dataesr/scientific-paragraphs-categorization huggingface dataset:
RDP Algorithm Description The RDP algorithm is widely applied in polyline simplification applications (a geophysical example being in the production of the Global Self-consistent, Hierarchical, High-resolution Shoreline Database  [Wessel and Smith, 1996] ), and functions by reducing the number of vertices of a given input according to a specified tolerance,. Figure  2  illustrates the application of the algorithm to a sample time series. Beginning with the straight line joining the beginning and end points (shown by the blue dashed line in Figure  2a ), the orthogonal distance between this line and each point comprising the input is calculated (Figure  2a , inset). If the orthogonal distance between the line and the vertex lying furthest from this line is greater than , the line is split at this point, and the procedure recursively applied to the two resulting pieces (Figure  2b ; note that at each recursion, the orthogonal distance is recalculated relative to the new segments of the line that result from the split at the previous recursion).
6); however, a robust link to the 2004 ice cover decline in the Barents Sea has not been proven  [Herbaut et al. , 2015]. Given that the recent warming of AW is one episode in a series of such events that are reported to have begun earlier (in the 1990s, e. g. ,  Quadfasel et al. [1991] ), another forcing mechanism may also be implicated in this transition. To investigate the viability of potential forcing mechanisms associated with the onset times found here, atmospheric fields from the ERA interim reanalysis  [Dee et al. , 2011]  are analyzed alongside ocean data from the EN4 objective analyses  [Good et al. , 2013]. In addition to observations drawn from the World Ocean Database (WOD)  [Boyer et al. , 2013] , the EN4 analysis also includes data compiled within the scope of the Arctic Synoptic Basin Wide Oceanography project, drawing on several sources not presently included in the WOD, with the aim of improving data coverage in the Arctic region.
Acknowledgments The research leading to these results has received funding from the  European Union   7th Framework Programme  ( FP7 2007 ( FP7 -2013)  ) under grant  308299 ,  NACLIM  Project. All sea ice data sets used in this work are available from the National Snow and Ice Data Center (http://nsidc. org/data). ERA interim reanalysis data are made available by the  European Centre for Medium-range Weather Forecasting  (http://apps. ecmwf. int/datasets/)and the EN4 data set by the  UK Met Office  (http://hadobs. metoffice. com/en4/index. html). This work has benefited from discussions during FAMOS meetings and support from the  FAMOS  project. We are grateful to two anonymous reviewers for their helpful comments on the manuscript. Journal of Geophysical Research: Oceans 10. 1002/2015JC011187.
Specimen with fixed circular inclusion A first example is a squared specimen with a fixed circular inclusion. The specimen is 0. 3 m by 0. 3 m, the inclusion has a radius equal to 0. 05 m and is located in the middle of the specimen. An imposed displacement is applied on the upper horizontal edge, while displacements of the inclusion are set to zero in all directions (see Fig. 9 ). The finite element code Code_Aster  [4]  is used. The specimen is computed up to its complete failure by means of the brittle damage model of Section 4. 1. Law parameters are: E ¼ 30; 000 MPa ; G f ¼ 100 N=m; m ¼ 0:2; D ¼ 0:01 m; r y ¼ 3 MPa. The lower part of the specimen (starting from its geometrical centre) is considered as elastic, with Young modulus and Poisson ratio equal to those of the upper part. The numerical implementation of the damage model is realized on elements with quadratic interpolations for displacements; damage is modelled as an additional degree of freedom, but adopting a linear interpolation on the finite element.
Statistical analysis All statistical tests were processed using STATISTICA Software (StatSoft, France). The data are expressed as mean9SD. Analysis of variance (ANOVA) was carried out to compare the responses of the different groups before and after the training program. Least significant difference (LSD) post-hoc analysis was used to identify significant group differences that were indicated by ANOVA. A probability level of 0. 05 was selected as the criterion for statistical significance.
More scientifically-based methods have been developed such as the use of climate envelope models  [21] , mechanistic niche modelling  [22]  and other statistical methods  [23] [24]  but the accuracy of the predictions still remains in question  [25]. An alternative approach proposed by Worner and Gevrey  [26] , Paini et al. [27] [28]  and Worner et al. [29]  is to use self-organizing maps (SOM), a form of artificial neural network, to analyze simultaneously large datasets of invasive species through the study of species assemblages; i. e. , groupings of species that co-occur in the same place and at the same time. This allows the identification of patterns of association amongst invasive species, whereby regions with similar suites of invasive species are clustered and a region-specific likelihood of establishment index is generated for each species.
We monitored the development of damage caused by native Chinese organisms in order to provide an early warning of the Asian pest species that could potentially affect European trees in the near future. Because the majority of the exotic insects related to woody plants apparently arrived in Europe through the 'plants for planting' pathway  [41] , one of the plantations was established in a nursery area whereas the other was planted in a forested zone. This paper provides the results concerning the colonization of the European trees by Chinese insects. Another paper will present the pathogen data (Vettraino et al. , in prep. ).
Insect identification The adults collected were sent for morphological identification to Chinese taxonomists, and if necessary to specialists elsewhere. Since in most cases it was impossible to identify the larvae collected due to the absence of taxonomic keys, they were first assigned to morphospecies and then systematically subjected to molecular analyses using the mtDNA barcode gene in order to compare them with the existing barcode datasets. Whole genomic DNA was extracted from individual specimens using a Nucleospin Tissue XS Kit (Macherey-Nagel, Düren, Germany). Identification was done by amplifying a 658 bp fragment of the mitochondrial gene (mtDNA) cytochrome oxidase c subunit 1 (COI) with the polymerase chain reaction (PCR). Reactions were performed in 25 μl volumes containing 2 μl of DNA template (concentration around 50ng/μl), 1x PCR Buffer with 1,5mM MgCl 2 (Qiagen, Hilden, Germany), 0,5 mM additional MgCl 2 , 100 μM of each dNTP, 2,5 U Taq DNA polymerase from Taq PCR Core Kit (Qiagen, Hilden, Germany), and 200 nM each of the primers LCO1490 (5'-GGTCAACAAATCATAAAGATATTGG-3') and HCO2198 (5'-TAAACTT CAGGGTGACCAAAAAATCA-3')  [42].
4 software. Sequences were corrected in BioEdit 7. 0. 9. 0  [43]  and primers sequences were removed from the analysis. COI sequences were translated by using the EMBOSS-Transeq website (http://www. ebi. ac. uk/Tools/emboss/transeq/index. html) to confirm the absence of nuclear pseudogenes  [44]. The sequences were compared with the data in the BOLDSYSTEMS databases (http://www. barcodinglife. com/) and with the search BLAST n available on NCBI (http://blast. ncbi. nlm. nih. gov/). The sequences analyzed in this study were deposited in GenBank [accession numbers KP662045 à KP662072].
Insect identification Only a small proportion of the insects collected could be directly identified to species using classical taxonomy (22 out of 104 species; i. e. 21. 1%). The sequencing of morphospecies using the 'barcode' gene suggested a specific identity for 5 more organisms with a match of at least 99% in the barcode database. Their identification was then confirmed from the relevant literature. The sequencing of all the lepidopteran larvae and pupae provided 5 species identities (match >99%), 13 genus identities (match between 98% and 97%), and 18 family identities (match >95%). However, the families of 2 Lepidoptera larvae were unknown (match <90%). In total, 27 of the 104 morphospecies were identified to the species (26. 0%), and 25 to the genus level (24. 0%). These percentages were higher in the species that had more than 5 colonization events, with 19 identified to species (50.
A major one is the difficulty of taxonomic identification since a large proportion of the collected specimens are larvae for which identification keys do not exist in most groups. Rearing larvae to adults is usually complicated because of limitations in food availability, particularly because the sentinel plants need to be preserved. In addition, some species could still be unknown to science; e. g. the weevil Compsapoderus continentalis was only described in 2007  [50]. A systematic molecular analysis of all collected specimens could also be used in taxonomic identification of immature stages given that data from established barcodes datasets are steadily increasing and becoming more accepted by biosecurity agencies  [57]. However, such molecular analyses revealed considerable limitations in our work because the development of reference molecular databases is, as yet, unequal between taxonomic groups.
Acknowledgments We greatly acknowledge the help of  Bo Liu ,  Jun-guo Meng  and  Ya-ping Luo , students at the  School of Forestry and Biotechnology of Zhejiang A & M University , in the survey of the colonization of the sentinel plantings at Fuyang. We thank  Christian Stauffer  and  Coralie Bertheau ,  BOKU Wien , for their help with genetic identifications. We are also greatly indebted to the following taxonomist colleagues who supplied insect identifications, especially  Andrei Legalov  (Russia),  Dr. Run-zhi Zhang  and other colleagues from the  Institute of Zoology of the Chinese Academy of Sciences, Beijing (China).
The authors greatly acknowledge the financial support for this work from the  EU projects ALARM  (Assessing large-scale environmental risks with tested methods-GOCE-CT-2003-506675), PRATIQUE (Enhancements of pest risk analysis techniques;  KBBE-2007-212459 ), and  ISEFOR (Increasing Sustainability of European Forests: Modelling for Security Against Invasive Pests and Pathogens under Climate Change-collaborative  project  245268 ). The  EU   COST projects PERMIT (Pathway Evaluation and pest Risk Management In Transport -FP1002-181110-06882 ) and GLOBAL WARNING (A global network of nurseries as early warning system against alien tree pests-FP1401) allowed fruitful discussions about the project design and results. JT Fan was also supported by a grant from  National Forestry Industry Research Special Funds for Public Welfare  Projects (20130440) in China.
A Si (311) double-crystal monochromator and platinum-coated focusing cylindrical mirror were inserted into the X-ray beam path. The X-ray intensity was maintained at 65% of the maximum flux using a piezo translator set to the crystal. The slit opening size was 1 mm (vertical) 9 2 mm (horizontal) in front of the ionization chamber. Part of the XAFS measurements were performed for a sample in a reactor equipped with polyethylene naphthalate windows (Q51-16, Teijin) irradiated by a xenon arc lamp  (Morikawa et al. , 2014a; Izumi et al. , 2007). The Cu K-edge absorption energy was calibrated to 8 980. 3 eV for the spectrum of Cu metal foil  (Bearden, 1967). The XAFS data were analyzed using an XDAP (X-ray absorption fine structure Data Analysis Program) package  (Vaarkamp et al. , 2006). The pre-edge background was approximated by a modified Victoreen function C 2 /E 2 + C 1 /E + C 0.
ACKNOWLEDGMENTS The authors are grateful for the financial support from the  Grant-in-Aid for Scientific Research C  ( 26410204 ,  22550117 ) from the  Japan Society for the Promotion of Science, Asahi Grass Foundation ,  Promotion Section of Technology Innovation, Daikin Industries , and from the  Romanian National Authority for Scientific Research  ( PN-II-IDEI-PCE-75/2013 ). X-ray absorption experiments were conducted under the approval of the  Photon Factory Proposal Review Committee  ( 2011G033 ,  2009G552 ,  2007G576 ) and Grant of the  Priority Program for Disaster-Affected Quantum Beam Facilities  ( 2011A1977 ,  SPring-8 & KEK ).
Acknowledgements This work at  RWTH Aachen University and Jülich Centre for Neutron Science JCNS Outstation at ILL  was funded by the  BMBF  under contract No. 05K10PA3. C. D. C at  NPU  (Xi'an) acknowledges supports from  National Basic Research Program of China  (No. 2012CB821404 ) and  National Natural Science Foundation of China  (No. 51471135 ). W. L at IFW (Dresden) acknowledges support from  DFG  through project  SFB 463. H. F. L is grateful to  Bachir Ouladdiaf  at  ILL  for his helpful assistance in the neutron Laue experiments, and  Thomas Brückel  at JCNS for helpful comments and discussions and a critical reading of the manuscript.
The stems chosen for this condition appeared in the Celex English database  (Baayen, Piepenbrock, & Gulikers, 1995)  only as a noun, and no instances (or a single instance only) of use as a verb were found in the British National Corpus (www. natcorp. ox. ac. uk/). Two baseline conditions were included that did not contain a potential affix: pseudostem (scandal ) and no stem/no affix (biscuit). Participants also saw the 450 embedded stems and pseudostems (or first syllables for words without embedded stems) extracted from these complex forms. These were accompanied by 160 strings of random consonants, matched to the length of the target items (both stems and whole forms), and varying in length from three to nine letters. These were included both as a general length-matched baseline and to allow specific contrasts with word and pseudoword stimuli to select out regions sensitive to orthographic structure.
For use as test items in the recognition task, a set of 50 filler items (words, pseudowords, and consonant strings) were also presented. An additional 10 filler items were included as dummy items at the beginning of each block. The total number of stimuli in the study was 1120 items. For all conditions where an embedded stem was present, pairs of items were presented to native English speakers who rated the semantic relatedness between the two words (e. g. , corner/corn) on a scale of 1-7 (unrelated to highly related ). Test items selected for the morphologically transparent condition were rated as 6. 5 or above. For the pseudoderived and pseudo-stem conditions, test items were rated as 3. 5 or below (weakly related). Items for the nine conditions were selected using the Celex database and the conditions were matched (Table  2 ) on whole form and stem length, percentage of orthographic overlap between stem and whole form (where applicable), and frequency of the whole form and embedded stem (where applicable).
We tested 29 new participants (none of whom took part in the MEG study), all right-handed native British English speakers between the ages of 18-34 (mean age of 24). Each trial began with a set of hashmarks as a premask, which appeared in the center of the screen for 500 msec. This was followed by the prime in the same location in lower-case letters for 40 msec and which itself was immediately followed by the target in uppercase letters. The experiment was run in a sound-proof, dimly lit room, using a PC-compatible microcomputer using DMDX software  (Forster & Forster, 2003). Trial order was pseudorandomized online using DMDX software, with two items from each condition appearing in each scrambling block (one related prime and one unrelated prime from each condition). Outliers (RTs over 1500 msec) were discarded, accounting for 0.
The order of the two blocks was alternated for each participant, so that presentation of the whole form and equivalent stem ( farmer and farm) were alternated, with the stem appearing first for half of the participants. The order of the five subblocks was randomized for each participant in a cyclical order (e. g. , subblock order 1-2-3-4-5 for Participant 1, and 2-3-4-5-1 for Participant 2). This preserved the order of the subblocks so that the repeated stem and whole form were always separated by the same number of subblocks, with a mean distance of 559 trials (range of 448-670 trials). Trial order was randomized within each subblock using E-Prime 1. 0 software (Psychology Software Tools, Inc. ). Each trial began with a fixation cross in the middle of the screen for 500 msec to direct the attention of the participant to the appropriate location on the screen.
MEG Acquisition MEG data were continuously acquired at a sampling rate of 1000 Hz (passband 0. 01-300 Hz), with triggers placed at the onset of each stimulus. Neuromagnetic signals were recorded continuously with a 306-channel Vectorview MEG system (Elekta Neuromag, Helsinki, Finland). Before recording, four electromagnetic coils were positioned on the head and digitized using the Polhemus Isotrak digital tracker system (Polhemus, Colchester, VT) with respect to three standard anatomical landmarks (nasion, left and right preauricular points). During the recording, the position of the magnetic coils was tracked using continuous head position identification, providing information on the exact head position within the MEG dewar for later movement correction. Four EOG electrodes were placed laterally to each eye and above and below the left eye to monitor horizontal and vertical eye movements.
MEG Preprocessing Continuous raw data were preprocessed offline with the MaxFilter (Elekta Neuromag) implementation of the signal-space separation technique with a temporal extension  (Taulu & Simola, 2006). Averaging was performed using the MNE Suite (Athinoula A. Martinos Center for Biomedical Imaging). Epochs containing gradiometer, magnetometer, or EOG peak-to-peak amplitudes larger than 3000 fT/cm, 6500 fT, or 200 μV, respectively, were rejected. Trials were averaged by condition with epochs generated from -100 to 500 msec from onset of the target word. Averaged data were baseline corrected using -100 to 0 msec interval and low-pass filtered at 45 Hz. For sensor-level analyses, MEG data were transformed to the head position coordinates of the participant with the median head position within the helmet to minimize transformation distance.
Sensor-level Analyses These analyses were conducted on gradiometers and magnetometers separately using the SensorSPM analysis method implemented in SPM5 (www. fil. ion. ucl. ac. uk/ spm/). Magnetometer data were used as such, whereas for each pair of gradiometer channels, a vector sum was calculated that reconstructed the field gradient from its two orthogonal components and its amplitude (computed as a square root of the sum of squared amplitudes in the two channels). For each participant and condition, a series of F tests were performed on a three-dimensional topography (2-D sensors by time image), which extended through 601 samples (1 msec each), allowing for the application of random field theory as in fMRI analysis  (Kiebel & Friston, 2004). The 3-D images were thresholded at a voxel level of p <.
Acknowledgments This research was supported by a grant to W. M. W. from the  European Research Council  ( NEUROLEX 230570 ) and by  MRC Cognition and Brain Sciences Unit funding (U. 1055. 04. 002. 00001. 01 ). C. W. was supported by funding from the  Cambridge Trusts  and a  Howard Research Studentship  from  Sidney Sussex College, Cambridge. Y. S. was supported by  MRC core program  funding (MC- A060-5PQ90 ). We thank  Daniel Wakeman  for his assistance with MNE and FreeSurfer;  Kathy Rastle ,  Lorraine Tyler ,  Tim Shallice , and  Ram Frost  for their comments on the manuscript; and the MEG operators at the  MRC CBU  for their help. Reprint requests should be sent to Caroline Whiting or  William Marslen-Wilson ,  Department of Psychology, University of Cambridge ,  Downing Street , Cambridge  CB2 3EB ,  UK , or via e-mail: cmw59@cam.
RESULTS In total, 42 individuals were identified, 23 men and 19 women from 21 kinships (see online supplementary tables S1A, B). Based on our data, the expected point prevalence of IBMPFD in the UK is 0. 066/100 000 population. Eighteen unrelated patients harbour a previously described mutation. In addition, three patients from two families harbour two novel variants (c. 604G>T, p. G202W in exon 6 and c. 1316C>G, p. A439G in exon 11) that are predicted to be pathogenic by in silico analysis (Alamut interpretation software V. 2. 4) and segregate with disease. Three previously described mutations were identified in exon 5 of the VCP gene. The mutation p. R155H (c. 464G>A) was found in 11 families. The mutation p. R191Q (c. 572G>A) was found in three unrelated patients, p. R155C (c. 463C>T) in two families, and p.
Back pain (4 patients), cramps and muscle pain (12 patients) were frequently reported. Forced vital capacity systematically assessed in 20 patients, was reduced in 2, requiring non-invasive ventilation after, respectively, 16 and 18 years of disease duration. ECG was performed in 14 patients. Three patients from the same family had moderate left ventricular dysfunction, 10, 11 and 17 years after the first symptoms. For the last patient, there was a past history of myocardial infarct (MCI). Severe progressive FTD or MCI was observed in 14 of 29 patients (48. 2%); in 5 patients, data were not available. PDB was confirmed in eight patients, and five other reported bone pain. In three cases, despite normal X-rays, bone alkaline phosphatase serum levels were high. Serum creatine kinase (CK) levels were measured in 19 of 40 patients.
DISCUSSION At present, only 43 families with VCP mutations have been reported worldwide to the Leiden Open Variation Database (LVOD). Our data indicate a point prevalence of IBMPFD of 0. 066/100 000 for the UK population as a whole. Although we accept that these figures need to be interpreted with caution, and cases may remain unrecognised, they suggest that IBMPFD is a very rare disease. As our department is a specialised service for muscle diseases, it is not surprising that muscle weakness was the first symptom in the majority of patients; with either a limb-girdle or combined proximal-distal distribution. Distal weakness, mostly affecting the small hand muscles, generally an extremely rare presentation of myopathy, was identified in several patients with IBMPFD. Approximately half of our patients remained ambulant after 17.
To identify such ncRVDs, we generated and screened collections of TALEN containing alternative combinations of amino acids at position 12 and 13 at defined positions of an array. Among the thousands TALEN/targets combinations tested (,18,000), we identified ncRVDs that presented novel valuable specificity features (exclusion properties). The additional levels of specificity control offered by these alternative DNA targeting modules will clearly represent a major advantage to alleviate off-site targeting. Off-site targets are defined as sequences within the genome that contain a few mismatches relative to the targeted sequence of interest. When considering an intended target and a related off-site sequence, the adequate implementation of ncRVDs that discriminate between the nucleotides present at the position of the mismatches (exclusion properties) will prevent the TALEN activity at the off-site sequences while allowing processing of the desired locus.