scholarly journals Photo images, 3D models and CT scanned data of loaches (Botiidae, Cobitidae and Nemacheilidae) of Japan

2018 ◽  
Vol 6 ◽  
pp. e26265 ◽  
Author(s):  
Yuichi Kano ◽  
Jun Nakajima ◽  
Takeshi Yamasaki ◽  
Jyun-ichi Kitamura ◽  
Ryoichi Tabata

Loach is one of the major cypriniform fishes in freshwater habitats of Japan; 35 taxa/clades have, until now, been recognised. Parallel to genetic studies, morphological examinations are needed for further development of loach study, eventually ichthyology and fish biology. Digital archiving, concerning taxonomy, ecology, ethology etc., is one of the progressive challenges for the open science of biology. This paper aimed to online publish photo images, 3D models and CT scanned data of all the known clades of loaches inhabiting Japan (103 individuals in total with several type specimens), contributing to ichthyology and public interest of biodiversity/biology.Photo images, 3D models and CT scanned data of all the known 35 taxa/clades of loaches inhabiting in Japan were online published at http://ffish.asia/loachesOfJapan and http://ffish.asia/loachesOfJapan3D.

2019 ◽  
pp. 112-141
Author(s):  
Paola Casu ◽  
Claudia Pisu

The digital archiving process of complex historical architectural 3D models is a key point in the field of tangible cultural heritage. A lot of research focus on the definition of methodologies and tools that exploit the full potential of ICT applied to the documentation of cultural heritage. This chapter illustrates a part of a study in this line of investigation. It focuses on the use of BIM for the reconstruction of lost architectural heritage. BIM will be applied to virtual reconstruct the nineteenth-century covered food market of Cagliari that was demolished in 1957. Thanks to the properties of BIM to enter information related to each element constituting a building, every part of the model will be accompanied by information on the degree of reliability and references adopted for its creation. In this way, each family of elements could more easily and knowingly be reused for other similar projects.


Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1108
Author(s):  
Patrick S. Osmer ◽  
Gatikrushna Singh ◽  
Kathleen Boris-Lawrie

Tertiary structure (3D) is the physical context of RNA regulatory activity. Retroviruses are RNA viruses that replicate through the proviral DNA intermediate transcribed by hosts. Proviral transcripts form inhomogeneous populations due to variable structural ensembles of overlapping regulatory RNA motifs in the 5′-untranslated region (UTR), which drive RNAs to be spliced or translated, and/or dimerized and packaged into virions. Genetic studies and structural techniques have provided fundamental input constraints to begin predicting HIV 3D conformations in silico. Using SimRNA and sets of experimentally-determined input constraints of HIVNL4-3 trans-activation responsive sequence (TAR) and pairings of unique-5′ (U5) with dimerization (DIS) or AUG motifs, we calculated a series of 3D models that differ in proximity of 5′-Cap and the junction of TAR and PolyA helices; configuration of primer binding site (PBS)-segment; and two host cofactors binding sites. Input constraints on U5-AUG pairings were most compatible with intramolecular folding of 5′-UTR motifs in energetic minima. Introducing theoretical constraints predicted metastable PolyA region drives orientation of 5′-Cap with TAR, U5 and PBS-segment helices. SimRNA and the workflow developed herein provides viable options to predict 3D conformations of inhomogeneous populations of large RNAs that have been intractable to conventional ensemble methods.


Open Medicine ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. 720-724 ◽  
Author(s):  
Emilia Mikołajewska ◽  
Dariusz Mikołajewski

AbstractNervous system disorders are among the most severe disorders. Significant breakthroughs in contemporary clinical practice may provide brain-computer interfaces (BCIs) and neuroprostheses (NPs). The aim of this article is to investigate the extent to which the ethical considerations in the clinical application of brain-computer interfaces and associated threats are being identified. Ethical considerations and implications may significantly influence further development of BCIs and NPs. Moreover, there is significant public interest in supervising this development. Awareness of BCIs’ and NPs’ threats and limitations allow for wise planning and management in further clinical practice, especially in the area of long-term neurorehabilitation and care.


PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4247 ◽  
Author(s):  
Matteo Belvedere ◽  
Matthew R. Bennett ◽  
Daniel Marty ◽  
Marcin Budka ◽  
Sally C. Reynolds ◽  
...  

Vertebrate tracks are subject to a wide distribution of morphological types. A single trackmaker may be associated with a range of tracks reflecting individual pedal anatomy and behavioural kinematics mediated through substrate properties which may vary both in space and time. Accordingly, the same trackmaker can leave substantially different morphotypes something which must be considered in creating ichnotaxa. In modern practice this is often captured by the collection of a series of 3D track models. We introduce two concepts to help integrate these 3D models into ichnological analysis procedures. The mediotype is based on the idea of using statistically-generated three-dimensional track models (median or mean) of the type specimens to create a composite track to support formal recognition of a ichno type. A representative track (mean and/or median) is created from a set of individual reference tracks or from multiple examples from one or more trackways. In contrast, stat-tracks refer to other digitally generated tracks which may explore variance. For example, they are useful in: understanding the preservation variability of a given track sample; identifying characteristics or unusual track features; or simply as a quantitative comparison tool. Both concepts assist in making ichnotaxonomical interpretations and we argue that they should become part of the standard procedure when instituting new ichnotaxa. As three-dimensional models start to become a standard in publications on vertebrate ichnology, the mediotype and stat-track concepts have the potential to help guiding a revolution in the study of vertebrate ichnology and ichnotaxonomy.


Author(s):  
Toluwase Asubiaro

This study investigated if there is a difference in the number of articles, datasets and computer codes that foreign and Nigerian authors of scientific publications on natural language processing (NLP) of Nigerian languages deposited in digital archives. Relevant articles were systematically retrieved from Google, Web of Science and Scopus. Authorship type and data archiving information was extracted from the full text of the relevant publications. Result shows that papers with foreign authorship (80.4%) published their articles in non-commercial repositories, more than papers with Nigerian authorship (55.3%). Similarly, few papers with foreign authorship deposited research data (19.1%) and computer codes (10.4%), while none of the papers with Nigerian authorship did. It was recommended that librarians in Nigeria should create awareness on the benefits of digital archiving and open science. Cette étude a eximané les différences dans le nombre d'articles, d'ensembles de données et de codes informatiques dans les articles scientifiques sur le traitement du langage naturel que les auteurs nigériens et les auteurs étrangers ont soumis dans les dépôts d'autoarchivage. Les articles pertinents ont été systématiquement extraits de Google, Web of Science et Scopus. Les informations relatives au type d'auteur et à l'archivage des données ont été extraites du texte intégral des publications pertinentes. Les résultats montrent que les articles écrits par des auteurs étrangers ont davantage publié leurs articles dans des dépôts non commerciaux (80,4%) que les auteurs nigériens (55,3%). Peu d'auteurs étrangers ont déposé des données de recherche (19,1%) et des codes informatiques (10,4%) tandis qu'aucun auteur nigérien ne l'a fait. Ces résultats démontrent l'importance de la sensibilisation aux avantages des dépôt d'archivage et de la science ouverte pour les bibliothécaires nigériens.


2021 ◽  
pp. 1-31
Author(s):  
Lutz Bornmann ◽  
Raf Guns ◽  
Michael Thelwall ◽  
Dietmar Wolfram

Open Science is an umbrella term that encompasses many recommendations for possible changes in research practices, management, and publishing with the objective to increase transparency and accessibility. This has become an important science policy issue that all disciplines should consider. Many Open Science recommendations may be valuable for the further development of research and publishing but not all are relevant to all fields. This opinion paper considers the aspects of Open Science that are most relevant for scientometricians, discussing how they can be usefully applied.


2021 ◽  
Vol 7 ◽  
Author(s):  
Natalie Evans ◽  
Marc van Hoof ◽  
Laura Hartman ◽  
Ana Marusic ◽  
Bert Gordijn ◽  
...  

Background: The areas of Research Ethics and Research Integrity (RE+RI) are rapidly evolving. In the EU and internationally, new legislation, codes of conduct and good practices are constantly being developed. New technologies (e.g. gene editing), complex statistical methods (e.g. biostatistics), pressure to publish and obtain grants, and growing emphasis on stakeholder driven science (e.g. public-private partnerships) increase the complexity of conducting science. In this complex and dynamic environment, researchers cannot easily identify the correct rules and best tools for responsible conduct of research. This also increasingly constitutes a challenge for RE+RI experts. Aim: Our aim is to create a platform that makes the normative framework governing RE+RI easily accessible, supports application in research and evaluation, and involves all stakeholders in a participatory way, thus achieving sustainability. The platform will foster uptake of ethical standards and responsible conduct of research, and ultimately support research excellence and strengthen society’s confidence in research and its findings. Vision: Our vision is that in order to make the normative framework governing RE+RI accessible, a dynamic online Wiki-platform, owned by the community of RE+RI stakeholders, is needed. The value of this platform will lie in the availability of practical information on how to comply with EU, national and discipline-specific RE+RI standards and legislation, including information on rules and procedures, educational materials, and illustrative cases and scenarios. Adopting open science (open source and open data) approaches, the platform will be easy to use, by applying novel techniques for data collection and comparison, enabling users to navigate quickly and intuitively to appropriate content. In order to keep the platform up-to-date and sustainable, it will be based upon active involvement of the RE+RI community, and will contribute to further development of this community by providing a podium for reflection and dialogue on RE+RI norms and practices. Objectives: EnTIRE’s work packages (WP) will: undertake an in-depth stakeholder consultation across EU countries exploring RE+RI experiences and practices in order to define the boundaries of data to be collected, and developing a mapping structure adapted to user needs (WP 2); assemble the relevant normative elements, including RE+RI rules and procedures, educational materials, and illustrative casuistry, and identify relevant institutions across EU countries (WP 3-5); develop a user-friendly Wiki-platform and online resources to foster and facilitate responsible research practices and to promote compliance amongst European researchers with RE+RI standards and pertinent legislation and regulations (WP 6); and foster further development of the RE+RI community, that will support the platform and be supported by it, will keep the information up-to-date, disseminate the project’s findings and develop innovative strategies for maintaining the platform and building relationships to relevant organisations for further dissemination, including sustainable funding (WP 7). Relevance to the work programme: The proposed project responds directly to the core requirement of call SwafS-16-2016 to ‘provide a dynamic mapping of the RE+RI normative framework which applies to scientific research conducted in the EU and beyond’. Our proposal does this by using a participatory approach, stimulating knowledge transfer regarding codes and regulations, resources and institutions, and cases, by applying innovative ICT solutions and open science approaches, and by further developing a community of active users, to enable sustainability after the end of the project.


Zootaxa ◽  
2012 ◽  
Vol 3360 (1) ◽  
pp. 1 ◽  
Author(s):  
HOSSEIN RAJAEI SH. ◽  
DIETER STÜNING ◽  
ROBERT TRUSCH

The genus Gnopharmia Staudinger, 1892 is revised, based on more than 2000 specimens from the entire area ofdistribution and study of type material of all described taxa, as far asmap available. Seven species and three subspeciesare confirmed as valid for the genus. All important morphological characters have been studied and compared, includingmale and female genitalia. In addition, preliminary results of DNA-Barcoding were used to reassess our taxonomicdecisions, based on morphological studies. Type specimens and their labels are illustrated and additional specimens,demonstrating the variability of certain species, are also figured. Male genitalia of all valid species are figured and SEMphotos of the aedeagus are illustrated. Further important structures, the so-called ‘octavals’ on the male pre-genitalabdomen, are also figured. Female genitalia revealed a high similarity between species, combined with a considerablevariability, and were unsuitable for characterisation of species. Female genitalia of three species are figured to exemplifythis situation. As a result of the morphological and genetic studies, 12 out of the 21 described species and subspecies aresynonymised or transferred to the closely related genus Neognopharmia Wehrli, 1953. In addition, G. colchidariacocandaria (Erschoff, 1874) is revived as a valid species, G. sinesefida Wehrli, 1941 is downgraded to a subspecies of G.colchidaria Lederer, 1870. Five new records for the fauna of the following countries are presented: G. colchidariaobjectaria: new for Pakistan; G. irakensis: new for Turkey and Pakistan; G. kasrunensis: new for Oman and G. sarobiana: new for Pakistan. Distribution maps and an identification key are given for all species.


1983 ◽  
Vol 61 (5) ◽  
pp. 1402-1410 ◽  
Author(s):  
Richard C. Summerbell

A wide range of habitats in and near southern British Columbia was sampled for the presence of Leucosporidium spp. Leucosporidium scottii, the only species capable of growth at mesic temperatures, occurred abundantly on marine substrates. The thalli of phaeophyte algae yielded particularly large numbers of isolates, but only in the colder months of the year. Leucosporidium scottii was found less frequently in terrestrial or freshwater habitats but was a major component of the yeast mycobiota of organic materials decaying in cold moist soils. The remaining five known species of Leucosporidium were not found. Genetic studies revealed that the tetrapolar mating system of L. scottii is characterized by the presence of multiple alleles at the A locus. The B locus appears to be biallelic.


Author(s):  
Erica B. Crampton ◽  
Ariana D. Sellers ◽  
John L. Salmon ◽  
Spencer P. Magleby

Applying an origami pattern to thick, non-paper-like materials is a challenging task. Though many techniques have been developed to accommodate thickness in origami, creating 3D models of such thick-origami mechanisms is complex. The time and knowledge required to manually model an origami mechanism can impede the exploration of the design space and creation of robust designs. This work presents data structures based on origami that can be used in the automation of thick-origami mechanism design. These structures are described and an example computer program that implements them is investigated. The program automatically generates all the necessary 3D CAD part models and an assembly model for a user-specified origami crease pattern. Models resulting from the program for several crease patterns are demonstrated with a discussion of the advantages and limitations of the system. With further development of the data structures and program, this framework has the potential to help mitigate some of the barriers to more widespread use of origami-based design.


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