dataesr/scientific-paragraphs-categorization huggingface dataset:
Typus. south AfricA, Eastern Cape Province, Haga Haga, on leaves of Carissa macrocarpa (Apocynaceae), Dec. 2014, M. J. Wingfield (holo- type CBS H-22399, culture ex-type CPC 25665; ITS sequence GenBank KT950849, LSU sequence GenBank KT950863, actA sequence GenBank KT950872, gapdh sequence GenBank KT950876, tef1 sequence GenBank KT950879, MycoBank MB814926). Colour illustrations. Symptomatic leaves of Carissa macrocarpa; conidiomata sporulating on PNA, conidiophores and conidia. Scale bars = 10 µm. Pedro W. Crous & Johannes Z. Groenewald, CBS-KNAW Fungal Biodiversity Centre, P. O. Box 85167, 3508 AD Utrecht, The Netherlands; e-mail: p. crous@cbs. knaw. nl & e. groenewald@cbs. knaw. nl Michael J. Wingfield, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; e-mail: mike.
2004). Pilidium eucalyptorum is most similar to Pilidium acerinum (GenBank AY487091; identity 449/470 (96 %), gaps 7/470 (1 %) and Pili-dium concavum (GenBank KF255414; identity 439/466 (94 %), gaps 2/466 (0 %) based on ITS sequence data. The species frequently constricted at septa, apex and base with prominent mucoid caps, and conidia undergoing microcyclic conidiation in older cultures. Chalara-like synasexual morph present in some species. commonly associated with diseased cutting in Eucalyptus nurseries is Pilidium concavum (synasexual morph Hainesia Type genus: Strelitziana Arzanlou & Crous. MycoBank MB814933. lythri; Crous et al. 1989). Genera included in family -Neophaeococcomyces, Strelit- ziana. Typus. frAncE, La Réunion, S21°15'52. 4" E55°36'3. 3", Cd 36 Nd de la Paix, on leaves of Eucalyptus robusta (Myrtaceae), 8 Mar.
2014, P. W. Crous & M. J. Wingfield (holotype CBS H-22398, culture ex-type CPC 26594 = CBS 140662; ITS sequence GenBank KT950854, LSU sequence GenBank KT950868, MycoBank MB814932). Colour illustrations. Coastline of La Réunion; conidiomata forming on OA, conidiogenous cells and conidia. Scale bars: conidiomata = 300 µm, all others = 10 µm. Colour illustrations. Mountain gorge in La Réunion; symptomatic flower of Syzygium jambos, chalara-like synasexual morph with small conidia, and hyphae giving rise to long, flexuous conidia of Strelitziana syzygii. Scale bars = 10 µm.
thAilAnd, Chaing Mai, from soil collected on Doi Suthep mountain, Nov. 2012, P. W. Crous (holotype CBS H-22376, culture ex-type CBS 140645 = CPC 28835; ITS sequence GenBank KT964775, LSU sequence GenBank KT983443, tub2 sequence GenBank KT964769, tef1 sequence GenBank KT964773, cmdA sequence GenBank KT964771, MycoBank MB814941), CPC 28836 (ITS sequence GenBank KT964776, LSU sequence GenBank KT983444, tub2 sequence GenBank KT964770, tef1 sequence GenBank KT964774, cmdA sequence GenBank KT964772). 100 Calonectria fujianensis CBS 127201 (--;HQ285792;HQ285820) Calonectria paraensis LPF306 (KM396012;KM395925;KM395838) Calonectria nymphaeae CBS 131802 (--;JN984864;KC555273) Calonectria pseudocolhounii CBS 127195 (--;HQ285788;HQ285816) Calonectria colhounii CBS 293. 79 (GQ267373;DQ190564;GQ267301) Calonectria brassicae CBS 111869 (GQ267382;AF232857;FJ918567) Calonectria paraensis CBS 134669 (KM396011;KM395924;KM395837) Calonectria pentaseptata CBS 136087 (KJ463083;KJ462966;KJ462853) Calonectria telluricola CBS 134663 (KM396016;KM395929;KM395842) Calonectria brassicae CBS 143.
Tosteberga, in a pasture on sandy calcareous soil, in a thicket of Crataegus and Corylus, 2 Aug. 2011, L. Örstadius, Herb. Örstadius 99-11 (ITS, LSU sequences GenBank KR261438, KR233831); Skåne, Ravlunda, Klammersbäck, in a pasture with Crataegus, 5 Oct. 2012, L. Örstadius, Herb. Örstadius 149-12 (ITS, LSU sequences GenBank KR261437, KR233830). Psathyrella purpureobadia: spAin, Alcalá de Henares, in calcareous pasture under Kochia prostrata, 12 Dec. 1991, A. Altés & G. Moreno, AH 23690 (ITS sequence GenBank KR261436). de Henares, Additional specimens examined. Psathyrella complutensis: spAin, Alcalá de Henares, Parque de los Cerros, under Kochia prostrata on slopes on loamy soil among mosses, 4 Dec. 2014, M. Heykoop, G. Moreno & M. Lizárraga, paratype AH 45541; ibid. , paratype AH 45542 (ITS, LSU se- quences GenBank KR261442, KR233835); ibid.
Chlorophyllum lusitanicum: spAin Typus. spAin, Extremadura, Cáceres, Navalmoral de la Mata, Jaral del Romeral, beside the reservoir Arroyo de Barrancas Altas, 280 m asl, nitrified grasslands with cow manure, 16 Nov. 2011, J. M. Mohedano & J. A. Suárez (holotype AH 45540, ITS sequence GenBank KR233482, LSU sequence GenBank KR233491, MycoBank MB 812380). , beside the reservoir Arroyo de Barrancas Altas, Jara del Romeral, Navalmoral de la Mata, Cáceres, grassland of Quercus suber, 23 Nov. 2011, J. M. Mohedano, C. Gelpi, J. A. Suárez & G. Moreno, AH 43927 (ITS, LSU sequences GenBank KR233483, KR233492); Turuñuelo farm, Navalmoral de la Mata, Cáceres, dehesa grassland, Nov. 2011, J. A. Suárez, AH 45643; Navalmoral de la Mata, Cáceres, dehesa grassland, 12 Nov. 2012, J. M. Mohedano, AH 45539 (ITS, LSU sequences GenBank KR233484, KR233493); dehesa grassland, beside the reservoir Arroyo de Barrancas Altas, Jara del Romeral, Cáceres, 5 Apr.
2013, F. Melgar, AH 44060; Madrid, prairie of holm oak, 15 Nov. 2013, Soc. Micol. Madrid, AH 44064. Chlorophyllum arizonicum: MExico, km 31 Hermosillo-Yécora, La Colorada, Sonora, thorny bushes, 11 Nov. 1996, M. Esqueda, A. Armenta, A. Núñez, R. Rodríguez & R. Santos, AH 31724 (ITS, LSU sequences GenBank KR233490, KR233499). Additional specimens examined.
Additional specimens examined. ArgEntinA, La Rioja, Castro Barros, Anjullón, on Prosopis spp. (Leguminosae) litter, growing close to old adobe edifications, 8 Apr. 2012, L. Papinutti & J. C. Zamora, MA-Fungi 83789, duplo AH 47603 (ITS sequence GenBank KF988453, LSU sequence GenBank KF988588, rpb1 sequence GenBank KF988723, atp6 sequence GenBank KF988854); ibid. , AH 47604. Typus. ArgEntinA, La Rioja, Castro Barros, Anjullón, on the ground, with Prosopis spp. (Leguminosae) litter, growing close to old adobe buildings, 8 Apr. 2012, L. Papinutti & J. C. Zamora (holotype AH 47602, isotypes in MA- Fungi 83788 and UPS; ITS sequence GenBank KF988452, LSU sequence GenBank KF988587, rpb1 sequence GenBank KF988722, atp6 sequence GenBank KF988853, MycoBank MB812569).
Typus. indonEsiA, Northern Kalimantan, near to the town of Berau, isolated from the exposed xylem tissues of Gmelina arborea (Lamiaceae), Dec. 2010, M. J. Wingfield (holotype PREM 61244, dried culture of CBS 134694, culture ex-holotype CBS 134694 = CMW 37146; isotype PREM 61245, dried culture of CBS 134695, culture ex-isotype CBS 134695 = CMW 37140; tub2 se- quences GenBank KT164794 (CBS 134694), KT164793 (CBS 134695), rpb2 sequences GenBank KT164796 (CBS 134694), KT164795 (CBS 134695), tef1 sequences GenBank KT164798 (CBS 134694), KT164797 (CBS 134695), LSU sequences GenBank KT164792 (CBS 134694), KT164791 (CBS 134695), MycoBank MB814898).
Typus. spAin, Bizkaia, Muskiz, Mount Posadero, in muddy soil, under moss, with Eucalyptus nitens and Pinus radiata, 4 Apr. 2003, J. L. Pérez-Butrón (holotype Herbarium Sociedad Ciencias Naturales Sestao, SESTAO 2003040401; ITS sequence GenBank KP195730, LSU sequence GenBank KP195729, tef1 sequence GenBank KP195727, MycoBank MB814903). specimens examined. spAin, Bizkaia, Muskiz, Mount Posadero, UTM 30TVN8896, 310 m, growing isolated or in dense groups in muddy soil of a forest track, with presence of Eucalyptus nitens and Pinus radiata, 15 Mar. 2001, J. L. Additional.
acknowledgments We would like to express our deepest gratitude to those who have directly facilitated this project, especially Dr. Federico Ramos, Luz Andrea Ramirez, Blanca Martinez, and Catalina Basaguren. We would also like to sincerely thank the staff of CasaNicolás and the Casa Santa Martha for always being approachable as well as all the migrants that shared their valuable experiences and time with us. Finally, we thank Irene Meester for critically reviewing and modifying the manuscript. Funding: The study was partially financed by a research grant from the University of Monterrey (Project grant #UIN15012, www. udem. edu. mx).
Immunocytochemistry Flip-out clones were performed as described  [21]. MARCM clones  [67]  were heat-shock induced at 4-6h embryogenesis and the larvae were allowed to grow on various sucrose-supplemented media until mid/late L3 stage. FB were dissected as described  [21]  but fixed with 3. 7% formaldehyde in PBT (PBS 0. 1% Tween20). FB were stained with Phalloidin-Rhodamine B (sigma) at 625 ηg/ml for 2h at RT, extensively washed and mounted in DABCO (sigma). Relative cell size was expressed as a ratio, clonal:neighboring control cells, which was estimated using the image-j software. The insulin responsive assay was performed as described  [27]. tGPH quantification was measured in squares (10X10 pixels) positioned either at the membrane or at the nuclei. Measurements for each assay were recorded from 8 cells taken from 2 different FBs.
Invasive aspergillosis is characterized by vascular invasion and thrombosis. In order to determine the antifungal activity of human platelets, hyphal elongation and metabolic activity of a clinical A. fumigatus isolate were measured. Genome-wide identification of differentially expressed genes in A. fumigatus was performed after exposure to platelets for 15, 30, 60 and 180 min. Data were analyzed by gene ontology annotation as well as functional categories (FunCat) and KEGG enrichment analyses. Platelets attenuated hyphal elongation and viability of A. fumigatus and in total 584 differentially expressed genes were identified, many of which were associated with regulation of biological processes, stress response, transport and metabolism. FunCat and KEGG enrichment analyses showed stress response and metabolic adaptation to be increased in response to platelets.
Reverse transcribed qPCR validation of microarray data Two-step RT-PCR was performed from total RNA using i-script reverse transcription supermix for RTqPCR and SsoFast EvaGreen Supermix (Bio-Rad). For cDNA synthesis 750 ng RNA was used as template, cDNA synthesis was performed according to the manufacturers recommendation. First strand cDNA was diluted 20× and 2 l were used as template for PCR. Total volume of real time qPCR reactions came to 20 l; SsoFast EVAGreen master mix, forward and reverse primer and cDNA. Cycling parameters were set up according to the recommendation of SsoFast EvaGreen Supermix (Bio-Rad). Non-template controls for each primer set were assayed to confirm no DNA contamination or primer dimer formation being present. Real time PCRs were performed in triplicates, and the expression levels of all genes of interest were normalized to ß-tubulin.
Histology Quadriceps muscles from 3-5-mo-old WT and cavin-1 -/-mice were fixed in 4% PFA and embedded in paraffin for sectioning. Routine hematoxylin and eosin staining was performed on paraffin sections by the Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute histology service. Digital images were captured at RT under bright-field illumination using DP Capture software (Olympus) on a microscope (BX-51; Olympus; 20×/0. 75 NA Plan Apochromat differential interference contrast [DIC] objective) with a color camera (DP-71 12 Mp; Olympus) and raw images assembled using Photoshop (Adobe).
Bright-field images were captured at RT using DP Capture software on a microscope (BX-51; Plan Apochromat 60×/1. 35 NA oil DIC objective) with a color camera (DP-71 12 Mp). Raw images were assembled using Photoshop (Adobe). For muscle cryosections, gastrocnemius mouse muscle was snap frozen in isopentane-cooled liquid N 2 and 8-µm-thick cryosections obtained using a Leica microtome. Cryosections were then blocked in 0. 2% fish skin gelatin/0. 2% BSA; immunostaining and confocal imaging were performed as described in this section for isolated muscle fibers.
EM Ruthenium red labeling of muscle fibers was performed as described previously  (Parton et al. , 2002). Electron tomography and segmentation was performed using methods described previously  (Kremer et al. , 1996; Mastronarde, 2005; Richter et al. , 2008). In brief, 300-nm-thick sections were cut using an ultramicrotome (EM UC6; Leica). Dual-axis tilt series data were collected on an field-emission gun-transmission electron microscope (Tecnai F30; FEI Company) operating at 300 kV, over a tilt range of ±66° at 1. 5° increments, using SerialEM software (The Boulder Lab for 3D Electron Microscopy). Tilt series were reconstructed with the R-weighted back projection algorithm using IMOD/ Etomo software (The Boulder Lab for 3D Electron Microscopy) and segmented using IMOD's automated isosurface rendering function.
Quantitative RT-PCR Total RNA was isolated using TRIzol reagent (Life Technologies), treated with Turbo DNase I (Life Technologies) and RNA purified using the RNeasy mini kit (QIAGEN), all according to the manufacturer's instructions. 1 µg of total RNA was reverse transcribed with oligo(dT)12-18 primers using the SuperScript III First-Strand Synthesis System for RT-PCR (Life Technologies). Quantitative PCR was performed in duplicate for four independent cDNA preparations using the TaqMan Universal Master Mix (Life Technologies) on a real-time PCR system (ViiA7; Applied Biosystems). Gene expression data were analyzed using the ΔΔCt method. TaqMan Gene Expression Assay PCR primers were purchased from Life Technologies: Mm00489257_m1 (DHPR/CACNA1S), Mm00441975_m1 (TRPC1), Mm00458050_m1 (DYSF), Mm00437457_m1 (BIN1), and Mm00446968_m1 (HPRT1).
Isolation of zebrafish fibers from 5-d-old embryos was performed as previously described  (Nixon et al. , 2005). Fibers were allowed to settle onto 3-cm Matrigel-coated dishes for 2 h followed by ruthenium red labeling as described in the EM section. To make the cavin1a-GFP MO target sequence, we fused the 47 bp 5′ of the ATG of cavin1a (which includes the cavin1a-MO target sequence) to EGFP. The vector for in vitro transcription was made by recombining p5E-CMV/SP6, p3E-pA, pDEST-Tol2-pA2  (Kwan et al. , 2007) , and pME-cavin1a-MO control (this study; GenBank accession no. KM211533). mRNA was transcribed using the SP6 mMessage mMachine kit (Ambion) and purified using the MEGAclear kit (Ambion). Images of live embryos in E3 were captured at RT with NIS Elements software (Nikon) on a stereomicroscope (SMZ1500; Nikon) using the GFP filter with a HR Plan Apochromat 1× objective and a camera (CoolSNAP ES2 MonoChrome; Roper Scientific).
Acknowledgments Confocal microscopy was performed at the  Australian Cancer Research Foundation (ACRF)/Institute for Molecular Bioscience Dynamic Imaging Facility for Cancer Biology , established with funding from the  ACRF. The authors acknowledge the use of the  Australian Microscopy & Microanalysis Research Facility at the Center for Microscopy and Microanalysis at The University of Queensland. Molecular graphics images were produced using the  UCSF Chimera package from the Resource for Biocomputing, Visualization , and  Informatics  at the  University of California, San Francisco  (supported by  National Institutes of Health   P41 RR001081 ). We are also grateful to the  University of Queensland Major Equipment and Infrastructure Scheme , the  Welford Donation , and members of the  Parton laboratory  for comments on the manuscript.
The pedagogical expressiveness of designed courses using Learning Management Systems (LMS) is highly dependent on the teachers' expertise about how to use the LMS at their disposal. The GraphiT project aims to help teachers in focusing on the specification of pedagogically sound learning scenarios that can be technically executable for automatically setting-up the LMS. We propose to provide teachers with LMS-specific instructional design languages and editors. The LMS semantics has to be raised in order to enrich the pedagogical expressiveness of the produced models. This paper deals with the proposition of a specific LMS-centered approach for abstracting the LMS low-level parameterizations and turning them into higher-level pedagogical building blocks. We choose to present and illustrate our propositions about the Moodle LMS.
, 12). The GraphiT project (Graphical Visual Instructional Design Languages for Teachers) is based on this approach. Its main objective is to investigate Model Driven Engineering (MDE) techniques for supporting the specification of LMS-centered graphical instructional design languages and the development of dedicated editors. This paper deals with one central challenge: raising the pedagogical expressiveness of LMSs learning design semantics by using MDE techniques. To this end, we detail in section 2 our research context, including the presentation of the GraphiT project, as well as a position of our current results. Section 3 of this paper is dedicated to a survey and series of interviews we conducted with designers in order to collect needs and requirements for the Moodle LMS. A global presentation of our abstraction proposition is done in section 4: a 4-level abstract syntax, formalized as a metamodel, for the future learning design language.
, 07). Educational Modeling Languages  (Berggren et al. , 05)  fail to provide a support for operationalizing EML-conformed learning scenarios into existing LMSs. For now widely spread LMSs like Moodle still do not propose an IMS-LD compliance. Moodle proposes its own format for importing questions into quizzes. Our idea is to generalise it to the whole instructional design aspects. Similarly to the SCORM (ADL, 14) compliance about Learning Objects, the rationale of the GraphiT project is based on the idea that LMSs should make explicit their learning design format in order to facilitate the import/export of compliant learning scenarios, and, in addition, to encourage LMS-dedicated instructional design editors.
Existing and Relevant Learning Design Tools and Languages The project main goal is to study the possibilities and limitations about the pedagogical expressiveness of operationalizable languages. According to the classification of Educational Modeling Languages proposed by  (Botturi et al. , 06) , our objectives map to formal languages, i. e. with closed set of concepts and rules for composing the designs, with an implementation level of elaboration, i. e. the highest level of detail achieving maximum precision, with a visual notation system. The Glue! architecture, including the Glue!PS editor  12) , and the CADMOS editor  (Katsamani et al. , 12)  are two recent research works sharing our learning design criteria about pedagogical sound and executable learning design editors. They both propose an LMS-independent solution offering an LMS deployment feature towards the most widespread and used platform: Moodle (Moodle, 14).
They both achieve the deployment by generating a Moodle course backup with all the information and mapping their own data model concepts to Moodle data model concepts; this backup is then imported and deployed within a Moodle course using the Moodle restoration process. Such approaches result in semantics adaptations and semantics losses during their internal mappings because of the gap between the instructional design language, the specific learning design capabilities as well as features of the targeted LMS. Other research  (Abdallah et al. , 08)  shows that model transformations techniques from the MDE theories and tools can be useful to translate a designercentered and LMS-independent learning scenario to a one that is LMS specific. Nevertheless, they also highlighted the complex transformation model to specify, the LMS metamodel to capture, the semantics losses during translation, and the requirement of an LMS-dedicated tool for embedding the scenarios into the LMS.
We aim at guaranteeing that learning scenarios could be fully operationalized into the LMS without semantics losses. Our approach can take advantage of this LMS-dependance but it has also the disadvantage to be restricted to one LMS and one of its versions. The LMS instructional design semantics has first to be identified and formalized as a domain metamodel. This metamodel drives the elaboration of an XSD (XML Schema Definition) schema that will be used as a format reference for the API to develop. This API will be used through an import facility available to teachers-designers in their LMS courses. Its function is to parse the XML-based scenario and fill-up the LMS database. According to DSM techniques and tools (like the EMF/GMF ones for example (Eclipse, 14)), the visual instructional design language will be composed of an abstract syntax (based on an extension of the LMS metamodel) from which the graphical, tooling and mapping models will be derived.
They approve the approach, emphasising its relevance if templates or concrete cases about pedagogical uses of Moodle tools can be handled within the editor. They highlight the need for a language/editor covering large pedagogical uses but without being too generic. Some of them consider important to continue using the editor for adapting the scenario after the import step although they agree that a round-trip use of both editor and Moodle can be an obstacle. One issue highlighted is that practitioners did not expressed common design practises, as we expected them to, mainly because of the heterogeneity of their Moodle expertises and pedagogical backgrounds. Nevertheless they have in common to think about Moodle tools according to their basic pedagogical uses. Indeed, they all point the heavy parameterizations of tools and resources and the need for having an abstract view of what are the pedagogical uses in order to help and guide them in selecting and configuring the right implementation activities.
Requirements for Our Language/editor From all these practitioners feedback we listed some specific requirements for our Moodle language/editor to develop. First, they mentioned the need for the graphical authoring-tool to allow designers to select pedagogical blocks on top of the LMS semantics as TurningRecurrentUsesofE-learningToolsintoReusablePedagogicalActivities-AMeta-modelingApproachAppliedto aMoodleCase-study well as with Moodle building blocks to compose with. In their mind, the editor will not have to strictly follow a top-down process from abstracted specification elements to implementation one expressed in terms of Moodle; abstractions from Moodle and its own concepts should be mixed up together according to practitioners' expertise about instructional design (specification and implementation concepts mix).
Activity Structures According to  (Gedera & Williams, 13) , successful implementation of an online course that is facilitated by an LMS needs careful planning, including structural strategies in the design of the course. In order to ease and assist the practitioners when assembling and setting-up combinations of activities or resources we propose then usual structural elements (selection, sequence, conditional activities, etc. ). These blocks will be composed of activities or other activity structures. Every instructional design language feature some of them. In the case of Moodle they will be concretely translated as complex combinations of labels (stating the structure name, kind and use for users), shifted content (move left/right feature) according to the activity structure components in the learning scenario.
A 4-levels Abstract Syntax The global architecture we propose for the abstract syntax of the Moodle-centered instructional design language is composed of four levels. Figure  1  illustrates our proposition with a graphical representation of the ecore domain model. Level 1 fits the Moodle metamodel. Readers have to consider Figure  1  as a part of the whole metamodel. Only important structural relations and concepts are depicted because of our current interest. Level 1 elements (restricted to the Moodle activities the Moodle name given to the tools -and resources) can be directly used by teachers-designers and parameterized for building a learning session. From the Moodle metamodel point of view these elements require a global Course and a Section container to be attached to. In the extended metamodel they will be specified at first as child of level 4 elements.