dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGEMENTS The use of trade, product, or firm names in this document is for descriptive purposes only and does not imply endorsement by the  U. S. Government. The tests described and the resulting data presented herein, unless otherwise noted, are based upon work supported by the  US Army ERDC  under  PE 0603119a , Project  T26  " Military Engineering   Applied Research", Task "Innovative Construction Materials for the Arctic ". Permission was granted by the Director,  Cold Regions Research and Engineering Laboratory  to publish this information. This project was supported in part by an appointment to the  Research Participation Program  at the  US Army Cold Regions Research and Engineering Laboratory (CRREL) ,  US Army ERDC ,  U. S. Department of Defense (DoD) , administered by the  Oak Ridge Institute for Science and Education  through an interagency agreement between the  U.
ACKNOWLEDGMENTS The work presented in this paper is part of a research project ( RP [19][20][21 ] sponsored by the  Georgia Department of Transportation. The contents of this paper reflect the views of the authors, who are solely responsible for the facts and accuracy of the data, opinions, and conclusions presented herein. The contents may not reflect the views of the funding agency or other individuals. The authors would like to acknowledge the financial support provided by the  Georgia Department of Transportation  for this study.
The objectives, covering most of today's major aspects of empirical graphs analysis, and the dataset used in this study, were unusual at the time, due to their ambition and size respectively. The reconstruction of the Assyrian trade network was based on the corpus of cuneiform tablets found at the Kültepe site (near Kayseri, see Figure  2 ). These tablets have two characteristics: first, they document with text very ancient human activities (the 2 nd millennium BC), and second, there is a large amount of information available because these tablets have been collected, translated and published since the 19 th century, first by orientalists and then by specialized Assyriologists. In the early 1920s, about 500 tablets had been published; by the end of the 1950s, this number had risen to about 2600.
This overabundance of material was an obstacle for research 3. Gardin considered overcoming it by data sampling and the use of computer. Sampling was carried out on two levels: first the tablets (the texts) and then the names of the identified merchants. At a meeting held in March 1961, Gardin indicated that the completion of the project presupposed the coding of the 2000 tablets studied by Garelli. The results which had been obtained so far were based on about 200 of them 4. Nothing was mentioned about the criteria used to select the tablets to be analysed. In a presentation in Paris at the "Séminaire sur les modèles mathématiques dans les sciences sociales", Gardin announced the number of "approximately" 1000 tablets  (Gardin 1961, p. 23). The number of merchants' names stated in the tablets was estimated at 1500 in the 1961 article, although the authors pointed out the possible problems of homonymy 5.
An organizational move from an interdisciplinary to a computing science space The analysis of the Assyrian trade network was the result of cooperation between two new research organizations focused on methods and interdisciplinarity, the Centre d'analyse documentaire pour l'archéologie (Cada) led by Gardin in Paris, and the European Scientific Information Processing Center (Cetis), a service created in 1961 as part of the Joint Research Centre of the European Atomic Energy Community (Euratom). After presenting these organizations and their collaboration, this section shows 1) how the development of non-numerical data processing was the common background and motivation for this cooperation and 2) how this unusual interdisciplinary effort terminated, to be pursued by organizations dedicated to computer science.
A complementary study: social networks in the New Hebrides The methods developed for the Assyrian trade network were immediately reused in the Cada for another project on contemporary social networks in the New Hebrides (South Pacific Ocean, then a French condominium). 25 "Réunion du comité scientifique et technique du 14-3-1961. Progrès de l'automatique appliquée au domaine du traitement des informations", 20  February 1961 , BAC-118-1986 1431, Haeu. The ethnographer Jean  Guiart (1925 Guiart ( -2019) )  conducted research on the local social structure, focusing on the system by which individuals could receive "titles" of prestige which were also related to places. Guiart collected a dataset of about 1200 titles and 500 places, related to individuals with about 2700 relations  (Espirat et al.
1973, p. 370 ). This research is first mentioned in relation to the Cada in 1962, after Guiart asked for support in running an experimental computer-based analysis of this large dataset  (Gardin 1962b)   26. Two of Gardin's colleagues supervised this collaboration: Marie-Salomé Lagrange , a member of the Cada, and Monique Renaud, a member of another research group led by Gardin, the Section d'automatique documentaire (Sad) 27  at the Institut Blaise Pascal, then the main place for computing research in Paris. A person was recruited to code the data on punched cards, Mrs A. -M. Nougaret 28  , preliminary tabulations were performed by the Service mécanographique of the Cnrs, and the main calculations were executed in 1963 on the IBM 1401 and 704 computers of the Institut Blaise Pascal  (Espirat et al.
The "graph contract" of the Institut de programmation The Institut de programmation was founded in 1963 in Paris and placed under the direction of Jacques Arsac. It was intended to be a counterpart to the Institut Blaise-Pascal to develop the teaching of programming and computer science (Mounier-Kuhn 2012, p. 428). However, research was also conducted at the Institut, in particular on non-numerical information and graphs. In 1964, the Institut benefited from a contract on graphs funded by the Dgrst. This research was carried out by Jean Berstel (1941-) and Jean-François Perrot (1941-), two former Schützenberger's students, who co-signed the final report 32. Arsac, Perrot and Berstel were trained in mathematics and dedicated to the different aspects of computer science. This contrasted with Cada's perspective where research in computing was a consequence of the data applications from the SSH.
e. community detection), written for a Univac 1 machine by Duncan MacRae and co-published with the sociologist James  Coleman (1926 Coleman ( -1995) )   (Coleman and MacRae 1960). This highlights the state-of-the-art when Gardin and Jaulin worked on the Assyrian trade network, for which the dataset size required a computer: The mathematical problem of clique detection has been approached by many authors, from varying angles. The main issue, here, is in the size of the matrix which has to be analysed to that end (ca. 200 rows x 200 columns); for any given detection method, it is unrealistic to consider its application on so large a matrix without the help of a computer. (Gardin 1965c, p. 389)  Harary's method was known by the authors, but they believed it could be improved in terms of efficiency and speed  (Jaulin 1961, p.
However, the description in the 1961 working paper was so incomplete and muddled that it failed. A workaround was to extract the data sample presented in the paper on the Assyrian trade network to illustrate the detection of cliques and process it with other methods to compare the results. Some of these results are contradictory in this paper, e. g. the adjacency matrix presented in Figure  7  contains six cliques whereas the legend indicates three cliques and a singleton, which is actually part of a clique. Consequently, the data was extracted from a network plot (Figure  4 ). Five methods were applied, including Harary's algorithm, which was implemented in R language for this research 41. All the methods identified the same six cliques as reported in Gardin and Garelli's paper (Table  1 ).
0 nM Cas13a bound to precursor crRNA-1 (E). Lines show single-exponential fit to yield k obs. (F-G) Simultaneously recorded target and trans cleavage: RNP reacted with a mixture of Alexa 488 (F 1 )-tagged target RNA and Alexa 594 (F 2 )-tagged trans-substrate. Time courses were recorded on 5. 0 nM Cas13a bound to mature or precursor crRNA-1, then reacted with a mixture of 1. 0 nM Alexa 488-labeled Target RNA-1 and varied Alexa 594-labeled trans-RNA U 10. Lines show single-exponential fit (where applicable) for target (top) or trans cleavage (bottom) to yield k obs. In panels (A-C and E) data represent mean G standard deviation (SD). See also Figures  S2  and S3. S3G and S3H). Again, precursor crRNA stimulated a more active Cas13a trans-RNase than mature, processed forms for two different crRNA-target pairs (Figures 3E, 3F, S3D, S3E, S3G, and S3H; Tables  S1  and S4 ).
DISCUSSION Cas13a: target RNA cleavage and trans-nuclease activation Target RNA binding to Cas13a RNP is rapid, achieving equilibrium within seconds, and does not limit its cleavage rate. We estimate the K d for initial encounter complex formation is < 1 nM, approximately 20-fold lower than   S5 ). (H) IS2404 in DNA samples isolated from 38 patient skin swabs quantified by Cas12a trans-activity (y axis) or by qPCR (x axis). Color-coded patient qPCR status was determined from DNA extracted initially at test site. Solid line, detailed in Inset, indicates linear fit to yield k app (Table  S5 ); gray shading indicates 95% confidence interval. In all panels data represent mean G SD. See also Figure  S6  and Table  S5. measured for LbuCas13a in the presence of tRNA  (Tambe et al. , 2018) , a potential competitive inhibitor that decreases trans-cleavage efficiency by approximately 100-fold.
Fluorophore quantification and data analysis Fluorescence readings of supernatants from which uncleaved substrates were removed by magnetic beads were compared to standard curves derived from titrations of starting solutions of fluorescent substrates to derive estimates of fluorophore concentrations (molarity). No adjustments were made to values to account for changes in fluorescence due to nuclease digestion of substrates (see below, Figure  S1  and Table  S2 ). Analytical limits of detection (LOD) and 95% confidence intervals were calculated using unweighted four-parameter logistic fit of raw fluorescence values of assay supernatants  (Holstein et al. , 2015)  from selected experiments (Table  S5 ). In transient-state kinetic experiments, time-dependent changes in fluorescence reporter levels were processed as follows.
Control fluorescence values collected in parallel were subtracted and converted to molarity, and the resulting values, F(t), were subjected to ordinary least-squares fitting in GraphPad Prism v8. 2 (GraphPad Software, Inc. ). The single-exponential equation is given by: FðtÞ = ðF 0 À F f Þ e Àk obs t + F f where t is time, F 0 and F f are initial and final fluorescent reporter values, respectively, and k obs is the apparent first-order rate constant. The double-exponential (sequential) equation is given by: FðtÞ = ðF 0 À F f Þ 1 À k obs 2 k obs 2 À k obs 1 e Àk obs 1 t + k obs 1 k obs 2 À k obs 1 e Àk obs 2 t + F f where k obs1 and k obs2 represent the apparent first-order rate constants for the two sequential steps  (Fierke and Hammes, 1995). In steady-state kinetic experiments, linear fitting of control-corrected reporter values was performed to obtain initial velocities (V 0 ).
The validity of all Cas13a trans-kinetic constants was corroborated by similarly analyzing rate data at low substrate concentrations (Table  S4 ). Steady-state kinetic constants were also estimated from endpoint experiments, as follows. For a given trans-substrate concentration, under conditions in which substrate conversion is low, V 0 is maintained throughout the experiment, and product increases linearly with time. Under such conditions, trans-product increases in direct proportion to target concentration (which serves as proxy for activated enzyme), and an apparent turnover rate (k app ) can be determined from the constant of proportionality (the slope) by taking into account the duration of the reaction. Since k app represents k cat ([S]/([S] + K M ), k cat and K M may be estimated from the ratio of k app calculated from two widely differing trans-substrate concentrations.
ACKNOWLEDGMENTS The authors thank  Brittney Thornton  for technical assistance and  Ted Baughman ,  Joshua Bishop ,  Shannon Kuyper ,  Akos Somoskovi ,  David Bell , and  Robert Jenison  for valuable discussions. E. A. N. , N. P. , P. J. Y. L. , Z. I. , R. M. K. , I. P, A-L. M. L. N, and D. M. were supported by the  Intellectual Ventures Global Good Fund. J. A. D. was supported by  NIH  grant nos. RM1HG009490  and  U01AI142817-02 , the  William M. Keck Foundation , the  National Multiple Sclerosis Society ,  NSF  grant no. 1817593 , the  Paul Allen Frontiers Group , and the  Howard Hughes Medical Institute. G. J. K. was supported by an  NHMRC   Investigator Grant  ( EL1 ,  1175568 ) and previously by an  American Australian Association Fellowship. E. M. was supported by the  Raoul Follereau Fondation.
LCA approach The Life Cycle Assessment was carried out with the SimaPro LCA software, version 8. 5. 2. The impact assessment method ILCD 2001 Midpoint+ was used but slightly adapted based on the recommendations from the European Commission (EC) "product environmental footprint category rules" (PEFCR; EC 2017), themselves based upon the IPCC update published in their Fifth Assessment Report (AR5; IPCC 2013). This affects the GWP100 of i) biogenic methane (34 kg CO2 eq); ii) non-biogenic methane (36. 75 kg CO2 eq) and iii) carbon monoxide, fossil and from land use changes (1. 57 kg CO2 eq). From the 16 impact categories proposed by ILCD 2001 Midpoint+, the following were selected to be part of the assessment, being explicitly mentioned in the European Commission policy recommendation  (EC 2013)  for the methods to use for LCA, namely: Climate change, Ozone depletion, Particulate matter, Photochemical ozone formation, Acidification, Freshwater eutrophication, Marine eutrophication and Mineral, fossil & renewable resource depletion.
Accordingly, a system expansion approach was taken, and allocation techniques were avoided, as recommended in  ISO 14040 and 14044 (ISO 14040 2006; ISO 14044 2006). Background data were extracted from two life cycle inventory databases, namely Ecoinvent v3. 4 and Agribalyse v1. 3 (a French specific agricultural database) from which "consequential processes"  (Weidema et al. 2013; Wernet et al. 2016)  or identified marginal processes were selected.
Functional Unit The functional unit is defined as the production of 2330 m² flax-based technical textile per year, having the required properties for an eventual use in the aviation sector. This corresponds to one hectare of cultivated land, from which about 7000 kg of flax green stems (wet weight; ww) are harvested per year (mean yield value of the last ten years according to data from FAOSTAT, 2017). For tractability reasons, the results will be here expressed per ha of land used for the cultivation of flax.
The hypothesis, calculations and data source behind these inventories are detailed in the Supporting Information (SI) Word document. All background processes (e. g. agricultural activities, production of fertilizers) involved were retrieved from the Ecoinvent v 3. 4 database; the exact processes used are documented in the SI Excel document. As previously discussed, system expansion was used to quantify the environmental impacts stemming from the co-products. Their inclusion into the system boundaries was done by identifying their most common use in the market, along with identifying the marginal (avoided) processes that would most likely be reacting to the demand change induced by their introduction to the market (Figure  2 ). These choices were validated by experts and professionals of the sector.
It was then considered that the 770 kg of short fibers produced per functional unit, avoid the production of 693 kg of glass fibers (considering a 90% DM content for the short fibers). To represent the displaced glass fibers production (from the 770 kg of short fibers produced per functional unit), the process avoided glass fiber production was modelled, adapted from an existing process of the Ecoinvent v3. 4 database, as further detailed in the SI Excel document. Seeds. Linseeds are flat-shaped and have a bright, brown color. They are small and light, 2000 seeds weight around 10 g; which corresponds to the dose required to sow one m² of land (GNIS 2018a). They come inside a structure known as a capsule; each capsule is made up of two lobes that can contain 1-2 seeds. In total, 8-10 seeds can be obtained from one capsule.
(2016) , the marginal protein to be soybean meal  (Dalgaard et al. 2008) , and the marginal lipid as palm oil  (Schmidt and Weidema 2007 ). Substitution factors were derived based on the nutritional valued of linseed meal and those of the marginal displaced feed ingredients (detailed in Table  1  and the SI), an approach similar to that taken by e. g. Tonini et al. (2016). The life cycle inventory of the displaced ingredients was retrieved from the Ecoinvent v3. 4 database (consequential processes; exact processes documented in the SI). The so-called "oil loop" documented in  Dalgaard et al. (2008) , i. e. reflecting that the substituted palm oil is produced along with palm meal, whose displacement in turns affect other commodities, is taken into account through the use of these consequential processes of the Ecoinvent database.
This is based upon the findings of Projet AF Filières (2018), presenting a detailed material flow analysis of woody resources for the whole of France. The heat produced by these wood residues would then induce a decrease on the use of natural gas, the latter representing the marginal heat source for France. The composition of flax shives and wood chips, in terms of DM, C and N, is very similar (C -51% vs 50%; N -0. 6% vs 0. 4%; expressed as % of the DM and retrieved from the Phyllis database). This involves that the emissions and impacts linked to their respective management (prior to their use) can be expected to be very similar to one another; these were thus neglected herein. In a nutshell, the overall management of shives implies two key processes, namely: • Induced woody residues combustion, to represent the emissions from generating district heating heat from the displaced wood residues and, • Avoided heat production from natural gas, which would have otherwise been used to generate that heat.
work was carried out as part of the doctoral thesis of A. Gomez-Campos, her work being financed by a scholarship awarded by the French Ministry of Higher Education, Research and Innovation (Ministère de lʼEnseignement supérieur, de la Recherche et de lʼInnova5on in French). The research leading to these results has received funding from ADEME under the grant agreement n°1501C0050. The time used by L. Hamelin during this research was funded by the Cambioscop project, supported by the French National Research Agency, Programme Investissement d'Avenir (ANR-17-MGPA-0006).
Background: Although aminoglycosides are often used as treatment for Gram-negative infections, optimal dosing regimens remain unclear, especially in ICU patients. This is due to a large between-and within-subject variability in the aminoglycoside pharmacokinetics in this population. Objective: This review provides comprehensive data on the pharmacokinetics of aminoglycosides in patients hospitalized in the ICU by summarizing all published PopPK models in ICU patients for amikacin, gentamicin, and tobramycin. The objective was to determine the presence of a consensus on the structural model used, significant covariates included, and therapeutic targets considered during dosing regimen simulations. Method: A literature search was conducted in the Medline/PubMed database, using the terms: 'amikacin', 'gentamicin', 'tobramycin', 'pharmacokinetic(s)', 'nonlinear mixed effect', 'population', 'intensive care', and 'critically ill'.
Data Sources 2. 1. Search Strategy A literature search was conducted in the Medline/PubMed database, from its inception until March 2020, using the following terms: (amikacin OR gentamicin OR tobramycin) AND [(pharmacokinetics/or renal elimination/) OR (pharmacokinetic* OR ((pharmaco OR drug) ADJ kinetic*) OR area under curve? OR AUC OR (renal ADJ (elimination? or excretion? or clearance?))) OR (((nonlinear OR non-linear) ADJ mixed effect model*) OR NONMEM OR Win-NonMix OR P-PHARM OR NLMIXED OR ADAPT)] AND (EXP population/OR population groups/OR (population? OR ethnic group?)) AND [critical care/OR intensive care or EXP intensive care units/OR critical illness/OR ((intensive OR critical) ADJ care?) OR ICU OR ((respiratory OR coronary) ADJ care unit?) OR (critical* ADJ (ill OR illness? OR disease?))].
Data Extraction The following information was extracted from relevant articles: first author, year of publication, population characteristics (number of males and females, age, bodyweight, height, and body mass index), study design, dosage regimen, sample collection (samples per patient, total samples, and sample frequency), population PK modeling methods (software used, model and evaluation method used), the formula of PopPK structural and statistical models, PK parameters, and tested and retained covariates. The model evaluation methods were divided into basic internal (goodness-of-fit plots), advanced internal (bootstrap resampling, Monte Carlo simulations, visual predictive check, normalized prediction distribution error, etc. ), and external evaluation. This step was done by two authors, and cross-verification was performed to ensure the accuracy of information extracted.
Study Selection A total of 78 studies were identified through the Medline/PubMed database, of which there were 26 articles for amikacin, 38 for gentamicin, and 14 for tobramycin. After assessing the articles for eligibility by applying the inclusion and exclusion criteria, 19 publications were selected. In total, six, 11, and five PopPK models were analyzed for amikacin  [16] [17] [18] [19] [20] [21] , gentamicin  [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] , and tobramycin  [32] [33] [34] , respectively (Figure  1 ).
Population Pharmacokinetic Analysis All 19 studies included in this review used nonlinear mixed effect methods to analyze their data and develop PopPK models. As per Table  2 , a version of NONMEM software was used for the modeling in more than half of the studies (n = 10)  [19, [22] [23] [24] [25] [26] [27] [32] [33] [34]. Other software used included NPAG, a function from the software Pmetrics (n = 2), and the NPEM software (n = 2). For model evaluation, more than half of these studies only used advanced internal evaluation, such as the bootstrap resampling method (n = 10), while three studies used both advanced internal and/or external evaluation with several external subjects ranging from 13 to 32  [19, 29, 33]. Tobramycin pharmacokinetics was described by a two-compartment model (n = 3)  [32] [33] [34] , while amikacin and gentamicin pharmacokinetics were described by single-compartment (amikacin n = 1  [19] , gentamicin n = 7  [23] [24] [25] [28] [29] [30] [31] ) and two-compartment models (amikacin n = 5  [16] [17] [18] 20, 21] , gentamicin n = 4  [21, 22, 26, 27] ).