dataesr/scientific-paragraphs-categorization huggingface dataset:
Materials and Methods Patients 112 serum samples were obtained from chronic hepatitis B patients receiving nucleos(t)ide analogues (NAs) therapy in The First Affiliated Hospital of Fujian Medical University. 83 were male and 29 were female. The mean age was 38613 years. Clinical data such as alanine aminotransferase (ALT) was measured. The study was in accordance with the approval of the ethics committee of The First Affiliated Hospital of Fujian Medical University and the ethical principles of the 1975 Declaration of Helsinki. Written informed consent was also obtained from each patient.
Primers for RT-AS-LNA-qPCR Primers for RT-AS-LNA-qPCR were designed using Primer Premier 5. 0 software (Premier Biosoft International, USA) according to the principle of AS-PCR technique. The design guidelines were provided by Exiqon (http://www. exiqon. com/ oligo-tools). The polymorphism analysis of the most common genotypes (B and C) in China obtained from GenBank was performed on DNAMAN software (Lynnon BioSoft, Canada). The forward primer (KF) was at nucleotide positions 396,416 for the amplification of both YMDD and YIDD (tyrosine-isoleucineaspartate-aspartate). The reverse primers modified with a LNA at the 39-end terminal position (L1) or penultimate position (L2) were designed to detect YIDD and YMDD, respectively. Wild type primer with last position of the nucleic acids lock (L2 l ) was synthesized.
Statistical analysis Results obtained from RT-AS-LNA-qPCR were compared with those from sequencing. The statistical analysis was performed using statistical analysis software SPSS version 16. 0 (SPSS Inc, USA) and GraphPad Prism software version 5. 0 (GraphPad Software, USA). Complete concordance was considered if the results detected by RT-AS-LNA-qPCR and direct sequencing were identical. Partial concordance was considered if (1) RT-AS-LNA-qPCR provided additional information compared to that provided by sequencing, meaning that RT-AS-LNA-qPCR showed a mixture of wild-type and mutant sequences, whereas sequencing showed only one of the two results, or (2) sequencing showed a mixture of wild-type and mutant sequences but RT-AS-LNA-qPCR showed only a wild-type or a mutant sequence. Complete discordance was considered if one test showed a wild type and the other showed a mutant.
Identification of recombinant plasmids by sequencing The pMD-18-YMDD and pMD-18-YIDD recombinant clones were picked out and sequenced. The obtained DNA sequences were subjected to BLAST alignment against HBV genome database (http://www. ncbi. nlm. nih. gov/BLAST/). Blast results indicated the sequences were completely consistent with HBV reference genome. Therefore, the pMD-18-YMDD and pMD-18-YIDD recombinant plasmids were successfully constructed. Linear range and detection limit 1610 10 copies/ml,1610 1 copies/ml recombinant plasmids were used to test the linear range and detection limit of RT-AS-LNA-qPCR (Figure  1  and Figure  2 ). There was an excellent linear correlation between the cycle number and the HBV DNA copy number from the concentration of 1610 9 copies/ml to 1610 2 copies/ml with correlation coefficients of 0.
Sampled specimens are located in the Field Museum of Natural History, Chicago (USA); Forschungsinstitut und Naturmuseum Senckenberg, Frankfurt (Germany); Museum National d'Histoire Naturelle, Paris (France); Musee Royal de l'Afrique Centrale, Tervuren (Belgium); Museum fu ¨r Naturkunde, Berlin (Germany); Natural History Museum, London (UK); National Museums of Kenya, Nairobi (Kenya); Naturhistorisches Museum, Bern (Switzerland); South African Museum, Cape Town (South Africa). These data were collected by AS and JRB.
Methods Observations reported below are based on the complete suid collection from TM. They describe the major morphological variations observed. Male and female morphotypes were recognized based on the assembly of characters recorded from published data and observations of extant material. These characters include, most prominently: canine size, cranio-mandibular proportions (widening of mandibular symphysis, rostrum, and parietals), and development of cranial superstructures (supracanine flange, cranial roof swellings, zygomatic expansion). For comparisons with other fossil species, we used parameters of third molar size and morphology, ratios within dental rows, and craniomandibular features. Comparative observations reported below mention the most significant specimens as references, but they as well apply to all other specimens observed for the relevant taxa, unless indicated otherwise.
Acknowledgments This research was developed under the auspices of the following institutions:  Chadian Ministere de l'Enseignement Superieur et de la Recherche ;  Centre National d'Appui ala Recherche, N'Djamena; University of N'Djamena; French Ministere de l'Enseignement Superieur et de la Recherche ;  Centre National de la Recherche Scientifique, Institut National E ´cologie et Environnement; University of Poitiers (UFR SFA );  French Ministere des Affaires E ´trangeres (French Embassy in Chad). In addition, we would like to thank the following institutions and all their staff for authorizing the study of their collections: Authority for  Research and Conservation of Cultural Heritage ,  Addis Ababa , Ethiopia;  CNAR, N'Djamena, Chad ;  Field Museum, Chicago, USA; Forschunginstitut und Naturmuseum Senkenberg, Frankfurt, Germany; HERC, University of California, Berkeley, USA; iPHEP, University of Poitiers, France; Iziko South African Museum, Cape Town, South Africa; Laboratory of Evolutionary Biology, Howard University, Washington D.
The funders of our work are:  Agence Nationale de la Recherche  (latest funding:  ANR-09-BLAN-0238 , PI:  M. Brunet );  French Ministere des Affaires E ´trange  `res (DCUR/RECH in Paris,  French Embassy in Chad ,  FSP  nu  2005-54  of the Franco-Chadian cooperation); Region Poitou-Charentes ;  Revealing Hominid Origins Initiative (U. S. National Science Foundation  Award # BCS-0321893 );  European Union Synthesis program  (grant  GB-TAF 886  to AS for work at  NHM ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Baseline system Since this the time first we are trying to develop a spellchecker and correction tool for Arabic, we wanted to have some figures about the performance of spellcheckers on Arabic. We used the development set to test the performance of various spellchecker and correction tools. We corrected the development set automatically using the spellchecker module of the following softwares: • Microsoft Word 2013 • OpenOffice 2014 • Hunspell For Microsoft Word and OpenOffice we used the default configuration for correcting Arabic text and disabled the grammar correction. Hunspell is an open source spellchecker widely used in the open source community. It is the spellchecker of many well-known applications such as OpenOffice, LibreOffice, Firefox, Thunderbird, Chrome, etc. It is the next generation of lexical based spellcheckers in line with Myspell, Ispell and Aspell.
Moses requires a parallel corpus to train a translation model, a development set to tune the translation model and also a monolingual language model in the target language. Since we had to evaluate the performance on the development data provided by the organizers, we had to use part of the training data as a development data for Moses. So we split the 20k sentences included in the training data in a new training set of 18k and a new development data of 2k sentences. We trained standard phrase based models using the surface word form with no morphological analysis or segmentation. For the word alignment in the training process, we used GIZA++  (Och, 2003). The 2k sentences were used to tune the SMT models. For the language models we used corpora of newspapers publicly available or collected by Techlimed.
Conclusion This paper has reported on the participation of Techlimed in the QALB Shared Task on Automatic Arabic Error Correction. This is the first time we tried to develop a spellchecker for Arabic and have investigated two approaches. The first one is a lexicon driven approach using Hunspell as a spellchecker and correction tool and the second one is a SMT systems using Moses for training a statistical machine translation model on the 1 million tokens corpus provided by the organizers. The best results were obtained with the SMT system which, especially, was able to deal with the punctuation marks corrections. We also tested an hybrid system by combining Hunspell and the SMT system but didn't get better results than the SMT system alone. Our perspective is to improve the results by using hybrid systems based on the Di-iNAR lexical database  (Abbes, 2004)  and also a large arabic named entity dictionary, both owned and developped by Techlimed We will also try to used factored translation models with the Techlimed Part-Of-Speech taggers.
Care was taken to guarantee normal incidence of the scanning beam. Ellipsometry. The mesoporous thin films without infiltration were first characterized by ellipso-porosimetry (EP). This technique allows the determination of the thickness and the optical constants n(λ) and k(λ) in the 300-950 nm range. Film porosity was determined by spectrometric ellipsometry while varying the water vapor pressure in a controlled humidity chamber. By the use of a Lorentz-Lorenz effective medium theory, a water adsorption isotherm is obtained from which the total accessible volume and, through the Kelvin equation, the pore size distribution can be extracted. 56 The measurements were performed in a commercial SOPRA GES5 spectrometric ellipsometer in microspot configuration and the data was analyzed by the use of Winelli II software.
Before the EP measurements, samples were washed with acetone, ethanol, and water and dried at 130 °C, in order to avoid pore blocking. The thermo-ellipsometry measurements were performed using a spectroscopic ellipsometer (Woollam M200U, software VASE) at a fixed incident angle of 70°and a polarization angle fixed at 45°. Thermal ellipsometry measurements were performed by placing the film samples on a hot plate, controlled by a home modified LINKAM heating cell. By setting the dynamical scan mode in the WVASE software, measurements were periodically taken to follow the changes in the optical parameters of the samples, as described by Bass et al. 53  The data obtained was then analyzed by proposing a model for the film optical properties and fitting the model parameters to match the experimental data.
For the proper modeling of the samples studied in this work, the substrate material, i. e. , silicon, was first measured at different temperatures and described by a model consisting on a Cauchy-Urbach law for the optical range of the spectra, two Tauc-Lorentz functions for the transitions in the UV region, and two Gaussian absorptions, provided that Kramers-Kronig relations were properly satisfied. In addition, a thin layer of SiO 2 , which is normally present in silicon wafers, was added to the model with the optical constant of silica taken from Palik. 57 or the description of mesoporous thin films loaded with gold nanoparticles, several effective medium models were tested The Journal of Physical Chemistry C including Bruggeman and Maxwell-Garnett. Although the fitting of the experimental data was good, the gold filling fraction and the intensity of the plasmon absorption could not be obtained simultaneously, as they are strongly related; therefore, a simpler model was proposed in which a Cauchy-Urbach dispersion law (eq 2a) is considered for TiO 2 and a Lorentz oscillator (eqs 2a and 2b) accounts for the LSPR absorption of gold nanoparticles.
0 mm•s -1 and calcined at 350 °C. The adsorption-desorption curves correspond to a type IV isotherm presenting H2 hysteresis loops. This feature is attributable to a three-dimensional pore array with restrictions, which is a typical feature of distorted cubic mesopore systems. 68  pore volume fraction of 46% was obtained for this system with a sample to sample variation of less than 4%. The pore size distribution (PSD) calculated by applying the Kelvin equation to the isotherm data leads to a pore average radius of 5 ± 1 nm and an average interpore neck radius of 3. 0 ± 0. 3 nm, obtained from the adsorption and desorption curves, respectively. Gold Infiltration. The procedure of gold reduction on TF films deposited on glass substrate was studied by UV-visible spectrophotometry on films deposited on transparent substrates.
The results show firstly that palaeolatitudes are slightly higher than predicted by the latest apparent polar wander path (APWP) for Eurasia by Torsvik et al. These data support an early Permian Pangaea A configuration and do not necessitate a Pangaea B configuration. The larger data set also allows us to assess the distribution of the characteristic remanent magnetization directions of the Oslo Graben in terms of geomagnetic field behaviour, which were acquired during a long period of dominantly single polarity the Permo-Carboniferous Reversed Superchron (PCRS). The distributions show a significantly lower virtual geomagnetic pole (VGP) scatter at the observed (low) latitudes than expected from a compilation from lavas of the last 5 Myr. The data do however show excellent agreement with the scatter observed both during the Cretaceous Normal Superchron and the PCRS.
I N T RO D U C T I O N The Earth's magnetic field is produced by a geodynamo process in the molten outer core of our planet. It varies dramatically at various timescales, becoming stronger and weaker and occasionally reversing its polarity altogether. The geomagnetic field plays a crucial role, not only in providing a means of navigation for humans and other species, but also in protecting the Earth's surface and atmosphere from the solar wind and cosmic radiation. It is important to study variations in the Earth's magnetic field in detail because they reveal core and core-mantle boundary (CMB) processes taking place in the deepest Earth. Short-term variations of the magnetic field are studied using data obtained by magnetic observatories and satellites. Longer term variations are preserved in rocks, which can contain reliable records of the direction and intensity of the magnetic field at the time of their formation.
Our significantly enlarged data set provides important information for analysing the behaviour of the geomagnetic field and for comparison to the PSV database for lavas of the last 5 Myr and Giant Gaussian Process (GGP;  Constable & Parker 1988 ) model predictions using TK03. GAD  (Tauxe & Kent 2004). PSV analyses are represented as VGP dispersion (S) of our data and existing data from the Oslo Graben plotted versus their palaeolatitude, while we also determine the elongation (E) of the directional distributions for comparison to the TK03. GAD field model  (Tauxe & Kodama 2009). The sampled rocks are lower Permian in age, which is a critical time span for Pangaea reconstructions, and until today still much debated (e. g. Domeier et al. 2012). The reconstruction of the youngest supercontinent Pangaea that existed from the late Palaeozoic to early Mesozoic was first made by  Wegener (1915) , who recognized the fit between the present-day Atlantic margins.
His reconstruction was further constrained by palaeontological and lithostratigraphical evidence  (Köppen & Wegener 1924; Du Toit 1937). The break-up of Pangaea is well known, thanks to the availability of marine magnetic anomalies  (Heezen 1960; Dietz 1961) , hotspot tracks  (Richards et al. 1989; Müller et al. 1993; Norton 2000)  and apparent polar wander paths (APWPs;  Creer et al. 1954; Besse & Courtillot 2002; Torsvik et al. 2012 ). Pangaea's configuration before its break-up, that commenced when the Atlantic Ocean started opening in the early Jurassic, is less well constrained and solely relies on APWPs. In classical Pangaea A-type reconstructions, present-day North America is placed north of South America, and Eurasia is placed north of Africa. Early reconstructions derived from the APWPs however, showed an overlap between the Gondwana and Laurussia part of Pangaea in the late Carboniferous and Permian as large as ∼15 • (equivalent to ∼1650 km).
This led  Irving (1977)  to introduce an alternative configuration, resulting in a controversy that prevails Pangaea reconstructions ever since. Irving's (1977)  Pangaea B-type reconstruction places present-day North America west of South America. A large, mainly longitudinal ∼3500 km shear zone would need to accommodate the necessary right-lateral motion between Gondwana and Laurussia necessary to bring the continents back into their pre-Pangaea break-up position. In addition to palaeomagnetic research aiming at resolving the Pangaea controversy, many studies introducing a variation of geological data types have been performed  (Angiolini et al. 2007; Schaltegger & Brack 2007; Gutierrez-Alonso et al. 2008; Torsvik et al. 2008a ). The controversy however, is of palaeomagnetic origin. The data from Permian rocks with well-determined and revised ages provided in this study are relevant to the Pangaea controversy, and we will discuss the implications of our data and ex-isting data from the Oslo Graben for the position of the northern Pangaea continent (Laurussia).
There is an increasing trend in all three groups, indicated by the (dotted) linear regression lines. The age of the Vestfold B series must be younger than the Skien and Brunlanes basalts, and older than the (average) age of the RP series. and rock magnetic techniques. A reassessment is warranted because the Oslo Graben volcanics provide an important constraint on the Permian Eurasian APWP, and have implications for the Pangaea A versus Pangaea B controversy. We also use revised and better constrained ages of the Oslo lava flows, based on the Rb-Sr and 40 Ar/ 39 Ar measurements of  Sundvoll & Larsen (1990). We have divided the Krokskogen lava formation in two age ranges (Fig. 2 ), one for the Vestmarka formation (290. 3 ± 10. 5 Ma) and one for the Kjaglia formation (279. 2 ± 3. 1 Ma). The Vestfold volcanics ages range 288.
Acquisition curves of isothermal remanent magnetization (IRM) To further characterize the NRM of the samples, the magnetic mineralogy was assessed by carrying out rock magnetic measurements. A MicroMag Model 2900 alternating gradient magnetometer was used, equipped with a 2 Tesla magnet-but effectively 1. 6 Tesla because of partial saturation of the pole shoes-(Princeton Measurements Corporation, noise level 2 × 10 -9 Am 2 ). Successively, hysteresis loops and IRM acquisition curves were measured, all at room temperature. We carried out the IRM measurements on 15 samples in order to identify the different IRM components using the fitting method of  Kruiver et al. (2001). The IRM acquisition curves contain 200 data points; examples of representative samples are given with the fitted IRM components (Fig.
Palaeomagnetic discussion and implications for Pangaea reconstructions The ctmd between our overall mean of the four formations and the study by  van Everdingen (1960)  implicates that the AF demagnetization technique used half a century ago successfully recovered the mean direction of the Oslo Graben volcanics from the Krokskogen and Vestfold lava plateaus. The earlier results are therefore confirmed by our study that was carried out with modern TH and AF demagnetization techniques and comprises a larger number of successful sites (104 versus 27). Our re-analysis of age data (Fig. 2 ) from the Oslo Graben volcanics allowed a subdivision of the data in two different areas (that do not share a ctmd) and four formations that show a clear northward palaeolatitude trend with decreasing ages. The trend is similar to the northward trend calculated from the APWPs  (Torsvik et al.
9b ) clearly results in a counterclockwise rotation of our reconstruction with respect to the reconstruction based on the spline path (Fig. 10b ). The recent study by  Dominguez et al. (2011)  on younger dykes from northern part of the Oslo Graben (∼270 Ma) was incorporated in the latest pole path and is in good agreement with  Torsvik et al. (2012). Compared to our data, it does not show an evident ongoing northward motion of the Oslo Graben region throughout the Permian. This can be ascribed to the error in palaeolatitude which leaves room for different fits through the data. Before discussing the data presented in this study in the light of the Pangaea controversy, its origin and developments will be discussed below. The first Pangaea B reconstruction by  Irving (1977;  see Introduction) was quickly followed by a publication by  Arthaud & Matte (1977).
They presented evidence for the existence of a right-lateral shear zone displacing Laurussia and Gondwana by linking a series of rifts that extended from the Urals to the Appalachians. Proposed timing of a transition from Pangaea B to Pangaea A has varied widely throughout the years, from Permian and Triassic  (Morel & Irving 1981) , Triassic  (Torcq et al. 1997)  to Permian  (Muttoni et al. 2003 (Muttoni et al. , 2009)). Interestingly,  Torsvik et al. (2012)  mention that the initial stages of Pangaea formation are unclear as a result of data paucity in the concerned time window and show an early Carboniferous (∼350 Ma) Pangaea B configuration. This configuration supposedly transformed into Pangaea A by the late Carboniferous, as was also suggested by Domeier et al. 1. (2012). The Gondwana reconstructions by  Muttoni et al.
(2003 Muttoni et al. ( , 2009 Muttoni et al. ( , 2013 ) that point to Pangaea B rely on palaeomagnetic data from North Africa (Sudan, N = 1; Morocco, N = 2) and Adria (N = 7), a promontory of the African plate. Their mean 280 Ma pole for Gondwana derived from these data results in a significantly more northern position of Gondwana compared to  Torsvik et al. 's (2012)  280 Ma pole (N = 56) from the global APWP (GAPWaP) which also includes the three North African poles selected by  Muttoni et al. (2013) , therefore resulting in an overlap of Gondwana and Laurussia (see Figs  10b  and c  for reconstructions). Even though the Sudanese, Moroccan and Adrian poles are derived from magmatic rocks and have therefore not been affected by inclination shallowing, the choice of using these poles for Gondwana reconstructions is questioned by several authors (see  Domeier et al.
2012). One argument is based on the publication year of the individual poles and their associated errors, since eight of the 10 poles were published between 1969 and 1984 (see references in  Muttoni et al. 2013). The intrusive nature of many sites selected by  Muttoni et al. (2013)  raises questions about the determination of the palaeohorizontal as well. Revisiting and resampling the early Permian (Adria and Africa) sites included in  Muttoni et al. 's (2013)  compilation would likely reduce the (often large) error of the individual data sets which are based on fewer flows than is presently the norm. In addition, the poles from Adria may need correction because of a possible rotation of Adria with respect to Africa since 20 Ma  (Van Hinsbergen et al. 2014). From the palaeomagnetic community, various approaches aimed at resolving the problem of the overlapping northern and southern continents without involving a Pangaea B configuration.
A review by  Domeier et al. (2012)  discusses the development of Pangaea reconstructions over decades and the various approaches that have been presented to solve the debate. As we stated above, the problem is of a purely palaeomagnetic origin and therefore  Domeier et al. (2012)  extensively discuss the effect of all palaeomagnetic bi-ases that may influence the reconstructions (e. g. non-dipole fields, inclination shallowing, age errors and the effect of (partial) remagnetizations) and present new reconstructions based on the latest updated GAPWaP of  Torsvik et al. (2012)  that introduces a flattening factor of 0. 6 to detrital sediment data sets uncorrected for inclination shallowing. Their reconstructions based on a combination of these revised palaeomagnetic data with newly available Euler poles Downloaded from https://academic.