Artykuły w czasopismach: „Combination sequences”

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Tachikawa, Shin-Ichi, i Gen Marubayashi. "Majority logic combination sequences using m-sequences for rapid acquisition in direct sequence/spread spectrum communication systems". Electronics and Communications in Japan (Part I: Communications) 74, nr 7 (lipiec 1991): 42–56. http://dx.doi.org/10.1002/ecja.4410740705.

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Stadje, Wolfgang. "On two combination rules for {$0$}-{$1$}-sequences". Bulletin of the Belgian Mathematical Society - Simon Stevin 3, nr 3 (1996): 295–99. http://dx.doi.org/10.36045/bbms/1105554387.

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Venkataraman, Ganesh, Zachary Shriver, Rahul Raman i Ram Sasisekharan. "Sequencing Complex Polysaccharides". Science 286, nr 5439 (15.10.1999): 537–42. http://dx.doi.org/10.1126/science.286.5439.537.

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Although rapid sequencing of polynucleotides and polypeptides has become commonplace, it has not been possible to rapidly sequence femto- to picomole amounts of tissue-derived complex polysaccharides. Heparin-like glycosaminoglycans (HLGAGs) were readily sequenced by a combination of matrix-assisted laser desorption ionization mass spectrometry and a notation system for representation of polysaccharide sequences. This will enable identification of sequences that are critical to HLGAG biological activities in anticoagulation, cell growth, and differentiation.

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Kassaei, Gholamreza, i Mohammad Amouzadeh. "The combination of Discourse Markers in Persian". International Review of Pragmatics 12, nr 1 (13.02.2020): 135–63. http://dx.doi.org/10.1163/18773109-01201102.

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Abstract This paper sets out to investigate the ways in which some of the Discourse Markers (DM s) in Persian are used by looking at a corpus of 475 million words. By adopting Fraser’s notion of DM (2009), it will analyse all possible combinations of thirty DMs categorized into three groups: contrastive, elaborative, and inferential. This categorization will be based on the types of semantic relationship they signal between the propositions of the discourse segments preceding and following them. Their deployment in the attested data demonstrates that the ordering of these DM s is by no means arbitrary. The result of our investigation also reveals that Persian contrastive DM s show a strong tendency to combine with the members of their own category, while elaborative DM s tend to combine with inferential DM s. Inferential DM s, too, have a tendency for intra-category combinations; however, such combinations are much less frequent than those of contrastive DM s. Contrastive DM s have the lowest predisposition for combining with inferential DM s. In short, by exploring the frequency of all sequences of DM s under investigation, a hierarchy of DM combinations in Persian will be proposed, which can be argued to predict certain possible configurations of DM sequences in Persian, and such empirical findings will build up some basis for future typological research as well as for the theorization of DM sequences in general.

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Hill, Janet E., Robyn P. Seipp, Martin Betts, Lindsay Hawkins, Andrew G. Van Kessel, William L. Crosby i Sean M. Hemmingsen. "Extensive Profiling of a Complex Microbial Community by High-Throughput Sequencing". Applied and Environmental Microbiology 68, nr 6 (czerwiec 2002): 3055–66. http://dx.doi.org/10.1128/aem.68.6.3055-3066.2002.

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ABSTRACT Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned cpn60 sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned cpn60 sequences from the four libraries were sequenced. Among the 1,125 cloned cpn60 sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.

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Carbonera Luvizon, Diogo, Hedi Tabia i David Picard. "Learning features combination for human action recognition from skeleton sequences". Pattern Recognition Letters 99 (listopad 2017): 13–20. http://dx.doi.org/10.1016/j.patrec.2017.02.001.

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NILSSON, MARKUS. "RETRIEVING HEART RATE SEQUENCES". International Journal on Artificial Intelligence Tools 15, nr 06 (grudzień 2006): 1091–106. http://dx.doi.org/10.1142/s0218213006003132.

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In this paper, we present a method with a low complexity for analysing short and dynamic biomedical sequences. The method uses the Daubechies D4 wavelet in combination with similarity fitness schemes for retrieval. We also present a more traditional way of retrieving dynamical biomedical sequences based on stretching the sequences in time. The first mentioned method has been shown to outperform Fourier based methods in retrieving biomedical sequences of dynamic lengths, as well as the Haar wavelet.

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Wang, Lei, Deborah Rothemund, Heather Curd i Peter R. Reeves. "Sequence Diversity of the Escherichia coli H7 fliC Genes: Implication for a DNA-Based Typing Scheme for E. coli O157:H7". Journal of Clinical Microbiology 38, nr 5 (2000): 1786–90. http://dx.doi.org/10.1128/jcm.38.5.1786-1790.2000.

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Flagellar (H) antigens are mostly encoded by genes at thefliC locus in E. coli. We have sequenced 11 H7fliC genes from Escherichia coli strains that belong to seven O serotypes. These sequences, together with those of nine other H7 fliC genes (from strains of three different O serotypes) sequenced recently (S. D. Reid, R. K. Selander, and T. S. Whittam, J. Bacteriol. 181:153–160, 1999), include 10 different sequences. The differences between these 10 sequences range from 0.06 to 3.12%. By comparison with other E. coliflagellin genes, we have identified primer length sequences specific for H7 genes in general and others specific for H7 genes of O157 and O55 strains: the specificity was confirmed by PCR testing the type strains for all 53 E. coli H types. We have previously identified genes specific for the E. coli O157 antigen, and use of the combination of O157- and H7-specific primers allows the sensitive and rapid detection of O157:H7 E. coli strains, which cause the majority of hemorrhagic colitis cases.

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Sancetta, Alessio. "RECURSIVE FORECAST COMBINATION FOR DEPENDENT HETEROGENEOUS DATA". Econometric Theory 26, nr 2 (30.09.2009): 598–631. http://dx.doi.org/10.1017/s0266466609100105.

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This paper studies a procedure to combine individual forecasts that achieve theoretical optimal performance. The results apply to a wide variety of loss functions and only require a tail condition on the data sequences. The theoretical results show that the bounds are also valid in the case of time varying combination weights.

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Qiu, Chengshu, Wenjuan Yan, Wangqiu Deng, Bin Song i Taihui Li. "Genetic Diversity Analysis ofHypsizygus marmoreuswith Target Region Amplification Polymorphism". Scientific World Journal 2014 (2014): 1–7. http://dx.doi.org/10.1155/2014/619746.

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Hypsizygus marmoreusis an industrialized edible mushroom. In the present paper, the genetic diversity among 20 strains collected from different places of China was evaluated by target region amplification polymorphism (TRAP) analysis; the common fragment of TRAPs was sequenced and analyzed. Six fixed primers were designed based on the analysis ofH. marmoreussequences from GenBank database. The genomic DNA extracted fromH. marmoreuswas amplified with 28 TRAP primer combinations, which generated 287 bands. The average of amplified bands per primer was 10.27 (mean polymorphism is 69.73%). The polymorphism information content (PIC) value for TRAPs ranged from 0.32 to 0.50 (mean PIC value per TRAP primer combination is 0.48), which indicated a medium level of polymorphism among the strains. A total of 36 sequences were obtained from TRAP amplification. Half of these sequences could encode the known or unknown proteins. According to the phylogenetic analysis based on TRAP result, the 20 strains ofH. marmoreuswere classified into two main groups.

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Bertók, Csanád, Lajos Hajdu, István Pink i Zsolt Rábai. "Linear combinations of prime powers in binary recurrence sequences". International Journal of Number Theory 13, nr 02 (7.02.2017): 261–71. http://dx.doi.org/10.1142/s1793042117500166.

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We give finiteness results concerning terms of linear recurrence sequences having a representation as a linear combination, with fixed coefficients, of powers of fixed primes. On one hand, under certain conditions, we give effective bounds for the terms of binary recurrence sequences with such a representation. On the other hand, in the case of some special binary recurrence sequences, all terms having a representation as sums of powers of [Formula: see text] and [Formula: see text] are explicitly determined.

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Buchman, A. R., i R. D. Kornberg. "A yeast ARS-binding protein activates transcription synergistically in combination with other weak activating factors." Molecular and Cellular Biology 10, nr 3 (marzec 1990): 887–97. http://dx.doi.org/10.1128/mcb.10.3.887.

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ABFI (ARS-binding protein I) is a yeast protein that binds specific DNA sequences associated with several autonomously replicating sequences (ARSs). ABFI also binds sequences located in promoter regions of some yeast genes, including DED1, an essential gene of unknown function that is transcribed constitutively at a high level. ABFI was purified by specific binding to the DED1 upstream activating sequence (UAS) and was found to recognize related sequences at several other promoters, at an ARS (ARS1), and at a transcriptional silencer (HMR E). All ABFI-binding sites, regardless of origin, provided weak UAS function in vivo when examined in test plasmids. UAS function was abolished by point mutations that reduced ABFI binding in vitro. Analysis of the DED1 promoter showed that two ABFI-binding sites combine synergistically with an adjacent T-rich sequence to form a strong constitutive activator. The DED1 T-rich element acted synergistically with all other ABFI-binding sites and with binding sites for other multifunctional yeast activators. An examination of the properties of sequences surrounding ARS1 left open the possibility that ABFI enhances the initiation of DNA replication at ARS1 by transcriptional activation.

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Buchman, A. R., i R. D. Kornberg. "A yeast ARS-binding protein activates transcription synergistically in combination with other weak activating factors". Molecular and Cellular Biology 10, nr 3 (marzec 1990): 887–97. http://dx.doi.org/10.1128/mcb.10.3.887-897.1990.

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ABFI (ARS-binding protein I) is a yeast protein that binds specific DNA sequences associated with several autonomously replicating sequences (ARSs). ABFI also binds sequences located in promoter regions of some yeast genes, including DED1, an essential gene of unknown function that is transcribed constitutively at a high level. ABFI was purified by specific binding to the DED1 upstream activating sequence (UAS) and was found to recognize related sequences at several other promoters, at an ARS (ARS1), and at a transcriptional silencer (HMR E). All ABFI-binding sites, regardless of origin, provided weak UAS function in vivo when examined in test plasmids. UAS function was abolished by point mutations that reduced ABFI binding in vitro. Analysis of the DED1 promoter showed that two ABFI-binding sites combine synergistically with an adjacent T-rich sequence to form a strong constitutive activator. The DED1 T-rich element acted synergistically with all other ABFI-binding sites and with binding sites for other multifunctional yeast activators. An examination of the properties of sequences surrounding ARS1 left open the possibility that ABFI enhances the initiation of DNA replication at ARS1 by transcriptional activation.

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Lv, Tu, Cheng-Lin Hou i Peter R. Johnston. "Three new species and a new combination of Triblidium". MycoKeys 60 (31.10.2019): 1–15. http://dx.doi.org/10.3897/mycokeys.60.46645.

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Triblidiaceae (Rhytismatales) currently consists of two genera: Triblidium and Huangshania. Triblidium is the type genus and is characterised by melanized apothecia that occur scattered or in small clusters on the substratum, cleistohymenial (opening in the mesohymenial phase), inamyloid thin-walled asci and hyaline muriform ascospores. Before this study, only the type species, Triblidium caliciiforme, had DNA sequences in the NCBI GenBank. In this study, six specimens of Triblidium were collected from China and France and new ITS, mtSSU, LSU and RPB2 sequences were generated. Our molecular phylogenetic analysis and morphological study demonstrated three new species of Triblidium, which are formally described here: T. hubeiense, T. rostriforme and T. yunnanense. Additionally, our results indicated that Huangshania that was considered to be distinct from Triblidium because of its elongated, transversely-septate ascospores, is congeneric with Triblidium. Therefore, we have placed Huangshania in synonymy under Triblidium, rendering Triblidiaceae a monotypic family.

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Durie, Brian GM, Julia Beck, Sundar Jagannath, Howard B. Urnovitz i Ekkehard Schutz. "Personalized Genetic Monitoring of myeloma using analytic multivariate analysis of total Fully-Sequenced Circulating DNA". Blood 112, nr 11 (16.11.2008): 5120. http://dx.doi.org/10.1182/blood.v112.11.5120.5120.

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Abstract There is no single sequence or breakpoint region linked to all patients with myeloma. It was thus elected to extract, amplify and fully sequence all (total) DNA present in circulating blood (CNA) using pyrosequencing with the Roche/454 sequencer (GSFLX). The origin of circulating DNA was investigated by local alignment analyses using BLAST and compared with the circulating DNA of 47 healthy individuals, aged 18 to 64 years. Thirty-one samples were subjected to total CNA sequencing during the course of the disease for a patient with lambda Bence Jones myeloma sequentially monitored from relapse, through complete response for 38 months and then with development of subsequent relapse. Conventional monitoring included both serum free light chain analyses and whole body CT-PET imaging. For comparative purposes the CNA was categorized by origin, functionality, chromosomal localization and genes, based on public databases (human reference genome build 36.2 and corresponding annotation file seq_gene.md as downloaded from NCBI (ftp.ncbi.nih.gov). The average length of sequenced nucleotides was 185.7 nucleotides and the total number of nucleotides sequenced per sample was 1.2 – 2.6 million. CNA sequences occurring with a frequency significantly greater or less than those observed for healthy controls were evaluated in detail. The next steps were to examine correlations with initial active myeloma, response to treatment, the complete remission state off all therapy, and subsequent relapse. The presence of 10 DNA sequences was highly correlated with the disease course: ZMYM2; TSPAN5; TLL1; PRKD1; ANTXR1; SYT14; PRKCH; MBNL1; EGFR and EDG7. Of these ZYMYM2 was highly correlated with disease reactivation and relapse off therapy. TSPAN5 showed a clear pattern with reduction to background levels during remission, but increase at the very earliest sign of relapse evident on CT-PET. Conversely, other sequences (GRID1; KIF16B) increased substantially during the peak impact of successful therapy. Multivariate analyses were used to identify the best combinations of gene sequences predictive of disease course and outcome. The combination of four genes (GRID1; PRKD1; ANTXR1; GAB1) was sufficient to define the early active disease data points vs the normal controls (odds-ratio OR: 135 [10.6 to 172]; p<.0001). When the resulting model was kept and used as a search engine for the whole 2 years course, the time course followed the treatment success (OR: 54; p=.0017) and failure as well as the final relapse(OR: 13.3; p=.004) In conclusion: Total sequencing of DNA has proved promising in providing personalized molecular monitoring for myeloma. The details of associated DNA sequences provide insights to the underlying molecular pathophysiology linked to myeloma disease progression, response to successful therapy as well as subsequent relapse. Further testing is ongoing.

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Ulusu, Uğur, i Fatih Nuray. "On Asymptotically Lacunary Statistical Equivalent Set Sequences". Journal of Mathematics 2013 (2013): 1–5. http://dx.doi.org/10.1155/2013/310438.

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This paper presents three definitions which are natural combination of the definitions of asymptotic equivalence, statistical convergence, lacunary statistical convergence, and Wijsman convergence. In addition, we also present asymptotically equivalent (Wijsman sense) analogs of theorems in Patterson and Savaş (2006).

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Georgiou, D. N., T. E. Karakasidis i A. C. Megaritis. "A Short Survey on Genetic Sequences, Chou’s Pseudo Amino Acid Composition and its Combination with Fuzzy Set Theory". Open Bioinformatics Journal 7, nr 1 (13.12.2013): 41–48. http://dx.doi.org/10.2174/1875036201307010041.

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The study of genetic sequences is of great importance in biology and medicine. Sequence analysis and taxonomy are two major fields of application of bioinformatics. In this survey, we present results concerning genetic sequences and Chou's pseudo amino acid composition as well as methodologies developed based on this concept along with elements of fuzzy set theory, and emphasize on fuzzy clustering and its application in analysis of genetic sequences.

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Devran, Zübeyir, Ahmet Fikret Firat, Mahmut Tör, Nedim Mutlu i Ibrahim Halil Elekçioğlu. "AFLP and SRAP markers linked to the mj gene for root-knot nematode resistance in cucumber". Scientia Agricola 68, nr 1 (luty 2011): 115–19. http://dx.doi.org/10.1590/s0103-90162011000100017.

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Root-knot nematodes (Meloidogyne spp.) are an important worldwide pest of cucumber (Cucumis sativus L.). Molecular markers linked to the Javanese root-knot nematode (M. javanica) resistance gene mj in cucumber may aid marker assisted selection. One-hundred AFLP (EcoRI-MseI) and 112 SRAP were used to screen resistant and susceptible parents for polymorphisms to develop molecular markers linked to the mj gene. Of the 100 AFLP primers, 92 produced bands and two yielded candidate markers (E-ATT/M-CAA and E-AAC/M-CTG). These two bands were cut off from polyacrylamide gel, cloned and sequenced. Primers designed from the sequences did not yield polymorphic bands between the parents. In addition, the sequences did not contain any restriction site or indel to be used to convert them to CAPS or SCAR markers. The two sequences obtained from polymorphic AFLP markers were used primarily to design D1F, D1R, D17F and D17R primers. SRAP forward and reverse primers were used in combination with these four specific primers to search for polymorphisms between parents. Of the 112 primer combinations 11 yielded polymorphisms between parents. MapMaker Exp 3.0 software was used to analyze the 11 markers. Two markers were identified that flanked the mj gene at distance of 16.3 and 19.3 cM. The results indicated that these markers should be useful to develop molecular markers flanking the mj gene.

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Jung, Jaehee, Heung Ki Lee i Gangman Yi. "A Novel Method for Functional Annotation Prediction Based on Combination of Classification Methods". Scientific World Journal 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/542824.

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Automated protein function prediction defines the designation of functions of unknown protein functions by using computational methods. This technique is useful to automatically assign gene functional annotations for undefined sequences in next generation genome analysis (NGS). NGS is a popular research method since high-throughput technologies such as DNA sequencing and microarrays have created large sets of genes. These huge sequences have greatly increased the need for analysis. Previous research has been based on the similarities of sequences as this is strongly related to the functional homology. However, this study aimed to designate protein functions by automatically predicting the function of the genome by utilizing InterPro (IPR), which can represent the properties of the protein family and groups of the protein function. Moreover, we used gene ontology (GO), which is the controlled vocabulary used to comprehensively describe the protein function. To define the relationship between IPR and GO terms, three pattern recognition techniques have been employed under different conditions, such as feature selection and weighted value, instead of a binary one.

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SKELLEY, PAUL, GUANG XU, WILLIAM TANG, ANDERS J. LINDSTRÖM, THOMAS MARLER, JIBANKUMAR SINGH KHURAIJAM, RITA SINGH, P. RADHA i STEPHEN RICH. "Review of Cycadophila Xu, Tang & Skelley (Coleoptera: Erotylidae: Pharaxonothinae) inhabiting Cycas (Cycadaceae) in Asia, with descriptions of a new subgenus and thirteen new species". Zootaxa 4267, nr 1 (12.05.2017): 1. http://dx.doi.org/10.11646/zootaxa.4267.1.1.

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The genus Cycadophila Xu, Tang & Skelley (Coleoptera: Erotylidae: Pharaxonothinae) associated with Cycas L. (Cycadacaeae) in Asia is reviewed. Strobilophila, new subgenus, with five species is described: Cycadophila (Strobilophila) assamensis new species, C. (S.) hiepi new species, C. (S.) kwaiensis new species, C. (S.) tansachai new species and C. (S.) yangi new species, all associated with Cycas. For the nominate subgenus Cycadophila eight new species are described, Cycadophila (Cycadophila) abyssa new species, C. (C.) collina new species,C. (C.) samara new species, C. (C.) convexa new species, C. (C.) cyclochasma new species, C. (C.) eurynota new species, C. (C.) papua new species, and C. (C.) torquata new species and four new generic combinations are proposed: C. (C.) vittata (Arrow) new combination, C. (C.) discimaculata (Mader) new combination, C. (C.) intermedia (Chûjô) new combination, and C. (C.) lata (Grouvelle) new combination. Only the first three listed species of the nominate subgenus have known associations with Cycas. Species are distinguished on the basis of morphology and/or by analysis of 16S rRNA gene sequences. The larva of subgenus Strobilophila is described based on individuals collected together with adults and matched with analysis of 16S rRNA gene sequences. Keys to subgenera and species of known adults and larvae are provided.

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Drew, Patrick J., i L. F. Abbott. "Model of Song Selectivity and Sequence Generation in Area HVc of the Songbird". Journal of Neurophysiology 89, nr 5 (1.05.2003): 2697–706. http://dx.doi.org/10.1152/jn.00801.2002.

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In songbirds, nucleus HVc plays a key role in the generation of the syllable sequences that make up a song. Auditory responses of neurons in HVc are selective for single syllables and for combinations of syllables occurring in temporal sequences corresponding to those in the bird's own song. We present a model of HVc that produces syllable- and temporal-combination-selective responses on the basis of input from recorded bird songs filtered through spectral temporal receptive fields similar to those measured in field L, a primary auditory area. Normalization of the field L outputs, similar to that proposed in models of visual processing, plays an important role in the generation of syllable-selective responses in the model. For temporal-combination-selective responses, N-methyl-d-aspartate (NMDA) conductances provide a memory that allows inhibitory neurons to gate responses to a final syllable in a sequence on the basis of responses to earlier syllables. When the same network that produces temporal-combination-selective responses is excited by a nonspecific timing signal, it generates a similar pattern of output as it does in response to auditory song input. Thus the same model network can perform both sensory and motor functions.

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Kışı, Ömer, i Fatıh Nuray. "On -Asymptotically Statistical Equivalence of Sequences of Sets". ISRN Mathematical Analysis 2013 (15.09.2013): 1–6. http://dx.doi.org/10.1155/2013/602963.

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This paper presents the notion of -asymptotically statistical equivalence, which is a natural combination of asymptotic -equivalence, and -statistical equivalence for sequences of sets. We find its relations to -asymptotically statistical convergence, strong -asymptotically equivalence, and strong Cesaro -asymptotically equivalence for sequences of sets.

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Jiang, Peng, Yi-Chung Hu, Wenbao Wang, Hang Jiang i Geng Wu. "Interval Grey Prediction Models with Forecast Combination for Energy Demand Forecasting". Mathematics 8, nr 6 (11.06.2020): 960. http://dx.doi.org/10.3390/math8060960.

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Time series data for decision problems such as energy demand forecasting are often derived from uncertain assessments, and do not meet any statistical assumptions. The interval grey number becomes an appropriate representation for an uncertain and imprecise observation. In order to obtain nonlinear interval grey numbers with better forecasting accuracy, this study proposes a combined model by fusing interval grey numbers estimated by neural networks (NNs) and the grey prediction models. The proposed model first uses interval regression analysis using NNs to estimate interval grey numbers for a real valued sequence; and then a grey residual modification model is constructed using the upper and lower wrapping sequences obtained by NNs. It turns out that two different kinds of interval grey numbers can be estimated by nonlinear interval regression analysis. Forecasting accuracy on real data sequences was then examined by the best non-fuzzy performance values of the combined model. The proposed combined model performed well compared with the other interval grey prediction models considered.

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Smit, Eric, Paula Leeflang, Boet Glandorf, Jan Dirk van Elsas i Karel Wernars. "Analysis of Fungal Diversity in the Wheat Rhizosphere by Sequencing of Cloned PCR-Amplified Genes Encoding 18S rRNA and Temperature Gradient Gel Electrophoresis". Applied and Environmental Microbiology 65, nr 6 (1.06.1999): 2614–21. http://dx.doi.org/10.1128/aem.65.6.2614-2621.1999.

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ABSTRACT Like bacteria, fungi play an important role in the soil ecosystem. As only a small fraction of the fungi present in soil can be cultured, conventional microbiological techniques yield only limited information on the composition and dynamics of fungal communities in soil. DNA-based methods do not depend on the culturability of microorganisms, and therefore they offer an attractive alternative for the study of complex fungal community structures. For this purpose, we designed various PCR primers that allow the specific amplification of fungal 18S-ribosomal-DNA (rDNA) sequences, even in the presence of nonfungal 18S rDNA. DNA was extracted from the wheat rhizosphere, and 18S rDNA gene banks were constructed in Escherichia coli by cloning PCR products generated with primer pairs EF4-EF3 (1.4 kb) and EF4-fung5 (0.5 kb). Fragments of 0.5 kb from the cloned inserts were sequenced and compared to known rDNA sequences. Sequences from all major fungal taxa were amplified by using both primer pairs. As predicted by computer analysis, primer pair EF4-EF3 appeared slightly biased to amplify Basidiomycota and Zygomycota, whereas EF4-fung5 amplified mainly Ascomycota. The 61 clones that were sequenced matched the sequences of 24 different species in the Ribosomal Database Project (RDP) database. Similarity values ranged from 0.676 to 1. Temperature gradient gel electrophoresis (TGGE) analysis of the fungal community in the wheat rhizosphere of a microcosm experiment was carried out after amplification of total DNA with both primer pairs. This resulted in reproducible, distinctive fingerprints, confirming the difference in amplification specificity. Clear banding patterns were obtained with soil and rhizosphere samples by using both primer sets in combination. By comparing the electrophoretic mobility of community fingerprint bands to that of the bands obtained with separate clones, some could be tentatively identified. While 18S-rDNA sequences do not always provide the taxonomic resolution to identify fungal species and strains, they do provide information on the diversity and dynamics of groups of related species in environmental samples with sufficient resolution to produce discrete bands which can be separated by TGGE. This combination of 18S-rDNA PCR amplification and TGGE community analysis should allow study of the diversity, composition, and dynamics of the fungal community in bulk soil and in the rhizosphere.

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Igarashi, Yoji, Daisuke Mori, Susumu Mitsuyama, Kazutoshi Yoshitake, Hiroaki Ono, Tsuyoshi Watanabe, Yukiko Taniuchi i in. "A Preliminary Metagenome Analysis Based on a Combination of Protein Domains". Proteomes 7, nr 2 (29.04.2019): 19. http://dx.doi.org/10.3390/proteomes7020019.

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Metagenomic data have mainly been addressed by showing the composition of organisms based on a small part of a well-examined genomic sequence, such as ribosomal RNA genes and mitochondrial DNAs. On the contrary, whole metagenomic data obtained by the shotgun sequence method have not often been fully analyzed through a homology search because the genomic data in databases for living organisms on earth are insufficient. In order to complement the results obtained through homology-search-based methods with shotgun metagenomes data, we focused on the composition of protein domains deduced from the sequences of genomes and metagenomes, and we utilized them in characterizing genomes and metagenomes, respectively. First, we compared the relationships based on similarities in the protein domain composition with the relationships based on sequence similarities. We searched for protein domains of 325 bacterial species produced using the Pfam database. Next, the correlation coefficients of protein domain compositions between every pair of bacteria were examined. Every pairwise genetic distance was also calculated from 16S rRNA or DNA gyrase subunit B. We compared the results of these methods and found a moderate correlation between them. Essentially, the same results were obtained when we used partial random 100 bp DNA sequences of the bacterial genomes, which simulated raw sequence data obtained from short-read next-generation sequences. Then, we applied the method for analyzing the actual environmental data obtained by shotgun sequencing. We found that the transition of the microbial phase occurred because the seasonal change in water temperature was shown by the method. These results showed the usability of the method in characterizing metagenomic data based on protein domain compositions.

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Kitanovic, Smiljka, Chad A. Marks-Fife, Quincy A. Parkes, P. Ross Wilderman, James R. Halpert i M. Denise Dearing. "Cytochrome P450 2B diversity in a dietary specialist—the red tree vole (Arborimus longicaudus)". Journal of Mammalogy 99, nr 3 (5.05.2018): 578–85. http://dx.doi.org/10.1093/jmammal/gyy039.

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Abstract Although herbivores rely on liver enzymes to biotransform plant secondary metabolites ingested in plant-based diets, only a few enzymes from a handful of species have been characterized at the genomic level. In this study, we examined cytochrome P450 2B (CYP2B) sequence diversity and gene copy number in a conifer specialist, the red tree vole (Arborimus longicaudus). We fed captive individuals exclusively Douglas-fir (Pseudotsuga menziesii) foliage, cloned and sequenced their liver CYP2B cDNA, and estimated CYP2B gene copy number. We identified 21 unique CYP2B nucleotide sequences, and 20 unique CYP2B amino acid sequences. Gene copy number of CYP2B was estimated at 7.7 copies per haploid genome. We compared red tree vole CYP2B with CYP2B sequences of a generalist, the prairie vole (Microtus ochrogaster), found in GenBank. Our study revealed that the CYP2B enzymes of red tree voles possess unique sequences compared to CYP2B enzymes of other herbivorous species. The unique combination of amino acid residues at key substrate recognition sites of CYP2B enzymes may underlie the ability of the red tree vole to specialize on a highly toxic diet of Douglas-fir.

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Hsieh, Pi-Chou, Hui-Ting Lin, Wen-Yih Chen, Jeffrey J. P. Tsai i Wen-Pin Hu. "The Combination of Computational and Biosensing Technologies for Selecting Aptamer against Prostate Specific Antigen". BioMed Research International 2017 (2017): 1–11. http://dx.doi.org/10.1155/2017/5041683.

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Herein, we report a method of combining bioinformatics and biosensing technologies to select aptamers against prostate specific antigen (PSA). The main objective of this study is to select DNA aptamers with higher binding affinity for PSA by using the proposed method. Based on the five known sequences of PSA-binding aptamers, we adopted the functions of reproduction and crossover in the genetic algorithm to produce next-generation sequences for the computational and experimental analysis. RNAfold web server was utilized to analyze the secondary structures, and the 3-dimensional molecular models of aptamer sequences were generated by using RNAComposer web server. ZRANK scoring function was used to rerank the docking predictions from ZDOCK. The biosensors, the quartz crystal microbalance (QCM) and a surface plasmon resonance (SPR) instrument, were used to verify the binding ability of selected aptamer for PSA. By carrying out the simulations and experiments after two generations, we obtain one aptamer that can have the highest binding affinity with PSA, which generates almost 2-fold and 3-fold greater measured signals than the responses produced by the best known DNA sequence in the QCM and SPR experiments, respectively.

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Kravchenko, YuE, SV Ivanov, DS Kravchenko, EI Frolova i SP Chumakov. "Combination of ribosome and phage display for fast selection of high affinity VHH antibody fragments". Laboratory diagnostics, nr 1 (24.02.2019): 27–33. http://dx.doi.org/10.24075/brsmu.2019.002.

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Selection of antibodies using phage display involves the preliminary cloning of the repertoire of sequences encoding antigen-binding domains into phagemid, which is considered the bottleneck of the method, limiting the resulting diversity of libraries and leading to the loss of poorly represented variants before the start of the selection procedure. Selection in cell-free conditions using a ribosomal display is devoid from this drawback, however is highly sensitive to PCR artifacts and the RNase contamination. The aim of the study was to test the efficiency of a combination of both methods, including pre-selection in a cell-free system to enrich the source library, followed by cloning and final selection using phage display. This approach may eliminate the shortcomings of each method and increase the efficiency of selection. For selection, alpaca VHH antibody sequences suitable for building an immune library were used due to the lack of VL domains. Analysis of immune libraries from the genes of the VH3, VHH3 and VH4 families showed that the VHH antibodies share in the VH3 and VH4 gene groups is insignificant, and selection from the combined library is less effective than from the VHH3 family of sequences. We found that the combination of ribosomal and phage displays leads to a higher enrichment of high-affinity fragments and avoids the loss of the original diversity during cloning. The combined method allowed us to obtain a greater number of different high-affinity sequences, and all the tested VHH fragments were able to specifically recognize the target, including the total protein extracts of cell cultures.

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Hazarika, Bipan. "Wijsman Orlicz Asymptotically Ideal -Statistical Equivalent Sequences". Journal of Function Spaces and Applications 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/257181.

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An ideal is a family of subsets of positive integers which is closed under taking finite unions and subsets of its elements. In this paper, we introduce a new definition of asymptotically ideal -statistical equivalent sequence in Wijsman sense and present some definitions which are the natural combination of the definition of asymptotic equivalence, statistical equivalent, -statistical equivalent sequences in Wijsman sense. Finally, we introduce the notion of Cesaro Orlicz asymptotically -equivalent sequences in Wijsman sense and establish their relationship with other classes.

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30

JOHNSON, RODNEY W., STANLEY E. CURTIS i ROGER D. SHANKS. "Effects on Chick Performance of Ammonia and Heat Stressors in Various Combination Sequences". Poultry Science 70, nr 5 (maj 1991): 1132–37. http://dx.doi.org/10.3382/ps.0701132.

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Wu, F. "Genomic subtraction in combination with PCR for enrichment of Listeria monocytogenes-specific sequences". International Journal of Food Microbiology 27, nr 2-3 (październik 1995): 161–74. http://dx.doi.org/10.1016/0168-1605(94)00162-y.

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Arumugam, Paritha, Fabrizia Urbinati, Chinavenmeni S. Velu, Tomoyasu Higashimoto, H. Leighton Grimes i Punam Malik. "A Novel Combination of Chicken Hypersensitive Site-4 Insulator Elements Improves Titers and Restores Full Insulator Activity." Blood 114, nr 22 (20.11.2009): 3566. http://dx.doi.org/10.1182/blood.v114.22.3566.3566.

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Abstract Abstract 3566 Poster Board III-503 Chromatin insulators separate active transcriptional domains and block the spread of heterochromatin in the genome. A prototypic insulator, the 1.2Kb chicken hypersensitive site-4 (cHS4) element utilizes CTCF and USF-1/2 motifs in the proximal 250bp. This smaller “core” cHS4 element provides enhancer blocking activity and reduces position effects. However, the cHS4 core sequences alone do not insulate viral vectors effectively. Two copies of the core, while effective in plasmid based systems, are unstable in viral vectors. In contrast, the full-length cHS4 has excellent insulating properties, but its large size severely compromises vector titers (Urbinati et al, Mol Ther 2009). Therefore, we performed a structure-function analysis of the full-length cHS4 in the context of self inactivating lentivirus-vectors to identify minimal insulator elements required for optimal insulation. Specifically, we analyzed transgene expression in the clonal progeny of primary murine hematopoietic stem cells using the secondary bone marrow transplant assay, and analyzed epigenetic changes in cHS4 and the transgene promoter in vitro in clonal integrants. As expected, the full length cHS4 insulator reduced clonal variegation in transgene expression, reduced position effects and blocked silencing-associated epigenetic modifications over the insulator core and the transgene promoter. However, while either the 5′ cHS4 250bp core or the 3′ cHS4 400bp sequences similarly effected only lower clonal variegation in transgene expression, when they were combined these 650bp sequences recapitulated the activity of the full length 1.2kb insulator, with minimal impact on viral titer. The distal 3′ 400bp fragment contains no consensus sites for USF or CTCF. However, ChIP analysis on proviruses carrying only the 3′ 400bp showed that it binds CTCF. USF-1 binding to the 3′ 400bp, however, only occurred when both the 5′ 250bp core and the 3′ 400bp fragment were present in the proviruses. Indeed, the silencing associated epigenetic marks over the 3′ 400bp region were blocked only when the vector carried both these ends of cHS4 insulator sequences, suggesting that USF-1 bridges the 5′ core and the 3′ 400bp to confer full insulator activity. Furthermore, the 650bp sequences or the full length insulator had the maximal reduction in clonal dominance in the in vitro immortalization assay of lineage negative primary murine hematopoietic cells (Arumugam et al, Mol Ther. In press). Our studies confirm and extend earlier observations on the 5′ 250bp insulator core and identify a new “core-like” insulator activity in the 3′ end of cHS4. The specific elements in the 3′ 400bp sequences that promote interaction with the 5′ 250bp sequences would be important to determine, and may be present in other insulators in and across the genome/s. In the meanwhile, new vector systems flanked by this optimized ‘650bp’ cHS4 sequences, can provide excellent insulation of the transgene without significant loss in viral titers and have important safety and efficacy implications for gene therapy. Our data have important implications in understanding the molecular basis of insulator function and design of gene therapy vectors. Disclosures: No relevant conflicts of interest to declare.

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Searle, Jeremy B., Paul M. Jamieson, İslam Gündüz, Mark I. Stevens, Eleanor P. Jones, Chrissen E. C. Gemmill i Carolyn M. King. "The diverse origins of New Zealand house mice". Proceedings of the Royal Society B: Biological Sciences 276, nr 1655 (30.09.2008): 209–17. http://dx.doi.org/10.1098/rspb.2008.0959.

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Molecular markers and morphological characters can help infer the colonization history of organisms. A combination of mitochondrial (mt) d -loop DNA sequences, nuclear DNA data, external measurements and skull characteristics shows that house mice ( Mus musculus ) in New Zealand and its outlying islands are descended from very diverse sources. The predominant genome is Mus musculus domesticus (from western Europe), but Mus musculus musculus (from central Europe) and Mus musculus castaneus (from southern Asia) are also represented genetically. These subspecies have hybridized to produce combinations of musculus and domesticus nuclear DNA coupled with domesticus mtDNA, and castaneus or musculus mtDNA with domesticus nuclear DNA. The majority of the mice with domesticus mtDNA that we sampled had d -loop sequences identical to two haplotypes common in Britain. This is consistent with long-term British–New Zealand cultural linkages. The origins of the castaneus mtDNA sequences widespread in New Zealand are less easy to identify.

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Compton, James A., Brian D. Schrire, Kálmán Könyves, Félix Forest, Panagiota Malakasi, Sawai Mattapha i Yotsawate Sirichamorn. "The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences". PhytoKeys 125 (26.06.2019): 1–112. http://dx.doi.org/10.3897/phytokeys.125.34877.

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The Tribe Wisterieae (Zhu 1994), founded on the single genus Wisteria, is emended and recircumscribed based on morphology and data from nuclear ITS and ndhJ-trnF, matK and rbcL chloroplast DNA sequences. This newly enlarged tribe comprises 36 species and 9 infraspecific taxa within 13 described genera. Six genera are new, two are reinstated and five were previously placed in Tribe Millettieae. The genus Adinobotrys is also reinstated comprising two species including the new combination A.vastus. Other reinstated genera include Whitfordiodendron, with four species, and Padbruggea, with three species, including the reinstatement of P.filipes and the new combination P.filipesvar.tomentosa. The existing genera Afgekia, Callerya, Endosamara (with the new combination E.racemosavar.pallida), Sarcodum and Wisteria, with the new combinations W.frutescenssubsp.macrostachya are evaluated. The new genera comprise three Australasian species in Austrocallerya: A.australis, A.megasperma and A.pilipes; Wisteriopsis with five species from east Asia has six new combinations: W.japonica, W.kiangsiensis, W.championii, W.eurybotrya, W.reticulata and W.reticulatavar.stenophylla. Two species comprise the new Thai genus Kanburia: K.tenasserimensis and K.chlorantha. Nanhaia comprises the two species: N.fordii and N.speciosa and the monotypic genera Sigmoidala and Serawaia are based respectively on the species S.kityana and S.strobilifera. Lectotypes are designated for the names Adinobotrysfilipes, A.myrianthus, Millettiabonatiana, Millettiabracteosa, Millettiachampionii, Millettiacinerea, Millettiadielsiana, Millettiakityana, M.maingayi, Millettianitida, Millettiaoocarpa, Millettiapurpurea, M.reticulata, M.reticulatavar.stenophylla, Padbruggeadasyphylla, Pterocarpusaustralis, Robiniaracemosa, Whitfordiodendronscandens, W.sumatranum and Wisteriapallida. A neotype is designated for the name Millettialeiogyna.

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Frey, Katharina, i Boas Pucker. "Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites". Cells 9, nr 2 (18.02.2020): 458. http://dx.doi.org/10.3390/cells9020458.

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Most protein-encoding genes in eukaryotes contain introns, which are interwoven with exons. Introns need to be removed from initial transcripts in order to generate the final messenger RNA (mRNA), which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides, which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5′ end and AG at the 3′ end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice site combinations, which have been known for years. Recently, various minor non-canonical splice site combinations were detected with numerous dinucleotide permutations. Here, we expand systematic investigations of non-canonical splice site combinations in plants across eukaryotes by analyzing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences, such as an apparently increased CT-AC frequency in fungal genome sequences. Canonical GT-AG splice site combinations in antisense transcripts are a likely explanation for this observation, thus indicating annotation errors. In addition, high numbers of GA-AG splice site combinations were observed in Eurytemora affinis and Oikopleura dioica. A variant in one U1 small nuclear RNA (snRNA) isoform might allow the recognition of GA as a 5′ splice site. In depth investigation of splice site usage based on RNA-Seq read mappings indicates a generally higher flexibility of the 3′ splice site compared to the 5′ splice site across animals, fungi, and plants.

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Biagolini, Carlos, i Regina H. Macedo. "GenTag: a package to improve animal color tagging protocol". Revista Brasileira de Ornitologia 27, nr 4 (grudzień 2019): 253–60. http://dx.doi.org/10.1007/bf03546071.

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AbstractThe individual identification of animals by means of tagging is a common methodological approach in ornithology. However, several studies suggest that specific colors may affect animal behavior and disrupt sexual selection processes. Thus, methods to choose color tagging combinations should be carefully evaluated. However, reporting of this information is usually neglected. Here, we introduce the GenTag, an R package developed to support biologists in creating color tag sequence combinations using a random process. First, a single-color tag sequence is created from an algorithm selected by the user, followed by verification of the combination. We provide three methods to produce color tag sequences. GenTag provides accessible and simple methods to generate color tag sequences. The use of a random process to define the color tags to be applied to each animal is the best way to deal with the influence of tag color upon behavior and life history parameters.

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37

Theys, K., K. Deforche, P. Libin, R. J. Camacho, K. Van Laethem i A. M. Vandamme. "Resistance pathways of human immunodeficiency virus type 1 against the combination of zidovudine and lamivudine". Journal of General Virology 91, nr 8 (1.08.2010): 1898–908. http://dx.doi.org/10.1099/vir.0.022657-0.

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A better understanding of human immunodeficiency virus type 1 drug-resistance evolution under the selective pressure of combination treatment is important for the design of long-term effective treatment strategies. We applied Bayesian network learning to sequences from patients treated with the reverse transcriptase inhibitor combination of zidovudine (AZT) and lamivudine (3TC) to identify the role of many treatment-selected mutations in the development of resistance. Based on the Bayesian network structure, an in vivo fitness landscape was built, reflecting the necessary selective pressure under treatment, to evolve naive sequences to sequences obtained from patients treated with the combination. This landscape, combined with an evolutionary model, was used to predict resistance evolution in longitudinal sequence pairs. In our analysis, mutations 41L, 70R, 184V and 215F/Y were identified as major resistance mutations to the combination of AZT and 3TC, as they were associated directly with treatment experience. The network also suggested a possible role in resistance development for a number of novel mutations. Estimated fitness, using the landscape, correlated significantly with in vitro resistance phenotype in genotype–phenotype pairs (R 2=0.70). Variation in predicted evolution under selective pressure correlated significantly with observed in vivo evolution during AZT plus 3CT treatment. In conclusion, we confirmed current knowledge on resistance development to the combination of AZT and 3CT, but additional novel mutations were identified. Moreover, a model to predict resistance evolution during AZT and 3CT treatment has been built and validated.

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VINK, COR J., NADINE DUPÉRRÉ, PIERRE PAQUIN, BRIAN M. FITZGERALD i PHIL J. SIRVID. "The cosmopolitan spider Cryptachaea blattea (Urquhart 1886) (Araneae: Theridiidae): Redescription, including COI sequence, and new synonymy". Zootaxa 2133, nr 1 (16.06.2009): 55–63. http://dx.doi.org/10.11646/zootaxa.2133.1.5.

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Cryptachaea blattea (Urquhart 1886) new combination, a cosmopolitan species of the spider family Theridiidae, is redescribed, including notes on its distribution and DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1. Based on morphological evidence and mitochondrial DNA sequences, Cryptachaea acoreensis Berland 1932 is a junior synonym of Cryptachaea blattea.

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Jun, Kyungkoo. "Human Activity Recognition using Fourier Transform Inspired Deep Learning Combination Model". International Journal of Sensors, Wireless Communications and Control 9, nr 1 (15.07.2019): 16–31. http://dx.doi.org/10.2174/2210327908666180727123657.

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Background & Objective: This paper proposes a Fourier transform inspired method to classify human activities from time series sensor data. Methods: Our method begins by decomposing 1D input signal into 2D patterns, which is motivated by the Fourier conversion. The decomposition is helped by Long Short-Term Memory (LSTM) which captures the temporal dependency from the signal and then produces encoded sequences. The sequences, once arranged into the 2D array, can represent the fingerprints of the signals. The benefit of such transformation is that we can exploit the recent advances of the deep learning models for the image classification such as Convolutional Neural Network (CNN). Results: The proposed model, as a result, is the combination of LSTM and CNN. We evaluate the model over two data sets. For the first data set, which is more standardized than the other, our model outperforms previous works or at least equal. In the case of the second data set, we devise the schemes to generate training and testing data by changing the parameters of the window size, the sliding size, and the labeling scheme. Conclusion: The evaluation results show that the accuracy is over 95% for some cases. We also analyze the effect of the parameters on the performance.

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Merante, Frank, Mingfu Ling, Catherine Duff, Brian H. Robinson i Alessandra M. V. Duncan. "Cloning, characterization, and chromosomal localization of human liver form cytochrome c oxidase subunit VIa related genes". Genome 40, nr 3 (1.06.1997): 325–31. http://dx.doi.org/10.1139/g97-045.

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The chromosomal location of human cytochrome c oxidase (COX) subunit VIa Liver (VIa-L) isoform related sequences has been determined by a combination of in situ hybridization and analysis of human–hamster somatic cell hybrid panels. COX VIa-L related sequences were present on chromosomes 6 and 12. It has been verified that at least two COX VIa-L genes are on chromosome 6, one of which is a pseudogene. In total, four COX VIa-L related sequences have been cloned and their nucleotide sequences analyzed. At least three of these sequences represent pseudogenes; their relatedness to the COX VIa-L cDNA is discussed.Key words: human, cytochrome c oxidase, chromosomal localization, COX VIa, cloning.

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Seatla, Kaelo K., Dorcas Maruapula, Wonderful T. Choga, Olorato Morerinyane, Shahin Lockman, Vladimir Novitsky, Ishmael Kasvosve, Sikhulile Moyo i Simani Gaseitsiwe. "Limited HIV-1 Subtype C nef 3′PPT Variation in Combination Antiretroviral Therapy Naïve and Experienced People Living with HIV in Botswana". Pathogens 10, nr 8 (13.08.2021): 1027. http://dx.doi.org/10.3390/pathogens10081027.

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Dolutegravir (DTG) is a potent anti-HIV drug that is used to treat HIV globally. There have been reports of mutations in the HIV-1 3′-polypurine tract (3′PPT) of the nef gene, contributing to DTG failure; however, there are limited ‘real-world’ data on this. In addition, there is a knowledge gap on the variability of 3′PPT residues in patients receiving combination antiretroviral therapy (cART) with and without viral load (VL) suppression. HIV-1 subtype C (HIV-1C) whole-genome sequences from cART naïve and experienced individuals were generated using next-generation sequencing. The nef gene sequences were trimmed from the generated whole-genome sequences using standard bioinformatics tools. In addition, we generated separate integrase and nef gene sequences by Sanger sequencing of plasma samples from individuals with virologic failure (VF) while on a DTG/raltegravir (RAL)-based cART. Analysis of 3′PPT residues was performed, and comparison of proportions computed using Pearson’s chi-square test with p-values < 0.05 was considered statistically significant. A total of 6009 HIV-1C full genome sequences were generated and had a median log10 HIV-1 VL (Q1, Q3) copies/mL of 1.60 (1.60, 2.60). A total of 12 matching integrase and nef gene sequences from therapy-experienced participants failing DTG/ RAL-based cART were generated. HIV-1C 3′PPT nef gene sequences from therapy-experienced patients failing DTG cART (n = 12), cART naïve individuals (n = 1263), and individuals on cART with and without virological suppression (n = 4696) all had a highly conserved 3′PPT motif with no statistically significant differences identified. Our study confirms the high conservation of the HIV-1 nef gene 3′PPT motif in ‘real-world’ patients and showed no differences in the motif according to VL suppression or INSTI-based cART failure. Future studies should explore other HIV-1 regions outside of the pol gene for associations with DTG failure.

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Hella, Olli, i Mikko Stenlund. "Quenched Normal Approximation for Random Sequences of Transformations". Journal of Statistical Physics 178, nr 1 (20.11.2019): 1–37. http://dx.doi.org/10.1007/s10955-019-02390-5.

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AbstractWe study random compositions of transformations having certain uniform fiberwise properties and prove bounds which in combination with other results yield a quenched central limit theorem equipped with a convergence rate, also in the multivariate case, assuming fiberwise centering. For the most part we work with non-stationary randomness and non-invariant, non-product measures. Independently, we believe our work sheds light on the mechanisms that make quenched central limit theorems work, by dissecting the problem into three separate parts.

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Yang, Runtao, Feng Wu, Chengjin Zhang i Lina Zhang. "iEnhancer-GAN: A Deep Learning Framework in Combination with Word Embedding and Sequence Generative Adversarial Net to Identify Enhancers and Their Strength". International Journal of Molecular Sciences 22, nr 7 (30.03.2021): 3589. http://dx.doi.org/10.3390/ijms22073589.

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As critical components of DNA, enhancers can efficiently and specifically manipulate the spatial and temporal regulation of gene transcription. Malfunction or dysregulation of enhancers is implicated in a slew of human pathology. Therefore, identifying enhancers and their strength may provide insights into the molecular mechanisms of gene transcription and facilitate the discovery of candidate drug targets. In this paper, a new enhancer and its strength predictor, iEnhancer-GAN, is proposed based on a deep learning framework in combination with the word embedding and sequence generative adversarial net (Seq-GAN). Considering the relatively small training dataset, the Seq-GAN is designed to generate artificial sequences. Given that each functional element in DNA sequences is analogous to a “word” in linguistics, the word segmentation methods are proposed to divide DNA sequences into “words”, and the skip-gram model is employed to transform the “words” into digital vectors. In view of the powerful ability to extract high-level abstraction features, a convolutional neural network (CNN) architecture is constructed to perform the identification tasks, and the word vectors of DNA sequences are vertically concatenated to form the embedding matrices as the input of the CNN. Experimental results demonstrate the effectiveness of the Seq-GAN to expand the training dataset, the possibility of applying word segmentation methods to extract “words” from DNA sequences, the feasibility of implementing the skip-gram model to encode DNA sequences, and the powerful prediction ability of the CNN. Compared with other state-of-the-art methods on the training dataset and independent test dataset, the proposed method achieves a significantly improved overall performance. It is anticipated that the proposed method has a certain promotion effect on enhancer related fields.

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Ghosheh, Hani Z., i James M. Chandler. "Johnsongrass (Sorghum halepense) Control Systems for Field Corn (Zea mays) Utilizing Crop Rotation and Herbicides". Weed Technology 12, nr 4 (grudzień 1998): 623–30. http://dx.doi.org/10.1017/s0890037x0004447x.

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Johnsongrass control systems that included commercially available corn herbicides applied to crop sequences of continuous corn or corn–cotton–corn rotation were evaluated over a 3-yr period at the Texas Agricultural Experiment Station in Burleson County. Herbicide treatments evaluated were EPTC + R-25788 applied preplant incorporated (PPI); metolachlor applied preemergence (PRE); nicosulfuron applied postemergence (POST); and the combination of metolachlor PRE and glyphosate POST applied after corn harvest. Weed control practices applied to plots planted to cotton in the second growing season provided excellent johnsongrass control (≈ 95%). Visual control ratings indicated that nicosulfuron provided the best johnsongrass control (> 80%) among the herbicides evaluated all three years. Metolachlor and glyphosate combinations provided acceptable johnsongrass control the third year of the experiment in both cropping sequences. Corn grain yield and johnsongrass control were best in cotton-rotated plots. The highest returns observed in continuous corn were from either nicosulfuron or the combination of metolachlor and glyphosate. Net returns for all control systems in corn–cotton–corn rotated plots were greater than the weedy check and were equivalent to the lead systems in continuous corn.

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Delogu, Giovanni, Amy Li, Charlene Repique, Frank Collins i Sheldon L. Morris. "DNA Vaccine Combinations Expressing Either Tissue Plasminogen Activator Signal Sequence Fusion Proteins or Ubiquitin-Conjugated Antigens Induce Sustained Protective Immunity in a Mouse Model of Pulmonary Tuberculosis". Infection and Immunity 70, nr 1 (styczeń 2002): 292–302. http://dx.doi.org/10.1128/iai.70.1.292-302.2002.

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ABSTRACT DNA vaccination has emerged as a powerful approach in the search for a more efficacious vaccine against tuberculosis. In this study, we evaluated the effectiveness of immunizing with combinations of 10 different tuberculosis DNA vaccines that expressed mycobacterial proteins fused at the N terminus to eukaryotic intracellular targeting sequences. In one vaccine combination, the genes were fused to the tissue plasminogen activator signal sequence (TPA), while in a second combination the same 10 genes were expressed as ubiquitin (Ub)-conjugated proteins. In ex vivo studies in which the secretion of gamma interferon was measured, cellular immune responses were detected in mice vaccinated with either the TPA DNA vaccine combination or the Ub DNA vaccine combination at 7 and 14 days following a low-dose Mycobacterium tuberculosis challenge. Moreover, mice vaccinated with the TPA combination, the Ub combination, and Mycobacterium bovis BCG were able to limit the growth of tubercle bacilli in the lung and spleen after a virulent tuberculous aerosol challenge. Histopathological analyses also showed that mice immunized with the DNA vaccine combinations had substantially improved postinfection lung pathology relative to the naïve controls. Finally, in three different long-term experiments, the survival periods following aerogenic challenge were extended as much as sevenfold for vaccinated mice compared to naïve controls. Interestingly, in all three experiments, no significant differences were detected in the mean times to death for mice immunized with the TPA combination or the Ub combination relative to the BCG controls. In conclusion, these studies demonstrate the effectiveness of immunization with DNA vaccine combinations against tuberculosis and suggest that further testing of these plasmid cocktails is warranted.

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Rowinsky, E. K., S. H. Kaufmann, S. D. Baker, L. B. Grochow, T. L. Chen, D. Peereboom, M. K. Bowling i in. "Sequences of topotecan and cisplatin: phase I, pharmacologic, and in vitro studies to examine sequence dependence." Journal of Clinical Oncology 14, nr 12 (grudzień 1996): 3074–84. http://dx.doi.org/10.1200/jco.1996.14.12.3074.

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PURPOSE A phase I and pharmacologic study was performed to evaluate the feasibility of administering the topoisomerase I (topo I) inhibitor topotecan (TPT) in combination with cisplatin (CDDP) in minimally pretreated adults with solid tumors. The study was designed to evaluate the magnitude of the toxicologic and pharmacologic differences between the two sequences of drug administration. MATERIALS AND METHODS TPT was administered as a 30-minute infusion daily for 5 days and CDDP was given either before TPT on day 1 or after TPT on day 5. Each patient was treated with both schedules on an alternating basis every 3 weeks. Sequential dose escalation of TPT or CDDP resulted in three dosage permutation of TPT/CDDP (mg/m2): 0.75/50, 1/50, and 0.75/75. After the maximum-tolerated dose (MTD) level was achieved, the feasibility of using granulocyte colony-stimulating factor (G-CSF) to permit further dose escalation was studied. To examine the interaction of TPT and CDDP in vitro, human A549 lung cancer cells were exposed to these agents concurrently and sequentially. RESULTS Dose-limiting neutropenia and thrombocytopenia resulted after the doses of TPT or CDDP were increased to greater than 0.75 and 50 mg/m2, respectively, without and with G-CSF. The sequence of CDDP before TPT induced significantly worse neutropenia and thrombocytopenia than the alternate sequence. In vitro studies failed to provide any evidence for the differences in the cytotoxicity of these two sequences. Instead, pharmacokinetic studies suggested that the differences in toxicity were due, in part, to lower TPT clearance and exposure when CDDP preceeds TPT, possibly due to subclinical renal tubular toxicity induced by CDDP. CONCLUSION The sequence of CDDP before TPT at doses of 50 and 0.75 mg/m2, respectively, is recommended for subsequent clinical trials in tumor types in which both agents have significant single-agent activity. The potential for sequence-dependent cytotoxic, toxicologic, and pharmacologic effects should be evaluated in concurrent clinical and laboratory studies in the course of developing combination chemotherapy regimens that consist of topo I-targeting agents and other antineoplastic agents, particularly DNA-damaging agents.

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Tran, Minh-Thai, Bac Le i Bay Vo. "Combination of dynamic bit vectors and transaction information for mining frequent closed sequences efficiently". Engineering Applications of Artificial Intelligence 38 (luty 2015): 183–89. http://dx.doi.org/10.1016/j.engappai.2014.10.021.

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Zhao, Yaou. "Predicting Protein-protein Interactions from Protein Sequences Using Probabilistic Neural Network and Feature Combination". Journal of Information and Computational Science 11, nr 7 (1.05.2014): 2397–406. http://dx.doi.org/10.12733/jics20103423.

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García, Carolina Carrizo. "Combination of sequences of cell divisions in the anther wall formation in Solanaceae species". Flora - Morphology, Distribution, Functional Ecology of Plants 198, nr 3 (styczeń 2003): 243–46. http://dx.doi.org/10.1078/0367-2530-00091.

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Deisingh, Anil K., i Michael Thompson. "Sequences of E. coli O157:H7 detected by a PCR-acoustic wave sensor combination". Analyst 126, nr 12 (7.11.2001): 2153–58. http://dx.doi.org/10.1039/b107117n.

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