dataesr/scientific-paragraphs-categorization huggingface dataset:
Name refers to the host genus Eucalyptus from which it was isolated. MG098280. 1; Identities = 581/588 (99 %), no gaps), Pseudocamarosporium tilicola (strain MFLUCC 13-0550, GenBank KJ747050. 1; Identities = 551/558 (99 %), no gaps), and Pseudocamarosporium piceae (strain cp48, GenBank MK796148. 1; Identities = 518/525 (99 %), no gaps). Closest hits using the LSU sequence are Pseudocamaro- sporium propinquum (strain MFLUCC 17-1211, GenBank MG812621. 1; Identities = 844/844 (100 %), no gaps), Pseudo- camarosporium ulmi-minoris (strain MFLUCC 17-0671, Gen- Bank MG829062. 1; Identities = 844/844 (100 %), no gaps), and Pseudocamarosporium pteleae (strain MFLUCC 17-0724, GenBank MG829061. 1; Identities = 844/844 (100 %), no gaps). Closest hits using the tef1 sequence had highest similarity to Pseudocamarosporium pteleae (strain MFLUCC 17-0724, GenBank MG829233.
1; Identities = 434/442 (98 %), no gaps), Paraconiothyrium cyclothyrioides (strain UTHSC DI16-327, GenBank LT797124. 1; Identities = 456/468 (97 %), no gaps), and Paraconiothyrium brasiliense (strain UTHSC DI16-311, GenBank LT797116. 1; Identities = 428/440 (97 %), no gaps). Colour illustrations. Leaves of Eucalyptus sp. in California Pseudocamarosporium eucalypti was isolated from. Conidiomata on pine needle agar; conidiogenous cells; conidia. Scale bars: conidiomata = 200 µm, all others = 10 µm. Pedro W. Crous, Lorenzo Lombard & Johannes Z. Groenewald, Westerdijk Fungal Biodiversity Institute, P. O. Box 85167, 3508 AD Utrecht, The Netherlands; e-mail: p. crous@wi. knaw. nl, l. lombard@wi. knaw. nl & e. groenewald@wi. knaw. nl Etymology.
Conidia single, pale brown, smooth, multiseptate, coiled in three rings (13 -17 µm diam), base truncate, 2 µm diam. Culture characteristics -Colonies flat, spreading, with sparse aerial mycelium and smooth, lobate margin, reaching 20 mm diam after 2 wk at 25 °C. On MEA, PDA and OA surface brown vinaceous, reverse honey. USA, California, Davis, UC Davis, on leaves of Melaleuca styphelioides × lanceolata (Myrtaceae), 2 Apr. 2019, P. W. Crous, HPC 2897 (holotype CBS H-24209, culture ex-type CPC 38042 = CBS 146081, ITS, LSU and tef1 sequences GenBank MN562154. 1, MN567661. 1 and MN556835. 1, MycoBank MB832914). Classification -Tubeufiaceae, Tubeufiales, Dothideomy- cetes. Mycelium consisting of pale to medium brown, smooth, septate, branched, 3 -4 µm diam hyphae. Conidiophores reduced to conidiogenous cells, integrated on hyphae, pale brown, smooth, 3 -15(-35) × 3 -4 µm, with one to several flat-tipped denticles, 2 µm diam; at times reduced to a single denticles directly on hyphae.
Typus. South africa, Eastern Cape Province, Haga Haga, on leaves Rhoicissus digitata (Vitaceae) with dieback, 12 Dec. 2016, M. J. Wingfield, HPC 2296 (holotype CBS H-23936, culture ex-type CPC 35297 = CBS 145536, ITS, LSU, rpb2, tef1 and tub2 sequences GenBank MN562156. 1, MN567663. 1, MN556817. 1, MN556827. 1 and MN556846. 1, MycoBank MB832918).
Boletopsis mediterraneensisG. Moreno, Carlavilla, Bellanger, Olariaga, P. -A. Moreau,   Bidaud, Loizides & Manjón, sp. nov. Referring to its Mediterranean distribution. Fungal Planet 1001 -18 December 2019 1; Identities = 215/241 (89 %), 8 gaps (3 %)), Pestalotiopsis colombiensis (strain CBS 118553, GenBank KM199488. 1; Identities = 215/241 (89 %), 8 gaps (3 %)), and Pestalotiopsis terricola (strain CBS 141. 69, GenBank MH554438. 1; Identities = 217/244 (89 %), 17 gaps (6 %)). Closest hits using the tub2 sequence had highest similarity to Monochaetia ilexae (strain CBS 101009, GenBank MH554612. 1; Identities = 474/598 (79 %), 31 gaps (5 %)), Nonappendiculata quercina (strain CBS 270. 82, GenBank MH554701. 1; Identities = 331/405 (82 %), 27 gaps (7 %)), and Monochaetia quercus (strain CBS 144034, GenBank MH554844.
, mountain polydominant rainforest with the participation of Fagaceae, Magnoliaceae, Theaceae, Podocarpaceae, 27 May 2014, A. V. Alexandrova & T. H. G. Pham (LE315543, ITS sequence GenBank MN511176). Supplementary material FP1001-1 Additional specimens examined. FP1001-2 Fungal Planet 1002 -18 December 2019 Q = (2. 5 -)3 -3. 5(-4), fusoid, subfusoid and inequilateral in side view with weak suprahilar depression, yellowish brown in Classification -Boletaceae, Boletales, Agaricomycetes. Basidiomata medium sized, boletoid. Pileus 18 -35 mm diam, initially hemispherical, becoming convex with slightly appen-diculate margin, projecting 1-2 mm beyond the pores, white (4A1, Kornerup & Wanscher 1978), cream (4A2 -3) on drying, surface dry, velutinous, tomentose or felted. Spores (12. 5 -)13. 5 -14(-15.
Cladosporium fildesenseC. Gil-Durán, Vaca & R. Chávez, sp. nov. Fungal Planet 1006 -18 December 2019 1; Identities 549/ 549 (100 %), no gaps), Cladosporium cladosporioides SLBB (GenBank JN565298. 1; Identities 549/549 (100 %), no gaps), and Cladosporium cucumerinum (GenBank DQ681347. 1; Iden- tities 549/551 (99 %), 2 gaps (0 %)). The closest hits using the LSU sequence are Cladosporium phlei CBS 358. 69 (GenBank MH877726. 1; Identities 608/608 (100 %), no gaps), Clado- sporium herbarum CBS 128892 69 (GenBank MH876581. 1; Identities 608/608 (100 %), no gaps), and Cladosporium cladosporioides CBS 127051 (GenBank MH875838. 1; Iden- tities 608/608 (100 %), no gaps). The closest hits using the actA sequences were Cladosporium spinulosum CBS 102044 (GenBank EF679541. 1; Identities 213/231 (92 %), 1 gap (0 %)), Cladosporium ossifragi CBS 842.
91 (GenBank EF679535. 1; Identities 212/233 (91 %), 4 gaps (1 %)), and Cladosporium soldanellae CPC 13153 (GenBank JN907001. 1 Identities 207/231 (90 %), 4 gaps (1 %)). The closest hits with tef1 sequen- ces were Clado sporium ramotenellum (GenBank LN834482. 1; Identities 214/245 (87 %), 6 gaps (2 %)), Cladosporium solda- nellae CPC 13153 (GenBank JN906994. 1; Identities 207/236 (88 %), 5 gaps (2 %)), and Cladosporium ossifragi CBS 843. 91 (GenBank EF679460. 1; Identities 204/236 (88 %), 5 gaps (2 %)).
Typus. cypruS, Dora, on calcareous substrate under Quercus coccifera subsp. calliprinos, Pinus brutia and Cistus shrubs, 5 Mar. 2015, M. Loizides (holotype in Herbarium of the Faculty of Pharmacy of Lille: LIP 0401586; isotype in herb. pers. M. Loizides n° ml5135C1, ITS and LSU sequences GenBank MN028412 and MN028396, MycoBank MB832755). Additional materials examined. cypruS (var. iris), Souni, 2 Mar. 2015, M. Loizides, ML5132C/LIP 0001618 (paratype, GenBank MN028411); Dora, 5 Mar. 2015, M. Loizides, ML5135C2 (GenBank MN028413); Anogyra, 17 Feb. 2015, M. Loizides, ML51271-CC (GenBank MN028414); Kelefos, 3 Jan. 2019, M. Loizides, ML9113CLI (GenBank MN028415). -france (var. occidentalis), Bonifacio, îlot Fazzio, 21 Nov. 2005, P. -A. Moreau, PAM05112103 (as 'C. cristata var. curta', GenBank MN028407); Mérindol, 27 Nov.
2011, J. -M. Bellanger, D. Borgarino, G. Corriol, P. -A. Moreau & F. Richard, PAM11122702 (GenBank MN028408); Pézilla-de-Conflent, Chenil Sauvage, under Quercus ilex on calcareous soil, 27 Nov. 2012, F. Richard & P. -A. Moreau, PAM12112740 (GenBank MN028409).
Typus. argentina, Catamarca, Dpto. Paclin, La Merced, close to the tunnels entrance, on humus in mixed forest, in ecotone with the Chaco Serrano/ Yungas, May 2009, M. M. Dios 589 (holotype AH 49090, isotype BAFC 52280, ITS, 28S nrDNA, RPB1 and ATP6 sequences GenBank MK732525, MK732526, MK732533 and MK732530, MycoBank MB832754). materials examined. argentina, Chaco, Dpto. Sargento Cabral y Presidencia de la Plaza, Parque Nacional Chaco, on humus in mixed forest with Aspidosperma quebracho-blanco as a dominant species, 5 May 2010, L. Hernández Caffot MLHC 526 (CORD, ITS/28S nrDNA, RPB1 and ATP6 sequences GenBank MK732527, MK732534 and MK732531); ibid. , MLHC 1903 (CORD, ITS/28S nrDNA, RPB1 and ATP6 sequences GenBank MK732528, MK732535 and MK732532). Additional.
Typus. french weSt indieS, Martinique, Prêcheur, Anse Couleuvre, coastal mesophilic forest, on dead blackened wood, associated with old stromata of Hypoxylon investiens, N14. 84 W61. 22, 9 June 2014, J. Fournier & C. Lechat, MJF 14113 (holotype ILLS00121145 (ILLS), ITS-LSU sequence GenBank MN447129, MycoBank MB832757). material examined. french weSt indieS, Martinique, Prêcheur, Anse Couleuvre, coastal mesophilic forest, on dead blackened wood, associated with old stromata of Hypoxylon investiens, N14. 84 W61. 22, 16 Aug. 2013, J. Fournier & C. Lechat, MJF 13262 = ILLS00121146. Additional.
Typus. uSa, Florida, Putnam County, Ordway-Swisher Biological Station, c. 50 m asl, in oak-dominated forest, 14 June 2017, L. Kaminsky (holotype FLAS-F-60908, ITS sequence GenBank MH016883, MycoBank MB830772). Paratypus. uSa, Tennessee, Anderson County, Oak Ridge, beneath Quercus, 21 Aug. 2015, H. Hitchcock, ARB1260 (FLAS-F-60333, ITS, LSU, rpb1, rpb2 and tef1 sequences GenBank MF098659, MF614166, MF614168, MF614169 and MF614165).
Typus. pakiStan, Khyber Pakhtunkhwa province, Malakand division, Swat district, Upper Shawar, alt. 1300 m, on the floor of Quercus floribunda dominated forest mixed with a few pines, 29 July 2018, Z. Ullah BS59 (holotype LAH 36219, ITS, LSU, mtSSU and rpb2 sequences GenBank MN053395, MN513043, MN053397 and MN053389, MycoBank MB831387). material examined. pakiStan, Upper Shawar, Malakand division, Swat district, Upper Shawar, alt. 1300 m, on the floor of Quercus floribunda dominated forest mixed with a few pines, 29 July 2018, Z. Ullah BS80 (LAH 36220, ITS, LSU, mtSSU and rpb2 sequences GenBank MN053391, MN513043, MN053396 and MN053390). Additional.
dalatensis, 23 May 2014, O. V. Morozova (LE315545); Dak Lak Province, Krong Bong District, Chu Yang Sin National Park, Krong Kmar, 7 km northwest of Chu Yang Sin, 12. 40856°N, 108. 38856°E, 1 530 m alt. , on soil in mountain polydominant rainforest with the participation of Pinus kempfii, 21 May 2014, A. V. Alexandrova (LE315547, ITS, tef1α and LSU sequences GenBank MN511178, MN597965 and MN511171; ibid. , LE315546, ITS and tef1α sequence GenBank MN511179 and MN597964). Additional.
Samples were genotyped using the classical P. falciparum marker msp2 according to published protocols  13. Fluorescently labelled nested PCR products were sized by CE on an automated sequencer and analysed using GeneMarker software. Fragments were accepted if the following cut-off criteria were met: peak height >500 intensity units and >10% of the height of the majority peak. Electropherograms were inspected visually to exclude obvious stutter peaks. All DNA samples were genotyped in 2 independent laboratories to assess reproducibility of clone detection and measures of MOI. Marker selection for Amplicon deep sequencing. Amp-Seq was performed on three amplicons located in two different P. falciparum marker genes, namely PF3D7_0104100, "conserved Plasmodium membrane protein" (cpmp), and PF3D7_1133400, "apical membrane antigen 1" (ama1) whose genetic diversity has been studied in great detail  7, [14] [15] [16].
Sequencing was performed on an Illumina MiSeq platform in paired-end mode (2 × 250 bp) using Illumina MiSeq reagent kit v2 (500-cycles) together with Enterobacteria phage PhiX control (Illumina, PhiXControl v3). Sequence read analysis and haplotype calling. Samples yielding a sequence coverage of <25 reads were excluded from the analysis. An overview of sequence read coverage for all Amp-Seq markers is given in Supplementary Table  S3. Several pipelines to process Amp-Seq data have recently been published, including HaplotypR (https://github. com/lerch-a/HaplotypR. git) that was used for this study  9, [18] [19] [20] [21]. Haplotype calling is explained in full detail in an earlier publication  9. In short: Low quality sequences were removed by trimming reads to a final size of 240 bp forward and 170 bp reverse for all amplicons.
1% and an occurrence of this haplotype in ≥2 samples over the entire data set including technical replicates. The chosen cut-off criteria where studied in great detail and discussed in an earlier publication  9. Multi-locus haplotype inference in longitudinal samples. Amp-Seq quantifies the frequency of each haplotype within a sample. This permits the inference of multi-locus haplotypes, an approach also used earlier by software DEploid  23. In this study a semi-automated procedure was applied for multi-locus haplotype inference that utilized longitudinal sample information to solve complex mixtures. A multi-locus haplotype was deduced iteratively and separately for each sample. In the first round, the multi-locus haplotype of the dominant clone of a sample was inferred by selecting each marker's dominant haplotype (>54% within-host haplotype frequency, i.
Additionally, false-negative (FN ii ) haplotypes were imputed for samples in which no sequence read was detected. These false-negative haplotypes were imputed only when (a) the haplotype was detected in the preceding as well as the succeeding bleed as a true-positive. Presence in only one of preceding or succeeding sample was not considered sufficient evidence for assuming a case of missed detection. For the Amp-Seq markers but not msp2-CE, false-negative haplotypes were also imputed when (b) data for the other two markers was present and the corresponding multi-locus haplotype was established in the preceding or succeeding sample. The sensitivity to detect parasite clones was estimated based on selected individuals who had not received antimalarial treatment during the timespan analysed and harboured at least one haplotype that was detected at 3 consecutive bleeds.
Inference also is impossible for complex patterns with shared haplotypes, i. e. if a haplotype has a high population frequency and therefore is present in 2 or more clones of a blood sample. Shared haplotypes may even lead to inference of wrong multi-locus haplotypes, e. g. when three clones were present at an equal within-host frequency, though only two haplotypes were measured at each locus. However, the risk of erroneous multi-locus haplotype inference decreases if more than 2 unlinked markers are used, as the likelihood of shared multi-locus haplotypes decreases with increasing number of loci. In the present study, multi-locus haplotypes up to MOI = 3 were inferred. For multiplicity >3 and for resolving complex patterns of shared haplotypes, additional longitudinal samples could be analysed simultaneously, for example by incorporating the within-host haplotype frequencies of all consecutive samples of an individual into DEploid software  23.
Acknowledgements We are grateful to the study participants and their guardians and to the field and laboratory team of the  PNG Institute of Medical Research, in particular Alice Ura. We would also like to thank  Stephen Wilcox  for supervising sequence library preparation and sequencing. This work was supported by the  Swiss National Science Foundation  [grant number  310030_159580 ] and the  International Centers of Excellence for Malaria Research  [grant number  1U19AI129392 ]. A. L. was partly funded by  Novartis Foundation for Medical-Biological Research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
2015) ; and other approaches of analysis on sampled imagery  (Dumas et al. , 2009; Teixidò et al. , 2011; Kipson et al. , 2011). The next step forward has consisted in employing automatic computer-vision and photogrammetric methods for processing the acquired underwater video footages and producing typical photogrammetric output (i. e. orthophoto mosaics, 3D point clouds, digital surface models). Compared to traditional methods used in the scientific diving community, the advantages are enormous, allowing also for objective postprocessing analyses (i. e. not in situ diver-operated estimations) with benthic image analysis softwares (e. g. Seascape,  Teixidò et al. 2011, and photoQuad, Trygonis and Sini, 2012). Underwater photogrammetry has then been exploited in hostile environments or remote areas  (Westoby et al.
Photogrammetric processing The original video streams from 2006 and 2015 were processed according to the following steps: 1. the analogue video were digitized with the Sony frame grabber (model DVBK2000E); 2. the frames were de-interlaced and extracted at the full frame rate with the VideoLAN software (VLC). Videos from the Sony A7IIs were processed in ffmpeg (www. ffmpeg. org) by extracting only the keyframes. A mixed procedure of image orientation and self-calibrating bundle adjustment was done using the commercial software Agisoft Photoscan and the open source damped bundle adjustment toolbox DBAT (Börlin and Grussenmeyer, 2013) v0. 7. 2. 0 for MATLAB environment. The use of DBAT software allowed to reprocess the image observations automatically extracted from Photoscan thus providing a more advanced tool for the analysis and revision of the bundle adjustment results.
Through for example the analysis of the full variance-covariance and correlation matrices it was possible to understand the precision of self-calibrated parameters, their significance and dangerous correlations between interior and exterior orientation parameters. With the aim of highlighting some critical issues of the photogrammetric processing, the video from 2017 (T1-2017) was processed twice: i) single nadir strip configuration and ii) together with two additional oblique looking strips, in order to emphasize the benefit of multiple strips on the global accuracy of 3D measurements. All the datasets were processed with a minimally constrained self-calibrating BA. Six degrees of freedom (DOF) needed for datum definition were solved by fixing the six exterior orientation parameters (three translations and three rotations) of the camera located nearest to the barycentre of the camera network.
Self-calibrating BA Table  1  summarises the main statistics from the self-calibrating BA. The processing of the video footage from 2006 and 2015 shows the highest RMS of image residuals and σ0, while the dataset T1-2017 with only nadir images provides the highest standard deviation value of the principal distance (focal length). In Figure  3 , the camera network and 3D tie points are reported for all the processed dataset. The dataset S1-2006 shows a light bending of the photogrammetric model (Fig. 3. a), deformation that is much more critical for the T1-2017 only nadir (Fig. 3c ). The bending is significantly reduced when the oblique images are included in the BA, as shown in Figure  3  The trend suggests a bending toward the extremities where the standard deviation can be as high as 15 mm (Fig.
Statistical ecological analysis Geospatial packages of R (R-project. org) and GIS (e. g. QGIS, qgis. org) software and specific image analysis software, such as those based on chromatic hierarchical segmentation processes (e. g. Seascape, Teixidò et al. 2011, and photoQuad, Trigonis & Sini, 2012) , allow to obtain quantitative measures useful to document the changes occurring in the benthos and hence establish a monitoring program of the communities studied. A first ecological outcome of the image analysis procedures concerns spatial patterns of S. neumayeri, that thanks to the application of appropriate indices (K-Ripley index,  Ripley, 1976, Fig. 5 ) resulted to be clustered. It is important to highlight that, from an ecological point of view, the possibility to quantitatively describe this kind of phenomena (probably already studied and described, but only qualitatively), it's an original and relevant outgrowth allowed by photogrammetric output (e.
Karimzadeh and MacEachren (2019)   [19]  thus offer a new bespoke and interactive visual analytics system, the GeoAnnotator, to speed up the process. The GeoAnnotator precomputes potential matches and then allows a multiuser collaborative approach to improve individual results. Its main purpose is geoparsing, but the algorithms can be further developed for other tasks related to recognition of patterns in spatial language. Further, the GeoAnnotator is provided as free and open source software (FOSS) at https://github. com/geovista/GeoTxt, thus the paper also supports open code provision and through it scientific reproducibility. In the next paper, Sarın and Ulu gtekin (2019)  [20]  take an entirely different approach to finding and analyzing content in newspapers collections. The effort can be viewed as a manual annotation of a training set for a future machine learning algorithm.
Authors document cartographic choices made by newspapers in communicating earthquake-related news in a historical period based on a manual collection, classification, and qualitative analysis. The objective of the work is to examine the role and the potential impact of newspaper maps and map-like contents to enhance spatial thinking abilities. Scanning the newspaper archives from 1928-2000 from eight major newspapers distributed throughout Turkey, a country with frequent earthquakes, authors first set up a geospatial database, coding the spatial and thematic features of map-like contents. The article describes the design of the database and the possible queries based on map title, type, purpose, scale, and elements such as text, location inside the newspaper, etc. , that could be relevant in classifying maps.
We homogenise the magnitudes to the moment magnitude scale of Kanamori  55  producing a catalogue which contains a total of 56 earthquakes with moment magnitudes ranging from 4. 3 to 7 M w. We then convert from moment magnitude (M w ) to seismic moment release (N m ) using the method of Kanamori  55. To represent the spatial variation in seismic moment release we sum the seismic moment release in grid cells with dimensions of 0. 5×0. 5 degrees. Numerical modelling. 3D rift evolution has been investigated by using the massively parallel finite element code ASPECT  [33] [34] [35] [36] [37]. ASPECT's mesh refinement capabilities enable us to focus resolution on the regions of interest (i. e. the nearsurface and the region of Kenya/Ethiopia rift interaction), while leaving other areas such as the undisturbed mantle at coarse resolution, leading to kilometre-scale local mesh resolution in 3D.
Acknowledgements This research was supported by the  National Geographic Society  (Grant # 9976-16 ,  P. I. G. Corti ). We thank the  DigitalGlobe Foundation  for providing the satellite image in Fig. 3. We warmly thank  Antonio Zeoli  for the processing of the satellite images and  Pablo Tierz  for valuable discussions. Inversion of fault-slip data and volcanic alignments was obtained using  Win-Tensor , a software developed by  Dr. Damien Delvaux ,  Royal Museum  for  Central Africa, Tervuren, Belgium. D. K. is supported by  NERC  grant  NE/ L013932. F. I. -K. is supported by the  ECLIPSE Program  funded by the  New Zealand Ministry of Business, Innovation and Employment. S. B. and A. G. are supported by the  Helmholtz Young Investigators Group CRYSTALS  ( VH-NG-1132 ). Numerical models were conducted on HLRN cluster Konrad.
Blank experiments were also carried out by inserting ampoules that were not inoculated and, as expected, no heat flux was observed confirming the medium sterility. Each experiment was repeated thrice. The heat flux dQ dt À � , also called thermal power output P, was measured for each methanogen and blank samples with a precision � 0. 2 μW. The heat flux data of each sample were collected every 5 minutes during more than 10 days. The total heat Q was obtained by integrating the overall heat flux time curve using the TAM Assistant Software and its integrating function (TA Instruments, France). Classically, the heat flux-time curve for a growing culture starts like the S-shaped biomass curve (a lag phase followed by an exponential growth phase) but differs beyond the growth phase, the heat flux being then modulated by transition periods  [37].