scholarly journals Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers

2021 ◽  
Author(s):  
Xiang Liu ◽  
Bo Zhao ◽  
Timothy Shaw ◽  
Brooke Fridley ◽  
Derek Duckett ◽  
...  
Keyword(s):  
Computational Method ◽  
Differential Analysis ◽  
Internal Dynamics ◽  
Functional Interpretation ◽  
Disease Mechanisms ◽  
Structural Differences ◽  
Different Types ◽  
Public Datasets ◽  
Regulatory Properties ◽  
State Of Art

Super enhancers (SEs) are broad enhancer domains usually containing multiple constitute enhancers with significantly elevated activities. The constitute enhancers work together through chromatin looping to build up distinct regulatory properties of SEs. Aberrant SE activities, which are critical to understand disease mechanisms, could be raised by the alterations of one or more of their constitute enhancers. However, the state-of-art binary strategy in calling differential SEs only relies on overall activity changes, neglecting the local differences of constitute enhancers within SEs. We propose a computational method to identify differential SEs by accounting for the combinatorial effects of constitute enhancers weighted with their activities and locations (internal dynamics). In addition to overall changes, our method finds four novel types of differential SEs pointing to the structural differences within SEs. When applied to public datasets for six cancer cells, we demonstrate that different types of differential SEs complement each other with distinct sets of gene targets and varied degrees of regulatory impacts. More importantly, we found that some cell-specific genes are linked to SE structural differences specifically, suggesting improved sensitivity by our methods in identifying and interpreting differential SEs. Such improvements further lead to increased discernment of cell identifies.

scholarly journals SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Wei Zhang ◽  
Meng Bo Wang ◽  
Shuai Cheng Li
Keyword(s):  
Structural Information ◽  
Current Method ◽  
Structural Proteins ◽  
Robust Detection ◽  
Topologically Associating Domains ◽  
Topologically Associated Domains ◽  
Significant Enrichment ◽  
High Consistency ◽  
Public Datasets ◽  
State Of Art

AbstractTopologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees. However, the current method for computing coding trees is not optimal. In this paper, we propose optimal algorithms for this computation. In comparison with seven state-of-art methods using two public datasets, from GM12878 and IMR90 cells, SuperTAD shows a significant enrichment of structural proteins around detected boundaries and histone modifications within TADs and displays a high consistency between various resolutions of identical Hi-C matrices.

Optimization of Cold-Formed Channel Sections Using Imperialist Competitive Algorithm

2012 ◽  
Vol 166-169 ◽  
pp. 493-496
Author(s):  
Roya Kohandel ◽  
Behzad Abdi ◽  
Poi Ngian Shek ◽  
M.Md. Tahir ◽  
Ahmad Beng Hong Kueh
Keyword(s):  
Sequential Quadratic Programming ◽  
Optimization Problems ◽  
Imperialist Competitive Algorithm ◽  
Computational Method ◽  
Compression Force ◽  
Sqp Method ◽  
Competitive Algorithm ◽  
Different Types ◽  
Formed Channel ◽  
Good Agreement

The Imperialist Competitive Algorithm (ICA) is a novel computational method based on the concept of socio-political motivated strategy, which is usually used to solve different types of optimization problems. This paper presents the optimization of cold-formed channel section subjected to axial compression force utilizing the ICA method. The results are then compared to the Genetic Algorithm (GA) and Sequential Quadratic Programming (SQP) algorithm for validation purpose. The results obtained from the ICA method is in good agreement with the GA and SQP method in terms of weight but slightly different in the geometry shape.

scholarly journals B-1 cell: the precursor of a novel mononuclear phagocyte with immuno-regulatory properties

2009 ◽  
Vol 81 (3) ◽  
pp. 489-496 ◽  
Author(s):  
José Daniel Lopes ◽  
Mario Mariano
Keyword(s):  
Mammalian Cells ◽  
Giant Cells ◽  
Mononuclear Phagocyte ◽  
Different Types ◽  
Series Of Experiments ◽  
B1 Cells ◽  
Regulatory Properties

Characterization of the origin, properties, functions and fate of cells is a fundamental task for the understanding of physiological and pathological phenomena. Despite the bulk of knowledge concerning the diverse characteristics of mammalian cells, some of them, such as B-1 cells, are still poorly understood. Here we report the results obtained in our laboratory on these cells in the last 10 years. After showing that B-1 cells could be cultured and amplified in vitro, a series of experiments were performed with these cells. They showed that B1 cells reside mostly in the peritoneal and pleural cavities, migrate to distant inflammatory foci, coalesce to form giant cells and participate in granuloma formation, both in vitro and in vivo. They are also able to present antigens to immunologically responsive cells and are endowed with regulatory properties. Further, we have also shown that these cells facilitate different types of infection as well as tumor growth and spreading. These data are presently reviewed pointing to a pivotal role that these cells may play in innate and acquired immunity.

scholarly journals Air quality sensors in public transport stops and cross-system communication

2021 ◽  
Vol 3 (1) ◽  
pp. 5-10
Author(s):  
Dan-Marius Mustață
Keyword(s):  
Air Quality ◽  
Public Transport ◽  
Traffic Management ◽  
Transport Systems ◽  
View Point ◽  
System Communication ◽  
Warning Messages ◽  
Different Types ◽  
Cross System ◽  
State Of Art

The purpose of this article is to present a state of art implementation of air quality sensors in public transport stops. Effects on health due to different types of pollutants are summarized as well. Functional scope of the solutions, via warning messages displayed for passengers waiting at these stops, including a cross system communication between traffic management and public transport systems, are also focused. Analysis of existing sensor types from multiple view point including functions, types of measured pollutants, price ranges and comparisons are outlined.

scholarly journals Amyloid Oligomer Structures and Toxicity

2009 ◽  
Vol 2 (1) ◽  
pp. 222-227
Author(s):  
Charles G. Glabe
Keyword(s):  
Neurodegenerative Diseases ◽  
Broad Spectrum ◽  
Degenerative Diseases ◽  
Mechanisms Of Toxicity ◽  
Membrane Pores ◽  
Disease Mechanisms ◽  
Amyloid Accumulation ◽  
Amyloid Oligomers ◽  
Different Types ◽  
Amyloid Oligomer

Amyloid accumulation is commonly associated with a number of important human degenerative diseases and recent findings indicate that soluble amyloid oligomers may represent the primary pathological species in degenerative diseases. Amyloid oligomers are structurally and morphologically diverse, raising the question on whether this diversity is pathologically significant and whether different types of oligomers may have different toxic activities. Many of the amyloids associated with neurodegenerative diseases form three immunologically distinct types of oligomers. Fibrillar oligomers are structurally related to fibrils and may represent small pieces of fibrils or fibril protofilaments. Prefibrillar oligomers are kinetic intermediates in fibril formation and annular protofibrils that resemble membrane pores. These three classes of oligomers share common structures and toxic activities. Focus on these common mechanisms of toxicity provides a means of simplifying the list of primary disease mechanisms and opens the possibility of developing broad spectrum therapeutics that target several amyloid related degenerative diseases.

Assessing the Utilization of Automata in Representing Players' Behaviors in Game Theory

Game Theory ◽  
2017 ◽  
pp. 106-119
Author(s):  
Khaled Suwais
Keyword(s):  
Game Theory ◽  
Cellular Automata ◽  
Finite Automata ◽  
The State ◽  
The Other ◽  
Direct Impact ◽  
Complex Environments ◽  
Other Hand ◽  
Different Types ◽  
State Of Art

Representing players' strategies in game theory has a direct impact on the players' performance. The state of art shows that automata are one of the primary techniques used for representing players' strategies and behaviors. In this paper, the author will identify different types of automata and assess their utilization in the field of game theory. Is has been found that finite automata, adaptive automata, and cellular automata are widely adopted in game theory. The utilization of finite automata is found to be limited to represent simpler players' behavior. On the other hand, adaptive automata and cellular automata are intensively applied in complex environments, where the number of interacted players is large and therefore, representing complex behaviors are needed.

An Approach to Legal Principles Based on Their Justifying Function

2019 ◽  
Vol 32 (02) ◽  
pp. 321-342 ◽  
Author(s):  
Juan B. Etcheverry
Keyword(s):  
Legal Reasoning ◽  
Legal Principles ◽  
Structural Differences ◽  
Different Types ◽  
The Way

AbstractThis paper intends to throw light upon some aspects of the debate on the characterization of legal principles and on their differences when compared to rules. Particularly, this analysis proposes differentiating principles from rules by considering the functions they perform in law instead of their structural differences. To achieve this, we distinguish between the functions of guidance and justification that legal principles fulfill. From that distinction, we observe that the attempt to characterize legal principles based on the way in which they guide conduct does not seem to be the most appropriate either. In contrast, this paper tries to show that all the different types of precepts known as principles perform a justifying function in legal reasoning.

scholarly journals Synchronisation phenomenon in three blades rotor driven by regular or chaotic oscillations

2018 ◽  
Vol 148 ◽  
pp. 06002
Author(s):  
Zofia Szmit ◽  
Jerzy Warmiński
Keyword(s):  
Time Series ◽  
Numerical Calculation ◽  
Duffing Oscillator ◽  
Equations Of Motion ◽  
Composite Beams ◽  
Chaotic Oscillations ◽  
Rotating System ◽  
Chaotic Motions ◽  
Structural Differences ◽  
Different Types

The goal of the paper is to analysed the influence of the different types of excitation on the synchronisation phenomenon in case of the rotating system composed of a rigid hub and three flexible composite beams. In the model is assumed that two blades, due to structural differences, are de-tuned. Numerical calculation are divided on two parts, firstly the rotating system is exited by a torque given by regular harmonic function, than in the second part the torque is produced by chaotic Duffing oscillator. The synchronisation phenomenon between the beams is analysed both either for regular or chaotic motions. Partial differential equations of motion are solved numerically and resonance curves, time series and Poincaré maps are presented for selected excitation torques.

scholarly journals PRESEE: An MDL/MML Algorithm to Time-Series Stream Segmenting

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Kaikuo Xu ◽  
Yexi Jiang ◽  
Mingjie Tang ◽  
Changan Yuan ◽  
Changjie Tang
Keyword(s):  
Time Series ◽  
Real Time ◽  
Processing Speed ◽  
Data Stream ◽  
Minimum Description Length ◽  
Data Types ◽  
Minimum Message Length ◽  
Message Length ◽  
Different Types ◽  
State Of Art

Time-series stream is one of the most common data types in data mining field. It is prevalent in fields such as stock market, ecology, and medical care. Segmentation is a key step to accelerate the processing speed of time-series stream mining. Previous algorithms for segmenting mainly focused on the issue of ameliorating precision instead of paying much attention to the efficiency. Moreover, the performance of these algorithms depends heavily on parameters, which are hard for the users to set. In this paper, we proposePRESEE(parameter-free, real-time, and scalable time-series stream segmenting algorithm), which greatly improves the efficiency of time-series stream segmenting. PRESEE is based on both MDL (minimum description length) and MML (minimum message length) methods, which could segment the data automatically. To evaluate the performance of PRESEE, we conduct several experiments on time-series streams of different types and compare it with the state-of-art algorithm. The empirical results show that PRESEE is very efficient for real-time stream datasets by improving segmenting speed nearly ten times. The novelty of this algorithm is further demonstrated by the application of PRESEE in segmenting real-time stream datasets from ChinaFLUX sensor networks data stream.

scholarly journals WhichTF is dominant in your open chromatin data?

2019 ◽  
Author(s):  
Yosuke Tanigawa ◽  
Ethan S. Dyer ◽  
Gill Bejerano
Keyword(s):  
Cell Fate ◽  
Molecular Mechanisms ◽  
Computational Prediction ◽  
Cell Types ◽  
Mouse Cell ◽  
Careful Consideration ◽  
Computational Method ◽  
Open Chromatin ◽  
Differential Analysis ◽  
Putative Gene

AbstractWe present WhichTF, a novel computational method to identify dominant transcription factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF integrates high-confidence genome-wide computational prediction of TF binding sites based on evolutionary sequence conservation, putative gene-regulatory models, and ontology-based gene annotations. Applying WhichTF, we find that the identified dominant TFs have been implicated as functionally important in well-studied cell types, such as NF-κB family members in lymphocytes and GATA factors in cardiac tissue. To distinguish the transcriptional regulatory landscape in closely related samples, we devise a differential analysis framework and demonstrate its utility in lymphocyte, mesoderm developmental, and disease cells. We also find TFs known for stress response in multiple samples, suggesting routine experimental caveats that warrant careful consideration. WhichTF yields biological insight into known and novel molecular mechanisms of TF-mediated transcriptional regulation in diverse contexts, including human and mouse cell types, cell fate trajectories, and disease-associated tissues.

Sign in / Sign up

Export Citation Format

Share Document