Redundant Bases Research Articles

Highly-efficient selection of interferon gamma-specific aptamers and development of a sensitive fiber-optic evanescent wave aptasensor

Interferon-gamma (IFN-γ) is a critical indicator of the immune response to many infections and diseases. Identifying excellent IFN-γ recognition molecules is of great significance for the early diagnosis and treatment of diseases. Herein, anti-IFN-γ aptamers were selected based on capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) and their affinities were characterized by the biolayer interferometry (BLI) assay. A rational molecular docking strategy was utilized to predict precisely the binding behavior between aptamer and IFN-γ and remove redundant bases of original sequence. Therefore, aptamer IFNG-8 with the highest affinity can be efficiently identified within only three rounds and the truncated aptamer IFNG-8 T with comparable affinity is eventually obtained. With IFNG-8 T as the detection probe, a fiber-optic evanescent wave aptasensor is constructed for the detection of IFN-γ, which shows a wide linear range from 0.1 to 10000 pM and a low limit of detection (LOD) of 0.0718 pM. The developed aptasensor exhibits high selectivity and can be utilized for IFN-γ detection in human serum samples with good recoveries. In summary, the truncated aptamer can serve as a novel optional transducing element and the developed aptasensor provides an innovative methodology for detection of IFN-γ in trace amount.

Digest: The non-redundancy of non-ephemeral reproductive isolation.

What factors determine the stability of intrinsic reproductive barriers in the face of hybridization? In a set of theoretical analyses, Xiong and Mallet (2022) show that intrinsic incompatibilities are more prone to collapse when the incompatible genotypes encode biological functions with redundant genetic bases. These findings suggest that stable reproductive barriers often will be based on non-redundant genetic complexes that evolve among diverging lineages.

Adaptive Cost Volume Fusion Network for Multi-Modal Depth Estimation in Changing Environments

In this letter, we propose an adaptive cost volume fusion algorithm for multi-modal depth estimation in changing environments. Our method takes measurements from multi-modal sensors to exploit their complementary characteristics and generates depth cues from each modality in the form of adaptive cost volumes using deep neural networks. The proposed adaptive cost volume considers sensor configurations and computational costs to resolve an imbalanced and redundant depth bases problem of conventional cost volumes. We further extend its role to a generalized depth representation and propose a geometry-aware cost fusion algorithm. Our unified and geometrically consistent depth representation leads to an accurate and efficient multi-modal sensor fusion, which is crucial for robustness to changing environments. To validate the proposed framework, we introduce a new multi-modal depth in changing environments (MMDCE) dataset. The dataset was collected by our own vehicular system with RGB, NIR, and LiDAR sensors in changing environments. Experimental results demonstrate that our method is robust, accurate, and reliable in changing environments. Our codes and dataset are available at our project page.

Utilizing the DNA Aptamer to Determine Lethal α-Amanitin in Mushroom Samples and Urine by Magnetic Bead-ELISA (MELISA).

Amanita poisoning is one of the most deadly types of mushroom poisoning. α-Amanitin is the main lethal toxin in amanita, and the human-lethal dose is about 0.1 mg/kg. Most of the commonly used detection techniques for α-amanitin require expensive instruments. In this study, the α-amanitin aptamer was selected as the research object, and the stem-loop structure of the original aptamer was not damaged by truncating the redundant bases, in order to improve the affinity and specificity of the aptamer. The specificity and affinity of the truncated aptamers were determined using isothermal titration calorimetry (ITC) and gold nanoparticles (AuNPs), and the affinity and specificity of the aptamers decreased after truncation. Therefore, the original aptamer was selected to establish a simple and specific magnetic bead-based enzyme linked immunoassay (MELISA) method for α-amanitin. The detection limit was 0.369 μg/mL, while, in mushroom it was 0.372 μg/mL and in urine 0.337 μg/mL. Recovery studies were performed by spiking urine and mushroom samples with α-amanitin, and these confirmed the desirable accuracy and practical applicability of our method. The α-amanitin and aptamer recognition sites and binding pockets were investigated in an in vitro molecular docking environment, and the main binding bases of both were T3, G4, C5, T6, T7, C67, and A68. This study truncated the α-amanitin aptamer and proposes a method of detecting α-amanitin.

A Blind Filtering Framework for Noisy Neonatal Chest Sounds

Chest sound— as the first and most commonly available vital signal for newborns— contains affluent information about their cardiac and respiratory health. However, neonatal lung sound auscultation is currently challenging and often unreliable due to the noise and interference, particularly for preterm infants. The noise often overlaps with the heart and lung contents in both time and frequency. Moreover, the frequency band of the useful components varies from one case to another, making it difficult to separate by fixed band-pass filtering. In this study, a single-channel Blind Source Separation (SCBSS) framework is proposed to separate newborns’ lung and heart sounds from noisy chest sounds recorded by a digital stethoscope. This method first decomposes the signal into a multi-resolution representation using a time-frequency transform, and then applies source separation algorithms, to find proper ad hoc frequency filters. In the simulation scenario, two different time-frequency transforms are considered; Stationary Wavelet Transform (SWT) with dyadic bases, and Continuous Wavelet Transform (CWT) with redundant bases. The transforms are followed by three different source separation methods, namely Principal Component Analysis (PCA), Periodic Component Analysis (πCA), and Second Order Blind Identification (SOBI). The yielded combinations are applied to the chest sounds recorded from ninety-one preterm and full-term newborns. The results show that compared to raw signals, fixed band-pass filtering and seven other separation methods, the heart and lung sounds extracted by the proposed methods have higher quality index and also result in more reliable heart and respiratory rate estimation.

The Role of Redundant Bases and Shrinkage Functions in Image Denoising.

Wavelet denoising is a classical and effective approach for reducing noise in images and signals. Suggested in 1994, this approach is carried out by rectifying the coefficients of a noisy image, in the transform domain, using a set of shrinkage functions (SFs). A plethora of papers deals with the optimal shape of the SFs and the transform used. For example, it is widely known that applying SFs in a redundant basis improves the results. However, it is barely known that the shape of the SFs should be changed when the transform used is redundant. In this paper, we introduce a complete picture of the interrelations between the transform used, the optimal shrinkage functions, and the domains in which they are optimized. We suggest three schemes for optimizing the SFs and provide bounds of the remaining noise, in each scheme, with respect to the other alternatives. In particular, we show that for subband optimization, where each SF is optimized independently for a particular band, optimizing the SFs in the spatial domain is always better than or equal to optimizing the SFs in the transform domain. Furthermore, for redundant bases, we provide the expected denoising gain that can be achieved, relative to the unitary basis, as a function of the redundancy rate.

Mitigating Mechanisms for the Dark Side of Collaborative Buyer–Supplier Relationships: A Mixed‐Method Study

Scholars have called attention to the dark side of collaborative buyer–supplier relationships (BSRs). For instance, the loss of objectivity, relational inertia, and redundant knowledge bases emerging from too much collaboration may result in declining performance. We extend this line of research by investigating the feasibility of potential mitigating mechanisms. Drawing from the literature on governance in inter‐organizational relationships and the interviews with practitioners that have experienced the dark side, we have identified three mechanisms: challenging goals, contractual explicitness, and expectation of continuity. We examine these mechanisms empirically through two consecutive studies. The first study collected data on 132 buying firms and 28 matched suppliers from two sources (survey and archival database). The results provide support for challenging goals and contractual explicitness but offer mixed results for expectation of continuity. The data also allow us to identify buyers suffering from excessive collaboration with their suppliers. In the second study, we gathered qualitative data on five pairs of such buyers and their matched suppliers. Different pairs show different behaviors. Some buyer and supplier firms seem unaware of their predicament, while others are grappling with fighting back the dark side. This qualitative study also offers additional manifestations of the dark side and mechanisms beyond the ones examined in our first study and explains why expectation of continuity received mixed results. This research advances the BSR literature by demonstrating that it is possible to mitigate the dysfunctionalities emerging from too much collaboration and by providing some evidence for its subtle manifestations. It also reveals the managerial complexity surrounding the dark side and provides future research directions for this important topic.

Gradient Boosts the Approximate Vanishing Ideal

In the last decade, the approximate vanishing ideal and its basis construction algorithms have been extensively studied in computer algebra and machine learning as a general model to reconstruct the algebraic variety on which noisy data approximately lie. In particular, the basis construction algorithms developed in machine learning are widely used in applications across many fields because of their monomial-order-free property; however, they lose many of the theoretical properties of computer-algebraic algorithms. In this paper, we propose general methods that equip monomial-order-free algorithms with several advantageous theoretical properties. Specifically, we exploit the gradient to (i) sidestep the spurious vanishing problem in polynomial time to remove symbolically trivial redundant bases, (ii) achieve consistent output with respect to the translation and scaling of input, and (iii) remove nontrivially redundant bases. The proposed methods work in a fully numerical manner, whereas existing algorithms require the awkward monomial order or exponentially costly (and mostly symbolic) computation to realize properties (i) and (iii). To our knowledge, property (ii) has not been achieved by any existing basis construction algorithm of the approximate vanishing ideal.

A morphological way to remove baseline and spike separation in EEG.

In this work, we have considered the problem of inconsistent sequence order and varying quality of decompositions by independent component analysis (ICA) and presented an alternate way to separate source signals from the electroencephalogram (EEG) using morphological component analysis (MCA) method based on explicit dictionary of independent redundant bases. Using correlation, qualitatively we have compared ICA with MCA's capability to segregate baseline and spike in different EEG data.

How to explore the patch space

Patches are small images (typically $8\times 8$ to $12\times 12$) extracted from natural images. The ``patch space'' is the set of all observable patches extracted from digital images in the world. This observable space is huge and should permit a sophisticated statistical analysis. In the past ten years, statistical inquiries and applications involving the ``patch space'' have tried to explore its structure on several levels. The first attempts have invalidated models based on PCA or Fourier analysis. Redundant bases (or patch dictionaries) obtained by independent component analysis (ICA) or related processes have tried to find a reduced set of patches on which every other patch obtains a sparse decomposition. Optimization algorithms such as EM have been used to explore the patch space as a Gaussian mixture. The goal of the present paper is to review this literature, and to extend its methodology to gain more insight on the independent components of the patch space.  &nbsp The conclusion of our analysis is that the sophisticated ICA tools introduced to analyze the patch space require a previous geometric normalization step to yield non trivial results. Indeed, we demonstrate by a simple experimental setup and by the analysis of the literature that, without this normalization, the patch space structure is actually hidden by the rotations, translations, and contrast changes. Thus, ICA models applied on a random set of patches boil down to segmenting the patch space depending on insignificant dimensions such as the patch orientation or the position of its gradient barycenter. When, instead of exploring the raw patches, one decides to explore the quotient of the set of patches by these action groups, a geometrically interpretable patch structure is revealed.

Sparse polynomials, redundant bases, gauss periods, and efficient exponentiation of primitive elements for small characteristic finite fields

Gauss periods give an exponentiation algorithm that is fast for many finite fields but slow for many other fields. The current paper presents a different method for construction of elements that yield a fast exponentiation algorithm for finite fields where the Gauss period method is slow or does not work. The basic idea is to use elements of low multiplicative order and search for primitive elements that are binomial or trinomial of these elements. Computational experiments indicate that such primitive elements exist, and it is shown that they can be exponentiated fast.

Indications that "codon boundaries" are physico-chemically defined and that protein-folding information is contained in the redundant exon bases

BackgroundAll the information necessary for protein folding is supposed to be present in the amino acid sequence. It is still not possible to provide specific ab initio structure predictions by bioinformatical methods. It is suspected that additional folding information is present in protein coding nucleic acid sequences, but this is not represented by the known genetic code.ResultsNucleic acid subsequences comprising the 1st and/or 3rd codon residues in mRNAs express significantly higher free folding energy (FFE) than the subsequence containing only the 2nd residues (p < 0.0001, n = 81). This periodic FFE difference is not present in introns. It is therefore a specific physico-chemical characteristic of coding sequences and might contribute to unambiguous definition of codon boundaries during translation. The FFEs of the 1st and 3rd residues are additive, which suggests that these residues contain a significant number of complementary bases and that may contribute to selection for local RNA secondary structures in coding regions. This periodic, codon-related structure-formation of mRNAs indicates a connection between the structures of exons and the corresponding (translated) proteins. The folding energy dot plots of RNAs and the residue contact maps of the coded proteins are indeed similar. Residue contact statistics using 81 different protein structures confirmed that amino acids that are coded by partially reverse and complementary codons (Watson-Crick (WC) base pairs at the 1st and 3rd codon positions and translated in reverse orientation) are preferentially co-located in protein structures.ConclusionExons are distinguished from introns, and codon boundaries are physico-chemically defined, by periodically distributed FFE differences between codon positions. There is a selection for local RNA secondary structures in coding regions and this nucleic acid structure resembles the folding profiles of the coded proteins. The preferentially (specifically) interacting amino acids are coded by partially complementary codons, which strongly supports the connection between mRNA and the corresponding protein structures and indicates that there is protein folding information in nucleic acids that is not present in the genetic code. This might suggest an additional explanation of codon redundancy.

Recovery of Exact Sparse Representations in the Presence of Bounded Noise

The purpose of this contribution is to extend some recent results on sparse representations of signals in redundant bases developed in the noise-free case to the case of noisy observations. The type of question addressed so far is as follows: given an (n,m)-matrix A with m>n and a vector b=Axo, i.e., admitting a sparse representation xo, find a sufficient condition for b to have a unique sparsest representation. The answer is a bound on the number of nonzero entries in xo. We consider the case b=Axo+e where xo satisfies the sparsity conditions requested in the noise-free case and e is a vector of additive noise or modeling errors, and seek conditions under which xo can be recovered from b in a sense to be defined. The conditions we obtain relate the noise energy to the signal level as well as to a parameter of the quadratic program we use to recover the unknown sparsest representation. When the signal-to-noise ratio is large enough, all the components of the signal are still present when the noise is deleted; otherwise, the smallest components of the signal are themselves erased in a quite rational and predictable way

Efficient reconstruction from frame-based multiple descriptions

Redundant bases or frames are a promising technique for multiple description signal coding. Frames can provide sufficient redundancy for recovery in case of coefficient losses due, for instance, to packet transmission errors. In this paper, we consider the problem of dual frame computation in the context of finite impulse response (FIR) analysis and synthesis filterbanks. In particular, we propose an algorithm for dual frame computation which recovers the missing frame coefficients, followed by synthesis with the original filterbank. It is shown that the algorithm operates locally and allows for reduced complexity and low-delay reconstruction of the original signal. The case of excessive losses and incomplete bases is also considered. Experiments are provided to evaluate the algorithm performance and test its applicability in practical contexts.

On Sparse Representations in Arbitrary Redundant Bases

The purpose of this contribution is to generalize some recent results on sparse representations of signals in redundant bases. The question that is considered is the following: given a matrix A of dimension (n,m) with m>n and a vector b=Ax, find a sufficient condition for b to have a unique sparsest representation x as a linear combination of columns of A. Answers to this question are known when A is the concatenation of two unitary matrices and either an extensive combinatorial search is performed or a linear program is solved. We consider arbitrary A matrices and give a sufficient condition for the unique sparsest solution to be the unique solution to both a linear program or a parametrized quadratic program. The proof is elementary and the possibility of using a quadratic program opens perspectives to the case where b=Ax+e with e a vector of noise or modeling errors.

Eutactic quantum codes

We consider sets of quantum observables corresponding to eutactic stars. Eutactic stars are systems of vectors which are the lower-dimensional ``shadow'' image, the orthogonal view, of higher-dimensional orthonormal bases. Although these vector systems are not comeasurable, they represent redundant coordinate bases with remarkable properties. One application is quantum secret sharing.

More on sparse representations in arbitrary bases

The purpose of this contribution is to generalize some recent results on sparse representations of signals in redundant bases. The question that is considered is thc following : let A be a known (n, m) matrix with m > n. one observes b = AX where X is known to have p < n nonzero components. under which couditions on A and p is it possible to recover X by solving a convex optimization problem such as a linear or quadratic program? The solution is known when A is the concatination of two unitary matrices. we extend it to arbitrary matrices.

Digital geographic data exchange standards and products: descriptions, comparisons and opinions

As the 21st century begins and this nation's economy continues to be transformed by technology from one dominated by production utilising natural resources to one based on service, transportation, and information, it will require the support of an information infrastructure. This infrastructure will include not only myriad data sets, but also complex systems for coordinating, storing, processing, managing, and distributing them. From this perspective it would appear that ‘(the major mapping and charting organizations)’ should be transformed from mapping service organisations to the federal agencies responsible for structuring and coordinating the geographic or spatial component of the national infrastructure. They would serve and be served by data users in all sectors of the economy, not just organisations with natural resource or earth science management responsibilities. Such a transformation can take place gradually, but it requires a clear vision of ultimate goals so that technological and institutional developments occur in an orderly, purposeful fashion. Such a transformation will not take place without substantial investment in the public and private sectors and a reordering of traditional priorities and organizational structures. Although the field is still emerging, it is clear that GIS technology, to which computers are central, will be pervasive. The need for a high-quality, comprehensive, current national base data to serve as the geometric framework to which specialized data sets (themes, overlays, coverages, layers—whatever terminology comes to be widely accepted) can be registered is developing at a faster rate than anyone could have predicted. Pressure is mounting for the immediate digital equivalent of topographic maps that were decades in the making. If such data are not available soon, untold millions and possibly even billions of dollars will be spent to create redundant data bases that will only meet users' short-term needs. This country has a tradition of localized control in the public sector and a belief in the power of free-market forces operating in the private sector to best serve the national interest. But in an era of instantaneous nationwide and worldwide transmission of information, it no longer may make sense to compartmentalise data production responsibility in quite the same ways as in the past. Survival in an increasingly global economy, dominated by ever larger private/public sector coalitions may be possible only if commitments are made in this country to a national policy for increased information development and sharing.

Treatment of redundancies among internal coordinates in optimizing molecular mechanics force constants

The use of redundant coordinate bases in the construction of molecular mechanics force fields is discussed. It is shown that the intrinsic indeterminacy in a force field in redundant coordinates in general stems from the squares of the first-order redundancy relations. The necessity to use constraints in such a force field is pointed out, and a method to check whether or not a set of constraints makes the force field determinate is described. It is also explained how force fields corresponding to different sets of constraints can be transformed into one another. To facilitate the utilization of ab initio or other spectroscopic force fields, a procedure is given by which force constants pertaining to a nonredundant coordinate basis can be optimized in molecular mechanics calculations where redundant coordinates are used. © 1992 by John Wiley & Sons, Inc.

On the general theoretical foundations of methods for optimum hybrids

This paper is intended as an attempt to establish a badly needed common theoretical background for different criteria for optimum hybrids. First, it is shown that hybridisation can be defined within the CI scheme and is not a specific feature of either the VB or the MO schemes. Next, using the MO scheme as a reference model, a description of the way in which hybrids follow from the search for bond orbitals is given. After analysing various physical and mathematical conditions, the hybrids thus defined are shown to be maximum-overlap hybrids, so that optimum hybrids determined by the maximum-localisation condition and hybrids determined by the maximum total overlap criterion coincide up to a choice of weights which is free in either case. Secondary hybridisation associated with lone pairs and redundant AO bases is shown to fit within the same general scheme. Its relation with orbital occupation is also discussed. Finally, the physical meaning of the various conditions and parameters (maximisation of overlap, orthogonality of hybrids, limiting form of lone pair hybrids, etc.) is discussed.