Simple Sequence Research Articles

Technique to Determine the Optimized Harmonic Switching Angles of a Cascaded Multilevel Inverter for Minimum Harmonic Distortion

ABSTRACTMultilevel inverters have received considerable attention from industries and researchers for its high power and voltage applications. Various switching techniques have been suggested for improving the quality and performance of inverters. One of the conventional techniques for implementing the switching algorithm in these inverters is optimized harmonic-stepped waveform. However, this technique involves the major problem of solving non-linear and complex equations, which indicates a possibility of multiple solutions. This paper describes a novel technique that uses the simple arithmetic sequence of natural numbers to determine the optimized switching angles of a single-phase cascaded multilevel inverter of any number of levels and fed by equal dc sources. The basic objective was to avoid the laborious process of solving the non-linear equations using complex switching algorithm for finding the optimal solution of the switching angles. This technique is implemented to calculate the optimized switching angles of a nine-level cascaded inverter that reduces the total harmonic distortion to below 9%.

Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing.

Monitoring antigen-specific T cells is critical for the study of immune responses and development of biomarkers and immunotherapeutics. We developed a novel multiplex assay that combines conventional immune monitoring techniques and immune receptor repertoire sequencing to enable identification of T cells specific to large numbers of antigens simultaneously. We multiplexed 30 different antigens and identified 427 antigen-specific clonotypes from 5 individuals with frequencies as low as 1 per million T cells. The clonotypes identified were validated several ways including repeatability, concordance with published clonotypes, and high correlation with ELISPOT. Applying this technology we have shown that the vast majority of shared antigen-specific clonotypes identified in different individuals display the same specificity. We also showed that shared antigen-specific clonotypes are simpler sequences and are present at higher frequencies compared to non-shared clonotypes specific to the same antigen. In conclusion this technology enables sensitive and quantitative monitoring of T cells specific for hundreds or thousands of antigens simultaneously allowing the study of T cell responses with an unprecedented resolution and scale.

Novel tridentate ligands derived from (+)-camphoric acid for enantioselective ethylation of aromatic aldehydes

Novel tridentate ligands were prepared from (+)-camphoric acid, using simple synthetic sequences. The synthesized ligands were used in enantioselective ethylations of benzaldehydes, showing enantioselectivities up to 92%, at room temperature. Extending the reaction to other aromatic aldehydes, very good results (almost quantitative yields and ee up to 97%, for m-anisaldehyde) were obtained. Structural features such as no substitution in the salicylaldehyde moiety of the Schiff base and an ethyl group in the nitrogen at the C1 position of the cyclopentane ring seem to be essential for obtaining high enantioselectivities.

Recursive sequences in first-year calculus

This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

Male mice song syntax depends on social contexts and influences female preferences.

In 2005, Holy and Guo advanced the idea that male mice produce ultrasonic vocalizations (USV) with some features similar to courtship songs of songbirds. Since then, studies showed that male mice emit USV songs in different contexts (sexual and other) and possess a multisyllabic repertoire. Debate still exists for and against plasticity in their vocalizations. But the use of a multisyllabic repertoire can increase potential flexibility and information, in how elements are organized and recombined, namely syntax. In many bird species, modulating song syntax has ethological relevance for sexual behavior and mate preferences. In this study we exposed adult male mice to different social contexts and developed a new approach of analyzing their USVs based on songbird syntax analysis. We found that male mice modify their syntax, including specific sequences, length of sequence, repertoire composition, and spectral features, according to stimulus and social context. Males emit longer and simpler syllables and sequences when singing to females, but more complex syllables and sequences in response to fresh female urine. Playback experiments show that the females prefer the complex songs over the simpler ones. We propose the complex songs are to lure females in, whereas the directed simpler sequences are used for direct courtship. These results suggest that although mice have a much more limited ability of song modification, they could still be used as animal models for understanding some vocal communication features that songbirds are used for.

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions.

Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The neutralizing antibody (KZ52) derived from a human survivor of the 1995 Kikwit outbreak recognizes a protein epitope on this AH, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' ( http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/index.html).

Design of CID-cleavable protein cross-linkers: identical mass modifications for simpler sequence analysis.

The cross-linking Mass Spectrometry (XL-MS) technique has enormous potential for studying the interactions between proteins, and it can provide detailed structural information about the interaction interfaces in large protein complexes. Such information has been difficult to obtain by conventional structural methods. One of the primary impediments to the wider use of the XL-MS technique is the extreme challenge in sequencing cross-linked peptides because of their complex fragmentation patterns in MS. A recent innovation is the development of MS-cleavable cross-linkers, which allows direct sequencing of component peptides for facile identification. Sulfoxides are an intriguing class of thermally-cleavable compounds that have been shown to fragment selectively during low-energy collisional induced dissociation (CID) analysis. Current CID-cleavable cross-linkers create fragmentation patterns in MS(2) of multiple peaks for each cross-linked peptide. Reducing the complexity of the fragmentation pattern in MS(2) facilitates subsequent MS(3) sequencing of the cross-linked peptides. The first authentic identical mass linker (IML) has now been designed, prepared, and evaluated. Multistage tandem mass spectrometry (MS(n)) analysis has demonstrated that the IML cross-linked peptides indeed yield one peak per peptide constituent in MS(2) as predicted, thus allowing effective and sensitive MS(3) analysis for unambiguous identification. Selective fragmentation for IML cross-linked peptides from the 19S proteasome complex was observed, providing a proof-of-concept demonstration for XL-MS studies on protein complexes.

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions

Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The neutralizing antibody (KZ52) derived from a human survivor of the 1995 Kikwit outbreak recognizes a protein epitope on this AH, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' (http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/index.html).

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions

Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The neutralizing antibody (KZ52) derived from a human survivor of the 1995 Kikwit outbreak recognizes a protein epitope on this AH, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' ( http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/index.html).

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions

Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The ability of this AH to bind to other host proteins is disrupted by a neutralizing antibody derived from a human survivor of the 1995 Kikwit outbreak, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' (http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/index.html).

RANDTRAN: Random transcriptome sequence generator that accounts for partition specific features in eukaryotic mRNA datasets

The generation of true random and pseudorandom control sequences is an important problem of computational biology. Available random sequence generators differ in underlying probabilistic models that often remain undisclosed to users. Random sequences produced by differing probabilistic models substantially differ in their outputs commonly used as baselines for evaluations of the motif frequencies. Moreover, modern bioinformatics studies often require generation of matching control transcriptome with emulated partitions into ORFs, 5'- and 3'-UTRs as well as the proportion of non-coding RNAs within model transcriptome rather than relatively simple continuous control sequences. Here we describe novel random sequence generating tool RANDTRAN that accounts for the length distribution of 5' and 3' non-translated regions in given transcriptome and the partition-specific di- and trinucleotide compositions in translated and non-translated regions. RANDRAN presents matching control transcriptomes in ready-to-use UCSC genome browser-compatible input files. These features may be useful for generating of control sequence sets for common types of computational analysis of various sequence motifs within various sets of RNA. RANDTRAN is available for free download at http://www.genereseairch.ru/images/Randtran.rar.

Zipf's law for randomly generated frequencies: explicit tests for the goodness-of-fit

The question, whether Zipf's law arises only in consequence of interactions in a complex system or if it is also valid for random structures, has been controversially discussed in the literature over several decades. We show by means of simulations that the frequency distributions of simple random sequences usually obey this regularity. For tens of thousands of cases the goodness-of-fit is explicitly demonstrated by estimating the parameter and calculating the corresponding chi-square value. From the study it becomes clear that some existing results in the literature should be revised, and some ideas concerning the explanation of Zipf's law are provided.

Ultrasonic Automatic Tracking System

Ultrasonic ranging system has many characteristics, such as well-directionality, small volume, and low price, but fails to realize a long distance measured. In order to realize exactly locating motion objects, multiple ultrasonic sensors are adopted to measure their motion orientation so that their 2D coordinates should be located and positioned, which results in calculations complicated and meanwhile measurement subject to errors. This study addresses a measurement method to realize automatically tracking motion objects. It has a reasonable distribution structure of the ultrasonic sensors adopted, critical tracking calculation method, which makes it possible to solve complex problems of equations. As it has simple control instruction sequence, it is able to precisely control timing period and effectively solve measure error caused by irregular delay from commands. These programs and methods are well deployed in the parameters collection and status control system for a moving object. DOI: http://dx.doi.org/10.11591/telkomnika.v12i6.5449 Full Text: PDF

Dominance Orders, Generalized Binomial Coefficients, and Kummer's Theorem

SummaryWe discuss the connections between a family of partial orders known as b-dominance orders, arithmetic in base b, and generalized binomial coefficients. In particular, we investigate theorems of Lucas and Kummer in relation to these orders and attempt to extend and explain these theorems using a family of generalized binomial coefficients derived from a simple integer sequence.

Transcription Factor Binding Sites Prediction Based on Modified Nucleosomes

In computational methods, position weight matrices (PWMs) are commonly applied for transcription factor binding site (TFBS) prediction. Although these matrices are more accurate than simple consensus sequences to predict actual binding sites, they usually produce a large number of false positive (FP) predictions and so are impoverished sources of information. Several studies have employed additional sources of information such as sequence conservation or the vicinity to transcription start sites to distinguish true binding regions from random ones. Recently, the spatial distribution of modified nucleosomes has been shown to be associated with different promoter architectures. These aligned patterns can facilitate DNA accessibility for transcription factors. We hypothesize that using data from these aligned and periodic patterns can improve the performance of binding region prediction. In this study, we propose two effective features, “modified nucleosomes neighboring” and “modified nucleosomes occupancy”, to decrease FP in binding site discovery. Based on these features, we designed a logistic regression classifier which estimates the probability of a region as a TFBS. Our model learned each feature based on Sp1 binding sites on Chromosome 1 and was tested on the other chromosomes in human CD4+T cells. In this work, we investigated 21 histone modifications and found that only 8 out of 21 marks are strongly correlated with transcription factor binding regions. To prove that these features are not specific to Sp1, we combined the logistic regression classifier with the PWM, and created a new model to search TFBSs on the genome. We tested the model using transcription factors MAZ, PU.1 and ELF1 and compared the results to those using only the PWM. The results show that our model can predict Transcription factor binding regions more successfully. The relative simplicity of the model and capability of integrating other features make it a superior method for TFBS prediction.

DNA divergence as a criterion of a sweet pepper (Capsicum annuum L.) selection for heterosis

The identification of perspective parental lines for the creation of highyield hybrids is the most laborconsuming stage of selection, because it needs exte nsive trials of combining ability. Based on evaluation of the genetic divergence of the parental lines, the prediction accuracy of F1 hybrids performance was inves� tigated. The value of the divergence was calculated using biometric and molecular methods, such as inter sim� ple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD). Based on estimates of diver� gence, 10 lines were chosen for cyclic cross (scheme I) and testcross (scheme II). In most crosses, the F1 hybrids were significantly superior to the parents in the main economically valuable traits. The level of het� erosis was higher among hybrids of scheme I. Analysis of the relationship between parental divergence and F1 performance showed that the hybrid productivity of scheme I was predetermined by ISSR divergence in 86%, and productivity was caused by RAPD divergence in 69%, whereas the F1 yield of scheme II was not related to the value of genetic distances. Since the values of DNA divergence were closely associated both with mid� parent level and F1 performance, we assumed that part of the polymorphic DNA fragments of the parental lines of scheme I is related to heterotic loci (HTL), which may be considered potential key markers for the heterotic selection of the sweet pepper.

Cognitive and neural foundations of discrete sequence skill: A TMS study

Executing discrete movement sequences typically involves a shift with practice from a relatively slow, stimulus-based mode to a fast mode in which performance is based on retrieving and executing entire motor chunks. The dual processor model explains the performance of (skilled) discrete key-press sequences in terms of an interplay between a cognitive processor and a motor system. In the present study, we tested and confirmed the core assumptions of this model at the behavioral level. In addition, we explored the involvement of the pre-supplementary motor area (pre-SMA) in discrete sequence skill by applying inhibitory 20min 1-Hz off-line repetitive transcranial magnetic stimulation (rTMS). Based on previous work, we predicted pre-SMA involvement in the selection/initiation of motor chunks, and this was confirmed by our results. The pre-SMA was further observed to be more involved in more complex than in simpler sequences, while no evidence was found for pre-SMA involvement in direct stimulus–response translations or associative learning processes. In conclusion, support is provided for the dual processor model, and for pre-SMA involvement in the initiation of motor chunks.

Interlimb Practice and Aging: Coding a Simple Movement Sequence

Background/Study Context: The purpose was to determine if aging interacts with the coding of a simple spatial-temporal movement sequence. Methods: An interlimb practice paradigm (24 participants; 12 young adults [age: 23–29]; 12 old adults [age: 65–78]) was designed to determine the coordinate system (visual-spatial/motor) that is used to code the movement sequence. Practice was scheduled over 2 days involving either the same visual-spatial or the same motor coordinates. On Day 3, two retention tests (Day 1/Day 2) were conducted. Results: Keeping the motor coordinates the same during acquisition resulted in superior retention only for younger adults. Conclusion: The data provide strong evidence that the motor code plays a dominant role in acquiring simple movement sequences for younger adults, but not for older adults.

Transcriptomics: Better Resolutions

Copyright: © 2014 Gupta S. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. In the post Human Genome Project era there are efforts to understand translation of the genomic sequence into the transcriptome. The human transcriptome is represented by >100,000 distinct transcripts presently described for ~20,000 protein-coding genes. Additionally, mRNA isoforms are produced by alternative processing of primary RNA transcripts. This alternative splicing affects >90% of the human genes and has been suggested to the primary driver of phenotypic complexity [1]. Despite this diversity in the coding sequence, the nonprotein-coding molecules contribute to > 95% of the transcriptome [2]. Numerous technologies and experimental platforms have facilitated the investigation of the complexity in the transcriptome that greater than that of the simple genome sequence.

RLS patients can also develop compulsions on dopaminergic agonists

Introduction The aim of this study was to assess the frequency of self-reported compulsive behaviours, depressive and stress symptoms and sleep disorders in a population of Restless legs patients treated with DA agonists. Reports by Tippmann-Peikert et al. (2007) and Ritz et al. (2006) extend the risk of developing DA agonists related impulse control disorders such as gambling, heightened sexual drive or unreasonably overinvested repetitive activities to RLS patients. Materials and methods A questionnaire covering RLS severity (IRLSSG-Walters et al. 2003), mood variables, The Beck Depression Inventory II (Beck et al. 2003), a visual Analog Scale of current level of stress and sleep parameters (The MOS Sleepscale, Hays & Stewart 1992) was sent at 3 points in time over twelve months in 2005 (February, June, October) to 150 RLS patients cared for at the Quebec Memory & Motor Skills Disorders Clinic. A last section exploring changes in hobbies, development of new habits and compulsions was added at the third mailing. Results Data derived from a population of 97 patients having answered all three mailings identified 17 positive responses to compulsions. After re-evaluation only 12 (8 women and 4 men) were found to have truly compulsive behaviours. In two women, simple motor stereotyped sequences in response to sensory urge evoked the phenomenology of Gilles de La Tourette Syndrome. In two other, one male, one female, a reactivation of trichotillomania previously exhibited in childhood was observed. For the other eight patients, abnormal behavioural display was similar to complex compulsory behaviours with short-term rewarding properties such as buying clothes, buying food, eating or gambling. In addition BDI and stress scores significantly contrasted the compulsion (+) vs. compulsion (−) patients. Their MOS sub-scale sleep problem Index I and II showed significantly higher scores and finally, the augmentation phenomenon was of higher prevalence in the C + group at the time of the 3rd questionnaire. Conclusion In summary, 12 out of 97 RLS patients on stable DA agonist therapy presented with progressive dishinibition of behaviour possibly shaped by pre treatment gender and individual specificities. None had a previous diagnosis of anxious generalized disorder or obsessive compulsive disorder. They showed more dysphoric and recognized themselves as more stressed than the compulsion (-) group of RLS patients.