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101.
Vinga S Carvalho AM Francisco AP Russo LM Almeida JS 《Algorithms for molecular biology : AMB》2012,7(1):10-12
Background
Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2 -L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations.Results
The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm.Conclusions
The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems. 相似文献102.
A Traboulsee A AL-Sabbagh R Bennett P Chang DKB Li the EVIDENCE Study Group the UBC MS/MRI Research Group 《BMC neurology》2008,8(1):11
Background
The EVIDENCE (EVidence of Interferon Dose-response: European North American Comparative Efficacy) study was an international, randomized, open-label, assessor-blinded, parallel-group study assessing the efficacy and tolerability of interferon (IFN) beta-1a, 44 mcg subcutaneously (sc) three times weekly (tiw), and IFN beta-1a, 30 mcg intramuscularly (im) once weekly (qw), in patients with relapsing-remitting multiple sclerosis (RRMS). The aim of this analysis was to assess whether reductions in T2 burden of disease (BOD) were greater for patients receiving IFN beta-1a, 44 mcg sc tiw, than for those treated with IFN beta-1a, 30 mcg im qw, and to assess the impact of neutralizing antibodies (NAbs). 相似文献103.
Ganoderma microsporum immunomodulatory protein induces apoptosis and potentiates mitomycin C‐induced apoptosis in urinary bladder urothelial carcinoma cells 下载免费PDF全文
104.
Sohrab?P?Shah Yong?Huang Tao?Xu Macaire?MS?Yuen John?Ling BF?Francis?OuelletteEmail author 《BMC bioinformatics》2005,6(1):34
Background
We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. 相似文献105.
Role of C5a in multiorgan failure during sepsis 总被引:18,自引:0,他引:18
Huber-Lang M Sarma VJ Lu KT McGuire SR Padgaonkar VA Guo RF Younkin EM Kunkel RG Ding J Erickson R Curnutte JT Ward PA 《Journal of immunology (Baltimore, Md. : 1950)》2001,166(2):1193-1199
In humans with sepsis, the onset of multiorgan failure (MOF), especially involving liver, lungs, and kidneys, is a well known complication that is associated with a high mortality rate. Our previous studies with the cecal ligation/puncture (CLP) model of sepsis in rats have revealed a C5a-induced defect in the respiratory burst of neutrophils. In the current CLP studies, MOF occurred during the first 48 h with development of liver dysfunction and pulmonary dysfunction (falling arterial partial pressure of O(2), rising partial pressure of CO(2)). In this model an early respiratory alkalosis developed, followed by a metabolic acidosis with increased levels of blood lactate. During these events, blood neutrophils lost their chemotactic responsiveness both to C5a and to the bacterial chemotaxin, fMLP. Neutrophil dysfunction was associated with virtually complete loss in binding of C5a, but binding of fMLP remained normal. If CLP animals were treated with anti-C5a, indicators of MOF and lactate acidosis were greatly attenuated. Under the same conditions, C5a binding to blood neutrophils remained intact; in tandem, in vitro chemotactic responses to C5a and fMLP were retained. These data suggest that, in the CLP model of sepsis, treatment with anti-C5a prevents development of MOF and the accompanying onset of blood neutrophil dysfunction. This may explain the protective effects of anti-C5a in the CLP model of sepsis. 相似文献
106.
Complement-induced impairment of innate immunity during sepsis 总被引:6,自引:0,他引:6
Huber-Lang MS Younkin EM Sarma JV McGuire SR Lu KT Guo RF Padgaonkar VA Curnutte JT Erickson R Ward PA 《Journal of immunology (Baltimore, Md. : 1950)》2002,169(6):3223-3231
This study defines the molecular basis for defects in innate immunity involving neutrophils during cecal ligation/puncture (CLP)-induced sepsis in rats. Blood neutrophils from CLP rats demonstrated defective phagocytosis and defective assembly of NADPH oxidase, the latter being due to the inability of p47(phox) to translocate from the cytosol to the cell membrane of neutrophils after cell stimulation by phorbol ester (PMA). The appearance of these defects was prevented by in vivo blockade of C5a in CLP rats. In vitro exposure of neutrophils to C5a led to reduced surface expression of C5aR and defective assembly of NADPH oxidase, as defined by failure in phosphorylation of p47(phox) and its translocation to the cell membrane, together with failure in phosphorylation of p42/p44 mitogen-activated protein kinases. These data identify a molecular basis for defective innate immunity involving neutrophils during sepsis. 相似文献
107.
Lake Ichkeul in northern Tunisia is a Ramsar site, a MAB Biosphere Reserve and a UNESCO World Heritage Site. The system is one of the most important coastal wetlands in North Africa, especially as an over-wintering area for migratory birds, particularly Palaearctic waterfowl. The present study was aimed at diagnosing the status of fish species in Lake Ichkeul and documenting their annual and seasonal occurrence within the system. Fish samples were collected monthly at 22 sites from March 2011 to April 2012 using a variety of gears, including a dragnet, gillnet, trammelnet, frynet and beach-seine. Temperature and salinity measurements were taken at each site, while fishes were obtained from only 11 sites, representing mainly lacustrine stations. A total of 18 fish species belonging to 14 genera and 12 families were identified, with Mugilidae dominating with four species, followed by Syngnathidae with three species. This study represents a relative recovery in terms of fish species richness, since only 13 species were recorded here between 2003 and 2007. However, the numbers of fish caught, especially of the commercial taxa, seem to have declined in recent years, and the number of species currently present is much lower than that of several decades ago. Increasing human pressures, particularly reductions in catchment freshwater inputs, a breakdown in ecosystem connectivity, pollution and over-fishing appear to be the principal causes for the decline in fish abundance and diversity. 相似文献
108.
Nazeh M. Al-Abd Zurainee Mohamed Nor Marzida Mansor MS Hasan Mustafa Kassim 《The Korean journal of parasitology》2016,54(3):273-280
We evaluated the activity of methanolic extracts of Melaleuca cajuputi flowers against the filarial worm Brugia pahangi and its bacterial endosymbiont Wolbachia. Anti-Wolbachia activity was measured in worms and in Aedes albopictus Aa23 cells by PCR, electron microscopy, and other biological assays. In particular, microfilarial release, worm motility, and viability were determined. M. cajuputi flower extracts were found to significantly reduce Wolbachia endosymbionts in Aa23 cells, Wolbachia surface protein, and microfilarial release, as well as the viability and motility of adult worms. Anti-Wolbachia activity was further confirmed by observation of degraded and phagocytized Wolbachia in worms treated with the flower extracts. The data provided in vitro and in vivo evidence that M. cajuputi flower extracts inhibit Wolbachia, an activity that may be exploited as an alternative strategy to treat human lymphatic filariasis. 相似文献
109.
The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution 总被引:1,自引:0,他引:1
Suoniemi A; Tanskanen J; Pentikainen O; Johnson MS; Schulman AH 《Molecular biology and evolution》1998,15(9):1135-1144
Propagation of long terminal repeat (LTR)-bearing retrotransposons and
retroviruses requires integrase (IN, EC 2.7.7.-), encoded by the
retroelements themselves, which mediates the insertion of cDNA copies back
into the genome. An active retrotransposon family, BARE-1, comprises
approximately 7% of the barley (Hordeum vulgare subsp. vulgare) genome. We
have generated models for the secondary and tertiary structure of BARE-1 IN
and demonstrate their similarity to structures for human immunodeficiency
virus 1 and avian sarcoma virus INs. The IN core domains were compared for
80 clones from 28 Hordeum accessions representative of the diversity of the
genus. Based on the structural model, variations in the predicted, aligned
translations from these clones would have minimal structural and functional
effects on the encoded enzymes. This indicates that Hordeum retrotransposon
IN has been under purifying selection to maintain a structure typical of
retroviral INs. These represent the first such analyses for plant INs.
相似文献
110.
OI Klychnikov AV Drabkin OV Vasilenko YS Pavlov MS Trofimova IN Smolenskaya AA Rozenkranz AS Sobolev AV Babakov 《Biochemistry. Biokhimii?a》1998,63(9):1083-1089
Higher plant plasma membranes carry receptors of different affinity for the phytotoxin fusicoccin. Reception of fusicoccin involves proteins belonging to the highly conserved 14-3-3 family, but the complete structure of the fusicoccin receptor (FCR) is unknown. Using radiation inactivation analysis, we estimated the molecular masses of low-affinity and high-affinity FCR at 63 +/- 7 and 130 +/- 15 kD, respectively. The dose dependences of receptor inactivation indicate that microsomal specimens contain "silent" FCRs of 420 +/- 90 kD in amounts commensurate with that of the active FCRs. Both low- and high-affinity FCRs are inactivated by hydrolytic enzymes from the outer surface of the plasma membrane, and impairment of protoplast integrity causes an irreversible transition of the low-affinity binding site into the high-affinity one. A scheme is proposed for the organization of different types of FCR in the plasma membrane, implying that the membrane affinity for fusicoccin reflects the interaction between proteins in the FCR complex. 相似文献