scholarly journals Using the Paleobiology Database and MorphoBank to facilitate collaborative research and data archival

2019 ◽  
Author(s):  
Melanie J Hopkins
Keyword(s):  
Collaborative Research ◽  
Review Process ◽  
Morphological Data ◽  
Statistical Computing ◽  
Data Services ◽  
Public Resource ◽  
Online Tools ◽  
R Project ◽  
History Of ◽  
Visualization Tools

The internet has made it possible to share and store large quantities of data, and as a result, there is an increasing imperative to make data easily accessible and results reproducible. This has been facilitated by the proliferation of online tools available for archiving and sharing data. In this talk I will describe two databases that are structured in different ways but provide useful platforms for collaboration, reproducibility, and data archival. The first is the Paleobiology Database (PBDB), which is a public resource for paleontological data in support of global, collection-based occurrence and taxonomic data for organisms of all geologic ages. I will give a brief history of the PBDB; describe how data is contributed; describe data services for browsing data, downloading data, and the independent development of analytical and visualization tools; and describe how to make research based on data from the PBDB replicable. The second is MorphoBank, which is a project-based platform for organizing and archiving morphological data and images affiliated with that data, and whose primary use has been for building morphological matrices for use in phylogenetic and disparity analyses. I will give a brief history of MorphoBank; describe tools for data creation, editing, and export; and describe how the platform is best used for replicability and data archival during the review process and after publication. Finally, I will discuss the future of both databases, focusing particularly on initiatives for connecting each with other databases and with the R Project for Statistical Computing, as well as educational resources and funding.

scholarly journals Using the Paleobiology Database and MorphoBank to facilitate collaborative research and data archival

2019 ◽  
Author(s):  
Melanie J Hopkins
Keyword(s):  
Collaborative Research ◽  
Review Process ◽  
Morphological Data ◽  
Statistical Computing ◽  
Data Services ◽  
Public Resource ◽  
Online Tools ◽  
R Project ◽  
History Of ◽  
Visualization Tools

The internet has made it possible to share and store large quantities of data, and as a result, there is an increasing imperative to make data easily accessible and results reproducible. This has been facilitated by the proliferation of online tools available for archiving and sharing data. In this talk I will describe two databases that are structured in different ways but provide useful platforms for collaboration, reproducibility, and data archival. The first is the Paleobiology Database (PBDB), which is a public resource for paleontological data in support of global, collection-based occurrence and taxonomic data for organisms of all geologic ages. I will give a brief history of the PBDB; describe how data is contributed; describe data services for browsing data, downloading data, and the independent development of analytical and visualization tools; and describe how to make research based on data from the PBDB replicable. The second is MorphoBank, which is a project-based platform for organizing and archiving morphological data and images affiliated with that data, and whose primary use has been for building morphological matrices for use in phylogenetic and disparity analyses. I will give a brief history of MorphoBank; describe tools for data creation, editing, and export; and describe how the platform is best used for replicability and data archival during the review process and after publication. Finally, I will discuss the future of both databases, focusing particularly on initiatives for connecting each with other databases and with the R Project for Statistical Computing, as well as educational resources and funding.

scholarly journals Demographic and Comorbidities Data Description of Population in Mexico with SARS-CoV-2 Infected Patients(COVID19): An Online Tool Analysis

2020 ◽  
Vol 17 (14) ◽  
pp. 5173
Author(s):  
Carlos E. Galván-Tejada ◽  
Laura A. Zanella-Calzada ◽  
Karen E. Villagrana-Bañuelos ◽  
Arturo Moreno-Báez ◽  
Huizilopoztli Luna-García ◽  
...  
Keyword(s):  
Demographic Data ◽  
Statistical Computing ◽  
Online Tool ◽  
Data Description ◽  
Graphic Information ◽  
R Project ◽  
Visualization Tools ◽  
Health Organization ◽  
National Governments ◽  
Web Platform

The Word Health Organization (WHO) declared in March 2020 that we are facing a pandemic designated as COVID-19, which is the acronym of coronavirus disease 2019, caused by a new virus know as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In Mexico, the first cases of COVID-19, was reported by the Secretary of Health on 28 February 2020. More than sixteen thousand cases and more than fifteen thousand deaths have been reported in Mexico, and it continues to rise; therefore, this article proposes two online visualization tools (a web platform) that allow the analysis of demographic data and comorbidities of the Mexican population. The objective of these tools is to provide graphic information, fast and updated, based on dataset obtained directly from National Governments Health Secretary (Secretaría de Salud, SSA) which is daily refreshed with the information related to SARS-CoV-2. To allow a dynamical update and friendly interface, and approach with R-project, a well-known Open Source language and environment for statistical computing and Shiny package, were implemented. The dataset is loaded automatically from the latest version released by the federal government of Mexico. Users can choose to study particular groups determined by gender, entity, type of result (positive, negative, pending outcome) and comorbidity. The image results are plots that can be instantly interpreted and supported by the text summary. This tool, in addition to being a consultation for the general public, is useful in Public Health to facilitate the visualization of the data, allowing its timely interpretation due to the changing nature of COVID-19, it can even be used for decision-making by leaders, for the benefit of the health of the community.

scholarly journals The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data

2014 ◽  
Vol 14 (1) ◽  
pp. 52 ◽  
Author(s):  
Ralph S Peters ◽  
Karen Meusemann ◽  
Malte Petersen ◽  
Christoph Mayer ◽  
Jeanne Wilbrandt ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Morphological Data ◽  
History Of

Alternative Futures for Forest-Based Nanomaterials

2016 ◽  
Vol 8 (4) ◽  
pp. 197-221 ◽  
Author(s):  
David N. Bengston ◽  
Jim Dator ◽  
Michael J. Dockry ◽  
Aubrey Yee
Keyword(s):  
Forest Management ◽  
Collaborative Research ◽  
Research Agenda ◽  
Forest Products ◽  
The United States ◽  
Solar Panels ◽  
Alternative Futures ◽  
Environmental Consequences ◽  
History Of ◽  
The U.S

Forestry and forest products research has entered into a robust research agenda focused on creating nano-sized particles and nanoproducts from wood. As wood-based materials can be sustainably produced, the potential of these renewable products could be limitless and include high-end compostable electronics, paint-on solar panels, and lightweight materials for airplanes and cars. Others warn about potential serious negative health and environmental consequences. Either way, wood-based nanomaterials could disrupt forestry as we know it. This article is a summary and analysis of a collaborative research project exploring the futures of wood-based nanomaterials within the context of the futures of forests and forest management within the United States. We start by describing the history of forestry through the lens of the U.S. Forest Service, then describe nanotechnology in general and wood-based nanocellulose specifically. Next, we outline the Manoa School alternative futures method, and how we used it to design and carry out a “complete futures of x” project. Following the Manoa School approach, we describe four alternative futures for forestry and forest management. We conclude with implications for the future of forestry, forests, and forest-based nanomaterials, as well as a discussion on the implementation of a complete “futures of x” project.

scholarly journals The taxonomic history of Indo-Papuan groundsnakes, genus Stegonotus Duméril et al., 1854 (Colubridae), with some taxonomic revisions and the designation of a neotype for S. parvus (Meyer, 1874)

Zootaxa ◽  
2018 ◽  
Vol 4512 (1) ◽  
pp. 1
Author(s):  
CHRISTINE M. KAISER ◽  
HINRICH KAISER ◽  
MARK O’SHEA
Keyword(s):  
New Guinea ◽  
Molecular Data ◽  
The Philippines ◽  
Morphological Data ◽  
Valid Species ◽  
Museum Specimens ◽  
Type Specimens ◽  
History Of ◽  
Original Species ◽  
Species Specific

Since its conceptualization in 1854, 29 species of the colubrid genus Stegonotus have been recognized or described, of which 15 (admiraltiensis, batjanensis, borneensis, cucullatus, derooijae, diehli, florensis, guentheri, iridis, heterurus, melanolabiatus, modestus, muelleri, parvus, poechi) are still considered valid today. Original species descriptions for the members of this genus were published in Dutch, English, French, German, and Italian and, perhaps as a consequence of these polyglot origins, there has been a considerable amount of confusion over which species names should be applied to which populations of Stegonotus throughout its range across Borneo, the Philippines, Wallacea, New Guinea, Australia, and associated archipelagos. In addition, the terminology used to notate characteristics in the descriptions of these forms was not uniform and may have added to the taxonomic confusion. In this paper, we trace in detail the history of the type specimens, the species, and the synonyms currently associated with the genus Stegonotus and provide a basic, species-specific listing of their characteristics, derived from our examination of over 1500 museum specimens. Based on our data, we are able to limit the distribution of S. modestus to the islands of Ambon, Buru, and Seram in the central Moluccas of Indonesian Wallacea. We correct the type locality of S. cucullatus to the Manokwari area on the Bird’s Head Peninsula of West Papua, Indonesian New Guinea and designate a neotype for S. parvus, a species likely to be a regional endemic in the Schouten Archipelago of Cenderawasih Bay (formerly Geelvink Bay), Indonesian New Guinea. We unequivocally identify and explain the problematic localities of the type specimens of S. muelleri and Lycodon muelleri, which currently reside in the same specimen jar. We remove L. aruensis and L. lividum from the synonymy of S. modestus and recognize them as S. aruensis n. comb. and S. lividus n. comb., respectively. We remove S. keyensis and Zamenophis australis from the synonymy of S. cucullatus and recognize them as S. keyensis n. comb. and S. australis n. comb., respectively. We further remove S. reticulatus from the synonymy of S. cucullatus, S. dorsalis from the synonymy of S. diehli, and S. sutteri from the synonymy of S. florensis. We designate lectotypes for S. guentheri, S. heterurus, S. lividus, and S. reticulatus. Lastly, we introduce S. poechi, a valid species not mentioned in the scientific literature since its description in 1924. This brings the diversity in the genus Stegonotus to 22 species. We also caution that in a complex group of organisms like Stegonotus any rush to taxonomic judgment on the basis of molecular and incomplete morphological data sets may perpetuate errors and introduce incongruities. Only through the careful work of connecting type material with museum specimens and molecular data can the taxonomy and nomenclature of complex taxa be stabilized. 

Notes on the generic position of Brassica deserti (Brassicaceae)

2019 ◽  
Vol 66 (1-2) ◽  
pp. 89-93
Author(s):  
Jotham Ziffer-Berger ◽  
Alexandra Keren-Keiserman ◽  
Adi Doron-Faigenboim ◽  
Klaus Mummenhoff ◽  
Oz Barazani
Keyword(s):  
Mediterranean Area ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Molecular Tools ◽  
East Mediterranean ◽  
Phylogenetic Groups ◽  
5.8S Rdna ◽  
The Core ◽  
Generic Position ◽  
History Of

Molecular tools provide new insights into phylogenetic relationships of plant species, and by relating phylogenetic groups to their geographical distribution, we can cast light upon the evolution history of plant clades. In the current study, we evaluated the phylogenetic position of the Sinai endemic Brassica deserti (Brassicaceae), later renamed as Erucastrum deserti, based on morphological data and 5.8S rDNA and ITS (Internal Transcribed Spacer) regions. Our results indicate that B. deserti belongs to an East-Mediterranean – Saharo Arabian clade and was not assigned to the core Brassica and Erucastrum clades, respectively, which evolved in the West Mediterranean area. We tentatively conclude that Brassica deserti evolved independently of core Brassica and Erucastrum.

scholarly journals Three new Cenomanian conifers from El Chango (Chiapas, Mexico) offer a snapshot of the geographic mosaic of the Mesozoic conifer decline

2021 ◽  
Author(s):  
Ixchel Gonzalez-Ramirez ◽  
Sergio RS Cevallos-Ferriz ◽  
Carl Rothfels
Keyword(s):  
Evolutionary History ◽  
Mixed Forest ◽  
Freshwater Ecosystems ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Dominant Group ◽  
Geographic Mosaic ◽  
History Of ◽  
Rare Opportunity

Premise of study: El Chango is a recently discovered quarry that contains extremely well preserved fossils. The Cenomanian age of the locality corresponds to a time when the global flora was transitioning from gymnosperm- to angiosperm-dominated, yet conifers predominate in this locality. These fossils thus provide a rare opportunity to understand the replacement of conifers by angiosperms as the dominant group of plants. Methods: We collected material from El Chango in annual expeditions (2010 to 2014). We selected the three most abundant and best preserved conifer morphotypes and conducted a total-evidence (i.e., including molecular and morphological data) phylogenetic analysis of a sample of 72 extant conifer species plus the three fossils. We use these results to inform our taxonomic decisions. Results: We obtained four equally most-parsimonious trees (consistency index = 44.1%, retention index = 78.8%). Despite ambiguous relationships among some extant taxa, the three fossil conifers had the same phylogenetic position in all four most parsimonious trees; we describe these species as new: Sequoiadendron helicalancifolium sp. nov. (Cupressaceae), and Microcachrys rhomboidea sp. nov. and Dacrydium bifoliosus sp. nov (Podocarpaceae). The ecosystem is interpreted as a coastal humid mixed forest. Conclusions: Our findings contribute to the understanding of Cenomanian equatorialregions, and support the hypothesis of a geographically and ecologically structured rise of angiosperms, with conifers remaining dominant in brackish-water and angiosperms becoming dominant in freshwater-ecosystems. These fossils fill in gaps in the evolutionary history of lineages like Microcachrys, which we demonstrate occurred in the Northern hemisphere before becoming restricted to its current range (Tasmania).

scholarly journals Taxonomic status of Flexopecten glaber ponticus (Bucquoy, Dautzenberg & Dollfus, 1889) – the Black Sea Flexopecten glaber (Linnaeus, 1758) (Bivalvia: Pectinidae)

2018 ◽  
Vol 3 (4) ◽  
pp. 14-28 ◽  
Author(s):  
I. P. Bondarev
Keyword(s):  
Comparative Analysis ◽  
Black Sea ◽  
Taxonomic Status ◽  
Morphological Data ◽  
Valid Species ◽  
The Black Sea ◽  
Marmara Sea ◽  
History Of ◽  
The Mediterranean ◽  
The Republic

The name Flexopecten glaber ponticus (Bucquoy, Dautzenberg & Dollfus, 1889) is generally used for the only Pectinidae representative inhabiting the Black Sea. It is registered in the Red Book of the Republic of Crimea as endemic subspecies reducing in amount. F. glaber ponticus is listed in WoRMS MolluscaBase as the only accepted subspecies of Flexopecten glaber (Linnaeus, 1758). In the past its taxonomic status has been changed from a geographic variety to valid species. The purpose of this study is to establish its correct taxonomic status. The study is based on a comparative analysis of conchological features of Flexopecten glaber and F. glaber ponticus in relation with the brief natural history of population in the Black Sea. Sampling was performed by snorkel equipment in Kazach’ya Bay (Black Sea, Crimea, Sevastopol) at 2–6 m depths. A total of 100 scallop specimens were sampled in September 2017. To assure a better understanding in a broader context those results are compared with the previously published morphological data based on the analysis of a large amount of material from the Black Sea and the Mediterranean Sea – Marmara Sea regions. Comparative analysis of conchological features of F. glaber ponticus from the Black Sea with F. glaber from the Mediterranean region has not revealed any distinct differences between them. Thus, there are no evidenced data for the diagnosis of F. glaber ponticus as a subspecies. Species F. glaber appeared in the Black Sea not earlier than 7,000 years ago and formed a well developed population less than 3,000 years ago. We have to conclude that the specified divergence period is not long enough to form a subspecies. As a result of the present survey the subspecific status of F. glaber ponticus is not retained and the name is placed in synonymy of the parent species Flexopecten glaber.

scholarly journals Research ethics by design: A collaborative research design proposal

2016 ◽  
Vol 13 (2) ◽  
pp. 84-91
Author(s):  
Donald S Borrett ◽  
Heather Sampson ◽  
Ann Cavoukian
Keyword(s):  
Research Ethics ◽  
Research Design ◽  
Collaborative Research ◽  
Review Process ◽  
Personal Data ◽  
Ethics Committees ◽  
Research Ethics Committees ◽  
Regulatory Frameworks ◽  
Collective Benefit ◽  
Design Proposal

Privacy by Design, a globally accepted framework for personal data management and privacy protection, advances the view that privacy cannot be assured solely by compliance with regulatory frameworks but must become an organisation’s default mode of operation. We are proposing a similar template for the research ethics review process. The Research Ethics by Design framework involves research ethics committees engaging researchers during the design phase of the proposal so that ethical considerations may be directly embedded in the science as opposed to being viewed as addendums after the fact. This collaborative research design proposal results in the establishment of a culture of ethical research rather than research with ethical oversight. Both researchers and research ethics committees come to view the review process as one in which individual protection and collective benefit co-exist in a doubly-enabling positive-sum manner.

Collecting Folk Histories

2015 ◽  
Vol 37 (3) ◽  
pp. 45-75
Author(s):  
William S. Walker
Keyword(s):  
New York ◽  
Collaborative Research ◽  
Public History ◽  
New York State ◽  
Field Research ◽  
Community Based ◽  
Community Based Research ◽  
Student Community ◽  
History Of

This article explores the shared intellectual tradition in folklore, public history, and oral history of involving students in community-based field research. This case study of the collaborative research New York State folklorist Harold W. Thompson and his students undertook in the 1930s contributes to ongoing efforts to enrich our understanding of public history’s genealogy. It also demonstrates that a counter-tradition to the “lone genius” model of humanities research emerged through faculty-student community-based research projects in history and folklore.

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