scholarly journals Guiding the interactive exploration of metabolic pathway interconnections

2011 ◽  
Vol 11 (2) ◽  
pp. 136-150 ◽  
Author(s):  
Ilir Jusufi ◽  
Christian Klukas ◽  
Andreas Kerren ◽  
Falk Schreiber
Keyword(s):  
Real Data ◽  
Biochemical Networks ◽  
Large Set ◽  
Biological Processes ◽  
Comprehensive Understanding ◽  
Topological Information ◽  
Common Solution ◽  
The Past ◽  
Complete Network ◽  
Research Areas

Approaches to investigate biological processes have been of strong interest in the past few years and are the focus of several research areas, especially Systems Biology. Biochemical networks as representations of processes are very important for a comprehensive understanding of living beings. Drawings of these networks are often visually overloaded and do not scale. A common solution to deal with this complexity is to divide the complete network, for example, the metabolism, into a large set of single pathways that are hierarchically structured. If those pathways are visualized, this strategy generates additional navigation and exploration problems as the user loses the context within the complete network. In this article, we present a general solution to this problem of visualizing interconnected pathways and discuss it in context of biochemical networks. Our new visualization approach supports the analyst in obtaining an overview to related pathways if they are working within a particular pathway of interest. By using glyphs, brushing, and topological information of the related pathways, our interactive visualization is able to intuitively guide the exploration and navigation process, and thus the analysis processes too. To deal with real data and current networks, our tool has been implemented as a plugin for the VANTED system.

scholarly journals Iron biogeochemistry across marine systems – progress from the past decade

2010 ◽  
Vol 7 (3) ◽  
pp. 1075-1097 ◽  
Author(s):  
E. Breitbarth ◽  
E. P. Achterberg ◽  
M. V. Ardelan ◽  
A. R. Baker ◽  
E. Bucciarelli ◽  
...  
Keyword(s):  
Global Climate ◽  
International Workshop ◽  
Review Article ◽  
Future Research ◽  
Biological Processes ◽  
Colloidal Iron ◽  
Marine Systems ◽  
The Past ◽  
Research Areas ◽  
Interdisciplinary Knowledge

Abstract. Based on an international workshop (Gothenburg, 14–16 May 2008), this review article aims to combine interdisciplinary knowledge from coastal and open ocean research on iron biogeochemistry. The major scientific findings of the past decade are structured into sections on natural and artificial iron fertilization, iron inputs into coastal and estuarine systems, colloidal iron and organic matter, and biological processes. Potential effects of global climate change, particularly ocean acidification, on iron biogeochemistry are discussed. The findings are synthesized into recommendations for future research areas.

scholarly journals Biological Prescience: The Role of Anticipation in Organismal Processes

2021 ◽  
Vol 12 ◽  
Author(s):  
Carrie Deans
Keyword(s):  
Human Mind ◽  
Genetic Networks ◽  
Biochemical Networks ◽  
Neural Systems ◽  
Future Scenarios ◽  
Biological Processes ◽  
Unique Type ◽  
The Past ◽  
Physiological Systems

Anticipation is the act of using information about the past and present to make predictions about future scenarios. As a concept, it is predominantly associated with the psychology of the human mind; however, there is accumulating evidence that diverse taxa without complex neural systems, and even biochemical networks themselves, can respond to perceived future conditions. Although anticipatory processes, such as circadian rhythms, stress priming, and cephalic responses, have been extensively studied over the last three centuries, newer research on anticipatory genetic networks in microbial species shows that anticipatory processes are widespread, evolutionarily old, and not simply reserved for neurological complex organisms. Overall, data suggest that anticipatory responses represent a unique type of biological processes that can be distinguished based on their organizational properties and mechanisms. Unfortunately, an empirically based biologically explicit framework for describing anticipatory processes does not currently exist. This review attempts to fill this void by discussing the existing examples of anticipatory processes in non-cognitive organisms, providing potential criteria for defining anticipatory processes, as well as their putative mechanisms, and drawing attention to the often-overlooked role of anticipation in the evolution of physiological systems. Ultimately, a case is made for incorporating an anticipatory framework into the existing physiological paradigm to advance our understanding of complex biological processes.

A Review of Chinese Raman Spectroscopy Research Over the Past Twenty Years

2019 ◽  
Vol 74 (2) ◽  
pp. 130-159
Author(s):  
Jie Wang ◽  
Kaiyuan Liu ◽  
Shangzhong Jin ◽  
Li Jiang ◽  
Pei Liang
Keyword(s):  
Raman Spectroscopy ◽  
Material Research ◽  
Testing Material ◽  
Research Groups ◽  
Comprehensive Understanding ◽  
Research Directions ◽  
Environmental Testing ◽  
The Past ◽  
Research Areas ◽  
Spectroscopy Research

This paper introduces the major Chinese research groups in the fields of biomedicine, food safety, environmental testing, material research, archaeological and cultural relics, gem identification, forensic science, and other research areas of Raman spectroscopy and combined methods spanning the two decades from 1997 to 2017. Briefly summarized are the research directions and contents of the major Chinese Raman spectroscopy research groups, giving researchers engaged in Raman spectroscopy research a more comprehensive understanding of the state of Chinese Raman spectroscopy research and future development trends to further develop Raman spectroscopy and its applications.

scholarly journals Iron biogeochemistry across marine systems at changing times – conclusions from the workshop held in Gothenburg, Sweden (14–16 May 2008)

2009 ◽  
Vol 6 (4) ◽  
pp. 6635-6694 ◽  
Author(s):  
E. Breitbarth ◽  
E. P. Achterberg ◽  
M. V. Ardelan ◽  
A. R. Baker ◽  
E. Bucciarelli ◽  
...  
Keyword(s):  
Global Climate ◽  
International Workshop ◽  
Future Research ◽  
Biological Processes ◽  
Colloidal Iron ◽  
Marine Systems ◽  
The Past ◽  
Research Areas ◽  
Interdisciplinary Knowledge ◽  
Changing Times

Abstract. Based on an international workshop (Gothenburg, 14–16 May 2008), this review article aims to combine interdisciplinary knowledge from coastal and open ocean research on iron biogeochemistry. The major scientific findings of the past decade are structured into sections on natural and artificial iron fertilization, iron inputs into coastal and estuarine systems, colloidal iron and organic matter, and biological processes. Potential effects of global climate change, particularly ocean acidification, on iron biogeochemistry are discussed. The findings are synthesized into recommendations for future research areas.

Fluorescent potentiometric dyes for membrane-potential imaging

1994 ◽  
Vol 52 ◽  
pp. 166-167
Author(s):  
Leslie M. Loew
Keyword(s):  
Membrane Potential ◽  
Single Cells ◽  
Quantitative Imaging ◽  
Optical Recording ◽  
Biological Processes ◽  
Major Focus ◽  
The Past ◽  
Excitable Systems ◽  
Major Application ◽  
The Impact

A major application of potentiometric dyes has been the multisite optical recording of electrical activity in excitable systems. After being championed by L.B. Cohen and his colleagues for the past 20 years, the impact of this technology is rapidly being felt and is spreading to an increasing number of neuroscience laboratories. A second class of experiments involves using dyes to image membrane potential distributions in single cells by digital imaging microscopy - a major focus of this lab. These studies usually do not require the temporal resolution of multisite optical recording, being primarily focussed on slow cell biological processes, and therefore can achieve much higher spatial resolution. We have developed 2 methods for quantitative imaging of membrane potential. One method uses dual wavelength imaging of membrane-staining dyes and the other uses quantitative 3D imaging of a fluorescent lipophilic cation; the dyes used in each case were synthesized for this purpose in this laboratory.

Comparison and Analysis of Computational Methods for Identifying N6 - methyladenosine Sites in Saccharomyces Cerevisiae

2020 ◽  
Vol 26 ◽  
Author(s):  
Pengmian Feng ◽  
Lijing Feng ◽  
Chaohui Tang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Computational Methods ◽  
Computational Analysis ◽  
Computational Prediction ◽  
Experimental Methods ◽  
Biological Processes ◽  
Biological Functions ◽  
Precise Location ◽  
Future Directions ◽  
The Past

Background and Purpose: N 6 -methyladenosine (m6A) plays critical roles in a broad set of biological processes. Knowledge about the precise location of m6A site in the transcriptome is vital for deciphering its biological functions. Although experimental techniques have made substantial contributions to identify m6A, they are still labor intensive and time consuming. As good complements to experimental methods, in the past few years, a series of computational approaches have been proposed to identify m6A sites. Methods: In order to facilitate researchers to select appropriate methods for identifying m6A sites, it is necessary to give a comprehensive review and comparison on existing methods. Results: Since researches on m6A in Saccharomyces cerevisiae are relatively clear, in this review, we summarized recent progresses on computational prediction of m6A sites in S. cerevisiae and assessed the performance of existing computational methods. Finally, future directions of computationally identifying m6A sites were presented. Conclusion: Taken together, we anticipate that this review will provide important guides for computational analysis of m 6A modifications.

Temporal Focus

2020 ◽  
Author(s):  
Abbie J. Shipp
Keyword(s):  
Well Being ◽  
Psychology Research ◽  
The Past ◽  
Research Areas ◽  
The Future ◽  
Behavior Based ◽  
The Individual ◽  
And Behavior ◽  
Temporal Focus

Temporal focus is the individual tendency to characteristically think more or less about the past, present, and future. Although originally rooted in early work from psychology, research on temporal focus has been steadily growing in a number of research areas, particularly since Zimbardo and Boyd’s (1999) influential article on the topic. This chapter will review temporal focus research from the past to the present, including how temporal focus has been conceptualized and measured, and which correlates and outcomes have been tested in terms of well-being and behavior. Based on this review, an agenda for research is created to direct temporal focus research in the future.

Experience

2021 ◽  
Vol 13 (1) ◽  
pp. 1-16
Author(s):  
Michela Fazzolari ◽  
Francesco Buccafurri ◽  
Gianluca Lax ◽  
Marinella Petrocchi
Keyword(s):  
Relative Frequency ◽  
Service Providers ◽  
Real Data ◽  
Online Reviews ◽  
Purchase Decision ◽  
The Past ◽  
Supervised Classifiers ◽  
Relative Frequency Distribution ◽  
Opinion Spam ◽  
Fake Reviews

Over the past few years, online reviews have become very important, since they can influence the purchase decision of consumers and the reputation of businesses. Therefore, the practice of writing fake reviews can have severe consequences on customers and service providers. Various approaches have been proposed for detecting opinion spam in online reviews, especially based on supervised classifiers. In this contribution, we start from a set of effective features used for classifying opinion spam and we re-engineered them by considering the Cumulative Relative Frequency Distribution of each feature. By an experimental evaluation carried out on real data from Yelp.com, we show that the use of the distributional features is able to improve the performances of classifiers.

scholarly journals MicroRNAs: Biological Regulators in Pathogen–Host Interactions

Cells ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 113 ◽  
Author(s):  
Stephanie Maia Acuña ◽  
Lucile Maria Floeter-Winter ◽  
Sandra Marcia Muxel
Keyword(s):  
Immune Response ◽  
Infectious Diseases ◽  
Small Rnas ◽  
Immune Cell ◽  
Fine Tuning ◽  
Biological Processes ◽  
Host Interactions ◽  
The Past ◽  
Biological Aspects

An inflammatory response is essential for combating invading pathogens. Several effector components, as well as immune cell populations, are involved in mounting an immune response, thereby destroying pathogenic organisms such as bacteria, fungi, viruses, and parasites. In the past decade, microRNAs (miRNAs), a group of noncoding small RNAs, have emerged as functionally significant regulatory molecules with the significant capability of fine-tuning biological processes. The important role of miRNAs in inflammation and immune responses is highlighted by studies in which the regulation of miRNAs in the host was shown to be related to infectious diseases and associated with the eradication or susceptibility of the infection. Here, we review the biological aspects of microRNAs, focusing on their roles as regulators of gene expression during pathogen–host interactions and their implications in the immune response against Leishmania, Trypanosoma, Toxoplasma, and Plasmodium infectious diseases.

scholarly journals The crucial roles of N6-methyladenosine (m6A) modification in the carcinogenesis and progression of colorectal cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhihao Fang ◽  
Yiqiu Hu ◽  
Jinhui Hu ◽  
Yanqin Huang ◽  
Shu Zheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Nuclear Export ◽  
Messenger Rna ◽  
Regulatory Proteins ◽  
Biological Processes ◽  
The Past ◽  
Common Cancer ◽  
Potential Applications ◽  
Regulated Gene Expression

AbstractAs the predominant modification in RNA, N6-methyladenosine (m6A) has attracted increasing attention in the past few years since it plays vital roles in many biological processes. This chemical modification is dynamic, reversible and regulated by several methyltransferases, demethylases and proteins that recognize m6A modification. M6A modification exists in messenger RNA and affects their splicing, nuclear export, stability, decay, and translation, thereby modulating gene expression. Besides, the existence of m6A in noncoding RNAs (ncRNAs) could also directly or indirectly regulated gene expression. Colorectal cancer (CRC) is a common cancer around the world and of high mortality. Increasing evidence have shown that the changes of m6A level and the dysregulation of m6A regulatory proteins have been implicated in CRC carcinogenesis and progression. However, the underlying regulation laws of m6A modification to CRC remain elusive and better understanding of these mechanisms will benefit the diagnosis and therapy. In the present review, the latest studies about the dysregulation of m6A and its regulators in CRC have been summarized. We will focus on the crucial roles of m6A modification in the carcinogenesis and development of CRC. Moreover, we will also discuss the potential applications of m6A modification in CRC diagnosis and therapeutics.

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