dataesr/scientific-paragraphs-categorization huggingface dataset:
The phylogenetic tree was created using Mesquite 3. 04 software  73. Klingenberg & Gidaszewski  67  remind us that geometric morphometrics results cannot be directly used as phylogenetic characters. An ordination method and splitting the shape into a set of multiple characters are methods already used (see Klingenberg & Gidaszewski  67  for an exhaustive review). Mennecart & Costeur  28  and Mennecart et al. 30  have shown that morphological characters of the bony labyrinth may be phylogenetically significant when used separately in a cladistics analysis. Moreover, Costeur et al. 31  have demonstrated the timing of the bony labyrinth ossification in an ontogenetic series of a pecoran ruminant. The different structures ossify diachronously and may be independent  31. We should also highlight that the ecological impact on the morphology the bony labyrinth, if existing, is limited because all the studied ruminants possess a similar kind of locomotion and live in relatively similar environments.
Mennecart & Costeur  29  and Costeur et al. 31  already pointed out that the open structures (i. e. the endolymphatic sac and the cochlear aqueduct) suffer from a strong intraspecific allometric effect due to continuous ossification of these structures long after birth (contrary to the rest of the bony labyrinth). Thus, these regions are not analyzed to avoid a Pinocchio effect. Similarly to Billet et al. 25, 74  , we observed a weak allometric effect on bony labyrinth shape (see Supplementary data 5). The allometric effect is mainly based on the semi-circular canal proportions in comparison to the entire bony labyrinth. In our dataset, the centroid size may predict 8. 5% of the total shape changes and there is a highly significant covariation between the bony labyrinth shape and the centroid size (p-value < 0.
0001). However, the centroid size is not predictive for the bony labyrinth shape (R 2 = 0. 6672) and is not influenced by phylogeny (p-value = 0. 2586). Since our data matrix for the phylogeny uses the semi-circular canal shape individually, and not the ratio between the canals and the bony labyrinth, the allometric effect does not affect our dataset. Thus, the semi-circular canals, the fenestra vestibuli, and the cochlea were treated here as separate and independent structures using an ordination method (CVA). This method was applied to maximise the between-group variation, relative to within-group groups according to the specified chosen grouping variable; here the well-defined cervid subfamilies Procervulinae, Dicrocerinae, Cervinae, and Capreolinae. Shape differences expressed along the axes are scaled morphological distances relative to within group variation.
These shape differences are used as morphological characters in our cladistics matrix as additional characters to the matrix proposed by Mennecart and Costeur  28  and coded for all the studied specimens (fossil and extant). We have included fossil specimens of well-known subfamilies (2 Capreolinae and 5 Cervinae), that were not in the PCA since their precise phylogenic position is still under discussion, to increase the number of observation per subfamilies (9 Procervulinae, 3 Dicrocerinae, 13 Cervinae, and 11 Capreolinae). Nevertheless, the low number of Dicrocerinae specimens may influence its morphospace relative to the other subfamilies. All statistical results are shown in the Supplementary data 5.
Calibrated tree. The complete mitochondrial genome matrix of Hassanin et al. 7  was pruned down to include just cervids plus a few outgroup representatives of the remaining pecoran families. Cytochrome b gene data was added for Megaloceros giganteus (Genbank Accession number AM182644)  6. After some tests of the combined morphological and molecular datasets, the early fossil artiodactyl Homacodon vagans (~47 Ma) was not included in the analysis because there is far too much of a temporal and phylogenetic gap between it and the next taxa for which morphological data was scored (Lagomeryx parvulus, Procervulus prealucidens, ~18 Ma). Its inclusion or exclusion did not significantly affect divergence estimates for the critical part of the tree (Pan-Cervidae), which, as detailed below, were largely controlled by the prior setting for the age of Pecora.
The 34 partitions of the mtDNA data used in Hassanin et al. 7  were analyzed in Partition Finder v. 1. 1  78  using the greedy search and GTR + G model. Best partitioning scheme indicated eight partitions. The morphological dataset comprised a ninth partition. Analysis xml files from the morphological and molecular data matrices were set up using Beastmaster 79 and R  80. The GTR + G model was used for all molecular partitions, the MK model for morphology. The SABDSKY treemodel was used, which allows for fossil tips to be ancestral nodes (though experimental runs with BDSKY produced similar results, not shown). Two main analyses were run. 1) A minimal constraint analysis in which the root age (Pecora) was set to a uniform distribution of 19-25 Ma (dubbed the 'Min Constraint' analysis), and only a single topological constraint forcing all extant fossil cervids and stem cervids to be monophyletic; and 2) an analysis with the same root prior plus many constraints (' All Constraints' analysis) following previous the topology of previous molecular studies as well as the parsimony analysis based only on the inner ear characters in this paper.
Acknowledgements This research was supported by the  Swiss National Foundation  ( SNF  Project  200021_159854/1  and  P2ZHP3_162102 ), the  Stiftung zur Förderung des NMB , and the  Kugler-Werdenberg Stiftung. We also thank support from the  Spanish Ministerio de Economía y Competitividad  (project  CGL2016-76431-P ) and the  National Natural Science Foundation of China  (Grant No. 41430102 ). We thank the  MNHN UMS 2700 , and the  AST-RX , plate-forme for CT scanning, especially  M. Garcia-Sanz  ( UMR7207 ). BMe warmly thanks  Soledad De Esteban-Trivagno  ( Transmitting Science and ICP ),  Chris Klingenberg  ( University of Manchester ) and  Melissa Tallman  ( Grand Valley State University ) for their precious help in geometric morphometrics through the  Transmitting Science programm. Maeva Orliac (CNRS)  is thanked for providing Homacodon' data and  Thomas Hiller  for providing new comparative material.
A 3D numerical model of Gas Tungsten Arc welding has been developed to predict weld bead shape, fluid flow in the weld pool as well as thermal field in the workpiece. This model accounts for coupled electromagnetism, heat transfer and fluid flow with a moving free surface to simulate different welding positions. The solution strategy of the coupled non-linear equations that has been implemented in the Cast εM finite element code is also discussed. The capabilities of our numerical model are first assessed by comparison to experimental results. Then, as fluid flows in weld pool play a prominent role in the weld quality as well as in the final shape of the weld bead seam, the effect of various welding positions on the weld pool shape has been investigated which constitutes the main novelty of this work.
Solution strategy The model involves a non-linear coupling between electromagnetism, heat transfer, fluid flow and free surface deformation. The non-linearities arise from convective terms in Navier-Stokes equations, radiative loss term in energy equation, phase change and the unknown melted pool shape. To handle this problem numerically, a segregated solution algorithm is used to compute the unknowns incrementally (Newton-like), as depicted in algorithm 1 implemented in the Cast εM finite element code  [24]. The solution strategy is as follows: one computes first the electromagnetic fields, so that the Lorentz force is updated into the fluid flow equations together with the Joule effect in the heat transfer problem. Then, one computes the fluid flow with driving forces (Marangoni, Lorentz and buoyancy) weighted by an intensity factor f α set to a starting value of 1 %.
1 9 9 8 1 9 9 9 2 0 0 0 2 0 0 1 2 0 0 2 2 0 0 3 2 0 0 4 2 0 0 5 2 0 0 6 2 0 0 7 2 0 0 8 2 0 0 9 2 0 1 0 2 0 1 1 2 0 1 2 2 0 1 3 2 0 1 4 2 0 1 5 The goal of this paper is to analyze the existing literature pertaining to OR models applied to the HHCRSP that are found in relevant journal papers, conference proceedings, Ph. D. theses, and books that represent 17 years of work in this field. HHC routing and scheduling solutions differ from existing models since problems considered often originate from different national and regulatory settings. Existing publications were initially selected by browsing the bibliographic databases Web of Science, Science Direct, Jstor, semanticscholar, CiteSeerX and using Google Scholar. Keywords used in the search were: "home health care", "home care", "resource scheduling", "routing", and "vehicle routing problem".
Thus, we propose a finer classification of the available literature, which is based on constraints in existing models and objective functions. Finally, we propose a deeper analysis of methods developed thus far to solve HHC routing and scheduling problems and a benchmark for instances and data sets used in the available literature. Two other literature reviews related to HHC routing and scheduling problem are available: a technical report  [Yalcindag et al. , 2012a] , which deals with human resource scheduling and routing problems in a home health care context, and a conference paper  [Mutingi and Mbohwa, 2013] , which focuses on HHC staff scheduling. Papers included in the present paper are partially found in  [Fikar and Hirsch, 2017]. Hence, our paper verifies some of the existing classifications in the literature and extends the topic by developing a more comprehensive and up-to-date review on the HHCRSP.
The problem is decomposed into a master problem using a set-partitioning formulation and pricing subproblems that are solved by a label-correcting algorithm adapted to take the lunch breaks into account. Several improvement techniques have been proposed: extension rules, dominance rules, cutting-edge column generation strategies, and hierarchical branching scheme. Experimental results shows the effectiveness of the proposed algorithm comparing to the results obtained by solving the mathematical model using CPLEX solver. Two types of instances have been used: instances derived from the literature (Solomon's VRPPTW benchmarks) and real-life data provided by an HHC company in China.
1% from the lower bound. For larger instances, CPLEX does not find any feasible solutions, except in one case. Conversely, the heuristic is able to find optimal solutions for very small instances in less than one second and find better solutions than CPLEX for instances of 25 patients. This heuristic finds solutions in less than 6 seconds for instances up to 100 patients and 20 care workers, but it needs more than 2 hours if the number of patients reaches 300. [Trautsamwieser et al. , 2011]  studied a daily planning problem of HHC services. The problem is laden with assignment constraints (qualification, language, rejection), working time restrictions, time windows, and mandatory break times. The objective function is to minimize the sum of driving and waiting times, and the dissatisfaction levels of patients and care givers.
An extended version of the cheapest insertion heuristic computes the initial solution. The solution is then improved with successive intensification and diversification phases. The diversification phase is an iterative "destroy and reinsert" method  [Pisinger and Ropke, 2007b]. For the VND intensification phase, a set of well known local search operators in routing literature are used: Relocate, 2-opt*, CROSS-exchange, 2-ot, 3-opt and Tour Depletion. Experimental results are presented from real data sets from the Finnish city of Jyväskylä. Seven best feasible solution by randomly generating new pre-assignments based on this solution and solving the resulting restricted mixed-integer program within a predetermined time limit. The proposed approach is tested on randomly generated instances that include up to 16 care workers and 80 services; results are compared with those of the CPLEX solver.
[Cappanera and Scutellà, 2015]  developed an integer linear programming (ILP) formulation for the weekly planning of the HHCRSP where patterns from different generation policies are used to visit patients according to the continuity of care and skill compatibility issues. In particular, maximum daily working times of care workers are considered while taking into account the workload balancing objective. Firstly, the proposed model is tested on realistic instances with the use of CPLEX solver where these instances are composed of 40 to 162 patients and 4 to 11 care workers. Then, data sets developed by  [Nickel et al. , 2012]  and  [Jensen, 2012]  are used to compare the quality of the proposed model's solutions with ones from literature. [Wirnitzer et al. , 2016]  proposed a mixed integer programming model for the monthly planning of the HHCRSP where weekly master tour plans are predefined and the care workers should be assigned to tours while taking into account continuity of care, availability, compatibility, and capacity restrictions.
Production of PiCV Recombinant Capsid Protein (rCP) Specific oligonucleotide primers harboring restriction sites for HindIII and SalI enzymes were designed on the basis of Columbid circovirus PiCV1 (Accession number: JF33089) to amplify the entire region encoding capsid protein. Primer sequences were as follows: PiCoV F: 5 -CCAAAGCTTATGAGGAGGCGGAGATTCAGACG -3 and PiCoV R: 5 -GTGGTCGACTTATTCAGAA TCCACAGCTGAGT-3. PCR reaction volume was 25 μL, and it contained: 2. 5 μL of 10x concentrated PCR buffer (50 mM KCl, pH 9, 50 mM NaCl, 5 mM MgCl 2) (A&A Biotechnology, Gdynia, Poland), 0. 5 μL (0. 2 mM) of each primer, 1 μL of dNTP (0. 2 mM) (A&A Biotechnology, Gdynia, Poland), 4 μL of betaine (1 M), 0. 5 μL of Taq DNA polymerase (5 U/mL) (A&A Biotechnology, Gdynia, Poland), and 14. 5 μL of deionized water.
The MD simulated results have a similar trend as the test results. The property analysis showed that: (1) the density of the xGNP modified model is higher than that of the control model; (2) the glass transition temperature of the xGNP modified model is closer to the laboratory data of the Strategic Highway Research Program (SHRP) asphalt binders than that of the control model; (3) the viscosities of the xGNP modified model at different temperatures are higher than those of the control model, and it coincides with the trend in the laboratory data; (4) the thermal conductivities of the xGNP modified asphalt model are higher than those of the control asphalt model at different temperatures, and it is consistent with the trend in the laboratory data.
The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)  [16]  and the Monte Carlo for Complex Chemical Systems (MCCCS) program  [17]  were commonly used for MD simulations. The computation algorithm of the MD simulation is shown in Figure  1. In addition, compared to other methods (such as Finite Element Method (FEM) and Discrete Element Method (DEM)), the MD method helps address specific problems or principles of atoms or materials, and also, a specific property can be studied by altering specific contributions. Moreover, the material behaviors or response can be analyzed under extreme conditions on a nanoscale. Recently, three components of mixtures (asphaltenes, aromatics and saturates) were chosen to represent the asphalt using MD simulation. In this reference model, 1,7-dimethylnaphthalene (C 12 H 12 ) and docosane (n-C 22 H 46 ) were represented as naphthene aromatics and saturates, respectively  [18].
Acknowledgments: The authors appreciate the financial support of the  U. S. National Science Foundation (NSF)  under grant  1300286. The computational studies were performed using Scienomics MAPS software suite (MAPS, Version 3. 4, Scienomics, Paris, France, 2014) and computer cluster (Superior research center) at  Michigan Technological University. The last author also acknowledges the fellowship support from  China Scholarship Council  under No. 201406370141. Any opinion, finding, and conclusion expressed in this paper are those of the authors and do not necessarily represent the view of any organization.
STUDY FUNDING Study funded by  Genome Canada  and the  Ontario Brain Institute. This work was supported by the  Ontario Brain Institute ,  Genome Canada ,  The McLaughlin Foundation ,  The Centre for Applied Genomics  and the  EU   FP7  project  GENCODYS , grant number  241995  (to V. M. K. , H. N. , and K. K. ). B. A. M. holds the  University of Toronto Michael Bahen chair in Epilepsy Research. DISCLOSURE Dr. Alber has received travel funding/speaker honoraria from AES Fellows Program 2015. Dr. Kalscheuer  reports no disclosures. Dr. Marco  has been a consultant for Grand Rounds Second Opinions (Clinical opinions through  UCSF ) and has received research support from the  Wallace Research Foundation. Dr. Sherr  has served on the scientific advisory board of InVitae; holds a patent for Blood-based diagnostic for autism; has been a consultant for Personalis; has received research support from  National Institute of Neurological Disorders and Stroke ,  Simons Foundation ,  CURE Foundation , and the  John and Marsha Goldman Foundation ; holds stock/stock options in InVitae and ChemoCentryx; has worked with the following law firms:  Sheuerman ,  Martini & Tabari ; Galloway and Lucchese;  Zuger Kirmis & Smith ;  Donahoe & Kearney ; LaFollette, Johnson;  Huff Powell & Bailey ; and Bell, Roper and Kohlmyer; and has served on the  Board of Directors of the National Organization of Disorders of the Corpus Callosum.
Chromatin Preparation and Immunoprecipitation Performed Equivalently between X-ChIP and N-ChIP In order to compare both fixed and native methods for preparing chromatin for ChIP-seq, we sampled in parallel 5 weeks-old male chicken muscle tissues (Pectoralis major) that were either cross-linked or snap frozen (unfixed). For cross-linked samples, we found that incubating muscle in the RBI relaxation buffer before fixation did improve tissue grinding by requiring less strength to grind despite this had no visible impact on chromatin shearing (  [9]  and data not shown). We determined the optimal cross-linking conditions by testing the following parameters: formaldehyde (FA) concentrations (1 and 2%), cross-linking duration (5 to 30 min) and sonication parameters (10 to 30 min with cycles 30 s ON / 30 s OFF) (Additional file 1: Fig.
Acknowledgements The authors wish to thank  A. Vitorino Carvalho ,  E. Godet ,  C. Praud ,  A. Jacques ,  Y. Wang ,  S. Metayer-Coustard ,  E. Cailleau-Audouin ,  P. Chartrin ,  E. Coudert ,  C. Combémorel ,  E. Dominguez-Romero ,  E. Baéza ,  D. Nyuiadzi  ( URA, INRA, 37380 Nouzilly, France ) and  L. Beauclair  ( PRC, CNRS, IFCE, INRA, Université de Tours, 37380, Nouzilly, France ) for their technical support, and  F. Mercerand ,  D. Gourichon ,  H. Rigoreau ,  J. Delaveau ,  C. Rat ,  P. Ganier ,  O. Callut  ( UE PEAT, INRA, 37380 Nouzilly, France ) for the rearing and care of the animals. We are grateful to  V. Moncollin  ( Université de Lyon 1 and Laboratoire de Biologie Moléculaire de la Cellule, ENS Lyon, Lyon, France ) for methodology discussions. Sequencing was performed by the  IGBMC Microarray and Sequencing platform , a member of the ' France Génomique' consortium  ( ANR-10-INBS-0009 ).
Alignments and population genetics pipeline A custom concatenated reference file "All3U" was built based on the Vectorbase AaegL3. 3 gene build, and SNPs were called with respect to this build. The reference was used for the detailed analysis of 18,840 transcripts among 15,735 genes. A FORTRAN program used the coordinates of the features of each gene appearing in Aedes-aegypti Liver-pool_ BASEFEATURES_Aaegl3. 3. GTF to extract: (1) 600 bp of the cis region 59 to each annotated transcript (59 nontranscribed = 59NTR), (2) all 59UTRs, (3) exons, (4) introns, (5) 39UTRs, and (6) a 600 bp cis region in the 39 direction (39 nontranscribed = 39NTR). Each SNP was given an ordered SNPID number according to its position in the gene, the location of the gene in the supercontig, and where the supercontig mapped physically  (Timoshevskiy et al.
html). A series of FORTRAN programs then read the "readcount" files to produce a flat file containing the SNPID number, the Aaegl3. 3 reference nucleotide, its coverage at each sequenced position, and the coverages of insertions or deletions at that position. The program "Trim" removed all SNPs that had ,15 counts, and capped all SNP coverage at 2000 to avoid regions of repetitive DNA. The program "2 • 2" read two files, one from each replicate at a collection site, and produced a single "2 • 2. out" file that contained SNPs that occurred in both replicate datasets for each collection (Mexico, Thailand male, Thailand female, PK10 male, PK10 female, and Kaolack). A program "2 • 2 • 2" then read two 2 • 2. out files to produce a list of SNPs common to a pair of collections. A program "Tables" then read the two "2 • 2.
Reassociation kinetics of the Ae. aegypti genome  (Warren and Crampton 1991)  indicated that 40% of the genome consisted of fold-back, highly repetitive, and middle repetitive DNA. Perusal of VectorBase indicates that much of the remaining "unique" DNA consists of transposable elements. Most importantly, analysis of these unenriched datasets provided no resolution of subspecies (Figure  1  and Figure  2 ), nor did it identify many differences between sexes (Figure  4  and Figure  5 ). The results of this study suggest that genes from throughout the genome are similar between Aaa from two geographically distinct locations. SenAae genomes also differed from one another to a large extent in the present study, but, more notably, differ greatly between Aaa and SenAae. We have yet to determine how SenAae are related to East African Aaf, but this same pattern was evident in the recent study of worldwide collections of Ae.
(2015). First, collection sites in Thailand differed between the two studies. Second, referring to Panel B of the PCA in Figure  3  of  Evans et al. (2015) , the Thailand (purple squares) and Tapachula (gold diamonds) collections are extremely close along the PC1 axis that accounts for 13. 2% of the variation in SNP frequencies. Thailand and Tapachula only separate along PC2, which accounts for only 4. 5% of the variation. Third, PC1+PC2 account for only 17. 7% of the overall variation, indicating that 82% of the variation in SNP frequencies is unexplained by the first two PCs. Fourth, PCA is an analysis of individuals, while our analysis of F ST is based on collections of individuals. Evans et al. (2015)  does not indicate how much variation exists among individuals in a collection (this appears for our data in Figure  1 ).
The latest and most precise measurements at √ s = 1. 96TeV can be found in Refs. [14, 15]. At the LHC, the ALICE, ATLAS and CMS collaborations have measured inclusive jet cross-sections in proton-proton collisions at centre-of-mass energies of √ s = 2. 76TeV  [16] [17] [18]  and √ s = 7 TeV  [19] [20] [21] [22] [23] , and recently the CMS Collaboration has also measured them at √ s = 8 TeV  [24]  and √ s = 13 TeV  [25]. This paper presents the measurement of the inclusive jet cross-sections in proton-proton collisions at a centre-of-mass energy of √ s = 8 TeV using data collected by the ATLAS experiment in 2012 corresponding to an integrated luminosity of 20. 2 fb -1. The cross-sections are measured double-differentially and presented as a function of the jet transverse momentum, p T , in six equal-width bins of the absolute jet rapidity, |y|.