917 research outputs found
SmartCanvas: Context-inferred Interpretation of Sketches for Preparatory Design Studies
In early or preparatory design stages, an architect or designer sketches out rough ideas, not only about the object or structure being considered, but its relation to its spatial context. This is an iterative process, where the sketches are not only the primary means for testing and refining ideas, but also for communicating among a design team and to clients. Hence, sketching is the preferred media for artists and designers during the early stages of design, albeit with a major drawback: sketches are 2D and effects such as view perturbations or object movement are not supported, thereby inhibiting the design process. We present an interactive system that allows for the creation of a 3D abstraction of a designed space, built primarily by sketching in 2D within the context of an anchoring design or photograph. The system is progressive in the sense that the interpretations are refined as the user continues sketching. As a key technical enabler, we reformulate the sketch interpretation process as a selection optimization from a set of context-generated canvas planes in order to retrieve a regular arrangement of planes. We demonstrate our system (available at http:/geometry.cs.ucl.ac.uk/projects/2016/smartcanvas/) with a wide range of sketches and design studies
A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex determining gene in the flatfish Solea senegalensis
Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 SNP variants in the follicle stimulating hormone receptor (fshr) consistent with an XX / XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. Fshr displayed differential gene expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 non-synonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.info:eu-repo/semantics/acceptedVersio
Management of visual clutter in annotated 3D CAD models: A comparative study
The use of annotations in CAD models has been an active area of research because of their ability to connect design information to specific aspects of the model s geometry. The effectiveness of annotations is determined by the ability to clearly communicate information. However, annotations can quickly create clutter and confusion as they increase both in number and complexity. Consequently, efficient interaction and visualization mechanisms become crucial. Despite recent standardizations of procedures for the presentation of textual information in CAD models, no explicit guidelines are available as to how to make annotated models more readable and manageable. In this paper, we present the results of a comparative study of different mechanisms to manage visual clutter in annotated 3D CAD models and offer recommendations based on our findings. Our results show that even basic interaction mechanisms have a substantial impact on user s performanceCamba, J.; Contero, M.; Johnson, M. 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FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform
BACKGROUND: Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. RESULTS: Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset). The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. CONCLUSION: The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest
CAD-Based Porous Scaffold Design of Intervertebral Discs in Tissue Engineering
With the development and maturity of three-dimensional (3D) printing technology over the past decade, 3D printing has been widely investigated and applied in the field of tissue engineering to repair damaged tissues or organs, such as muscles, skin, and bones, Although a number of automated fabrication methods have been developed to create superior bio-scaffolds with specific surface properties and porosity, the major challenges still focus on how to fabricate 3D natural biodegradable scaffolds that have tailor properties such as intricate architecture, porosity, and interconnectivity in order to provide the needed structural integrity, strength, transport, and ideal microenvironment for cell- and tissue-growth. In this dissertation, a robust pipeline of fabricating bio-functional porous scaffolds of intervertebral discs based on different innovative porous design methodologies is illustrated. Firstly, a triply periodic minimal surface (TPMS) based parameterization method, which has overcome the integrity problem of traditional TPMS method, is presented in Chapter 3. Then, an implicit surface modeling (ISM) approach using tetrahedral implicit surface (TIS) is demonstrated and compared with the TPMS method in Chapter 4. In Chapter 5, we present an advanced porous design method with higher flexibility using anisotropic radial basis function (ARBF) and volumetric meshes. Based on all these advanced porous design methods, the 3D model of a bio-functional porous intervertebral disc scaffold can be easily designed and its physical model can also be manufactured through 3D printing. However, due to the unique shape of each intervertebral disc and the intricate topological relationship between the intervertebral discs and the spine, the accurate localization and segmentation of dysfunctional discs are regarded as another obstacle to fabricating porous 3D disc models. To that end, we discuss in Chapter 6 a segmentation technique of intervertebral discs from CT-scanned medical images by using deep convolutional neural networks. Additionally, some examples of applying different porous designs on the segmented intervertebral disc models are demonstrated in Chapter 6
Towards the Understanding of the Human Genome: A Holistic Conceptual Modeling Approach
[EN] Understanding the human genome is a great scientific challenge, whose achievement requires effective data manipulation mechanisms. The non-stop evolution of both new knowledge and more efficient sequencing technologies generates a kind of genome data chaos. This chaos complicates the use of computational resources that obtain data and align them into specific actions. Conceptual model-based techniques should play a fundamental role in turning data into actionable knowledge. However, current solutions do not give a crucial role in the task of modeling that it should have to obtain a precise understanding of this domain. Hundreds of different data sources exist, but they have heterogeneous, imprecise, and inconsistent data. It is remarkably hard to have a unified data perspective that covers the genomic data from genome to transcriptome and proteome, which could facilitate semantic data integration. This paper focuses on how to design a conceptual model of the human genome that could be used as the key artifact to share, integrate, and understand the various types of datasets used in the genomic domain. We provide a full conceptual picture of relevant data in genomics and how semantic data integration is much more effective by conceptually integrating the diverse types of existing data. We show how such a conceptual model has been built, focusing on the conceptual problems that were solved to adequately model concepts whose knowledge is under constant evolution. We show how the use of the initial versions of the conceptual model in practice has allowed us to identify new features to incorporate in the model, achieving a continuous improvement process. The current version is ready to be used as the key artifact in projects where conceptually combining multiple levels of data helps to provide valuable insights that would be hard to obtain without it.This work was supported in part by the Spanish State Research Agency, in part by the Generalitat Valenciana under Grant TIN2016-80811-P and Grant PROMETEO/2018/176, and in part by European Regional Development Fund (ERDF).García-Simón, A.; León-Palacio, A.; Reyes Román, JF.; Casamayor Rodenas, JC.; Pastor López, O. (2020). Towards the Understanding of the Human Genome: A Holistic Conceptual Modeling Approach. IEEE Access. 8:197111-197123. https://doi.org/10.1109/ACCESS.2020.3034793S197111197123
Procedures as Programs: Hierarchical Control of Situated Agents through Natural Language
When humans conceive how to perform a particular task, they do so
hierarchically: splitting higher-level tasks into smaller sub-tasks. However,
in the literature on natural language (NL) command of situated agents, most
works have treated the procedures to be executed as flat sequences of simple
actions, or any hierarchies of procedures have been shallow at best. In this
paper, we propose a formalism of procedures as programs, a powerful yet
intuitive method of representing hierarchical procedural knowledge for agent
command and control. We further propose a modeling paradigm of hierarchical
modular networks, which consist of a planner and reactors that convert NL
intents to predictions of executable programs and probe the environment for
information necessary to complete the program execution. We instantiate this
framework on the IQA and ALFRED datasets for NL instruction following. Our
model outperforms reactive baselines by a large margin on both datasets. We
also demonstrate that our framework is more data-efficient, and that it allows
for fast iterative development
Depict: A Tool to Represent Classroom Scenarios
A functional version of Depict can be found at www.lessonsketch.orgThis document describes design features of Depict, a web based software that allows users to represent classroom scenarios using comics. The document provides the conceptual bases of the design and a description of the user interface. The document also sketches out a direction for further development.This work has been done with support from NSF grants ESI-0353285 and DRL- 0918425 to Patricio Herbst.http://deepblue.lib.umich.edu/bitstream/2027.42/87949/1/Depict_2011.pdf-
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