Target morphology and cell memory: a model of regenerative pattern formation Cell Memory Can Regulate Morphogenesis and Regeneration

International audienceDespite the growing body of work on molecular components required for regenerative repair, westill lack a deep understanding of the ability of some animal species to regenerate their appropriatecomplex anatomical structure following damage. A key question is how regenerating systemsknow when to stop growth and remodeling – what mechanisms implement recognition of correctmorphology that signals a stop condition? In this work, we review two conceptual modelsof pattern regeneration that implement a kind of pattern memory. In the first one, all cells communicatewith each other and keep the value of the total signal received from the other cells. If apart of the pattern is amputated, the signal distribution changes. The difference from the originalsignal distribution stimulates cell proliferation and leads to pattern regeneration, in effect implementingan error minimization process that uses signaling memory to achieve pattern correction.In the second model, we consider a more complex pattern organization with different cell types.Each tissue contains a central (coordinator) cell that controls the tissue and communicates withthe other central cells. Each of them keeps memory about the signals received from other centralcells. The values of these signals depend on the mutual cell location, and the memory allowsregeneration of the structure when it is modified. The purpose of these models is to suggestpossible mechanisms of pattern regeneration operating on the basis of cell memory which arecompatible with diverse molecular implementation mechanisms within specific organisms

The dialectic as driver of complexity in urban and social systems

This chapter considers what can be learned from the study of urban systems considered as complex networks of spatial relations that might shed light on the rapid acceleration in human progress after their first invention around 10,000 BC. Using Hillier’s key notion of the objective subject, Karl Marx and Vilfredo Pareto’s distinct notions of the dialectic are reviewed. The contribution of space syntax research to consideration of the objective and subjective experience of urban systems is described, before finally proposing a dynamic bi-directional process in which the dialectic delivers continued progress in human development

A Multiple-Systems Approach in the Symbolic Modelling of Human Vision

For most of the thirty years or so of machine vision research, activity has been concentrated mainly in the domain of metric-based approaches: there has been negligible attention to the psychological factors in human vision. With the recent resurgence of interest in neural systems, that is now changing. This thesis discusses relevant aspects of basic visual neuroanatomy, and psychological phenomena, in an attempt to relate the concepts to a model of human vision and the prospective goals of future machine vision systems. It is suggested that, while biological vision is complex, the underlying mechanisms of human vision are more tractable than is often believed. We also argue here that the controversial subject of direct vision plays a crucial role in natural vision, and we attempt to relate this to the model. The recognition of massive parallelism in natural vision has led to proposals for emulating aspects of neural networks in technology. The systems model developed in this work demonstrates software-simulated cellular automata (CAs) in the role of mainly low-level image processing. It is shown that CAs are able to efficiently provide both conventional and neurally-inspired vision functions. The thesis also discusses the use of Prolog as the means of realising higher level image understanding. The symbolic processing developed is basic, but is nevertheless sufficient for the purposes of the present. demonstrations. Extensions to the concepts can be easily achieved. The modular systems approach adopted blends together several ideas and processes, and results in a more robust model of human vision that is able to translate a noisy real image into an accessible symbolic form for expert-domain interpretation

The evaluation of Corona and Ikonos satellite imagery for archaeological applications in a semi-arid environment

Archaeologists have been aware of the potential of satellite imagery as a tool almost since the first Earth remote sensing satellite. Initially sensors such as Landsat had a ground resolution which was too coarse for thorough archaeological prospection although the imagery was used for geo-archaeological and enviro-archaeological analyses. In the intervening years the spatial and spectral resolution of these sensing devices has improved. In recent years two important occurrences enhanced the archaeological applicability of imagery from satellite platforms: The declassification of high resolution photography by the American and Russian governments and the deregulation of commercial remote sensing systems allowing the collection of sub metre resolution imagery. This thesis aims to evaluate the archaeological application of three potentially important resources; Corona space photography and Ikonos panchromatic and multispectral imager). These resources are evaluated in conjunction with Landsat Thematic Mapper (TM) imagery over a 600 square km study area in the semi-arid environment around Homs, Syria. The archaeological resource in this area is poorly understood, mapped and documented. The images are evaluated for their ability to create thematic layers and to locate archaeological residues in different environmental zones. Further consideration is given to the physical factors that allow archaeological residues to be identified and how satellite imagery and modern technology may impact on Cultural Resource Management. This research demonstrates that modern high resolution and historic satellite imagery can be important tools for archaeologists studying in semi-arid environments. The imagery has allowed a representative range of archaeological features and landscape themes to be identified. The research shows that the use of satellite imagery can have significant impact on the design of the archaeological survey in the middle-east and perhaps in other environments

P. patens genomic and transcriptomic analyses

The model organism Physcomitrium patens, formerly Physcomitrella patens is a moss in the Funariaceae family. Due to P. patens ability to generate easily transgenic plants via homologous recombination, the interest of scientists worldwide was attracted. P. patens was the world's first completely sequenced non-seed plant genome (V1). Constant improvements of the genome assembly and the associated gene annotations resulted in the current P. patens pseudo-chromosomal genome version (V3). This genome version is the basis of all analyses performed in this thesis. Since P. patens became a U.S. Department of Energy Joint Genome Institute (DOE JGI) plant flagship genome 1 and a member of the JGI Gene Atlas project 2, hundreds of P. patens RNA-seq samples were generated. During my time as a PhD student, I analysed the JGI Gene Atlas RNA-seq samples and several dozen other RNA-seq samples from different projects. These RNA-seq samples contained data from five different P. patens ecotypes/accessions (Gransden, Kaskaskia, Reute, Villersexel, and Wisconsin).To efficiently analyse this data, I developed a powerful RNA-seq pipeline to perform differentially expressed gene (DEG) calling. The performance of the RNA-seq pipeline was tested by comparing its results to commercial software solutions and multiple RNA-seq samples from different species. My newly generated gene expression results, together with previous published expression data from a variety of other projects, were stored at our novel online tool PEATmoss. Furthermore, my gene version lookup tables were implemented in a database structure. This, allows PEATmoss users to find gene models of different gene annotation versions and to use them in PEATmoss. With an updated version of my RNA-seq pipeline, I identified and analysed sequence variations in P. patens accessions. A clear clustering by individual accessions could be shown. I could demonstrate, that due to decades of vegetative propagation in laboratories, somatic mutations have accumulated in Gransden laboratory plants. In addition, we used restriction fragment length polymorphism (RFLP) to offer a simple method for quick identification of unknown P. patens plants. 1 https://jgi.doe.gov/our-science/science-programs/plant-genomics/plant-flagship-genomes/ 2 https://jgi.doe.gov/doe-jgi-plant-flagship-gene-atlas

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Next generation transduction pathways for nano-bio-chip array platforms

textIn the following work, nanoparticle quantum dot (QD) fluorophores have been exploited to measure biologically relevant analytes via a miniaturized sensor ensemble to provide key diagnostic and prognostic information in a rapid, yet sensitive manner—data essential for effective treatment of many diseases including HIV/AIDS and cancer. At the heart of this “nano-bio-chip” (NBC) sensor is a modular chemical/cellular processing unit consisting of either a polycarbonate membrane filter for cell-based assays, or an agarose bead array for detection of biomarkers in serum or saliva. Two applications of the NBC sensor system are described herein, both exhibiting excellent correlation to reference methods ((R² above 0.94), with analysis times under 30 minutes and sample volumes below 50 [mu]L. First, the NBC sensor was employed for the sequestration and enumeration of T lymphocytes, cells specifically targeted by HIV, from whole blood samples. Several different conjugation methods linking QDs to recognition biomolecules were extensively characterized by biological and optical methods, with a thiol-linked secondary antibody labeling scheme yielding intense, specific signal. Using this technique, the photostability of QDs was exploited, as was the ability to simultaneously visualize different color QDs via a single light pathway, effectively reducing optical requirements by half. Further, T-cell counts were observed well below the 200/[mu]L discriminator between HIV and AIDS and across the common testing region, demonstrating the first reported example of cell counting via QDs in an enclosed, disposable device. Next, multiplexed bead-based detection of cancer protein biomarkers CEA, Her-2/Neu, and CA125 in serum and saliva was examined using a sandwich immunoassay with detecting antibodies covalently bound to QDs. This nano-based signal was amplified 30 times versus molecular fluorophores and cross talk in multiplexed experiments was less than 5%. In addition, molecular-level tuning of recognition elements (size, concentration) and agarose porosity resulted in NBC limits of detection two orders of magnitude lower than ELISA, values competitive with the most sensitive methods yet reported (0.021 ng/mL CEA). Taken together, these efforts serve to establish the valuable role of QDs in miniaturized diagnostic devices with potential for delivering biomedical information rapidly, reliably, and robustly.Chemistry and Biochemistr

The Evolution of Language Universals: Optimal Design and Adaptation

Inquiry into the evolution of syntactic universals is hampered by severe limitations on the available evidence. Theories of selective function nevertheless lead to predictions of local optimaliiy that can be tested scientifically. This thesis refines a diagnostic, originally proposed by Parker and Maynard Smith (1990), for identifying selective functions on this basis and applies it to the evolution of two syntactic universals: (I) the distinction between open and closed lexical classes, and (2) nested constituent structure. In the case of the former, it is argued that the selective role of the closed class items is primarily to minimise the amount of redundancy in the lexicon. In the case of the latter, the emergence of nested phrase structure is argued to have been a by-product of selection for the ability to perform insertion operations on sequences - a function that plausibly pre-dated the emergence of modem language competence. The evidence for these claims is not just that these properties perform plausibly fitness-related functions, but that they appear to perform them in a way that is improbably optimal. A number of interesting findings follow when examining the selective role of the closed classes. In particular, case, agreement and the requirement that sentences have subjects are expected consequences of an optimised lexicon, the theory thereby relating these properties to natural selection for the first time. It also motivates the view that language variation is confined to parameters associated with closed class items, in turn explaining why parameter confiicts fail to arise in bilingualism. The simplest representation of sequences that is optimised for efficient insertions can represent both nested constituent structure and long-distance dependencies in a unified way, thus suggesting that movement is intrinsic to the representation of constituency rather than an 'imperfection'. The basic structure of phrases also follows from this representation and helps to explain the interaction between case and theta assignment. These findings bring together a surprising array of phenomena, reinforcing its correctness as the representational basis of syntactic structures. The diagnostic overcomes shortcomings in the approach of Pinker and Bloom (1990), who argued that the appearance of 'adaptive complexity' in the design of a trait could be used as evidence of its selective function, but there is no reason to expect the refinements of natural selection to increase complexity in any given case. Optimality considerations are also applied in this thesis to filter theories of the nature of unobserved linguistic representations as well as theories of their functions. In this context, it is argued that, despite Chomsky's (1995) resistance to the idea, it is possible to motivate the guiding principles of the Minimalist Program in terms of evolutionary optimisation, especially if we allow the possibility that properties of language were selected for non-communicative functions and that redundancy is sometimes costly rather than beneficial

Mental-State Estimation, 1987

Reports on the measurement and evaluation of the physiological and mental state of operators are presented