Digital Atlas Research Articles

Open access digital tools’ contribution for mapping and monitoring of biodiversity

Biodiversity constitutes a source of natural richness of life on Earth, including all the variety of living organisms. The United Nations Organization proclaimed the period between 2011 and 2020 as the International Decade of Biodiversity. Knowing that the majority of the existing information about species distribution is not promptly reachable, the adoption of Georeferencing tolls as a brace for mapping, managing and handling of the biodiversity stands out. The present essay aims to describe the development and implementation of the Digital Atlas of Herpetofauna from the state of Pernambuco, a new digital tool of open access, which integrates data about species, their natural histories and their spacial distribution. For its development, the Joomla!, version 1.5.26, was adopted as Content Management System and the MySQL as Database System, these were integrated to the Library System PROJ.4 in order to enable graphic projections. The result is the developed tool itself, applying the combination of geographic data stored by mapping based on web browser. This study presented advantages found in the use of open access digital tools for mapping and monitoring species, pointing that its use is a very effective way to aggregate and communicate information about biodiversity.

Mapping the Human Brain: What Is the Next Frontier?

Abstract The structure and function of the human brain have long been the topic of exploration by scientists. To understand how the brain works, researchers have created various brain navigation maps, i.e. brain atlases, which are still being developed and improved. To clarify the trend of human brain mapping and to achieve better applications in brain science and diseases, this commentary briefly traces the history of human brain mapping and describes insights into the next stage of building brain atlases.

Mapping Mexican COVID-19 vulnerability at municipal scale

This paper presents an interactive map related to the population vulnerability concerning COVID-19 at the municipal level for Mexico. A vulnerability index was modeled using seven socioeconomic/sociodemographic variables and one health-care related variable, all with relevance to a health contingency such as COVID-19. The resulting indicator expresses the municipal vulnerability to face a sanitary crisis such as COVID-19 in five categories. Data for each of the eight variables were first categorized in quintiles. A pairwise comparison matrix was used to weight these variables in relation to their estimated relevance for the municipal vulnerability. With respect to COVID-19 vulnerability, Mexican municipalities show the following results: 1.6% (very low), 18.7% (low), 46.6% (medium), 24.6% (high), 8.5% (very high).
 The map forms part of a dashboard providing daily information on the development of the pandemic in Mexico, and is complemented by a digital atlas visualizing information for each variable of the indicator.

Scales of justice: putting remembrance back on the map in Palestine and Mi’kma’ki

ABSTRACT This paper considers two remarkable efforts to counter the repressive effects of ‘colonial cartography’: the Nakba map project in Israel, and the Ta’n Weji-sqalia’tiek Mi’kmaw Place Names Digital Atlas and Website Project in Mi’kma’ki (Nova Scotia, Canada). Undertaken by the Israeli NGO Zochrot (‘remembering’ in Hebrew), the Nakba ‘counter-mapping’ project seeks to challenge settler foundation myths utilized to perpetuate ongoing oppression. The Ta’n Weji-sqalia’tiek Mi’kmaw Place Names project deploys cartographic revelation – the recovery of erased place names – as a mode of cultural reclamation, confronting settlers with the natural and human realities of the ‘world’ they ‘discovered.’ In addition, by delineating the legends and lore encoded and embedded in those place names, the project helps place the Mi’kmaw language and worldview back ‘on the map’ of remembrance and dialogue. Linkages between the two examples of settler occupation are highlighted through a consideration of the ways the Canadian government assists with the ongoing oppression of Palestine, as well as the ways Palestinian-Indigenous solidarity efforts seek to resist entrenched settler-centric narratives (mental maps). The case studies are presented as part of a necessarily larger, on-going effort to give voice to those long silenced by the hegemonic ‘truth’ of settler societies.

Current state of whole slide imaging use in cytopathology: Pros and pitfalls.

Whole slide imaging (WSI) allows generation of large whole slide images and their navigation with zoom in and out like a true virtual microscope. It has become widely used in surgical pathology for many purposes, such as education and training, research activity, teleconsultation, and primary diagnosis. However, in cytopathology, the use of WSI has been lagging behind histology, mainly due to the cytological specimen's characteristics, as groups of cells of different thickness are distributed throughout the slide. To allow the same focusing capability of light microscope, slides have to be scanned at multiple focal planes, at the cost of longer scan times and larger file size. These are the main technical pitfalls of WSI for cytopathology, partly overcome by solutions like liquid-based preparations. Validation studies for the use in primary diagnosis are less numerous and more heterogeneous than in surgical pathology. WSI has been proved effective for training students and successfully used in proficiency testing, allowing the creation of digital cytology atlases. Longer scan times are also a barrier for use in rapid on-site evaluation, but WSI retains its advantages of easy sharing of images for consultation, multiple simultaneous viewing in different locations, the possibility of unlimited annotations and easy integration with medical records. Moreover, digital slides set the laboratory free from reliance on a physical glass slide, with no more concern of fading of stain or slide breakage. Costs are still a problem for small institutions, but WSI can also represent the beginning of a more efficient way of working.

WebGIS Implementation and Effectiveness in Secondary Education Using the Digital Atlas for Schools

The Digital Atlas for Schools is an innovative WebGIS development contributing to the use of geospatial information in schools. Based on a story map tool, it creates a geography curriculum constructed on ArcGIS Online. This article discusses the implications of implementing geospatial technologies so that learners can acquire spatial thinking and geographical knowledge, but also develop responsible and active spatial citizenship. Based on the learning progression approach, it presents results showing the effectiveness of this instructional resource, both for secondary school students and for geography teachers in training. The article concludes with a discussion on how results confirm the need for geospatial technologies to be better incorporated into the geography curriculum at secondary schools.

An Updated Small Magellanic Cloud and Magellanic Bridge Catalog of Star Clusters, Associations, and Related Objects

Abstract We present a catalog of star clusters, associations, and related extended objects in the Small Magellanic Cloud (SMC) and the Magellanic Bridge with 2741 entries, a factor 2 more than a previous version from a decade ago. Literature data up until 2018 December are included. The identification of star clusters was carried out with digital atlases in various bands currently available in the Digitized Sky Survey and the Machine Automatique à Mésurer pour l’Astronomie. imaging surveys. In particular, we cross-identified recent cluster samples from the Visible and Infrared Survey Telescope for Astronomy near-infrared YJK s survey of the Magellanic System, Optical Gravitational Lensing Experiment IV, and Survey of the MAgellanic Stellar History surveys, confirming new clusters and pointing out equivalencies. A major contribution of the present catalog consists of the accurate central positions for clusters and small associations, including a new sample of 45 clusters or candidates in the SMC and 19 in the Magellanic Bridge, as well as a compilation of the most reliable age and metallicity values from the literature. A general catalog must also deal with the recent discoveries of 27 faint and ultra-faint star clusters and galaxies projected on the far surroundings of the Clouds, most of them from the Dark Energy Survey. The information on these objects has been complemented with photometric, spectroscopic, and kinematical follow-up data from the literature. The underluminous galaxies around the Magellanic System, still very few as compared to the predictions from Λ Cold Dark Matter simulations, can bring constraints to galaxy formation and hierarchical evolution. Furthermore, we provide diagnostics, when possible, of the nature of the ultra-faint clusters, searching for borders of the Magellanic System extensions into the Milky Way gravitational potential.

The basic repository of digital thematic maps and atlases of the regions of Siberia and neighboring territories.

The basic repository of digital thematic maps and atlases of the regions of Siberia and neighboring territories.

Diversidade lexical do português de comunidades indígenas do Médio Xingu

O presente estudo apresenta resultados do mapeamento da diversidade lexical do português brasileiro falado em comunidades Asuriní do Xingu e em comunidades Araweté, etnias indígenas que habitam no município de Altamira no estado do Pará. Os resultados limitam-se aos itens lexicais “banguela” e “cigarro de palha” do questionário semântico-lexical que integra o projeto Atlas Linguístico do Brasil. O estudo segue a orientação da Dialetologia pluridimensional e adota procedimentos de projetos de pesquisa que visam mapear línguas faladas por populações indígenas: o Atlas Linguístico do Português em Áreas Indígenas (ALIPAI) e o Atlas Linguístico Sonoro das Línguas Indígenas do Brasil (ALSLIB).

Relato de experiências exitosas na iniciação científica

Este estudo teve por objetivos relatar e refletir sobre duas experiências interdisciplinares na iniciação científica, desenvolvidas em conjunto por dois docentes que atuam em áreas distintas do conhecimento(saúdee tecnologia), em uma Instituição de Ensino Superior. Trata-se de uma pesquisa que descreve a trajetória metodológica dos projetos orientados, nos anos de 2015 e 2018. Discute-se a relação da integração e articulação ocorrida entre os docentes e, destes, com os discentes das duas áreas. Os produtos obtidos desta parceria, isto é, um atlas digital para o estudo de tecidos e um jogo educativo sobre a esquistossomose, do tipo serious game, demonstram a importância do desenvolvimento de trabalhos colaborativos e interdisciplinares na promoção de trocas de experiências, informações, desenvolvimento de habilidades e criação de ferramentas educativas que atendam às demandas de inovação tecnológica da educação contemporânea no ensino superior.

Comparative determination of skeletal maturity by hand-wrist radiograph, cephalometric radiograph and cone beam computed tomography.

The purpose of this study is to assess the stages of skeletal maturity in cone beam computed tomography (CBCT), hand-wrist radiography (HWR) and cephalometric radiography (CR) techniques of orthodontic patients, and associate skeletal maturity stages with chronological age, in a Turkish subpopulation. Hand-wrist radiographs, cephalometric radiographs and CBCT of 105 patients were evaluated. For evaluation of HWR, the "Hand Bone Age A Digital Atlas of Skeletal Maturity" of Vicente Gilsanz and Osman Ratib (2005) was used. Skeletal maturation in the cephalometric radiographs and sagittal sections of cervical vertebrae obtained by CBCT were evaluated with Hassel and Farman's method (1995). All results were re-evaluated 3weeks later to assess intra-observer reliability. Intra-observer reliability coefficients of the skeletal maturity stages in HWR, CR, and CBCT were 0.912, 0.595, 0.756 respectively (p < 0.05). Spearman's correlation coefficient value between skeletal developmental stages in in HWR, CR, and CBCT was found to be 0.785, 0.875, and 0.791, respectively (p < 0.05). Results of this study reveal that the determination of the skeletal development status with analysis of cervical vertebrae using cephalometric radiographs and CBCT is as reliable method as the evaluation of the hand-wrist radiographs and is compatible with chronological age in a subgroup of the Turkish population. When assessingthe skeletal development stages of patients, both CBCT and CR can be used validly, so no extra hand-wrist radiography is required. This information is important for the prevention of increased radiation doses in patients.

Characterization of the olfactory system of the giant honey bee, Apis dorsata

Apis dorsata is an open-nesting, undomesticated, giant honey bee found in southern Asia. We characterized a number of aspects of olfactory system of Apis dorsata and compared it with the well-characterized, western honeybee, Apis mellifera, a domesticated, cavity-nesting species. A. dorsata differs from A. mellifera in nesting behavior, foraging activity, and defense mechanisms. Hence, there can be different demands on its olfactory system. We elucidated the glomerular organization of A. dorsata by creating a digital atlas for the antennal lobe and visualized the antennal lobe tracts and localized their innervations. We showed that the neurites of Kenyon cells with cell bodies located in a neighborhood in calyx retain their relative neighborhoods in the pedunculus and the vertical lobe forming a columnar organization in the mushroom body. The vertical lobe and the calyx of the mushroom body were found to be innervated by extrinsic neurons with cell bodies in the lateral protocerebrum. We found that the species was amenable to olfactory conditioning and showed good learning and memory retention at 24h after training. It was also amenable to massed and spaced conditioning and could distinguish trained odor from an untrained novel odor. We found that all the abovementioned features in A. dorsata are very similar to those in A. mellifera. We thereby establish A. dorsata as a good model system, strikingly similar to A. mellifera despite the differences in their nesting and foraging behavior.

Структура и информационное наполнение электронного атласа изменений климата Урала

Структура и информационное наполнение электронного атласа изменений климата Урала

Topic Selection and Structure in the National Atlas of Switzerland

Topic Selection and Structure in the National Atlas of Switzerland

Creating a Digital Atlas of French Public Architecture (1795–1840)

Abstract. After the French Revolution, a national council called Conseil des bâtiments civils was put in charge of the nation's public architecture. Its aim was to build the Republic, providing the necessary infrastructure to establish the new political power and to control public space. The CONBAVIL database consists in the compiled statements of the council meetings, from its creation in 1795 until 1840. It therefore contains all civil building projects pertaining to this time, as each project was examined by the council due to nation-wide administrative centralisation. This database is currently available on the web, yet its use is constrained to interrogation through a static form. Each query returns a list of results which can be studied individually. This model makes limited use of the digital potential within the database and restricts exploration of its contents.In this presentation, the focus will be set on the intrinsically spatial nature of the data. Beyond the immediate implementation of architecture in space, civil buildings were planned and constructed with spatial awareness on local, regional and national scales. What kind of interface can render these characteristics of the CONBAVIL data? Furthermore, how can it impact discovery and knowledge production? My hypothesis is that creating an interactive interface focused on visual and spatial approaches to the data will enable discovery and foster new theories on its contents. My thesis therefore consists in the editorialization and visualization of the CONBAVIL database into a Digital Atlas of French Public Architecture.

3DCellAtlas Meristem: a tool for the global cellular annotation of shoot apical meristems

Modern imaging approaches enable the acquisition of 3D and 4D datasets capturing plant organ development at cellular resolution. Computational analyses of these data enable the digitization and analysis of individual cells. In order to fully harness the information encoded within these datasets, annotation of the cell types within organs may be performed. This enables data points to be placed within the context of their position and identity, and for equivalent cell types to be compared between samples. The shoot apical meristem (SAM) in plants is the apical stem cell niche from which all above ground organs are derived. We developed 3DCellAtlas Meristem which enables the complete cellular annotation of all cells within the SAM with up to 96% accuracy across all cell types in Arabidopsis and 99% accuracy in tomato SAMs. Successive layers of cells are identified along with the central stem cells, boundary regions, and layers within developing primordia. Geometric analyses provide insight into the morphogenetic process that occurs during these developmental processes. Coupling these digital analyses with reporter expression will enable multidimensional analyses to be performed at single cell resolution. This provides a rapid and robust means to perform comprehensive cellular annotation of plant SAMs and digital single cell analyses, including cell geometry and gene expression. This fills a key gap in our ability to analyse and understand complex multicellular biology in the apical plant stem cell niche and paves the way for digital cellular atlases and analyses.

Landmark‐based multi‐region ensemble convolutional neural networks for bone age assessment

AbstractBone age assessment based on hand X‐ray imaging is important in pediatry medicine. At present, prediction of bone age is mainly performed by the manual comparison with the existing atlas. To develop an automatic regression framework based on deep learning with high performance and efficiency. A landmark‐based multi‐region convolutional neural networks for automatic bone age assessment based on left hand X‐ray images was proposed. The deep alignment network localized multiple landmarks distributed over the hand, and cropped the local regions to establish the multi‐region ensemble convolutional neural networks with different sub‐network combinations. The modified loss function and the optimized bone sub‐regions were applied to train the networks. The experiments on Digital Hand Atlas Database revealed that the mean absolute error of bone age assessment was 0.52 ± 0.25 years. It is the first study to predict bone age using deep learning methods throughout the entire process including image preprocessing, landmark localization and bone age predication. The proposed method outperformed most of the existing state‐of‐the‐art deep learning methods and achieved good results compared with the expert's experience. It can improve the efficiency of the medical doctors while minimizing the subjective errors.

The Digital Urban Atlas of Jeddah: Some Raised Issues and &amp;lt;i&amp;gt;Semiological&amp;lt;/i&amp;gt; Principles

The “Technological Transition” has had a tremendous impact on cartographic processes and outputs. Atlases, whether national, regional or urban, were affected as they moved from a static to an animated and interactive era. The overall positive development, consolidated by map automation and map animation, has taken various forms and directions. Nevertheless, some graphic and cartographic outputs, especially atlases, still suffer from serious pitfalls, regarding some semiological aspects of the resulting maps and graphics. The Digital Urban Atlas of Jeddah (DUAJ) is a research in progress aware of such deficiencies. It tries to spare it from some frequent errors in map design related to: the choice of the base map, the use of some frequent symbols such as columns and pie charts for multivariate quantitative data, and the alternative solutions to choropleth maps. These deficiencies are selected and examined among others. The authors are convinced that the generated maps and diagrams that should be produced in digital atlases must be examined with regards to the semiological rules that drew upon the theory of signs perception. They try to incorporate the basic principles of graphic semiology reviewed, corrected and adapted to the GIS requirements. This is also meant to avoid map noises and deficiencies. The goal is to attract future Digital Atlases producers towards developing higher interest in map look and design and users to grasp messages rapidly. Specifically, the use of GIS and linked spatial databases within the DUAJ should not pay attention only to data handling and crossing, but also, to the semiological features of the outputs and relevant visual communication. In its preliminary stage, the DUAJ should give answers not only to the three questions raised in this research but also to others not examined here. This is to prevent from incorrect, irrelevant or inadequate use of the cartographic tools and, following the analysis of concrete examples, to propose a set of recommendations in establishing maps and graphics. When necessary, the DUAJ GIS-based outputs are inserted in CAD or CAC systems to benefit from some their specific visual tricks and subtleties that yield better legibility and efficiency of communication for Atlases users as recommended by authors. This experience is discussed regarding its eventual contribution to better map reading through some examples of maps and graphics from the DUAJ project (in progress).

Primary study on computer-aided qualitative and quantitative radial thin-layer chromatography methods for analysis of Yiqing tablets

Radial thin-layer chromatography (RTLC) is a form of chromatography in which the sample and developing agent/solvent are applied at the edge of a circle on the silica-layered TLC plate. The sample components are radially transported from the center of the circle toward the periphery by the solvent flow. RTLC is an efficient separation and semi-preparation method, with the advantages of fast separation, low diffusion, and absence of tailing at a certain distance. Although RTLC isolation has been well documented in the literature, there are only a few qualitative and quantitative reports on this technique. In this study, a self-programming module combined with image processing software was adopted for digital processing of RTLC images, and a digital atlas was created. Qualitative and quantitative verification of RTLC was then conducted. With the aid of computer technology, qualitative and quantitative methods of radially expanded TLC for Yiqing tablets were investigated. The results showed that the qualitative RTLC method has good reliability, but the quantitative RTLC method has inherent drawbacks, which may be associated with the experimental environment. We strongly believe that better separation and data acquisition equipment, as well as the combination of computer image processing and programming methods, will open up infinite possibilities of analysis/separation using RTLC-based techniques. We also believe that TLC will take a new step in the future with the assistance of computer technology.

Statistical Shape Models: Understanding and Mastering Variation in Anatomy.

In our chapter we are describing how to reconstruct three-dimensional anatomy from medical image data and how to build Statistical 3D Shape Models out of many such reconstructions yielding a new kind of anatomy that not only allows quantitative analysis of anatomical variation but also a visual exploration and educational visualization. Future digital anatomy atlases will not only show a static (average) anatomy but also its normal or pathological variation in three or even four dimensions, hence, illustrating growth and/or disease progression.Statistical Shape Models (SSMs) are geometric models that describe a collection of semantically similar objects in a very compact way. SSMs represent an average shape of many three-dimensional objects as well as their variation in shape. The creation of SSMs requires a correspondence mapping, which can be achieved e.g. by parameterization with a respective sampling. If a corresponding parameterization over all shapes can be established, variation between individual shape characteristics can be mathematically investigated.We will explain what Statistical Shape Models are and how they are constructed. Extensions of Statistical Shape Models will be motivated for articulated coupled structures. In addition to shape also the appearance of objects will be integrated into the concept. Appearance is a visual feature independent of shape that depends on observers or imaging techniques. Typical appearances are for instance the color and intensity of a visual surface of an object under particular lighting conditions, or measurements of material properties with computed tomography (CT) or magnetic resonance imaging (MRI). A combination of (articulated) Statistical Shape Models with statistical models of appearance lead to articulated Statistical Shape and Appearance Models (a-SSAMs).After giving various examples of SSMs for human organs, skeletal structures, faces, and bodies, we will shortly describe clinical applications where such models have been successfully employed. Statistical Shape Models are the foundation for the analysis of anatomical cohort data, where characteristic shapes are correlated to demographic or epidemiologic data. SSMs consisting of several thousands of objects offer, in combination with statistical methods or machine learning techniques, the possibility to identify characteristic clusters, thus being the foundation for advanced diagnostic disease scoring.