Power-law distributions occur in many situations of scientific interest and have significant consequences for our understanding of natural and man-made phenomena. Unfortunately, the detection and characterization of power laws is complicated by the large fluctuations that occur in the tail of the distribution—the part of the distribution representing large but rare events—and by the difficulty of identifying the range over which power-law behavior holds. Commonly used methods for analyzing power-law data, such as least-squares fitting, can produce substantially inaccurate estimates of parameters for power-law distributions, and even in cases where such methods return accurate answers they are still unsatisfactory because they give no indication of whether the data obey a power law at all. Here we present a principled statistical framework for discerning and quantifying power-law behavior in empirical data. Our approach combines maximum-likelihood fitting methods with goodness-of-fit tests based on the Kolmogorov-Smirnov (KS) statistic and likelihood ratios. We evaluate the effectiveness of the approach with tests on synthetic data and give critical comparisons to previous approaches. We also apply the proposed methods to twenty-four real-world data sets from a range of different disciplines, each of which has been conjectured to follow a power-law distribution. In some cases we find these conjectures to be consistent with the data, while in others the power law is ruled out.

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Power-Law Distributions in Empirical Data

Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at http://www.thebiogrid.org. BioGRID release version 2.0 includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. Over 30 000 interactions have recently been added from 5778 sources through exhaustive curation of the Saccharomyces cerevisiae primary literature. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.

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BioGRID: a general repository for interaction datasets

Protein-protein interactions play crucial roles in the execution of various biological functions. Accordingly, their comprehensive description would contribute considerably to the functional interpretation of fully sequenced genomes, which are flooded with novel genes of unpredictable functions. We previously developed a system to examine two-hybrid interactions in all possible combinations between the approximately 6,000 proteins of the budding yeast Saccharomyces cerevisiae. Here we have completed the comprehensive analysis using this system to identify 4,549 two-hybrid interactions among 3,278 proteins. Unexpectedly, these data do not largely overlap with those obtained by the other project [Uetz, P., et al. (2000) Nature (London) 403, 623-627] and hence have substantially expanded our knowledge on the protein interaction space or interactome of the yeast. Cumulative connection of these binary interactions generates a single huge network linking the vast majority of the proteins. Bioinformatics-aided selection of biologically relevant interactions highlights various intriguing subnetworks. They include, for instance, the one that had successfully foreseen the involvement of a novel protein in spindle pole body function as well as the one that may uncover a hitherto unidentified multiprotein complex potentially participating in the process of vesicular transport. Our data would thus significantly expand and improve the protein interaction map for the exploration of genome functions that eventually leads to thorough understanding of the cell as a molecular system.

/pdf/a-comprehensive-two-hybrid-analysis-to-explore-the-yeast-2tmnxjrhto.pdf

A comprehensive two-hybrid analysis to explore the yeast protein interactome

We review the recent rapid progress in the statistical physics of evolving networks. Interest has focused mainly on the structural properties of complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of this kind have recently been created, which opens a wide field for the study of their topology, evolution, and the complex processes which occur in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of the large sizes of these networks, the distances between most of their vertices are short - a feature known as the 'small-world' effect. We discuss how growing networks self-organize into scale-free structures, and investigate the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation and disease spread on these networks. We present a number of models demonstrat...

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Evolution of networks

Proteomics, the large-scale analysis of proteins, will contribute greatly to our understanding of gene function in the post-genomic era. Proteomics can be divided into three main areas: (1) protein micro-characterization for large-scale identification of proteins and their post-translational modifications; (2) 'differential display' proteomics for comparison of protein levels with potential application in a wide range of diseases; and (3) studies of protein-protein interactions using techniques such as mass spectrometry or the yeast two-hybrid system. Because it is often difficult to predict the function of a protein based on homology to other proteins or even their three-dimensional structure, determination of components of a protein complex or of a cellular structure is central in functional analysis. This aspect of proteomic studies is perhaps the area of greatest promise. After the revolution in molecular biology exemplified by the ease of cloning by DNA methods, proteomics will add to our understanding of the biochemistry of proteins, processes and pathways for years to come.

/pdf/proteomics-to-study-genes-and-genomes-p3gszdgohu.pdf

Proteomics to study genes and genomes

tions, constituting '10% of the total to be tested, has revealed 183 independent two-hybrid interactions, more than half of which are entirely novel. Notably, the obtained binary data allow us to extract more complex interaction networks, including the one that may explain a currently unsolved mechanism for the connection between distinct steps of vesicular transport. The approach de- scribed here thus will provide many leads for integration of various cellular functions and serve as a major driving force in the com- pletion of the protein-protein interaction map.

/pdf/toward-a-protein-protein-interaction-map-of-the-budding-4ghe7q3yu7.pdf

Toward a protein–protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins

A marked improvement in the thermoelectric performance of dense ZnO ceramics is achieved by employing a third element as a co-dopant with Al. Dual doping of ZnO with Al and Ga results in a drastic decrease in the thermal conductivity of the oxide, while the decrease in the electrical conductivity is relatively small. With the aid of a significant enhancement in the thermopower, the dually doped oxide shows thermoelectric figure of merit values, ZT, values of 0.47 at 1000 K and 0.65 at 1247 K at the composition Zn 0.96 Al 0.02 Ga 0.02 O. These results appear to be the highest ZT values so far reported for bulk n-type oxides. Microscopic observation of the samples reveals a granular texture in the densely sintered oxide matrix, suggesting that considerable reduction of the thermal conductivity while maintaining high electrical conductivity could be achieved by such a bulk nanocomposite structure in the samples.

High Thermoelectric Performance of Dually Doped ZnO Ceramics

Gene regulatory networks elucidated from strategic, genome-wide experimental data can aid in the discovery of novel gene function information and expression regulation events from observation of transcriptional regulation among genes of known and unknown biological function. To create a reliable and comprehensive data set for the elucidation of transcription regulation networks, we conducted systematic genome-wide disruption expression experiments of yeast on 118 genes with known involvement in transcription regulation. We report several novel regulatory relationships between known transcription factors and other genes with previously unknown biological function discovered with this expression library. Here we report the downstream regulatory subnetworks for UME6 and MET28. The elucidated network topology among these genes demonstrates MET28's role as a nodal point between genes involved in cell division and those involved in DNA repair mechanisms.

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Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries.

Computational fluid dynamics (CFD) is one of the promising methods that can precisely predict non-uniform air flow and contaminant distribution in indoor environments. The overarching objective of ...

https://journals.sagepub.com/doi/pdf/10.1177/1420326X19854499

Computational fluid dynamics modelling of the visible light photocatalytic oxidation process of toluene for indoor building materials with locally doped titanium dioxide

Kiyoshi Yamamoto

Papers

Toward a protein–protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins

High Thermoelectric Performance of Dually Doped ZnO Ceramics

Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries.

Computational fluid dynamics modelling of the visible light photocatalytic oxidation process of toluene for indoor building materials with locally doped titanium dioxide

The Effects of Intrauterine Injection with Prostaglandin F2α, Arachidonic Acid and Phosphate Solution on the Eggshell Formation of Japanese Quail Hen