced by the modes of subsistence adopted by past populations, and in particular their diets  (Patin et al.
ACKNOWLEDGMENTS The authors wish to thank  Lydie Brunet ,  Eli ska Podgorná ,  Ilham Bahechar  and  Juan Montoya , for technical assistance,  Ronald Bontrop  and  Gaby Doxiadis  for help with the BPRC samples, and  Gaby Doxiadis ,  José Manuel Nunes , and  André Langaney  for helpful discussions. We are also very grateful to the anonymous reviewer for providing constructive comments and suggestions on a former version of the manuscript. Supported by  Swiss National Science Foundation  grant no. 320030  to ESP.
The consequent repeating of this simulation for all possible combinations of parameters p 10 , p 20 , q 20 , starting from the triple (0,0,0) up to the triple (1,1,1) with a step 0,01 for each parameter p 10 , p 20 , q 20 allowed detecting the intervals of initial conditions: p min 10 � p 10 � p max 10 ; p min 20 � p 20 � p max 20 ; q min 20 � q 20 � q max 20 ; which satisfy (A14) for all time period T and thus provide a desired corridors of all probabilities. A user interface is developed allowing to input the parameters of the model and to output the results in the graphical form and in the form of numerical files. The corresponding program code can be found at: https://github. com/nickbessonov/CSC-article/blob/master/CSC%20(17. 05. 18). rar) 2. Algorithm for the solution of the system of Eq  (25).
The system (B1) was solved with the help of iterations. Trial initial values a 0 q ; c 0 q , and b 0 iq q = 1. K, i = 1. 6 were set. Substituting these values into the right-hand side of the Eq (B1), we determined the values of unknown parameters in the next pseudo time step a 1 q ; c 1 q , and b 1 iq. Then this process was repeated until the required accuracy of the solution was reached. The only one difficulty arises at the beginning of application of this trick when it is necessary to determine the signs of time steps. This problem was solved easy by several numerical experiments. The sign minus in right part of (B1) is a result of these computational experiments. The corresponding program code can be found at: https://github. com/nickbessonov/CSC-article/blob/master/CSC%20(17. 05. 18).
Materials Chitosan (obtained from France Chitine, France) had a degree of deacetylation ( ) of 80% (supplier's data determined by nuclear magnetic resonance) and a weight-average molecular weight ( ) of 180,000 g. mol -1 (supplier's data determined by size-exclusion chromatography). Urea, urease and hydrochloric acid were purchased from Sigma (France). Urease (type III, EC 3. 5. 1. 5) from Canavalia ensiformis (Jack bean) was supplied as a glycerol solution and the specific activity of this enzymatic solution was 778,000 U. L -1  [16].
L -1 urease concentration and an initial pH equal to 4. 7 ± 0. 1: (ii) A second set of experiments for a temperature of 298. 15K and 0. 075, 0. 100, 0. 150 and 0. 200 mol. L -1 for the urea concentration. Experiment at 0. 200 mol. L -1 is from the present study while others are from  [16]. (i) A first For each experiment, data of pH versus time were used. At each reaction time, urea concentration was calculated from pH using the chitosan gelation and chemical equilibrium reactions, i. e. the set of Equations 1, 2, 13, 14, 15, 16, 17, 20, 21 and 22 using build-in fsolve MATLAB®software function (least square method). Experimental hydrolysis reaction rate A aHU (mol. L -1. min -  ) was then calculated using Equation  23 : [^= ? ?.
L -1 , an urea concentration between 0 and 0. 200 mol. L -1 , a pH between 4. 0 and 9. 0 and a temperature between 274 and 310 K. However, some differences can be still raised between modeling and experimental data that should be investigated more deeply. First, except for the experiments where urea is a limiting parameter due to its too low concentration (below 0. 050 mol. L -1 ), the modeling results always underestimate the plateau of pH at the end of the experiments (Figure  3a ). This plateau indicates the end of the experiment, i. e. the depletion of urea. It would indicate that the depletion of urea occurred later and that there was initially more urea in the solution than expected (which allows reaching a higher pH value). In Section 4. 1, urea concentration during the reaction, used for the determination of kinetics parameters of the reaction involved in enzymatic gelation, was estimated using pH value.
, 1985). Normalised data was analysed using the Seahorse XF Mitochondrial Stress Test Generator from Agilent. OCR values were used to calculate non-mitochondrial respiration (NMR = minimum rate measurement after rotenone/antimycin A injection), basal respiration (BR = last measurement before oligomycin injection -NMR), proton leak (PL = minimum measurement after oligomycin injection -NMR), ATP-linked respiration (ALR = BR -PL), maximum respiration (MR = maximum measurement after FCCP injection -NMR) and spare respiratory capacity (SRC = MR -BR) (Fig. 1 ).
1. Illustration of a typical mitochondrial stress test only using injection ports A-C. Oligomycin is released from port A, FCCP from port B and rotenone and antimycin A from port C. OCR data can be manipulated to determine mitochondrial parameters such as basal respiration (BR), ATP-linked respiration (ALR), proton leak (PL), maximum respiration (MR), spare respiratory capacity (SCR) and non-mitochondrial respiration (NMR). 1000 x BA mix was used. Although the 1000 x BA mix is supra-physiological of serum levels, it is similar to the concentrations BAs are postulated to rise to in the bile, albeit not identical. Although it is suspected that biliary levels of BAs are responsible for hepatotoxicity in obstructive cholestasis, it remains unclear whether during DIC hepatocytes are exposed to such biliary fluids containing high levels of BAs.
Acknowledgements We are grateful to the patients who took part in the study and their families. We would like to thank all local investigators who have conducted the clinical studies (Alfred B Tiono,  Marielle Bouyou-Akotet ,  Halidou Tinto ,  Quique Bassat ,  Saadou Issifou ,  Afizi Kibuuka ,  Peter G Kremsner ,  Alphonse Ouedraogo ,  Michael Ramharter ) and  MMV  staff involved in study conduct, data collection and reporting ( Helen Demarest ,  Stephan Duparc ,  Sophie Biguenet ). We thank  Drs. M. Adamy  and  T. N. Wells  for their critical reading of the manuscript. MMV would also like to acknowledge their development partner Sanofi-Aventis.
Israel's National Digital Health Program (2018) Following the National Digital Strategy introduced in 2017, the government of Israel has introduced the national digital health program as a way of increasing access and availability to health information and improve the overall health care system in Israel  [11]. Japan 2035 (2015) Japan has been among the pioneers in developing innovative healthcare. Introduced in 2015, the Japan 2035 vision aims to build and design a health care system for all members of society by 2035. Among others, this includes  1 3  the need to improve the supporting infrastructure through technological development, including the development of health care databases to support telemedicine applications and a strong online database for disease management and treatments  [12].
Italy The Italian Drug Agency's Drug Data Bank provides patients with up-to-date information on medicines. Companies are asked to provide the updated information to the database within 30 days of approval. Patients are allowed to have onsite printing through pharmacies. https ://farma ci. agenz iafar maco. gov. it/banca datif armac i/home Spain Spain's Agency of Medicine and Medical Devices developed a Medicine Online Information Center that displays information on medicines, including leaflet information, in various formats including in sign language. The website also provides information on available medicines in community centres or pharmacy, as well as details referring to a product's authorization and marketing status. https ://cima. aemps. es/cima/publi co/home. html Sweden Fass. se is a trade-association online service that is updated daily and provides information on available medicines in the EU.
It serves as a repository for summary of product characteristics and package leaflets approved by the Swedish Medical Products Agency and the EMA. It is regarded as one of the most consulted database on medicine information in the world, and is also accessible via a smartphone. https ://www. fass. se/LIF/start page United States DailyMed is FDA's official provider for trustworthy drugs marketed in the US, including information on package inserts. It provides standard, comprehensive, up-todate, and downloadable content on the medical product and its respective inserts as well as manufacturing information intended to provide visibility into the supply chain for health care professionals and patients. https ://daily med. nlm. nih. gov/daily med.
Conditions for the time of flight mass spectrometer scan mode were as follows: scan range 100-1000 m/z at 6 eV (low energy) and 50-1000 m/z with a collision energy ramp from 10-40 eV (high energy). Data process was performed using ChromaLynx, TargetLynx, MassFragment and MetaboLynx associated softwares (Waters) using a homemade database of more than 1. 600 substances including more than 600 (feb 2018) NPS or metabolites.
HLM incubate samples were consequently analysed using the LC-HRMS method described above. Data process was performed using ChromaLynx, TargetLynx, MassFragment and MetaboLynx associated softwares (Waters, Manchester, UK). A software algorithm (MetaboLynx™) was used in order to in silico predict CaF biotransformations. Data about CaF metabolism were available since 2016: 12 metabolites were identified and N-dealkylation and monohydroxylation of the piperidine ring were the dominant metabolic pathways. Two Noxide metabolites and one glucuronide metabolite were also observed  [52]. As a consequence, taking into account these data, sets of theoretically possible biotransformations of CaF were created, and the automated metabolite profiling process was completed (i) in agreement with main fragment ions preliminary established, and (ii) through the use of the fragmentation interpretation software tool MassFragmentTM 4.
2016). In Europe, Estonia has seen a large epidemic since the 2000s. It is almost the only European country that has epidemiological data on fentanyl use. In 2008, according to a national survey, the prevalence of fentanyl use in the general population (18-64 years old) was 0. 1%. This proportion reached 1. 1% among males aged 15 to 24. In 2011, the Estonian drug treatment database recorded 407 primary fentanyl/3methylfentanyl users among their 532 registered patients (EMCDDA 2012). Users are predominantly injectors with a profile of social precariousness and from the Russian-speaking minority (EMCDDA 2012). The particularity of Estonia is that fentanyls are mainly produced clandestinely inside the country. In France, the latest report published by the French Monitoring Centre for Drugs and Drug Addiction stated that, between 2000 and 2017, 10 SOs were identified on the French territory: AH-7921 (notified in 2013), acetylfentanyl, despropiopyl-o-fluoro-fentanyl (reported in 2014), ocfentanyl, methylfentanyl, U-47700, valerylfentanyl (reported in 2015), and W-15, metafluorofentanyl, furanylfentanyl (reported in 2016) (OFDT 2017).
Negative DNA supercoiling specific activities were not significantly different between WT and ∆Cloop gyrases (triplicate experiments led to mean values of 2 10 5 and 1. 5 10 5 U/mg, respectively) (Figure  5C ). Similar results were also observed for DNA decatenation (data not shown), confirming that the mutation has little effect on DNA strand passage despite clear impact on basal ATPase rate (e. g. in absence of DNA). We next questioned whether the C-loop affects DNA binding. GyrBA57 or C-loopdeleted GyrBA57 gyrases were incubated with a fluorescein-labeled 50-bp duplex oligonucleotide and their binding activities were assessed using electrophoretic mobility shift assays (EMSAs). We found that the C-loop-deleted gyrase keeps its capacity of binding small DNA fragment and we observed a shift of migration between the apo and DNA-bound forms (Figure  5D , right panel).
Reactions were analyzed by a 5h to 16h electrophoresis at 50 V through 1% agarose gels with a 0. 5x TBE running buffer, in a gel which was stained with ethidium bromide (0. 5 µg/ml) after running. Supercoiling activity was assessed by scanning the fluorescence of the bands corresponding to the supercoiled pBR322 DNA the using Molecular Analyst® software (Bio-Rad). One unit of enzyme activity was defined as the minimum amount of gyrase that converted 0. 3 µg of relaxed pBR322 to the supercoiled form in 1 h at 37°C.
Analytical ultracentrifugation and hydrodynamic. Sedimentation coefficients were determined at 20°C, using a Beckman Coulter XL-I centrifuge equipped with an AN60-Ti rotor equipped with Rayleigh interference detection. Samples diluted in 20 mM Tris-HCl (pH 7. 5), 6 mM MgCl 2 were centrifuged for 17 h at 36 000 rpm and profiles were recorded every 5 min. Sedimentation scans were analyzed by the continuous size distribution procedure c(S) with the program Sedfit 15. 01 (available at analyticalultracentrifugation. com). All c(S) distributions were calculated with a fitted frictional ratio f/f0 and a maximum entropy regularization procedure with a confidence level of 0. 95. The theoretical sedimentation coefficients of the different atomic models were calculated using HYDROPRO  (Ortega et al. , 2011)  and compared to the experimental sedimentation coefficients obtained from ultracentrifugation analysis.
Small-angle X-ray scattering. For GyrBA57 apo and GyrBA57 ∆C-loop , protein (50µl at 7mg/ml) was eluted into buffer D5 (20 mM Tris-HCl (pH 7. 5), 6 mM MgCl 2 , 5% (v/v) glycerol,) plus 100 mM KCl. For GyrBA57 holo 2 mM AMPPNP and 2 mM MgCl 2 were added to the buffer and the sample. SAXS data were collected in line at beamline SWING at the synchrotron SOLEIL after elution on an increase superose 6 column (5 x 150 mm). The curves were background-subtracted using FOXTROT. Data were then processed using the HPLC-SAXS module of US-SOMO. Then, data were analyzed using the ATSAS 2. 7. 1 software suite. The normalized Kratky was calculated according to  (Durand et al. , 2010 , Pérez et al. , 2001)  using the value determined by Guinier analysis. P(r) functions were computed from the scattering curves by an indirect transform method in GNOM  (Svergun, 1992) , and theoretical scattering curves for model structures were calculated with CRYSOL  (Svergun et al.