Unifying Schemes Research Articles

FERONIA: A Receptor Kinase at the Core of a Global Signaling Network.

Initially identified as a key regulator of female fertility in Arabidopsis, the FERONIA (FER) receptor kinase is now recognized as crucial for almost all aspects of plant growth and survival. FER partners with a glycosylphosphatidylinositol-anchored protein of the LLG family to act as coreceptors on the cell surface. The FER-LLG coreceptor interacts with different RAPID ALKALINIZATION FACTOR (RALF) peptide ligands to function in various growth and developmental processes and to respond to challenges from the environment. The RALF-FER-LLG signaling modules interact with molecules in the cell wall, cell membrane, cytoplasm, and nucleus and mediate an interwoven signaling network. Multiple FER-LLG modules, each anchored by FER or a FER-related receptor kinase, have been studied, illustrating the functional diversity and the mechanistic complexity of the FER family signaling modules. The challenges going forward are to distill from this complexity the unifying schemes where possible and attain precision and refinement in the knowledge of critical details upon which future investigations can be built. By focusing on the extensively characterized FER, this review provides foundational information to guide the next phase of research on FER in model as well as crop species and potential applications for improving plant growth and resilience.

Projective method for spinorial techniques: Unifying calculational schemes of Dirac amplitudes

There have been numerous approaches to the calculation of spin dependent amplitudes for Dirac particles. All of them have their own advantages, particularly, the standard method of calculation, based on the multiplication by the unit, has a few shortcomings. In this work we use the closure property of the Dirac spinors to present a general method for the amplitude computation. It is shown that the massless spinor method and the helicity spinor method can be formulated through this method. Finally, we get an example of this calculation procedure computing the spin dependentamplitude for the Compton process.

Molecular aspects of eye evolution and development: from the origin of retinal cells to the future of regenerative medicine.

A central issue of evolutionary developmental biology is how the eye is diverged morphologically and functionally. However, the unifying mechanisms or schemes that govern eye diversification remain unsolved. In this review, I first introduce the concept of evolutionary developmental biology of the eye with a focus on photoreception, the fundamental property of retinal cells. Second, I summarize the early development of vertebrate eyes and the role of a homeobox gene, Lhx1, in subdivision of the retina into 2 domains, the neural retina and retinal pigmented epithelium of the optic primordium. The 2 retinal domains are essential components of the eye as they are found in such prototypic eyes as the extant planarian eye. Finally, I propose the presence of novel retinal cell subtypes with photosensory functions based on our recent work on atypical photopigments (opsins) in vertebrates. Since human diseases are attributable to the aberration of various types of cells due to alterations in gene expression, understanding the precise mechanisms of cellular diversification and unraveling the molecular profiles of cellular subtypes are essential to future regenerative medicine.

Transglutaminase Inhibition Protects against Oxidative Stress-Induced Neuronal Death Downstream of Pathological ERK Activation

Molecular deletion of transglutaminase 2 (TG2) has been shown to improve function and survival in a host of neurological conditions including stroke, Huntington's disease, and Parkinson's disease. However, unifying schemes by which these cross-linking or polyaminating enzymes participate broadly in neuronal death have yet to be presented. Unexpectedly, we found that in addition to TG2, TG1 gene expression level is significantly induced following stroke in vivo or due to oxidative stress in vitro. Forced expression of TG1 or TG2 proteins is sufficient to induce neuronal death in Rattus norvegicus cortical neurons in vitro. Accordingly, molecular deletion of TG2 alone is insufficient to protect Mus musculus neurons from oxidative death. By contrast, structurally diverse inhibitors used at concentrations that inhibit TG1 and TG2 simultaneously are neuroprotective. These small molecules inhibit increases in neuronal transamidating activity induced by oxidative stress; they also protect neurons downstream of pathological ERK activation when added well after the onset of the death stimulus. Together, these studies suggest that multiple TG isoforms, not only TG2, participate in oxidative stress-induced cell death signaling; and that isoform nonselective inhibitors of TG will be most efficacious in combating oxidative death in neurological disorders.

COLLECTIVE TREATMENT OF HIGH ENERGY THRESHOLDS IN SUSY GUT's

Supersymmetric GUT's are the most natural extension of the Standard Model unifying electroweak and strong forces. Despite their indubitable virtues, among these the gauge coupling unification and the quantization of the electric charge, one of their shortcomings is the large number of parameters used to describe the high energy thresholds, which are hard to handle. We present a new method according to which the effects of the high energy thresholds, in any GUT model, can be described by fewer parameters that are randomly produced from the original set of the parameters of the model. In this way, regions favored by the experimental data are easier to locate, avoiding a detailed and time-consuming exploration of the parameter space, which is multidimensional even in the most economic unifying schemes. To check the efficiency of this method, we directly apply it to a SUSY SO(10) GUT model in which the doublet–triplet splitting is realized through the Dimopoulos–Wilczek mechanism. We show that the demand of gauge coupling unification, in conjunction with precision data, locates regions of the parameter space in which values of the strong coupling α strong are within the experimental limits, along with a suppressed nucleon decay, mediated by a higgsino driven dimension five operators, yielding lifetimes that are comfortably above the current experimental bounds. These regions open up for values of the SUSY breaking parameters m0, M1/2 < 1 TeV being therefore accessible to LHC.

FDR-FET: an optimizing gene set enrichment analysis method

Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as “gene sets”. Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the P value of the overrepresentation of a gene set using a Fisher’s exact test (FET) in each of these gene lists. The lowest P value is retained to represent the significance of the gene set. We also implemented improved methods to define a more relevant global reference set for the FET. We demonstrate the validity of the method using a published microarray study of three protease inhibitors of the human immunodeficiency virus and compare the results with those from other popular gene set enrichment analysis algorithms. Our results show that combining FDR with multiple cutoffs allows us to control the error while retaining genes that increase information content. We conclude that FDR-FET can selectively identify significant affected biological processes. Our method can be used for any user-generated gene list in the area of transcriptome, proteome, and other biological and scientific applications.

Message from the Series Editor

Presents the editorial for this issue of the publication.

A unified interaction scheme for information sources

Commonly, for retrieving the desired information from an information source (knowledge base or information base), the user has to use the query language that is provided by the system. This is a big barrier for many ordinary users and the resulting interaction style is rather inflexible. In this paper we give the theoretical foundations of an interaction scheme that allows users to retrieve the objects of interest without having to be familiar with the conceptual schema of the source or with the supported query language. Specifically, we describe an interaction manager that provides a quite flexible interaction scheme by unifying several well-known interaction schemes. Furthermore, we show how this scheme can be applied to taxonomy-based sources by providing all needed algorithms and reporting their computational complexity.

Weighted two-valued digit-set encodings: unifying efficient hardware representation schemes for redundant number systems

We introduce the notion of two-valued digit (twit) as a binary variable that can assume one of two different integer values. Posibits, or simply bits, in {0,1} and negabits in {-1,0}, commonly used in two's-complement representations and (n,p) encoding of binary signed digits, are special cases of twits. A weighted bit-set (WBS) encoding, which generalizes the two's-complement encoding by allowing one or more posibits and/or negabits in each radix-2 position, has been shown to unify many efficient implementations of redundant number systems. A collection of equally weighted twits, including ones with noncontiguous values (e.g., {-1,1} or {0,2}), can lead to wider representation range without the added storage and interconnection costs associated with multivalued digit sets. We present weighted twit-set (WTS) encodings as a generalization of WBS encodings, examine key properties of this new class of encodings, and show that any redundant number system (e.g., generalized signed-digit and hybrid-redundant systems), including those that are based on noncontiguous and/or zero-excluded digit sets, is faithfully representable by WTS encoding. We highlight this broad coverage by a tree chart having WTS representations at its root and various useful redundant representations at its many internal nodes and leaves. We further examine how highly optimized conventional components such as standard full/half-adders and compressors may be used for arithmetic on WTS-encoded operands, thus allowing highly efficient and VLSI-friendly circuit implementations. For example, focusing on the WBS-like subclass of WTS encodings, we describe a twit-based implementation of a particular stored-transfer representation which offers area and speed advantages over other similar designs based on WBS and hybrid-redundant representations.

An X-ray selected sample of radio-loud quasars

We construct the first X-ray selected sample of broad line radio-loud AGN from the EMSS survey. In order to test unifying schemes for radio-loud objects, their spectral and statistical properties (both flat and steep spectrum objects) are examined and compared with those of other samples of blazars. The X-ray selection allows us to explore properties of radio-loud quasars 10-100 weaker in the radio band than classical samples. The most convincing interpretation of our results is that there are no radio-loud quasars whose synchrotron emission peak reaches the EUV-soft X-ray band at these (radio) flux levels. Moreover, due to the comparatively weak non-thermal emission, a quasi-thermal component appears to contribute at optical-UV energies. The detection of sources at low radio fluxes also reveals a large population of steep spectrum quasars and the lack of the predicted turnover in the quasar (radio) counts. The evolution of X-ray selected radio-loud quasars does not significantly differ from that of radio-selected ones, and flat spectrum and steep spectrum sources appear to behave quite similarly.

Structuring user interfaces with a meta-model of mental models

This article presents a meta-model of user interfaces, based on the idea of mental models. This meta-model provides its utility in single-user environments as well as those for multiusers. A prototype is presented that implements the meta-model and two trial areas are chosen for discussing its operation. The most innovative aspect is unifying different use schemes in one interface, like temporary, spatial, networked or structured data organizations.

A direct image of the obscuring disk surrounding an active galactic nucleus

Active galactic nuclei (AGN) are generally accepted to be powered by the release of gravitational energy in a compact accretion disk surrounding a massive black hole. Such disks are also necessary to collimate powerful radio jets seen in some AGN. The unifying classification schemes for AGN further propose that differences in their appearance can be attributed to the opacity of the accreting material, which may obstruct our view of the central region of some systems. The popular model for the obscuring medium is a parsec-scale disk of dense molecular gas, although evidence for such disks has been mostly indirect, as their angular size is much smaller than the resolution of conventional telescopes. Here we report the first direct images of a pc-scale disk of ionised gas within the nucleus of NGC 1068, the archetype of obscured AGN. The disk is viewed nearly edge-on, and individual clouds within the ionised disk are opaque to high-energy radiation, consistent with the unifying classification scheme. In projection, the disk and AGN axes align, from which we infer that the ionised gas disk traces the outer regions of the long-sought inner accretion disk.

HSTand Merlin Observations of 3C 264—A Laboratory for Jet Physics and Unified Schemes

We present new HST optical continuum and emission line WFPC2 images and MERLIN radio observations of 3C 264 at ~01 resolution. The jet is well resolved in both the optical and radio images. In addition, we report the discovery of an apparent optical at a projected radius of ~300-400 pc. The ring is most likely the manifestation of absorption by a nearly face-on circumnuclear dust disk. We discuss the evolution of the jet properties with distance. The jet collimation, brightness, and orientation change dramatically as it crosses the outer boundary of the suggesting an interaction between the jet and dense circumnuclear gas. We present a model for the jet propagation in which an initially relativistic jet decelerates as it crosses through a region of dense cold gas in the inner region of the galaxy. We derive the equations for brightness variations along an adiabatically expanding relativistic jet, and we model the jet brightness in 3C 264 as the combined effects of Doppler boosting, and adiabatic losses as traced through the jet velocity and width. We find that the data are consistent with a model in which the jet is initially highly relativistic (v ~ 0.98c, γ = 5) and we view it at roughly 50° inclination. We suggest that 3C 264 may serve as a laboratory for the study of relativistic entraining jets and may help us to understand the deceleration of jets, which is required in unifying schemes for FRI radio galaxies and BL Lac objects.

The polarization-redshift relation in radio galaxies

We analyze the properties of a sample of optically polarized radio galaxies with a wide range of redshifts. The galaxies were selected both from our survey and from the literature. The aim of this work is checking whether high linear polarization is a general property of high redshift radio galaxies and how it depends on redshift. This provides a critical test on the suggestion that a considerable fraction of rest frame UV light in high redshift radio galaxies is scattered nuclear radiation. Our results show that radio galaxies with z > 0.7 are strongly polarized and that there is a strong dependence of the degree of linear polarization on the redshift. We discuss the possible origin of this correlation. Our results provide support to the validity of the Radio Quasar and Radio Galaxies unifying schemes.

Integrating GIS's and remote sensing image analysis systems by unifying knowledge representation schemes

The major barriers to the integration of remote sensing image analysis and geographical information system (GIS) technologies include the problems with data format, data accuracy, and system communication. This research explores a new path for achieving the integration. The three problems, which at first may seem to be independent of each other, are considered as different aspects of a problem with knowledge (information) representation and are tackled by unifying the systems on a common knowledge representation framework. Three new techniques-relational-linear quadtree, fuzzy representation method, and communication subschema-have been developed to provide such a framework. >

About Group Representations in Grand Unified Theories

The main purpose of this article is to systematize group theory methods in Grand Unified Theories (GUTs). An exact representation structure for all admissible groups that unify elementary forces is analysed. The implications of requirements asymptotic freedom for standard SU (3)c ⊗ SU(2)L ⊗ U(1)y model is investigated in detail. It is shown how restrictive are such assumptions in unified model building. As a result the maximal number of families is five independently on the kind of considered model. In several cases this number is even smaller. The maximal horizontal structure of interactions which is possible to embed into unification scheme is also discussed for all admissible models. The number of superheavy particles is evaluated in different unifying schemes.

Hyperleptonic generations in unifying schemes

It is shown that the requirement of having a fully spectator ${N}_{g}$-dimensional generation structure, in the presence of a confining $\mathrm{SU}{(n)}_{\mathrm{HC}}$ interaction, can be fulfilled in a conventional $\mathrm{SU}(N)$ grand unified manner only provided $n={N}_{g}=3$. A possible origin for the exclusive smallness of ${m}_{u}$, ${m}_{d}$, and ${m}_{s}$ is then suggested by the global group-theoretical properties of the associated fermionic representation. The price of such a hyperleptonic scenario is briefly discussed.

Toward the unification of weak, electromagnetic, and strong interactions: SU(5)

The successes of the Weinberg-Salam model and quantum chromodynamics have made the attempt at the unification of weak, electromagnetic, and strong interactions of leptons and quarks in the framework of a single group into a serious proposition. The simplest and most economic unifying group is SU(5). The review is devoted to a detailed study of some of the questions associated with the unification of the interactions of the elementary particles in the example of the group SU(5). The questions considered include the part played by natural conservation of the quark flavor by neutral weak currents in searches for unifying groups, the quantization of charge (connection between the charges of quarks and leptons), the renormalization of unified groups to present-day energies, the instability of the nucleon, the finiteness of the number of flavors, the hierarchy of interactions unified in a single scheme, and the cosmological aspects of unification schemes. Other grand unification schemes are also considered briefly. Some possible ways of constructing unifying schemes are discussed in the conclusions.

Machines, Programs and Languages

Recently, several unifying schemes have been presented by various authors [1, 3, 4, 5] for the study of automata and formal languages. Among the various approaches, the one which deals with the concept of machines with standard input/output, introduced by Scott [5], seems to be the simplest and the most natural. Unfortunately, as it stands, machines with standard input/output are essentially one-way devices, and hence fail to encompass such machines as the two-way stack automata. In the present paper, we extend the concept to two-way machines. This provides a general framework for the study of the various two-way as well as one-way devices, deterministic or otherwise, which appeared in the literature.