cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 2 of In vitro performance and in vivo fertility of antibiotic-free preserved boar semen stored at 5 °C
Creators: name: Jäkel, Helen
name: Scheinpflug, Kathi
name: Mühldorfer, Kristin
name: Gianluppi, Rafael
name: Lucca, Matheus Schardong
name: Mellagi, Ana Paula Gonçalves
name: Bortolozzo, Fernando Pandolfo
name: Waberski, Dagmar
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Physiology
subject: Sociology
subject: FOS: Sociology
subject: Cancer

description: Additional file 2: Table S2. Sublethal damage of sperm function in semen samples: Semen samples were extended in AndroStar® Premium and stored at 17 °C with antibiotics (17 °C w/AB; 0.25 g/L gentamicin sulphate) or at 5 °C without antibiotics (5 °C w/o AB). After 72 h of storage, sublethal damage of sperm function were determined under capacitating (Tyrode A) and non-capacitating (Tyrode C) conditions: Distribution of viable (Hoechst 33258 negative) spermatozoa (%; means ± SEM) with high (JC-1 aggregate positive) or low (JC-1 aggregate negative) mitochondria membrane potential and high (Calbryte 630 positive) or low (Calbryte 630 negative) intracellular calcium (n = 9 boars, experiment 1).
Cetopsis gobioides Kner 1858
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Siluriformes
Cetopsidae
Cetopsis
Cetopsis gobioides

description: Cetopsis gobioides Kner, 1858 Fig. 19 Body elongated; greatest depth contained 3.7 to 3.9, head depth 4.9 to 5.0 and caudal peduncle depth 8.4 to 9.6 times in SL; head length 4.1 to 4.4, anal-fin base length 3.6 to 3.8, maxillary-barbel length 11.1 to 11.4 in SL; snout length 3.1 to 3.5, horizontal orbital diameter 7.8 to 8.6 and least interorbital width 2.4 to 2.8 in HL. Mouth terminal; premaxilla and dentary with viliform teeth, maxilla with no teeth and vomer with one row of conical teeth. Dorsal fin with 7, pectoral fin with 10 or 11, pelvic fin with 10 and anal fin with 21-24 rays. Ground color darker dorsally, lighter ventrally; dorsum with few scattered dark-grey chromatophores. Hyaline fins (Graça, Pavanelli, 2007). Maximum standard length. 112.4 mm (Graça, Pavanelli, 2007). Distribution. Upper rio São Francisco, río Paraná and río Uruguay basins.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on page 65, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
ENVRI-FAIR D5.4: ENVRI Service Catalogue
Creators: name: Bailo, Daniele
name: Jeffery, Keith
Publisher: name: Zenodo
Year: 2023
Subjects: ENVRI-FAIR
deliverable
FAIR data
research infrastructures

description: The Deliverable "D5.4 ENVRI Service Catalogue" presents the development, implementation, and operation of a comprehensive service catalogue within the context of the ENVRI-FAIR project. The deliverable outlines the creation of a FAIR compliant and EOSC-ready catalogue, primarily focusing on services providing access to data. The innovative design and implementation of the catalogue embrace the adoption of rich metadata standards for ingestion and storage, namely EPOS-DCAT-AP metadata profile and the CERIF model, facilitating the description of diverse services across different research infrastructures (RIs). The validation processes, including service validation at the subdomain level, FAIRness evaluation, and an implementation phase, ensure the robustness, accuracy, and FAIR compliance of the catalogue, promoting its interoperability with the EOSC catalogue.

The deliverable further details the operation of the catalogue, which involves a harmonised effort among service providers, backend developers, and front-end developers. It underscores the ongoing endeavour to ingest more metadata records, provide support for metadata curation, and work towards semantic interoperability. Future work, as outlined in the deliverable, involves enhancing the catalogue's operation by improving metadata quality, enhancing semantic interoperability, and adapting to the diversity of service types from different RIs.

The ENVRI Service Catalogue represents a pivotal step towards advancing FAIR practices in environmental research. Its development, implementation, and operation symbolise an ongoing commitment to continuous improvement, adaptation, and learning, with the ultimate goal of propelling environmental research towards new horizons of discovery and innovation. By aligning with the EOSC catalogue requirements, it envisions a broader, more integrated network of scientific resources, thus empowering global researchers. The ENVRI Service Catalogue, as the embodiment of the ENVRI-FAIR project's vision, promises to facilitate open, FAIR, and efficient access to services and data in the environmental research domain.
Representation of gender, marriage, Punjabi diaspora and the homeland in Punjabi cinema
Creators: name: Kaur, Reetinder
Publisher: name: University of British Columbia
Year: 2023

description: This thesis examines the construction of gender, marriage, homeland, and diaspora in three transnational Punjabi films set in Indian Punjab, Canada and the United Kingdom. Three major themes emerge from the films under study: construction of masculinities and femininities; imagined and embodied homeland; and desires to ‘return’ to the homeland within diasporic communities. The discussion relevant to the broader themes of migration, marriage, homeland, and the diaspora are presented under each of these themes.
Clarias gariepinus
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Siluriformes
Clariidae
Clarias
Clarias gariepinus

description: Clarias gariepinus (Burchell, 1822) Fig. 19 Body elongated; greatest depth contained 5.5 to 9.3 and caudal peduncle depth 9.9 to 16.1 times in SL; head length 2.9 to 3.8, anal-fin base length 2.1 to 2.7, maxillary-barbel length 1.6 to 6.5 in SL; snout length 3.7 to 5.7, horizontal orbital diameter 7.6 to 19.2, least interorbital width 2.2 to 2.7 in HL. Mouth terminal with dentigerous tooth plates in both premaxilla, vomer and dentary. Dorsal fin with 61- 79, pectoral fin with I,9-12, pelvic fin with 6 and anal fin with 45-60 rays (Hanssens, 2009). Ground color grey to yellowish, abdominal region white. Maximum standard length. 700.0 mm. Biological data. Lives in lakes, rivers and seasonally swampy areas (Winemiller, Kelso-Winemiller, 1996). Feeds on plant material, plankton, arthropods, mollusks, fish, reptiles, and amphibians (Yalçin et al., 2001). Distribution. Africa and Asia Minor; introduced elsewhere (Eschmeyer et al., 2017). Remarks. Clarias gariepinus, native of Africa, has been captured in the upper rio Paraná floodplain since 2005 by Nupélia staff. Its occurrence in the region can be associated with fish-farming and escapes from recreational angling ponds.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on page 65, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Hanssens M. A review of the Clarias species (Pisces; Siluriformes) from the lower Congo and the Pool Malebo. J Afrotrop Zool. 2009; 5: 27 - 40.", "Winemiller KO, Kelso-Winemiller LC. Comparative ecology of catfishes of the upper Zambezi River floodplain. J Fish Biol. 1996; 49 (6): 1043 - 61.", "Yalcin S, Akyurt I, Solak K. Stomach contents of the catfish (Clarias gariepinus Burchell, 1822) in the River Asi (Turkey). Turk J Zool. 2001; 25: 461 - 68.", "Eschmeyer WN, Fricke R, van der Laan R, editors. Catalog of fishes: genera, species, references [Internet]. San Francisco: California Academy of Science; 2017 [updated 2017 Jan 31; cited 2017 Feb 24]. Available from: http: // researcharchive. calacademy. org / research / ichthyology / catalog / fishcatmain. asp"]}
A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
Creators: name: Veličković, Tijana
name: Snoj, Aleš
name: Simić, Vladica
name: Šanda, Radek
name: Vukić, Jasna
name: Barcytė, Dovilė
name: Stanković, David
name: Marić, Saša
Publisher: name: Brill Online
Year: 2023
Subjects: Evolutionary biology not elsewhere classified

description: To elucidate the historical biogeography of a species, the patterns of population divergence must be understood, and the evolutionary history of the species must be accurately known. For brown trout (Salmo trutta complex), estimating divergence times remains a challenge due to the lack of well-defined time calibration points and insufficient phylogeographic coverage in previous studies. The present work aims to improve molecular dating of mitochondrial control region sequences by using a multicalibration framework based on the latest paleogeological evidence for dating the origin of Lake Ohrid and two available Salmo fossils, including the overlooked Salmo immigratus. Our results clearly show that, contrary to common belief, the major divisions within the brown trout occurred in the Late Pliocene, not the Pleistocene. The Pliocene origin suggests that the brown trout lineages did not form because of geo(hydro)morphological changes during glaciation cycles but may be the result of orogeny and drainage evolution. In addition, increased sampling, particularly in Serbia, led to the identification of a new haplogroup (DA-INT) occupying an intermediate position with respect to DA-ES and DA-BS haplogroups. While the control region can delineate brown trout lineages, its phylogenetic resolution is limited, so even extensive sampling could not further resolve the lineage level polytomies.
ENVRI-FAIR D5.4: ENVRI Service Catalogue
Creators: name: Bailo, Daniele
name: Jeffery, Keith
Publisher: name: Zenodo
Year: 2023
Subjects: ENVRI-FAIR
deliverable
FAIR data
research infrastructures

description: The Deliverable "D5.4 ENVRI Service Catalogue" presents the development, implementation, and operation of a comprehensive service catalogue within the context of the ENVRI-FAIR project. The deliverable outlines the creation of a FAIR compliant and EOSC-ready catalogue, primarily focusing on services providing access to data. The innovative design and implementation of the catalogue embrace the adoption of rich metadata standards for ingestion and storage, namely EPOS-DCAT-AP metadata profile and the CERIF model, facilitating the description of diverse services across different research infrastructures (RIs). The validation processes, including service validation at the subdomain level, FAIRness evaluation, and an implementation phase, ensure the robustness, accuracy, and FAIR compliance of the catalogue, promoting its interoperability with the EOSC catalogue. The deliverable further details the operation of the catalogue, which involves a harmonised effort among service providers, backend developers, and front-end developers. It underscores the ongoing endeavour to ingest more metadata records, provide support for metadata curation, and work towards semantic interoperability. Future work, as outlined in the deliverable, involves enhancing the catalogue's operation by improving metadata quality, enhancing semantic interoperability, and adapting to the diversity of service types from different RIs. The ENVRI Service Catalogue represents a pivotal step towards advancing FAIR practices in environmental research. Its development, implementation, and operation symbolise an ongoing commitment to continuous improvement, adaptation, and learning, with the ultimate goal of propelling environmental research towards new horizons of discovery and innovation. By aligning with the EOSC catalogue requirements, it envisions a broader, more integrated network of scientific resources, thus empowering global researchers. The ENVRI Service Catalogue, as the embodiment of the ENVRI-FAIR project's vision, promises to facilitate open, FAIR, and efficient access to services and data in the environmental research domain.
D4.1.- Report on characterization of main processed materials
Creators: name: Santos, Fernando
name: Glasser, Björn
name: Niklas, Andrea
name: Surbhi Shivaji Jogdand
Publisher: name: Zenodo
Year: 2022
Subjects: High temperature steels
microestructure
grain size
Refractory stainless steels
hardening phases

description: This report contains the characterization resutls of different refaractory stainless steels develoved during the project HIPERMAT and that is used as the basis to understand the different behaviour of these alloys in relation to the mechanical properties in the working range of 800-950ºC.
Arpilleras of migration : an a/r/tography about female Latin American resilience
Creators: name: Rojas Farias, Mariela
Publisher: name: University of British Columbia
Year: 2023

description: This thesis is a metaphor for an Arpillera, since it assembles dialogues, poems and photographs collected during encounters between a pair of women who share similar and dissimilar life circumstances. The thesis addresses issues of gender inequality and how the empowering potential of the collaborative and socially engaged textile art of the arpilleras can be a tool to facilitate dialogic praxis within circles of women who have experienced and continue to experience oppressive situations. Through an a/r/tographic approach the thesis analyzes, discusses, and elaborates on elements derived from feminist theorists, critical pedagogy, and art education for social justice primarily. The concept of living inquiry informed by the methodological approach of a/r/tography is relevant and enlightening in the research since it holds the whole theory, collaborative artmaking, and writing–poetic or theoretical–into a unique and personal experience that generates knowledge about feminine migration, single parenthood, and Latin-American ways of being. The results show the transformative power of the arts. In the same way, sisterhood, collaboration, partnership, and reciprocity as key principles of Indigenous Knowledge are present along the whole text. Arpilleras- dialogue-transformation-socially engaged arts.
Ossancora eigenmanni
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Siluriformes
Doradidae
Ossancora
Ossancora eigenmanni

description: Ossancora eigenmanni (Boulenger, 1895) Fig. 20 Body deep; greatest body depth contained 2.8 to 3.8, head length 3.4 to 4.0 times in SL; snout length contained 1.9 to 2.1, horizontal orbital diameter 2.6 to 4.9 and least interorbital width 2.6 to 3.1 times in HL; orbital diameter contained 1.3 to 1.7 times in interorbital width. Mouth terminal; with dentigerous plates in both premaxilla and dentary. Lateral line with 27-30 plates. Dorsal fin with I,6 rays, pectoral fin with I,6-7 rays, pelvic fin with 7 rays and anal fin with 12-15 rays. Ground color brownish; dark-brown spots of varied sizes irregularly distributed. Fins light-brown with dark-brown spots. Maximum standard length. 125.0 mm. Distribution. Upper río Paraguay and rio Paraná basins. Remarks. Ossancora eigenmanni was identified as Oxydoras eigenmanni by Graça, Pavanelli (2007). Birindelli, Sabaj-Pérez (2011), in the description of the new genus, Ossancora, proposed the new combination. Ossancora eigenmanni is a non-native species from the upper rio Paraná, and its occurrence can be associated with the filling of the Itaipu Reservoir and the consequent inundation of the Sete Quedas Falls.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on page 65, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
Economic value of knowing BRCA status: BRCA testing for prostate cancer prevention and optimal treatment
Creators: name: Oh, Mok
name: McBride, Ali
name: Bhattacharjee, Sandipan
name: Slack, Marion
name: Jeter, Joanne
name: Abraham, Ivo
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: Hematology

description: We aimed to estimate the incremental lifetime effects, costs, and net-monetary-benefit (NMB) of knowing BRCA information by testing of patients with low-risk localized prostate cancer (PCa) in the US and guiding subsequent screening and treatment, and the cumulative savings or losses of yearly cohort testing over 16 years. We compared two strategies: (1)‘with BRCA information’ and (2)‘without BRCA information.’ We also estimated the expected value of perfect information. The incremental NMB (INMB) quantified the monetized benefit per person of knowing BRCA status. The net-monetized-value of knowing BRCA information was estimated by multiplying the INMB with the eligible population. The INMBs of knowing BRCA information were $43,357 (payer) and $43,487 (society). in payer and societal perspectives, respectively. Escalated to the eligible patients in 2020, knowing BRCA status resulted in net monetized lifetime value of $1.7 billion (payer and society) for the 2020 cohort; and yielded accumulated net-monetized-value of $28.0 billion (payer) and $28.1 billion (society) over 16 yearly cohorts of eligible PCa patients. The economic value of knowing BRCA status for all low-risk localized PCa patients in the US provides short-term and long-term evidence for BRCA testing to screen early and optimize treatment.
MPEC 2023-X248 : 2016 AH165
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2023
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
Platydoras armatulus
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Siluriformes
Doradidae
Platydoras
Platydoras armatulus

description: Platydoras armatulus (Valenciennes, 1840) Fig. 20 Body deep; greatest body depth contained 3.2 to 3.9, head length 3.8 to 4.0 times in SL; snout length contained 2.2 to 2.3, horizontal orbital diameter 4.8 to 5.5 and least interorbital width 2.5 to 2.7 times in HL; orbital diameter contained 1.8 to 2.1 times in interorbital width. Mouth terminal; with dentigerous plates in both premaxilla and dentary. Lateral line with 27-28 plates. Dorsal fin with I,6, pectoral fin with I,7, pelvic fin with 7 and anal fin with 10-12 rays (Graça, Pavanelli, 2007). Ground color darkbrown above pelvic-fin orign, whitish to yellowish below; yellowish longitudinal band, from dorsal region of head to distal margin of median caudal-fin rays. Dorsal, pelvic, anal and caudal fins hyaline or light-beige; dorsal fin with dark-brown blotch on distal margin; pectoral fin darkbrown, its spine light-beige; caudal fin with one dark-brown longitudinal band on each lobe. Maximum standard length. 178.0 mm (Graça, Pavanelli, 2007). Distribution. Paraná-Paraguay system. Remarks. Platydoras armatulus is a non-native species from the upper rio Paraná, and its occurrence can be associated with the filling of the Itaipu Reservoir and the consequent inundation of the Sete Quedas Falls.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on pages 65-66, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
MOESM1 of External quality assessment (EQA) program for the immunohistochemical detection of ER, PR and Ki-67 in breast cancer: results of an interlaboratory reproducibility ring study in China
Creators: name: Pu, Tianjie
name: Shui, Ruohong
name: Shi, Jie
name: Liang, Zhiyong
name: Yang, Wentao
name: Bu, Hong
name: Li, Qin
name: Zhang, Zhang
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Neuroscience
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Plant Biology
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Standardized IHC staining procedures of RCs. Figure S1. Observed agreement between 3 RCs and the reference value. Three RCs, the Department of Pathology, West China Hospital, Sichuan University, the Department of Pathology of Peking Union Medical College Hospital and the Shanghai Cancer Center of Fudan University, stained the slides by standardized procedures using three kinds of antibodies. As all RCs obtained the same results, the proportions of tumour nuclei positive for ER-1, ER-2 and ER-3 were 11–50%, > 50 and 0%, respectively. For the PR tests, the reference values were > 50% for PR-1, 1–10% for PR-2 and 0% for PR-3. For the Ki-67 tests, the reference values were > 30% for KI-1, KI-2 and KI-5; 10–30% for KI-3; and < 10% for KI-4. RCs: revising centres
Additional file 12 of An “expressionistic” look at serrated precancerous colorectal lesions
Creators: name: Marra, Giancarlo
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 12: Supplementary Figure 12. In situ hybridization analysis of APOBEC1 in serrated precursor lesions, cADNs and normal colorectal mucosa. APOBEC1 was expressed in all the lesion types investigated, especially in the upper portions of glands, and also in the superficial epithelium of the normal mucosa (H) (Table 1). However, the expression was higher in SSLs, where it was absent only at the bases of serrated glands (A and B), and in HPs, where high expression was more confined to the surface of the lesions (Table 1). In TSAs and cADNs, moderate expression of APOBEC1 was seen in glands with more evident goblet-cell differentiation (C-G).
Additional file 1 of Quality analysis of discharge instruction among 602 hospitalized patients in China: a multicenter, cross-sectional study
Creators: name: Yang, Miao-miao
name: Liang, Wei
name: Zhao, Hui Hua
name: Zhang, Ying
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 1. Demographic questionnaire.
Deliverable 1.1 Project Management Plan
Creators: name: Spella, Magda
Publisher: name: Zenodo
Year: 2023

description: The GRAPHEGIA project was launched on the 1st of October, 2023, for 3,5 years, and it is a research and innovation project co-funded by the European Union.  Deliverable 1.1 Project Management Plan was created by the project coordinator, Foundation For Research and Technology Hellas (FORTH), under work package 1," Scientific Coordination and Project Management". 
Abstract
This document is the deliverable "D1.1 – Project Management Plan" of the European project "GRAPHERGIA – Innovative pilot lines for sustainable graphene-based flexible and structural energy harvesting and storage devices" (Grant Agreement number 101120832). It is a management guide laying down standard workflows and processes for the management activities of GRAPHERGIA project. It will provide guidance and recommendations regarding the organisational structure, the work structure, the quality assurance workflow, the internal communication, the reporting procedure, and the risk assessment mechanisms of the project. The Project Management Plan will foster active collaboration and the smooth implementation of the project.
Pterodoras granulosus
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Siluriformes
Doradidae
Pterodoras
Pterodoras granulosus

description: Pterodoras granulosus (Valenciennes, 1821) Fig. 20 Body deep; greatest body depth contained 2.9 to 4.4, head length 3.4 to 4.4 times in SL; snout length contained 2.2 to 2.3, horizontal orbital diameter 8.3 to 11.8 and least interorbital width 2.5 to 3.1 times in HL; orbital diameter contained 3.1 to 4.3 times in interorbital width. Mouth terminal; with dentigerous plates in both premaxilla and dentary. Lateral line with 27-28 plates. Dorsal fin with I,6, pectoral fin with I,8- 10, pelvic fin with 7 and anal fin with 12 or 13 rays. Ground color pale brown to greyish, darker dorsally, lighter ventrally; dark-brown or grey chromatophores irregularly distributed on body. Dark-brown or yellowish fins (Graça, Pavanelli, 2007). Maximum standard length. 635.0 mm (Graça, Pavanelli, 2007). Distribution. Amazon, río Paraná and coastal drainages of Guyana, Surinam and French Guiana. Remarks. Pterodoras granulosus is a non-native species from the upper rio Paraná, and its occurrence can be associated with the filling of the Itaipu Reservoir and the consequent inundation of the Sete Quedas Falls.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on page 66, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
Additional file 13 of An “expressionistic” look at serrated precancerous colorectal lesions
Creators: name: Marra, Giancarlo
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 13: Supplementary Figure 13. In situ hybridization analysis of MUC5AC in serrated precursor lesions, cADNs and normal colorectal mucosa. MUC5AC expression, like that of APOBEC1, is not specific to serrated lesions. Very high levels were found in the mucous cells of all the lesions we tested, but not in those of the normal mucosa (H) (excluding rare positive cells in its surface; not shown). Very high MUC5AC expression was more extensive in SSLs and HPs (i.e., along the entire length of serrated crypts with lower levels only at their bases) (A-C), while patchier expression was observed in cADNs (D and E) and TSAs (F and G) (Table 1). MUC5AC therefore represents a marker of neoplastic goblet cells (e.g., panel E) but not of their normal mucosal counterparts (panel H).
The economic value of knowing BRCA status: universal BRCA testing for breast cancer prevention
Creators: name: Oh, Mok
name: McBride, Ali
name: Bhattacharjee, Sandipan
name: Slack, Marion
name: Jeter, Joanne
name: Abraham, Ivo
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy

description: This study aimed to estimate the incremental lifetime effects, costs, and net monetary benefit (NMB) of knowing BRCA information by universal genetic testing of all US women without breast cancer turning 40 in a given year, and the cumulative savings or losses of yearly cohort testing over 16 years. We compared two strategies: (1) ‘with BRCA information’ and (2) ‘without BRCA information.’ Incremental NMB (INMB) was calculated as the monetized benefit per person of knowing BRCA status. The net monetized value (cumulated INMB) of knowing BRCA information was estimated by multiplying the INMB with the eligible population or the year 2020 cohort of US women age 40 and extended for a total of 16 yearly cohorts. Universal testing of the female population at the age of 40 in a given year provided aan INMB of $663/person (payer) and $1,006/person (society).Escalated to the U.S. population of women age 40 , knowing BRCA status resulted in lifetime cumulated INMB of $1.3 billion (payer) and $2.0 billion (society) for the 2020 cohort; and yielded accumulated monetized value of $18.3 billion (payer) and $27.6 billion (society) over 16 yearly cohorts of 40-year-old women. The universal testing for BRCA status of all US women at age 40 provides compelling short-term and long-term economic value.
Additional file 14 of An “expressionistic” look at serrated precancerous colorectal lesions
Creators: name: Marra, Giancarlo
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 14: Supplementary Figure 14. In situ hybridization analysis of NKD1 in serrated precursor lesions, cADNs and normal colorectal mucosa. NKD1 is expressed only in a few cells within the stem-cell compartment at the bottom of serrated crypts in SSLs (A) and HPs (B) and at the bases of normal mucosal crypts (I). In cADNs, it is very highly and extensively expressed, with patchy variation of intensity (C and D), and similarly high expression was also observed in one of the TSAs (E and F). Its expression is much more limited in the other two TSAs (G and H, and Table 1). NKD1 is also expressed in some stromal cells and quite extensively in the muscularis mucosae (I).
Budget impact analysis of the freestyle libre flash continuous glucose monitoring system® in patients with diabetes mellitus type 1 in Chile
Creators: name: Palacios, Alfredo
name: Cairoli, Federico Rodriguez
name: Balan, Dario
name: Balmaceda, Carlos
name: Augustovski, Federico
name: Pichon-Riviere, Andres
name: Bardach, Ariel
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: To estimate the budget impact of covering the FreeStyle Libre Flash Continuous Glucose Monitoring System (FSL) for type 1 Diabetes Mellitus patients (T1DM), compared to self-monitoring of blood glucose (SMBG), from the perspective of public and private third-party payers in Chile. A budget impact model was developed to estimate the cost difference between SMBG and FSL over five years. Two FSL coverage schemes were assessed. Input parameters were retrieved from the literature review and complemented by expert opinion. Healthcare costs were estimated by a micro-costing approach and reported in USD. For a public sector third-party payer, incorporating FSL implied a cost increase up to USD 0.013 per member per month (PMPM) for the fifth year under the broad coverage scheme and a net saving of 0.0001 PMPM (all years) under the restricted coverage scheme. From a private sector third-party payer, incorporating FSL implied savings up to USD 0.028 PMPM (fifth year) for the broad coverage scheme and up to USD 0.012 PMPM (fifth year) for the restricted scheme. Incorporating the FSL for T1DM patients was associated with a marginal incremental cost for the public sector third-party payer and cost savings in Chile’s private healthcare sector.
Additional file 10 of An “expressionistic” look at serrated precancerous colorectal lesions
Creators: name: Marra, Giancarlo
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 10: Supplementary Figure 10. In situ hybridization analysis of ZIC5 and ZIC2 in serrated precursor lesions, cADNs and normal colorectal mucosa. ZIC5 and ZIC2 are neighboring transcription factor-encoding genes with similar expression profiles in the colorectal tissues investigated (Supplementary Figure 2G). They are consistently expressed at low levels at the bases of serrated crypts in SSLs and HPs (A, B, and F) (Table 1). Neither gene is expressed in cADNs (D), the normal mucosa (E), or TSAs (C) with the exception of a few SSL-like glands in the latter lesions (Table 1). The brown (instead of red) punctate labeling in panel F reflects the use of a different chromogen from that used in other hybridizations.
The economic value of knowing BRCA status: BRCA testing for optimizing treatment in recurrent epithelial ovarian cancer
Creators: name: Oh, Mok
name: McBride, Ali
name: Bhattacharjee, Sandipan
name: Slack, Marion
name: Jeter, Joanne
name: Abraham, Ivo
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy

description: This study aimed to estimate the incremental lifetime effects, costs, and net monetary benefit (NMB) of knowing BRCA information for recurrent ovarian cancer (ROC) patients in a given year and the cumulative savings of yearly hypothetical cohort testing over 16 years. We compared two strategies: (1) ‘with BRCA information’ and (2) ‘without BRCA information.’ Incremental NMB (INMB) was calculated as the average net monetized benefit of knowing BRCA status. The net monetized value (cumulative INMB) of knowing BRCA information was estimated by multiplying the INMB with the eligible ROC patients in year 2020 and extended for potential ROC patients over 16 yearly hypothetical cohorts of ROC patients Knowing BRCA information for ROC patients provided an additional monetized value of $3,528 in (payer) and $3,194 (society). Escalated to all ROC patients in the U.S. and future incidence ROC estimates, knowing BRCA information resulted in a lifetime cumulative INMB of $35.6 million (payer) and $32.2 million (society) for the 2020 cohort; and yielded an accumulated value of $97.3 million (payer) and $88.0 million (society) over 16 yearly hypothetical cohorts of ROC patients The economic value of knowing BRCA status of all U.S. ROC patients provides short-term and long-term evidence for optimizing treatment
ENVRI-FAIR D5.5: Guidelines for validation of ENVRI-FAIR services
Creators: name: Bailo, Daniele
name: Tarabusi, Gabriele
name: Jeffery, Keith
name: Adamaki, Angeliki
name: Thijsse, Peter
Publisher: name: Zenodo
Year: 2022
Subjects: ENVRI-FAIR
deliverable
service validation
quality of services
functionality of services
data services
EOSC catalogue of services

description: D5.5 “Guidelines for validation of ENVRI-FAIR services” formulates the criteria and test plan for validating the overall quality of the ENVRI-FAIR services and summarises the guidelines for testing and validating the functionality of the services developed in WP8-WP11 in synergy with WP7. The criteria will allow the developers of the ENVRI data services to validate the results towards the EOSC catalogue of services.
Additional file 11 of An “expressionistic” look at serrated precancerous colorectal lesions
Creators: name: Marra, Giancarlo
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 11: Supplementary Figure 11. In situ hybridization analysis of FOXD1 in serrated precursor lesions, cADNs and normal colorectal mucosa. FOXD1 is another marker of SSLs and HPs, where it is lowly expressed along the entire length of the serrated crypts (A-C). Limited areas of positivity were observed in 2 of the 3 TSAs (D and E) (Table 1), but no expression was found in cADNs (F and G) or in normal mucosa (H).
Deep learning framework for classification of neuroendocrine neoplasm whole slide images
Creators: name: Hadjifaradji, Amir
Publisher: name: University of British Columbia
Year: 2023

description: Neuroendocrine neoplasms (NENs) are uncommon neoplasms, which can arise in cells across the body. The last few decades have seen NEN incidence increase by 7-fold. NEN grades are morphologically indistinguishable for well-differentiated tumours and are determined from the tumour proliferation. Cell proliferation is defined by the number of mitotic figures in a 2mm² area for H&E slides and by the percent of Ki-67 positive cells in Ki-67 slides. Unfortunately, these measures suffer inter- and intra-observer variability, and are cumbersome to quantify. We developed a novel machine learning framework to identify candidate mitotic figures in H&E images, calculate the Ki-67 index in Ki-67 images, and aggregate proliferating features to grade NENs. Our work included 186 gastroenteropancreatic NENs with 385 samples from across British Columbia with two different stains (247 H&E and 138 Ki-67 images) and patient-level labels for grade. The H&E portion of the framework achieved a balanced accuracy of 72.1% across 6-folds for three-class classification (G1, G2, G3). We demonstrated that the survival outcomes for computer assigned grades are comparable to those based on pathologist assessment, with c-index values of 0.63 and 0.64, respectively. Our Ki-67 algorithm achieves a balanced accuracy of 83.9% to predict the grade of Ki-67 slides. With Ki-67 added to our pipeline, grading improves the balanced accuracy to 78.5%. Analysis of the survival outcome for pathologist assessed G1s demonstrated significant (p-value=0.01) separation amongst samples the algorithm assigned to a higher grade (n=27; median survival 4.63 years) compared to concordant G1 samples (n=55; median survival 10.13 years). By identifying both mitotic figures and Ki-67 positive cells, our method may provide a tool to verify hot-spots in both H&E and Ki-67 slides for further analysis of grades. Misclassified G1 patients have lower median survival, and further analysis is needed to determine if this group should be considered a different clinical entity and if our machine learning approach has identified two distinct populations within the grade 1 group.
Rhinodoras dorbignyi
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Siluriformes
Doradidae
Rhinodoras
Rhinodoras dorbignyi

description: Rhinodoras dorbignyi (Kner, 1855) Fig. 20 Body deep; greatest body depth contained 3.5 to 4.5, head length 3.1 to 3.6 times in SL; snout length contained 1.9 to 2.2, horizontal orbital diameter 6.5 to 9.8 and least interorbital width 4.7 to 6.2 times in HL; orbital diameter contained 1.2 to 1.8 times in interorbital width. Mouth subterminal; with dentigerous plates in both premaxilla and dentary. Lateral line with 27-28 plates. Dorsal fin with I,6, pectoral fin with I,8-10, pelvic fin with 7 and anal fin with 8 or 9 rays. Ground color yellowish; dark-brown irregular blotches on body. Hyaline or light-beige fins with darkbrown blotches and spots (Graça, Pavanelli, 2007). Maximum standard length. 172.0 mm (Graça, Pavanelli, 2007). Distribution. Paraná-Paraguay system.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on page 67, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
Additional file 16 of An “expressionistic” look at serrated precancerous colorectal lesions
Creators: name: Marra, Giancarlo
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 16: Supplementary Figure 16. In situ hybridization analysis of HOXB13 in serrated precursor lesions, cADNs and normal colorectal mucosa. HOXB13 was generally more highly expressed than HOXD13 in colorectal tissues (Table 1; see also Supplementary Figures 2 and 3), but, similarly to HOXD13, it is a typical marker of the normal mucosal of the distal colon and rectum (H). In the normal mucosa of the proximal colon, expression was low or absent (G). Moderate-to-high HOXB13 expression was found in SSLs (A), HPs (B), TSAs (E and F), and cADNs (C and D), but in all four lesion types, more abundant expression was found in tumors taken from the distal colon and rectum (Table 1).
Additional file 15 of An “expressionistic” look at serrated precancerous colorectal lesions
Creators: name: Marra, Giancarlo
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 15: Supplementary Figure 15. In situ hybridization analysis of HOXD13 in serrated precursor lesions, cADNs and normal colorectal mucosa. In proximal-colon SSLs, HOXD13 is expressed only in a few cells at crypt bases (A) (Table 1). The two distal-colon HPs (especially HP 3, which arose in the rectum) displayed moderate expression at the crypt bases (C). Patchy, low-to-moderate HOXD13 expression was also present in cADNs and TSAs (B and D), and only a few sporadic positive crypts were noted in the normal mucosa of the proximal colon (E and F). In contrast, it was expressed in the normal mucosa of the distal colon and rectum at moderate levels, although patches of negative crypts were also seen (G and H).
Additional file 1 of Fruit and vegetable consumption is associated with lower prevalence of asymptomatic diverticulosis: a cross-sectional colonoscopy-based study
Creators: name: Maxner, Benjamin
name: McGoldrick, Jessica
name: Bellavance, Danielle
name: Liu, Po-Hong
name: Xavier, Ramnik J.
name: Yarze, Joseph C.
name: Ricciardi, Rocco
name: Staller, Kyle
name: Chung, Daniel C.
name: Khalili, Hamed
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Virology

description: Additional file 1: Supplementary Table 1. Brief dietary questionnaire. Dietary assessment instrument administered to each participant to evaluate nutritional intake.
title: Hyperspectral Imaging for Assessment of Initial Graft Function in Human Kidney Transplantation
Creators: name: Romann, Sophie
name: Wagner, Tristan
name: Katou, Shadi
name: Reuter, Stefan Johannes
name: Vogel, Thomas
name: Becker, Felix
name: Morgul, M. Haluk
name: Houben, Philipp
name: Wahl, Philip
name: Pascher, Andreas
name: Radunz, Sonia
Publisher: name: University of Muenster, Institutional Repository MIAMI
Year: 2023
Subjects: subject: 610 Medicine and health

description: The aim of our study was to evaluate hyperspectral imaging (HSI) as a rapid, non-ionizing technique for the assessment of organ quality and the prediction of delayed graft function (DGF) in kidney transplantation after static cold storage (SCS, n = 20), as well as hypothermic machine perfusion (HMP, n = 18). HSI assessment of the kidney parenchyma was performed during organ preservation and at 10 and 30 min after reperfusion using the TIVITA® Tissue System (Diaspective Vision GmbH, Am Salzhaff, Germany), calculating oxygen saturation (StO2), near-infrared perfusion index (NIR), tissue haemoglobin index (THI), and tissue water index (TWI). Recipient and donor characteristics were comparable between organ preservation groups. Cold ischemic time was significantly longer in the HMP group (14.1 h [3.6–23.1] vs. 8.7h [2.2–17.0], p = 0.002). The overall presence of DGF was comparable between groups (HMP group n = 10 (55.6%), SCS group n = 10 (50.0%)). Prediction of DGF was possible in SCS and HMP kidneys; StO2 at 10 (50.00 [17.75–76.25] vs. 63.17 [27.00–77.75]%, p = 0.0467) and 30 min (57.63 [18.25–78.25] vs. 65.38 [21.25–83.33]%, p = 0.0323) after reperfusion, as well as NIR at 10 (41.75 [1.0–58.00] vs. 48.63 [12.25–69.50], p = 0.0137) and 30 min (49.63 [8.50–66.75] vs. 55.80 [14.75–73.25], p = 0.0261) after reperfusion were significantly lower in DGF kidneys, independent of the organ preservation method. In conclusion, HSI is a reliable method for intraoperative assessment of renal microperfusion, applicable after organ preservation through SCS and HMP, and predicts the development of DGF.
description: Finanziert durch den Open-Access-Publikationsfonds der Westfälischen Wilhelms-Universität Münster (WWU Münster).
Additional file 7 of Gut microbiota is associated with the effect of photoperiod on seasonal breeding in male Brandt’s voles (Lasiopodomys brandtii)
Creators: name: Zhu, Hanyi
name: Li, Guoliang
name: Liu, Jing
name: Xu, Xiaoming
name: Zhang, Zhibin
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 7: Table S2. Spearman correlations between ASVs and serum hormones levels in the photoperiod experiment.