dataesr/scientific-paragraphs-categorization huggingface dataset:
Background First-line palliative treatment for patients with R/M SCCHN includes platinum-based chemotherapy. There are no standard second-line options upon relapse and median survival is limited. In SCCHN, tumors create a highly immunosuppressive environment and evade immune detection by exploiting inhibitory immune checkpoints such as the programmed cell death ligand-1 (PD-L1)/programmed cell death-1 (PD-1) axis, making immunotherapy an attractive option to study in this disease. Durvalumab (MEDI4736) is a selective, high affinity human IgG1 mAb that blocks PD-L1 binding to PD-1 (IC 50 0. 1 nM) and CD80 (IC 50 0. 04 nM) that has shown promising antitumor activity in the SCCHN cohort of a Phase I/II study (NCT01693562). Tremelimumab is a selective human IgG2 mAb inhibitor of cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) that has been combined with durvalumab in a Phase Ib study in patients with NSCLC (NCT02000947), with encouraging clinical activity and a manageable safety profile.
While anti-PD-1/PD-L1 monotherapy may be associated with greater clinical benefit in patients with PD-L1 + tumors, combination therapy has clinical activity in both PD-L1 + and PD-L1 -patients in several solid tumors, enhancing the antitumor activity of anti-PD-1/PD-L1 agents in patients with PD-L1 -tumors. The PD-L1 and CTLA-4 pathways are non-redundant and preclinical data indicate targeting both may induce synergistic antitumor effects. Here we describe the CONDOR study (NCT02319044), a Phase II study to determine the efficacy and safety of durvalumab monotherapy, tremelimumab monotherapy, and their combination in PD-L1 -R/M SCCHN patients who have failed prior platinumtherapy.
PCR products were visualized in 1. 5% agarose gels (1% TBE) stained with SYBR-Safe (Lonza, Belgium). The DNA size marker used was the Smart ladder Eurogentec ® (200 to 10,000 pb). Successful double-strand PCR products were purified with the Exo-SAP-IT buffer (USB, Cleveland, OH, USA) and then sequenced using the Big Dye v. 3. 1 Terminator Kit on a capillary automated sequencer ABI PRISM 3130 (PE Applied Biosystem, Carlsbad, CA, USA). For most samples, the forward and reverse sequences were obtained. In addition to the Sardinian individuals, we sequenced some specimens from Corsica and France; all the haplotypes are available in GenBank under the accession numbers KP866104-KP866115. Sequences from  Grandjean et al. (2000) ,  Largiadèr et al. (2000) ,  Zaccara et al. (2004) ,  Fratini et al.
Phylogenetic inference We restricted the location selection to Italy and Southern France. Sequences from A. torrentium from Switzerland were added as an outgroup to the overall dataset. First, we used a Bayesian inference implemented in BEAST 1. 8. 0  (Drummond et al. , 2012)  for computing the species phylogeny and detecting the taxonomical affiliation of the Sardinian population. We selected the HKY  (Hasegawa et al. , 1985)  substitution model in MEGA 6  (Tamura et al. , 2013)  with selection on the lowest Akaike Index Criterion (AIC). Three Metropolis-coupled Markov chains (MCMC) were run 10 million generations with trees sampled every 1,000 generations. We used TRACER 1. 6 (http://beast. bio. ed. ac. uk/Tracer) to check that all Effective Sample Size (ESS) were largely exceeding the minimum value of 100 to ensure the meaningful estimation of parameters.
The different runs were combined using LogCombiner 1. 8. 0. (http://beast. bio. ed. ac. uk/logcombiner). We discarded the first 10% trees in TreeAnnotator 1. 8 (http://beast. bio. ed. ac. uk/treeannotator). Then, we visualized the trees topologies in FigTree 1. 4. 2 (http://tree. bio. ed. ac. uk/software/figtree/). Secondly we added to the posterior probabilities of the Bayesian inference, the bootstrap values from a Maximum Likelihood analysis (1000 repetitions, MEGA 6;  Tamura et al. , 2013) , to support the main branches of the species complex phylogeny.
Phylogenetic inference The data matrix of 223 mitochondrial DNA 16S rRNA gene sequences of Austropotamobius spp. , consisted of eight samples from Sardinia, 19 from Corsica, nine from the Rhône (France) and six samples from the French Eastern Pyrénées, were supplemented by 181 sequences re-   1, data from previous published studies  (Fratini et al. , 2005 ; Grandjean et al. , 2000; Largiadèr et al. , 2000; Pedraza-Lara et al. , 2010; Zaccara et al. , 2004). 2, data obtained from the present study.
If this Sardinian population might result from a natural genetic divergence, both the Pleistocene climate and the regional geomorphological history might have influenced the splitting of species. As shown in Proseallus species  (Matthaeis et al. , 2001) , the natural genetic divergence of the Sardinian population is the largest within its Mediterranean distribution. This is not the case in our dataset; the Sardinian population is genetically very similar to the Southern Italian populations of A. i. meridionalis. However, given that the separation of the Corsica-Sardinia microplate ranged between 50-25 million years before present (MYBP) and 16-12 MYBP  (Alvarez, 1972) , the genetic pool of any endemic population in Sardinia would have been much more differentiated from the other Italian and European populations.
Novelty and relevance Radiation Physics and Chemistry aims to publish articles with significance to an international audience, containing substantial novelty and contributions to science. We expect that articles present new insight or hypothesis testing, that they focus on radiation effects or applications of ionizing radiation, provide uncertainties and statistical analysis where relevant, and present their findings in context with discussion of past and recent literature. The editors reserve the right to reject, with or without external review, articles which do not meet these criteria. This could include articles which are very similar to previous publications, except that target substrates, materials, analyzed sites or experimental methods have been changed. General considerations Note that each new submission will be checked against the CrossCheck database to detect (self)-plagiarism.
CrossCheck uses originality detection software to compare manuscripts against a unique database of 30+ million articles from 200+ publishers. Normally, RPC will not expect the total number of tables and figures to exceed 10 unless it concerns an extensive review article or in other exceptional cases. Figures and tables that are not essential to the paper can best be submitted as online supplementary material. Please provide reproducible data were possible and include measurement uncertainties and error analyses Data should be presented with a number of decimals that matches the data best.
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Oguro, M. , Imahiro, S. , Saito, S. , Nakashizuka, T. , 2015. Mortality data for Japanese oak wilt disease and surrounding forest compositions. Mendeley Data, v1. https://doi. org/10. 17632/xwj98nb39r. 1. Reference to software: Coon, E. , Berndt, M. , Jan, A. , Svyatsky, D. , Atchley, A. ,Kikinzon, E. , Harp, D. , Manzini, G. , Shelef,  E. , Lipnikov, K. , Garimella, R. , Xu, C. , Moulton, D. , Karra, S. , Painter, S. , Jafarov, E. , & Molins, S. ,  2020. Advanced Terrestrial Simulator (ATS) v0. 88 (Version 0. 88). Zenodo. https://doi. org/10. 5281/ zenodo. 3727209.
Oguro, M. , Imahiro, S. , Saito, S. , Nakashizuka, T. , 2015. Mortality data for Japanese oak wilt disease and surrounding forest compositions. Mendeley Data, v1. https://doi. org/10. 17632/xwj98nb39r. 1. Reference to software: Coon, E. , Berndt, M. , Jan, A. , Svyatsky, D. , Atchley, A. ,Kikinzon, E. , Harp, D. , Manzini, G. , Shelef,  E. , Lipnikov, K. , Garimella, R. , Xu, C. , Moulton, D. , Karra, S. , Painter, S. , Jafarov, E. , & Molins, S. ,  2020. Advanced Terrestrial Simulator (ATS) v0. 88 (Version 0. 88). Zenodo. https://doi. org/10. 5281/ zenodo. 3727209. [dataset] Journal abbreviations source Journal names should be abbreviated according to the List of Title Word Abbreviations. …. Or, as demonstrated (Jones, 1999; Allan, 2000)… Kramer et al. (2010) have recently shown …' List: References should be arranged first alphabetically and then further sorted chronologically if necessary.
, 2009. How to prepare an electronic version of your article, in: Jones, B. S. , Smith , R. Z. (Eds. ), Introduction to the Electronic Age. E-Publishing Inc. , New York, pp. 281-304. Reference to a website: Cancer Research UK, 1975. Cancer statistics reports for the UK. http://www. cancerresearchuk. org/ aboutcancer/statistics/cancerstatsreport/ (accessed 13 March 2003). Reference to a dataset:.
Several components are needed to achieve these goals: a multidisciplinary, multiscale observational network; a state of the art modelling suite integrating the primitive equations and solving explicitly for the particular physical processes characterizing the coastal area; a robust data assimilation scheme accounting for anisotropy and complex cross correlations between errors in environmental variables; and a suite of dissemination tools able to scientifically integrate the information collected and transform it into products serving the community (scientists, policy makers, maritime stakeholders). Coastal ocean disciplines are still advancing along active research topics. This evolution requires the development of adequate observational networks to monitor and further understand the coastal ocean.
Advanced understanding should provide new processes to be implemented and/or parameterized in ocean models to cover the observational gaps, but also to study the whole coastal ocean system and interactions that are impossible to solve analytically. Numerical models have limitations due to intrinsic errors, thus data assimilation schemes must be developed in parallel, accounting for the new processes and scales required to correct and drive the numerical results. Finally, methods integrating the very complex resulting information obtained in simple and usable ways must be developed. The goal of this paper is to discuss areas where scientific progress is crucial for the development of COFS and the expected benefits that COFS can provide to the society at large and to specific users. The next section focuses on four major scientific aspects that are currently active areas of research: downscaling, coastal data assimilation and two types of inter-disciplinary couplings (circulationwaves, physics-biogeochemistry).
Science in support of coastal forecasting Downscaling the ocean estimation problem The coastal ocean circulation is driven by a combination of local (winds, atmospheric fluxes, land drainage and tides) and deep-ocean forcings (along the shelf slope). Both of these influences must be included in COFS. Downscaling is accepted as the preferred methodology to propagate the large scale dynamics into COFS, through boundary conditions from Global Ocean Forecasting Systems (GOFS)  (Auclair et al. 2001; Dombrowsky et al. 2009 ). The boundary conditions must capture relevant far-field phenomena, such as swells from distant storms in wave models, or thermodynamic gradients and tidal information in circulation models. The forcing data and the representation of the coastal model geometry must be also appropriately scaled, with details that are often missing from the outer model.
In the U. S, the most reliable bathymetric data source is from the National Oceanic and Atmospheric Administration (NOAA) VDatum project, combining bathymetric (sounding) and topographic (LIDAR) data. Another challenge is that coastal topography and bathymetry change on both intraand inter-storm scales (e. g. bar formation during severe winter storms). It is, therefore, challenging to establish representative bathymetry in coastal models. Although it is possible to include morphological processes such as erosion and breaching, it is operationally unfeasible at present. Modelling at coastal scales also increases demands on atmospheric forcings: higher spatial resolutions and accurate land models (e. g. North American Mesoscale system, NAM, from NOAA's National Centers for Environmental Prediction, NCEP) are required to capture coastal features.
Coastal data assimilation and prediction Data assimilation (DA) frameworks have been used in coastal ocean models to control the model trajectory and minimize errors, toward enhancing the model's predictive  capabilities. These topics are discussed below. Such frameworks have also been used for array design (including Observing System Experiments/Observing System Simulation Experiments; OSE/OSSEs) and probabilistic forecasting  (Kourafalou et al. 2015).
Accounting for model uncertainties Many factors contribute to errors in coastal ocean model forecasts. These may include: imperfect atmospheric forcing fields; errors in boundary conditions propagating inside the finer scale model domain; bathymetric errors (more consequential in coastal regions); insufficient horizontal and vertical resolution and numerical noise and bias; errors in parameterizations of atmosphere-ocean interactions and sub-grid turbulence; intrinsic limited model predictability (strong non-linearity), etc. To improve the quality of prediction, the model estimates are combined with available data by means of DA. Many different flavors of DA have been developed, tested, and implemented in numerical weather prediction and ocean forecasting. Some methods, including Optimal Interpolation (OI), 3-dimensional variational (3DVAR), and Ensemble Kalman Filter (EnKF), provide instantaneous corrections to the present ocean estimate sequentially, at relatively short time intervals (several hours in the context of a shelf scale model)  (Oke et al.
Toward real-time data assimilation systems DA has been applied to multiple state estimation efforts for the California Current System (CCS, US West Coast, WC) with ROMS (4DVAR)  (Moore et al. 2011a; Moore et al. 2011b ). These include a near real-time (NRT) quasi-operational nowcast/forecast system (WCNRT) and the computation of two sequences of historical reanalyses for the CCS (West Coast ReAnalysis, WCRA). Both near real-time and historical systems are based on the nonlinear model configuration of  Veneziani et al. (2009). The model domain (Figure  6a ) extends from 30N to 48N and offshore to 134W, encompassing a substantial portion of the CCS. Horizontal resolution of 1/10°resolves regional mesoscale variability, and 42 terrain-following levels span the water column. One sequence of reanalyses spans the 31-year period 1980-2010 (hereafter WCRA31), while the second sequence spans the 14-year period 1999-2012 (hereafter WCRA14).
Main issues/challenges for couplings in the coastal ocean An important challenge in coupling coastal ocean models has been to ensure consistency in the fluxes that go between the various coupled models (atmosphere-toocean, atmosphere-to-wave, wave-to-ocean, etc. ). In the uncoupled paradigm, models are calibrated and validated mostly in isolation, often with limited data compared to the number of modeled processes. As a result, dissipation terms are often used as tuning parameters to force a desired model behavior. In coupled modelling, these same dissipation terms become the fluxes to other models, e. g. the dissipated energy from wind wave models that feeds into the mixing of the upper ocean in baroclinic circulation models. This has forced the community to reassess calibration strategies when applied to coupled model systems.
s160 V. H. Kourafalou et al. Downloaded by [University of Liege] at 01: 34 08 January 2016  Acknowledgements V. Kourafalou acknowledges NOAA support ( NA13OAR 4830224  and  NA12OAR4310073 ) and  H. Kang  ( UM/RSMAS ) for help with manuscript formatting. P. De Mey  and  N. Ayoub  have closely collaborated with  P. Marsaleix  ( CNRS/LA, France ) and have been supported from  CNES  through the  Ocean Surface Topography/Jason project MICSS  and from  CNRS/ INSU. A. Barth  was supported in part by the  National Fund for Scientific Research, Belgium (F. R. S. -FNRS)  and the  SANGOMA  project ( FP7-SPACE-2011-1-CT-283580-SANGOMA ). The research by  Y. Chao  was supported by  NOAA/IOOS  (through  CeNCOOS, SCCOOS)  and the  NASA   Interdisciplinary Science program. M. Herzfeld is thankful to the eReefs marine modelling team and partners (CSIRO: Commonwealth Industrial and Scientific Research Organization; SIEF:  Science and Industry Endowment Fund ; AIMS:  Australian Institute of Marine Science).
Single most parsimonious tree (TL = 523, CI = 0. 704, RI = 0. 635, RC = 0. 447) obtained from a heuristic search with 1 000 random addition sequences of the internal transcribed spacer and intervening 5. 8S (ITS) gene regions. Scale bar shows 20 changes and bootstrap support values (1 000 repetitions) are shown at the nodes. The species described here is indicated in bold face. The tree was rooted to Fusarium sambucinum. Notes -Phacidium grevilleae is closely related to a sequence deposited as Ceuthospora pinastri (= Phacidium lacerum) (GenBank FR717225), although its conidia are longer and somewhat narrower than those of P. lacerum (10-18 × 2. 5 -4 μm)  (Crous et al. 2014a) , which is a species commonly isolated from needles of Pinus sylvestris in Europe. It is also related to Phacidium pseudophacidioides (conidia 11-13 × 2-2.
5 μm), although it has much larger conidia than the latter species  (Crous et al. 2014a). First of five equally most parsimonious trees obtained from the ITS alignment based on a heuristic analysis with 100 random taxon additions and tree-bisection-reconnection algorithm using PAUP v. 4. 0b10  (Swofford 2003 ; TL = 538, CI = 0. 690, RI = 0. 613, RC = 0. 422). GenBank accession numbers are indicated behind the species names. Bootstrap support values > 50 % from 1 000 replicates are shown at the node and the scale bar indicates the number of changes. The tree was rooted to Infundibulomyces cupulata (GenBank EF113976) and the novel species described in this study is indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 17580). Notes -Soloacrosporiella is morphologically similar to Soloacrospora, but differs in that it has a much more complex arrangement of conidia, occurring in branched chains with ramoconidia and terminal conidia.
5-4 µm; hila thickened, darkened, 1. 5 -2 µm diam. Culture characteristics -Colonies erumpent with sparse aerial mycelium and even, lobed margins, reaching 25 mm diam after 1 mo at 25 °C. On MEA, PDA and OA surface and reverse iron grey. Typus. Malaysia, Sarawak, on leaf spots of Eucalyptus pellita (Myrtaceae), May 2014, M. J. Wingfield (holotype CBS H-22240 , culture ex-type CPC 24864 = CBS 139920; ITS sequence GenBank KR476727, LSU sequence GenBank KR476762, MycoBank MB812432); CPC 24863. Notes -The genus Myrtapenidiella (Teratosphaeriaceae) was introduced by  Quaedvlieg et al. (2014)  to accommodate penidiella-like genera occurring on Myrtaceae. Two species are presently known, namely M. corymbia (ramoconidia 0-2-septate, (7-)10-12(-14) × 2. 5-3 μm, intercalary conidia 0-1-septate, 7-9(-12.
Conidiogenous cells terminal to intercalary, subcylindrical to ampulliform, pale brown, smooth, terminating in a swollen apex 2-3 µm diam with several scars, polyblastic, 8-25 × 2. 5-4 µm. Conidia solitary, hyaline, smooth, falcate, slightly curved, widest in middle with subobtuse ends, (15 -)18 -21(-23) × 2 -3 µm. Culture characteristics -Colonies spreading, reaching up to 60 mm diam after 1 mo at 25 °C, with sparse aerial mycelium, and smooth, lobed margins. On OA surface honey with patches of isabelline. On MEA surface isabelline with patches of dirty white, reverse umber. On PDA surface and reverse fuscous black. Typus. Malaysia, Sabah, on leaf spots of Eucalyptus pellita (Myrtaceae), May 2014, M. J. Wingfield (holotype CBS H-22226 , culture ex-type CPC 24746 = CBS 139897; ITS sequence GenBank KR476723, LSU sequence GenBank KR476758, MycoBank MB812433); CPC 24747.
adansoniae (from South Africa), and G. madagascariense and G. fabiforme (from Madagascar)  (Cruywagen et al. 2010). Interestingly, the ITS sequence of G. jumulu is identical to a partial ITS sequence of a 'Graphium sp. ' isolated from an aneurysm in the abdominal aorta of a dog (GenBank LC007972) and several sequences (e. g. GenBank KF540218 -KF540225) associated with the polyphagous shot hole borer on avocado and landscape trees. The latter sequences are labelled as 'sp. ' in GenBank but the study title associated with these sequences indicates that the species was identified as 'Graphium euwallaceae sp. nov. '. Although the sequences were released on 24 November 2013, we were not able to find any evidence that this species was ever validly published. Fungal Planet 331 -10 June 2015  Barber & Crous, sp.
agric. za First of two equally most parsimonious trees obtained from the ITS alignment based on a heuristic analysis with 100 random taxon additions and tree-bisection-reconnection algorithm using PAUP v. 4. 0b10  (Swofford 2003 ; TL = 438, CI = 0. 826, RI = 0. 702, RC = 0. 580). GenBank accession numbers are indicated behind the species names. Bootstrap support values > 50 % from 1 000 replicates are shown at the node and the scale bar indicates the number of changes. The tree was rooted to Keller mania yuccigena (GenBank JX444868) and the novel species described in this study is indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 17580). Phaeophleospora hymenocallidicola  Crous, sp. nov. Etymology. Name reflects the host genus Hymenocallis, from which the species was isolated.
Scale bars = 10 µm. Single most parsimonious tree obtained from a heuristic analysis with 100 random taxon additions and tree-bisection-reconnection algorithm using PAUP v. 4. 0b10  (Swofford 2003 ; TL = 1 234, CI = 0. 713, RI = 0. 648, RC = 0. 462). The alignment consisted of four partial loci, namely ITS, actin, histone H3 and beta-tubulin (GenBank accession numbers separated by slash in the tree). Bootstrap support values > 50 % from 1 000 replicates are shown at the node and the scale bar indicates the number of changes. The tree was rooted to Colletotrichum cliviae CBS 125375 and the novel species described in this study is indicated in bold face. The alignment and tree were deposited in TreeBASE (Submission ID 17580). Classification -Incertae sedis, Phaeomoniellales, Eurotiomy cetes.
Conidia solitary, hyaline, smooth, subcylindrical with obtuse ends, (2. 5-)3(-3. 5) × 1-1. 5 µm. A yeast-like synasexual morph develops in culture on SNA. Culture characteristics -Colonies spreading, with sparse aerial mycelium and feathery margins, reaching 60 mm diam after 1 mo at 25 °C. On MEA surface olivaceous grey, centre buff, outer region olivaceous grey to buff. On OA surface olivaceous grey to buff. On PDA surface buff with zones of isabelline, also in reverse. Typus. iTaly, Province of Lecce, Trepuzzi, isolated from black-discoloured xylem of wilting Olea europaea (Oleaceae) branch of plant infected by Xylella fastidiosa 'CoDiRO strain', May 2014, F. Nigro (holotype CBS H-22251, culture ex-type M24 = CBS 139192; ITS sequence GenBank KP411807, LSU sequence GenBank KP635970, ACT sequence GenBank KP411805, TEF sequence GenBank KP411802, MycoBank MB812472).