Hierarchy Of Domains Research Articles

HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.

We present a major update of the HOCOMOCO collection that provides DNA binding specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make this release, we performed motif discovery in peak sets that originated from 14 183 ChIP-Seq experiments and reads from 2554 HT-SELEX experiments yielding more than 400 thousand candidate motifs. The candidate motifs were annotated according to their similarity to known motifs and the hierarchy of DNA-binding domains of the respective transcription factors. Next, the motifs underwent human expert curation to stratify distinct motif subtypes and remove non-informative patterns and common artifacts. Finally, the curated subset of 100 thousand motifs was supplied to the automated benchmarking to select the best-performing motifs for each transcription factor. The resulting HOCOMOCO v12 core collection contains 1443 verified position weight matrices, including distinct subtypes of DNA binding motifs for particular transcription factors. In addition to the core collection, HOCOMOCO v12 provides motif sets optimized for the recognition of binding sites in vivo and in vitro, and for annotation of regulatory sequence variants. HOCOMOCO is available at https://hocomoco12.autosome.org and https://hocomoco.autosome.org.

DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells.

Topologically associating domains (TADs) are functional chromatin units with hierarchical structure. However, the existence, prevalence, and dynamics of such hierarchy in single cells remain unexplored. Here, a new generation TAD-like domain (TLD) detection algorithm, named deDoc2, to decode the hierarchy of TLDs in single cells, is reported. With dynamic programming, deDoc2 seeks genome partitions with global minimal structure entropy for both whole and local contact matrix. Notably, deDoc2 outperforms state-of-the-art tools and is one of only two tools able to identify the hierarchy of TLDs in single cells. By applying deDoc2, it is showed that the hierarchy of TLDs in single cells is highly dynamic during cell cycle, as well as among human brain cortex cells, and that it is associated with cellular identity and functions. Thus, the results demonstrate the abundance of information potentially encoded by TLD hierarchy for functional regulation. The deDoc2 can be freely accessed at https://github.com/zengguangjie/deDoc2.

Personality change through a digital-coaching intervention: Using measurement invariance testing to distinguish between trait domain, facet, and nuance change

Recent intervention research has shown that personality traits can be modified through psychological interventions. However, it is unclear whether reported effects represent changes in the trait domain or only some facets or items. Using data ( N = 552) from a recent intervention trial, the present study examined the effects of a digital-coaching intervention on self- and observer-reported personality facets and items. We focused on participants who wanted to decrease in Negative Emotionality, increase in Conscientiousness or increase in Extraversion. We used measurement invariance testing to examine which level of the trait domain hierarchy changed during the intervention. For the self-reports, we found some heterogeneity in the effects on all three trait domains, but most notably Extraversion and Conscientiousness. Specifically, participants reported to increase strongly on sociability (Extraversion), and moderately on productiveness and organization (Conscientiousness), but not on the other facets of these trait domains. Observers generally reported small but non-significant changes, with no scalar invariance violations except for Extraversion. Overall, this suggests considerable heterogeneity in intervention-related personality change that can be overlooked if only focusing on the trait domain level. We discuss the relevance of measurement invariance testing and measurement approaches for personality development and intervention research.

A proof of the instability of AdS for the Einstein-massless Vlasov system

In recent years, the conjecture on the instability of Anti-de Sitter spacetime, put forward by Dafermos–Holzegel (Dynamic instability of solitons in 4 + 1 dimesnional gravity with negative cosmological constant, 2006. https://www.dpmms.cam.ac.uk/~md384/ADSinstability.pdf) and Dafermos (The Black Hole Stability problem, Talk at the Newton Institute, Cambridge, 2006. http://www-old.newton.ac.uk/webseminars/pg+ws/2006/gmx/1010/dafermos/) in 2006, has attracted a substantial amount of numerical and heuristic studies. Following the pioneering work (Phys Rev Lett 107(3):031102, 2011) of Bizon–Rostworowski, research efforts have been mainly focused on the study of the spherically symmetric Einstein-scalar field system. The first rigorous proof of the instability of AdS in the simplest spherically symmetric setting, namely for the Einstein-null dust system, was obtained in Moschidis (A proof of the instability of AdS for the Einstein-null dust system with an inner mirror, 2017. arXiv:1704.08681). In order to circumvent problems associated with the trivial break down of the Einstein-null dust system occuring at the center r=0, Moschidis (2017) studied the evolution of the system in the exterior of an inner mirror placed at r=r_{0}, r_{0}>0. However, in view of additional considerations on the nature of the instability, it was necessary for Moschidis (2017) to allow the mirror radius r_{0} to shrink to 0 with the size of the initial perturbation; well-posedness in the resulting complicated setup (involving low-regularity estimates of uniform modulus with respect to r_{0}) was obtained in Moschidis (The Einstein-null dust system in spherical symmetry with an inner mirror: structure of the maximal development and Cauchy stability, 2017. arXiv:1704.08685). In this paper, we establish the instability of AdS for the Einstein-massless Vlasov system in spherical symmetry; this will be the first proof of the AdS instability conjecture for an Einstein-matter system which is well-posed for regular initial data in the standard sense, without the addition of an inner mirror. The necessary well-posedness results for this system are obtained in our companion paper (Moschidis in The characteristic initial-boundary value problem for the Einstein-massless Vlasov system in spherical symmetry, 2018. arXiv:1812.04274). Our proof utilises an instability mechanism based on beam interactions which is superficially similar to the one appearing in Moschidis (A proof of the instability of AdS for the Einstein-null dust system with an inner mirror, 2017. arXiv:1704.08681). However, new difficulties associated with the Einstein-massless Vlasov system (such as the need for control on the paths of non-radial geodesics in a large curvature regime) will force us to develop a different strategy of proof involving a novel configuration of beam interactions. One of the main novelties of our construction is the introduction of a multi-scale hierarchy of domains in phase space, on which the initial support of the Vlasov field f is localised. The propagation of this hierarchical structure of the support of f along the evolution will be crucial both for controlling the geodesic flow under minimal regularity assumptions and for guaranteeing the existence of the solution until the time of trapped surface formation.

P440. Investigation of Multivariate Associations Between Brain Volume and Dimensions of Psychopathology in Children

Psychopathology can be conceptualized as a hierarchy of dimensional symptom domains, with common and dissociable neural substrates. While many studies of brain-behavior relationships rely on univariate analyses, multivariate approaches allow us to examine relationships between psychopathology and neural substrates simultaneously. There are multiple multivariate approaches to consider. Each approach has important effects on the interpretation of the results; however, there are few studies illustrating their potential differences.

Fractal and Knot-Free Chromosomes Facilitate Nucleoplasmic Transport

Chromosomes in the nucleus assemble into hierarchies of 3D domains that, during interphase, share essential features with a knot-free condensed polymer known as the fractal globule (FG). The FG-like chromosome likely affects macromolecular transport, yet its characteristics remain poorly understood. Using computer simulations and scaling analysis, we show that the 3D folding and macromolecular size of the chromosomes determine their transport characteristics. Large-scale subdiffusion occurs at a critical particle size where the network of accessible volumes is critically connected. Condensed chromosomes have connectivity networks akin to simple Bernoulli bond percolation clusters, regardless of the polymer models. However, even if the network structures are similar, the tracer's walk dimension varies. It turns out that the walk dimension depends on the network topology of the accessible volume and dynamic heterogeneity of the tracer's hopping rate. We find that the FG structure has a smaller walk dimension than other random geometries, suggesting that the FG-like chromosome structure accelerates macromolecular diffusion and target-search.

Secure Conflicts Avoidance in Multidomain Environments: A Distributed Approach

In a multidomain application environment, it is of paramount importance for different organizations to collaborate with each other to facilitate secure interoperation. However, various types of conflicts related to access control constraints may arise as a result of integrating access control policies for individual domains, such as role inheritance violations (RIVs) and separation of duty violations (SoDVs). Current methods solve the conflicts in a centralized way by withdrawing or removing all crossdomain relationships resulting in the violations with the knowledge of all domains. However, these methods are inappropriate for large-scale systems due to their high computational complexity. In this article, we propose a distributed approach to avoid secure conflicts in a multidomain environment. We first model the role inheritance hierarchies of multiple domains as an interoperation graph. We then develop RIVs and SoDVs avoidance algorithms based on the interoperation graph and the communications among different domains. Each domain can execute the algorithms autonomously and in real time by evaluating whether its succeeding activated role can result in RIVs and SoDVs. We show that the new algorithms perform well in contrast to the existing algorithms.

Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions.

A growing amount of evidence in literature suggests that germline sequence variants and somatic mutations in non-coding distal regulatory elements may be crucial for defining disease risk and prognostic stratification of patients, in genetic disorders as well as in cancer. Their functional interpretation is challenging because genome-wide enhancer–target gene (ETG) pairing is an open problem in genomics. The solutions proposed so far do not account for the hierarchy of structural domains which define chromatin three-dimensional (3D) architecture. Here we introduce a change of perspective based on the definition of multi-scale structural chromatin domains, integrated in a statistical framework to define ETG pairs. In this work (i) we develop a computational and statistical framework to reconstruct a comprehensive map of ETG pairs leveraging functional genomics data; (ii) we demonstrate that the incorporation of chromatin 3D architecture information improves ETG pairing accuracy and (iii) we use multiple experimental datasets to extensively benchmark our method against previous solutions for the genome-wide reconstruction of ETG pairs. This solution will facilitate the annotation and interpretation of sequence variants in distal non-coding regulatory elements. We expect this to be especially helpful in clinically oriented applications of whole genome sequencing in cancer and undiagnosed genetic diseases research.

Ferroelastic domain hierarchy in the intermediate state of PbZr0.98Ti0.02O3 single crystal

PbZrO3-based antiferroelectric crystals are of great interest in both fundamental and applied research, not only because of the antiferroelectric feature at room temperature but also because of the existence of a peculiar intermediate state at elevated temperatures. Here, we report a detailed description of domain structure change at the temperature-induced antiferroelectric-to-ferroelectric phase transition. A complex process of different types of domains is revealed to appear at different stages of the phase transition. A hierarchical ferroelastic domain structure forms in the stabilized intermediate state, where the dense domain walls show potential impact on the physical properties of the crystal.

How CSR Affects Polish Enterprises

Purpose: The article refers to the assessment of the activities of enterprises within CSR, according to the classification adopted in the Carroll’s pyramid model. Research on CSR issues in this approach has been conducted since the 1980s and is usually addressed to the top management. Design/Approach/Methodology: This article is based on research on the attitude to CSR activities of managers / employees at the operational level; in this way we endeavour to fill a certain cognitive gap. The research included a representative sample of large and medium-sized enterprises in Poland, including representativeness by economy sectors. Findings: The research results point to a different hierarchy of CSR domains than that suggested by the Carroll’s pyramid (and most of the results of previous research addressed to the top management). The highest rated by respondents was legal responsibility, before ethical, and only third place was taken by economic responsibility. Practical Implications: The research results could be useful for managers responsible for CSR impleneting and developing. Originality/Value: The article contributed to filling the cognitive gap regarding priorities declared by CSR managers, i.e. persons implementing CSR activities on behalf of enterprises in practice. The research results indicate that the respondent's job position (the scope of duties related to CSR) and the economic sector they represent have the greatest impact on the valuation of individual areas of CSR, while the size of the enterprise has a weak impact.

Collecting and analyzing data jointly from multiple services under local differential privacy

Users' sensitive data can be collected and analyzed under local differential privacy (LDP) without the need to trust the data collector. Most previous work on LDP can be applied when each user's data is generated and collected from a single service or data source. In a more general and practical setting, sensitive data of each user needs to be collected under LDP from multiple services independently and can be joined on, e.g. , user id. In this paper, we address two challenges in this setting: first, how to prevent the privacy guarantee from being weakened during the joint data collection; second, how to analyze perturbed data jointly from different services. We introduce the notation of user-level LDP to formalize and protect the privacy of a user when her joined data tuples are released. We propose mechanisms and estimation methods to process multidimensional analytical queries, each with sensitive attributes (in its aggregation and predicates) collected and perturbed independently in multiple services. We also introduce an online utility optimization technique for multi-dimensional range predicates, based on consistency in domain hierarchy. We conduct extensive evaluations to verify our theoretical results using synthetic and real datasets.

Tracking and Visualization of Functional Domains in Stratified Metal-Organic Frameworks Using Gold Nanoparticles.

We report here a new technique for the identification and visualization of functional domains in stratified metal–organic frameworks (MOFs). The technique, namely, gold diffusion enabled domain identification, utilizes the diffusion of Au nanoparticles within MOF cavities to track and selectively stain the more Au-philic domain in an MOF particle thereby allowing direct observation of domains, determination of domain sequences, and, in certain cases, domain boundaries under transmission electron microscopy. This method is an excellent tool for studying MOF materials with complex domain hierarchy.

“A Beautiful Mind” or “Proof of Life”: Historical Information Science and/or Digital History?

The article studies integration processes which have been characteristic of humanities in the second half of the twentieth century, the changing configuration of interdisciplinary fields and the redistribution of the interdisciplinary hierarchy of science domains as well as the role of historical information science in a strong or a weak integration type of scientific knowledge. Historical information science is a classical example of interdisciplinary interaction (match) of several fields (history, source studies, applied mathematics, mathematical statistics and information science). This supradisciplinary form of integration connects history with mathematization and informatization as well as principles and methods of the general theory of systems, the information theory, synergetics, etc. In this respect, the article focuses on the impact of the digital turn on the relationship between historical information science, digital history and digital humanities as well as methodological problems of information source studies rather than digital documents studies. The author states that new prospects provided by the “digital revolution” set new goals for history in the 21st century.

Construction of the REACHES climate database based on historical documents of China

This paper describes the methodology of an ongoing project of constructing an East Asian climate database REACHES based on Chinese historical documents. The record source is Compendium of Meteorological Records of China in the Last 3000 Years which collects meteorology and climate related records from mainly official and local chronicles along with a small number of other documents. We report the digitization of the records covering the period 1644–1795. An example of the original records is translated to illustrate the typical contents which contain time, location and type of events. Chinese historical times and location names are converted into Gregorian calendar and latitudes and longitudes. A hierarchical database system is developed that consists of the hierarchies of domains, main categories, subcategories, and further details. Historical events are then digitized and categorized into such a system. Code systems are developed at all levels such that the original descriptive entries are converted into digitized records suitable for treatment by computers. Statistics and characteristics of the digitized records in the database are described.

Clients’ Experiences With Internet-Based Psychological Treatments for Mental Disorders: Protocol for a Metasynthesis of Qualitative Studies

BackgroundGiven the rise of internet-based treatments as an effective therapeutic tool for psychological disorders, it is necessary to carry out research that examines clients’ experiences with this type of intervention. The qualitative methodology has been found to be useful for analyzing clients’ perceptions in terms of facilitators and barriers, acceptability, and negative effects of internet-based treatments. However, a lack of integration of these primary studies has prevented their findings from being applied to new research and in clinical practice.ObjectiveThe objective of this paper is to describe the protocol for a metasynthesis of qualitative studies exploring the experiences of clients who underwent an internet-based treatment.MethodsElliot and Timulak’s metasynthesis approach will be used to review and synthesize qualitative studies related to client experiences in terms of the barriers and facilitators they perceived when undergoing internet-based treatment. For each search string, the features in the Sample, Phenomenon of Interest, Design, Evaluation, Research type (SPIDER) tool will be considered. Electronic databases (PubMed, PsycINFO, and Web of Science) will be searched. Two independent reviewers will analyze the material in order to determine whether the eligibility criteria are fulfilled. Findings will make it possible to create a hierarchy of domains in terms of their relevance across all the primary studies. The data obtained from primary studies will be cross-analyzed using descriptive and interpretative procedures.ResultsThe search strategy is currently being conducted. First results are expected to be submitted for publication in 2019.ConclusionsWe will develop conceptual framework of the barriers and facilitators perceived by clients and propose their implications and recommendations for clinical practice, research, and training.Trial RegistrationPROSPERO CRD42018079894; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=79894 (Archived by WebCite at http://www.webcitation.org/73C6OtlS7).International Registered Report Identifier (IRRID)PRR1-10.2196/9722

SHOPPING CENTRE SAFETY PROVIDED BY ARCHITECTURAL MEANS

Purpose: The aim of this paper is to study the relationship between the architectural characteristics of shopping centres and their safety. The scope of the study covers the architectural means which create a safe building environment. The author suggests to reduce criminality by means of architecture, urban and landscape design. These means can be applied after carrying out five analyses of a future architectural and master plan of building. The main stages of the safety performance are described and the architectural safety algorithm is developed either for future or existing buildings. Methodology/Design: Efforts are made to adapt and naturalize the proposed principles to shopping centres in Russia. A safety assessment method is derived and a more subtle approach to creating safe shopping centres is developed. The methodological basis of the study includes: analysis of examples of modern shopping centres designed with possible threats of criminal nature; comparative analysis of research and design approaches to a safe architectural environment; analysis of scientific and normative documents on minimization of criminal accidents in shopping centres; comparative analysis of principles, means and design techniques which increase the safety level of buildings; individual space classification by the level of access and required safety protection. Findings and results: A study of the safety principles is carried out with adaptation to shopping centres. The main types of crime accidents are identified according to the specificity of shopping centres. The main safety principles (territory, access monitoring, surveillance, etc.) are adapted to this type of buildings. A study of examples and recommendations on shopping centres allows identifying the main design algorithms for shopping centres accounting for the safety protection. A comparison of different types of threats and relevant architectural and planning protection methods allows detecting the main safety means for shopping centres. Practical implications: Architectural and planning methods of decriminalizing shopping centres can be used in reconstruction or design of new buildings; a comprehensive analysis of safety and recommendations on decriminalization can be used in reconstruction of existing buildings; a design algorithm for shopping centres can be implemented in new building design. Originality/value: Architectural means determine the formation of safe and protected shopping centres; development of design approaches to safety protection and individual building types; comprehensive analysis provides the evaluation of the building safety including the hierarchy of spaces and domains, visibility, stream of people, etc.; design algorithm is proposed taking into account the safety requirements and recommendations on the use of architectural means for shopping centre safety.

Hierarchical topic modeling with automatic knowledge mining

Traditional topic modeling has been widely studied and popularly employed in expert systems and information systems. However, traditional topic models cannot discover structural relations among topics, thus losing the chance to explore the data more deeply. Hierarchical topic modeling has the capability of learning topics, as well as discovering the hierarchical topic structure from text data. But purely unsupervised models tend to generate weak topic hierarchies. To solve this problem, we propose a novel knowledge-based hierarchical topic model (KHTM), which can incorporate prior knowledge into topic hierarchy building. A key novelty of this model is that it can mine prior knowledge automatically from the topic hierarchies of multiple domains corpora. In this paper, the knowledge is represented as the word pairs which satisfy the requirement of frequent co-occurrence, and knowledge is organized in form of hierarchical structure. We also propose an iterative learning algorithm. For evaluation, we crawled two new multi-domain datasets and conducted comprehensive experiments. The experimental results show that our algorithm and model can generate more coherent topics, and more reasonable hierarchical structure.

A novel approach for analysing evolutional motivation of empirical engineering knowledge

Empirical engineering knowledge (EEK), a specific technical know-how about solving engineering problems, is frequently accumulated and reused in this era of mass innovation and knowledge-driven economy. Since EEK is abidingly evolving because of the intense business competitions, continual technical renovations and wide industrial concern, it’s a new challenge both in theories and applications of knowledge management to analyse EEK evolution and its motivations. This paper proposes a novel approach to tackle this non-trivial issue. Based on the constructed domain hierarchy and EEK networks, EEK clusters are grouped and represented with populations, latent topics and distributions. Then four kinds of evolutional patterns are defined and recognised from the EEK clusters in neighbouring time intervals. The evolutional motivations of these patterns are discovered from the important evolutional events, with the proposed abductive reasoning algorithm. This paper also integrates all techniques, and implements a knowledge management system EEK-KEAS in computer-aided design (CAD), a typical engineering field. Experimental result shows that EEK-KEAS operations well in revealing the evolutional motivations of CAD EEKs, and outperforms the former approaches in feasibility and effectiveness, thereby opening up a novel way for further understanding the evolution of EEK.

The Hierarchies of Multivalued Attribute Domains and Corresponding Applications in Data Mining

In mobile computing, machine learning models for natural language processing (NLP) have become one of the most attractive focus areas in research. Association rules among attributes are common knowledge patterns, which can often provide potential and useful information such as mobile users′ interests. Actually, almost each attribute is associated with a hierarchy of the domain. Given an relation R = (U, A) and any cut αa on the hierarchy for every attribute a, there is another rough relation RΦ, where Φ = (αa : a ∈ A). This paper will establish the connection between the functional dependencies in R and RΦ, propose the method for extracting reducts in RΦ, and demonstrate the implementation of proposed method on an application in data mining of association rules. The method for acquiring association rules consists of the following three steps: (1) translating natural texts into relations, by NLP; (2) translating relations into rough ones, by attributes analysis or fuzzy k‐means (FKM) clustering; and (3) extracting association rules from concept lattices, by formal concept analysis (FCA). Our experimental results show that the proposed methods, which can be applied directly to regular mobile data such as healthcare data, improved quality, and relevance of rules.

Preliminary assessment of ecosystem risk based on IUCN criteria in a hierarchy of spatial domains: A case study in Southwestern China

World ecosystems are suffering great losses from anthropogenic and natural pressures. To meet the demand of ecosystem-level risk assessment for biodiversity conservation, the IUCN has adopted a global standard to assess the risk to ecosystems. The IUCN Red List of Ecosystems (IUCN RLE) is a growing tool to raise the public awareness of ecosystem conservation and provide reasonable strategies to managers. As for managing ecosystems with the RLE, the spatial information of degraded patches is important for the efficient allocation of conservation resources. In this paper, a method for assessment across hierarchy of spatial domains was designed to provide spatial information for the IUCN RLE. 105 natural ecosystems of vegetation in Southwestern China were systematically assessed at the hierarchy of spatial domains. According to the results, the declining distributions of most ecosystems have slowed down recently due to protection policies. All vegetative ecosystems containing nationally protected species are threatened, supporting the robustness of this protocol. Limited distributions and degradation in area are the key risk to threatened ecosystems, as threatened ecosystems account for only 1.55% of the total area and the mean of its degradation in area is almost 45%. With the assessment in the hierarchy of spatial domains, the IUCN RLE was featured with spatial information of degraded patches. The hierarchical assessment markedly improved the practical applications of RLE and led to an efficient allocation of conservation resources. The scale effect of hierarchical assessment was significant and the representativeness of ecosystems in systematic assessments is extremely valuable.