pseudo random sequence generators and stream ciphers

... same notation as (Lafferty et al 2001) Let be a random variable over data sequences to be labeled, and be a random variable over corresponding label sequences All components, , of are assumed to ... Information Processing Systems, 17:529-536 and ¡¢ J Lafferty, A McCallum and F Pereira (2001) Conditional random fields: probabilistic models for segmenting and labeling sequence data Proceedings of the ... McDonald and Pereira (2005), and also to self-training (Celeux and Govaert 1992; Yarowsky 1995), using the same feature set as (McDonald and Pereira 2005) The CRF training procedures, supervised and...

Ngày tải lên: 17/03/2014, 04:20

... PR, and the respective S4 and S3 binding sites could accept a variety of residues [33,34,46] When compared to peptides having the same natural sequence background (peptides and 1, and 2, and ... frequently occurring mutations found as sequence polymorphisms and in drug resistance, with wild-type and five drug-resistant mutant PRs: M46L, V82A, I84V and L90M mutations that appeared together ... peptides representing NC/p1 cleavage site sequences by wild-type and mutant HIV-1 proteinases Oligopeptides including both natural sequence polymorphisms and resistant mutations of the NC/p1 cleavage...

Ngày tải lên: 21/02/2014, 03:20

... encompassing the conserved sequence boxes I-III (CSB), tRNA genes, L and H strand promoters (LSP and HSP), L and H strand transcription start sites (LSS and HSS) The L-strand sequence and position of the ... OL and OH represent the origin of L and H strand replication, respectively LSS, L strand start site; HSS, H strand start site The map positions of the rRNA, tRNAs and mRNAs (ND1 to ND6, A6 and ... from free and protein-bound DNA (complex II), respectively The arrows on the right and asterisks on the left hand sequence bar denote the protected nucleotides The Maxam and Gilbert sequence reactions...

Ngày tải lên: 08/03/2014, 08:20

... 601–641 Multi-critical unitary random matrix ensembles and the general Painlev´ II equation e By T Claeys, A.B.J Kuijlaars, and M Vanlessen Abstract We study unitary random matrix ensembles of the ... the double scaling limit Introduction and statement of results 1.1 Unitary random matrix ensembles For n ∈ N, N > 0, and α > −1/2, we consider the unitary random matrix ensemble (1.1) −1 Zn,N | ... the longest increasing subsequence of random permutations, J Amer Math Soc 12 (1999), 1119– 1178 [3] M Bertola and S Y Lee, First colonization of a spectral outpost in random matrix theory, Constr...

Ngày tải lên: 15/03/2014, 09:20

... (green) was split into the 5¢ and 3¢ parts by the SMN1 alternative splicing cassette (orange) including exon and parts of the upstream intron and downstream intron HBV-PRE and its derivatives were ... sense and antisense strands of HBV-PRE engineered in the upstream intron can repress the alternative splicing of SMN1 exon We constructed an ISS reporter in which exon and the adjacent intron sequences ... similarity was found between the sense and antisense strands of PRE-ISS, suggesting a sequence- independent silencer mechanism Third, both the sense and antisense strands of PRE-ISS form complex secondary...

Ngày tải lên: 28/03/2014, 23:20

... Cloning and sequencing of the StP gene Using the PCR primers p1 and p2, a 710-bp fragment was amplified from chromosomal C callunae DNA, blunt-end cloned into pUC 18, and sequenced The sequence ... StP is 41% identical to rmGP and 42% identical to EcMalP Figure maps structural and functional elements of rmGP [4] and EcMalP [3] onto the linear sequence of StP and thus measures the extent ... alignment of the amino acid sequences of StP, rmGP and maltodextrin phosphorylase from Escherichia coli (EcMalP) is shown in Fig rmGP and EcMalP were chosen for structure-based sequence comparison because...

Ngày tải lên: 31/03/2014, 01:20

... are imposed on each position in the sequence and can therefore aid in the multiple alignment of sequences (Chapters 1, 3, and 6) and the interpretaion of sequence patterns (Chapter 7) While computational ... without computers and to access the data you need to use a computer Bioinformatics has come of age Sequence analysis and searching Since the first efforts of Gilbert and Sanger, the DNA sequence databases ... Protein structure analysis and prediction Protein structure plays a central role in our understanding and use of sequence data A knowledge of the protein structure behind the sequences often makes...

Ngày tải lên: 10/04/2014, 11:05

... distribution, and stream set distribution at time k − Based on the stream set distribution at time k − 1, we assume that the distance between the object and the goal is fixed at 200 cm so that we only randomly ... 10.7 cm, and 10.2 cm, respectively The total standard deviations of tracking errors of KF, PF, and RBPFSF are 6.1 cm, 5.7 cm, and 5.2 cm, respectively The errors of standard deviation of KF and PF ... RBPF-SF, and ground truth in the 1st experiment tracking errors of PF and RBPF are 29.5 cm and 27.8 cm, respectively The standard deviations of tracking errors of PF and RBPF are 25.2 cm and 22.2...

Ngày tải lên: 21/06/2014, 20:20

... Figure 2: Equivalent system with a random bit flipping, s c Uk , Uk , Fk ∈ {+1, −1} As in Figure 1, we define LI,: = LO,: and s c LO,: = LI,: the presented ideas and concepts are compatible with ... [7] In the remainder, random variables are written with capital letters and realizations with small letters P(z) is the abbreviation of the probability P(Z = z) The subsequence (Zm , Zm+1 , ... Assumptions, Notations, and Consistency We assume that the channel code is linear and the channel is binary, symmetric, memoryless, and time invariant Besides, we assume that the channel and source decoders,...

Ngày tải lên: 21/06/2014, 20:20

... GO sequences, or (P, V , M) sequences as named by Yang and Wu [36], can effectively reduce the mutual interference among different transmitting antennas, compared with the pseudorandom binary sequences ... correlation functions and aperiodic GQO In the following sections, the GQO and GO sequence designs and the related periodic and aperiodic bounds will be discussed in details SPREADING SEQUENCES WITH ... of orthogonal sequences, GO sequences, and GQO sequences are briefly described Due to the limited space, only basic ideas and selected constructions are given without proofs Walsh sequences The...

Ngày tải lên: 23/06/2014, 00:20

... if x, y are Gaussian random variables with mean and variance 1/2, then the random variable z = x + iy is called a standard complex Gaussian √ Corollary 2.3 As d → ∞, the random variable duij converges ... of Theorem for truncations of random orthogonal and symplectic matrices Acknowledgements I am grateful to Roland Speicher and Jamie Mingo for helpful discussions, and to Richard Stanley for encouraging ... results regarding the moments and limiting distribution of the individual entries of a random unitary matrix The matrix Uk is called the kth truncation of U Truncations of random unitary matrices have...

Ngày tải lên: 07/08/2014, 15:22

... libraries PR and AM performed the hybrid selection MFB and JZL analyzed the sequence data XA and AG confirmed fusion transcripts and SNPs, respectively JZL, CN, LAG, and AG conceived and directed ... example, one upstream exon joined to two downstream exons, two upstream exons joined to one downstream exon, or alternating exons) were considered to be alternatively spliced For NUP214-XKR3 and SNHG3-RCC1-PICALM ... products First-strand cDNA was synthesized from K-562 mRNA with random hexamers (Invitrogen) or genespecific primers (Eurofins MWG Operon, Huntsville, AL, USA) as described earlier For random priming,...

Ngày tải lên: 09/08/2014, 20:20

... positions 634 and 714 A-B: Reverse strand sequences and arrows indicating a nucleotide change of C→G observed between mother-child pairs among the HIV1 non-transmitting group C-D: Forward strand sequences ... nucleotide positions 3742, 3743 and 3777 A-B: Forward strand sequences and arrows indicating nucleotide changes of T→A and G→C Underlined is the +/-14bp C-D: Sequences showing a nucleotide change ... motherchild pairs (lane and mother-child pair, lane and mother-child pair; and mother-child pair); lane 8–13; three non transmitting mother-child pairs (lane and mother-child pair, lane 10 and 11 mother-child...

Ngày tải lên: 10/08/2014, 05:20

... erika.varkonyi-gasic@plantandfood.co.nz The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand growth and ... class proteins AP3-1 and PI, as well as FUL and SEP4; weaker interactions were detected between AG and SEP4 and SEP3 and SEP4 No interactions were identified with FUL-like and SEP1 (Figure 2H) ... AG, SEP1, SEP3 and SEP4 were detected both in the flower and fruit tissue and PI was detected exclusively in flowers Kiwifruit FUL-like was detected in leaf and flower tissues and was relatively...

Ngày tải lên: 11/08/2014, 11:22

... AY421760, and AY421769), HEV-B (AF241359, AF081485, and AF029859), HEV-C (NC_001428, AF499640, and AF499635), HEV-D (NC_001430, EF107098, and DQ201177), and Polioviruses (V01150, X00595, and X00925) ... studies, participated in the sequence alignment and drafted the manuscript SP and KS participated in the sequence alignment PL and YP participated in the design of the study and performed the data ... size of 400 bp and a step size of 20 bp, and 1,000 bootstrap replicates conserved motif and functional domain of the HRVCU072 strain, the deduced amino acid sequences of protein VP1 and carboxy-terminal...

Ngày tải lên: 11/08/2014, 21:21

... 384-well plates and gDNA inserts were Sanger-sequenced from both ends Sequences were scanned and masked for vector sequences and contaminating bacterial sequences, eliminating 21.4% (PGB02) and 27.9% ... automated and manual sequence assemblies resulted in two contigs for PGB02 with a combined sequence length of 172,056 bp and 15.6× sequence coverage, and into a single contigs for PGB04 with a sequence ... for the PGB04 library Sequences were scanned and masked for vector sequences and contaminating bacterial sequences, eliminating 21.4% (PGB02) and 27.9% (PGB04) of the total sequences Using PHRAP,...

Ngày tải lên: 12/08/2014, 03:21

... Pox_N2L and Orthopox_C1 (Additional File 1) Thus the sequence relationships among the four families were confirmed and all sequences belonging to any of them were collected A multiple sequence ... http://www.virologyj.com/content/7/1/59 Page of 12 Figure Sequence conservation in A46 and related families (A) Multiple sequence alignment with the common sequence domain found in protein families A46, N1, N2 and C1 The alignment ... K7 (Arg37 and Asp61) and A52 (Arg67 and Asp87) proteins On the other hand there are a number of charged residues which are exposed on the surface of the proteins with known structure and seem...

Ngày tải lên: 12/08/2014, 04:20

... Arabidopsis sequences [18] Four of the conifer sequences (PgMYB2 and 4; PtMYB2 and 4) clustered with Arabidopsis sequences that not fit into a defined subgroup Several pairs of spruce and pine sequences ... consistent, and the end sequences (GT in 5' and AG in 3') were conserved among the sequences we analysed (Table 2) Phylogenetically close sequences, like PgMYB5, 10 and 13, had similar 5' and 3' splice ... Isolation and sequence analysis of 18 R2R3-MYB genes from spruce and pine We isolated and sequenced 18 full-length cDNAs encoding R2R3-MYB genes from conifer trees: 13 from spruce (PgMYB1-13) and five...

Ngày tải lên: 12/08/2014, 05:20

... EF519795–EF519811, EF519815–EF519834 and EF519838–EF519857 Excluding indels, sequence lengths varied from 365 to 621 base pairs (bp) per locus, and all sequences included both exons and introns (Table 3) Thus, ... burn-in and discarded Authors' contributions MAC and JMB conceived the investigation, carried out the analyses and wrote the paper MAC carried out the PCR and sequencing All authors read and approved ... clones per cloning reaction were then prepared and sequenced as above, except that the T7 and M13 universal vector primers were used Data analyses DNA sequences were edited using Chromas 2.12 (Technelysium,...

Ngày tải lên: 12/08/2014, 05:20

... now exploring if a specific signature sequence and RNA structural element was required for the 115-A-mediated strand transfer, as opposed to more random strand transfer from the other HIV-1 RNA ... elongation (245 nt T product; Figure 5B and 5C) Using primers specific for the strand transferred minus strand DNA products, we PCR amplified the recombinants and sequenced 35 clones from the 115-A/89-D ... D)) × 100) increase strand invasion and transfer The frequencies of strand transfer events along these templates were plotted in Figure 5D and 5E As observed in the in vitro and single cycle assays...

Ngày tải lên: 13/08/2014, 09:20