scholarly journals VOLTA: adVanced mOLecular neTwork Analysis

2021 ◽  
Author(s):  
Alisa Pavel ◽  
Antonio Federico ◽  
Giusy del Giudice ◽  
Angela Serra ◽  
Dario Greco
Keyword(s):  
Network Analysis ◽  
Clustering Algorithms ◽  
Expression Patterns ◽  
Direct Access ◽  
Supplementary Information ◽  
Complete Analysis ◽  
Wide Range ◽  
Novice Users ◽  
Analytical Step ◽  
The Individual

Abstract Motivation Network analysis is a powerful approach to investigate biological systems. It is often applied to study gene co-expression patterns derived from transcriptomics experiments. Even though co-expression analysis is widely used, there is still a lack of tools that are open and customizable on the basis of different network types and analysis scenarios (e.g. through function accessibility), but are also suitable for novice users by providing complete analysis pipelines. Results We developed VOLTA, a Python package suited for complex co-expression network analysis. VOLTA is designed to allow users direct access to the individual functions, while they are also provided with complete analysis pipelines. Moreover, VOLTA offers when possible multiple algorithms applicable to each analytical step (e.g. multiple community detection or clustering algorithms are provided), hence providing the user with the possibility to perform analysis tailored to their needs. This makes VOLTA highly suitable for experienced users who wish to build their own analysis pipelines for a wide range of networks as well as for novice users for which a ‘plug and play’ system is provided. Availability and implementation The package and used data are available at GitHub: https://github.com/fhaive/VOLTA and 10.5281/zenodo.5171719. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MOVICS: an R package for multi-omics integration and visualization in cancer subtyping

2020 ◽  
Author(s):  
Xiaofan Lu ◽  
Jialin Meng ◽  
Yujie Zhou ◽  
Liyun Jiang ◽  
Fangrong Yan
Keyword(s):  
Clustering Algorithms ◽  
R Package ◽  
Supplementary Information ◽  
Multiple Perspectives ◽  
Model Free ◽  
Omics Integration ◽  
Wide Range ◽  
Breast Cancer Cohort ◽  
The One ◽  
Minimal Effort

Abstract Summary Stratification of cancer patients into distinct molecular subgroups based on multi-omics data is an important issue in the context of precision medicine. Here, we present MOVICS, an R package for multi-omics integration and visualization in cancer subtyping. MOVICS provides a unified interface for 10 state-of-the-art multi-omics integrative clustering algorithms, and incorporates the most commonly used downstream analyses in cancer subtyping researches, including characterization and comparison of identified subtypes from multiple perspectives, and verification of subtypes in external cohort using two model-free approaches for multiclass prediction. MOVICS also creates feature rich customizable visualizations with minimal effort. By analysing two published breast cancer cohort, we signifies that MOVICS can serve a wide range of users and assist cancer therapy by moving away from the ‘one-size-fits-all’ approach to patient care. Availability and implementation MOVICS package and online tutorial are freely available at https://github.com/xlucpu/MOVICS. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Unsupervised Anomaly Detectors to Detect Intrusions in the Current Threat Landscape

2021 ◽  
Vol 2 (2) ◽  
pp. 1-26
Author(s):  
Tommaso Zoppi ◽  
Andrea Ceccarelli ◽  
Tommaso Capecchi ◽  
Andrea Bondavalli
Keyword(s):  
Intrusion Detection ◽  
Anomaly Detection ◽  
Binary Classification ◽  
Clustering Algorithms ◽  
Good Alternative ◽  
Experimental Comparison ◽  
Support Vector ◽  
Self Organizing Maps ◽  
Wide Range ◽  
The Individual

Anomaly detection aims at identifying unexpected fluctuations in the expected behavior of a given system. It is acknowledged as a reliable answer to the identification of zero-day attacks to such extent, several ML algorithms that suit for binary classification have been proposed throughout years. However, the experimental comparison of a wide pool of unsupervised algorithms for anomaly-based intrusion detection against a comprehensive set of attacks datasets was not investigated yet. To fill such gap, we exercise 17 unsupervised anomaly detection algorithms on 11 attack datasets. Results allow elaborating on a wide range of arguments, from the behavior of the individual algorithm to the suitability of the datasets to anomaly detection. We conclude that algorithms as Isolation Forests, One-Class Support Vector Machines, and Self-Organizing Maps are more effective than their counterparts for intrusion detection, while clustering algorithms represent a good alternative due to their low computational complexity. Further, we detail how attacks with unstable, distributed, or non-repeatable behavior such as Fuzzing, Worms, and Botnets are more difficult to detect. Ultimately, we digress on capabilities of algorithms in detecting anomalies generated by a wide pool of unknown attacks, showing that achieved metric scores do not vary with respect to identifying single attacks.

scholarly journals Transcriptome Analysis of Sugarcane in Response to Colletotrichum Falcatum Infection Reveals Repertoire of Transcription Factors and Host Targets

2021 ◽  
Author(s):  
C. Naveen Prasanth ◽  
Viswanathan Rasappa ◽  
P. Malathi ◽  
A.R. Sundar
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Complete Analysis ◽  
Colletotrichum Falcatum ◽  
Data Set ◽  
Challenge Inoculation ◽  
Wide Range ◽  
Pcr Assays

Abstract Background - Sugarcane (Saccharum spp hybrid), an important C4 perennial plantation crop, globally grown for white sugar and ethanol production. Red rot caused by Colletotrichum falcatum is one of the most important threats affecting sugarcane productivity in many countries including India.Materials and Methods - Comprehensive understanding is very much needed to define their transcription level differences and their key regulatory genes during interaction of sugarcane with C. falcatum. To compute and evaluate the molecular mechanism in sugarcane, transcriptome analysis of sugarcane challenged with C. falcatum was sequenced using Hi-Seq 2500 and gene expression profiles were generated by qRT-PCR assays in both compatible and incompatible interactions after challenge inoculation of C. falcatum in sugarcane.Results - A total of 15,728,914 reads were aligned to 48,935 unigenes using BOWTIE 2; the unigenes were annotated using BLASTX and found that 39,895 unigenes were annotated and 22,025 were unigenes with respect to host species, 8,830 with respect to Colletotrichum spp and 9,040 were found to be novel genes. A total of 243 transcription factors (TFs) were found to be predicted in sugarcane challenged with C. falcatum and those TFs were divided into 45 specific families. WRKY, MYB, NAC, bHLH and AUX/IAA transcription factors were found to be abundant which are considered to be key regulators in controlling wide range of molecular events such as defense response, oxidative stimuli, host signalling and triggering disease resistance. In addition, a lot of stress related genes and genes involved in gene ontological and KEGG pathway were significantly affected due to C. falcatum infection. Quantative real time PCR assays carried out to validate reliability of observed expression patterns in sugarcane in response to C. falcatum infection illustrates first transcriptome wide in planta identification and analysis of TF repertoire in the host pathogen interaction.Conclusion - The results of this study provide a benchmark discovery in finding host targets and provide tissue specific data set of genes that express in response to C. falcatum in sugarcane and also a complete analysis of main group of genes that significantly enriched under this condition. This is the first comprehensive work provides basis for the further studies to dissect role of TFs at molecular level in sugarcane defense to fungal pathogens.

THE VALUE OF LOVE IN THE SYSTEM OF FORMATION OF THE PROFESSIONAL MATURITY OF THE EDUCATOR

2020 ◽  
Vol 1 (10(79)) ◽  
pp. 12-18
Author(s):  
G. Bubyreva
Keyword(s):  
Russian Federation ◽  
The State ◽  
Educational Process ◽  
Wide Range ◽  
The Family ◽  
The Russian Federation ◽  
The Government ◽  
The Individual ◽  
The Right

The existing legislation determines the education as "an integral and focused process of teaching and upbringing, which represents a socially important value and shall be implemented so as to meet the interests of the individual, the family, the society and the state". However, even in this part, the meaning of the notion ‘socially significant benefit is not specified and allows for a wide range of interpretation [2]. Yet the more inconcrete is the answer to the question – "who and how should determine the interests of the individual, the family and even the state?" The national doctrine of education in the Russian Federation, which determined the goals of teaching and upbringing, the ways to attain them by means of the state policy regulating the field of education, the target achievements of the development of the educational system for the period up to 2025, approved by the Decree of the Government of the Russian Federation of October 4, 2000 #751, was abrogated by the Decree of the Government of the Russian Federation of March 29, 2014 #245 [7]. The new doctrine has not been developed so far. The RAE Academician A.B. Khutorsky believes that the absence of the national doctrine of education presents a threat to national security and a violation of the right of citizens to quality education. Accordingly, the teacher has to solve the problem of achieving the harmony of interests of the individual, the family, the society and the government on their own, which, however, judging by the officially published results, is the task that exceeds the abilities of the participants of the educational process.  The particular concern about the results of the patriotic upbringing served as a basis for the legislative initiative of the RF President V. V. Putin, who introduced the project of an amendment to the Law of RF "About Education of the Russian Federation" to the State Duma in 2020, regarding the quality of patriotic upbringing [3]. Patriotism, considered by the President of RF V. V. Putin as the only possible idea to unite the nation is "THE FEELING OF LOVE OF THE MOTHERLAND" and the readiness for every sacrifice and heroic deed for the sake of the interests of your Motherland. However, the practicing educators experience shortfalls in efficient methodologies of patriotic upbringing, which should let them bring up citizens, loving their Motherland more than themselves. The article is dedicated to solution to this problem based on the Value-sense paradigm of upbringing educational dynasty of the Kurbatovs [15].

Punk as Folk: Continuities and Tensions in the UK and Beyond

2020 ◽  
Author(s):  
Pete Dale
Keyword(s):  
Folk Music ◽  
Music Making ◽  
Collective Creativity ◽  
Living Tradition ◽  
Wide Range ◽  
The Us ◽  
The Common ◽  
The Individual ◽  
The Uk

Numerous claims have been made by a wide range of commentators that punk is somehow “a folk music” of some kind. Doubtless there are several continuities. Indeed, both tend to encourage amateur music-making, both often have affiliations with the Left, and both emerge at least partly from a collective/anti-competitive approach to music-making. However, there are also significant tensions between punk and folk as ideas/ideals and as applied in practice. Most obviously, punk makes claims to a “year zero” creativity (despite inevitably offering re-presentation of at least some existing elements in every instance), whereas folk music is supposed to carry forward a tradition (which, thankfully, is more recognized in recent decades as a subject-to-change “living tradition” than was the case in folk’s more purist periods). Politically, meanwhile, postwar folk has tended more toward a socialist and/or Marxist orientation, both in the US and UK, whereas punk has at least rhetorically claimed to be in favor of “anarchy” (in the UK, in particular). Collective creativity and competitive tendencies also differ between the two (perceived) genre areas. Although the folk scene’s “floor singer” tradition offers a dispersal of expressive opportunity comparable in some ways to the “anyone can do it” idea that gets associated with punk, the creative expectation of the individual within the group differs between the two. Punk has some similarities to folk, then, but there are tensions, too, and these are well worth examining if one is serious about testing out the common claim, in both folk and punk, that “anyone can do it.”

scholarly journals Epidemiological modeling in StochSS Live!

2021 ◽  
Author(s):  
Richard Jiang ◽  
Bruno Jacob ◽  
Matthew Geiger ◽  
Sean Matthew ◽  
Bryan Rumsey ◽  
...  
Keyword(s):  
Stochastic Model ◽  
Epidemiological Model ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Based ◽  
Epidemiological Modeling ◽  
Modeling Simulation ◽  
Wide Range ◽  
Biochemical Systems

Abstract Summary We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results. Availability and implementation StochSS Live! is freely available at https://live.stochss.org/ Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals BloodGen3Module: Blood transcriptional module repertoire analysis and visualization using R

2021 ◽  
Author(s):  
Darawan Rinchai ◽  
Jessica Roelands ◽  
Mohammed Toufiq ◽  
Wouter Hendrickx ◽  
Matthew C Altman ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
R Package ◽  
Supplementary Information ◽  
Illustrative Case ◽  
Bioinformatic Tools ◽  
Transcriptional Module ◽  
Wide Range ◽  
Downstream Analysis ◽  
Computing Module ◽  
Parallel Workflow

Abstract Motivation We previously described the construction and characterization of generic and reusable blood transcriptional module repertoires. More recently we released a third iteration (“BloodGen3” module repertoire) that comprises 382 functionally annotated gene sets (modules) and encompasses 14,168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results We have developed and describe here a R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. Availability The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals The OsERF115/AP2EREBP110 Transcription Factor Is Involved in the Multiple Stress Tolerance to Heat and Drought in Rice Plants

2021 ◽  
Vol 22 (13) ◽  
pp. 7181
Author(s):  
Seong-Im Park ◽  
Hyeok Jin Kwon ◽  
Mi Hyeon Cho ◽  
Ji Sun Song ◽  
Beom-Gi Kim ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Transcriptional Activation ◽  
Individual Plant ◽  
Hormone Signaling ◽  
Combined Stress ◽  
Drought Treatment ◽  
Wide Range ◽  
The Individual ◽  
Potential Use ◽  
Multiple Stress Tolerance

The AP2/EREBP family transcription factors play important roles in a wide range of stress tolerance and hormone signaling. In this study, a heat-inducible rice ERF gene was isolated and functionally characterized. The OsERF115/AP2EREBP110 was categorized to Group-IIIc of the rice AP2/EREBP family and strongly induced by heat and drought treatment. The OsERF115/AP2EREBP110 protein targeted to nuclei and suppressed the ABA-induced transcriptional activation of Rab16A promoter in rice protoplasts. Overexpression of OsERF115/AP2EREBP110 enhanced thermotolerance of seeds and vegetative growth stage plants. The OsERF115/AP2EREBP110 overexpressing (OE) plants exhibited higher proline level and increased expression of a proline biosynthesis P5CS1 gene. Phenotyping of water use dynamics of the individual plant indicates that the OsERF115/AP2EREBP110-OE plant exhibited better water saving traits under heat and drought combined stress. Our combined results suggest the potential use of OsERF115/AP2EREBP110 as a candidate gene for genetic engineering approaches to develop heat and drought stress-tolerant crops.

scholarly journals Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 311
Author(s):  
Zhenqiu Liu
Keyword(s):  
Single Cell ◽  
Free Parameter ◽  
Graphical Model ◽  
Expression Patterns ◽  
Information Criterion ◽  
Log P ◽  
Rna Seq ◽  
Clustering Methods ◽  
Wide Range ◽  
Free Parameters

Single-cell RNA-seq (scRNA-seq) is a powerful tool to measure the expression patterns of individual cells and discover heterogeneity and functional diversity among cell populations. Due to variability, it is challenging to analyze such data efficiently. Many clustering methods have been developed using at least one free parameter. Different choices for free parameters may lead to substantially different visualizations and clusters. Tuning free parameters is also time consuming. Thus there is need for a simple, robust, and efficient clustering method. In this paper, we propose a new regularized Gaussian graphical clustering (RGGC) method for scRNA-seq data. RGGC is based on high-order (partial) correlations and subspace learning, and is robust over a wide-range of a regularized parameter λ. Therefore, we can simply set λ=2 or λ=log(p) for AIC (Akaike information criterion) or BIC (Bayesian information criterion) without cross-validation. Cell subpopulations are discovered by the Louvain community detection algorithm that determines the number of clusters automatically. There is no free parameter to be tuned with RGGC. When evaluated with simulated and benchmark scRNA-seq data sets against widely used methods, RGGC is computationally efficient and one of the top performers. It can detect inter-sample cell heterogeneity, when applied to glioblastoma scRNA-seq data.

scholarly journals Entangling Lattice-Trapped Bosons with a Free Impurity: Impact on Stationary and Dynamical Properties

Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 290
Author(s):  
Maxim Pyzh ◽  
Kevin Keiler ◽  
Simeon I. Mistakidis ◽  
Peter Schmelcher
Keyword(s):  
Structural Changes ◽  
Many Body ◽  
Wide Range ◽  
Entropy Measures ◽  
Particle Level ◽  
The Many ◽  
The One ◽  
Tunneling Dynamics ◽  
The Individual ◽  
Trapped Bosons

We address the interplay of few lattice trapped bosons interacting with an impurity atom in a box potential. For the ground state, a classification is performed based on the fidelity allowing to quantify the susceptibility of the composite system to structural changes due to the intercomponent coupling. We analyze the overall response at the many-body level and contrast it to the single-particle level. By inspecting different entropy measures we capture the degree of entanglement and intraspecies correlations for a wide range of intra- and intercomponent interactions and lattice depths. We also spatially resolve the imprint of the entanglement on the one- and two-body density distributions showcasing that it accelerates the phase separation process or acts against spatial localization for repulsive and attractive intercomponent interactions, respectively. The many-body effects on the tunneling dynamics of the individual components, resulting from their counterflow, are also discussed. The tunneling period of the impurity is very sensitive to the value of the impurity-medium coupling due to its effective dressing by the few-body medium. Our work provides implications for engineering localized structures in correlated impurity settings using species selective optical potentials.

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