Redundant Entries Research Articles

Low-Complexity Direction-of-Arrival Estimation Based on Wideband Co-Prime Arrays

A class of low-complexity compressive sensing-based direction-of-arrival (DOA) estimation methods for wideband co-prime arrays is proposed. It is based on a recently proposed narrowband estimation method, where a virtual array model is generated by directly vectorizing the covariance matrix and then using a sparse signal recovery method to obtain the estimation result. As there are a large number of redundant entries in both the auto-correlation and cross-correlation matrices of the two sub-arrays, they can be combined together to form a model with a significantly reduced dimension, thereby leading to a solution with much lower computational complexity without sacrificing performance. A further reduction in complexity is achieved by removing noise power estimation from the formulation. Then, the two proposed low-complexity methods are extended to the wideband realm utilizing a group sparsity based signal reconstruction method. A particular advantage of group sparsity is that it allows a much larger unit inter-element spacing than the standard co-prime array and therefore leads to further improved performance.

Protein profile of Beta vulgaris leaf apoplastic fluid and changes induced by Fe deficiency and Fe resupply.

The fluid collected by direct leaf centrifugation has been used to study the proteome of the sugar beet apoplastic fluid as well as the changes induced by Fe deficiency and Fe resupply to Fe-deficient plants in the protein profile. Plants were grown in Fe-sufficient and Fe-deficient conditions, and Fe resupply was carried out with 45 μM Fe(III)-EDTA for 24 h. Protein extracts of leaf apoplastic fluid were analyzed by two-dimensional isoelectric focusing-SDS-PAGE electrophoresis. Gel image analysis revealed 203 consistent spots, and proteins in 81% of them (164) were identified by nLC-MS/MS using a custom made reference repository of beet protein sequences. When redundant UniProt entries were deleted, a non-redundant leaf apoplastic proteome consisting of 109 proteins was obtained. TargetP and SecretomeP algorithms predicted that 63% of them were secretory proteins. Functional classification of the non-redundant proteins indicated that stress and defense, protein metabolism, cell wall and C metabolism accounted for approximately 75% of the identified proteome. The effects of Fe-deficiency on the leaf apoplast proteome were limited, with only five spots (2.5%) changing in relative abundance, thus suggesting that protein homeostasis in the leaf apoplast fluid is well-maintained upon Fe shortage. The identification of three chitinase isoforms among proteins increasing in relative abundance with Fe-deficiency suggests that one of the few effects of Fe deficiency in the leaf apoplast proteome includes cell wall modifications. Iron resupply to Fe deficient plants changed the relative abundance of 16 spots when compared to either Fe-sufficient or Fe-deficient samples. Proteins identified in these spots can be broadly classified as those responding to Fe-resupply, which included defense and cell wall related proteins, and non-responsive, which are mainly protein metabolism related proteins and whose changes in relative abundance followed the same trend as with Fe-deficiency.

Reduced-Dimensional PARAFAC-Based Algorithm for Joint Angle and Doppler Frequency Estimation in Monostatic MIMO Radar

In this article, the problem of joint direction of arrival (DOA) and Doppler frequency estimation using parallel factor (PARAFAC) analysis in the monostatic multiple-input multiple-output radar is investigated and a reduced-dimensional PARAFAC (RD-PARAFAC) algorithm is proposed. In order to overcome the shortcoming of the heavy computational load in conventional PARAFAC algorithm, we firstly utilize a RD transformation by employing the property of uniform linear arrays, which can remove the redundant entries of steering matrix. By means of the reduced-dimensional transformation, the proposed algorithm can reduce the computational complexity, save memory capacity significantly and has very close joint DOA and Doppler frequency estimation performance when compared with conventional PARAFAC algorithm. Meanwhile, it outperforms the estimation of signal parameters via rotational invariance technique and the propagator method. Furthermore, our algorithm needs no spectral peak searching or pair matching. The complexity analysis and the Cramer-Rao Bound of the DOA and frequency estimation is derived. Simulations are provided to verify its effectiveness and superiority.

Layered interval codes for TCAM-based classification

Ternary content-addressable memories (TCAMs) are increasingly used for high-speed packet classification. TCAMs compare packet headers against all rules in a classification database in parallel and thus provide high throughput.TCAMs are not well-suited, however, for representing rules that contain range fields and previously published algorithms typically represent each such rule by multiple TCAM entries. The resulting range expansion can dramatically reduce TCAM utilization because it introduces a large number of redundant TCAM entries. This redundancy can be mitigated by making use of extra bits, available in each TCAM entry.We present a scheme for constructing efficient representations of range rules, based on the simple observation that sets of disjoint ranges may be encoded much more efficiently than sets of overlapping ranges. Since the ranges in real-world classification databases are, in general, non-disjoint, the algorithms we present split ranges between multiple layers, each of which consists of mutually disjoint ranges. Each layer is then coded and assigned its own set of extra bits.Our layering algorithms are based on approximations for specific variants of interval-graph coloring. We evaluate these algorithms by performing extensive comparative analysis on real-life classification databases. Our analysis establishes that our algorithms reduce the number of redundant TCAM entries caused by range rules by more than 60% as compared with best range-encoding prior work.

Axonal Transport Proteomics Reveals Mobilization of Translation Machinery to the Lesion Site in Injured Sciatic Nerve

Investigations of the molecular mechanisms underlying responses to nerve injury have highlighted the importance of axonal transport systems. To obtain a comprehensive view of the protein ensembles associated with axonal transport in injured axons, we analyzed the protein compositions of axoplasm concentrated at ligatures following crush injury of rat sciatic nerve. LC-MS/MS analyses of iTRAQ-labeled peptides from axoplasm distal and proximal to the ligation sites revealed protein ensembles transported in both anterograde and retrograde directions. Variability of replicates did not allow straightforward assignment of proteins to functional transport categories; hence, we performed principal component analysis and factor analysis with subsequent clustering to determine the most prominent injury-related transported proteins. This strategy circumvented experimental variability and allowed the extraction of biologically meaningful information from the quantitative neuroproteomics experiments. 299 proteins were highlighted by principal component analysis and factor analysis, 145 of which correlate with retrograde and 154 of which correlate with anterograde transport after injury. The analyses reveal extensive changes in both anterograde and retrograde transport proteomes in injured peripheral axons and emphasize the importance of RNA binding and translational machineries in the axonal response to injury.

The Reinstatement of Polyphony in Musical Construction: Fugal Finales in Haydn's Op. 20 String Quartets

The title, borrowed from Paul Henry Lang's description of Haydn's op. 20 string quartets in Music in Western Civilization, characterizes Haydn's endeavor to create more independent partwriting in the string quartet. First, Haydn's fugal practice is noteworthy particularly for the construction of the fugal exposition and his treatment of multiple subjects, the question of what constitutes a regular countersubject, and the treatment of redundant entries. Second, the chief strategy in these movements is the invention of invertible counterpoint in three voices. Haydn writes a double fugue (with a regular countersubject), as well as a triple and quadruple fugue, in which the principal issue is the ability of each subject (including the double fugue's countersubject) to serve as any voice—top, middle or bottom—in a texture of invertible counterpoint. The expertise he attained with these works then allows him to exploit the technique in later quartets, principally in the development sections of sonata-form movements. There, he uses invertible counterpoint to establish the independence of each voice, and to create longer passages unarticulated by cadences, sections distinct from the more clearly articulated periodic expositions and recapitulations. The three fugal finales of op. 20, therefore, constitute Haydn's advanced study not so much in fugal procedure as in the practice of invertible counterpoint.

An accurate and efficient system model of iterative image reconstruction in high-resolution pinhole SPECT for small animal research

Accurate modeling of the photon acquisition process in pinhole SPECT is essential for optimizing resolution. In this work, the authors develop an accurate system model in which pinhole finite aperture and depth-dependent geometric sensitivity are explicitly included. To achieve high-resolution pinhole SPECT, the voxel size is usually set in the range of sub-millimeter so that the total number of image voxels increase accordingly. It is inevitably that a system matrix that models a variety of favorable physical factors will become extremely sophisticated. An efficient implementation for such an accurate system model is proposed in this research. We first use the geometric symmetries to reduce redundant entries in the matrix. Due to the sparseness of the matrix, only non-zero terms are stored. A novel center-to-radius recording rule is also developed to effectively describe the relation between a voxel and its related detectors at every projection angle. The proposed system matrix is also suitable for multi-threaded computing. Finally, the accuracy and effectiveness of the proposed system model is evaluated in a workstation equipped with two Quad-Core Intel Xeon processors.

Quantitative proteomic analysis of radioresistant breast cancer cell lines.

Abstract Abstract #5074 Background: Resistance to radiotherapy may be a significant factor in the development of local recurrence following surgical resection and radiotherapy. We aimed to develop a novel in vitro model of radioresistance using a breast cancer cell line and to subsequently identify molecular biomarkers which may be associated with the radioresistant phenotype. We utilised a quantitative proteomics technique (iTRAQ) based on MALDI-TOF/TOF mass spectrometry (MS) to identify differentially expressed proteins.
 Material and Methods: We established 3 novel breast cancer cell sublines which were significantly resistant to radiotherapy when compared with the parental cells. The radioresistant sublines were created by irradiating cells in fractionated doses of 2Gy up to a total dose of 40Gy. Sufficient time was allowed for the cells to recover between subsequent irradiations. A dose response curve was assessed at the end of treatment to demonstrate a statistically significant increase in radioresistance for each novel cell subline when compared with parental cells. One radioresistant/parental cell pair was first analysed using in-solution digestion and liquid chromatographic separation with protein identification by MALDI-TOF/TOF (LC-MALDI analysis) on an Applied Biosystems 4800 Plus instrument. Quantitative iTRAQ (Applied Biosystems) was then performed on the same instrument for all 3 radioresistant/parental cell pairs.
 Results: A total of 586 and 652 proteins were identified in T47D and T47DRR cells respectively by LC-MALDI. Those proteins identified in both cell lines and any redundant entries were removed to reveal those proteins which were unique to each cell line. In total 244 unique proteins were identified in T47D cells and 311 unique proteins were identified in T47DRR cells.
 Comparison of the 3 pairs of radioresistant/parental cell samples by iTRAQ revealed a number of differentially expressed proteins. Using a standard ≥2-fold change in expression, these iTRAQ analyses revealed significant changes in the expression of 51 proteins in one or more of the radio-resistant derivatives.
 Further confirmation by immunoblotting is underway. Currently the decrease in expression of 26S proteasome associated subunits has been confirmed by this method.
 Conclusion: LC-MALDI and iTRAQ analysis has revealed a large number of candidate proteins which may be associated with a radioresistant phenotype. These now require further confirmatory studies. These MS-based techniques offer a powerful proteomic approach to identify candidate biomarkers which may be involved in radioresistance. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 5074.

Global Survey of Human T Leukemic Cells by Integrating Proteomics and Transcriptomics Profiling

A global protein survey is needed to gain systems-level insights into mammalian cell signaling and information flow. Human Jurkat T leukemic cells are one of the most important model systems for T cell signaling study, but no comprehensive proteomics survey has been carried out in this cell type. In the present study we combined subcellular fractionation, multiple protein enrichment methods, and replicate tandem mass spectrometry analyses to determine the protein expression pattern in a single Jurkat cell type. The proteome dataset was evaluated by comparison with the genome-wide mRNA expression pattern in the same cell type. A total of 5381 proteins were identified by mass spectrometry with high confidence. Rigorous comparison of RNA and protein expression afforded removal of the false positive identifications and redundant entries but rescued the proteins identified by a single high scoring peptide, resulting in the final identification of 6471 unique gene products among which 98% of the corresponding transcripts were detected with high probability. Using hierarchical clustering of the protein expression patterns in five subcellular fractions (cytosol, light membrane, heavy membrane, mitochondria, and nuclei), the primary subcellular localization of 2241 proteins was assigned with high confidence including 792 previously uncharacterized proteins. This proteome landscape can serve as a useful platform for systems-level understanding of organelle composition and cellular functions in human T cells.

Evaluation of Multiprotein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry

Strategies for removal of high abundance proteins have been increasingly utilized in proteomic studies of serum/plasma and other body fluids to enhance the detection of low abundance proteins and achieve broader proteome coverage; however, both the reproducibility and specificity of the high abundance protein depletion process still represent common concerns. Here we report a detailed evaluation of immunoaffinity subtraction performed applying the ProteomeLab IgY-12 system that is commonly used in human serum/plasma proteome characterization in combination with high resolution LC-MS/MS. Plasma samples were repeatedly processed using this approach, and the resulting flow-through fractions and bound fractions were individually analyzed for comparison. The removal of target proteins by the immunoaffinity subtraction system and the overall process was highly reproducible. Non-target proteins, including one spiked protein standard (rabbit glyceraldehyde-3-phosphate dehydrogenase), were also observed to bind to the column at different levels but also in a reproducible manner. The results suggest that multiprotein immunoaffinity subtraction systems can be readily integrated into quantitative strategies to enhance detection of low abundance proteins in biomarker discovery studies.

Eliminating redundant entries in bibliographic records

According to AACR2 21.4D1 and 21.4D3 for works by heads of state, other high government officials, popes, and other high ecclesiastical officials, catalogers are to enter a person's personal heading and a person's corporate heading as main entry and added entry in the same bibliographic record. Entering both a person's personal and corporate headings in the same bibliographic record leads to the retrieval of identical sets where a person is represented in the catalog in both an official and a private capacity. This paper proposes to eliminate redundant entries in bibliographic records in order to help users find resources by heads of state (etc.) through the authority structure of the catalog.

Faster Algorithms for Frobenius Numbers

The Frobenius problem, also known as the postage-stamp problem or the money-changing problem, is an integer programming problem that seeks nonnegative integer solutions to $ x_1 a_1 +\cdots + x_n a_n =M$, where $ a_i $ and $M$ are positive integers. In particular, the Frobenius number $f(A)$, where $A=\{ a_i \}$, is the largest $M$ so that this equation fails to have a solution. A simple way to compute this number is to transform the problem to a shortest-path problem in a directed weighted graph; then Dijkstra's algorithm can be used. We show how one can use the additional symmetry properties of the graph in question to design algorithms that are very fast. For example, on a standard desktop computer, our methods can handle cases where $n=10$ and $ a_1 = 10^7$. We have two main new methods, one based on breadth-first search and another that uses the number theory and combinatorial structure inherent in the problem to speed up the Dijkstra approach. For both methods we conjecture that the average-case complexity is $O( a_1 \sqrt{n} )$. The previous best method is due to Böcker and Lipták and runs in time $O( a_1 n)$. These algorithms can also be used to solve auxiliary problems such as (1) find a solution to the main equation for a given value of $M$; or (2) eliminate all redundant entries from a basis. We then show how the graph theory model leads to a new upper bound on $f(A)$ that is significantly lower than existing upper bounds. We also present a conjecture, supported by many computations, that the expected value of $f(A)$ is a small constant multiple of $ \left({1\over2} \, n! \, \Pi A\right)^{1/(n-1)} -\Sigma A$.

Development and Evaluation of a Quality-Controlled Ribosomal Sequence Database for 16S Ribosomal DNA-Based Identification of Staphylococcus Species

To establish an improved ribosomal gene sequence database as part of the Ribosomal Differentiation of Microorganisms (RIDOM) project and to overcome the drawbacks of phenotypic identification systems and publicly accessible sequence databases, both strands of the 5' end of the 16S ribosomal DNA (rDNA) of 81 type and reference strains comprising all validly described staphylococcal (sub)species were sequenced. Assuming a normal distribution for pairwise distances of all unique staphylococcal sequences and choosing a reporting criterion of > or =98.7% similarity for a "distinct species," a statistical error probability of 1.0% was calculated. To evaluate this database, a 16S rDNA fragment (corresponding to Escherichia coli positions 54 to 510) of 55 clinical Staphylococcus isolates (including those of the small-colony variant phenotype) were sequenced and analyzed by the RIDOM approach. Of these isolates, 54 (98.2%) had a similarity score above the proposed threshold using RIDOM; 48 (87.3%) of the sequences gave a perfect match, whereas 83.6% were found by searching National Center for Biotechnology Information (NCBI) database entries. In contrast to RIDOM, which showed four ambiguities at the species level (mainly concerning Staphylococcus intermedius versus Staphylococcus delphini), the NCBI database search yielded 18 taxon-related ambiguities and showed numerous matches exhibiting redundant or unspecified entries. Comparing molecular results with those of biochemical procedures, ID 32 Staph (bioMerieux, Marcy I'Etoile, France) and VITEK 2 (bioMerieux) failed to identify 13 (23.6%) and 19 (34.5%) isolates, respectively, due to incorrect identification and/or categorization below acceptable values. In contrast to phenotypic methods and the NCBI database, the novel high-quality RIDOM sequence database provides excellent identification of staphylococci, including rarely isolated species and phenotypic variants.

A local alignment metric for accelerating biosequence database search.

We introduce a metric for local sequence alignments that has utility for accelerating optimal alignment searches without loss of sensitivity. The metric's triangle inequality property permits identification of redundant database entries guaranteed to have optimal alignments to the query sequence that fall below a specified score threshold, thereby permitting comparisons to these entries to be skipped. We prove the existence of the metric for a variety of scoring systems, including the most commonly used ones, and show that a triangle inequality can be established as well for nucleotide-to-protein sequence comparisons. We discuss a database clustering and search strategy that takes advantage of the triangle inequality. The strategy permits moderate but significant acceleration of searches against the widely used "nr" protein database. It also provides a theoretically based method for database clustering in general and provides a standard against which to compare heuristic clustering strategies.

The listing and de-listing of invertebrate species for conservation in Australia

Formal listing of species for protection is a responsible action in conferring conservation priority, and must be undertaken as objectively as possible, and redundant entries that distract from priority need be removed. Diverse groups, such as invertebrates, pose problems for listing because criteria of ‘rarity’ and ‘threat’ are often confounded. Species de-listed as a result of recovery action are a special category, in which conservation investment has been made; the principle of recognising these as ‘rehabilitated species’ with a formal duty of aftercare is discussed. Although the paper focuses on invertebrates in Australia, the principles have wider relevance in species-level conservation focus.

Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry.

Blood serum is a complex body fluid that contains various proteins ranging in concentration over at least 9 orders of magnitude. Using a combination of mass spectrometry technologies with improvements in sample preparation, we have performed a proteomic analysis with submilliliter quantities of serum and increased the measurable concentration range for proteins in blood serum beyond previous reports. We have detected 490 proteins in serum by on-line reversed-phase microcapillary liquid chromatography coupled with ion trap mass spectrometry. To perform this analysis, immunoglobulins were removed from serum using protein A/G, and the remaining proteins were digested with trypsin. Resulting peptides were separated by strong cation exchange chromatography into distinct fractions prior to analysis. This separation resulted in a 3-5-fold increase in the number of proteins detected in an individual serum sample. With this increase in the number of proteins identified we have detected some lower abundance serum proteins (ng/ml range) including human growth hormone, interleukin-12, and prostate-specific antigen. We also used SEQUEST to compare different protein databases with and without filtering. This comparison is plotted to allow for a quick visual assessment of different databases as a subjective measure of analytical quality. With this study, we have performed the most extensive analysis of serum proteins to date and laid the foundation for future refinements in the identification of novel protein biomarkers of disease.

Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues.

A four-step procedure for the efficient and systematic mining of whole EST libraries for differentially expressed genes is presented. After eliminating redundant entries from the EST library under investigation (step 1), contigs of maximal length are built upon each remaining EST using about 4 000 000 public and proprietary ESTs (step 2). These putative genes are compared against a database comprising ESTs from 16 different tissues (both normal and tumour affected) to determine whether or not they are differentially expressed (step 3; electronic northern). Fisher's exact test is used to assess the significance of differential expression. In step 4, an attempt is made to characterise the contigs obtained in the assembly through database comparison. A case study of the CGAP library NCI_CGAP_Br1.1, a library made from three (well, moderately, and poorly differentiated) invasive ductal breast tumours (2126 ESTs in total) was carried out. Of the maximal contigs, 139 were found to be significantly (alpha = 0.05) over-expressed in breast tumour tissue, while 13 appeared to be down-regulated.

PROSET—a fast procedure to create non-redundant sets of protein sequences

The PROSET computer program described efficiently eliminates redundant entries from a set of proteins. It finds repeats between all the proteins of the original set, derives a block identity score between any two sequences that share at least one sufficiently long exact repeat, and discards the shorter of the two sequences if the score exceeds a user-defined threshold. The program finds application in generating control sets for statistical evaluation of sequence patterns. It may also serve to reduce the amount of redundancy in available databases.

Rethinking National Policy for Cataloging Microform Reproductions

Current national cataloging policy requires the creation of unique cataloging records for an original publication and each of its microfilm reproductions. Such redundant entries are difficult to decipher and expensive to produce and maintain. The case of serial publications is most urgent, especially due to the proliferation of preservation microfilming efforts and union list projects. The master record concept used in the United States Newspaper Project offers a viable alternative method. Librarians should lobby to have the single record approach adopted as national policy.