scholarly journals BHi-Cect: a top-down algorithm for identifying the multi-scale hierarchical structure of chromosomes

2020 ◽  
Vol 48 (5) ◽  
pp. e26-e26
Author(s):  
Vipin Kumar ◽  
Simon Leclerc ◽  
Yuichi Taniguchi
Keyword(s):  
Hierarchical Structure ◽  
Detection Methods ◽  
Interaction Patterns ◽  
Top Down ◽  
Chromosome Conformation ◽  
Multi Scale ◽  
Topologically Associating Domains ◽  
Genome Wide ◽  
The Hierarchical Structure ◽  
Respective Function

Abstract High-throughput chromosome conformation capture (Hi-C) technology enables the investigation of genome-wide interactions among chromosome loci. Current algorithms focus on topologically associating domains (TADs), that are contiguous clusters along the genome coordinate, to describe the hierarchical structure of chromosomes. However, high resolution Hi-C displays a variety of interaction patterns beyond what current TAD detection methods can capture. Here, we present BHi-Cect, a novel top-down algorithm that finds clusters by considering every locus with no assumption of genomic contiguity using spectral clustering. Our results reveal that the hierarchical structure of chromosome is organized as ‘enclaves’, which are complex interwoven clusters at both local and global scales. We show that the nesting of local clusters within global clusters characterizing enclaves, is associated with the epigenomic activity found on the underlying DNA. Furthermore, we show that the hierarchical nesting that links different enclaves integrates their respective function. BHi-Cect provides means to uncover the general principles guiding chromatin architecture.

scholarly journals Multi-scale Information Retrieval for BIM using Hierarchical Structure Modelling and Natural Language Processing

2021 ◽  
Vol 26 ◽  
pp. 409-426
Author(s):  
Jie Wang ◽  
Xinao Gao ◽  
Xiaoping Zhou ◽  
Qingshen Xie
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Natural Language ◽  
Hierarchical Structure ◽  
Language Processing ◽  
Tree Model ◽  
Multi Scale ◽  
Building Information ◽  
The Hierarchical Structure ◽  
Retrieval Scheme

Building Information Modelling (BIM) captures numerous information the life cycle of buildings. Information retrieval is one of fundamental tasks for BIM decision support systems. Currently, most of the BIM retrieval systems focused on querying existing BIM models from a BIM database, seldom studies explore the multi-scale information retrieval from a BIM model. This study proposes a multi-scale information retrieval scheme for BIM jointly using the hierarchical structure of BIM and Natural Language Processing (NLP). Firstly, a BIM Hierarchy Tree (BIH-Tree) model is constructed to interpret the hierarchical structure relations among BIM data according to Industry Foundation Class (IFC) specification. Secondly, technologies of NLP and International Framework for Dictionaries (IFD) are employed to parse and unify the queries. Thirdly, a novel information retrieval scheme is developed to find the multi-scale information associated with the unified queries. Finally, the retrieval method proposed in this study is applied to an engineering case, and the practical results show that the proposed method is effective.

scholarly journals Semantic Relatedness Emerges in Deep Convolutional Neural Networks Designed for Object Recognition

2021 ◽  
Vol 15 ◽  
Author(s):  
Taicheng Huang ◽  
Zonglei Zhen ◽  
Jia Liu
Keyword(s):  
Neural Networks ◽  
Object Recognition ◽  
Convolutional Neural Networks ◽  
Hierarchical Structure ◽  
Semantic Relatedness ◽  
Developmental Trajectory ◽  
Top Down ◽  
Deep Convolutional Neural Networks ◽  
Object Categories ◽  
The Hierarchical Structure

Human not only can effortlessly recognize objects, but also characterize object categories into semantic concepts with a nested hierarchical structure. One dominant view is that top-down conceptual guidance is necessary to form such hierarchy. Here we challenged this idea by examining whether deep convolutional neural networks (DCNNs) could learn relations among objects purely based on bottom-up perceptual experience of objects through training for object categorization. Specifically, we explored representational similarity among objects in a typical DCNN (e.g., AlexNet), and found that representations of object categories were organized in a hierarchical fashion, suggesting that the relatedness among objects emerged automatically when learning to recognize them. Critically, the emerged relatedness of objects in the DCNN was highly similar to the WordNet in human, implying that top-down conceptual guidance may not be a prerequisite for human learning the relatedness among objects. In addition, the developmental trajectory of the relatedness among objects during training revealed that the hierarchical structure was constructed in a coarse-to-fine fashion, and evolved into maturity before the establishment of object recognition ability. Finally, the fineness of the relatedness was greatly shaped by the demand of tasks that the DCNN performed, as the higher superordinate level of object classification was, the coarser the hierarchical structure of the relatedness emerged. Taken together, our study provides the first empirical evidence that semantic relatedness of objects emerged as a by-product of object recognition in DCNNs, implying that human may acquire semantic knowledge on objects without explicit top-down conceptual guidance.

scholarly journals Comparative Multi-scale Hierarchical Structure of the Tail, Plantaris, and Achilles Tendons in the Rat

2018 ◽  
Author(s):  
Andrea H. Lee ◽  
Dawn M. Elliott
Keyword(s):  
Hierarchical Structure ◽  
Single Species ◽  
Confocal Imaging ◽  
Multi Scale ◽  
Multiple Length Scales ◽  
Human Pathology ◽  
The Hierarchical Structure ◽  
Characteristic Features ◽  
Definition Of ◽  
Species Specific

AbstractRodent tendons are widely used to study human pathology, such as tendinopathy and repair, and to address fundamental physiological questions about development, growth, and remodeling. However, how the gross morphology and the multi-scale hierarchical structure of rat tendons, such as the tail, plantaris, and Achillles tendons, compare to that of human tendons are unknown. In addition, there remains disagreement about terminology and definitions. Specifically, the definition of fascicle and fiber are often dependent on the diameter size and not their characteristic features, which impairs the ability to compare across species where the size of the fiber and fascicle might change with animal size and tendon function. Thus, the objective of the study was to select a single species that is widely used for tendon research (rat) and tendons with varying mechanical functions (tail, plantaris, Achilles) to evaluate the hierarchical structure at multiple length scales. This study was designed including, histology, SEM, and confocal imaging. We confirmed that rat tendons do not contain fascicles, and thus the fiber is the largest tendon subunit in the rat. In addition, we provided a structurally-based definition of a fiber as a bundle of collagen fibrils that is surrounded by elongated cells, and this definition was supported by both histologically processed and unprocessed tendons. In all rat tendons studied, the fiber diameters were consistently 10-50 µm, and this diameter appears to be conserved across larger species. Specific recommendations were made for the strengths and limitations of each rat tendon as tendon research models. Understanding the hierarchical structure of tendon can advance the design and interpretation of experiments and development of tissue engineered constructs.

scholarly journals Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms

2018 ◽  
Author(s):  
Andres M Cardozo Gizzi ◽  
Diego I. Cattoni ◽  
Jean-Bernard Fiche ◽  
Sergio Espinola ◽  
Julian Gurgo ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Spatial Information ◽  
Multiple Scales ◽  
Simultaneous Detection ◽  
Chromosome Organization ◽  
Chromosome Conformation ◽  
Chromosome Architecture ◽  
Multi Scale ◽  
The Awakening ◽  
Genome Wide

Eukaryotic chromosomes are organized in multiple scales, from nucleosomes to chromosome territories. Recently, genome-wide methods identified an intermediate level of chromosome organization, topologically associating domains (TADs), that play key roles in transcriptional regulation. However, these methods cannot directly examine the interplay between transcriptional activation and chromosome architecture while maintaining spatial information. Here, we present a multiplexed, sequential imaging approach (Hi-M) that permits the simultaneous detection of chromosome organization and transcription in single nuclei. This allowed us to unveil the changes in 3D chromatin organization occurring upon transcriptional activation and homologous chromosome un-pairing during the awakening of the zygotic genome in intact Drosophila embryos. Excitingly, the ability of Hi-M to explore the multi-scale chromosome architecture with spatial resolution at different stages of development or during the cell cycle will be key to understand the mechanisms and consequences of the 4D organization of the genome.

Parafia unicka w Rachaniach do 1811 roku/ The Uniate Parish in Rachanie until 1811

2012 ◽  
Vol 67 (2) ◽  
Author(s):  
Janusz Adam Frykowski
Keyword(s):  
Hierarchical Structure ◽  
Geographical Location ◽  
Historical Sources ◽  
Holy Communion ◽  
The Hierarchical Structure ◽  
History Of ◽  
The Church ◽  
Ancillary Equipment

AbstractThe following paper depicts the history of Saint Simeon Stylites Uniate Parish in Rachanie since it became known in historical sources until 1811- that is the time it ceased to be an independent church unit. The introduction of the article contains the geographical location of the parish, its size and the position within the hierarchical structure of the Church. Having analysed post-visit inspection protocols left by Chelm Bishops, the appearance as well as fittings and ancillary equipment of the church in Rachanie in that particular period are reported. Moreover, the list of 4 local clergymen is recreated and their benefice is determined. As far as possible, both the number of worshipers and the number of Holy Communion receivers is determined.

Default Logic Models of Certain Inheritance Systems with Exceptions

1993 ◽  
Vol 18 (2-4) ◽  
pp. 129-149
Author(s):  
Serge Garlatti
Keyword(s):  
Hierarchical Structure ◽  
Formal Semantics ◽  
Sufficient Conditions ◽  
Nonmonotonic Reasoning ◽  
Default Logic ◽  
Representation Systems ◽  
The Hierarchical Structure ◽  
Necessary And Sufficient ◽  
Structure Of Knowledge ◽  
Made In

Representation systems based on inheritance networks are founded on the hierarchical structure of knowledge. Such representation is composed of a set of objects and a set of is-a links between nodes. Objects are generally defined by means of a set of properties. An inheritance mechanism enables us to share properties across the hierarchy, called an inheritance graph. It is often difficult, even impossible to define classes by means of a set of necessary and sufficient conditions. For this reason, exceptions must be allowed and they induce nonmonotonic reasoning. Many researchers have used default logic to give them formal semantics and to define sound inferences. In this paper, we propose a survey of the different models of nonmonotonic inheritance systems by means of default logic. A comparison between default theories and inheritance mechanisms is made. In conclusion, the ability of default logic to take some inheritance mechanisms into account is discussed.

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