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2,453 results for “Architecture”
Multiple Nuclei HeLa cell ground truth images with four labels (nuclear envelope, nucleus, rest of the cell, and background) for deep learning architecture training.
<p>This is a data set that contains <strong>labelled HeLa cell images</strong>, indicating the four different classes - nuclear envelope, nucleus, rest of the cell, and background. Similar ground truth have been published for this data set, but in this case, multiple nuclei have been labelled, whilst previous ones only focused on the central cell (https://doi.org/10.5281/zenodo.3874949)</p> <p>Details of the imaging, preparation and segmentation have been published in:</p> <ul> <li>Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro. Segmentation and Modelling of the Nuclear Envelope of HeLa Cells Imaged with Serial Block Face Scanning Electron Microscopy. <em>J. Imaging</em> <strong>2019</strong>, <em>5</em>(9), 75; <a href="https://doi.org/10.3390/jimaging5090075">https://doi.org/10.3390/jimaging5090075</a></li> <li>Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro. Semantic segmentation of HeLa cells: An objective comparison between one traditional algorithm and four deep-learning architectures, PLOS ONE, <strong>2020</strong>; <a href="https://doi.org/10.1371/journal.pone.0230605">https://doi.org/10.1371/journal.pone.0230605</a></li> <li> <p>Cefa Karabağ, Martin L. Jones, Constantino Carlos Reyes-Aldasoro, Segmentation of the Plasma Membrane of HeLa Cells,<em> J. Imaging</em> <strong>2021</strong>, <em>7</em>(6), 93; <a href="https://doi.org/10.3390/jimaging7060093">https://doi.org/10.3390/jimaging7060093</a></p> </li> </ul> <ul> <li>The data sets are freely available through EMPIAR: http://dx.doi.org/10.6019/EMPIAR-10094 EMPIAR.</li> </ul>
Additional Material for Architecture Smell Ontology
<p>This is the dataset of our literature review study on Architecture Smells. We provide the decisive exclusion criteria for excluded studies and the classification for included studies. We exported OWL file of the ontology from Protégé and included the tables of the architecture smells and the connected quality attributes and design principles. The study protocol is also included.</p> <p> </p>
The Surface Biology and Geology Architecture Study Science and Applications Traceability Matrix (SATM)
<p>This dataset provides a synthesis of the National Academies of Sciences 2017 Earth Science Decadal Survey mission most and very important objectives for the Surface Biology and Geology Earth Observing system consisting of a global visible to shortwave infrared imaging spectrometer and a multi-spectral thermal infrared radiometer. These objectives are traced to performance criteria used for assessing hundreds of potential architecture variants in an architecture study outlined in a paper titled: "Designing an Observing System to Study the Surface Biology and Geology (SBG) of the Earth in the 2020s".</p>
FIGURE 12 in Nest Architecture, Immature Stages, and Ethnoentomology of a New Species of Trigonisca from Northern Colombia (Hymenoptera: Apidae)
FIGURE 12. SEM micrographs of mature larva of Trigonisca (Trigonisca) mepecheu Engel and Gonzalez, new species. A. Entire larva, oblique frontal view. B. Close-up of pro- and mesothoracic segments showing paired segmental dorsolateral tubercles (arrows) and distribution of fine spicules. C. Close-up of meso- and metathoracic segments and of first abdominal segment showing dorsolateral tubercles along left side as well as distribution of fine spicules. D. Head, frontal view, demonstrating extreme width, and showing pronounced, dome-shaped antennae. E. Same, oblique lateral view. F. Close-up of labrum and mandibles, frontal view, showing cluster of multipronged spicules at lower edge of labrum as well as sharp-pointed mandibles. G. Close-up of left side of cluster of multipronged spicules along lower edge of labrum and sharply toothed upper edge of left mandible, possibly used as comb to push provisions through prongs toward esophagus.
Additional files for manuscript titled 'The double round-robin population unravels the genetic architecture of grain size in barley'
<p>Additional file 1: Parental allele for barley orthologs of genes controlling grain size in rice</p> <p>Additional file 2: Cross-validation of quantitative trait loci (QTLs) detected for grain size characters in rice</p> <p>Additional file 3: Adjusted entry means of recombinant inbred lines of 45 HvDRR sub-populations</p>
Manhattan and QQ plots of GWAS on salt stress responses in root system architecture parameters of wild tomato (S. pimpinellifolium)
<p>The population of +/2 200 accessions of wild tomato was screened with the protocol described <a href="https://www.protocols.io/view/studying-root-system-architecture-changes-in-tomat-2mqgc5w">here</a> with the only exception that the plants were transferred 4 days after germination (rather than 3 - described in the protocol). The images were analyzed using the <a href="https://smartroot.github.io/">SmartRoot</a> for days 0, 1, 2, 3, and 4 after transfer to treatment plates (0 or 100 mM NaCl, 1/4 MS, 0.5% sucrose, 0.1% MES, 1% Dashin agar). The data analysis was performed as described <a href="https://rpubs.com/mjulkowska/BIGpimp_RSA_salt">here</a>, while the pareto front calculations were done according to Chandrasekhar & Julkowska paper (<a href="https://www.biorxiv.org/content/10.1101/2021.08.12.456185v1">preprint here</a>). The GWAS was performed using the ASReml script similar to <a href="https://onlinelibrary.wiley.com/doi/10.1111/tpj.15310">Awlia et al. (2021)</a>. The raw GWAS outputs can be found <a href="https://zenodo.org/badge/DOI/10.5281/zenodo.5856310.svg">here</a>. This dataset represents Manhattan plots and QQ plots made out of the data. </p>
Genetic architecture of adaptive radiation across two trophic levels
<p>Evolution of trophic diversity is a hallmark of adaptive radiation. Yet, transitions between carnivory and herbivory are rare in young adaptive radiations. Haplochromine cichlid fish of the African Great Lakes are exceptional in this regard. Lake Victoria was colonized by an insectivorous generalist and in less than 20,000 years, several clades of specialized herbivores evolved. Carnivorous versus herbivorous lifestyles in cichlids require many different adaptations in functional morphology, physiology, and behaviour. Ecological transitions in either direction thus require many traits to change in a concerted fashion, which could be facilitated if genomic regions underlying these traits were physically linked or pleiotropic. However, linkage/pleiotropy could also constrain evolvability. To investigate components of the genetic architecture of a suite of traits that distinguish invertivores from algae scrapers, we performed Quantitative Trait Locus (QTL) mapping using a second-generation hybrid cross. While we found indications of linkage/pleiotropy within trait complexes, QTLs for distinct traits were distributed across several unlinked genomic regions. Thus, a mixture of independently segregating variation and some pleiotropy may underpin the rapid trophic transitions. We argue that the emergence and maintenance of associations between the different genomic regions underpinning co-adapted traits that evolved and persist against some gene flow required reproductive isolation.</p>
Trained Models from "General Cross-Architecture Distillation of Pretrained Language Models into Matrix Embeddings"
<p>Trained models from the paper:</p> <p>Lukas Galke, Isabell Cuber, Christoph Meyer, Henrik Ferdinand Noelscher, Angelina Sonderecker, and Ansgar Scherp: <strong>General Cross-Architecture Distillation of Pretrained Language Models into Matrix Embeddings</strong>, in: <em>International Joint Conference on Neural Networks (IJCNN), </em>2022.</p> <ul> <li>File seq2mat_hybrid_bidirectional_sbertlike-100p-bsz512 holds the model from pretraining</li> <li>File ws2020_transformer_final_models holds the fine-tuned models for each task of the GLUE benchmark</li> </ul>
API Description-Based Conformance Assessment of Architectural Design Decision: Dataset and Code
<p>This is the dataset and related code artifact for the article "API Description-Based Conformance Assessment of Architectural Design Decision".</p> <p><strong>Abstract of the article:</strong></p> <p>Microservice APIs are often designed based on Domain-Driven Design. It can be challenging to judge the quality<br> of the relation between such a design and the implemented API, especially when facing frequent releases and changes in an API and its design models. Conformance assessment aims to improve software quality by bridging the gap between design and implementation. However, manual conformance assessment is time-intensive and error prone. This paper proposes a novel approach for automated conformance assessment of API designs in relation to API design decisions. Our approach aims to provide<br> the first fully automated conformance assessment approach based solely on the code of API Descriptions such as OpenAPI. We<br> applied and exemplified our approach for checking conformance to the patterns and practices in an API design decision for mapping links in a system’s domain model to API representations. The total accuracy score (F1-measure) for decision option identification in our multi-case study for this decision is 97.22%.</p>
Additional Material for Debiasing architectural decision-making: a workshop-based training approach
<p>This additional material was created to enable full replication of the experiment described in the paper:<br> "Klara Borowa, Maria Jarek, Gabriela Mystkowska, Weronika Paszko and Andrzej Zalewski: <strong>Debiasing architectural decision-making: a workshop-based training approach</strong>".<br> The paper was accepted for publication at ECSA 2022 (The 16th European Conference on Software Architecture).<br> <br> The folder contains the following files:<br> Coding-details.xlsx - the coding scheme, as well as coding results. Contains all code counts for each team participating in the experiment.<br> Experiment-meeting-plan.pdf - contains the plan for the 3-hour meeting during which the experiment was conducted, as well as a timetable of when each meeting took place and who organised it.<br> Debiasing-workshop-slides.pdf - slides used during the debiasing workshop.<br> Debiasing-workshop-plan.pdf - detailed instruction for workshop organisers, what should be said and done during the workshop.<br> Participants_questionnaire_and_results.xlsx - questionnaire questions used to obtain information about participants, as well as questionnaire results for all 44 participants.</p>
Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
<p>These files are results obtained in<br><span><span><span><span>Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts</span></span></span></span><br>by Yoshito Hirata, Arisa H. Oda, Chie Motono, Masanori Shiro & Kunihiro Ohta.</p> <p>There are 33 files for the corresponding each reconstruction of three-dimensional chromosomone structures<br>for each cell.<br>There are 3D structures for 15 GM cells and 18 PBMC cells, which are obtained from the single cell Hi-C data of Tan et al. Science (2018).</p> <p>For each file, there are 6 columns:<br>The first column corresponds to the allele (0: maternal, 1: paternal)<br>The second column corresponds to the chromosome (1-22: chromosome's number, 23: X, 24: Y)<br>The third column corrsponds to the base point.<br>The fourth column, the fifth column and the sixth column correspond to x-, y-, and z-axes of our reconstruction.</p>
Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species
<p>These data are the numerical values that underlie the Figures 1 - 4, and the Supplementary Figures 1 - 10 for the article "Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species" by the same authors. The content of the data files is organized according to the figures and figure panels of this article. </p>
Consensus of Game Engine Architectures: an Overview of Coupling and Subsystems in Game Engines
<p>The video game industry is one of the most innovative, competitive, and rapidly growing industries. The industry's successes along with the increasing gamers’ expectations result in always larger and more complex games. These games thus must be developed with game engines, which have become correspondingly more sophisticated. Today, game engine developers find game engine development challenging. To support the process of creating and maintaining game engines, we propose applying an approach based on a consensus algorithm to a set of game engine architectures. Our approach generates a model that suggests the most commonly used subsystems in game engine architectures, ranked by their degree of coupling. The model can be used by developers as a starting point when deciding what subsystems to include when building a game engine and points out the most coupled subsystems, which can play an important role towards higher subsystems maintainability and reusability. We evaluate our approach by comparing the results of our approach against a predefined ground truth data. The result of our approach matches the subsystems defined in the ground truth data and it shows that the most coupled subsystems are core, low-level rendering, third-party SDKs and world editor. Additionally, when comparing game engine architectures, we observe that most architectures are composed of nearly the same set of subsystems. </p>
Data for: Associations between leaf developmental stability, canalization and phenotypic plasticity in an architectural perspective
<p class="MsoNormal"><span>Associations between developmental stability, canalization and phenotypic plasticity have been predicted, but rarely supported by direct evidence. Architectural analysis may provide a more powerful approach to finding correlations among these mechanisms in plants. T</span><span>o investigate the relationships among the three mechanisms in architectural perspective, w</span><span>e </span><span>subjected plants of </span><em><span>Abutilon theophrasti</span></em><span> to three densities, measured and calculated </span><span>fluctuating asymmetry (FA), coefficients of variation (CV)</span><span> and </span><span>plasticity (PI) of three leaf traits, to analyze the </span><span>correlations among these variables.</span><span> As density increased, mean leaf size, petiole length and angle of most layers and mean leaf FA of some layers decreased (at both stages), CV of petiole angle increased (at day 50), and PI of petiole length and angle across all layers decreased (at day 70); leaf FA and CV of traits generally increased with higher layers at all densities. At both stages, there were more positive correlations between FA and CV at lower vs. high densities; at day 50, little correlation of plasticity with FA or CV was found; at day 70, more positive correlations between FA and PI occurred for response to high vs. low density than for response to medium vs. low density, and more positive correlations between CV and PI occurred at lower vs. high densities. Results suggested that developmental instability, decreased canalization and plasticity can be cooperative and the relationships between decreased canalization and plasticity are more likely to be positive if decreased canalization is due to vibrant growth rather than stressful effects. The relationships of plasticity with developmental instability differed from its relationship with decreased canalization in the way of variation. Decreased canalization should be more beneficial for possible plasticity in the future, while canalization may result from already-expressed plasticity.</span></p>
Figure 4. Portal Logical Architecture-A Proposed Data Driven Architecture for Cardiology Network Application
<p>The applications that are based on a SOA environment can be configured to work both<br> as services exchanging data in point to point protocol and as a communication channel<br> between two entities that call a service provided by an entity that has the role of mediator or<br> broker. The letter can be seen as intermediary level that represents an “enterprise service bus”<br> (ESB) between service producers and consumers, offering messaging exchange services.</p>
Figure 2. System General View-A Proposed Data Driven Architecture for Cardiology Network Application
<p>Figure 2 presents a general schematic overview of the medical informational system,<br> underlying the main roles in the system together with their interactions. From an architectural<br> point of view one can identify the following main components:<br> • Host systems, named local (medical data) production systems<br> • General Practitioner system<br> • Analysis Laboratory system<br> • Hospital system<br> • Client system (interface to remote devices)<br> • Local portal (regional, national) for medical assistance, and long term data storage<br> Host systems consist of database servers connected through access points with<br> fixed/mobile medical devices. The portal will supply the functionality necessary to collect<br> information from the local interconnected systems into a centralized repository. Medical<br> services will be provided at portal level using specialized web-services that will allow access<br> to data stored in the repository.</p>
Figure 1. Schema for a data-integration solution-A Proposed Data Driven Architecture for Cardiology Network Application
<p>Data integration has favored loosening the coupling between data. This may involve<br> providing a uniform query interface over a mediated schema (see figure 1), thus transforming<br> a query into specialized queries over the original databases. One can also term this process<br> "view-based query-answering" because each of the data sources functions as a view over the<br> (nonexistent) mediated schema.</p>
Figure 3. Data Integration Sample-A Proposed Data Driven Architecture for Cardiology Network Application
<p>Pentaho Data Integration has implemented a metadata-driven approach where you<br> only specify the data you want integrated, but you do not specify the way you want it done.<br> One of the most important advantages of Pentaho is that one can create complex<br> transformations and jobs in a graphical, drag-and-drop environment without having to create<br> proprietary custom code that will work only with some proprietary application.</p>
Figure 2: The design tool architecture
<p>Taking in consideration the two important aspects considered above, we de¯ne<br> the architecture of the design tool (Figure. 2). We observe that there is a<br> database where we store the instances of each diagram and the details of the<br> di®erent users that, according to the metaphor, can participate in the de¯nition<br> of a speci¯c model (Storyboard Artist, Designer, Pedagogic people, Technical<br> users). The engine of the design tool accesses to the database using a database<br> access object layer (DAO). The DAO has the task to abstract and encapsulates<br> all accesses to the data source; it manages the connection with the data source<br> to obtain and store data. The output of the design will be an XML ¯le: the<br> xml ¯le will be the input for a CVE engine that will automatically generate<br> the collaboration virtual environment. It is important to note that the CVE<br> engine may use a set of template useful for the designer. The editor must<br> present to the user these templates in order to help him in its design task.</p>
Figure 1: The Architecture
<p>The application My E-Wall could permit to propose a more interesting section in a customized portal, and also it could permit to use semantics to filter the collected information,according to the user preferences. Until now we have only implemented the first two layer of the architecture that generates an ontology starting from the wesite’s database. In the section 2 we present the proposed architecture. In the sections 3 and 4 we explain and detail all the architecture layers, instead the section 5 contains conclusions and future works.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.