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Prediction Algorithms and Methods of Registering the Products on Warranty by Using RFID Technologies
Cristina Hurjui,Adrian Graur
Journal of Applied Computer Science & Mathematics , 2007,
Abstract: The RFID technology (Radio FrequencyIdentifi - cation) is used in the view of data transmission,by means of mobile transponders, known as tags and forreceiving that information, by means of reading devices,known as readers. Radio Frequency Identification (RFID)has become specific for tracking the items and carryingout solutions of data achieving within the supply chains ofenterprises, factories, trading companies or automationtechnologies. This present paper proposes creation of acomputerized system dedicated to selling companies,manufacturers and service units, with a view of usingproducts’ information and estimating by a predictionalgorithm the return time towards the customers ofchanged or repaired products being on warranty or postwarrantytime.
IsoPlotter+: A Tool for Studying the Compositional Architecture of Genomes
Eran Elhaik,Dan Graur
ISRN Bioinformatics , 2013, DOI: 10.1155/2013/725434
Abstract: Eukaryotic genomes, particularly animal genomes, have a complex, nonuniform, and nonrandom internal compositional organization. The compositional organization of animal genomes can be described as a mosaic of discrete genomic regions, called “compositional domains,” each with a distinct GC content that significantly differs from those of its upstream and downstream neighboring domains. A typical animal genome consists of a mixture of compositionally homogeneous and nonhomogeneous domains of varying lengths and nucleotide compositions that are interspersed with one another. We have devised IsoPlotter, an unbiased segmentation algorithm for inferring the compositional organization of genomes. IsoPlotter has become an indispensable tool for describing genomic composition and has been used in the analysis of more than a dozen genomes. Applications include describing new genomes, correlating domain composition with gene composition and their density, studying the evolution of genomes, testing phylogenomic hypotheses, and detect regions of potential interbreeding between human and extinct hominines. To extend the use of IsoPlotter, we designed a completely automated pipeline, called IsoPlotter+ to carry out all segmentation analyses, including graphical display, and built a repository for compositional domain maps of all fully sequenced vertebrate and invertebrate genomes. The IsoPlotter+ pipeline and repository offer a comprehensive solution to the study of genome compositional architecture. Here, we demonstrate IsoPlotter+ by applying it to human and insect genomes. The computational tools and data repository are available online. 1. Introduction While the genome sizes of multicellular eukaryotes are generally larger and more variable in length than those of prokaryotes, guanine and cytosine (GC) content exhibits a much smaller variation in eukaryotes than in prokaryotes. In particular, vertebrate genomes show quite a uniform GC content, distributing over a very narrow range from about 40% to 45% [1]. Despite the uniformity of their genomic GC content, vertebrate genomes have a much more complex compositional organization than prokaryotic genomes. Recent studies have shown that this narrow distribution cloaks a complex mosaic of homogeneous and nonhomogeneous compositional domains whose sizes range from 3 kilobases (kb) to more than 10 Mega bases (Mb) and whose GC contents range from ~7% to ~72% (e.g., [2, 3]). Molecular evolutionists have had a long-standing interest in deciphering the internal compositional organization of genomes, describing their
A Comparative Study and a Phylogenetic Exploration of the Compositional Architectures of Mammalian Nuclear Genomes
Eran Elhaik ,Dan Graur
PLOS Computational Biology , 2014, DOI: doi/10.1371/journal.pcbi.1003925
Abstract: For the past four decades the compositional organization of the mammalian genome posed a formidable challenge to molecular evolutionists attempting to explain it from an evolutionary perspective. Unfortunately, most of the explanations adhered to the “isochore theory,” which has long been rebutted. Recently, an alternative compositional domain model was proposed depicting the human and cow genomes as composed mostly of short compositionally homogeneous and nonhomogeneous domains and a few long ones. We test the validity of this model through a rigorous sequence-based analysis of eleven completely sequenced mammalian and avian genomes. Seven attributes of compositional domains are used in the analyses: (1) the number of compositional domains, (2) compositional domain-length distribution, (3) density of compositional domains, (4) genome coverage by the different domain types, (5) degree of fit to a power-law distribution, (6) compositional domain GC content, and (7) the joint distribution of GC content and length of the different domain types. We discuss the evolution of these attributes in light of two competing phylogenetic hypotheses that differ from each other in the validity of clade Euarchontoglires. If valid, the murid genome compositional organization would be a derived state and exhibit a high similarity to that of other mammals. If invalid, the murid genome compositional organization would be closer to an ancestral state. We demonstrate that the compositional organization of the murid genome differs from those of primates and laurasiatherians, a phenomenon previously termed the “murid shift,” and in many ways resembles the genome of opossum. We find no support to the “isochore theory.” Instead, our findings depict the mammalian genome as a tapestry of mostly short homogeneous and nonhomogeneous domains and few long ones thus providing strong evidence in favor of the compositional domain model and seem to invalidate clade Euarchontoglires.
Discovery of 90 Type Ia supernovae among 700,000 Sloan spectra: the Type-Ia supernova rate versus galaxy mass and star-formation rate at redshift ~0.1
Or Graur,Dan Maoz
Physics , 2012, DOI: 10.1093/mnras/sts718
Abstract: Using a method to discover and classify supernovae (SNe) in galaxy spectra, we find 90 Type Ia SNe (SNe Ia) and 10 Type II SNe among the ~700,000 galaxy spectra in the Sloan Digital Sky Survey Data Release 7 that have VESPA-derived star-formation histories (SFHs). We use the SN Ia sample to measure SN Ia rates per unit stellar mass. We confirm, at the median redshift of the sample, z = 0.1, the inverse dependence on galaxy mass of the SN Ia rate per unit mass, previously reported by Li et al. (2011b) for a local sample. We further confirm, following Kistler et al. (2011), that this relation can be explained by the combination of galaxy "downsizing" and a power-law delay-time distribution (DTD; the distribution of times that elapse between a hypothetical burst of star formation and the subsequent SN Ia explosions) with an index of -1, inherent to the double-degenerate progenitor scenario. We use the method of Maoz et al. (2011) to recover the DTD by comparing the number of SNe Ia hosted by each galaxy in our sample with the VESPA-derived SFH of the stellar population within the spectral aperture. In this galaxy sample, which is dominated by old and massive galaxies, we recover a "delayed" component to the DTD of 4.5 +/- 0.6 (statistical) +0.3 -0.5 (systematic) X 10^-14 SNe Msun^-1 yr^-1 for delays in the range > 2.4 Gyr. The mass-normalized SN Ia rate, averaged over all masses and redshifts in our galaxy sample, is R(Ia,M,z=0.1) = 0.10 +/- 0.01 (statistical) +/- 0.01 (systematic) SNuM, and the volumetric rate is R(Ia,V,z=0.1) = 0.247 +0.029 -0.026 (statistical) +0.016 -0.031 (systematic) X 10^-4 SNe yr^-1 Mpc^-3. This rate is consistent with the rates and rate evolution from other recent SN Ia surveys, which together also indicate a ~t^-1 DTD.
The multiple personalities of Watson and Crick strands
Reed A Cartwright, Dan Graur
Biology Direct , 2011, DOI: 10.1186/1745-6150-6-7
Abstract: The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus) strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics.This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin.In 1953, James Watson and Francis Crick published the structure of DNA [1], for which they were awarded a Nobel Prize in 1962. They determined that DNA consists of two antiparallel, complementary strands twisted around each other to form a right-handed double helix held in place by interactions between complementary base pairs: adenine (A) with thymine (T) and guanine (G) with cytosine (C). From this structure, it was straightforwardly evident how the genetic information was copied and maintained [2].As a couple, Watson and Crick were immediately hyphenated and eponymized, resulting in terms such as "Watson-Crick model" [3], "Watson-Crick structure" [4], "Watson-Crick helix" [5], "Watson-Crick duplex" [6], "Watson-Crick hydrogen bond" [7], "Watson-Crick bridge" [8], "Watson-Crick complementarity" [5], as well as "Watson-Crick base pair" [9] and its antonym "non-Watson-Crick base pair" [10]. These terms are unequiv
A candidate polar-ring galaxy in the Subaru Deep Field
Ido Finkelman,Or Graur,Noah Brosch
Physics , 2010, DOI: 10.1111/j.1365-2966.2010.17899.x
Abstract: We discuss the properties of an object in the Subaru Deep Field (SDF) classified as a galaxy in on-line data bases and revealed on the Subaru images as a genuine polar-ring galaxy (PRG) candidate. We analyse available photometric data and conclude that this object consists of a >5 Gyr old early-type central body surrounded by a faint, narrow inner ring tilted at a ~25 deg angle relative to the polar axis of the host galaxy. The halo surrounding the main stellar body exhibits a diversity of spatially extended stellar features of low surface brightness, including a faint asymmetric stellar cloud and two prominent loops. These faint features, together with the unperturbed morphology of the central host, are clear signs of a recent coalescence of two highly unequal mass galaxies, most likely a pre-existing early-type galaxy and a close-by gas-rich dwarf galaxy. The presumed stellar remnants observed near the edges of the ring, including possibly the surviving captured companion itself, indicate that the merger is still taking place.
A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes
Niv Sabath, Giddy Landan, Dan Graur
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003996
Abstract: Inferring the intensity of positive selection in protein-coding genes is important since it is used to shed light on the process of adaptation. Recently, it has been reported that overlapping genes, which are ubiquitous in all domains of life, seem to exhibit inordinate degrees of positive selection. Here, we present a new method for the simultaneous estimation of selection intensities in overlapping genes. We show that the appearance of positive selection is caused by assuming that selection operates independently on each gene in an overlapping pair, thereby ignoring the unique evolutionary constraints on overlapping coding regions. Our method uses an exact evolutionary model, thereby voiding the need for approximation or intensive computation. We test the method by simulating the evolution of overlapping genes of different types as well as under diverse evolutionary scenarios. Our results indicate that the independent estimation approach leads to the false appearance of positive selection even though the gene is in reality subject to negative selection. Finally, we use our method to estimate selection in two influenza A genes for which positive selection was previously inferred. We find no evidence for positive selection in both cases.
Same-strand overlapping genes in bacteria: compositional determinants of phase bias
Niv Sabath, Dan Graur, Giddy Landan
Biology Direct , 2008, DOI: 10.1186/1745-6150-3-36
Abstract: We examined the frequencies of initiation- and termination-codons in the two phases, and found that termination codons do not significantly differ between the two phases, whereas initiation codons are more abundant in phase 1. We found that the primary factors explaining the phase inequality are the frequencies of amino acids whose codons may combine to form start codons in the two phases. We show that the frequencies of start codons in each of the two phases, and, hence, the potential for the creation of overlapping genes, are determined by a universal amino-acid frequency and species-specific codon usage, leading to a correlation between long phase-1 overlaps and genomic GC content.Our model explains the phase bias in same-strand overlapping genes by compositional factors without invoking selection. Therefore, it can be used as a null model of neutral evolution to test selection hypotheses concerning the evolution of overlapping genes.This article was reviewed by Bill Martin, Itai Yanai, and Mikhail Gelfand.Overlapping genes were found in all cellular domains of life, as well as in viruses [1-3]. Overlapping genes are thought to have unique evolutionary constraints [4,5] and regulatory properties [6,7]. Genes can overlap on the same strand (→ →) or on the complementary strand ("tail-to-tail" → ←, or "head-to-head" ← →, Figure 1). Different nomenclatures have been used in the literature to denote "same-strand" ("unidirectional," "codirected," "parallel," and "tandem"), "tail-to-tail" ("convergent," "anti-parallel," and "end-on"), and "head-to-head" ("divergent" and "head-on") overlapping genes [8-11]. Here, we use the self-explanatory terms "same-strand" and "opposite-strand" overlapping genes.In bacteria, overlaps on the same strand are by far the most abundant [10,11], most likely because, on average, 70% of the genes in bacterial genomes, are located on one strand [9]. Same-strand overlaps occur in frameshifts of one nucleotide (phase 1) or two nucleotides (phas
'Genome order index' should not be used for defining compositional constraints in nucleotide sequences - a case study of the Z-curve
Eran Elhaik, Dan Graur, Kre?imir Josi?
Biology Direct , 2010, DOI: 10.1186/1745-6150-5-10
Abstract: In this work, we studied the basic properties of the Z-curve using the "genome order index" as a case study. We show that (1) the calculation of the radius of the inscribed sphere of a regular tetrahedron is incorrect, (2) the S index is narrowly distributed, (3) based on the second parity rule, the S index can be derived directly from the Shannon entropy and is, therefore, redundant, and (4) the Z-curve suffers from over dimensionality, and the dimension stands for GC content alone suffices to represent any given genome.The "genome order index" S does not represent a constraint on nucleotide composition. Moreover, S can be easily computed from the Gini-Simpson index and be directly derived from entropy and is redundant. Overall, the Z-curve and S are over-complicated measures to GC content and Shannon H index, respectively.This article was reviewed by Claus Wilke, Joel Bader, Marek Kimmel and Uladzislau Hryshkevich (nominated by Itai Yanai).The nucleotide composition of genomes varies dramatically between and among taxa. The GC content is the primary measure to characterize genomic regions in terms of homogeneity, compositional bias, and compositional constraints [1].Zhang and Zhang [2] proposed the Z-curve, an extension to the GC content measure, based on a three coordinate system of x, y, and z:where a, c, t, and g are the frequencies of the four nucleotides in a sequence. For instance, in the case of the sequence ACGTCGCG, the three coordinates are (0,0,-0.5).Since it was first proposed, the Z-curve has been used in many applications of sequence segmentation [3-5], horizontal gene transfer detection [6], isochoric domain inference [3,5], and sequence analysis [7].We study the characteristics of the Z-curve using a statistical quantity, the "genome order index" S, proposed to measure nucleotide composition. Zhang and Zhang [7] defined S aswhere a, c, t, and g are the frequencies of the four nucleotides in a sequence. It was observed [7,8] that S is negatively cor
A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives
Niv Sabath, Nicholas Price, Dan Graur
Virology Journal , 2009, DOI: 10.1186/1743-422x-6-144
Abstract: Colony collapse disorder (CCD) is a syndrome characterized by the mass disappearance of honeybees from hives [1]. CCD imperils a global resource estimated at approximately $200 billion [2]. For example, it has been estimated that up to 35% of hives in the US may have been affected [3]. Many culprits have been suggested as causal factors of CCD, among them fungal, bacterial, and protozoan diseases, external and internal parasites, in-hive chemicals, agricultural insecticides, genetically modified crops, climatic factors, changed cultural practices, and the spread of cellular phones [1]. The Israeli acute paralysis virus (IAPV), a positive-strand RNA virus belonging to the family Dicistroviridae, was found to be strongly correlated with CCD [4]. It was first isolated in Israel [5], but was later found to have a worldwide distribution [4,6,7].The genome of IAPV contains two long open reading frames (ORFs) separated by an intergenic region. The 5' ORF encodes a structural polyprotein; the 3' ORF encodes a non-structural polyprotein [5]. The non-structural polyprotein contains several signature sequences for helicase, protease, and RNA-dependent RNA polymerase [5]. The structural polyprotein, which is located downstream of the non-structural polyprotein, encodes two (and possibly more) capsid proteins.Overlapping genes are easily missed by annotation programs [8], as evidenced by the fact that several overlapping genes were only detected by using the signatures of purifying selection [9-13]. Here, we apply a recently developed method for the detection of selection in overlapping reading frames [14] to the genome of IAPV and its relatives.In the fourteen completely sequenced dicistroviral genomes (Table 1), we identified 43 same-strand overlapping ORFs of lengths equal or greater than 60 codons on the positive strand. Ten overlapping ORFs were found in concordant genomic locations in two or more genomes. The concordant overlapping ORFs were assigned to three orthologous c
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