Extended Molecular Evolutionary Biology: Artificial Life Bridging the Gap Between Chemistry and Biology

Molecular evolution provides an ample field for the extension of Nature's principles towards novel applications. Several examples are discussed here, among them are evolution in the test tube, nucleotide chemistry with new base pairs and new backbones, enzyme-free replication of polynucleotides and template chemistry aiming at replicating structures that have nothing in common with the molecules from nature. Molecular evolution in the test tube provides a uniquely simple system for the study of evolutionary phenomena: genotype and phenotype are two features of one and the same RNA molecule. Then fitness landscapes are nothing more than combined mappings from sequences to structures and from structures to functions, the latter being expressed in terms of rate constants. RNA landscapes are presented as examples for which an access to phenomena in reality by mathematical analysis and computer simulations is feasible. New questions concerning stability of structures in evolution can be raised and quantitative answers are given. Evolutionary biotechnology is a spin-off from molecular evolution. Darwin's principle of variation and selection is applied to design novel biopolymers with predetermined functions. Different approaches to achieve this goal are discussed and a survey of the current state of the art is given.

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Stability and reactivity control of carbenoids: recent advances and perspectives

Chemical Communications ◽

10.1039/c6cc05524a ◽

2016 ◽

Vol 52 (81) ◽

pp. 12011-12023 ◽

Cited By ~ 43

Author(s):

Viktoria H. Gessner

Keyword(s):

State Of The Art ◽

Main Group ◽

Feature Article ◽

Group Metal ◽

Current State ◽

Recent Advances ◽

Main Group Metal ◽

Metal Carbenoids ◽

Novel Applications

This feature article highlights the current state of the art in the chemistry of main group metal carbenoids with focus on stability and reactivity control and novel applications.

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Habitat, applications and genomics of the aerobic, thermophilic genus Geobacillus

Biochemical Society Transactions ◽

10.1042/bst0320214 ◽

2004 ◽

Vol 32 (2) ◽

pp. 214-217 ◽

Cited By ~ 61

Author(s):

G. McMullan ◽

J.M. Christie ◽

T.J. Rahman ◽

I.M. Banat ◽

N.G. Ternan ◽

...

Keyword(s):

Type Strain ◽

State Of The Art ◽

Thermophilic Bacteria ◽

Signal Molecules ◽

Gram Negative Bacteria ◽

Gene Products ◽

Current State ◽

Group 5 ◽

Novel Applications ◽

Herbicide Glyphosate

Thermophilic bacteria belonging to Bacillus genetic group 5 have been reclassified as being members of Geobacillus gen. nov., with G. stearothermophilus as the type strain. Geobacillus species, literally meaning earth or soil Bacillus, are widely distributed and readily isolated from natural and man-made thermophilic biotopes. Work within our group has however shown that an abundance of genetically distinct Geobacillus isolates can be obtained from temperate Irish soils. As with many thermophiles there is considerable interest in potential industrial application of these bacteria and their gene products. This review describes two novel applications for Geobacillus isolates, firstly in the metabolism of the herbicide glyphosate and secondly in the metabolism of quorum-sensing signal molecules from Gram-negative bacteria. Finally the current state of the art is described for Bacillus genomics, with details given of three independent genome-sequencing projects of Geobacillus isolates.

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SPATIAL-VARIANT MORPHOLOGICAL FILTERS WITH NONLOCAL-PATCH-DISTANCE-BASED AMOEBA KERNEL FOR IMAGE DENOISING

Image Analysis & Stereology ◽

10.5566/ias.1098 ◽

2015 ◽

Vol 33 (2) ◽

pp. 63 ◽

Cited By ~ 3

Author(s):

Shuo Yang ◽

Jian-Xun Li

Keyword(s):

Image Processing ◽

Medical Image ◽

State Of The Art ◽

Geodesic Distance ◽

Medical Image Processing ◽

Sar Image ◽

Morphological Filters ◽

Current State ◽

Spatially Variant ◽

Novel Applications

Filters of the Spatial-Variant amoeba morphology can preserve edges better, but with too much noise being left. For better denoising, this paper presents a new method to generate structuring elements for Spatially-Variant amoeba morphology. The amoeba kernel in the proposed strategy is divided into two parts: one is the patch distance based amoeba center, and another is the geodesic distance based amoeba boundary, by which the nonlocal patch distance and local geodesic distance are both taken into consideration. Compared to traditional amoeba kernel, the new one has more stable center and its shape can be less influenced by noise in pilot image. What’s more important is that the nonlocal processing approach can induce a couple of adjoint dilation and erosion, and combinations of them can construct adaptive opening, closing, alternating sequential filters, etc. By designing the new amoeba kernel, a family of morphological filters therefore is derived. Finally, this paper presents a series of results on both synthetic and real images along with comparisons with current state-of-the-art techniques, including novel applications to medical image processing and noisy SAR image restoration.

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Stereo Digital Image Correlation in MATLAB

Applied Sciences ◽

10.3390/app11114904 ◽

2021 ◽

Vol 11 (11) ◽

pp. 4904

Author(s):

Devan Atkinson ◽

Thorsten Hermann Becker

Keyword(s):

Digital Image Correlation ◽

Digital Image ◽

State Of The Art ◽

Deep Understanding ◽

Image Correlation ◽

Educational Resource ◽

Full Field ◽

Current State ◽

Out Of Plane ◽

Novel Applications

Digital Image Correlation (DIC) has found widespread use in measuring full-field displacements and deformations experienced by a body from images captured of it. Stereo-DIC has received significantly more attention than two-dimensional (2D) DIC since it can account for out-of-plane displacements. Although many aspects of Stereo-DIC that are shared in common with 2D DIC are well documented, there is a lack of resources that cover the theory of Stereo-DIC. Furthermore, publications which do detail aspects of the theory do not detail its implementation in practice. This literature gap makes it difficult for newcomers to the field of DIC to gain a deep understanding of the Stereo-DIC process, although this knowledge is necessary to contribute to the development of the field by either furthering its capabilities or adapting it for novel applications. This gap in literature acts as a barrier thereby limiting the development rate of Stereo-DIC. This paper attempts to address this by presenting the theory of a subset-based Stereo-DIC framework that is predominantly consistent with the current state-of-the-art. The framework is implemented in practice as a 202 line MATLAB code. Validation of the framework shows that it performs on par with well-established Stereo-DIC algorithms, indicating it is sufficiently reliable for practical use. Although the framework is designed to serve as an educational resource, its modularity and validation make it attractive as a means to further the capabilities of DIC.

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WebAL Comes of Age: A Review of the First 21 Years of Artificial Life on the Web

Artificial Life ◽

10.1162/artl_a_00211 ◽

2016 ◽

Vol 22 (3) ◽

pp. 364-407 ◽

Cited By ~ 4

Author(s):

Tim Taylor ◽

Joshua E. Auerbach ◽

Josh Bongard ◽

Jeff Clune ◽

Simon Hickinbotham ◽

...

Keyword(s):

Recent Work ◽

Artificial Life ◽

State Of The Art ◽

Web Based ◽

Web Technologies ◽

Current State ◽

The Many ◽

Exciting Area ◽

Future Work ◽

The Web

We present a survey of the first 21 years of web-based artificial life (WebAL) research and applications, broadly construed to include the many different ways in which artificial life and web technologies might intersect. Our survey covers the period from 1994—when the first WebAL work appeared—up to the present day, together with a brief discussion of relevant precursors. We examine recent projects, from 2010–2015, in greater detail in order to highlight the current state of the art. We follow the survey with a discussion of common themes and methodologies that can be observed in recent work and identify a number of likely directions for future work in this exciting area.

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Behavioral Genetics: Concepts for Research and Practice in Language Development and Disorders

Journal of Speech Language and Hearing Research ◽

10.1044/jshr.3805.1126 ◽

1995 ◽

Vol 38 (5) ◽

pp. 1126-1142 ◽

Cited By ~ 14

Author(s):

Jeffrey W. Gilger

Keyword(s):

Language Development ◽

Behavioral Genetics ◽

State Of The Art ◽

Genetic Research ◽

Great Promise ◽

Behavioral Genetic ◽

Fine Grained ◽

Future Goals ◽

Current State ◽

Research Designs

This paper is an introduction to behavioral genetics for researchers and practioners in language development and disorders. The specific aims are to illustrate some essential concepts and to show how behavioral genetic research can be applied to the language sciences. Past genetic research on language-related traits has tended to focus on simple etiology (i.e., the heritability or familiality of language skills). The current state of the art, however, suggests that great promise lies in addressing more complex questions through behavioral genetic paradigms. In terms of future goals it is suggested that: (a) more behavioral genetic work of all types should be done—including replications and expansions of preliminary studies already in print; (b) work should focus on fine-grained, theory-based phenotypes with research designs that can address complex questions in language development; and (c) work in this area should utilize a variety of samples and methods (e.g., twin and family samples, heritability and segregation analyses, linkage and association tests, etc.).

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Schizophrenia Research: Current State of the Art

Contemporary Psychology ◽

10.1037/015267 ◽

1976 ◽

Vol 21 (7) ◽

pp. 497-498

Author(s):

STANLEY GRAND

Keyword(s):

State Of The Art ◽

Current State

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Umbral Calculus

The Electronic Journal of Combinatorics ◽

10.37236/24 ◽

2002 ◽

Vol 1000 ◽

Author(s):

A. Di Bucchianico ◽

D. Loeb

Keyword(s):

19Th Century ◽

Finite Differences ◽

State Of The Art ◽

Umbral Calculus ◽

Current State ◽

Logical Foundation ◽

Complete Bibliography ◽

The 19Th Century ◽

Mathematical Literature

We survey the mathematical literature on umbral calculus (otherwise known as the calculus of finite differences) from its roots in the 19th century (and earlier) as a set of “magic rules” for lowering and raising indices, through its rebirth in the 1970’s as Rota’s school set it on a firm logical foundation using operator methods, to the current state of the art with numerous generalizations and applications. The survey itself is complemented by a fairly complete bibliography (over 500 references) which we expect to update regularly.

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