scholarly journals The Additivity Project - Use Cases and User Interface

2019 ◽  
Vol 3 ◽  
Author(s):  
Tilo Henning ◽  
Patrick Plitzner ◽  
Andreas Müller ◽  
Anton Güntsch ◽  
Walter G. Berendsohn ◽  
...  
Keyword(s):  
Data Exchange ◽  
Use Cases ◽  
Morphological Data ◽  
Herbarium Specimens ◽  
Data Set ◽  
Basic Set ◽  
Combine Structure ◽  
Individual Specimen ◽  
The Individual ◽  
And Storage

Herbarium specimens are central to botanical science and of rising importance thanks to increasing accessibility and broadened usability. Alongside the many new uses of specimen data, sit a range of traditional uses supporting the collection of morphological data and their application to taxonomy and systematics. (Henning et al. 2018). Technical workflows are needed to support the sustainable collection of this traditional information and maintain the high quality of the morphological data. Data exchange and re-usability requires the use of accepted controlled vocabularies (community approved) that are accessible (web-based ontologies and term vocabularies) and reliable (long-term availability/unique identifiers). The same applies to datasets that must be stored accessibly and sustainably by maintaining all data relationships that would facilitate convenient re-use. This project aims to construct a comprehensive workflow to optimise the delimitation and characterisation (“descriptions”) of taxa (see complementary talk by Plitzner et al.). It is implemented on the open-source software framework of the EDIT Platform for Cybertaxonomy (http://www.cybertaxonomy.org, Ciardelli et al. 2009) extending the workflow for sample data processing developed in a preceding project (Kilian et al. 2015). The principal goals of this new software component are: specimen-level recording and storage of character data in structured character matrices generating taxon characterisations by aggregating the individual specimen-based datasets using and developing community-coordinated, ontology-based exemplar vocabularies persistently linking character datasets with source specimens for high visibility and re-usability specimen-level recording and storage of character data in structured character matrices generating taxon characterisations by aggregating the individual specimen-based datasets using and developing community-coordinated, ontology-based exemplar vocabularies persistently linking character datasets with source specimens for high visibility and re-usability The angiosperm order, Caryophyllales, provides an exemplar use case through cooperation with the Global Caryophyllales Initiative (Borsch et al. 2015). A basic set of morphological terms and vocabularies has been obtained from various online sources (ontologies, glossaries) and can be used, searched and expanded in the EDIT platform. The terms are categorised into: structures, properties and states. Different editors have been developed to combine structure and property terms to characters and assign a customised state vocabulary (categorical) or suitable values and units (numerical) to them. The workflow is built around a data set defining the taxonomic environment of individual use cases. A data set is specified by the characters and a taxonomic group, which can be filtered by area or rank. The dataset can be opened in a tabular representation (character matrix) to enter preselected state terms or values for the individual specimen. The matrix provides several features for basic comparison and analysis and allows the entry of alternative datasets (e.g. literature). Finally, the aggregation of data subsets to potential taxonomic units by adding up the values and summarising character states, allows the convenient test of taxonomic hypotheses. The term additivity is used here to describe this set of workflows and processes adding value to herbarium specimens and accumulating the specimen data for a taxon description.

Control of Secretory Production in the Isopod Hepatopancreas

1972 ◽  
Vol 30 ◽  
pp. 166-167
Author(s):  
John W. Roberts ◽  
E. R. Witkus
Keyword(s):  
B Cells ◽  
Morphological Data ◽  
Secretory Product ◽  
Secretory Function ◽  
Secretory Material ◽  
Blind Ending ◽  
Secretory Production ◽  
Regenerative Cells ◽  
Immature Cells ◽  
And Storage

The isopod hepatopancreas, as exemplified by Oniscus ascellus. is comprised of four blind-ending diverticula. The regenerative cells at the tip of each diverticula differentiate into either club-shaped B-cells, which serve a secretory function, or into conoid S-cells, which serve in the absorption and storage of nutrients.The glandular B-cells begin producing secretory material with the development of rough endoplasmic reticulum during their process of maturation from the undifferentiated regenerative cells. Cytochemical and morphological data indicate that the hepatopancreas sequentially produces two types of secretory material within the large club-shaped cells. The production of the carbohydrate-like secretory product in immature cells seems to be phased out as the production of the osmiophilic secretion was phased in as the cell matured.

Algorithms for automated montage synthesis of images from laser-scanning confocal microscopes

1995 ◽  
Vol 53 ◽  
pp. 650-651
Author(s):  
D. E. Becker
Keyword(s):  
Image Analysis ◽  
High Resolution ◽  
Laser Scanning ◽  
Cell Counting ◽  
Wide Area ◽  
Data Set ◽  
Computational Synthesis ◽  
Automated Cell Counting ◽  
Partial View ◽  
The Individual

An efficient, robust, and widely-applicable technique is presented for computational synthesis of high-resolution, wide-area images of a specimen from a series of overlapping partial views. This technique can also be used to combine the results of various forms of image analysis, such as segmentation, automated cell counting, deblurring, and neuron tracing, to generate representations that are equivalent to processing the large wide-area image, rather than the individual partial views. This can be a first step towards quantitation of the higher-level tissue architecture. The computational approach overcomes mechanical limitations, such as hysterisis and backlash, of microscope stages. It also automates a procedure that is currently done manually. One application is the high-resolution visualization and/or quantitation of large batches of specimens that are much wider than the field of view of the microscope.The automated montage synthesis begins by computing a concise set of landmark points for each partial view. The type of landmarks used can vary greatly depending on the images of interest. In many cases, image analysis performed on each data set can provide useful landmarks. Even when no such “natural” landmarks are available, image processing can often provide useful landmarks.

Territorial Distribution of Alcohol and Drug Addictions Mortality Concerning Regional Disparities in the Slovak Republic from Year 1996 to Year 2015

2020 ◽  
Keyword(s):  
Mortality Rate ◽  
Slovak Republic ◽  
Regional Disparities ◽  
Point Of View ◽  
Extreme Position ◽  
Data Set ◽  
Female Sex ◽  
Male Sex ◽  
The Individual ◽  
High Level

BACKGROUND: This paper deals with territorial distribution of the alcohol and drug addictions mortality at a level of the districts of the Slovak Republic. AIM: The aim of the paper is to explore the relations within the administrative territorial division of the Slovak Republic, that is, between the individual districts and hence, to reveal possibly hidden relation in alcohol and drug mortality. METHODS: The analysis is divided and executed into the two fragments – one belongs to the female sex, the other one belongs to the male sex. The standardised mortality rate is computed according to a sequence of the mathematical relations. The Euclidean distance is employed to compute the similarity within each pair of a whole data set. The cluster analysis examines is performed. The clusters are created by means of the mutual distances of the districts. The data is collected from the database of the Statistical Office of the Slovak Republic for all the districts of the Slovak Republic. The covered time span begins in the year 1996 and ends in the year 2015. RESULTS: The most substantial point is that the Slovak Republic possesses the regional disparities in a field of mortality expressed by the standardised mortality rate computed particularly for the diagnoses assigned to the alcohol and drug addictions at a considerably high level. However, the female sex and the male sex have the different outcome. The Bratislava III District keeps absolutely the most extreme position. It forms an own cluster for the both sexes too. The Topoľčany District bears a similar extreme position from a point of view of the male sex. All the Bratislava districts keep their mutual notable dissimilarity. Contrariwise, evaluation of a development of the regional disparities among the districts looks like notably heterogeneously. CONCLUSIONS: There are considerable regional discrepancies throughout the districts of the Slovak Republic. Hence, it is necessary to create a common platform how to proceed with the solution of this issue.

scholarly journals Crystal growth of clathrate hydrate formed with H2 + CO2 mixed gas and tetrahydropyran

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Meku Maruyama ◽  
Riku Matsuura ◽  
Ryo Ohmura
Keyword(s):  
Crystal Growth ◽  
Synthesis Gas ◽  
Water System ◽  
Hydrate Formation ◽  
Growth Dynamics ◽  
Operating Conditions ◽  
Mixed Gas ◽  
Thermodynamic Conditions ◽  
The Individual ◽  
And Storage

AbstractHydrate-based gas separation technology is applicable to the CO2 capture and storage from synthesis gas mixture generated through gasification of fuel sources including biomass. This paper reports visual observations of crystal growth dynamics and crystal morphology of hydrate formed in the H2 + CO2 + tetrahydropyran (THP) + water system with a target for developing the hydrate-based CO2 separation process design. Experiments were conducted at a temperature range of 279.5–284.9 K under the pressure of 4.9–5.3 MPa. To simulate the synthesis gas, gas composition in the gas phase was maintained around H2:CO2 = 0.6:0.4 in mole fraction. Hydrate crystals were formed and extended along the THP/water interface. After the complete coverage of the interface to shape a polycrystalline shell, hydrate crystals continued to grow further into the bulk of liquid water. The individual crystals were identified as hexagonal, tetragonal and other polygonal-shaped formations. The crystal growth rate and the crystal size varied depending on thermodynamic conditions. Implications from the obtained results for the arrangement of operating conditions at the hydrate formation-, transportation-, and dissociation processes are discussed.

High-Resolution Facial Feature Saliency Mapping

Perception ◽  
1986 ◽  
Vol 15 (4) ◽  
pp. 373-386 ◽  
Author(s):  
Nigel D Haig
Keyword(s):  
Image Processing ◽  
High Resolution ◽  
Facial Feature ◽  
Human Beings ◽  
Comparison Process ◽  
Compression Technique ◽  
Feature Saliency ◽  
Basic Set ◽  
Computational Speed ◽  
The Individual

For recognition of a target there must be some form of comparison process between the image of that target and a stored representation of that target. In the case of faces there must be a very large number of such stored representations, yet human beings seem able to perform comparisons at phenomenal speed. It is possible that faces are memorised by fitting unusual features or combinations of features onto a bland prototypical face, and such a data-compression technique would help to explain our computational speed. If humans do indeed function in this fashion, it is necessary to ask just what are the features that distinguish one face from another, and also, what are the features that form the basic set of the prototypical face. The distributed apertures technique was further developed in an attempt to answer both questions. Four target faces, stored in an image-processing computer, were each divided up into 162 contiguous squares that could be displayed in their correct positions in any combination of 24 or fewer squares. Each observer was required to judge which of the four target faces was displayed during a 1 s presentation, and the proportion of correct responses for each individual square was computed. The resultant response distributions, displayed as brightness maps, give a vivid impression of the relative saliency of each feature square, both for the individual targets and for all of them combined. The results, while broadly confirming previous work, contain some very interesting and surprising details about the differences between the target faces.

scholarly journals Transport and storage of anthropogenic C in the North Atlantic Subpolar Ocean

2018 ◽  
Vol 15 (14) ◽  
pp. 4661-4682 ◽  
Author(s):  
Virginie Racapé ◽  
Patricia Zunino ◽  
Herlé Mercier ◽  
Pascale Lherminier ◽  
Laurent Bopp ◽  
...  
Keyword(s):  
Interannual Variability ◽  
North Atlantic ◽  
General Circulation ◽  
Meridional Overturning Circulation ◽  
Intermediate Water ◽  
Data Set ◽  
The North ◽  
Storage Rate ◽  
The North Atlantic ◽  
And Storage

Abstract. The North Atlantic Ocean is a major sink region for atmospheric CO2 and contributes to the storage of anthropogenic carbon (Cant). While there is general agreement that the intensity of the meridional overturning circulation (MOC) modulates uptake, transport and storage of Cant in the North Atlantic Subpolar Ocean, processes controlling their recent variability and evolution over the 21st century remain uncertain. This study investigates the relationship between transport, air–sea flux and storage rate of Cant in the North Atlantic Subpolar Ocean over the past 53 years. Its relies on the combined analysis of a multiannual in situ data set and outputs from a global biogeochemical ocean general circulation model (NEMO–PISCES) at 1∕2∘ spatial resolution forced by an atmospheric reanalysis. Despite an underestimation of Cant transport and an overestimation of anthropogenic air–sea CO2 flux in the model, the interannual variability of the regional Cant storage rate and its driving processes were well simulated by the model. Analysis of the multi-decadal simulation revealed that the MOC intensity variability was the major driver of the Cant transport variability at 25 and 36∘ N, but not at OVIDE. At the subpolar OVIDE section, the interannual variability of Cant transport was controlled by the accumulation of Cant in the MOC upper limb. At multi-decadal timescales, long-term changes in the North Atlantic storage rate of Cant were driven by the increase in air–sea fluxes of anthropogenic CO2. North Atlantic Central Water played a key role for storing Cant in the upper layer of the subtropical region and for supplying Cant to Intermediate Water and North Atlantic Deep Water. The transfer of Cant from surface to deep waters occurred mainly north of the OVIDE section. Most of the Cant transferred to the deep ocean was stored in the subpolar region, while the remainder was exported to the subtropical gyre within the lower MOC.

scholarly journals Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics

2018 ◽  
Vol 19 (12) ◽  
pp. 3780 ◽  
Author(s):  
Dingxuan He ◽  
Andrew Gichira ◽  
Zhizhong Li ◽  
John Nzei ◽  
Youhao Guo ◽  
...  
Keyword(s):  
Genome Structure ◽  
Morphological Data ◽  
Basal Angiosperm ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Gene Data ◽  
High Degree

The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.

Morphological and genetic variability of Baetis (Rhodobaetis) braaschi Zimmermann, 1980 (Ephemeroptera: Baetidae)

Zootaxa ◽  
2012 ◽  
Vol 3323 (1) ◽  
pp. 27 ◽  
Author(s):  
PAVEL SROKA ◽  
ALEXANDER V. MARTYNOV ◽  
ROMAN J. GODUNKO
Keyword(s):  
Genetic Variability ◽  
Methodological Approach ◽  
Morphological Variability ◽  
Geographic Origin ◽  
Intraspecific Variability ◽  
Morphological Data ◽  
Mtdna Coi ◽  
Geographic Regions ◽  
Coi Sequences ◽  
The Individual

Specimens of Baetis (Rhodobaetis) braaschi Zimmermann, 1980 from the three distant geographic regions (Crimean Pen-insula, Eastern Ukraine and Caucasus) are investigated and compared using a methodological approach combining mor-phological and molecular (partial mtDNA COI sequences) data. Intraspecific variability in several morphologicalcharacters is recognized and described, whereas COI sequences are found to be very uniform. The amount and distributionof the changes of COI sequences do not follow the pattern of morphological variability and/or geographic origin of thespecimens. This indicates that analysis of the changes in the COI sequence can contradict the pattern of morphologicalcharacters commonly used for the discrimination of the individual Rhodobaetis species. As a basis for the future taxonom-ic changes concerning subgenus Rhodobaetis, it is advised (where possible) to critically evaluate both molecular and morphological data.

scholarly journals Autonomous feature type selection based on environment using expectation maximization in self-localization

2018 ◽  
Vol 15 (6) ◽  
pp. 172988141881470
Author(s):  
Nezih Ergin Özkucur ◽  
H Levent Akın
Keyword(s):  
Expectation Maximization ◽  
Autonomous Robots ◽  
Expectation Maximization Algorithm ◽  
Sensory Information ◽  
Ground Truth ◽  
Local Environment ◽  
Localization Algorithm ◽  
Data Set ◽  
Public Data ◽  
The Individual

Self-localization in autonomous robots is one of the fundamental issues in the development of intelligent robots, and processing of raw sensory information into useful features is an integral part of this problem. In a typical scenario, there are several choices for the feature extraction algorithm, and each has its weaknesses and strengths depending on the characteristics of the environment. In this work, we introduce a localization algorithm that is capable of capturing the quality of a feature type based on the local environment and makes soft selection of feature types throughout different regions. A batch expectation–maximization algorithm is developed for both discrete and Monte Carlo localization models, exploiting the probabilistic pose estimations of the robot without requiring ground truth poses and also considering different observation types as blackbox algorithms. We tested our method in simulations, data collected from an indoor environment with a custom robot platform and a public data set. The results are compared with the individual feature types as well as naive fusion strategy.

scholarly journals Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
Author(s):  
W. Andrew Cox ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
New World ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Strong Support ◽  
Nuclear Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Mitochondrial Data ◽  
Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

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