Regulation of presynaptic Ca2+, synaptic plasticity and contextual fear conditioning by a N-terminal β-amyloid fragment.

Science.gov (United States)

Lawrence, James L M; Tong, Mei; Alfulaij, Naghum; Sherrin, Tessi; Contarino, Mark; White, Michael M; Bellinger, Frederick P; Todorovic, Cedomir; Nichols, Robert A

2014-10-22

Soluble β-amyloid has been shown to regulate presynaptic Ca(2+) and synaptic plasticity. In particular, picomolar β-amyloid was found to have an agonist-like action on presynaptic nicotinic receptors and to augment long-term potentiation (LTP) in a manner dependent upon nicotinic receptors. Here, we report that a functional N-terminal domain exists within β-amyloid for its agonist-like activity. This sequence corresponds to a N-terminal fragment generated by the combined action of α- and β-secretases, and resident carboxypeptidase. The N-terminal β-amyloid fragment is present in the brains and CSF of healthy adults as well as in Alzheimer's patients. Unlike full-length β-amyloid, the N-terminal β-amyloid fragment is monomeric and nontoxic. In Ca(2+) imaging studies using a model reconstituted rodent neuroblastoma cell line and isolated mouse nerve terminals, the N-terminal β-amyloid fragment proved to be highly potent and more effective than full-length β-amyloid in its agonist-like action on nicotinic receptors. In addition, the N-terminal β-amyloid fragment augmented theta burst-induced post-tetanic potentiation and LTP in mouse hippocampal slices. The N-terminal fragment also rescued LTP inhibited by elevated levels of full-length β-amyloid. Contextual fear conditioning was also strongly augmented following bilateral injection of N-terminal β-amyloid fragment into the dorsal hippocampi of intact mice. The fragment-induced augmentation of fear conditioning was attenuated by coadministration of nicotinic antagonist. The activity of the N-terminal β-amyloid fragment appears to reside largely in a sequence surrounding a putative metal binding site, YEVHHQ. These findings suggest that the N-terminal β-amyloid fragment may serve as a potent and effective endogenous neuromodulator. Copyright © 2014 the authors 0270-6474/14/3414210-09$15.00/0.

Role of the Cationic C-Terminal Segment of Melittin on Membrane Fragmentation.

Science.gov (United States)

Therrien, Alexandre; Fournier, Alain; Lafleur, Michel

2016-05-05

The widespread distribution of cationic antimicrobial peptides capable of membrane fragmentation in nature underlines their importance to living organisms. In the present work, we determined the impact of the electrostatic interactions associated with the cationic C-terminal segment of melittin, a 26-amino acid peptide from bee venom (net charge +6), on its binding to model membranes and on the resulting fragmentation. In order to detail the role played by the C-terminal charges, we prepared a melittin analogue for which the four cationic amino acids in positions 21-24 were substituted with the polar residue citrulline, providing a peptide with the same length and amphiphilicity but with a lower net charge (+2). We compared the peptide bilayer affinity and the membrane fragmentation for bilayers prepared from 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)/1,2-dipalmitoyl-sn-glycero-3-phospho-l-serine (DPPS) mixtures. It is shown that neutralization of the C-terminal considerably increased melittin affinity for zwitterionic membranes. The unfavorable contribution associated with transferring the cationic C-terminal in a less polar environment was reduced, leaving the hydrophobic interactions, which drive the peptide insertion in bilayers, with limited counterbalancing interactions. The presence of negatively charged lipids (DPPS) in bilayers increased melittin binding by introducing attractive electrostatic interactions, the augmentation being, as expected, greater for native melittin than for its citrullinated analogue. The membrane fragmentation power of the peptide was shown to be controlled by electrostatic interactions and could be modulated by the charge carried by both the membrane and the lytic peptide. The analysis of the lipid composition of the extracted fragments from DPPC/DPPS bilayers revealed no lipid specificity. It is proposed that extended phase separations are more susceptible to lead to the extraction of a lipid species in a specific manner

Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes

Science.gov (United States)

Braker, Gesche; Ayala-del-Río, Héctor L.; Devol, Allan H.; Fesefeldt, Andreas; Tiedje, James M.

2001-01-01

Steep vertical gradients of oxidants (O2 and NO3−) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of nirS clones. These clones belonged to clusters II, III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl. Environ. Microbiol. 66:2096–2104, 2000). T-RFLP analysis of nirS and bacterial rDNA revealed a high level of functional and phylogenetic diversity, whereas the level of diversity of Archaea was lower. A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequencies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the Washington margin populations. However, changes in community structure within sediment core sections during the transition from aerobic to anaerobic conditions were minor. Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of populations of similar communities, probably through mixing by marine invertebrates rather than from the development of distinct communities. PMID:11282647

Restriction fragment polymorphisms in the major histocompatibility complex of diabetic BB rats

DEFF Research Database (Denmark)

Kastern, W.; Dyrberg, T.; Scholler, J.

1984-01-01

DNA isolated from diabetic BB (BB/Hagedorn) rats was examined for restriction fragment length differences within the major histocompatibility complex (MHC) as compared with nondiabetic (W-subline) BB rats. Polymorphisms were detected using a mouse class I MHC gene as probe. Specifically, a 2-kb Bam......HI fragment was present in all the nondiabetic rats examined, but absent in the diabetic rats. Similar polymorphisms were observed with various other restriction enzymes, particularly XbaI, HindII, and SacI. There were no polymorphisms detected using either a human DR-alpha (class II antigen heavy chain...

Occurrence of C-Terminal Residue Exclusion in Peptide Fragmentation by ESI and MALDI Tandem Mass Spectrometry

Science.gov (United States)

Dupré, Mathieu; Cantel, Sonia; Martinez, Jean; Enjalbal, Christine

2012-02-01

By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (bn-1 + H2O) ion, corresponding to a shortened non-scrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases. Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride intermediate structure. The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment ions issued from non specific loss of neutral molecules (mainly H2O and NH3) and multiple backbone amide ruptures (b-type internal ions), the described C-terminal residue exclusion is highly identifiable giving raise to a single fragment ion in

Skin-Derived C-Terminal Filaggrin-2 Fragments Are Pseudomonas aeruginosa-Directed Antimicrobials Targeting Bacterial Replication.

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Britta Hansmann

2015-09-01

Full Text Available Soil- and waterborne bacteria such as Pseudomonas aeruginosa are constantly challenging body surfaces. Since infections of healthy skin are unexpectedly rare, we hypothesized that the outermost epidermis, the stratum corneum, and sweat glands directly control the growth of P. aeruginosa by surface-provided antimicrobials. Due to its high abundance in the upper epidermis and eccrine sweat glands, filaggrin-2 (FLG2, a water-insoluble 248 kDa S100 fused-type protein, might possess these innate effector functions. Indeed, recombinant FLG2 C-terminal protein fragments display potent antimicrobial activity against P. aeruginosa and other Pseudomonads. Moreover, upon cultivation on stratum corneum, P. aeruginosa release FLG2 C-terminus-containing FLG2 fragments from insoluble material, indicating liberation of antimicrobially active FLG2 fragments by the bacteria themselves. Analyses of the underlying antimicrobial mechanism reveal that FLG2 C-terminal fragments do not induce pore formation, as known for many other antimicrobial peptides, but membrane blebbing, suggesting an alternative mode of action. The association of the FLG2 fragment with the inner membrane of treated bacteria and its DNA-binding implicated an interference with the bacterial replication that was confirmed by in vitro and in vivo replication assays. Probably through in situ-activation by soil- and waterborne bacteria such as Pseudomonads, FLG2 interferes with the bacterial replication, terminates their growth on skin surface and thus may contributes to the skin's antimicrobial defense shield. The apparent absence of FLG2 at certain body surfaces, as in the lung or of burned skin, would explain their higher susceptibility towards Pseudomonas infections and make FLG2 C-terminal fragments and their derivatives candidates for new Pseudomonas-targeting antimicrobials.

Skin-Derived C-Terminal Filaggrin-2 Fragments Are Pseudomonas aeruginosa-Directed Antimicrobials Targeting Bacterial Replication.

Science.gov (United States)

Hansmann, Britta; Schröder, Jens-Michael; Gerstel, Ulrich

2015-09-01

Soil- and waterborne bacteria such as Pseudomonas aeruginosa are constantly challenging body surfaces. Since infections of healthy skin are unexpectedly rare, we hypothesized that the outermost epidermis, the stratum corneum, and sweat glands directly control the growth of P. aeruginosa by surface-provided antimicrobials. Due to its high abundance in the upper epidermis and eccrine sweat glands, filaggrin-2 (FLG2), a water-insoluble 248 kDa S100 fused-type protein, might possess these innate effector functions. Indeed, recombinant FLG2 C-terminal protein fragments display potent antimicrobial activity against P. aeruginosa and other Pseudomonads. Moreover, upon cultivation on stratum corneum, P. aeruginosa release FLG2 C-terminus-containing FLG2 fragments from insoluble material, indicating liberation of antimicrobially active FLG2 fragments by the bacteria themselves. Analyses of the underlying antimicrobial mechanism reveal that FLG2 C-terminal fragments do not induce pore formation, as known for many other antimicrobial peptides, but membrane blebbing, suggesting an alternative mode of action. The association of the FLG2 fragment with the inner membrane of treated bacteria and its DNA-binding implicated an interference with the bacterial replication that was confirmed by in vitro and in vivo replication assays. Probably through in situ-activation by soil- and waterborne bacteria such as Pseudomonads, FLG2 interferes with the bacterial replication, terminates their growth on skin surface and thus may contributes to the skin's antimicrobial defense shield. The apparent absence of FLG2 at certain body surfaces, as in the lung or of burned skin, would explain their higher susceptibility towards Pseudomonas infections and make FLG2 C-terminal fragments and their derivatives candidates for new Pseudomonas-targeting antimicrobials.

Linkage map of the fragments of herpesvirus papio DNA.

Science.gov (United States)

Lee, Y S; Tanaka, A; Lau, R Y; Nonoyama, M; Rabin, H

1981-01-01

Herpesvirus papio (HVP), an Epstein-Barr-like virus, causes lymphoblastoid disease in baboons. The physical map of HVP DNA was constructed for the fragments produced by cleavage of HVP DNA with restriction endonucleases EcoRI, HindIII, SalI, and PvuI, which produced 12, 12, 10, and 4 fragments, respectively. The total molecular size of HVP DNA was calculated as close to 110 megadaltons. The following methods were used for construction of the map; (i) fragments near the ends of HVP DNA were identified by treating viral DNA with lambda exonuclease before restriction enzyme digestion; (ii) fragments containing nucleotide sequences in common with fragments from the second enzyme digest of HVP DNA were examined by Southern blot hybridization; and (iii) the location of some fragments was determined by isolating individual fragments from agarose gels and redigesting the isolated fragments with a second restriction enzyme. Terminal heterogeneity and internal repeats were found to be unique features of HVP DNA molecule. One to five repeats of 0.8 megadaltons were found at both terminal ends. Although the repeats of both ends shared a certain degree of homology, it was not determined whether they were identical repeats. The internal repeat sequence of HVP DNA was found in the EcoRI-C region, which extended from 8.4 to 23 megadaltons from the left end of the molecule. The average number of the repeats was calculated to be seven, and the molecular size was determined to be 1.8 megadaltons. Similar unique features have been reported in EBV DNA (D. Given and E. Kieff, J. Virol. 28:524-542, 1978). Images PMID:6261015

Rumen bacterial community evaluated by 454 pyrosequencing and terminal restriction fragment length polymorphism analyses in dairy sheep fed marine algae.

Science.gov (United States)

Castro-Carrera, T; Toral, P G; Frutos, P; McEwan, N R; Hervás, G; Abecia, L; Pinloche, E; Girdwood, S E; Belenguer, A

2014-03-01

Developing novel strategies to increase the content of bioactive unsaturated fatty acids (FA) in ruminant-derived products requires a deeper understanding of rumen biohydrogenation and bacteria involved in this process. Although high-throughput pyrosequencing may allow for a great coverage of bacterial diversity, it has hardly been used to investigate the microbiology of ruminal FA metabolism. In this experiment, 454 pyrosequencing and a molecular fingerprinting technique (terminal restriction fragment length polymorphism; T-RFLP) were used concurrently to assess the effect of diet supplementation with marine algae (MA) on the rumen bacterial community of dairy sheep. Eleven lactating ewes were divided in 2 lots and offered a total mixed ration based on alfalfa hay and concentrate (40:60), supplemented with 0 (control) or 8 (MA) g of MA/kg of dry matter. After 54 d on treatments, animals were slaughtered and samples of rumen content and fluid were collected separately for microbial analysis. Pyrosequencing yielded a greater coverage of bacterial diversity than T-RFLP and allowed the identification of low abundant populations. Conversely, both molecular approaches pointed to similar conclusions and showed that relevant changes due to MA addition were observed within the major ruminal phyla, namely Bacteroidetes, Firmicutes, and Proteobacteria. Decreases in the abundance of unclassified Bacteroidales, Porphyromonadaceae, and Ruminococcaceae and increases in as-yet uncultured species of the family Succinivibrionaceae, might be related to a potential role of these groups in different pathways of rumen FA metabolism. Diet supplementation with MA, however, had no effect on the relative abundance of Butyrivibrio and Pseudobutyrivibrio genera. In addition, results from both 454 pyrosequencing and T-RFLP indicate that the effect of MA was rather consistent in rumen content or fluid samples, despite inherent differences between these fractions in their bacterial composition

Protection against β-amyloid neurotoxicity by a non-toxic endogenous N-terminal β-amyloid fragment and its active hexapeptide core sequence.

Science.gov (United States)

Forest, Kelly H; Alfulaij, Naghum; Arora, Komal; Taketa, Ruth; Sherrin, Tessi; Todorovic, Cedomir; Lawrence, James L M; Yoshikawa, Gene T; Ng, Ho-Leung; Hruby, Victor J; Nichols, Robert A

2018-01-01

High levels (μM) of beta amyloid (Aβ) oligomers are known to trigger neurotoxic effects, leading to synaptic impairment, behavioral deficits, and apoptotic cell death. The hydrophobic C-terminal domain of Aβ, together with sequences critical for oligomer formation, is essential for this neurotoxicity. However, Aβ at low levels (pM-nM) has been shown to function as a positive neuromodulator and this activity resides in the hydrophilic N-terminal domain of Aβ. An N-terminal Aβ fragment (1-15/16), found in cerebrospinal fluid, was also shown to be a highly active neuromodulator and to reverse Aβ-induced impairments of long-term potentiation. Here, we show the impact of this N-terminal Aβ fragment and a shorter hexapeptide core sequence in the Aβ fragment (Aβcore: 10-15) to protect or reverse Aβ-induced neuronal toxicity, fear memory deficits and apoptotic death. The neuroprotective effects of the N-terminal Aβ fragment and Aβcore on Aβ-induced changes in mitochondrial function, oxidative stress, and apoptotic neuronal death were demonstrated via mitochondrial membrane potential, live reactive oxygen species, DNA fragmentation and cell survival assays using a model neuroblastoma cell line (differentiated NG108-15) and mouse hippocampal neuron cultures. The protective action of the N-terminal Aβ fragment and Aβcore against spatial memory processing deficits in amyloid precursor protein/PSEN1 (5XFAD) mice was demonstrated in contextual fear conditioning. Stabilized derivatives of the N-terminal Aβcore were also shown to be fully protective against Aβ-triggered oxidative stress. Together, these findings indicate an endogenous neuroprotective role for the N-terminal Aβ fragment, while active stabilized N-terminal Aβcore derivatives offer the potential for therapeutic application. © 2017 International Society for Neurochemistry.

Enhanced resolution of DNA restriction fragments: A procedure by two-dimensional electrophoresis and double-labeling

International Nuclear Information System (INIS)

Yi, M.; Au, L.C.; Ichikawa, N.; Ts'o, P.O.

1990-01-01

A probe-free method was developed to detect DNA rearrangement in bacteria based on the electrophoretic separation of twice-digested restriction fragments of genomic DNA into a two-dimensional (2-D) pattern. The first restriction enzyme digestion was done in solution, followed by electrophoresis of the restriction fragments in one dimension. A second restriction enzyme digestion was carried out in situ in the gel, followed by electrophoresis in a second dimension perpendicular to the first electrophoresis. The 2-D pattern provides for the resolution of 300-400 spots, which are defined and indexed by an x,y coordinate system with size markers. This approach has greatly increased the resolution power over conventional one-dimensional (1-D) electrophoresis. To study DNA rearrangement, a 2-D pattern from a test strain was compared with the 2-D pattern from a reference strain. After the first digestion, genomic DNA fragments from the test strain were labeled with 35S, while those from the reference strain were labeled with 32P. This was done to utilize the difference in the energy emission of 35S and 32P isotopes for autoradiography when two x-ray films were exposed simultaneously on top of the gel after the 2-D electrophoresis. The irradiation from the decay of 35S exposed only the lower film, whereas the irradiation from the decay of 32P exposed both the lower and upper films. Different DNA fragments existed in the test DNA compared with the reference DNA can be identified unambiguously by the differential two 2-D patterns produced on two films upon exposure to the 35S and 32P fragments in the same gel. An appropriate photographic procedure further simplified the process, allowing only the difference in DNA fragments between these two patterns to be shown in the map

Differential diagnosis of genetic disease by DNA restriction fragment length polymorphisms

NARCIS (Netherlands)

Bolhuis, P. A.; Defesche, J. C.; van der Helm, H. J.

1987-01-01

DNA restriction fragment length polymorphisms (RFLPs) are used for diagnosis of genetic disease in families known to be affected by specific disorders, but RFLPs can be also useful for the differential diagnosis of hereditary disease. An RFLP pattern represents the inheritance of chromosomal markers

Analysis of proteolytic processes and enzymatic activities in the generation of huntingtin n-terminal fragments in an HEK293 cell model.

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Andrew T N Tebbenkamp

Full Text Available N-terminal fragments of mutant huntingtin (htt that terminate between residues 90-115, termed cleavage product A or 1 (cp-A/1, form intracellular and intranuclear inclusion bodies in the brains of patients with Huntington's disease (HD. These fragments appear to be proteolytic products of the full-length protein. Here, we use an HEK293 cell culture model to investigate huntingtin proteolytic processing; previous studies of these cells have demonstrated cleavage of htt to cp-A/1 like htt fragments.Recombinant N-terminal htt fragments, terminating at residue 171 (also referred to as cp-B/2 like, were efficiently cleaved to produce cp-A/1 whereas fragments representing endogenous caspase, calpain, and metalloproteinase cleavage products, terminating between residues 400-600, were inefficiently cleaved. Using cysteine-labeling techniques and antibody binding mapping, we localized the C-terminus of the cp-A/1 fragments produced by HEK293 cells to sequences minimally limited by cysteine 105 and an antibody epitope composed of residues 115-124. A combination of genetic and pharmacologic approaches to inhibit potential proteases, including γ-secretase and calpain, proved ineffective in preventing production of cp-A/1.Our findings indicate that HEK293 cells express a protease that is capable of efficiently cleaving cp-B/2 like fragments of htt with normal or expanded glutamine repeats. For reasons that remain unclear, this protease cleaves longer htt fragments, with normal or expanded glutamine expansions, much less efficiently. The protease in HEK293 cells that is capable of generating a cp-A/1 like htt fragment may be a novel protease with a high preference for a cp-B/2-like htt fragment as substrate.

Carboxyl-terminal parathyroid hormone fragments: role in parathyroid hormone physiopathology.

Science.gov (United States)

D'Amour, Pierre; Brossard, Jean-Hugues

2005-07-01

Carboxyl-terminal parathyroid hormone (C-PTH) fragments constitute 80% of circulating PTH. Since the first 34 amino acids of the PTH structure are sufficient to explain PTH classical biological effects on the type I PTH/PTHrP receptor and since C-PTH fragments do not bind to this receptor, they have long been considered inactive. Recent data suggest the existence of a C-PTH receptor through which C-PTH fragments exert biological effects opposite to those of human PTH(1-84) on the type I PTH/PTHrP receptor. This is why a lot of attention has been paid to these fragments recently. In vivo, synthetic C-PTH fragments are able to decrease calcium concentration, to antagonize the calcemic response to human PTH(1-34) and human PTH(1-84) and to decrease the high bone turnover rate induced by human PTH(1-84). In vitro, they inhibit bone resorption, promote osteocyte apoptosis and exert a variety of effects on bone and cartilaginous cells. These effects are opposite to those of human PTH(1-84) on the PTH/PTHrP type I receptor. This suggests that the molecular forms of circulating PTH may control bone participation in calcium homeostasis via two different receptors. Clinically, the accumulation of C-PTH fragments in renal failure patients may cause PTH resistance and may be associated with adynamic bone disease. Rare parathyroid tumors, without a set point error, overproduce C-PTH fragments. The implication of C-PTH fragments in osteoporosis is still to be explored. C-PTH fragments represent a new field of investigation in PTH biology. More studies are necessary to disclose their real importance in calcium and bone homeostasis in health and disease.

Detection of prosecretory mitogen lacritin in nonprimate tears primarily as a C-terminal-like fragment.

Science.gov (United States)

Laurie, Diane E; Splan, Rebecca K; Green, Kari; Still, Katherine M; McKown, Robert L; Laurie, Gordon W

2012-09-12

Lacritin is a human tear glycoprotein that promotes basal tear protein secretion in cultured rat lacrimal acinar cells and proliferation of subconfluent human corneal epithelial cells. When topically added to rabbit eyes, lacritin promotes basal tearing. Despite these activities on several species, lacritin's presence in nonprimate tears or other tissues has not been explored. Here we probed for lacritin in normal horse tears. Sequences were collected from the Ensembl genomic alignment of human LACRT gene with high-quality draft horse genome (EquCab2.0) and analyzed. Normal horse tears were collected and assayed by Western blotting, ELISA, and mass spectrometry. Newly generated rabbit antibodies, respectively, against N- and C-terminal regions of human lacritin were employed. Identity was 75% and 45%, respectively, at nucleotide and protein levels. Structural features were conserved, including a C-terminal amphipathic α-helix. Anti-C-terminal antibodies strongly detected a ∼13 kDa band in horse tears that was validated by mass spectrometry. In human tears, the same antibody detected uncleaved lacritin (∼24 kDa) strongly and C-terminal fragments of ∼13 and ∼11 kDa weakly. Anti-N-terminal antibodies were slightly reactive with a ∼24 kDa horse antigen and showed no reaction with the anti-C-terminal-reactive ∼13 kDa species. Similar respective levels of horse C-terminal versus N-terminal immunoreactivity were apparent by ELISA. Lacritin is present in horse tears, largely as a C-terminal fragment homologous to the mitogenic and bactericidal region in human lacritin, suggesting potential benefit in corneal wound repair.

Seasonal diversity of planktonic protists in Southwestern Alberta rivers over a 1-year period as revealed by terminal restriction fragment length polymorphism and 18S rRNA gene library analyses.

Science.gov (United States)

Thomas, Matthew C; Selinger, L Brent; Inglis, G Douglas

2012-08-01

The temporal dynamics of planktonic protists in river water have received limited attention despite their ecological significance and recent studies linking phagotrophic protists to the persistence of human-pathogenic bacteria. Using molecular-based techniques targeting the 18S rRNA gene, we studied the seasonal diversity of planktonic protists in Southwestern Alberta rivers (Oldman River Basin) over a 1-year period. Nonmetric multidimensional scaling analysis of terminal restriction fragment length polymorphism (T-RFLP) data revealed distinct shifts in protistan community profiles that corresponded to season rather than geographical location. Community structures were examined by using clone library analysis; HaeIII restriction profiles of 18S rRNA gene amplicons were used to remove prevalent solanaceous plant clones prior to sequencing. Sanger sequencing of the V1-to-V3 region of the 18S rRNA gene libraries from spring, summer, fall, and winter supported the T-RFLP results and showed marked seasonal differences in the protistan community structure. The spring library was dominated by Chloroplastidae (29.8%), Centrohelida (28.1%), and Alveolata (25.5%), while the summer and fall libraries contained primarily fungal clones (83.0% and 88.0%, respectively). Alveolata (35.6%), Euglenozoa (24.4%), Chloroplastida (15.6%), and Fungi (15.6%) dominated the winter library. These data demonstrate that planktonic protists, including protozoa, are abundant in river water in Southwestern Alberta and that conspicuous seasonal shifts occur in the community structure.

N-terminal region of gelsolin induces apoptosis of activated hepatic stellate cells by a caspase-dependent mechanism.

Directory of Open Access Journals (Sweden)

Budhaditya Mazumdar

Full Text Available Activated hepatic stellate cells (HSCs are the major source for alteration of extracellular matrix in fibrosis and cirrhosis. Conditioned medium (CM collected from immortalized human hepatocytes (IHH have earlier been shown to be responsible for apoptosis of HSCs. In this study, we have shown that antibodies raised against a peptide derived from a linear B-cell epitope in the N-terminal region of gelsolin identified a gelsolin fragment in IHH CM. Analysis of activated stellate cell death by CM collected from Huh7 cells transfected with plasmids encoding gelsolin deletion mutants suggested that the N-terminal half of gelsolin contained sequences which were responsible for stellate cell death. Further analysis determined that this activity was restricted to a region encompassing amino acids 1-70 in the gelsolin sequence; antibody directed to an epitope within this region was able to neutralize stellate cell death. Gelsolin modulation of cell death using this fragment involved upregulation of TRAIL-R1 and TRAIL-R2, and involved caspase 3 activation by extrinsic pathway. The apoptotic activity of N-terminal gelsolin fragments was restricted to activated but not quiescent stellate cells indicating its potential application in therapeutic use as an anti-fibrotic agent. Gelsolin fragments encompassing N-terminal regions in polypeptides of different molecular sizes were detected by N-terminal peptide specific antiserum in IHH CM immunoprecipitated with chronically HCV infected patient sera, suggesting the presence of autoantibodies generated against N-terminal gelsolin fragments in patients with chronic liver disease.

Characterization of gut microbiota profiles by disease activity in patients with Crohn's disease using data mining analysis of terminal restriction fragment length polymorphisms.

Science.gov (United States)

Andoh, Akira; Kobayashi, Toshio; Kuzuoka, Hiroyuki; Tsujikawa, Tomoyuki; Suzuki, Yasuo; Hirai, Fumihito; Matsui, Toshiyuki; Nakamura, Shiro; Matsumoto, Takayuki; Fujiyama, Yoshihide

2014-05-01

The gut microbiota plays a significant role in the pathogenesis of Crohn's disease (CD). In this study, we analyzed the disease activity and associated fecal microbiota profiles in 160 CD patients and 121 healthy individuals. Fecal samples from the CD patients were collected during three different clinical phases, the active (n=66), remission-achieved (n=51) and remission-maintained (n=43) phases. Terminal restriction fragment length polymorphism (T-RFLP) and data mining analysis using the Classification and Regression Tree (C&RT) approach were performed. Data mining provided a decision tree that clearly identified the various subject groups (nodes). The majority of the healthy individuals were divided into Node-5 and Node-8. Healthy subjects comprised 99% of Node-5 (91 of 92) and 84% of Node-8 (21 of 25 subjects). Node-3 was characterized by CD (136 of 160 CD subjects) and was divided into Node-6 and Node-7. Node-6 (n=103) was characterized by subjects in the active phase (n=48; 46%) and remission-achieved phase (n=39; 38%) and Node-7 was characterized by the remission-maintained phase (21 of 37 subjects; 57%). Finally, Node-6 was divided into Node-9 and Node-10. Node-9 (n=78) was characterized by subjects in the active phase (n=43; 55%) and Node-10 (n=25) was characterized by subjects in the remission-maintained phase (n=16; 64%). Differences in the gut microbiota associated with disease activity of CD patients were identified. Thus, data mining analysis appears to be an ideal tool for the characterization of the gut microbiota in inflammatory bowel disease.

Fragment-Based Drug Discovery in the Bromodomain and Extra-Terminal Domain Family.

Science.gov (United States)

Radwan, Mostafa; Serya, Rabah

2017-08-01

Bromodomain and extra-terminal domain (BET) inhibition has emerged recently as a potential therapeutic target for the treatment of many human disorders such as atherosclerosis, inflammatory disorders, chronic obstructive pulmonary disease (COPD), some viral infections, and cancer. Since the discovery of the two potent inhibitors, I-BET762 and JQ1, different research groups have used different techniques to develop novel potent and selective inhibitors. In this review, we will be concerned with the trials that used fragment-based drug discovery (FBDD) approaches to discover or optimize BET inhibitors, also showing fragments that can be further optimized in future projects to reach novel potent BET inhibitors. © 2017 Deutsche Pharmazeutische Gesellschaft.

Restriction map of the single-stranded DNA genome of Kilham rat virus strain 171, a nondefective parvovirus

International Nuclear Information System (INIS)

Banerjee, P.T.; Rathrock, R.; Mitra, S.

1981-01-01

A physical map of Kilham rat virus strain 171 DNA was constructed by analyzing the sizes and locations of restriction endonuclease-generated fragments of the replicative-form viral DNA synthesized in vitro. BglI, KpnI, BamHI, SmaI, XhoI, and XorII did not appear to have any cleavage sites, whereas 11 other enzymes cleaved the genome at one to eight sites, and AluI generated more than 12 distinct fragments. The 30 restriction sites that were mapped were distributed randomly in the viral genome. A comparison of the restriction fragments of in vivo- and in vitro-replicated replicative-form DNAs showed that these DNAs were identical except in the size or configuration of the terminal fragments

Pseudo-arthrosis repair of a posterior cruciate ligament avulsion fracture

OpenAIRE

Hoogervorst, Paul; Gardeniers, J. W. M.; Moret-Wever, S.; van Kampen, A.

2010-01-01

A pseudo-arthrosis repair of a 4-year-old bony avulsion fracture of the PCL using a minimally invasive technique, screw fixation, and bone grafting is reported. The case presented seems to be rather unique due to the fragment size and the approach for pseudo-arthrosis repair. There was a good functional result following minimally invasive pseudo-arthrosis repair of a posterior cruciate ligament avulsion fracture. There are no previous reports of similar pseudo-arthrosis repairs, and other aut...

Study on detection of mutation DNA fragment in gastric cancer by restriction endonuclease fingerprinting with capillary electrophoresis.

Science.gov (United States)

Wang, Rong; Xie, Hua; Xu, Yue-Bing; Jia, Zheng-Ping; Meng, Xian-Dong; Zhang, Juan-Hong; Ma, Jun; Wang, Juan; Wang, Xian-Hua

2012-03-01

The DNA fragment detection focusing technique has further enhanced the sensitivity and information of DNA targets. The DNA fragment detection method was established by capillary electrophoresis with laser-induced fluorescence detection and restriction endonuclease chromatographic fingerprinting (CE-LIF-REF) in our experiment. The silica capillary column was coated with short linear polyarclarylamide (SLPA) using nongel sieving technology. The excision product of various restricted enzymes of DNA fragments was obtained by REF with the molecular biology software Primer Premier 5. The PBR322/BsuRI DNA marker was used to establish the optimization method. The markers were focused electrophoretically and detected by CE-LIF. The results demonstrate that the CE-LIF-REF with SLPA can improve separation, sensitivity and speed of analysis. This technique may be applied to analysis of the excision product of various restricted enzymes of prokaryotic plasmid (pIRES2), eukaryote plasmid (pcDNA3.1) and the PCR product of codon 248 region of gastric cancer tissue. The results suggest that this method could very sensitively separate the excision products of various restricted enzymes at a much better resolution than the traditional agarose electrophoresis. Copyright © 2011 John Wiley & Sons, Ltd.

Phylogenetic analysis of Gossypium L. using restriction fragment length polymorphism of repeated sequences.

Science.gov (United States)

Zhang, Meiping; Rong, Ying; Lee, Mi-Kyung; Zhang, Yang; Stelly, David M; Zhang, Hong-Bin

2015-10-01

Cotton is the world's leading textile fiber crop and is also grown as a bioenergy and food crop. Knowledge of the phylogeny of closely related species and the genome origin and evolution of polyploid species is significant for advanced genomics research and breeding. We have reconstructed the phylogeny of the cotton genus, Gossypium L., and deciphered the genome origin and evolution of its five polyploid species by restriction fragment analysis of repeated sequences. Nuclear DNA of 84 accessions representing 35 species and all eight genomes of the genus were analyzed. The phylogenetic tree of the genus was reconstructed using the parsimony method on 1033 polymorphic repeated sequence restriction fragments. The genome origin of its polyploids was determined by calculating the diploid-polyploid restriction fragment correspondence (RFC). The tree is consistent with the morphological classification, genome designation and geographic distribution of the species at subgenus, section and subsection levels. Gossypium lobatum (D7) was unambiguously shown to have the highest RFC with the D-subgenomes of all five polyploids of the genus, while the common ancestor of Gossypium herbaceum (A1) and Gossypium arboreum (A2) likely contributed to the A-subgenomes of the polyploids. These results provide a comprehensive phylogenetic tree of the cotton genus and new insights into the genome origin and evolution of its polyploid species. The results also further demonstrate a simple, rapid and inexpensive method suitable for phylogenetic analysis of closely related species, especially congeneric species, and the inference of genome origin of polyploids that constitute over 70 % of flowering plants.

Progress towards construction of a total restriction fragment map of a human chromosome.

NARCIS (Netherlands)

H. Vissing; F.G. Grosveld (Frank); E. Solomon; G. Moore; N. Lench; N. Shennan; R. Williamson

1987-01-01

textabstractWe present an approach to the construction of an overlapping restriction fragment map of a single human chromosome. A genomic cosmid library genome was constructed from a mouse-human hybrid cell line containing chromosome 17 as its only human genetic component. Cosmids containing human

The Processed Amino-Terminal Fragment of Human TLR7 Acts as a Chaperone To Direct Human TLR7 into Endosomes

Science.gov (United States)

Shepherd, Dawn; Booth, Sarah; Waithe, Dominic; Reis e Sousa, Caetano

2015-01-01

TLR7 mediates innate immune responses to viral RNA in endocytic compartments. Mouse and human (h)TLR7 undergo proteolytic cleavage, resulting in the generation of a C-terminal fragment that accumulates in endosomes and associates with the signaling adaptor MyD88 upon receptor triggering by TLR7 agonists. Although mouse TLR7 is cleaved in endosomes by acidic proteases, hTLR7 processing can occur at neutral pH throughout the secretory pathway through the activity of furin-like proprotein convertases. However, the mechanisms by which cleaved hTLR7 reaches the endosomal compartment remain unclear. In this study, we demonstrate that, after hTLR7 proteolytic processing, the liberated amino (N)-terminal fragment remains bound to the C terminus through disulfide bonds and provides key trafficking information that ensures correct delivery of the complex to endosomal compartments. In the absence of the N-terminal fragment, the C-terminal fragment is redirected to the cell surface, where it is functionally inactive. Our data reveal a novel role for the N terminus of hTLR7 as a molecular chaperone that provides processed hTLR7 with the correct targeting instructions to reach the endosomal compartment, hence ensuring its biological activity and preventing inadvertent cell surface responses to self-RNA. PMID:25917086

Regression analysis of censored data using pseudo-observations

DEFF Research Database (Denmark)

Overgaard, Morten; Andersen, Per K.; Parner, Erik T.

2015-01-01

competing risks, the restricted mean survival-time function, and the causespecific lost-lifetime function. The pseudo-observations can be used to assess the effects of covariates on their respective functions at different times by fitting generalized linear models to the pseudo-observations. The updated...

Pseudo-arthrosis repair of a posterior cruciate ligament avulsion fracture.

NARCIS (Netherlands)

Hoogervorst, P.; Gardeniers, J.W.M.; Moret-Wever, S.; Kampen, A. van

2010-01-01

A pseudo-arthrosis repair of a 4-year-old bony avulsion fracture of the PCL using a minimally invasive technique, screw fixation, and bone grafting is reported. The case presented seems to be rather unique due to the fragment size and the approach for pseudo-arthrosis repair. There was a good

Expression, purification, crystallization and preliminary X-ray analysis of a C-terminal fragment of the Epstein–Barr virus ZEBRA protein

Energy Technology Data Exchange (ETDEWEB)

Morand, Patrice [European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble CEDEX 9 (France); Laboratoire de Virologie Moléculaire et Structurale, EA 2939, Université Joseph Fourier, Grenoble (France); Budayova-Spano, Monika [European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble CEDEX 9 (France); Perrissin, Monique [Laboratoire de Virologie Moléculaire et Structurale, EA 2939, Université Joseph Fourier, Grenoble (France); Müller, Christoph W., E-mail: mueller@embl-grenoble.fr; Petosa, Carlo [European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble CEDEX 9 (France)

2006-03-01

A C-terminal fragment of the Epstein–Barr virus lytic switch protein ZEBRA has been crystallized in complex with DNA. A C-terminal fragment of the Epstein–Barr virus immediate-early transcription factor ZEBRA has been expressed as a recombinant protein in Escherichia coli and purified to homogeneity. The fragment behaves as a dimer in solution, consistent with the presence of a basic region leucine-zipper (bZIP) domain. Crystals of the fragment in complex with a DNA duplex were grown by the hanging-drop vapour-diffusion technique using polyethylene glycol 4000 and magnesium acetate as crystallization agents. Crystals diffract to better than 2.5 Å resolution using synchrotron radiation (λ = 0.976 Å). Crystals belong to space group C2, with unit-cell parameters a = 94.2, b = 26.5, c = 98.1 Å, β = 103.9°.

Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities

Directory of Open Access Journals (Sweden)

Fei Cheng

Full Text Available Abstract Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants. Residual contaminants were precipitated by adding 0.6 mL of 0.5 M CaCl2. Four cell lysis methods were applied to test their compatibility with the pretreatment (prewashing + Ca2+ flocculation and to ultimately identify the optimal cell lysis method for analyzing fungal communities in forest soils. The results showed that pretreatment with TNP + Triton X-100 + skim milk (100 mM Tris, 100 mM Na4P2O7, 1% polyvinylpyrrolidone, 100 mM NaCl, 0.05% Triton X-100, 4% skim milk, pH 10.0 removed most soil humic contaminants. When the pretreatment was combined with Ca2+ flocculation, the purity of all soil DNA samples was further improved. DNA samples obtained by the fast glass bead-beating method (MethodFGB had the highest purity. The resulting DNA was successfully used, without further purification steps, as a template for polymerase chain reaction targeting fungal internal transcribed spacer regions. The results obtained by terminal restriction fragment length polymorphism analysis indicated that the MethodFGB revealed greater fungal diversity and more distinctive community structure compared with the other methods tested. Our study provides a protocol for fungal cell lysis in soil, which is fast, convenient, and effective for analyzing fungal communities in forest soils.

Crystallization and preliminary crystallographic studies of the single-chain variable fragment of antibody chA21 in complex with an N-terminal fragment of ErbB2

International Nuclear Information System (INIS)

Liu, Yang; Zhou, Huihao; Zhu, Juanjuan; Gao, Yongxiang; Niu, Liwen; Liu, Jing; Teng, Maikun

2009-01-01

An antibody–antigen complex consisting of a single-chain variable fragment of the potential therapeutic antibody chA21 and an N-terminal fragment (residues 1–192) of the human ErbB2 extracellular domain was expressed, purified and crystallized. X-ray diffraction data were collected to 2.45 Å resolution. ErbB2 is a transmembrane tyrosine kinase, the overexpression of which causes abnormality and disorder in cell signalling and leads to cell transformation. Previously, an anti-ErbB2 single-chain chimeric antibody chA21 that specifically inhibits the growth of ErbB2-overexpressing cancer cells in vitro and in vivo was developed. Here, an antibody–antigen complex consisting of the single-chain variable fragment (scFv) of chA21 and an N-terminal fragment (residues 1–192, named EP I) of the ErbB2 extracellular domain was crystallized using the sitting-drop vapour-diffusion method. An X-ray diffraction data set was collected to 2.45 Å resolution from a single flash-cooled crystal; the crystal belonged to space group P2 1 2 1 2 1

Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using restriction fragment length polymorphism.

Science.gov (United States)

Boyko, Alex; Kovalchuk, Igor

2010-01-01

Restriction fragment length polymorphism (RFLP) is a difference in DNA sequences of organisms belonging to the same species. RFLPs are typically detected as DNA fragments of different lengths after digestion with various restriction endonucleases. The comparison of RFLPs allows investigators to analyze the frequency of occurrence of mutations, such as point mutations, deletions, insertions, and gross chromosomal rearrangements, in the progeny of stressed plants. The assay involves restriction enzyme digestion of DNA followed by hybridization of digested DNA using a radioactively or enzymatically labeled probe. Since DNA can be digested with methylation sensitive enzymes, the assay can also be used to analyze a methylation pattern of a particular locus. Here, we describe RFLP analysis using methylation-insensitive and methylation-sensitive enzymes.

Diagnosis of invasive candidiasis by enzyme-linked immunosorbent assay using the N-terminal fragment of Candida albicans hyphal wall protein 1

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Pontón José

2007-04-01

Full Text Available Abstract Background The diagnosis of invasive candidiasis is difficult because there are no specific clinical manifestations of the disease and colonization and infection are difficult to distinguish. In the last decade, much effort has been made to develop reliable tests for rapid diagnosis of invasive candidiasis, but none of them have found widespread clinical use. Results Antibodies against a recombinant N-terminal fragment of the Candida albicans germ tube-specific antigen hyphal wall protein 1 (Hwp1 generated in Escherichia coli were detected by both immunoblotting and ELISA tests in a group of 36 hematological or Intensive Care Unit patients with invasive candidiasis and in a group of 45 control patients at high risk for the mycosis who did not have clinical or microbiological data to document invasive candidiasis. Results were compared with an immunofluorescence test to detect antibodies to C. albicans germ tubes (CAGT. The sensitivity, specificity, positive and negative predictive values of a diagnostic test based on the detection of antibodies against the N-terminal fragment of Hwp1 by immunoblotting were 27.8 %, 95.6 %, 83.3 % and 62.3 %, respectively. Detection of antibodies to the N-terminal fragment of Hwp1 by ELISA increased the sensitivity (88.9 % and the negative predictive value (90.2 % but slightly decreased the specificity (82.6 % and positive predictive values (80 %. The kinetics of antibody response to the N-terminal fragment of Hwp1 by ELISA was very similar to that observed by detecting antibodies to CAGT. Conclusion An ELISA test to detect antibodies against a recombinant N-terminal fragment of the C. albicans germ tube cell wall antigen Hwp1 allows the diagnosis of invasive candidiasis with similar results to those obtained by detecting antibodies to CAGT but without the need of treating the sera to adsorb the antibodies against the cell wall surface of the blastospore.

Restriction fragment length polymorphism of the major histocompatibility complex of the dog.

Science.gov (United States)

Sarmiento, U M; Storb, R F

1988-01-01

Human major histocompatibility complex (HLA) cDNA probes were used to analyze the restriction fragment length polymorphism (RFLP) of the DLA-D region in dogs. Genomic DNA from peripheral blood leucocytes of 23 unrelated DLA-D-homozygous dogs representing nine DLA-D types (defined by mixed leucocyte reaction) was digested with restriction enzymes (Bam HI, Eco RI, Hind III, Pvu II, Taq I, Rsa I, Msp I, Pst I, and Bgl II), separated by agarose gel electrophoresis, and transferred onto Biotrace membrane. The Southern blots were successively hybridized with radiolabeled HLA cDNA probes corresponding to DR, DQ, DP, and DO beta genes. The autoradiograms for all nine enzyme digests displayed multiple bands with the DRb, DQb, and DPb probes while the DOb probe hybridized with one to two bands. The RFLP patterns were highly polymorphic but consistent within each DLA-D type. Standard RFLP patterns were established for nine DLA-D types which could be discriminated from each other by using two enzymes (Rsa I and Pst I) and the HLA-DPb probe. Cluster analysis of the polymorphic restriction fragments detected by the DRb probe revealed four closely related supertypic groups or DLA-DR families: Dw3 + Dw4 + D1, Dw8 + D10, D7 + D16 + D9, and Dw1. This study provides the basis for DLA-D genotyping at a population level by RFLP analysis. These results also suggest that the genetic organization of the DLA-D region may closely resemble that of the HLA complex.

Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine.

Science.gov (United States)

Bythell, Benjamin J; Csonka, István P; Suhai, Sándor; Barofsky, Douglas F; Paizs, Béla

2010-11-25

The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.

Pseudo-stochastic signal characterization in wavelet-domain

International Nuclear Information System (INIS)

Zaytsev, Kirill I; Zhirnov, Andrei A; Alekhnovich, Valentin I; Yurchenko, Stanislav O

2015-01-01

In this paper we present the method for fast and accurate characterization of pseudo-stochastic signals, which contain a large number of similar but randomly-located fragments. This method allows estimating the statistical characteristics of pseudo-stochastic signal, and it is based on digital signal processing in wavelet-domain. Continuous wavelet transform and the criterion for wavelet scale power density are utilized. We are experimentally implementing this method for the purpose of sand granulometry, and we are estimating the statistical parameters of test sand fractions

NcoI restriction fragment length polymorphism (RFLP) of the tumour necrosis factor (TNF alpha) region in primary biliary cirrhosis and in healthy Danes

DEFF Research Database (Denmark)

Fugger, L; Morling, N; Ryder, L P

1989-01-01

The restriction fragment length polymorphism of the human tumour necrosis factor (TNF alpha) region was investigated by means of 20 different restriction enzymes and a human TNF alpha cDNA probe. Only one of the enzymes, NcoI, revealed a polymorphic pattern consisting of fragments of 10.5 and 5.5...

Regression analysis of censored data using pseudo-observations: An update

DEFF Research Database (Denmark)

Overgaard, Morten; Andersen, Per Kragh; Parner, Erik Thorlund

2015-01-01

competing risks, the restricted mean survival-time function, and the cause-specific lost-lifetime function. The pseudo-observations can be used to assess the effects of covariates on their respective functions at different times by fitting generalized linear models to the pseudo-observations. The updated...

N-terminal prolactin-derived fragments, vasoinhibins, are proapoptoptic and antiproliferative in the anterior pituitary.

Science.gov (United States)

Ferraris, Jimena; Radl, Daniela Betiana; Zárate, Sandra; Jaita, Gabriela; Eijo, Guadalupe; Zaldivar, Verónica; Clapp, Carmen; Seilicovich, Adriana; Pisera, Daniel

2011-01-01

The anterior pituitary is under a constant cell turnover modulated by gonadal steroids. In the rat, an increase in the rate of apoptosis occurs at proestrus whereas a peak of proliferation takes place at estrus. At proestrus, concomitant with the maximum rate of apoptosis, a peak in circulating levels of prolactin is observed. Prolactin can be cleaved to different N-terminal fragments, vasoinhibins, which are proapoptotic and antiproliferative factors for endothelial cells. It was reported that a 16 kDa vasoinhibin is produced in the rat anterior pituitary by cathepsin D. In the present study we investigated the anterior pituitary production of N-terminal prolactin-derived fragments along the estrous cycle and the involvement of estrogens in this process. In addition, we studied the effects of a recombinant vasoinhibin, 16 kDa prolactin, on anterior pituitary apoptosis and proliferation. We observed by Western Blot that N-terminal prolactin-derived fragments production in the anterior pituitary was higher at proestrus with respect to diestrus and that the content and release of these prolactin forms from anterior pituitary cells in culture were increased by estradiol. A recombinant preparation of 16 kDa prolactin induced apoptosis (determined by TUNEL assay and flow cytometry) of cultured anterior pituitary cells and lactotropes from ovariectomized rats only in the presence of estradiol, as previously reported for other proapoptotic factors in the anterior pituitary. In addition, 16 kDa prolactin decreased forskolin-induced proliferation (evaluated by BrdU incorporation) of rat total anterior pituitary cells and lactotropes in culture and decreased the proportion of cells in S-phase of the cell cycle (determined by flow cytometry). In conclusion, our study indicates that the anterior pituitary production of 16 kDa prolactin is variable along the estrous cycle and increased by estrogens. The antiproliferative and estradiol-dependent proapoptotic actions of this

N-terminal prolactin-derived fragments, vasoinhibins, are proapoptoptic and antiproliferative in the anterior pituitary.

Directory of Open Access Journals (Sweden)

Jimena Ferraris

Full Text Available The anterior pituitary is under a constant cell turnover modulated by gonadal steroids. In the rat, an increase in the rate of apoptosis occurs at proestrus whereas a peak of proliferation takes place at estrus. At proestrus, concomitant with the maximum rate of apoptosis, a peak in circulating levels of prolactin is observed. Prolactin can be cleaved to different N-terminal fragments, vasoinhibins, which are proapoptotic and antiproliferative factors for endothelial cells. It was reported that a 16 kDa vasoinhibin is produced in the rat anterior pituitary by cathepsin D. In the present study we investigated the anterior pituitary production of N-terminal prolactin-derived fragments along the estrous cycle and the involvement of estrogens in this process. In addition, we studied the effects of a recombinant vasoinhibin, 16 kDa prolactin, on anterior pituitary apoptosis and proliferation. We observed by Western Blot that N-terminal prolactin-derived fragments production in the anterior pituitary was higher at proestrus with respect to diestrus and that the content and release of these prolactin forms from anterior pituitary cells in culture were increased by estradiol. A recombinant preparation of 16 kDa prolactin induced apoptosis (determined by TUNEL assay and flow cytometry of cultured anterior pituitary cells and lactotropes from ovariectomized rats only in the presence of estradiol, as previously reported for other proapoptotic factors in the anterior pituitary. In addition, 16 kDa prolactin decreased forskolin-induced proliferation (evaluated by BrdU incorporation of rat total anterior pituitary cells and lactotropes in culture and decreased the proportion of cells in S-phase of the cell cycle (determined by flow cytometry. In conclusion, our study indicates that the anterior pituitary production of 16 kDa prolactin is variable along the estrous cycle and increased by estrogens. The antiproliferative and estradiol-dependent proapoptotic

Direct determination of the rate constant of propagation by pseudo-stationary polymerization technique: screening investigation for the (implicit) penultimate effect

International Nuclear Information System (INIS)

Schnoll-Bitai, I.; Friedrich Olaj, O.; Liu Song Yu

1999-01-01

The systems styrene-p-methylstyrene, styrene-p-chlorostyrene, methyl methacrylate-p-methylstyrene and methyl methacrylate-p-chlorostyrene were polymerized under pseudo-stationary conditions (rotating sector or pulsed laser) at 25 degree C, 40 degree C and 50 degree C. The respective molecular weight distributions measured by GPC were analysed in order to derive directly the phenomenological rate constant of propagation, κ sub ρ. Copolymer compositions as a function of monomer feed could be described by the terminal model, whereas the kinetic results could only be interpreted in terms of the restricted penultimate model

HLA-DPB1 typing with polymerase chain reaction and restriction fragment length polymorphism technique in Danes

DEFF Research Database (Denmark)

Hviid, Thomas Vauvert F.; Madsen, Hans O; Morling, Niels

1992-01-01

We have used the polymerase chain reaction (PCR) in combination with the restriction fragment length polymorphism (RFLP) technique for HLA-DBP1 typing. After PCR amplification of the polymorphic second exon of the HLA-DPB1 locus, the PCR product was digested with seven allele-specific restriction...... endonucleases: RsaI, FokI, ApaI, SacI, BstUI, EcoNI, and DdeI, and the DNA fragments were separated by electrophoresis in agarose gels. Altogether, 71 individuals were investigated and 16 different HLA-DPB1 types were observed in 26 different heterozygotic combinations, as well as five possible homozygotes....... Four heterozygotes could not be unequivocally typed with the PCR-RFLP method. The HLA-DPB1 typing results obtained with the PCR-RFLP method were compared with the typing results obtained with PCR allele-specific oligonucleotides (PCR-ASO) in 50 individuals. The results obtained with the two methods...

Rapid detection of dihydropteroate polymorphism in AIDS-related Pneumocystis carinii pneumonia by restriction fragment length polymorphism

DEFF Research Database (Denmark)

Helweg-Larsen, J; Eugen-Olsen, Jesper; Lundgren, B

2000-01-01

are associated with failure of sulpha prophylaxis and increased mortality in HIV-1 positive patients with PCP, suggesting that DHPS mutations may cause sulpha resistance. To facilitate detection of DHPS mutations we developed a restriction fragment length polymorphism (RFLP) assay, detecting mutations at codon...

Nuclear uptake of an amino-terminal fragment of apolipoprotein E4 promotes cell death and localizes within microglia of the Alzheimer's disease brain.

Science.gov (United States)

Love, Julia E; Day, Ryan J; Gause, Justin W; Brown, Raquel J; Pu, Xinzhu; Theis, Dustin I; Caraway, Chad A; Poon, Wayne W; Rahman, Abir A; Morrison, Brad E; Rohn, Troy T

2017-01-01

Although harboring the apolipoprotein E4 ( APOE4 ) allele is a well known risk factor in Alzheimer's disease (AD), the mechanism by which it contributes to disease risk remains elusive. To investigate the role of proteolysis of apoE4 as a potential mechanism, we designed and characterized a site-directed cleavage antibody directed at position D151 of the mature form of apoE4 and E3. Characterization of this antibody indicated a high specificity for detecting synthesized recombinant proteins corresponding to the amino acid sequences 1-151 of apoE3 and E4 that would generate the 17 kDa (p17) fragment. In addition, this antibody also detected a ~17 kDa amino-terminal fragment of apoE4 following incubation with collagenase and matrix metalloproteinase-9 (MMP-9), but did not react with full-length apoE4. Application of this amino-terminal apoE cleavage-fragment (nApoECFp17) antibody, revealed nuclear labeling within glial cells and labeling of a subset of neurofibrillary tangles in the human AD brain. A quantitative analysis indicated that roughly 80% of labeled nuclei were microglia. To confirm these findings, cultured BV2 microglia cells were incubated with the amino-terminal fragment of apoE4 corresponding to the cleavage site at D151. The results indicated efficient uptake of this fragment and trafficking to the nucleus that also resulted in significant cell death. In contrast, a similarly designed apoE3 fragment showed no toxicity and primarily localized within the cytoplasm. These data suggest a novel cleavage event by which apoE4 is cleaved by the extracellular proteases, collagenase and MMP-9, generating an amino-terminal fragment that is then taken up by microglia, traffics to the nucleus and promotes cell death. Collectively, these findings provide important mechanistic insights into the mechanism by which harboring the APOE4 allele may elevate dementia risk observed in AD.

Use of restriction fragment length polymorphisms to investigate strain variation within Neisseria meningitidis

Energy Technology Data Exchange (ETDEWEB)

Williams, S.D.

1989-01-01

Similarity within bacterial populations is difficult to assess due to the limited number of characters available for evaluation and the heterogeneity of bacterial species. Currently, the preferred method used to evaluate the structure of bacterial populations is multilocus enzyme electrophoresis. However, this method is extremely cumbersome and only offers an indirect measure of genetic similarities. The development of a more direct and less cumbersome method for this purpose is warranted. Restriction fragment length polymorphism analysis was evaluated as a tool for use in the study of bacterial population structures and in the epidemiology and surveillance of infectious disease. A collection of Neisseria meningitidis was available for use in the investigation of this technique. Neisseria meningitidis is the causative agent of epidemic cerebrospinal meningitis and septicemia as well as a variety of other clinical manifestations. Each isolate in the collection was defined in terms of serogroup specificity, clinical history, geographic source, and date of isolation. Forty-six strains were chosen for this study. The DNA from each strain was restricted with Pst1 and EcoR1 and electrophoresed on agarose gels. The DNA was transferred to nylon filters and hybridized with P{sup 32} labeled DNA probes. Two randomly generated probes and a gene-specific probe were used to estimate the genetic similarities between and among the strains in the study population. A total of 28 different restriction fragment migration types were detected by the probes used. Data obtained from the RFLP analysis was analyzed by cluster analysis and multivariate statistical methods. A total of 7 clones groups were detected. Two of these appear to be major clones that comprise 35% of the population.

Use of restriction fragment length polymorphisms to investigate strain variation within Neisseria meningitidis

International Nuclear Information System (INIS)

Williams, S.D.

1989-01-01

Similarity within bacterial populations is difficult to assess due to the limited number of characters available for evaluation and the heterogeneity of bacterial species. Currently, the preferred method used to evaluate the structure of bacterial populations is multilocus enzyme electrophoresis. However, this method is extremely cumbersome and only offers an indirect measure of genetic similarities. The development of a more direct and less cumbersome method for this purpose is warranted. Restriction fragment length polymorphism analysis was evaluated as a tool for use in the study of bacterial population structures and in the epidemiology and surveillance of infectious disease. A collection of Neisseria meningitidis was available for use in the investigation of this technique. Neisseria meningitidis is the causative agent of epidemic cerebrospinal meningitis and septicemia as well as a variety of other clinical manifestations. Each isolate in the collection was defined in terms of serogroup specificity, clinical history, geographic source, and date of isolation. Forty-six strains were chosen for this study. The DNA from each strain was restricted with Pst1 and EcoR1 and electrophoresed on agarose gels. The DNA was transferred to nylon filters and hybridized with P 32 labeled DNA probes. Two randomly generated probes and a gene-specific probe were used to estimate the genetic similarities between and among the strains in the study population. A total of 28 different restriction fragment migration types were detected by the probes used. Data obtained from the RFLP analysis was analyzed by cluster analysis and multivariate statistical methods. A total of 7 clones groups were detected. Two of these appear to be major clones that comprise 35% of the population

Inheritance of restriction fragment length polymorphisms, random amplified polymorphic DNAs and isozymes in coastal Douglas-fir

Science.gov (United States)

K.D. Jermstad; A.M. Reem; J.R. Henifin; N.C. Wheeler; D.B Neale

1994-01-01

A total of 225 new genetic loci [151 restriction fragment length polymorphisms (RFLP) and 74 random amplified polymorphic DNAs (RAPD)] in coastal Douglas- fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] have been identified using a three-generation outbred pedigree. The Mendelian inheritance of 16 RFLP loci and 29...

Analysis of DNA restriction fragments greater than 5.7 Mb in size from the centromeric region of human chromosomes.

Science.gov (United States)

Arn, P H; Li, X; Smith, C; Hsu, M; Schwartz, D C; Jabs, E W

1991-01-01

Pulsed electrophoresis was used to study the organization of the human centromeric region. Genomic DNA was digested with rare-cutting enzymes. DNA fragments from 0.2 to greater than 5.7 Mb were separated by electrophoresis and hybridized with alphoid and simple DNA repeats. Rare-cutting enzymes (Mlu I, Nar I, Not I, Nru I, Sal I, Sfi I, Sst II) demonstrated fewer restriction sites at centromeric regions than elsewhere in the genome. The enzyme Not I had the fewest restriction sites at centromeric regions. As much as 70% of these sequences from the centromeric region are present in Not I DNA fragments greater than 5.7 and estimated to be as large as 10 Mb in size. Other repetitive sequences such as short interspersed repeated segments (SINEs), long interspersed repeated segments (LINEs), ribosomal DNA, and mini-satellite DNA that are not enriched at the centromeric region, are not enriched in Not I fragments of greater than 5.7 Mb in size.

THE HUMAN FUMARYLACETOACETATE GENE : CHARACTERIZATION OF RESTRICTION-FRAGMENT-LENGTH-POLYMORPHISMS AND IDENTIFICATION OF HAPLOTYPES IN TYROSINEMIA TYPE-1 AND PSEUDODEFICIENCY

NARCIS (Netherlands)

ROOTWELT, H; KVITTINGEN, EA; HOIE, K; AGSTERIBBE, E; HARTOG, M; BERGER, R

Deficiency of human fumarylacetoacetase (FAH) activity results in hereditary tyrosinemia type I. Using the restriction enzymes BglII, KpnI and StuI and a 1.3-kb cDNA probe for the FAH gene, we have found 6 restriction fragment length polymorphisms (RFLPs). These RFLPs were utilised in 3 tyrosinemia

Identification of Pork Contamination in Meatballs of Indonesia Local Market Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP Analysis

Directory of Open Access Journals (Sweden)

Yuny Erwanto

2014-10-01

Full Text Available This research applied and evaluated a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP using cytochrome b gene to detect pork contamination in meatballs from local markets in Surabaya and Yogyakarta regions, Indonesia. To confirm the effectiveness and specificity of this fragment, thirty nine DNA samples from different meatball shops were isolated and amplified, and then the PCR amplicon was digested by BseDI restriction enzyme to detect the presence of pork in meatballs. BseDI restriction enzyme was able to cleave porcine cytochrome b gene into two fragments (131 bp and 228 bp. Testing the meatballs from the local market showed that nine of twenty meatball shops in Yogyakarta region were detected to have pork contamination, but there was no pork contamination in meatball shops in Surabaya region. In conclusion, specific PCR amplification of cytochrome b gen and cleaved by BseDI restriction enzymes seems to be a powerful technique for the identification of pork presence in meatball because of its simplicity, specificity and sensitivity. Furthermore, pork contamination intended for commercial products of sausage, nugget, steak and meat burger can be checked. The procedure is also much cheaper than other methods based on PCR, immunodiffusion and other techniques that need expensive equipment.

Identification of Pork Contamination in Meatballs of Indonesia Local Market Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis.

Science.gov (United States)

Erwanto, Yuny; Abidin, Mohammad Zainal; Sugiyono, Eko Yasin Prasetyo Muslim; Rohman, Abdul

2014-10-01

This research applied and evaluated a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using cytochrome b gene to detect pork contamination in meatballs from local markets in Surabaya and Yogyakarta regions, Indonesia. To confirm the effectiveness and specificity of this fragment, thirty nine DNA samples from different meatball shops were isolated and amplified, and then the PCR amplicon was digested by BseDI restriction enzyme to detect the presence of pork in meatballs. BseDI restriction enzyme was able to cleave porcine cytochrome b gene into two fragments (131 bp and 228 bp). Testing the meatballs from the local market showed that nine of twenty meatball shops in Yogyakarta region were detected to have pork contamination, but there was no pork contamination in meatball shops in Surabaya region. In conclusion, specific PCR amplification of cytochrome b gen and cleaved by BseDI restriction enzymes seems to be a powerful technique for the identification of pork presence in meatball because of its simplicity, specificity and sensitivity. Furthermore, pork contamination intended for commercial products of sausage, nugget, steak and meat burger can be checked. The procedure is also much cheaper than other methods based on PCR, immunodiffusion and other techniques that need expensive equipment.

Cut-and-Paste of DNA Using an Artificial Restriction DNA Cutter

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Makoto Komiyama

2013-02-01

Full Text Available DNA manipulations using a completely chemistry-based DNA cutter (ARCUT have been reviewed. This cutter, recently developed by the authors, is composed of Ce(IV/EDTA complex and two strands of pseudo-complementary peptide nucleic acid. The site-selective scission proceeds via hydrolysis of targeted phosphodiester linkages, so that the resultant scission fragments can be easily ligated with other fragments by using DNA ligase. Importantly, scission-site and site-specificity of the cutter are freely tuned in terms of the Watson–Crick rule. Thus, when one should like to manipulate DNA according to the need, he or she does not have to think about (1 whether appropriate “restriction enzyme sites” exist near the manipulation site and (2 whether the site-specificity of the restriction enzymes, if any, are sufficient to cut only the aimed position without chopping the DNA at non-targeted sites. Even the human genome can be manipulated, since ARCUT can cut the genome at only one predetermined site. Furthermore, the cutter is useful to promote homologous recombination in human cells, converting a site to desired sequence. The ARCUT-based DNA manipulation should be promising for versatile applications.

Structure of antigenetic determinants in the amino-terminal region of bovine fibrinogen Aα chain

International Nuclear Information System (INIS)

Tanswell, P.; Reiter, H.; Timpl, R.

1978-01-01

A radioimmunoassay was developed for peptide F-CB1α from the amino of bovine fibrinogen Aα chain, isolated after reduction and carboxymethylation of the multichain disulfide-linked cyanogen bromide peptide F-CB1. Seven out of twelve different rabbit antisera produced against fibrinogen, peptide F-CB1 or Aα chain showed distinct binding to 125 I-labelled F-CB1α. Thrombin cleavage of F-CB1α yielded two fragments: fibrinopeptide A (residues 1-19) and the carboxy-terminal fragment Th2 (residues 20-54). Antisera could be classified into three groups according to whether they recognized antigenic determinants on fibrinopeptide A, on peptide Th2 or as they showed diminished reactions with both fragments. Only little or no cross-reaction was observed with the amino-terminal cyanogen bromide peptides of Bβ and γ chain. Proteolytic fragments of fibrinopeptide A were isolated and tested for inhibitory activity with two antisera. One antiserum contained anitbodies binding selectively to the amino-terminal sequence (residues 4-11) and did not cross-react with human fibrinopeptide A. Another antiserum showed a specific binding restricted to the carboxy-terminal sequence (residues 11-18) and cross-reacted completely with human fibrinopeptide A. These results correlate well with the primary structures of the two fibrinopeptides. The antigenic activity of the peptide fragment Th2 was localized on a 15-residue tryptic peptide derived from the central portion of the sequence. These and further data indicate that at least six different antigenic determinants are present in peptide F-CB1α. (orig.) 891 AJ [de

Restriction Fragment Pattern (RFP) analysis of genomes from Danish isolates of Suid herpesvirus 1 (Aujeszky's disease virus)

DEFF Research Database (Denmark)

Christensen, Laurids Siig; Sørensen, K. J.; Lei, J. C.

1987-01-01

Purified DNA from 42 isolates of Suid herpesvirus 1 (SHV-1) collected during 1985 from clinical outbreaks of Aujezsky's disease on Danish farms was compared by restriction fragment pattern (RFP) analysis. The BamHI generated RFPs were found to be distinguishable, thus confirming RFP analysis...

Genotyping of major histocompatibility complex Class II DRB gene in Rohilkhandi goats by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing

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Kush Shrivastava

2015-10-01

Full Text Available Aim: To study the major histocompatibility complex (MHC Class II DRB1 gene polymorphism in Rohilkhandi goat using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP and nucleotide sequencing techniques. Materials and Methods: DNA was isolated from 127 Rohilkhandi goats maintained at sheep and goat farm, Indian Veterinary Research Institute, Izatnagar, Bareilly. A 284 bp fragment of exon 2 of DRB1 gene was amplified and digested using BsaI and TaqI restriction enzymes. Population genetic parameters were calculated using Popgene v 1.32 and SAS 9.0. The genotypes were then sequenced using Sanger dideoxy chain termination method and were compared with related breeds/species using MEGA 6.0 and Megalign (DNASTAR software. Results: TaqI locus showed three and BsaI locus showed two genotypes. Both the loci were found to be in Hardy–Weinberg equilibrium (HWE, however, population genetic parameters suggest that heterozygosity is still maintained in the population at both loci. Percent diversity and divergence matrix, as well as phylogenetic analysis revealed that the MHC Class II DRB1 gene of Rohilkhandi goats was found to be in close cluster with Garole and Scottish blackface sheep breeds as compared to other goat breeds included in the sequence comparison. Conclusion: The PCR-RFLP patterns showed population to be in HWE and absence of one genotype at one locus (BsaI, both the loci showed excess of one or the other homozygote genotype, however, effective number of alleles showed that allelic diversity is present in the population. Sequence comparison of DRB1 gene of Rohilkhandi goat with other sheep and goat breed assigned Rohilkhandi goat in divergence with Jamanupari and Angora goats.

Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking.

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Jiabing Ji

Full Text Available BACKGROUND: Insertion mutant isolation and characterization are extremely valuable for linking genes to physiological function. Once an insertion mutant phenotype is identified, the challenge is to isolate the responsible gene. Multiple strategies have been employed to isolate unknown genomic DNA that flanks mutagenic insertions, however, all these methods suffer from limitations due to inefficient ligation steps, inclusion of restriction sites within the target DNA, and non-specific product generation. These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner. METHODOLOGY/PRINCIPAL FINDINGS: We designed a novel strategy called Restriction Site Extension PCR (RSE-PCR to efficiently conduct large-scale isolation of unknown genomic DNA fragments linked to DNA insertions. The strategy is a modified adaptor-mediated PCR without ligation. An adapter, with complementarity to the 3' overhang of the endonuclease (KpnI, NsiI, PstI, or SacI restricted DNA fragments, extends the 3' end of the DNA fragments in the first cycle of the primary RSE-PCR. During subsequent PCR cycles and a second semi-nested PCR (secondary RSE-PCR, touchdown and two-step PCR are combined to increase the amplification specificity of target fragments. The efficiency and specificity was demonstrated in our characterization of 37 tex mutants of Arabidopsis. All the steps of RSE-PCR can be executed in a 96 well PCR plate. Finally, RSE-PCR serves as a successful alternative to Genome Walker as demonstrated by gene isolation from maize, a plant with a more complex genome than Arabidopsis. CONCLUSIONS/SIGNIFICANCE: RSE-PCR has high potential application in identifying tagged (T-DNA or transposon sequence or walking from known DNA toward unknown regions in large-genome plants, with likely application in other organisms as well.

33 CFR 334.450 - Cape Fear River and tributaries at Sunny Point Army Terminal, Brunswick County, N.C.; restricted...

Science.gov (United States)

2010-07-01

... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Cape Fear River and tributaries... AND RESTRICTED AREA REGULATIONS § 334.450 Cape Fear River and tributaries at Sunny Point Army Terminal, Brunswick County, N.C.; restricted area. (a) The area. That portion of Cape Fear River due west of the main...

Characterization of gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism: gut microbiota could be a diagnostic marker of coronary artery disease.

Science.gov (United States)

Emoto, Takuo; Yamashita, Tomoya; Kobayashi, Toshio; Sasaki, Naoto; Hirota, Yushi; Hayashi, Tomohiro; So, Anna; Kasahara, Kazuyuki; Yodoi, Keiko; Matsumoto, Takuya; Mizoguchi, Taiji; Ogawa, Wataru; Hirata, Ken-Ichi

2017-01-01

The association between atherosclerosis and gut microbiota has been attracting increased attention. We previously demonstrated a possible link between gut microbiota and coronary artery disease. Our aim of this study was to clarify the gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism (T-RFLP). This study included 39 coronary artery disease (CAD) patients and 30 age- and sex- matched no-CAD controls (Ctrls) with coronary risk factors. Bacterial DNA was extracted from their fecal samples and analyzed by T-RFLP and data mining analysis using the classification and regression algorithm. Five additional CAD patients were newly recruited to confirm the reliability of this analysis. Data mining analysis could divide the composition of gut microbiota into 2 characteristic nodes. The CAD group was classified into 4 CAD pattern nodes (35/39 = 90 %), while the Ctrl group was classified into 3 Ctrl pattern nodes (28/30 = 93 %). Five additional CAD samples were applied to the same dividing model, which could validate the accuracy to predict the risk of CAD by data mining analysis. We could demonstrate that operational taxonomic unit 853 (OTU853), OTU657, and OTU990 were determined important both by the data mining method and by the usual statistical comparison. We classified the gut microbiota profiles in coronary artery disease patients using data mining analysis of T-RFLP data and demonstrated the possibility that gut microbiota is a diagnostic marker of suffering from CAD.

Pharmacologic study of C-terminal fragments of frog skin calcitonin gene-related peptide.

Science.gov (United States)

Ladram, Ali; Besné, Isabelle; Breton, Lionel; de Lacharrière, Olivier; Nicolas, Pierre; Amiche, Mohamed

2008-07-01

The calcitonin gene-related peptide from the skin of the frog Phyllomedusa bicolor (pbCGRP) is a 37-residue neuropeptide that differs from human alpha CGRP (halphaCGRP) at 16 positions. The affinities of the C-terminal fragments of pbCGRP and halphaCGRP were evaluated in SK-N-MC cells: pbCGRP(8-37) (K(i)=0.2nM) and pbCGRP(27-37) (K(i)=95nM) were, respectively, 3 times and 20 times more potent than the human fragments halphaCGRP(8-37) and halphaCGRP(27-37). Their antagonistic potencies were measured in SK-N-MC and Col 29 cells, and the rat vas deferens. pbCGRP(8-37) inhibited the halphaCGRP-stimulated production of cAMP by SK-N-MC and Col 29 cells 3 to 4 times more strongly than halphaCGRP(8-37). Thus pbCGRP(8-37) is the most potent CGRP-1 competitive antagonist of all the natural sequences reported to date. pbCGRP(27-37) was also as potent as [D(31), A(34), F(35)] halphaCGRP(27-37), a prototypic antagonist analog derived from structure-activity relationship studies of halphaCGRP(8-37).

Termination of DNA synthesis in vitro at apurinic sites but not at ethyl adducts of the template

Energy Technology Data Exchange (ETDEWEB)

Lockhart, M.L.; Deutsch, J.F.; Yamaura, I.; Cavalieri, L.F.; Rosenberg, B.H.

1982-01-01

The effects of DNA lesions produced by the carcinogenic alkylating agents ethylnitrosourea and diethylsulfate on the extent of DNA synthesis have been studied in a system utilizing circular single-stranded phi X174 DNA as template and a 392-base restriction fragment as primer with E. coli polymerase I (Klenow fragment). Apurinic sites produced by loss of unstable ethylated bases from the template terminate DNA synthesis at the first such site encountered, but ethyl adducts at most, if not all, locations permit readthrough. 22 references, 3 figures, 1 table.

Simultaneous and rapid differential diagnosis of Mycoplasma genitalium and Ureaplasma urealyticum based on a polymerase chain reaction-restriction fragment length polymorphism

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R Mirnejad

2011-01-01

Full Text Available Objectives: The aim of this investigation was to simultaneously detect and differentiate Mycoplasma genitalium and Ureaplasma urealyticum in female patients suffering from genital complications by polymerase chain reaction (PCR-restriction fragment length polymorphism (RFLP. Materials and Methods : Genital swabs were taken from 210 patients. They were transported to the laboratory in phosphate-buffered saline. For PCR, samples were analysed with genus-specific MyUu-R and MyUu-F primers. This primer set, which was originally designed in our laboratory, amplified a 465 bp fragment (M. genitalium and a 559 bp fragment (U. urealyticum. Samples containing a band of the expected sizes for the Mycoplasma strains were subjected to digestion with a restriction endonuclease enzyme of TaqI and Cac8I. Results: Of the 210 samples, a total of 100 (47.6% samples were found to be positive for Mycoplasmas (seven M. genitalium isolates, 3.3%; and 89 U. urealyticum isolates, 42.4%, and coinfections with both species were detected in four samples (1.9%. The PCR-RFLP results showed that M. genitalium and U. urealyticum are different by enzyme patterns. Conclusion: PCR-RFLP offers a rapid and easily applicable protocol to simultaneous detection and differentiation of M. genitalium and U. urealyticum from clinical samples when specific primers and restriction enzymes are used.

Nondetectability of restriction fragments and independence of DNA fragment sizes within and between loci in RFLP typing of DNA

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, R.; Zhong, Y.; Jin, L. (Univ. of Texas Health Science Center, Houston, TX (United States)); Budowle, B. (FBI Academy, Quantico, VA (United States))

1994-08-01

The authors provide experimental evidence showing that, during the restriction-enzyme digestion of DNA samples, some of the HaeIII-digested DNA fragments are small enough to prevent their reliable sizing on a Southern gel. As a result of such nondetectability of DNA fragments, individuals who show a single-band DNA profile at a VNTR locus may not necessarily be true homozygotes. In a population database, when the presence of such nondetectable alleles is ignored, they show that a pseudodependence of alleles within as well as across loci may occur. Using a known statistical method, under the hypothesis of independence of alleles within loci, they derive an efficient estimate of null allele frequency, which may be subsequently used for testing allelic independence within and across loci. The estimates of null allele frequencies, thus derived, are shown to agree with direct experimental data on the frequencies of HaeIII-null alleles. Incorporation of null alleles into the analysis of the forensic VNTR database suggests that the assumptions of allelic independence within and between loci are appropriate. In contrast, a failure to incorporate the occurrence of null alleles would provide a wrong inference regarding the independence of alleles within and between loci. 47 refs., 2 figs., 4 tabs.

Restriction Fragment Length Polymorphism Analysis Reveals High Levels of Genetic Divergence Among the Light Organ Symbionts of Flashlight Fish.

Science.gov (United States)

Wolfe, C J; Haygood, M G

1991-08-01

Restriction fragment length polymorphisms within the lux and 16S ribosomal RNA gene regions were used to compare unculturable bacterial light organ symbionts of several anomalopid fish species. The method of Nei and Li (1979) was used to calculate phylogenetic distance from the patterns of restriction fragment lengths of the luxA and 16S rRNA regions. Phylogenetic trees constructed from each distance matrix (luxA and 16S rDNA data) have similar branching orders. The levels of divergence among the symbionts, relative to other culturable luminous bacteria, suggests that the symbionts differ at the level of species among host fish genera. Symbiont relatedness and host geographic location do not seem to be correlated, and the symbionts do not appear to be strains of common, free-living, luminous bacteria. In addition, the small number of hybridizing fragments within the 16S rRNA region of the symbionts, compared with that of the free-living species, suggests a decrease in copy number of rRNA operons relative to free-living species. At this level of investigation, the symbiont phylogeny is consistent with the proposed phylogeny of the host fish family and suggests that each symbiont strain coevolved with its host fish species.

Graph Theory. 1. Fragmentation of Structural Graphs

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Lorentz JÄNTSCHI

2002-12-01

Full Text Available The investigation of structural graphs has many fields of applications in engineering, especially in applied sciences like as applied chemistry and physics, computer sciences and automation, electronics and telecommunication. The main subject of the paper is to express fragmentation criteria in graph using a new method of investigation: terminal paths. Using terminal paths are defined most of the fragmentation criteria that are in use in molecular topology, but the fields of applications are more generally than that, as I mentioned before. Graphical examples of fragmentation are given for every fragmentation criteria. Note that all fragmentation is made with a computer program that implements a routine for every criterion.[1] A web routine for tracing all terminal paths in graph can be found at the address: http://vl.academicdirect.ro/molecular_topology/tpaths/ [1] M. V. Diudea, I. Gutman, L. Jäntschi, Molecular Topology, Nova Science, Commack, New York, 2001, 2002.

Effects of a one year physical activity program on serum C Terminal Agrin Fragment (CAF) concentrations among mobility limited older adults

Science.gov (United States)

OBJECTIVES: C terminal Agrin Fragment (CAF) has been proposed as a potential circulating biomarker for predicting changes in physical function among older adults. To determine the effect of a one year PA intervention on changes in CAF concentrations and to evaluate baseline and longitudinal associat...

Molecular identification of similar species of the genus Biomphalaria (Mollusca: Planorbidae determined by a polymerase chain reaction-restriction fragment length polymorphism

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Caldeira Roberta Lima

1998-01-01

Full Text Available The freshwater snails Biomphalaria straminea, B. intermedia, B. kuhniana and B. peregrina, are morphologically similar; based on this similarity the first three species were therefore grouped in the complex B. straminea. The morphological identification of these species is based on characters such as vaginal wrinkling, relation between prepuce: penial sheath:deferens vas and number of muscle layers in the penis wall. In this study the polymerase chain reaction restriction fragment length polymorphism technique was used for molecular identification of these molluscs. This technique is based on the amplification of the internal transcribed spacer regions ITS1 e ITS2 of the ribosomal RNA gene and subsequent digestion of these fragments by restriction enzymes. Six enzymes were tested: Dde I, Mnl I, Hae III, Rsa I, Hpa II e Alu I. The restriction patterns obtained with DdeI presented the best profile for separation of the four species of Biomphalaria. The profiles obtained with all the enzymes were used to estimate the genetic distances among the species through analysis of common banding patterns.

Mapped DNA probes from Ioblolly pine can be used for restriction fragment length polymorphism mapping in other conifers

Science.gov (United States)

M.R. Ahuja; M.E. Devey; A.T. Groover; K.D. Jermstad; D.B Neale

1994-01-01

A high-density genetic map based on restriction fragment length polymorphisms (RFLPs) is being constructed for loblolly pine (Pinus taeda L.). Consequently, a large number of DNA probes from loblolly pine are potentially available for use in other species. We have used some of these DNA probes to detect RFLPs in 12 conifers and an angiosperm....

Restriction fragment length polymorphism of the HLA-DP subregion and correlations to HLA-DP phenotypes

International Nuclear Information System (INIS)

Hyldig-Nielsen, J.J.; Morling, N.; Oedum, N.; Ryder, L.P.; Platz, P.; Jakobsen, B.; Svejgaard, A.

1987-01-01

The restriction fragment length polymorphism (RFLP) of the class II HLA-DP subregion of the major histocompatibility complex (MHC) of humans has been unraveled by Southern blotting using DP/sub α/ and DP/sub β/ probes in a study of 46 unrelated individuals with known HLA-DP types. Contrary to earlier preliminary findings with a limited number of enzymes, the RFLP appears to be quite extensive both with the DP/sub β/ (14 different DNA markers defined by individual fragments or clusters thereof) and the DP/sub α/ (8 markers) probes, especially when enzyme recognizing only four base pairs were used. A few markers were absolutely or strongly associated with individual DP antigens, whereas most were associated with two or more DP antigens as defined by primed lymphocyte typing. Thus, Southern blotting seems feasible for typing for most DP determinants by specific fragments or subtraction between the various more broadly reactive DNA markers, and the RFLP provides further information on the DP subregion in addition to that provided by primed lymphocyte typing. In two recombinant families, the DP/sub β/ and DP/sub α/ DNA markers segregated with DP antigens, whereas the DR/sub β/, DQ/sub β/, DQ/sub α/, and DX/sub α/ markers followed the DR and DQ antigens

Molecular markers. Amplified fragment length polymorphism

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Pržulj Novo

2005-01-01

Full Text Available Amplified Fragment Length Polymorphism molecular markers (AFLPs has been developed combining procedures of RFLPs and RAPDs molekular markers, i.e. the first step is restriction digestion of the genomic DNA that is followed by selective amplification of the restricted fragments. The advantage of the AFLP technique is that it allows rapid generation of a large number of reproducible markers. The reproducibility of AFLPs markers is assured by the use of restriction site-specific adapters and adapter-specific primers for PCR reaction. Only fragments containing the restriction site sequence plus the additional nucleotides will be amplified and the more selected nucleotides added on the primer sequence the fewer the number of fragments amplified by PCR. The amplified products are normally separated on a sequencing gel and visualized after exposure to X-ray film or by using fluorescent labeled primers. AFLP shave proven to be extremely proficient in revealing diversity at below the species level. A disadvantage of AFLP technique is that AFLPs are essentially a dominant marker system and not able to identify heterozygotes.

Aspergillus section Fumigati typing by PCR-restriction fragment polymorphism.

Science.gov (United States)

Staab, Janet F; Balajee, S Arunmozhi; Marr, Kieren A

2009-07-01

Recent studies have shown that there are multiple clinically important members of the Aspergillus section Fumigati that are difficult to distinguish on the basis of morphological features (e.g., Aspergillus fumigatus, A. lentulus, and Neosartorya udagawae). Identification of these organisms may be clinically important, as some species vary in their susceptibilities to antifungal agents. In a prior study, we utilized multilocus sequence typing to describe A. lentulus as a species distinct from A. fumigatus. The sequence data show that the gene encoding beta-tubulin, benA, has high interspecies variability at intronic regions but is conserved among isolates of the same species. These data were used to develop a PCR-restriction fragment length polymorphism (PCR-RFLP) method that rapidly and accurately distinguishes A. fumigatus, A. lentulus, and N. udagawae, three major species within the section Fumigati that have previously been implicated in disease. Digestion of the benA amplicon with BccI generated unique banding patterns; the results were validated by screening a collection of clinical strains and by in silico analysis of the benA sequences of Aspergillus spp. deposited in the GenBank database. PCR-RFLP of benA is a simple method for the identification of clinically important, similar morphotypes of Aspergillus spp. within the section Fumigati.

Aspergillus Section Fumigati Typing by PCR-Restriction Fragment Polymorphism▿

Science.gov (United States)

Staab, Janet F.; Balajee, S. Arunmozhi; Marr, Kieren A.

2009-01-01

Recent studies have shown that there are multiple clinically important members of the Aspergillus section Fumigati that are difficult to distinguish on the basis of morphological features (e.g., Aspergillus fumigatus, A. lentulus, and Neosartorya udagawae). Identification of these organisms may be clinically important, as some species vary in their susceptibilities to antifungal agents. In a prior study, we utilized multilocus sequence typing to describe A. lentulus as a species distinct from A. fumigatus. The sequence data show that the gene encoding β-tubulin, benA, has high interspecies variability at intronic regions but is conserved among isolates of the same species. These data were used to develop a PCR-restriction fragment length polymorphism (PCR-RFLP) method that rapidly and accurately distinguishes A. fumigatus, A. lentulus, and N. udagawae, three major species within the section Fumigati that have previously been implicated in disease. Digestion of the benA amplicon with BccI generated unique banding patterns; the results were validated by screening a collection of clinical strains and by in silico analysis of the benA sequences of Aspergillus spp. deposited in the GenBank database. PCR-RFLP of benA is a simple method for the identification of clinically important, similar morphotypes of Aspergillus spp. within the section Fumigati. PMID:19403766

Performance of PCR-restriction fragment length polymorphism analysis of the Helicobacter pylori ureB gene in differentiating gene variants

DEFF Research Database (Denmark)

Colding, H; Hartzen, S H; Mohammadi, M

2003-01-01

Recently, PCR-restriction fragment length polymorphism (PCR-RFLP) of the urease genes of Helicobacter pylori was evaluated in a meta-analysis; acceptable discriminatory indices of the ureAB and C genes were found. In the present investigation, we found a discriminatory index of 0.95 for 191...... is comparable to typing of other H. pylori urease genes....

Structure of a tropomyosin N-terminal fragment at 0.98 Å resolution

International Nuclear Information System (INIS)

Meshcheryakov, Vladimir A.; Krieger, Inna; Kostyukova, Alla S.; Samatey, Fadel A.

2011-01-01

The crystal structure of the N-terminal fragment of the short nonmuscle α-tropomyosin has been determined at a resolution of 0.98 Å. Tropomyosin (TM) is an elongated two-chain protein that binds along actin filaments. Important binding sites are localized in the N-terminus of tropomyosin. The structure of the N-terminus of the long muscle α-TM has been solved by both NMR and X-ray crystallography. Only the NMR structure of the N-terminus of the short nonmuscle α-TM is available. Here, the crystal structure of the N-terminus of the short nonmuscle α-TM (αTm1bZip) at a resolution of 0.98 Å is reported, which was solved from crystals belonging to space group P3 1 with unit-cell parameters a = b = 33.00, c = 52.03 Å, α = β = 90, γ = 120°. The first five N-terminal residues are flexible and residues 6–35 form an α-helical coiled coil. The overall fold and the secondary structure of the crystal structure of αTM1bZip are highly similar to the NMR structure and the atomic coordinates of the corresponding C α atoms between the two structures superimpose with a root-mean-square deviation of 0.60 Å. The crystal structure validates the NMR structure, with the positions of the side chains being determined precisely in our structure

Structure of a tropomyosin N-terminal fragment at 0.98 Å resolution

Energy Technology Data Exchange (ETDEWEB)

Meshcheryakov, Vladimir A. [Okinawa Institute of Science and Technology, Okinawa (Japan); Krieger, Inna [Texas A& M University, College Station, Texas (United States); Kostyukova, Alla S. [Robert Wood Johnson Medical School, Piscataway, New Jersey (United States); Samatey, Fadel A., E-mail: f.a.samatey@oist.jp [Okinawa Institute of Science and Technology, Okinawa (Japan)

2011-09-01

The crystal structure of the N-terminal fragment of the short nonmuscle α-tropomyosin has been determined at a resolution of 0.98 Å. Tropomyosin (TM) is an elongated two-chain protein that binds along actin filaments. Important binding sites are localized in the N-terminus of tropomyosin. The structure of the N-terminus of the long muscle α-TM has been solved by both NMR and X-ray crystallography. Only the NMR structure of the N-terminus of the short nonmuscle α-TM is available. Here, the crystal structure of the N-terminus of the short nonmuscle α-TM (αTm1bZip) at a resolution of 0.98 Å is reported, which was solved from crystals belonging to space group P3{sub 1} with unit-cell parameters a = b = 33.00, c = 52.03 Å, α = β = 90, γ = 120°. The first five N-terminal residues are flexible and residues 6–35 form an α-helical coiled coil. The overall fold and the secondary structure of the crystal structure of αTM1bZip are highly similar to the NMR structure and the atomic coordinates of the corresponding C{sup α} atoms between the two structures superimpose with a root-mean-square deviation of 0.60 Å. The crystal structure validates the NMR structure, with the positions of the side chains being determined precisely in our structure.

Characterization of European Yersinia enterocolitica 1A strains using restriction fragment length polymorphism and multilocus sequence analysis.

Science.gov (United States)

Murros, A; Säde, E; Johansson, P; Korkeala, H; Fredriksson-Ahomaa, M; Björkroth, J

2016-10-01

Yersinia enterocolitica is currently divided into two subspecies: subsp. enterocolitica including highly pathogenic strains of biotype 1B and subsp. palearctica including nonpathogenic strains of biotype 1A and moderately pathogenic strains of biotypes 2-5. In this work, we characterized 162 Y. enterocolitica strains of biotype 1A and 50 strains of biotypes 2-4 isolated from human, animal and food samples by restriction fragment length polymorphism using the HindIII restriction enzyme. Phylogenetic relatedness of 20 representative Y. enterocolitica strains including 15 biotype 1A strains was further studied by the multilocus sequence analysis of four housekeeping genes (glnA, gyrB, recA and HSP60). In all the analyses, biotype 1A strains formed a separate genomic group, which differed from Y. enterocolitica subsp. enterocolitica and from the strains of biotypes 2-4 of Y. enterocolitica subsp. palearctica. Based on these results, biotype 1A strains considered nonpathogenic should not be included in subspecies palearctica containing pathogenic strains of biotypes 2-5. Yersinia enterocolitica strains are currently divided into six biotypes and two subspecies. Strains of biotype 1A, which are phenotypically and genotypically very heterogeneous, are classified as subspecies palearctica. In this study, European Y. enterocolitica 1A strains isolated from both human and nonhuman sources were characterized using restriction fragment length polymorphism and multilocus sequence analysis. The European biotype 1A strains formed a separate group, which differed from strains belonging to subspecies enterocolitica and palearctica. This may indicate that the current division between the two subspecies is not sufficient considering the strain diversity within Y. enterocolitica. © 2016 The Society for Applied Microbiology.

Crystallization and preliminary X-ray analysis of a C-terminal fragment of FlgJ, a putative flagellar rod cap protein from Salmonella

International Nuclear Information System (INIS)

Kikuchi, Yuki; Matsunami, Hideyuki; Yamane, Midori; Imada, Katsumi; Namba, Keiichi

2008-01-01

A C-terminal fragment of Salmonella FlgJ, FlgJ 120–316 , which has peptidoglycan-hydrolysing activity, has been overproduced, purified and crystallized and the crystals have been characterized by X-ray diffraction. The formation of the bacterial flagellar axial structure, including the filament, the hook and the rod, requires the attachment of a cap complex to the distal end of the growing structure. Because the rod penetrates the peptidoglycan (PG) layer, the rod cap complex is thought to have PG-hydrolyzing activity. FlgJ is a putative rod cap protein whose C-terminal region shows sequence similarity to known muramidases. In this study, FlgJ 120–316 , a C-terminal fragment of FlgJ which contains the muramidase region, was overproduced, purified and crystallized. Crystals were obtained by the sitting-drop vapour-diffusion technique using PEG 3350 as a crystallizing agent and belonged to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 38.8, b = 43.9, c = 108.5 Å. Anomalous difference Patterson maps calculated from the diffraction data set of a selenomethionine-labelled crystal showed significant peaks in the Harker sections, indicating that the data were suitable for structure determination

Crystallization and preliminary X-ray crystallographic analysis of a 40 kDa N-terminal fragment of the yeast prion-remodeling factor Hsp104

Energy Technology Data Exchange (ETDEWEB)

Lee, Sukyeong; Tsai, Francis T. F., E-mail: ftsai@bcm.tmc.edu [Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 (United States)

2007-09-01

An N-terminal fragment of S. cerevisiae Hsp104 has been crystallized. This is the first report of the crystallization of a eukaryotic member of the Hsp100 family of molecular chaperones. A 40 kDa N-terminal fragment of Saccharomyces cerevisiae Hsp104 was crystallized in two different crystal forms. Native 1 diffracted to 2.6 Å resolution and belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 66.6, b = 75.8, c = 235.7 Å. Native 2 diffracted to 2.9 Å resolution and belonged to space group P6{sub 1}22 or P6{sub 5}22, with unit-cell parameters a = 179.1, b = 179.1, c = 69.7 Å. This is the first report of the crystallization of a eukaryotic member of the Hsp100 family of molecular chaperones.

An Algebra for Program Fragments

DEFF Research Database (Denmark)

Kristensen, Bent Bruun; Madsen, Ole Lehrmann; Møller-Pedersen, Birger

1985-01-01

Program fragments are described either by strings in the concrete syntax or by constructor applications in the abstract syntax. By defining conversions between these forms, both may be intermixed. Program fragments are constructed by terminal and nonterminal symbols from the grammar and by variab...

Structure and inhibition analysis of the mouse SAD-B C-terminal fragment.

Science.gov (United States)

Ma, Hui; Wu, Jing-Xiang; Wang, Jue; Wang, Zhi-Xin; Wu, Jia-Wei

2016-10-01

The SAD (synapses of amphids defective) kinases, including SAD-A and SAD-B, play important roles in the regulation of neuronal development, cell cycle, and energy metabolism. Our recent study of mouse SAD-A identified a unique autoinhibitory sequence (AIS), which binds at the junction of the kinase domain (KD) and the ubiquitin-associated (UBA) domain and exerts autoregulation in cooperation with UBA. Here, we report the crystal structure of the mouse SAD-B C-terminal fragment including the AIS and the kinase-associated domain 1 (KA1) at 2.8 Å resolution. The KA1 domain is structurally conserved, while the isolated AIS sequence is highly flexible and solvent-accessible. Our biochemical studies indicated that the SAD-B AIS exerts the same autoinhibitory role as that in SAD-A. We believe that the flexible isolated AIS sequence is readily available for interaction with KD-UBA and thus inhibits SAD-B activity.

Typing of Human Mycobacterium avium Isolates in Italy by IS1245-Based Restriction Fragment Length Polymorphism Analysis

Science.gov (United States)

Lari, Nicoletta; Cavallini, Michela; Rindi, Laura; Iona, Elisabetta; Fattorini, Lanfranco; Garzelli, Carlo

1998-01-01

All but 2 of 63 Mycobacterium avium isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS1245 restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS1245 patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS1245 RFLP pattern. PMID:9817900

Plasminogen fragments K 1-3 and K 5 bind to different sites in fibrin fragment DD.

Science.gov (United States)

Grinenko, T V; Kapustianenko, L G; Yatsenko, T A; Yusova, O I; Rybachuk, V N

2016-01-01

Specific plasminogen-binding sites of fibrin molecule are located in Аα148-160 regions of C-terminal domains. Plasminogen interaction with these sites initiates the activation process of proenzyme and subsequent fibrin lysis. In this study we investigated the binding of plasminogen fragments K 1-3 and K 5 with fibrin fragment DD and their effect on Glu-plasminogen interaction with DD. It was shown that the level of Glu-plasminogen binding to fibrin fragment DD is decreased by 50-60% in the presence of K 1-3 and K 5. Fragments K 1-3 and K 5 have high affinity to fibrin fragment DD (Kd is 0.02 for K 1-3 and 0.054 μМ for K 5). K 5 interaction is independent and K 1-3 is partly dependent on C-terminal lysine residues. K 1-3 interacts with complex of fragment DD-immobilized K 5 as well as K 5 with complex of fragment DD-immobilized K 1-3. The plasminogen fragments do not displace each other from binding sites located in fibrin fragment DD, but can compete for the interaction. The results indicate that fibrin fragment DD contains different binding sites for plasminogen kringle fragments K 1-3 and K 5, which can be located close to each other. The role of amino acid residues of fibrin molecule Аα148-160 region in interaction with fragments K 1-3 and K 5 is discussed.

Restriction Fragment Length Polymorphisms of Virulence Plasmids in Rhodococcus equi

Science.gov (United States)

Takai, Shinji; Shoda, Masato; Sasaki, Yukako; Tsubaki, Shiro; Fortier, Guillaume; Pronost, Stephane; Rahal, Karim; Becu, Teotimo; Begg, Angela; Browning, Glenn; Nicholson, Vivian M.; Prescott, John F.

1999-01-01

Virulent Rhodococcus equi, which is a well-known cause of pyogranulomatous pneumonia in foals, possesses a large plasmid encoding virulence-associated 15- to 17-kDa antigens. Foal and soil isolates from five countries—Argentina, Australia, Canada, France, and Japan—were investigated for the presence of 15- to 17-kDa antigens by colony blotting, using the monoclonal antibody 10G5, and the gene coding for 15- to 17-kDa antigens by PCR. Plasmid DNAs extracted from positive isolates were digested with restriction endonucleases BamHI, EcoRI, EcoT22I, and HindIII, and the digestion patterns that resulted divided the plasmids of virulent isolates into five closely related types. Three of the five types had already been reported in Canadian and Japanese isolates, and the two new types had been found in French and Japanese isolates. Therefore, we tentatively designated these five types 85-kb type I (pREAT701), 85-kb type II (a new type), 87-kb type I (EcoRI and BamHI type 2 [V. M. Nicholson and J. F. Prescott, J. Clin. Microbiol. 35:738–740, 1997]), 87-kb type II (a new type), and 90-kb (pREL1) plasmids. The 85-kb type I plasmid was found in isolates from Argentina, Australia, Canada, and France. Plasmid 87-kb type I was isolated in specimens from Argentina, Canada, and France. The 85-kb type II plasmid appeared in isolates from France. On the other hand, plasmids 87-kb type II and 90-kb were found only in isolates from Japan. These results revealed geographic differences in the distribution of the virulence plasmids found in the five countries and suggested that the restriction fragment length polymorphism of virulence plasmids might be useful to elucidate the molecular epidemiology of virulent R. equi in the world. PMID:10488224

Restriction fragment length polymorphism of two HLA-B-associated transcripts genes in five autoimmune diseases

DEFF Research Database (Denmark)

Fugger, L; Morling, N; Ryder, L P

1991-01-01

The restriction fragment length polymorphism of the two human HLA-B-associated transcripts (BATs) genes, BAT1 and BAT2, identifying polymorphic bands of 12, 8, 2.5, and 1.1 kb, and at 3.3, 2.7, 2.3, and 0.9 kb, respectively, was investigated in patients with primary biliary cirrhosis (PBC......), systemic lupus erythematosus (SLE), pauciarticular juvenile rheumatoid arthritis (P-JRA), rheumatoid arthritis (RA), and primary Sjögren's syndrome (pSS), and in healthy Danes. The BAT2/RsaI 2.7-kb band fragment was more frequent in PBC, pSS, and SLE than in controls, but the p values did not reach...... significance when corrected for multiple comparisons. For pSS and SLE, the associations may be secondary to primary associations with HLA-B8 because the BAT2/RsaI 2.3-kb band, which is allelic to the BAT2/RsaI 2.7-kb band, is strongly negatively associated with HLA-B8 and HLA-DR3. The only significance...

Restriction fragment length polymorphism (RFLP) of two HLA-B-associated transcripts (BATs) genes in healthy Danes

DEFF Research Database (Denmark)

Fugger, L; Morling, N; Ryder, L P

1990-01-01

The restriction fragment length polymorphism (RFLP) of the two human HLA-B-associated transcripts (BATs) genes, BAT1 and BAT2, was investigated using 5 different restriction enzymes and two human BAT1 and BAT2 cDNA probes. Two of the enzymes, NcoI and RsaI, revealed polymorphic patterns which were...... investigated in healthy Danes. The cDNA/restriction enzyme combination BAT1/NcoI identifies polymorphic bands at 12 kb, 8 kb, 2.5 kb, and 1.1 kb, while the BAT2/RsaI combination identifies polymorphic bands at 3.3 kb, 2.7 kb, 2.3 kb, and 0.9 kb. The frequencies of these markers were determined in 90 unrelated...... Danes. Co-dominant segregation and allelic behavior was seen for the BAT1/NcoI 12 kb and 8 kb bands and the BAT2/RsaI 2.7 kb and 2.3 kb bands, respectively. It is possible that the BAT2/RsaI 3.3 kb band represents a rare allele of the BAT2/RsaI system. The BAT2/RsaI 2.3 kb marker was strongly negatively...

Pseudo color ghost coding imaging with pseudo thermal light

Science.gov (United States)

Duan, De-yang; Xia, Yun-jie

2018-04-01

We present a new pseudo color imaging scheme named pseudo color ghost coding imaging based on ghost imaging but with multiwavelength source modulated by a spatial light modulator. Compared with conventional pseudo color imaging where there is no nondegenerate wavelength spatial correlations resulting in extra monochromatic images, the degenerate wavelength and nondegenerate wavelength spatial correlations between the idle beam and signal beam can be obtained simultaneously. This scheme can obtain more colorful image with higher quality than that in conventional pseudo color coding techniques. More importantly, a significant advantage of the scheme compared to the conventional pseudo color coding imaging techniques is the image with different colors can be obtained without changing the light source and spatial filter.

Analyzing Internal Fragmentation of Electrosprayed Ubiquitin Ions During Beam-Type Collisional Dissociation

Science.gov (United States)

Durbin, Kenneth R.; Skinner, Owen S.; Fellers, Ryan T.; Kelleher, Neil L.

2015-05-01

Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis.

Structure-activity studies with carboxy- and amino-terminal fragments of neurotensin on hypothalamic neurons in vitro.

Science.gov (United States)

Baldino, F; Davis, L G; Wolfson, B

1985-09-09

The purpose of this study was to determine the structural requirements for the activity of neurotensin (NT1-13) on preoptic/anterior hypothalamic (POAH) neurons in vitro. Standard explant culture electrophysiological techniques were employed. NT was administered to POAH cultures through the superfusion fluid, or, to the vicinity of individual neurons by pressure ejection (0.5-10 psi) from micropipettes. Computer-generated, peri-event histograms were used to quantitate neuronal responses. Pressure ejection of NT1-13 (50 pM to 1 microM) consistently produced an excitatory effect on 30 of 42 neurons. The remaining cells were either inhibited or unaffected. Application of the C-terminal hexapeptide, NT8-13, but not the N-terminal octapeptide, NT1-8 (less than or equal to 1 mM), produced an excitatory response in 21 of 30 neurons, but was less potent than NT1-13. Application of an N-acetylated NT8-13 fragment (NTAC8-13) produced a response that was similar to that produced by NT8-13. The excitatory effects of NT1-13 and NT8-13 were maintained in medium which effectively blocked synaptic transmission (0 mM Ca2+/12 mM Mg2+ 1 mM EGTA). These data indicate that the C-terminal hexapeptide, but not the N-terminal octapeptide, produces a dose-related, excitatory effect on single neurons in the POAH in vitro. The persistence of these effects in Ca2+-free medium supports a postsynaptic site of action for these peptides.

Events per variable for risk differences and relative risks using pseudo-observations

DEFF Research Database (Denmark)

Hansen, Stefan Nygaard; Andersen, Per Kragh; Parner, Erik Thorlund

2014-01-01

A method based on pseudo-observations has been proposed for direct regression modeling of functionals of interest with right-censored data, including the survival function, the restricted mean and the cumulative incidence function in competing risks. The models, once the pseudo-observations have...... been computed, can be fitted using standard generalized estimating equation software. Regression models can however yield problematic results if the number of covariates is large in relation to the number of events observed. Guidelines of events per variable are often used in practice. These rules...

Percolation versus microcanonical fragmentation - comparison of fragment size distribution: Where is the liquid-gas transition in nuclei?

International Nuclear Information System (INIS)

Jaqaman, H.R.; Birzeit Univ.; Papp, G.; Eoetvoes Lorand Tudomanyegyetem, Budapest; Gross, D.H.E.; Freie Univ. Berlin

1990-01-01

The distributions of fragments produced by microcanonical multifragmentation of hot nuclei are compared with the cluster distributions predicted by a bond percolation model on a finite lattice. The conditional moments of these distributions are used together with the correlations between the largest three fragments in each event. Whereas percolation and statistical nuclear fragmentation agree in many details as in the usual plots of the averaged moments of the fragment distributions which yield the critical exponents, they turn out to be essentially different when less averaged quantities or correlations are considered. The differences between the predictions of the two models are mainly due to the particularities of the nuclear problem, especially the effect of the long-range Coulomb force which favours the break-up of the highly excited nucleus into two large fragments (pseudo-fission) and, to a somewhat lesser extent, enhances the possibility for the cracking of the nucleus into more than two large fragments. The fission events are, however, clearly separated from a second branch of critical correlations which shows up clearly in both nuclear fragmentation and percolation. We think that this critical correlation branch is due to the liquid-gas phase transition in finite nuclei. (orig.)

Heparan sulfate regulates fibrillin-1 N- and C-terminal interactions

DEFF Research Database (Denmark)

Cain, Stuart A; Baldwin, Andrew K; Mahalingam, Yashithra

2008-01-01

Fibrillin-1 N- and C-terminal heparin binding sites have been characterized. An unprocessed monomeric N-terminal fragment (PF1) induced a very high heparin binding response, indicating heparin-mediated multimerization. Using PF1 deletion and short fragments, a heparin binding site was localized w......-terminal interactions with heparin/heparan sulfate directly influence cell behavior, whereas C-terminal interactions with heparin/heparan sulfate regulate elastin deposition. These data highlight how heparin/heparan sulfate controls fibrillin-1 interactions....

Identification of planorbids from Venezuela by polymerase chain reaction amplification and restriction fragment length polymorphism of internal transcriber spacer of the RNA ribosomal gene

Directory of Open Access Journals (Sweden)

Caldeira Roberta L

2000-01-01

Full Text Available Snails of the genus Biomphalaria from Venezuela were subjected to morphological assessment as well as polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP analysis. Morphological identification was carried out by comparison of characters of the shell and the male and female reproductive apparatus. The PCR-RFLP involved amplification of the internal spacer region ITS1 and ITS2 of the RNA ribosomal gene and subsequent digestion of this fragment by the restriction enzymes DdeI, MnlI, HaeIII and MspI. The planorbids were compared with snails of the same species and others reported from Venezuela and present in Brazil, Cuba and Mexico. All the enzymes showed a specific profile for each species, that of DdeI being the clearest. The snails were identified as B. glabrata, B. prona and B. kuhniana.

Crystallization of the two-domain N-terminal fragment of the archaeal ribosomal protein L10(P0) in complex with a specific fragment of 23S rRNA

Science.gov (United States)

Kravchenko, O. V.; Mitroshin, I. V.; Gabdulkhakov, A. G.; Nikonov, S. V.; Garber, M. B.

2011-07-01

Lateral L12-stalk (P1-stalk in Archaea, P1/P2-stalk in eukaryotes) is an obligatory morphological element of large ribosomal subunits in all organisms studied. This stalk is composed of the complex of ribosomal proteins L10(P0) and L12(P1) and interacts with 23S rRNA through the protein L10(P0). L12(P1)-stalk is involved in the formation of GTPase center of the ribosome and plays an important role in the ribosome interaction with translation factors. High mobility of this stalk puts obstacles in determination of its structure within the intact ribosome. Crystals of a two-domain N-terminal fragment of ribosomal protein L10(P0) from the archaeon Methanococcus jannaschii in complex with a specific fragment of rRNA from the same organism have been obtained. The crystals diffract X-rays at 3.2 Å resolution.

Crystallization of the two-domain N-terminal fragment of the archaeal ribosomal protein L10(P0) in complex with a specific fragment of 23S rRNA

Energy Technology Data Exchange (ETDEWEB)

Kravchenko, O. V.; Mitroshin, I. V.; Gabdulkhakov, A. G.; Nikonov, S. V.; Garber, M. B., E-mail: garber@vega.protres.ru [Institute of Protein Research RAS (Russian Federation)

2011-07-15

Lateral L12-stalk (P1-stalk in Archaea, P1/P2-stalk in eukaryotes) is an obligatory morphological element of large ribosomal subunits in all organisms studied. This stalk is composed of the complex of ribosomal proteins L10(P0) and L12(P1) and interacts with 23S rRNA through the protein L10(P0). L12(P1)-stalk is involved in the formation of GTPase center of the ribosome and plays an important role in the ribosome interaction with translation factors. High mobility of this stalk puts obstacles in determination of its structure within the intact ribosome. Crystals of a two-domain N-terminal fragment of ribosomal protein L10(P0) from the archaeon Methanococcus jannaschii in complex with a specific fragment of rRNA from the same organism have been obtained. The crystals diffract X-rays at 3.2 Angstrom-Sign resolution.

Analysis of ORF 1 in European porcine reproductive and respiratory syndrome virus by long RT-PCR and restriction fragment length polymorphism (RFLP) analysis

DEFF Research Database (Denmark)

Nielsen, H. S.; Storgaard, Torben; Oleksiewicz, M.B.

2000-01-01

A rapid method was developed for partial characterization of the replicase-encoding open reading frame 1 (ORF 1) of porcine reproductive and respiratory syndrome virus (PRRSV). It comprised long RT-PCR amplification of 11.1 kb (94%) of ORF 1, followed by restriction fragment length polymorphism a...

DEMONSTRATION BY MASS-SPECTROMETRY THAT PSEUDO-HEVEIN AND HEVEIN HAVE RAGGED C-TERMINAL SEQUENCES

NARCIS (Netherlands)

SOEDJANAATMADJA, UMS; HOFSTEENGE, J; JERONIMUSSTRATINGH, CM; BRUINS, AP; BEINTEMA, JJ

1994-01-01

The primary structure of pseudo-hevein, a minor hevein component from the latex of the rubber tree, Hevea brasiliensis, was determined. Six differences with the sequence of the major hevein component were found, one of which is a replacement of tryptophan by tyrosine in the carbohydrate binding

Caspase-3-mediated cleavage of p65/RelA results in a carboxy-terminal fragment that inhibits IκBα and enhances HIV-1 replication in human T lymphocytes

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Alcamí José

2008-12-01

Full Text Available Abstract Background Degradation of p65/RelA has been involved in both the inhibition of NF-κB-dependent activity and the onset of apoptosis. However, the mechanisms of NF-κB degradation are unclear and can vary depending on the cell type. Cleavage of p65/RelA can produce an amino-terminal fragment that was shown to act as a dominant-negative inhibitor of NF-κB, thereby promoting apoptosis. However, the opposite situation has also been described and the production of a carboxy-terminal fragment that contains two potent transactivation domains has also been related to the onset of apoptosis. In this context, a carboxy-terminal fragment of p65/RelA (ΔNH2p65, detected in non-apoptotic human T lymphocytes upon activation, has been studied. T cells constitute one of the long-lived cellular reservoirs of the human immunodeficiency virus type 1 (HIV-1. Because NF-κB is the most important inducible element involved in initiation of HIV-1 transcription, an adequate control of NF-κB response is of paramount importance for both T cell survival and viral spread. Its major inhibitor IκBα constitutes a master terminator of NF-κB response that is complemented by degradation of p65/RelA. Results and conclusions In this study, the function of a caspase-3-mediated carboxy-terminal fragment of p65/RelA, which was detected in activated human peripheral blood lymphocytes (PBLs, was analyzed. Cells producing this truncated p65/RelA did not undergo apoptosis but showed a high viability, in spite of caspase-3 activation. ΔNH2p65 lacked most of DNA-binding domain but retained the dimerization domain, NLS and transactivation domains. Consequently, it could translocate to the nucleus, associate with NF-κB1/p50 and IκBα, but could not bind -κB consensus sites. However, although ΔNH2p65 lacked transcriptional activity by itself, it could increase NF-κB activity in a dose-dependent manner by hijacking IκBα. Thus, its expression resulted in a persistent

Pseudo-set framing.

Science.gov (United States)

Barasz, Kate; John, Leslie K; Keenan, Elizabeth A; Norton, Michael I

2017-10-01

Pseudo-set framing-arbitrarily grouping items or tasks together as part of an apparent "set"-motivates people to reach perceived completion points. Pseudo-set framing changes gambling choices (Study 1), effort (Studies 2 and 3), giving behavior (Field Data and Study 4), and purchase decisions (Study 5). These effects persist in the absence of any reward, when a cost must be incurred, and after participants are explicitly informed of the arbitrariness of the set. Drawing on Gestalt psychology, we develop a conceptual account that predicts what will-and will not-act as a pseudo-set, and defines the psychological process through which these pseudo-sets affect behavior: over and above typical reference points, pseudo-set framing alters perceptions of (in)completeness, making intermediate progress seem less complete. In turn, these feelings of incompleteness motivate people to persist until the pseudo-set has been fulfilled. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

MRT of scaphoid pseudo-arthrosis using Gd-DTPA. Staging and clinical correlation

International Nuclear Information System (INIS)

Vogl, T.J.; Beutel, F.; Wilhelm, K.; Tempka, A.; Schedel, H.; Haas, R.; Felix, R.

1994-01-01

During a period of two years, 134 patients with pseudo-arthrosis of the scaphoid were examined by conventional radiography and by MRI in the course of a prospective study. The aim of the study was to define radiological staging using contrast enhanced MRI in order to improve the prognostic criteria. All MRI examinations were carried out with a 1.5 Tesla scanner (SP63) using a surface coil and T 1 weighted spin echo sequences in sagittal and frontal projection and frontal FLASH T 2 -sequences and axial spin echo T 2 sequences. The T 1 weighted SE sequences in frontal projection were carried out before and after iv contrast (0.1 mmol Gd-DTPA/kg KG). All sequences were compared with conventional radiographs and the operative findings. Eight patients in stage 0 showed high signal intensity of both fragments in T 1 weighted SE sequences and at surgery there was good vascularisation. In 22 cases there was reduced signal intensity in at least one fragment (stage I). 45 patients with scaphoid pseudo-arthrosis showed complete signal loss but marked contrast uptake with still vital nuclei at surgery (stage II). In 22 patients, there was no increase in signal intensity after contrast and complete loss of vitality of the fragments at surgery. Staging was not possible in 37 patients because of previous operative intervention. The use of contrast enhanced MRI provides additional information compared with conventional radiography or plain MRI. (orig.) [de

Quark fragmentation in e+e- collisions

International Nuclear Information System (INIS)

Oddone, P.

1984-12-01

This brief review of new results in quark and gluon fragmentation observed in e + e - collisions concentrates mostly on PEP results and, within PEP, mostly on TPC results. The new PETRA results have been reported at this conference by M. Davier. It is restricted to results on light quark fragmentation since the results on heavy quark fragmentation have been reported by J. Chapman

Molecular analysis of Leptospira spp. isolated from humans by restriction fragment length polymorphism, real-time PCR and pulsed-field gel electrophoresis.

Science.gov (United States)

Turk, Nenad; Milas, Zoran; Mojcec, Vesna; Ruzic-Sabljic, Eva; Staresina, Vilim; Stritof, Zrinka; Habus, Josipa; Postic, Daniele

2009-11-01

A total of 17 Leptospira clinical strains isolated from humans in Croatia were serologically and genetically analysed. For serovar identification, the microscopic agglutination test (MAT) and pulsed-field gel electrophoresis (PFGE) were used. To identify isolates on genomic species level, PCR-based restriction fragment length polymorphism (RFLP) and real-time PCR were performed. MAT revealed the following serogroup affinities: Grippotyphosa (seven isolates), Icterohaemorrhagiae (eight isolates) and Javanica (two isolates). RFLP of PCR products from a 331-bp-long fragment of rrs (16S rRNA gene) digested with endonucleases MnlI and DdeI and real-time PCR revealed three Leptospira genomic species. Grippotyphosa isolates belonged to Leptospira kirschneri, Icterohaemorrhagiae isolates to Leptospira interrogans and Javanica isolates to Leptospira borgpetersenii. Genomic DNA from 17 leptospiral isolates was digested with NotI and SgrAI restriction enzymes and analysed by PFGE. Results showed that seven isolates have the same binding pattern to serovar Grippotyphosa, eight isolates to serovar Icterohaemorrhagiae and two isolates to serovar Poi. Results demonstrate the diversity of leptospires circulating in Croatia. We point out the usefulness of a combination of PFGE, RFLP and real-time PCR as appropriate molecular methods in molecular analysis of leptospires.

The isolation and localization of arbitrary restriction fragment length polymorphisms in Southern African populations

International Nuclear Information System (INIS)

Conn, V.

1987-01-01

The main aim of this study was to contribute to the mapping of the human genome by searching for and characterizing a number of RFLPs (restriction fragment length polymorphisms) in the human genome. The more specific aims of this study were: 1. To isolate single-copy human DNA sequences from a human genomic library. 2. To use these single-copy sequences as DNA probes to search for polymorphic variation among Caucasoid individuals. 3. To show by means of family studies that the RFLPs were inherited in a co-dominant Mendelian fashion. 4. To determine the population frequencies of these RFLPs in Southern African Populations, namely the Bantu-speaking Negroids and the San. 5. To assign these RFLP-detecting DNA sequences to human chromosomes using somatic cell hybrid lines. In this study DNA was labelled with Phosphorus 32

Identification of an N-terminal 27 kDa fragment of Mycoplasma pneumoniae P116 protein as specific immunogen in M. pneumoniae infections

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Chourasia Bishwanath

2010-12-01

Full Text Available Abstract Background Mycoplasma pneumoniae is an important cause of respiratory tract infection and is increasingly being associated with other diseases such as asthma and extra-pulmonary complications. Considerable cross-reactivity is known to exist between the whole cell antigens used in the commercial serological testing assays. Identification of specific antigens is important to eliminate the risk of cross-reactions among different related organisms. Adherence of M. pneumoniae to human epithelial cells is mediated through a well defined apical organelle to which a number of proteins such as P1, P30, P116 and HMW1-3 have been localized, and are being investigated for adhesion, gliding and immunodiagnostic purposes. Methods A 609 bp fragment P116(N-27, corresponding to the N-terminal region of M. pneumoniae P116 gene was cloned and expressed. A C-terminal fragment P1(C-40, of P1 protein of M. pneumoniae was also expressed. Three IgM ELISA assays based on P116(N-27, P1(C-40 and (P116 (N-27 + P1(C-40 proteins were optimized and a detailed analysis comparing the reactivity of these proteins with a commercial kit was carried out. Comparative statistical analysis of these assays was performed with the SPSS version 15.0. Results The expressed P116(N-27 protein was well recognized by the patient sera and was immunogenic in rabbit. P1(C-40 of M. pneumoniae was also immunogenic in rabbit. In comparison to the reference kit, which is reported to be 100% sensitive and 75% specific, ELISA assay based on purified P116(N-27, P1(C-40 and (P116(N-27 + P1(C-40 proteins showed 90.3%, 87.1% and 96.8% sensitivity and 87.0%, 87.1% and 90.3% specificity respectively. The p value for all the three assays was found to be Conclusion This study shows that an N-terminal fragment of P116 protein holds a promise for serodiagnosis of M. pneumoniae infection. The IgM ELISA assays based on the recombinant proteins seem to be suitable for the use in serodiagnosis of acute M

The Pseudo signal peptide of the corticotropin-releasing factor receptor type 2A prevents receptor oligomerization.

Science.gov (United States)

Teichmann, Anke; Rutz, Claudia; Kreuchwig, Annika; Krause, Gerd; Wiesner, Burkhard; Schülein, Ralf

2012-08-03

N-terminal signal peptides mediate the interaction of native proteins with the translocon complex of the endoplasmic reticulum membrane and are cleaved off during early protein biogenesis. The corticotropin-releasing factor receptor type 2a (CRF(2(a))R) possesses an N-terminal pseudo signal peptide, which represents a so far unique domain within the large protein family of G protein-coupled receptors (GPCRs). In contrast to a conventional signal peptide, the pseudo signal peptide remains uncleaved and consequently forms a hydrophobic extension at the N terminus of the receptor. The functional consequence of the presence of the pseudo signal peptide is not understood. Here, we have analyzed the significance of this domain for receptor dimerization/oligomerization in detail. To this end, we took the CRF(2(a))R and the homologous corticotropin-releasing factor receptor type 1 (CRF(1)R) possessing a conventional cleaved signal peptide and conducted signal peptide exchange experiments. Using single cell and single molecule imaging methods (fluorescence resonance energy transfer and fluorescence cross-correlation spectroscopy, respectively) as well as biochemical experiments, we obtained two novel findings; we could show that (i) the CRF(2(a))R is expressed exclusively as a monomer, and (ii) the presence of the pseudo signal peptide prevents its oligomerization. Thus, we have identified a novel functional domain within the GPCR protein family, which plays a role in receptor oligomerization and which may be useful to study the functional significance of this process in general.

Restriction fragment length polymorphism (RFLP) analysis of PCR products amplified from 18S ribosomal RNA gene of Trypanosoma congolense

International Nuclear Information System (INIS)

Osanyo, A.; Majiwa, P.W.

2006-01-01

Oligonucleotide primers were designed from the conserved nucleotide sequences of 18S ribosomal RNA (18S rRNA) gene of protozoans: Trypanosoma brucei, Leishmania donovani, Triponema aequale and Lagenidium gigantum. The primers were used in polymerace chain reaction (PCR) to generate PCR products of approximately 1 Kb using genomic DNA from T. brucei and the four genotypic groups of T. congolense as template. The five PCR products so produced were digested with several restriction enzymes and hybridized to a DNA probe made from T. brucei PCR product of the same 18S rRNA gene region. Most restriction enzyme digests revealed polymorphism with respect to the location of their recognition sites on the five PCR products. The restriction fragment length polymorphism (RFLP) pattern observed indicate that the 18S rRNA gene sequences of trypanosomes: T. brucei and the four genotypes of T.congolence group are heterogeneous. The results further demonstrate that the region that was amplified can be used in specific identification of trypanosomes species and subspecies.(author)

Discrete pseudo-integrals

Czech Academy of Sciences Publication Activity Database

Mesiar, Radko; Li, J.; Pap, E.

2013-01-01

Roč. 54, č. 3 (2013), s. 357-364 ISSN 0888-613X R&D Projects: GA ČR GAP402/11/0378 Institutional support: RVO:67985556 Keywords : concave integral * pseudo-addition * pseudo-multiplication Subject RIV: BA - General Mathematics Impact factor: 1.977, year: 2013 http://library.utia.cas.cz/separaty/2013/E/mesiar-discrete pseudo-integrals.pdf

Regression analysis of censored data using pseudo-observations

DEFF Research Database (Denmark)

Parner, Erik T.; Andersen, Per Kragh

2010-01-01

We draw upon a series of articles in which a method based on pseu- dovalues is proposed for direct regression modeling of the survival function, the restricted mean, and the cumulative incidence function in competing risks with right-censored data. The models, once the pseudovalues have been...... computed, can be fit using standard generalized estimating equation software. Here we present Stata procedures for computing these pseudo-observations. An example from a bone marrow transplantation study is used to illustrate the method....

C-terminal agrin fragment is inversely related to neuromuscular fatigue in older men.

Science.gov (United States)

Stout, Jeffrey R; Fragala, Maren S; Hoffman, Jay R; Robinson, Edward H; Mccormack, William P; Townsend, Jeremy R; Jatjner, Adam R; Emerson, Nadia S; Oliveira, Leonardo P; Fukuda, David H

2015-01-01

The aim of this study was to examine the relationship between serum C-terminal agrin fragment (CAF) concentrations and neuromuscular fatigue in older adults. Twenty-two healthy older men and women volunteered for this study. Resting fasted blood samples were collected and prepared for measurement of serum CAF concentration by a commercially available ELISA kit. The onset of neuromuscular fatigue was measured by monitoring electromyographic fatigue curves from the vastus lateralis muscle using the physical working capacity at fatigue threshold (PWCFT ) test. A significant inverse correlation for men was observed between CAF and PWCFT (r = -0.602; P = 0.05), but not for women (r = 0.208; P = 0.54). After controlling for age and body mass index, significant correlations (r = -0.69; P = 0.042) remained for men, but not for women (r = 0.12; P = 0.76). These data suggest that serum CAF concentrations were significantly related to the onset of neuromuscular fatigue independent of age and BMI in men only. © 2014 Wiley Periodicals, Inc.

Comparison by restriction fragment pattern analyses and molecular characterization of some European isolates of Suid herpesvirus 1: A contribution to strain differentiation of European isolates

DEFF Research Database (Denmark)

Christensen, Laurids Siig

1988-01-01

Eleven European isolates of Suid herpesvirus type 1 (SHV-1) were compared by restriction fragment pattern analyses and Southern blot hybridization using different genomic probes. The presence of strain discriminative 4 major genome types and several subtypes as well as the molecular distinctions...

Calorie Restriction Attenuates Terminal Differentiation of Immune Cells.

Science.gov (United States)

White, Matthew J; Beaver, Charlotte M; Goodier, Martin R; Bottomley, Christian; Nielsen, Carolyn M; Wolf, Asia-Sophia F M; Boldrin, Luisa; Whitmore, Charlotte; Morgan, Jennifer; Pearce, Daniel J; Riley, Eleanor M

2016-01-01

Immune senescence is a natural consequence of aging and may contribute to frailty and loss of homeostasis in later life. Calorie restriction increases healthy life-span in C57BL/6J (but not DBA/2J) mice, but whether this is related to preservation of immune function, and how it interacts with aging, is unclear. We compared phenotypic and functional characteristics of natural killer (NK) cells and T cells, across the lifespan, of calorie-restricted (CR) and control C57BL/6 and DBA/2 mice. Calorie restriction preserves a naïve T cell phenotype and an immature NK cell phenotype as mice age. The splenic T cell populations of CR mice had higher proportions of CD11a - CD44 lo cells, lower expression of TRAIL, KLRG1, and CXCR3, and higher expression of CD127, compared to control mice. Similarly, splenic NK cells from CR mice had higher proportions of less differentiated CD11b - CD27 + cells and correspondingly lower proportions of highly differentiated CD11b + CD27 - NK cells. Within each of these subsets, cells from CR mice had higher expression of CD127, CD25, TRAIL, NKG2A/C/E, and CXCR3 and lower expression of KLRG1 and Ly49 receptors compared to controls. The effects of calorie restriction on lymphoid cell populations in lung, liver, and lymph nodes were identical to those seen in the spleen, indicating that this is a system-wide effect. The impact of calorie restriction on NK cell and T cell maturation is much more profound than the effect of aging and, indeed, calorie restriction attenuates these age-associated changes. Importantly, the effects of calorie restriction on lymphocyte maturation were more marked in C57BL/6 than in DBA/2J mice indicating that delayed lymphocyte maturation correlates with extended lifespan. These findings have implications for understanding the interaction between nutritional status, immunity, and healthy lifespan in aging populations.

Rapid identification of Campylobacter, Arcobacter, and Helicobacter isolates by PCR-restriction fragment length polymorphism analysis of the 16S rRNA gene.

Science.gov (United States)

Marshall, S M; Melito, P L; Woodward, D L; Johnson, W M; Rodgers, F G; Mulvey, M R

1999-12-01

A rapid two-step identification scheme based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 16S rRNA gene was developed in order to differentiate isolates belonging to the Campylobacter, Arcobacter, and Helicobacter genera. For 158 isolates (26 reference cultures and 132 clinical isolates), specific RFLP patterns were obtained and species were successfully identified by this assay.

PCR-Restriction Fragment Length Polymorphism for Rapid, Low-Cost Identification of Isoniazid-Resistant Mycobacterium tuberculosis▿

Science.gov (United States)

Caws, Maxine; Tho, Dau Quang; Duy, Phan Minh; Lan, Nguyen Thi Ngoc; Hoa, Dai Viet; Torok, Mili Estee; Chau, Tran Thi Hong; Van Vinh Chau, Nguyen; Chinh, Nguyen Tran; Farrar, Jeremy

2007-01-01

PCR-restriction fragment length poymorphism (PCR-RFLP) is a simple, robust technique for the rapid identification of isoniazid-resistant Mycobacterium tuberculosis. One hundred consecutive isolates from a Vietnamese tuberculosis hospital were tested by MspA1I PCR-RFLP for the detection of isoniazid-resistant katG_315 mutants. The test had a sensitivity of 80% and a specificity of 100% against conventional phenotypic drug susceptibility testing. The positive and negative predictive values were 1 and 0.86, respectively. None of the discrepant isolates had mutant katG_315 codons by sequencing. The test is cheap (less than $1.50 per test), specific, and suitable for the rapid identification of isoniazid resistance in regions with a high prevalence of katG_315 mutants among isoniazid-resistant M. tuberculosis isolates. PMID:17428939

Proximal Region of the Gene Encoding Cytadherence-Related Protein Permits Molecular Typing of Mycoplasma genitalium Clinical Strains by PCR-Restriction Fragment Length Polymorphism

Science.gov (United States)

Musatovova, Oxana; Herrera, Caleb; Baseman, Joel B.

2006-01-01

Restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified proximal region of the gene encoding cytadherence accessory protein P110 (MG192) revealed DNA sequence divergences among 54 Mycoplasma genitalium clinical strains isolated from the genitourinary tracts of women attending a sexually transmitted disease-related health clinic, plus one from the respiratory tract and one from synovial fluid. Seven of 56 (12.5%) strains exhibited RFLPs following digestion of the proximal region with restriction endonuclease MboI or RsaI, or both. No sequence variability was detected in the distal portion of the gene. PMID:16455921

Characterisation of Toxoplasma gondii isolates using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of the non-coding Toxoplasma gondii (TGR)-gene sequences

DEFF Research Database (Denmark)

Høgdall, Estrid; Vuust, Jens; Lind, Peter

2000-01-01

of using TGR gene variants as markers to distinguish among T. gondii isolates from different animals and different geographical sources. Based on the band patterns obtained by restriction fragment length polymorphism (RFLP) analysis of the polymerase chain reaction (PCR) amplified TGR sequences, the T...

Diversity of the marine picocyanobacteria Prochlorococcus and Synechococcus assessed by terminal restriction fragment length polymorphisms of 16S-23S rRNA internal transcribed spacer sequences Diversidad de las picocianobacterias marinas Prochlorococcus y Synechococcus por medio de polimorfismos de longitud de fragmentos de restricción terminal en secuencias del espaciador transcrito interno del ARNr 16S - 23S

Directory of Open Access Journals (Sweden)

PARIS LAVIN

2008-12-01

Full Text Available In order to assess the appropriateness of the use of internal transcribed spacer (ITS sequences for the study of population genetics of marine cyanobacteria, we amplified and cloned the 16S rRNA gene plus the 16S-23S ITS regions of six strains of Prochlorococcus and Synechococcus. We analyzed them by denaturing gradient gel electrophoresis (DGGE and terminal restriction fragment length polymorphisms (T-RFLP. When using the standard application of these techniques, we obtained more than one band or terminal restriction fragment (T-RF per strain or cloned sequence. Reports in literature have suggested that these anomalies can result from the formation of secondary structures. Secondary structures of the ITS sequences of Prochlorococcus and Synechococcus strains were computationally modelled at the different temperatures that were used during the polymerase chain reaction (PCR. Modelling results predicted the existence of hairpin loops that would still be present at the extensión temperature; it is likely that these loops produced incomplete and single stranded PCR products. We modified the standard T-RFLP procedure by adding the labelled ITS primer in the last two cycles of the PCR reaction; this resulted, in most cases, in only one T-RF per ribotype. Application of this technique to a natural picoplankton community in marine waters off northern Chile, showed that it was possible to identify the presence, and determine the relative abundance, of several phylogenetic lineages within the genera Prochlorococcus and Synechococcus inhabiting the euphotic zone. Phylogenetic analysis of ITS sequences obtained by cloning and sequencing DNA from the same sample confirmed the presence of the different genotypes. With the proposed modification, T-RFLP profiles should therefore be suitable for studying the diversity of natural populations of cyanobacteria, and should become an important tool to study the factors influencing the genetic structure and

Study of Particle Production and Nuclear Fragmentation in Collisions of $^{16}$O Beams with Emulsion Nuclei at 13-200 A GeV

CERN Multimedia

2002-01-01

.SK 2\\\\ \\\\ The aim of the experiment is to study, on an event by event basis, multiplicities of produced charged particles, pseudo-rapidity density distributions globally and in selected regions of pseudo-rapidity, density fluctuations, multiplicity and angular distributions of nuclear fragments and recoiling protons (30-400~A~MeV) and cross sections for production and interation of light and medium (Z=2-8) projectile fragments. \\\\ \\\\ The detectors are emulsion chambers as well as conventional emulsion stacks. The emulsion chambers consist of several layers of a plastic substrate, each coated with nuclear emulsion on both sides. Since the best measurement accuracy is obtained for the particles with the smallest emission angles, this design is especially suited for the pseudo-rapidity determination. The emulsion stacks, of both high and low sensitivity, have been exposed in the conventional way, with the beam parallel to the emulsion sheets. These stacks are used to study the fragmentation of the interaction n...

ALIS-FLP: Amplified ligation selected fragment-length polymorphism method for microbial genotyping

DEFF Research Database (Denmark)

Brillowska-Dabrowska, A.; Wianecka, M.; Dabrowski, Slawomir

2008-01-01

A DNA fingerprinting method known as ALIS-FLP (amplified ligation selected fragment-length polymorphism) has been developed for selective and specific amplification of restriction fragments from TspRI restriction endonuclease digested genomic DNA. The method is similar to AFLP, but differs...

Isolation and characterization of DNA probes from a flow-sorted human chromosome 8 library that detect restriction fragment length polymorphism (RFLP).

Science.gov (United States)

Wood, S; Starr, T V; Shukin, R J

1986-01-01

We have used a recombinant DNA library constructed from flow-sorted human chromosome 8 as a source of single-copy human probes. These probes have been screened for restriction fragment length polymorphism (RFLP) by hybridization to Southern transfers of genomic DNA from five unrelated individuals. We have detected six RFLPs distributed among four probes after screening 741 base pairs for restriction site variation. These RFLPs all behave as codominant Mendelian alleles. Two of the probes detect rare variants, while the other two detect RFLPs with PIC values of .36 and .16. Informative probes will be useful for the construction of a linkage map for chromosome 8 and for the localization of mutant alleles to this chromosome. Images Fig. 1 PMID:2879441

Antifungal properties of durancins isolated from Enterococcus durans A5-11 and of its synthetic fragments.

Science.gov (United States)

Belguesmia, Y; Choiset, Y; Rabesona, H; Baudy-Floc'h, M; Le Blay, G; Haertlé, T; Chobert, J-M

2013-04-01

The aim of this work was to study the antifungal properties of durancins isolated from Enterococcus durans A5-11 and of their chemically synthesized fragments. Enterococcus durans A5-11 is a lactic acid bacteria strain isolated from traditional Mongolian airag cheese. This strain inhibits the growth of several fungi including Fusarium culmorum, Penicillium roqueforti and Debaryomyces hansenii. It produces two bacteriocins: durancin A5-11a and durancin A5-11b, which have similar antimicrobial properties. The whole durancins A5-11a and A5-11b, as well as their N- and C-terminal fragments were synthesized, and their antifungal properties were studied. C-terminal fragments of both durancins showed stronger antifungal activities than other tested peptides. Treatment of D. hansenii LMSA2.11.003 strain with 2 mmol l(-1) of the synthetic peptides led to the loss of the membrane integrity and to several changes in the ultra-structure of the yeast cells. Chemically synthesized durancins and their synthetic fragments showed different antimicrobial properties from each other. N-terminal peptides show activities against both bacterial and fungal strains tested. C-terminal peptides have specific activities against tested fungal strain and do not show antibacterial activity. However, the C-terminal fragment enhances the activity of the N-terminal fragment in the whole bacteriocins against bacteria. © 2012 The Society for Applied Microbiology.

DNA fragmentation in spermatozoa

DEFF Research Database (Denmark)

Rex, A S; Aagaard, J.; Fedder, J

2017-01-01

Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...

Peri/nuclear localization of intact insulin-like growth factor binding protein-2 and a distinct carboxyl-terminal IGFBP-2 fragment in vivo

International Nuclear Information System (INIS)

Hoeflich, A.; Reisinger, R.; Schuett, B.S.; Elmlinger, M.W.; Russo, V.C.; Vargas, G.A.; Jehle, P.M.; Lahm, H.; Renner-Mueller, I.; Wolf, E.

2004-01-01

Insulin-like growth factor binding protein-2 (IGFBP-2) as one of the most important IGFBPs has never been assessed in the intracellular compartment in vivo. Since there is evidence for novel intracellular functions of distinct IGFBPs, we investigated the presence of IGFBP-2 inside the cell. In peri/nuclear fractions of various tissues isolated from IGFBP-2 transgenic and non-transgenic mice we were able to show the presence of intact IGFBP-2. In addition, we demonstrate the presence of a highly conserved carboxyl-terminal IGFBP-2 fragment in the peri/nuclear fraction by using different peptide-induced antibodies. In pancreatic sections, confocal microscopy revealed the presence of IGFBP-2 on the nuclear surface but not within the nucleus. Our findings suggest novel functions of intact IGFBP-2 and IGFBP-2 fragments within the cell

Perisplenic Pseudo

International Nuclear Information System (INIS)

Kim, Hyo Heon; Cho, Sin Young; Suh, Hong Kil; Kim, Ji Hyeon; Choi, Chul Soon; Lee, Eil Seong; Kang, Ik Won

1995-01-01

Perisplenic pseudo 'fluid collection' is one of the rare normal variations. Its frequency and sonographic findings for the differentiation from true perisplenic fluid collection have not been well described. Thus, we performed this study. The examination was performed with special attention to the splenic and perisplenic areas. We excluded patients with proved or suspected liver cirrhosis, pancreatic diseases,and abdominal trauma from the study population, but did not exclude the patients with chronic hepatitis and the carriers of hepatitis B virus. Of the examined 4794 patients, 8 cases showed perisplenic pseudo 'fluid collection'. Two of them were confirmed with computed tomography and liver scan, and six were inferred from the fact proved to be a part of the left lobe extension of the liver by tracing with the transducer. All cases ofperisplenic pseudo 'fluid collection' showed hypoechoic crescent area with hepatic ductal echoes. Perisplenic pseudo 'fluid collection' is very rare. The helpful findings for the differentiation from true fluid collection are the hepatic ductal echoes seen in the normal liver, proof of continuation into remained voluminous liver by tracing with the transducer. High awareness of it would prevent further unnecessary studies such as computed tomography and liver scan

A C-terminal fragment of fibulin-7 interacts with endothelial cells and inhibits their tube formation in culture.

Science.gov (United States)

de Vega, Susana; Suzuki, Nobuharu; Nonaka, Risa; Sasaki, Takako; Forcinito, Patricia; Arikawa-Hirasawa, Eri; Yamada, Yoshihiko

2014-03-01

We have previously demonstrated that fibulin-7 (Fbln7) is expressed in teeth by pre-odontoblast and odontoblast cells, localized in the basement membrane and dentin matrices, and is an adhesion molecule for dental mesenchyme cells and odontoblasts. Fbln7 is also expressed in blood vessels by endothelial cells. In this report, we show that a recombinant C-terminal Fbln7 fragment (Fbln7-C) bound to Human Umbilical Vein Endothelial Cells (HUVECs) but did not promote cell spreading and actin stress fiber formation. Fbln7-C binding to HUVECs induced integrin clustering at cell adhesion sites with other focal adhesion molecules, and sustained activation of FAK, p130Cas, and Rac1. In addition, RhoA activation was inhibited, thereby preventing HUVEC spreading. As endothelial cell spreading is an important step for angiogenesis, we examined the effect of Fbln7-C on angiogenesis using in vitro assays for endothelial cell tube formation and vessel sprouting from aortic rings. We found that Fbln7-C inhibited the HUVEC tube formation and the vessel sprouting in aortic ring assays. Our findings suggest potential anti-angiogenic activity of the Fbln7 C-terminal region. Published by Elsevier Inc.

Pst I restriction fragment length polymorphism of the human placental alkaline phosphatase gene in normal placentae and tumors

International Nuclear Information System (INIS)

Tsavaler, L.; Penhallow, R.C.; Kam, W.; Sussman, H.H.

1987-01-01

The structure of the human placental alkaline phosphatase gene from normal term placentae was studied by restriction enzyme digestion and Southern blot analysis using a cDNA probe to the gene for the placental enzyme. The DNA digests fall into three distinct patterns based on the presence and intensity of an extra 1.1-kilobase Pst I Band. The extra 1.1-kilobase band is present in 9 of 27 placenta samples, and in 1 of these samples the extra band is present at double intensity. No polymorphism was revealed by digestion with restriction enzymes EcoRI, Sma I, BamHI, or Sac I. The extra Pst I-digestion site may lie in a noncoding region of the gene because no correlation was observed between the restriction fragment length polymorphism and the common placental alkaline phosphatase alleles identified by starch gel electrophoresis. In addition, because placental alkaline phosphatase is frequently re-expressed in neoplasms, the authors examined tissue from ovarian, testicular, and endometrial tumors and from BeWo choriocarcinoma cells in culture. The Pst I-DNA digestion patterns from these cells and tissues were identical to those seen in the normal ovary and term placentae. The consistent reproducible digestion patterns seen in DNA from normal and tumor tissue indicate that a major gene rearrangement is not the basis for the ectopic expression of placental alkaline phosphatase in neoplasia

Pseudo-Riemannian Novikov algebras

Energy Technology Data Exchange (ETDEWEB)

Chen Zhiqi; Zhu Fuhai [School of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071 (China)], E-mail: chenzhiqi@nankai.edu.cn, E-mail: zhufuhai@nankai.edu.cn

2008-08-08

Novikov algebras were introduced in connection with the Poisson brackets of hydrodynamic-type and Hamiltonian operators in formal variational calculus. Pseudo-Riemannian Novikov algebras denote Novikov algebras with non-degenerate invariant symmetric bilinear forms. In this paper, we find that there is a remarkable geometry on pseudo-Riemannian Novikov algebras, and give a special class of pseudo-Riemannian Novikov algebras.

Fragmentation of percolation cluster perimeters

Science.gov (United States)

Debierre, Jean-Marc; Bradley, R. Mark

1996-05-01

We introduce a model for the fragmentation of porous random solids under the action of an external agent. In our model, the solid is represented by a bond percolation cluster on the square lattice and bonds are removed only at the external perimeter (or `hull') of the cluster. This model is shown to be related to the self-avoiding walk on the Manhattan lattice and to the disconnection events at a diffusion front. These correspondences are used to predict the leading and the first correction-to-scaling exponents for several quantities defined for hull fragmentation. Our numerical results support these predictions. In addition, the algorithm used to construct the perimeters reveals itself to be a very efficient tool for detecting subtle correlations in the pseudo-random number generator used. We present a quantitative test of two generators which supports recent results reported in more systematic studies.

Perisplenic Pseudo

Energy Technology Data Exchange (ETDEWEB)

Kim, Hyo Heon; Cho, Sin Young; Suh, Hong Kil; Kim, Ji Hyeon; Choi, Chul Soon; Lee, Eil Seong; Kang, Ik Won [Hallym University College of Medicine, Chuncheon (Korea, Republic of)

1995-12-15

Perisplenic pseudo 'fluid collection' is one of the rare normal variations. Its frequency and sonographic findings for the differentiation from true perisplenic fluid collection have not been well described. Thus, we performed this study. The examination was performed with special attention to the splenic and perisplenic areas. We excluded patients with proved or suspected liver cirrhosis, pancreatic diseases,and abdominal trauma from the study population, but did not exclude the patients with chronic hepatitis and the carriers of hepatitis B virus. Of the examined 4794 patients, 8 cases showed perisplenic pseudo 'fluid collection'. Two of them were confirmed with computed tomography and liver scan, and six were inferred from the fact proved to be a part of the left lobe extension of the liver by tracing with the transducer. All cases ofperisplenic pseudo 'fluid collection' showed hypoechoic crescent area with hepatic ductal echoes. Perisplenic pseudo 'fluid collection' is very rare. The helpful findings for the differentiation from true fluid collection are the hepatic ductal echoes seen in the normal liver, proof of continuation into remained voluminous liver by tracing with the transducer. High awareness of it would prevent further unnecessary studies such as computed tomography and liver scan

Genotypic lineages and restriction fragment length polymorphism of canine distemper virus isolates in Thailand.

Science.gov (United States)

Radtanakatikanon, Araya; Keawcharoen, Juthatip; Charoenvisal, Na Taya; Poovorawan, Yong; Prompetchara, Eakachai; Yamaguchi, Ryoji; Techangamsuwan, Somporn

2013-09-27

Canine distemper virus (CDV) is known to cause multisystemic disease in all families of terrestrial carnivores. Attenuated live vaccines have been used to control CDV in a variety of species for many decades, yet a number of CDV infections in vaccinated dogs are still observed. The aims of this study were to investigate the genetic diversity of CDV lineages based on phosphoprotein (P), hemagglutinin (H) and fusion protein (F) genes and to develop the restriction fragment length polymorphism (RFLP) technique for effective differentiation among individual wild-type and vaccine lineages in Thailand. Four commercial vaccine products, thirteen conjunctival swabs and various tissues from 9 necropsied dogs suspected of having CDV infections were included. Virus isolation was performed using Vero cell expressing canine signaling lymphocyte activation molecules (Vero-DST cells). Reverse-transcription polymerase chain reaction (RT-PCR) on 3 gene regions from the dog derived specimens and the vaccines were carried out, then RFLP analysis upon F-gene amplified fragments was developed. Nucleotide sequence and phylogenetic analysis were compared with other CDV lineages in Genbank. Phylogenetic relationships revealed that CDV field isolates were separated from the vaccine lineage and could be divided into two clusters; one of which belonged to the Asia-1 lineage and another, not related to any previous recognized lineages was proposed as 'Asia-4'. RFLP patterns demonstrating concordance with phylogenetic trees of the distemper virus allowed for differentiation between the Asia-1, Asia-4 and vaccine lineages. Thus, RFLP technique is able to effectively distinguish individual wild-type canine distemper virus from vaccine lineages in Thailand. Copyright © 2013 Elsevier B.V. All rights reserved.

Genetic identification of the main opportunistic Mucorales by PCR-restriction fragment length polymorphism.

Science.gov (United States)

Machouart, M; Larché, J; Burton, K; Collomb, J; Maurer, P; Cintrat, A; Biava, M F; Greciano, S; Kuijpers, A F A; Contet-Audonneau, N; de Hoog, G S; Gérard, A; Fortier, B

2006-03-01

Mucormycosis is a rare and opportunistic infection caused by fungi belonging to the order Mucorales. Recent reports have demonstrated an increasing incidence of mucormycosis, which is frequently lethal, especially in patients suffering from severe underlying conditions such as immunodeficiency. In addition, even though conventional mycology and histopathology assays allow for the identification of Mucorales, they often fail in offering a species-specific diagnosis. Due to the lack of other laboratory tests, a precise identification of these molds is thus notoriously difficult. In this study we aimed to develop a molecular biology tool to identify the main Mucorales involved in human pathology. A PCR strategy selectively amplifies genomic DNA from molds belonging to the genera Absidia, Mucor, Rhizopus, and Rhizomucor, excluding human DNA and DNA from other filamentous fungi and yeasts. A subsequent digestion step identified the Mucorales at genus and species level. This technique was validated using both fungal cultures and retrospective analyses of clinical samples. By enabling a rapid and precise identification of Mucorales strains in infected patients, this PCR-restriction fragment length polymorphism-based method should help clinicians to decide on the appropriate treatment, consequently decreasing the mortality of mucormycosis.

Single Cystosorus Isolate Production and Restriction Fragment Length Polymorphism Characterization of the Obligate Biotroph Spongospora subterranea f. sp. subterranea.

Science.gov (United States)

Qu, Xinshun; Christ, Barbara J

2006-10-01

ABSTRACT Spongospora subterranea f. sp. subterranea causes powdery scab in potatoes and is distributed worldwide. Genetic studies of this pathogen have been hampered due, in part, to its obligate parasitism and the lack of molecular markers for this pathogen. In this investigation, a single cystosorus inoculation technique was developed to produce large amounts of S. subterranea f. sp. subterranea plasmodia or zoosporangia in eastern black nightshade (Solanum ptycanthum) roots from which DNA was extracted. Cryopreservation of zoosporangia was used for long-term storage of the isolates. S. subterranea f. sp. subterranea-specific restriction fragment length polymorphism (RFLP) markers were developed from randomly amplified polymorphic DNA (RAPD) fragments. Cystosori of S. subterranea f. sp. subterranea were used for RAPD assays and putative pathogen-specific RAPD fragments were cloned and sequenced. The fragments were screened for specificity by Southern hybridization and subsequent DNA sequence BLAST search. Four polymorphic S. subterranea f. sp. subterranea-specific probes containing repetitive elements, and one containing single copy DNA were identified. These RFLP probes were then used to analyze 24 single cystosorus isolates derived from eight geographic locations in the United States and Canada. Genetic variation was recorded among, but not within, geographic locations. Cluster analysis separated the isolates into two major groups: group I included isolates originating from western North America, with the exception of those from Colorado, and group II included isolates originating from eastern North America and from Colorado. The techniques developed in this study, i.e., production of single cystosorus isolates of S. subterranea f. sp. subterranea and development of RFLP markers for this pathogen, provide methods to further study the genetic structure of S. subterranea f. sp. subterranea.

Conformal maps between pseudo-Finsler spaces

Science.gov (United States)

Voicu, Nicoleta

The paper aims to initiate a systematic study of conformal mappings between Finsler spacetimes and, more generally, between pseudo-Finsler spaces. This is done by extending several results in pseudo-Riemannian geometry which are necessary for field-theoretical applications and by proposing a technique that reduces some problems involving pseudo-Finslerian conformal vector fields to their pseudo-Riemannian counterparts. Also, we point out, by constructing classes of examples, that conformal groups of flat (locally Minkowskian) pseudo-Finsler spaces can be much richer than both flat Finslerian and pseudo-Euclidean conformal groups.

Lack of a 5.9 kDa peptide C-terminal fragment of fibrinogen α chain precedes fibrosis progression in patients with liver disease.

Directory of Open Access Journals (Sweden)

Santiago Marfà

Full Text Available Early detection of fibrosis progression is of major relevance for the diagnosis and management of patients with liver disease. This study was designed to find non-invasive biomarkers for fibrosis in a clinical context where this process occurs rapidly, HCV-positive patients who underwent liver transplantation (LT. We analyzed 93 LT patients with HCV recurrence, 41 non-LT patients with liver disease showing a fibrosis stage F≥1 and 9 patients without HCV recurrence who received antiviral treatment before LT, as control group. Blood obtained from 16 healthy subjects was also analyzed. Serum samples were fractionated by ion exchange chromatography and their proteomic profile was analyzed by SELDI-TOF-MS. Characterization of the peptide of interest was performed by ion chromatography and electrophoresis, followed by tandem mass spectrometry identification. Marked differences were observed between the serum proteome profile of LT patients with early fibrosis recurrence and non-recurrent LT patients. A robust peak intensity located at 5905 m/z was the distinguishing feature of non-recurrent LT patients. However, the same peak was barely detected in recurrent LT patients. Similar results were found when comparing samples of healthy subjects with those of non-LT fibrotic patients, indicating that our findings were not related to either LT or HCV infection. Using tandem mass-spectrometry, we identified the protein peak as a C-terminal fragment of the fibrinogen α chain. Cell culture experiments demonstrated that TGF-β reduces α-fibrinogen mRNA expression and 5905 m/z peak intensity in HepG2 cells, suggesting that TGF-β activity regulates the circulating levels of this protein fragment. In conclusion, we identified a 5.9 kDa C-terminal fragment of the fibrinogen α chain as an early serum biomarker of fibrogenic processes in patients with liver disease.

Clustering of Beijing genotype Mycobacterium tuberculosis isolates from the Mekong delta in Vietnam on the basis of variable number of tandem repeat versus restriction fragment length polymorphism typing.

NARCIS (Netherlands)

Huyen, M.N.; Kremer, K.; Lan, N.T.; Buu, T.N.; Cobelens, F.G.; Tiemersma, E.W.; Haas, P. de; Soolingen, D. van

2013-01-01

BACKGROUND: In comparison to restriction fragment length polymorphism (RFLP) typing, variable number of tandem repeat (VNTR) typing is easier to perform, faster and yields results in a simple, numerical format. Therefore, this technique has gained recognition as the new international gold standard

A 19-kDa C-terminal tryptic fragment of the α chain of Na/K-ATPase is essential for occlusion and transport of cations

International Nuclear Information System (INIS)

Karlish, S.J.D.; Goldshleger, R.; Stein, W.D.

1990-01-01

Tryptic digestion of pig renal Na/K-ATPase in the presence of Rb and absence of Ca ions removes about half of the protein but leaves a stable 19-kDa membrane-embedded fragment derived from the α chain, a largely intact β chain, and essentially normal Rb- and Na-occlusion capacity. Subsequent digestion with trypsin in the presence of Ca or absence of Rb ions leads to rapid loss of the 19-kDa fragment and a parallel loss of Rb occlusion, demonstrating that the fragment is essential for occlusion. The N-terminal sequence of the 19-kDa fragment is Asn-Pro-Lys-Thr-Asp-Lys-Leu-Val-Asn-Glu-Arg-Leu-Ile-Ser-Met-Ala, beginning at residue 830 and extending toward the C terminus. Membranes containing the 19-kDa fragment have the following functional properties. (i) ATP-dependent functions are absent. (ii) The apparent affinity for occluding Rb is unchanged, the affinity for Na is lower than in the control enzyme, and activation is now strongly sigmoidal rather than hyperbolic. (iii) Membranes containing the 19-kDa fragment can be reconstituted into phospholipid vesicles and sustain slow Rb-Rb exchange. Thus the transport pathway is retained. The authors conclude that cation occlusion sites and the transport pathway within transmembrane segments are quite separate from the ATP binding sites, located on the cytoplasmic domain of the α chain. Interactions between cation and ATP sites, the heart of active transport, must be indirect - mediated, presumably, by conformational changes of the protein

A 19-kDa C-terminal tryptic fragment of the. alpha. chain of Na/K-ATPase is essential for occlusion and transport of cations

Energy Technology Data Exchange (ETDEWEB)

Karlish, S.J.D.; Goldshleger, R. (Weizmann Institute of Science, Rehovot (Israel)); Stein, W.D. (Hebrew Univ. Jerusalem (Israel))

1990-06-01

Tryptic digestion of pig renal Na/K-ATPase in the presence of Rb and absence of Ca ions removes about half of the protein but leaves a stable 19-kDa membrane-embedded fragment derived from the {alpha} chain, a largely intact {beta} chain, and essentially normal Rb- and Na-occlusion capacity. Subsequent digestion with trypsin in the presence of Ca or absence of Rb ions leads to rapid loss of the 19-kDa fragment and a parallel loss of Rb occlusion, demonstrating that the fragment is essential for occlusion. The N-terminal sequence of the 19-kDa fragment is Asn-Pro-Lys-Thr-Asp-Lys-Leu-Val-Asn-Glu-Arg-Leu-Ile-Ser-Met-Ala, beginning at residue 830 and extending toward the C terminus. Membranes containing the 19-kDa fragment have the following functional properties. (i) ATP-dependent functions are absent. (ii) The apparent affinity for occluding Rb is unchanged, the affinity for Na is lower than in the control enzyme, and activation is now strongly sigmoidal rather than hyperbolic. (iii) Membranes containing the 19-kDa fragment can be reconstituted into phospholipid vesicles and sustain slow Rb-Rb exchange. Thus the transport pathway is retained. The authors conclude that cation occlusion sites and the transport pathway within transmembrane segments are quite separate from the ATP binding sites, located on the cytoplasmic domain of the {alpha} chain. Interactions between cation and ATP sites, the heart of active transport, must be indirect - mediated, presumably, by conformational changes of the protein.

Clustering of Beijing genotype Mycobacterium tuberculosis isolates from the Mekong delta in Vietnam on the basis of variable number of tandem repeat versus restriction fragment length polymorphism typing

NARCIS (Netherlands)

Huyen, Mai N. T.; Kremer, Kristin; Lan, Nguyen T. N.; Buu, Tran N.; Cobelens, Frank G. J.; Tiemersma, Edine W.; de Haas, Petra; van Soolingen, Dick

2013-01-01

In comparison to restriction fragment length polymorphism (RFLP) typing, variable number of tandem repeat (VNTR) typing is easier to perform, faster and yields results in a simple, numerical format. Therefore, this technique has gained recognition as the new international gold standard in typing of

Molecular Characterization of Yeast Strains Isolated from Different Sources by Restriction Fragment Length Polymorphism

International Nuclear Information System (INIS)

Ali, M. S.; Latif, Z.

2016-01-01

Various molecular techniques like analysis of the amplified rDNA internal transcribed spacers (ITS), intragenic spacers and total ITS region analysis by restriction fragment length polymorphism (RFLP) has been introduced for yeast identification but there are limited databases to identify yeast species on the basis of 5.8S rDNA. In this study, twenty nine yeast strains from various sources including spoiled fruits, vegetables, foodstuffs, and concentrated juices were characterized by PCR-RFLP. PCR-RFLP has been used to characterize yeasts present in different spoiled food samples after isolation of the yeasts. By using this technique, the isolated yeast strains were characterized by direct 5.8S-ITS rDNA region amplification. RFLP analysis was applied to each of the amplification products (varied from 400bp to 800bp) detected, and the corresponding yeast identifications were made according to each specific restriction patterns obtained after treatment with two endonucleases TaqI and HaeIII which yielded a specific banding pattern for each species. For further confirmation amplified products of eleven selected isolates were sequenced and blast on NCBI. Both RFLP and sequence analyses of the strains with accession nos. KF472163, KF472164, KF472165, KF472166, KF472167, KF472168, KF472169, KF472170, KF472171, KF472172, KF472173 gave significantly similar results. The isolates were found to belong five different yeast species including; Candida spp., Pichia spp., Kluyveromyces spp., Clavispora spp. and Hanseniaspora spp. This method provides a fast, easy, reliable and authentic way for determining yeast population present in different type of samples, as compared to traditional characterization technique. (author)

THE PSEUDO-SMARANDACHE FUNCTION

OpenAIRE

David Gorski

2007-01-01

The Pseudo-Smarandache Function is part of number theory. The function comes from the Smarandache Function. The Pseudo-Smarandache Function is represented by Z(n) where n represents any natural number.

Distinguishing Heterodera filipjevi and H. avenae using polymerase chain reaction-restriction fragment length polymorphism and cyst morphology.

Science.gov (United States)

Yan, Guiping; Smiley, Richard W

2010-03-01

The cereal cyst nematodes Heterodera filipjevi and H. avenae impede wheat production in the Pacific Northwest (PNW). Accurate identification of cyst nematode species and awareness of high population density in affected fields are essential for designing effective control measures. Morphological methods for differentiating these species are laborious. These species were differentiated using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) of internal transcribed spacer (ITS)-ribosomal (r)DNA with up to six restriction endonucleases (TaqI, HinfI, PstI, HaeIII, RsaI, and AluI). The method was validated by inspecting underbridge structures of cyst vulval cones. Grid soil sampling of an Oregon field infested by both species revealed that H. filipjevi was present at most of the infested grid sites but mixtures of H. avenae and H. filipjevi also occurred. These procedures also detected and differentiated H. filipjevi and H. avenae in soil samples from nearby fields in Oregon and H. avenae in samples from Idaho and Washington. Intraspecific polymorphism was not observed within H. filipjevi or PNW H. avenae populations based on the ITS-rDNA. However, intraspecific variation was observed between H. avenae populations occurring in the PNW and France. Methods described here will improve detection and identification efficiencies for cereal cyst nematodes in wheat fields.

Dangerous relations in the Arctic marine food web: Interactions between toxin producing Pseudo-nitzschia diatoms and Calanus copepodites

DEFF Research Database (Denmark)

Hardardottir, Sara; Pancic, Marina; Tammilehto, Anna

2015-01-01

Diatoms of the genus Pseudo-nitzschia produce domoic acid (DA), a toxin that is vectored in the marine food web, thus causing serious problems for marine organisms and humans. In spite of this, knowledge of interactions between grazing zooplankton and diatoms is restricted. In this study, we...... examined the interactions between Calanus copepodites and toxin producing Pseudo-nitzschia. The copepodites were fed with different concentrations of toxic P. seriata and a strain of P. obtusa that previously was tested to be non-toxic. The ingestion rates did not differ among the diets (P. seriata, P...

Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments

DEFF Research Database (Denmark)

Priemé, Anders; Wolsing, Martin

2004-01-01

Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kg N ha-1 year-1) and cattle manure (75 and 150 kg N ha-1 year-1) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified...... nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed...... a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different...

Comparative study of IS6110 restriction fragment length polymorphism and variable-number tandem-repeat typing of Mycobacterium tuberculosis isolates in the Netherlands, based on a 5-year nationwide survey

NARCIS (Netherlands)

de Beer, Jessica L.; van Ingen, Jakko; de Vries, Gerard; Erkens, Connie; Sebek, Maruschka; Mulder, Arnout; Sloot, Rosa; van den Brandt, Anne-Marie; Enaimi, Mimount; Kremer, Kristin; Supply, Philip; van Soolingen, Dick

2013-01-01

In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a

Comparative Study of IS6110 Restriction Fragment Length Polymorphism and Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Isolates in the Netherlands, Based on a 5-Year Nationwide Survey

NARCIS (Netherlands)

Beer, J.L. de; Ingen, J. van; Vries, G. de; Erkens, C.; Sebek, M.; Mulder, A.; Sloot, R.; Brandt, A.M. van den; Enaimi, M.; Kremer, K.; Supply, P.; Soolingen, D. van

2013-01-01

In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a

Algebra of pseudo-differential C*-operators

International Nuclear Information System (INIS)

Mohammad, N.

1987-11-01

In this paper the algebra of pseudo-differential operators is studied in the framework of C * -algebras. It is proved that every pseudo-differential operator of order m admits an adjoint operator, in this case, which is again a pseudo-differential operator. Consequently, the space of all pseudo-differential operators on a compact manifold is an involutive algebra. 10 refs

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments.

Science.gov (United States)

Harvey, David J; Seabright, Gemma E; Vasiljevic, Snezana; Crispin, Max; Struwe, Weston B

2018-05-01

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man 8 GlcNAc 2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. Graphical Abstract ᅟ.

Pseudo-Haptic Feedback in Teleoperation.

Science.gov (United States)

Neupert, Carsten; Matich, Sebastian; Scherping, Nick; Kupnik, Mario; Werthschutzky, Roland; Hatzfeld, Christian

2016-01-01

In this paper, we develop possible realizations of pseudo-haptic feedback in teleoperation systems based on existing works for pseudo-haptic feedback in virtual reality and the intended applications. We derive four potential factors affecting the performance of haptic feedback (calculation operator, maximum displacement, offset force, and scaling factor), which are analyzed in three compliance identification experiments. First, we analyze the principle usability of pseudo-haptic feedback by comparing information transfer measures for teleoperation and direct interaction. Pseudo-haptic interaction yields well above-chance performance, while direct interaction performs almost perfectly. In order to optimize pseudo-haptic feedback, in the second study we perform a full-factorial experimental design with 36 subjects performing 6,480 trials with 36 different treatments. Information transfer ranges from 0.68 bit to 1.72 bit in a task with a theoretical maximum of 2.6 bit, with a predominant effect of the calculation operator and a minor effect of the maximum displacement. In a third study, short- and long-term learning effects are analyzed. Learning effects regarding the performance of pseudo-haptic feedback cannot be observed for single-day experiments. Tests over 10 days show a maximum increase in information transfer of 0.8 bit. The results show the feasibility of pseudo-haptic feedback for teleoperation and can be used as design basis for task-specific systems.

Restricted N-terminal truncation of cardiac troponin T: a novel mechanism for functional adaptation to energetic crisis.

Science.gov (United States)

Feng, Han-Zhong; Biesiadecki, Brandon J; Yu, Zhi-Bin; Hossain, M Moazzem; Jin, J-P

2008-07-15

The N-terminal variable region of cardiac troponin T (TnT) is a regulatory structure that can be selectively removed during myocardial ischaemia reperfusion by mu-calpain proteolysis. Here we investigated the pathophysiological significance of this post-translational modification that removes amino acids 1-71 of cardiac TnT. Working heart preparations were employed to study rat acute myocardial infarction and transgenic mouse hearts over-expressing the N-terminal truncated cardiac TnT (cTnT-ND). Ex vivo myocardial infarction by ligation of the left anterior descending coronary artery induced heart failure and produced cTnT-ND not only in the infarct but also in remote zones, including the right ventricular free wall, indicating a whole organ response in the absence of systemic neurohumoral mechanisms. Left ventricular pressure overload in mouse working hearts produced increased cTnT-ND in both ventricles, suggesting a role of haemodynamic stress in triggering an acute whole organ proteolytic regulation. Transgenic mouse hearts in which the endogenous intact cardiac TnT was partially replaced by cTnT-ND showed lowered contractile velocity. When afterload increased from 55 mmHg to 90 mmHg, stroke volume decreased in the wild type but not in the transgenic mouse hearts. Correspondingly, the left ventricular rapid-ejection time of the transgenic mouse hearts was significantly longer than that of wild type hearts, especially at high afterload. The restricted deletion of the N-terminal variable region of cardiac troponin T demonstrates a novel mechanism by which the thin filament regulation adapts to sustain cardiac function under stress conditions.

Restricted fragmentation of poliovirus type 1, 2, and 3 RNAs by ribonuclease III

Energy Technology Data Exchange (ETDEWEB)

Nomoto, A. (State Univ. of New York, Stony Brook); Lee, Y.F.; Babich, A.; Jacobson, A.; Dunn, J.J.; Wimmer, E.

1979-01-01

Cleavage of the genome RNAs of poliovirus type 1, 2, and 3 with the ribonuclease III of Escherichia coli has been investigated with the following results: (1) at or above physiological salt concentration, the RNAs are completely resistant to the action of the enzyme, an observation suggesting that the RNAs lack primary cleavage sites; (2) lowering the salt concentration to 0.1 M or below allows RNase III to cleave the RNAs at secondary sites. Both large and small fragments can be obtained in a reproducible manner depending on salt conditions chosen for cleavage. Fingerprints of three large fragments of poliovirus type 2 RNA show that they originate from unique segments and represent most if not all sequences of the genome. Based upon binding to poly(U) filters of poly(A)-linked fragments, a physical map of the large fragments of poliovirus type 2 RNA was constructed. The data suggest that RNase III cleavage of single-stranded RNA provides a useful method to fragment the RNA for further studies.

Allelic sequence variations in the hypervariable region of a T-cell receptor β chain: Correlation with restriction fragment length polymorphism in human families and populations

International Nuclear Information System (INIS)

Robinson, M.A.

1989-01-01

Direct sequence analysis of the human T-cell antigen receptor (TCR) V β1 variable gene identified a single base-pair allelic variation (C/G) located within the coding region. This change results in substitution of a histidine (CAC) for a glutamine (CAG) at position 48 of the TCR β chain, a position predicted to be in the TCR antigen binding site. The V β1 polymorphism was found by DNA sequence analysis of V β1 genes from seven unrelated individuals; V β1 genes were amplified by the polymerase chain reaction, the amplified fragments were cloned into M13 phage vectors, and sequences were determined. To determined the inheritance patterns of the V β1 substitution and to test correlation with V β1 restriction fragment length polymorphism detected with Pvu II and Taq I, allele-specific oligonucleotides were constructed and used to characterize amplified DNA samples. Seventy unrelated individuals and six families were tested for both restriction fragment length polymorphism and for the V β1 substitution. The correlation was also tested using amplified, size-selected, Pvu II- and Taq I-digested DNA samples from heterozygotes. Pvu II allele 1 (61/70) and Taq I allele 1 (66/70) were found to be correlated with the substitution giving rise to a histidine at position 48. Because there are exceptions to the correlation, the use of specific probes to characterize allelic forms of TCR variable genes will provide important tools for studies of basic TCR genetics and disease associations

Pseudo-color processing in nuclear medical image

International Nuclear Information System (INIS)

Wang Zhiqian; Jin Yongjie

1992-01-01

The application of pseudo-color technology in nuclear medical image processing is discussed. It includes selection of the number of pseudo-colors, method of realizing pseudo-color transformation, function of pseudo-color transformation and operation on the function

Molecular identification of Giardia duodenalis in Ecuador by polymerase chain reaction-restriction fragment length polymorphism

Directory of Open Access Journals (Sweden)

Richard Atherton

2013-06-01

Full Text Available The aim of this study was to determine the genetic diversity of Giardia duodenalis present in a human population living in a northern Ecuadorian rain forest. All Giardia positive samples (based on an ELISA assay were analysed using a semi-nested polymerase chain reaction-restriction fragment length polymorphism assay that targets the glutamate dehydrogenase (gdh gene; those amplified were subsequently genotyped using NlaIV and RsaI enzymes. The gdh gene was successfully amplified in 74 of 154 ELISA positive samples; 69 of the 74 samples were subsequently genotyped. Of these 69 samples, 42 (61% were classified as assemblage B (26 as BIII and 16 as BIV, 22 (32% as assemblage A (3 as AI and 19 as AII and five (7% as mixed AII and BIII types. In this study site we observe similar diversity in genotypes to other regions in Latin America, though in contrast to some previous studies, we found similar levels of diarrheal symptoms in those individuals infected with assemblage B compared with those infected with assemblage A.

Estados de pseudo-Cushing

OpenAIRE

Romanholi, Daniella J.P.C.; Salgado, Luiz Roberto

2007-01-01

Síndromes de pseudo-Cushing são um grupo heterogêneo de doenças, incluindo alcoolismo, anorexia nervosa, obesidade visceral e depressão, que compartilham muitas das características clínicas e bioquímicas da síndrome de Cushing. Os mecanismos responsáveis para a gênese da síndrome de pseudo-Cushing são fracamente compreendidos. Tem sido sugerido que o hipercortisolismo da síndrome de pseudo-Cushing pode ser resultante do aumento da secreção do hormônio liberador de corticotrofina (CRH) hipotal...

Yeast two-hybrid screening of proteins interacting with plasmin receptor subunit: C-terminal fragment of annexin A2.

Science.gov (United States)

Li, Qun; Laumonnier, Yves; Syrovets, Tatiana; Simmet, Thomas

2011-11-01

To identify proteins that interact with the C-terminal fragment of annexin A2 (A2IC), generated by plasmin cleavage of the plasmin receptor, a heterotetramer (AA2t) containing annexin A2. The gene that encodes the A2IC fragment was obtained from PCR-amplified cDNA isolated from human monocytes, and was ligated into the pBTM116 vector using a DNA ligation kit. The resultant plasmid (pBTM116-A2IC) was sequenced with an ABI PRISM 310 Genetic Analyzer. The expression of an A2IC bait protein fused with a LexA-DNA binding domain (BD) was determined using Western blot analysis. The identification of proteins that interact with A2IC and are encoded in a human monocyte cDNA library was performed using yeast two-hybrid screening. The DNA sequences of the relevant cDNAs were determined using an ABI PRISM BigDye terminator cycle sequencing ready reaction kit. Nucleotide sequence databases were searched for homologous sequences using BLAST search analysis (http://www.ncbi.nlm.nih.gov). Confirmation of the interaction between the protein LexA-A2IC and each of cathepsin S and SNX17 was conducted using a small-scale yeast transformation and X-gal assay. The yeast transformed with plasmids encoding the bait proteins were screened with a human monocyte cDNA library by reconstituting full-length transcription factors containing the GAL4-active domain (GAL4-AD) as the prey in a yeast two-hybrid approach. After screening 1×10(7) clones, 23 independent β-Gal-positive clones were identified. Sequence analysis and a database search revealed that 15 of these positive clones matched eight different proteins (SNX17, ProCathepsin S, RPS2, ZBTB4, OGDH, CCDC32, PAPD4, and actin which was already known to interact with annexin A2). A2IC A2IC interacts with various proteins to form protein complexes, which may contribute to the molecular mechanism of monocyte activation induced by plasmin. The yeast two-hybrid system is an efficient approach for investigating protein interactions.

Comparison of CHROMagar, polymerase chain reaction-restriction fragment length polymorphism, and polymerase chain reaction-fragment size for the identification of Candida species.

Science.gov (United States)

Jafari, Zahra; Motamedi, Marjan; Jalalizand, Nilufar; Shokoohi, Gholam R; Charsizadeh, Arezu; Mirhendi, Hossein

2017-09-01

The epidemiological alteration in the distribution of Candida species, as well as the significantly increasing trend of either intrinsic or acquired resistance of some of these fungi highlights the need for a reliable method for the identification of the species. Polymerase chain reaction (PCR) is one of the methods facilitating the quick and precise identification of Candida species. The aim of this study was to compare the efficiency of CHROMagar, PCR-restriction fragment length polymorphism (PCR-RFLP), and PCR-fragment size polymorphism (PCR-FSP) assays in the identification of Candida species to determine the benefits and limitations of these methods. This study was conducted on 107 Candida strains, including 20 standard strains and 87 clinical isolates. The identification of the isolates was accomplished by using CHROMagar as a conventional method. The PCR-RFLP assay was performed on the entire internal transcribed spacer (ITS) region of ribosomal DNA (rDNA), and the consequent enzymatic digestion was compared with PCR-FSP results in which ITS1 and ITS2 regions were separately PCR amplified. In both molecular assays, yeast identification was carried out through the specific electrophoretic profiles of the PCR products. According to the results, the utilization of CHROMagar resulted in the identification of 29 (33.3%) Candida isolates, while the PCR-RFLP and PCR-FSP facilitated the identification of 83 (95.4%) and 80 (91.9%) clinical isolates, respectively. The obtained concordances between CHROMagar and PCR-RFLP, between CHROMagar and PCR-FSP, as well as between PCR-RFLP and PCR-FSP were 0.23, 0.20, and 0.77, respectively. The recognition of the benefits and limitations of PCR methods allows for the selection of the most efficient technique for a fast and correct differentiation. The PCR-RFLP and PCR-FSP assays had satisfactory concordance. The PCR-FSP provides a rapid, technically simple, and cost-effective method for the identification of Candida species

Heavy quark fragmentation functions for D-wave quarkonium and charmed beauty mesons

International Nuclear Information System (INIS)

Cheung, K.; Yuan, T.C.

1995-09-01

At the large transverse momentum region, the production of heavy-heavy bound-states such as charmonium, bottomonium, and anti bc mesons in high energy e + e - and hadronic collisions is dominated by parton fragmentation. The authors calculate the heavy quark fragmentation functions into the D-wave quarkonium and anti bc mesons to leading order in the strong coupling constant and in the non-relativistic expansion. In the anti bc meson case, one set of its D-wave states is expected to lie below the open flavor threshold. The total fragmentation probability for a anti b antiquark to split into the D-wave anti bc mesons is about 2 x 10 -5 , which implies that only 2% of the total pseudo-scalar ground state B c comes from the cascades of these orbitally excited states

Minimal groundwater leakage restricts salinity in a hydrologically terminal basin of northwest Australia

Science.gov (United States)

Skrzypek, Grzegorz; Dogramaci, Shawan; Rouillard, Alexandra; Grierson, Pauline

2016-04-01

The Fortescue Marsh (FM) is one of the largest wetlands of arid northwest Australia (~1200 km2) and is thought to act as a terminal basin for the Upper Fortescue River catchment. Unlike the playa lake systems that predominate in most arid regions, where salinity is driven by inflow and evaporation of groundwater, the hydrological regime of the FM is driven by inundation from irregular cyclonic events [1]. Surface water of the FM is fresh to brackish and the salinity of the deepest groundwater (80 m b.g.l.) does not exceed 160 g/L; salt efflorescences are rarely present on the surface [2]. In this study, we tested the hypothesis that persistent but low rates of groundwater outflow have restricted the accumulation of salt in the FM over time. Using hydrological, hydrochemical data and dimensionless time evaporation modelling along with the water and salt budget, we calculated the time and the annual groundwater discharge volume that would be required to achieve and maintain the range of salinity levels observed in the Marsh. Groundwater outflow from alluvial and colluvial aquifers to the Lower Fortescue catchment is limited by an extremely low hydraulic gradient of 0.001 and is restricted to a relatively small 'alluvial window' of 0.35 km2 because of the elevation of the basement bedrock at the Marsh outflow. We show that if the Marsh was 100% "leakage free" i.e., a true terminal basin for the Upper Fortescue Catchment, the basin water would have achieved salt saturation after ~45 ka. This is not the case and only a very small outflow of saline groundwater of water volume) is needed to maintain the current salinity conditions. The minimum time required to develop the current hydrochemical composition of the water in the Marsh and the steady-state conditions for salt concentration is between 58 and 164 ka. This is a minimum age of the Marsh but it can be much older as nearly steady-state conditions could be maintained infinitely. Our approach using a combined water

Structure of the Escherichia coli RNA polymerase α subunit C-terminal domain

International Nuclear Information System (INIS)

Lara-González, Samuel; Birktoft, Jens J.; Lawson, Catherine L.

2010-01-01

The crystal structure of the dimethyllysine derivative of the E. coli RNA polymerase α subunit C-terminal domain is reported at 2.0 Å resolution. The α subunit C-terminal domain (αCTD) of RNA polymerase (RNAP) is a key element in transcription activation in Escherichia coli, possessing determinants responsible for the interaction of RNAP with DNA and with transcription factors. Here, the crystal structure of E. coli αCTD (α subunit residues 245–329) determined to 2.0 Å resolution is reported. Crystals were obtained after reductive methylation of the recombinantly expressed domain. The crystals belonged to space group P2 1 and possessed both pseudo-translational symmetry and pseudo-merohedral twinning. The refined coordinate model (R factor = 0.193, R free = 0.236) has improved geometry compared with prior lower resolution determinations of the αCTD structure [Jeon et al. (1995 ▶), Science, 270, 1495–1497; Benoff et al. (2002 ▶), Science, 297, 1562–1566]. An extensive dimerization interface formed primarily by N- and C-terminal residues is also observed. The new coordinates will facilitate the improved modeling of αCTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction

Restriction fragment polymorphism (RFLP) of a "new" HLA-DP specificity, CDP-HEI

DEFF Research Database (Denmark)

Hyldig-Nielsen, J J; Ødum, Niels; Morling, Niels

1988-01-01

Southern blotting with a DP beta cDNA probe of MspI digested DNA from 83 healthy unrelated individuals revealed a 1.8 kb fragment present in all four individuals (and no others) possessing the newly determined DP specificity, CDP-HEI.......Southern blotting with a DP beta cDNA probe of MspI digested DNA from 83 healthy unrelated individuals revealed a 1.8 kb fragment present in all four individuals (and no others) possessing the newly determined DP specificity, CDP-HEI....

Sortilin Fragments Deposit at Senile Plaques in Human Cerebrum

Directory of Open Access Journals (Sweden)

Xia Hu

2017-06-01

Full Text Available Genetic variations in the vacuolar protein sorting 10 protein (Vps10p family have been linked to Alzheimer’s disease (AD. Here we demonstrate deposition of fragments from the Vps10p member sortilin at senile plaques (SPs in aged and AD human cerebrum. Sortilin changes were characterized in postmortem brains with antibodies against the extracellular and intracellular C-terminal domains. The two antibodies exhibited identical labeling in normal human cerebrum, occurring in the somata and dendrites of cortical and hippocampal neurons. The C-terminal antibody also marked extracellular lesions in some aged and all AD cases, appearing as isolated fibrils, mini-plaques, dense-packing or circular mature-looking plaques. Sortilin and β-amyloid (Aβ deposition were correlated overtly in a region/lamina- and case-dependent manner as analyzed in the temporal lobe structures, with co-localized immunofluorescence seen at individual SPs. However, sortilin deposition rarely occurred around the pia, at vascular wall or in areas with typical diffuse Aβ deposition, with the labeling not enhanced by section pretreatment with heating or formic acid. Levels of a major sortilin fragment ~15 kDa, predicted to derive from the C-terminal region, were dramatically elevated in AD relative to control cortical lysates. Thus, sortilin fragments are a prominent constituent of the extracellularly deposited protein products at SPs in human cerebrum.

Generation of the beta-amyloid peptide and the amyloid precursor protein C-terminal fragment gamma are potentiated by FE65L1.

Science.gov (United States)

Chang, Yang; Tesco, Giuseppina; Jeong, William J; Lindsley, Loren; Eckman, Elizabeth A; Eckman, Christopher B; Tanzi, Rudolph E; Guénette, Suzanne Y

2003-12-19

Members of the FE65 family of adaptor proteins, FE65, FE65L1, and FE65L2, bind the C-terminal region of the amyloid precursor protein (APP). Overexpression of FE65 and FE65L1 was previously reported to increase the levels of alpha-secretase-derived APP (APPs alpha). Increased beta-amyloid (A beta) generation was also observed in cells showing the FE65-dependent increase in APPs alpha. To understand the mechanism for the observed increase in both A beta and APPs alpha given that alpha-secretase cleavage of a single APP molecule precludes A beta generation, we examined the effects of FE65L1 overexpression on APP C-terminal fragments (APP CTFs). Our data show that FE65L1 potentiates gamma-secretase processing of APP CTFs, including the amyloidogenic CTF C99, accounting for the ability of FE65L1 to increase generation of APP C-terminal domain and A beta 40. The FE65L1 modulation of these processing events requires binding of FE65L1 to APP and APP CTFs and is not because of a direct effect on gamma-secretase activity, because Notch intracellular domain generation is not altered by FE65L1. Furthermore, enhanced APP CTF processing can be detected in early endosome vesicles but not in endoplasmic reticulum or Golgi membranes, suggesting that the effects of FE65L1 occur at or near the plasma membrane. Finally, although FE65L1 increases APP C-terminal domain production, it does not mediate the APP-dependent transcriptional activation observed with FE65.

Ca-C backbone fragmentation dominates in electron detachment dissociation of gas-phase polypeptide polyanions

DEFF Research Database (Denmark)

Kjeldsen, Frank; Silivra, Oleg A; Ivonin, Igor A

2005-01-01

the dissociation of oxidized radical anions [M-nH]((n-1)-*. We demonstrate that C(alpha)-C cleavages, which are otherwise rarely observed in tandem mass spectrometry, can account for most of the backbone fragmentation, with even-electron x fragments dominating over radical a* ions. Ab initio calculations at the B3...... LYP level of theory with the 6-311+G(2 p,2 d)//6-31+G(d,p) basis set suggested a unidirectional mechanism for EDD (cleavage always N-terminal to the radical site), with a*, x formation being favored over a, x* fragmentation by 74.2 kJ mol(-1). Thus, backbone C(alpha)-C bonds N-terminal to proline...

The human immunodeficiency virus-1 protein Tat and its discrete fragments evoke selective release of acetylcholine from human and rat cerebrocortical terminals through species-specific mechanisms.

Science.gov (United States)

Feligioni, Marco; Raiteri, Luca; Pattarini, Roberto; Grilli, Massimo; Bruzzone, Santina; Cavazzani, Paolo; Raiteri, Maurizio; Pittaluga, Anna

2003-07-30

The effect of the human immunodeficiency virus-1 protein Tat was investigated on neurotransmitter release from human and rat cortical nerve endings. Tat failed to affect the release of several neurotransmitters, such as glutamate, GABA, norepinephrine, and others, but it evoked the release of [3H]ACh via increase of cytosolic [Ca2+]. In human nerve terminals, the Tat effect partly depends on Ca2+ entry through voltage-sensitive Ca2+ channels, because Cd2+ halved the Tat-evoked release. Activation of group I metabotropic glutamate receptors (mGluR) and mobilization of Ca2+ from IP3-sensitive intraterminal stores are also involved, because the Tat effect was prevented by mGluR antagonists 2-methyl-6-(phenylethynyl)pyridine hydrochloride and 7-(hydroxyimino)cyclopropa[b]chromen-1a-carboxylate ethyl ester and by the IP3 receptor antagonists heparin and xestospongin C. Furthermore, the group I selective mGlu agonist (RS)-3,5-dihydroxyphenylglycine enhanced [3H]ACh release. In rat nerve terminals, the Tat-evoked release neither depends on external Ca2+ ions entry nor on IP3-mediated mechanisms. Tat seems to cause mobilization of Ca2+ from ryanodine-sensitive internal stores because its effect was prevented by both 8-bromo-cyclic adenosine diphosphate-ribose and dantrolene. The Tat-evoked release from human synaptosomes was mimicked by the peptide sequences Tat 32-62, Tat 49-86, and Tat 41-60. In contrast, the Tat 49-86 and Tat 61-80 fragments, but not the Tat 32-62 fragment, were active in rat synaptosomes. In conclusion, Tat elicits Ca2+-dependent [3H]ACh release by species-specific intraterminal mechanisms by binding via discrete amino acid sequences to different receptive sites on human and rat cholinergic terminals.

Rapid identification and classification of bacteria by 16S rDNA restriction fragment melting curve analyses (RFMCA).

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Rudi, Knut; Kleiberg, Gro H; Heiberg, Ragnhild; Rosnes, Jan T

2007-08-01

The aim of this work was to evaluate restriction fragment melting curve analyses (RFMCA) as a novel approach for rapid classification of bacteria during food production. RFMCA was evaluated for bacteria isolated from sous vide food products, and raw materials used for sous vide production. We identified four major bacterial groups in the material analysed (cluster I-Streptococcus, cluster II-Carnobacterium/Bacillus, cluster III-Staphylococcus and cluster IV-Actinomycetales). The accuracy of RFMCA was evaluated by comparison with 16S rDNA sequencing. The strains satisfying the RFMCA quality filtering criteria (73%, n=57), with both 16S rDNA sequence information and RFMCA data (n=45) gave identical group assignments with the two methods. RFMCA enabled rapid and accurate classification of bacteria that is database compatible. Potential application of RFMCA in the food or pharmaceutical industry will include development of classification models for the bacteria expected in a given product, and then to build an RFMCA database as a part of the product quality control.

Genetic Diversity among Rhizobium leguminosarum bv. Trifolii Strains Revealed by Allozyme and Restriction Fragment Length Polymorphism Analyses

Science.gov (United States)

Demezas, David H.; Reardon, Terry B.; Watson, John M.; Gibson, Alan H.

1991-01-01

Allozyme electrophoresis and restriction fragment length polymorphism (RFLP) analyses were used to examine the genetic diversity of a collection of 18 Rhizobium leguminosarum bv. trifolii, 1 R. leguminosarum bv. viciae, and 2 R. meliloti strains. Allozyme analysis at 28 loci revealed 16 electrophoretic types. The mean genetic distance between electrophoretic types of R. leguminosarum and R. meliloti was 0.83. Within R. leguminosarum, the single strain of bv. viciae differed at an average of 0.65 from strains of bv. trifolii, while electrophoretic types of bv. trifolii differed at a range of 0.23 to 0.62. Analysis of RFLPs around two chromosomal DNA probes also delineated 16 unique RFLP patterns and yielded genetic diversity similar to that revealed by the allozyme data. Analysis of RFLPs around three Sym (symbiotic) plasmid-derived probes demonstrated that the Sym plasmids reflect genetic divergence similar to that of their bacterial hosts. The large genetic distances between many strains precluded reliable estimates of their genetic relationships. PMID:16348600

Haplotyping the human T-cell receptor β-chain gene complex by use of restriction fragment length polymorphisms

International Nuclear Information System (INIS)

Charmley, P.; Chao, A.; Gatti, R.A.; Concannon, P.; Hood, L.

1990-01-01

The authors have studied the genetic segregation of human T-cell receptor β-chain (TCRβ) genes on chromosome 7q in 40 CEPH (Centre d'Etude du Polymorphisme Humain) families by using restriction fragment length polymorphisms (RFLPs). They constructed haplotypes from eight RFLPs by using variable- and constant-region cDNA probes, which detect polymorphisms that span more than 600 kilobases of the TCRβ gene complex. Analysis of allele distributions between TCRβ genes revealed significant linkage disequilibrium between only 6 of the 28 different pairs of RFLPs. This linkage disequilibrium strongly influences the most efficient order to proceed for typing of these RFLPs in order to achieve maximum genetic informativeness, which in this study revealed a 97.3% level of heterozygosity within the TCRβ gene complex. The results should provide new insight into recent reports of disease associations with the TCRβ gene complex and should assist in designing future experiments to detect or confirm the existence of disease-susceptibility loci in this region of the human genome

77 FR 21981 - Maher Terminal, LLC

Science.gov (United States)

2012-04-12

... continues to agree with another marine terminal operator or common carrier to boycott and/or unreasonably... costs and other undue and unreasonable payments, economic considerations, restrictions on transfers and...

SEARCHING FOR LOW WEIGHT PSEUDO-CODEWORDS

International Nuclear Information System (INIS)

Chertkov, Michael; Stepanov, Mikhail

2007-01-01

Belief Propagation (BP) and Linear Programming (LP) decodings of LDPC codes are discussed. The authors summarize results of instanton/pseudo-codeword approach developed for analysis of the error-floor domain of the codes. Instantons are special, code and decoding specific, configurations of the channel noise contributing most to the Frame-Error-Rate (FER). Instantons are decoded into pseudo-codewords. Instanton/pseudo-codeword with the lowest weight describes the largest Signal-to-Noise-Ratio (SNR) asymptotic of FER, while the whole spectra of the low weight instantons is descriptive of the FER vs. SNR profile in the extended error-floor domain. First, they describe a general optimization method that allows to find the instantons for any coding/decoding. Second, they introduce LP-specific pseudo-codeword search algorithm that allows efficient calculations of the pseudo-codeword spectra. Finally, they discuss results of combined BP/LP error-floor exploration experiments for two mode codes.

SEARCHING FOR LOW WEIGHT PSEUDO-CODEWORDS

Energy Technology Data Exchange (ETDEWEB)

CHERTKOV, MICHAEL [Los Alamos National Laboratory; STEPANOV, MIKHAIL [Los Alamos National Laboratory

2007-01-23

Belief Propagation (BP) and Linear Programming (LP) decodings of LDPC codes are discussed. The authors summarize results of instanton/pseudo-codeword approach developed for analysis of the error-floor domain of the codes. Instantons are special, code and decoding specific, configurations of the channel noise contributing most to the Frame-Error-Rate (FER). Instantons are decoded into pseudo-codewords. Instanton/pseudo-codeword with the lowest weight describes the largest Signal-to-Noise-Ratio (SNR) asymptotic of FER, while the whole spectra of the low weight instantons is descriptive of the FER vs. SNR profile in the extended error-floor domain. First, they describe a general optimization method that allows to find the instantons for any coding/decoding. Second, they introduce LP-specific pseudo-codeword search algorithm that allows efficient calculations of the pseudo-codeword spectra. Finally, they discuss results of combined BP/LP error-floor exploration experiments for two mode codes.

Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriae

DEFF Research Database (Denmark)

Leser, Thomas D.; Lindecrona, Rikke Hvid; Jensen, Tim Kåre

2000-01-01

Bacterial communities in the large intestines of pigs were compared using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S ribosomal DNA. The pigs were fed different experimental diets based on either modified standard feed or cooked rice supplemented with die......Bacterial communities in the large intestines of pigs were compared using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S ribosomal DNA. The pigs were fed different experimental diets based on either modified standard feed or cooked rice supplemented...

Causal inference in survival analysis using pseudo-observations.

Science.gov (United States)

Andersen, Per K; Syriopoulou, Elisavet; Parner, Erik T

2017-07-30

Causal inference for non-censored response variables, such as binary or quantitative outcomes, is often based on either (1) direct standardization ('G-formula') or (2) inverse probability of treatment assignment weights ('propensity score'). To do causal inference in survival analysis, one needs to address right-censoring, and often, special techniques are required for that purpose. We will show how censoring can be dealt with 'once and for all' by means of so-called pseudo-observations when doing causal inference in survival analysis. The pseudo-observations can be used as a replacement of the outcomes without censoring when applying 'standard' causal inference methods, such as (1) or (2) earlier. We study this idea for estimating the average causal effect of a binary treatment on the survival probability, the restricted mean lifetime, and the cumulative incidence in a competing risks situation. The methods will be illustrated in a small simulation study and via a study of patients with acute myeloid leukemia who received either myeloablative or non-myeloablative conditioning before allogeneic hematopoetic cell transplantation. We will estimate the average causal effect of the conditioning regime on outcomes such as the 3-year overall survival probability and the 3-year risk of chronic graft-versus-host disease. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Fragmentation of organic ions bearing fixed multiple charges observed in MALDI MS.

Science.gov (United States)

Lou, Xianwen; Li, Bao; de Waal, Bas F M; Schill, Jurgen; Baker, Matthew B; Bovee, Ralf A A; van Dongen, Joost L J; Milroy, Lech-Gustav; Meijer, E W

2018-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) was used to analyze a series of synthetic organic ions bearing fixed multiple charges. Despite the multiple intrinsic charges, only singly charged ions were recorded in each case. In addition to the pseudo-molecular ions formed by counterion adduction, deprotonation and electron capture, a number of fragment ions were also observed. Charge splitting by fragmentation was found to be a viable route for charge reduction leading to the formation of the observed singly charged fragment ions. Unlike multivalent metal ions, organic ions can rearrange and/or fragment during charge reduction. This fragmentation process will evidently complicate the interpretation of the MALDI MS spectrum. Because MALDI MS is usually considered as a soft ionization technique, the fragment ion peaks can easily be erroneously interpreted as impurities. Therefore, the awareness and understanding of the underlying MALDI-induced fragmentation pathways is essential for a proper interpretation of the corresponding mass spectra. Due to the fragment ions generated during charge reduction, special care should be taken in the MALDI MS analysis of multiply charged ions. In this work, the possible mechanisms by which the organic ions bearing fixed multiple charges fragment are investigated. With an improved understanding of the fragmentation mechanisms, MALDI TOF MS should still be a useful technique for the characterization of organic ions with fixed multiple charges. Copyright © 2017 John Wiley & Sons, Ltd.

Optimal decision procedures for satisfiability in fragments of alternating-time temporal logics

DEFF Research Database (Denmark)

Goranko, Valentin; Vester, Steen

2014-01-01

We consider several natural fragments of the alternating-time temporal logics ATL*and ATL with restrictions on the nesting between temporal operators and strate-gicquantifiers. We develop optimal decision procedures for satisfiability in these fragments, showing that they have much lower complexi...

Severe delayed complication after percutaneous endoscopic colostomy for chronic intestinal pseudo-obstruction: A case report and review of the literature

Science.gov (United States)

Bertolini, David; De Saussure, Philippe; Chilcott, Michael; Girardin, Marc; Dumonceau, Jean-Marc

2007-01-01

Percutaneous endoscopic colostomy (PEC) is increasingly proposed as an alternative to surgery to treat various disorders, including acute colonic pseudo-obstruction, chronic intestinal pseudo-obstruction and relapsing sigmoid volvulus. We report on a severe complication that occurred two months after PEC placement. A 74-year-old man with a history of chronic intestinal pseudo-obstruction evolving since 8 years was readmitted to our hospital and received PEC to provide long-standing relief. The procedure was uneventful and greatly improved the patient’s quality of life. Two months later, the patient developed acute stercoral peritonitis. At laparotomy, the colostomy flange was embedded in the abdominal wall but no pressure necrosis was found at the level of the colonic wall. This complication was likely related to inadvertent traction of the colostomy tube. Subtotal colectomy with terminal ileostomy was performed. We review the major features of 60 cases of PEC reported to date, including indications and complications. PMID:17465514

Pseudo-simple heteroclinic cycles in R4

Science.gov (United States)

Chossat, Pascal; Lohse, Alexander; Podvigina, Olga

2018-06-01

We study pseudo-simple heteroclinic cycles for a Γ-equivariant system in R4 with finite Γ ⊂ O(4) , and their nearby dynamics. In particular, in a first step towards a full classification - analogous to that which exists already for the class of simple cycles - we identify all finite subgroups of O(4) admitting pseudo-simple cycles. To this end we introduce a constructive method to build equivariant dynamical systems possessing a robust heteroclinic cycle. Extending a previous study we also investigate the existence of periodic orbits close to a pseudo-simple cycle, which depends on the symmetry groups of equilibria in the cycle. Moreover, we identify subgroups Γ ⊂ O(4) , Γ ⊄ SO(4) , admitting fragmentarily asymptotically stable pseudo-simple heteroclinic cycles. (It has been previously shown that for Γ ⊂ SO(4) pseudo-simple cycles generically are completely unstable.) Finally, we study a generalized heteroclinic cycle, which involves a pseudo-simple cycle as a subset.

28-mer Fragment Derived from Enterocin CRL35 Displays an Unexpected Bactericidal Effect on Listeria Cells.

Science.gov (United States)

Masias, Emilse; Sanches, Paulo R S; Dupuy, Fernando G; Acuna, Leonardo; Bellomio, Augusto; Cilli, Eduardo; Saavedra, Lucila; Minahk, Carlos

2015-01-01

Two shorter peptides derived from enterocin CRL35, a 43-mer bacteriocin, were synthesized i.e. the N-terminal fragment spanning from residues 1 to 15, and a 28-mer fragment that represents the C-terminal of enterocin CRL35, the residues 16 to 43. The separate peptides showed no activity when combined. On one hand, the 28-mer peptide displayed an unpredicted antimicrobial activity. On the other, 15- mer peptide had no consistent anti-Listeria effect. The dissociation constants calculated from experimental data indicated that all peptides could bind at similar extent to the sensitive cells. However, transmembrane electrical potential was not dissipated to the same level by the different peptides; whereas the full-length and the C-terminal 28-mer fragment induced almost full dissipation, 15-mer fragment produced only a slow and incomplete effect. Furthermore, a different interaction of each peptide with membranes was demonstrated based on studies carried out with liposomes, which led us to conclude that activity was related to structure rather than to net positive charges. These results open up the possibility of designing new peptides based on the 28-mer fragment with enhanced activity, which would represent a promising approach for combating Listeria and other pathogens.

Scaphoid pseudo-arthrosis: Frequency, pathogenesis and course

Energy Technology Data Exchange (ETDEWEB)

Schunk, K.; Teifke, A.; Benning, R.; Dahm, M.; Thelen, R.; Schild, H.

1989-06-01

Eighty-three scaphoid pseudo-arthroses were found amongst 1.104 scaphoid examinations. Sixtyseven were present at the first examination and 16 pseudo-arthroses developed amongst 252 scaphoid fractures. Men were affected predominantly, particularly in the 20 to 40-year old group. Fractures in the proximal third of the scaphoid and vertical oblique fractures had a particular tendency to pseudo-arthrosis formation. The operative treatment of choice is a Matti-Russe bone graft. Only one patient in seven with definite scaphoid pseudo-arthrosis showed firm fusion. (orig.).

Scaphoid pseudo-arthrosis: Frequency, pathogenesis and course

International Nuclear Information System (INIS)

Schunk, K.; Teifke, A.; Benning, R.; Dahm, M.; Thelen, R.; Schild, H.; Mainz Univ.

1989-01-01

Eighty-three scaphoid pseudo-arthroses were found amongst 1.104 scaphoid examinations. Sixtyseven were present at the first examination and 16 pseudo-arthroses developed amongst 252 scaphoid fractures. Men were affected predominantly, particularly in the 20 to 40-year old group. Fractures in the proximal third of the scaphoid and vertical oblique fractures had a particular tendency to pseudo-arthrosis formation. The operative treatment of choice is a Matti-Russe bone graft. Only one patient in seven with definite scaphoid pseudo-arthrosis showed firm fusion. (orig.) [de

Fragmentation of Ceramics in Rapid Expansion Mode

Science.gov (United States)

Maiti, Spandan; Geubelle, Philippe H.; Rangaswamy, Krishnan

The study of the fragmentation process goes back to more than a century, motivated primarily by problems related to mining and ore handling (Grady and Kipp, 1985). Various theories have been proposed to predict the fragmentation stress and the fragment size and distribution. But the investigations are generally case specific and relate to only a narrow set of fragmentation processes. A number of theoretical studies of dynamic fragmentation in a rapidly expanding body can be found in the literature. For example, the study summarized in (Grady, 1982) presents a model based on a simple energy balance concept between the surface energy released due to fracture and the kinetic energy of the fragments. Subsequent refinements of the energy balance model have been proposed by (Glenn and Chudnovsky, 1986), which take into account the strain energy of the fragments and specify a threshold stress below which no fragmentation occurs. These models assume that the fracture events are instantaneous and occur simultaneously. Evidently, these assumptions are quite restrictive and these models can not take into account the transient nature of the fragmentation process after the onset of fracture in the material. A more recent model proposed by (Miller et al., 1999) however takes into account this time-dependent nature of the fragmentation event and the distribution of flaws of various strengths in the original material.

Maintaining heterokaryosis in pseudo-homothallic fungi.

Science.gov (United States)

Grognet, Pierre; Silar, Philippe

2015-01-01

Among all the strategies displayed by fungi to reproduce and propagate, some species have adopted a peculiar behavior called pseudo-homothallism. Pseudo-homothallic fungi are true heterothallics, i.e., they need 2 genetically-compatible partners to mate, but they produce self-fertile mycelium in which the 2 different nuclei carrying the compatible mating types are present. This lifestyle not only enables the fungus to reproduce without finding a compatible partner, but also to cross with any mate it may encounter. However, to be fully functional, pseudo-homothallism requires maintaining heterokaryosis at every stage of the life cycle. We recently showed that neither the structure of the mating-type locus nor hybrid-enhancing effect due to the presence of the 2 mating types accounts for the maintenance of heterokaryosis in the pseudo-homothallic fungus P. anserina. In this addendum, we summarize the mechanisms creating heterokaryosis in P. anserina and 2 other well-known pseudo-homothallic fungi, Neurospora tetrasperma and Agaricus bisporus. We also discuss mechanisms potentially involved in maintaining heterokaryosis in these 3 species.

Pst I restriction fragment length polymorphism of human placental alkaline phosphatase gene: Mendelian in segregation and localization of mutation site in the gene

International Nuclear Information System (INIS)

Tsavaler, L.; Penhallow, R.C.; Sussman, H.H.

1988-01-01

The pattern of inheritance of a Pst I restriction fragment length polymorphism (RFLP) of the human placental alkaline phosphatase gene was studied in nine nuclear families by Southern blot hybridization analysis of genomic DNA. The dimorphic RFLP is defined by the presence of allelic fragments 1.0 kilobase and 0.8 kilobase long. The results of this study show that the two alleles of the Pst I RFLP of the placental alkaline phosphatase gene segregate as codominant traits according to Mendelian expectations. For a polymorphism to be useful as a genetic marker the probability that an offspring is informative (PIC) must be at least 0.15. The allelic frequency of the 1.0-kilobase allele is 0.21, which correlates to a probability that an offspring is informative of 0.275 and is indicative of a useful polymorphism. By using probes derived from different regions of the placental alkaline phosphatase cDNA, the mutated Pst I site causing the RFLP was located in the penultimate intron 2497 base pairs downstream from the transcriptional initiation site

[Pseudo-Bartter syndrome--2 cases].

Science.gov (United States)

Jóźwiak, Lucyna; Jaroszyński, Andrzej; Baranowicz-Gaszczyk, Iwona; Borowicz, Ewa; Ksiazek, Andrzej

2010-01-01

Bartter syndrome represents the group of renal disturbances characterized by hypokaliemia and metabolic alkalosis. Some diseases could display hypokalemic metabolic alkalosis without primary tubular dysfunction. These disorders are called pseudo-Bartter syndrome. In this paper we present 2 cases of pseudo-Bartter syndrome related among to other things to overuse of diuretic drugs.

Rapid differentiation of closely related isolates of two plant viruses by polymerase chain reaction and restriction fragment length polymorphism analysis.

Science.gov (United States)

Barbara, D J; Morton, A; Spence, N J; Miller, A

1995-09-01

Immunocapture reverse transcriptase-polymerase chain reaction (RT-PCR) followed by restriction fragment length polymorphism (RFLP) analysis of the product has been shown to be an effective procedure for discriminating serologically indistinguishable isolates of two plant viruses, raspberry bushy dwarf (RBDV) and zucchini yellow mosaic (ZYMV). For both viruses, only limited sequence information was available at the time of primer design, but most of the isolates which were tested could be amplified (the one exception being a serologically quite distinct isolate of ZYMV). Restriction endonucleases revealing diagnostic RFLPs were readily identified. Each of two isolates of ZYMV could be detected in the presence of the other and the relative proportions approximately quantified by visual estimation of the relative intensity of the appropriate bands. A range of isolates of different RBDV pathotypes were compared; isolates were grouped in ways that accorded with their known history. Computer analysis of the published sequence from which the primers had been derived showed the sequenced isolate to be identical with an isolate imported from the USSR. The PCR/RFLP procedure is rapid (it can be completed in less than 2 days), effective and will probably be generally applicable to distinguishing closely related virus isolates, even where little sequence information is available.

Loss of Nat4 and its associated histone H4 N-terminal acetylation mediates calorie restriction-induced longevity.

Science.gov (United States)

Molina-Serrano, Diego; Schiza, Vassia; Demosthenous, Christis; Stavrou, Emmanouil; Oppelt, Jan; Kyriakou, Dimitris; Liu, Wei; Zisser, Gertrude; Bergler, Helmut; Dang, Weiwei; Kirmizis, Antonis

2016-12-01

Changes in histone modifications are an attractive model through which environmental signals, such as diet, could be integrated in the cell for regulating its lifespan. However, evidence linking dietary interventions with specific alterations in histone modifications that subsequently affect lifespan remains elusive. We show here that deletion of histone N-alpha-terminal acetyltransferase Nat4 and loss of its associated H4 N-terminal acetylation (N-acH4) extend yeast replicative lifespan. Notably, nat4Δ-induced longevity is epistatic to the effects of calorie restriction (CR). Consistent with this, (i) Nat4 expression is downregulated and the levels of N-acH4 within chromatin are reduced upon CR, (ii) constitutive expression of Nat4 and maintenance of N-acH4 levels reduces the extension of lifespan mediated by CR, and (iii) transcriptome analysis indicates that nat4Δ largely mimics the effects of CR, especially in the induction of stress-response genes. We further show that nicotinamidase Pnc1, which is typically upregulated under CR, is required for nat4Δ-mediated longevity. Collectively, these findings establish histone N-acH4 as a regulator of cellular lifespan that links CR to increased stress resistance and longevity. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

Complementarily addressed modification and cleavage of a single-stranded fragment of DNA with the aid of alkylating derivatives of oligonucleotides

International Nuclear Information System (INIS)

Brosalina, E.B.; Vlasov, V.V.; Kutyavin, I.V.; Mamaev, S.V.; Pletnev, A.G.; Podyminogin, M.A.

1986-01-01

The chemical modification of a 303-nucleotide single-stranded fragment of DNA by alkylating oligonucleotide derivatives bearing 4-[N-methyl-N-(2-chloroethyl)amino]benzyl groups in the 5'-terminal phosphate of the 3'-terminal ribose residue has been investigated. It has been shown that under the conditions of the formation of a complex with the DNA fragment both types of derivatives specifically alkylate nucleotides of the DNA fragments that are located directly adjacent to the sections complementary to the oligonucleotides bearing the reactive groups. Alkylation takes place with a high efficiency, and the DNA fragment can be cleaved specifically at the position of the alkylated nucleotides

Limits of a rapid identification of common Mediterranean sandflies using polymerase chain reaction-restriction fragment length polymorphism

Directory of Open Access Journals (Sweden)

Azzedine Bounamous

2014-07-01

Full Text Available A total of 131 phlebotomine Algerian sandflies have been processed in the present study. They belong to the species Phlebotomus bergeroti, Phlebotomus alexandri, Phlebotomus sergenti, Phlebotomus chabaudi, Phlebotomus riouxi, Phlebotomus perniciosus, Phlebotomus longicuspis, Phlebotomus perfiliewi, Phlebotomus ariasi, Phlebotomus chadlii, Sergentomyia fallax, Sergentomyia minuta, Sergentomyia antennata, Sergentomyia schwetzi, Sergentomyia clydei, Sergentomyia christophersi and Grassomyia dreyfussi. They have been characterised by sequencing of a part of the cytochrome b (cyt b, t RNA serine and NADH1 on the one hand and of the cytochrome C oxidase I of the mitochondrial DNA (mtDNA on the other hand. Our study highlights two sympatric populations within P. sergenti in the area of its type-locality and new haplotypes of P. perniciosus and P. longicuspis without recording the specimens called lcx previously found in North Africa. We tried to use a polymerase chain reaction-restriction fragment length polymorphism method based on a combined double digestion of each marker. These method is not interesting to identify sandflies all over the Mediterranean Basin.

Evaluation of the use of amplified 16S rRNA gene-restriction fragment length polymorphism analysis to detect enterobacter cloacae and bacillus licheniformis for microbial enhanced oil recovery field pilot

Energy Technology Data Exchange (ETDEWEB)

Fujiwara, Kazuhiro; Tanaka, Shinji; Otsuka, Makiko; Ichimura, Naoya [Lansai Research Institute, Kyoto (Japan); Yonebayashi, Hideharu [Japan National Oil Corp., Chiba (Japan); Hong, Chengxie; Enomoto, Heiji [Tohoku University, Miyagi (Japan)

1999-09-01

Evaluation of effectiveness of restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene of microorganisms injected into an oil reservoir, for monitoring their levels over time, was conducted. Two microorganisms, enterobacter cloacae TRC-322 and Bacillus licheniformis TRC-18-2-a, were focused in this paper among the microorganisms selected for injection, and gene fragments of the 16S rRNA gene of these microorganisms were amplified by polymerase chain reaction (PCP), using one set of universal primers. Samples of the reservoir brine and reservoir rock were obtained; the microorganisms inhabiting in the reservoir were isolated from these samples, and the 16S rRNA gene of these microorganisms was amplified, condition remaining the same. RFLP analysis was performed on the 16S rRNA gene of each of these microorganisms, using restriction endonucleases HhaI, MspI, AluI and TaqI as necessary. Comparison of the resultant rRNA gene fragments, demonstrated that closely-related species displaying RFLP profile similar to that of E. cloacae TRC-322 or B. licheniformis TRC-18-2-a were not among the microorganisms isolated from the reservoir. PCR-RFLP analysis of the 16S rRNA gene, using the protocol; presented in this paper, is effective to detect the presence appropriate injecting microorganisms. This method was also effective for studying microorganisms isolated from the reservoir, which have the ability to grow on a molasses. (author)

Characterization of Erwinia amylovora strains from different host plants using repetitive-sequences PCR analysis, and restriction fragment length polymorphism and short-sequence DNA repeats of plasmid pEA29.

Science.gov (United States)

Barionovi, D; Giorgi, S; Stoeger, A R; Ruppitsch, W; Scortichini, M

2006-05-01

The three main aims of the study were the assessment of the genetic relationship between a deviating Erwinia amylovora strain isolated from Amelanchier sp. (Maloideae) grown in Canada and other strains from Maloideae and Rosoideae, the investigation of the variability of the PstI fragment of the pEA29 plasmid using restriction fragment length polymorphism (RFLP) analysis and the determination of the number of short-sequence DNA repeats (SSR) by DNA sequence analysis in representative strains. Ninety-three strains obtained from 12 plant genera and different geographical locations were examined by repetitive-sequences PCR using Enterobacterial Repetitive Intergenic Consensus, BOX and Repetitive Extragenic Palindromic primer sets. Upon the unweighted pair group method with arithmetic mean analysis, a deviating strain from Amelanchier sp. was analysed using amplified ribosomal DNA restriction analysis (ARDRA) analysis and the sequencing of the 16S rDNA gene. This strain showed 99% similarity to other E. amylovora strains in the 16S gene and the same banding pattern with ARDRA. The RFLP analysis of pEA29 plasmid using MspI and Sau3A restriction enzymes showed a higher variability than that previously observed and no clear-cut grouping of the strains was possible. The number of SSR units reiterated two to 12 times. The strains obtained from pear orchards showing for the first time symptoms of fire blight had a low number of SSR units. The strains from Maloideae exhibit a wider genetic variability than previously thought. The RFLP analysis of a fragment of the pEA29 plasmid would not seem a reliable method for typing E. amylovora strains. A low number of SSR units was observed with first epidemics of fire blight. The current detection techniques are mainly based on the genetic similarities observed within the strains from the cultivated tree-fruit crops. For a more reliable detection of the fire blight pathogen also in wild and ornamentals Rosaceous plants the genetic

Examples of pseudo-bosons in quantum mechanics

International Nuclear Information System (INIS)

Bagarello, F.

2010-01-01

We discuss two physical examples of the so-called pseudo-bosons, recently introduced in connection with pseudo-hermitian quantum mechanics. In particular, we show that the so-called extended harmonic oscillator and the Swanson model satisfy all the assumptions of the pseudo-bosonic framework introduced by the author. We also prove that the biorthogonal bases they produce are not Riesz bases.

THE PSEUDO-EVOLUTION OF HALO MASS

International Nuclear Information System (INIS)

Diemer, Benedikt; Kravtsov, Andrey V.; More, Surhud

2013-01-01

A dark matter halo is commonly defined as a spherical overdensity of matter with respect to a reference density, such as the critical density or the mean matter density of the universe. Such definitions can lead to a spurious pseudo-evolution of halo mass simply due to redshift evolution of the reference density, even if its physical density profile remains constant over time. We estimate the amount of such pseudo-evolution of mass between z = 1 and 0 for halos identified in a large N-body simulation, and show that it accounts for almost the entire mass evolution of the majority of halos with M 200ρ-bar ≲ 10 12 h -1 M ☉ and can be a significant fraction of the apparent mass growth even for cluster-sized halos. We estimate the magnitude of the pseudo-evolution assuming that halo density profiles remain static in physical coordinates, and show that this simple model predicts the pseudo-evolution of halos identified in numerical simulations to good accuracy, albeit with significant scatter. We discuss the impact of pseudo-evolution on the evolution of the halo mass function and show that the non-evolution of the low-mass end of the halo mass function is the result of a fortuitous cancellation between pseudo-evolution and the absorption of small halos into larger hosts. We also show that the evolution of the low-mass end of the concentration-mass relation observed in simulations is almost entirely due to the pseudo-evolution of mass. Finally, we discuss the implications of our results for the interpretation of the evolution of various scaling relations between the observable properties of galaxies and galaxy clusters and their halo masses.

Newtonian and pseudo-Newtonian Hill problem

International Nuclear Information System (INIS)

Steklain, A.F.; Letelier, P.S.

2006-01-01

A pseudo-Newtonian Hill problem based on the Paczynski-Wiita pseudo-Newtonian potential that reproduces general relativistic effects is presented and compared with the usual Newtonian Hill problem. Poincare maps, Lyapunov exponents and fractal escape techniques are employed to study bounded and unbounded orbits. In particular we consider the systems composed by Sun, Earth and Moon and composed by the Milky Way, the M2 cluster and a star. We find that some pseudo-Newtonian systems-including the M2 system-are more stable than their Newtonian equivalent

(PCR) for direct cloning of blunt-end DNA fragments

African Journals Online (AJOL)

Administrator

2011-09-19

Sep 19, 2011 ... Key words: Blunt-end cloning, phosphorylated DNA fragment, dephosphorylated blunt-end vector. INTRODUCTION ... With this method, a lot of steps are saved, which includes restriction .... pBSK-blunt (data not shown).

Structural Basis for Toughness and Flexibility in the C-terminal Passenger Domain of an Acinetobacter Trimeric Autotransporter Adhesin*

Science.gov (United States)

Koiwai, Kotaro; Hartmann, Marcus D.; Linke, Dirk; Lupas, Andrei N.; Hori, Katsutoshi

2016-01-01

Trimeric autotransporter adhesins (TAAs) on the cell surface of Gram-negative pathogens mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows nonspecific high adhesiveness to abiotic material surfaces as well as to biotic surfaces. It consists of a passenger domain secreted by the C-terminal transmembrane anchor domain (TM), and the passenger domain contains an N-terminal head, N-terminal stalk, C-terminal head (Chead), and C-terminal stalk (Cstalk). The Chead-Cstalk-TM fragment, which is conserved in many Acinetobacter TAAs, has by itself the head-stalk-anchor architecture of a complete TAA. Here, we show the crystal structure of the Chead-Cstalk fragment, AtaA_C-terminal passenger domain (CPSD), providing the first view of several conserved TAA domains. The YadA-like head (Ylhead) of the fragment is capped by a unique structure (headCap), composed of three β-hairpins and a connector motif; it also contains a head insert motif (HIM1) before its last inner β-strand. The headCap, Ylhead, and HIM1 integrally form a stable Chead structure. Some of the major domains of the CPSD fragment are inherently flexible and provide bending sites for the fiber between segments whose toughness is ensured by topological chain exchange and hydrophobic core formation inside the trimer. Thus, although adherence assays using in-frame deletion mutants revealed that the characteristic adhesive sites of AtaA reside in its N-terminal part, the flexibility and toughness of the CPSD part provide the resilience that enables the adhesive properties of the full-length fiber across a wide range of conditions. PMID:26698633

Construction of the mathematical concept of pseudo thinking students

Science.gov (United States)

Anggraini, D.; Kusmayadi, T. A.; Pramudya, I.

2018-05-01

Thinking process is a process that begins with the acceptance of information, information processing and information calling in memory with structural changes that include concepts or knowledges. The concept or knowledge is individually constructed by each individual. While, students construct a mathematical concept, students may experience pseudo thinking. Pseudo thinking is a thinking process that results in an answer to a problem or construction to a concept “that is not true”. Pseudo thinking can be classified into two forms there are true pseudo and false pseudo. The construction of mathematical concepts in students of pseudo thinking should be immediately known because the error will have an impact on the next construction of mathematical concepts and to correct the errors it requires knowledge of the source of the error. Therefore, in this article will be discussed thinking process in constructing of mathematical concepts in students who experience pseudo thinking.

Oncogenic transformation of rat lung epithelioid cells by SV40 DNA and restriction enzyme fragments

International Nuclear Information System (INIS)

Daya-Grosjean, L.; Lasne, C.; Nardeux, P.; Chouroulinkov, I.; Monier, R.

1979-01-01

Rat epithelioid lung cells were transformed with various preparations of SV40 DNA using the Ca 2+ -precipitation technique. The amount of SV40 genetic information integrated into transformed clones was evaluated by DNA-DNA renaturation kinetics. The growth properties on plastic and in soft-agar were examined, as well as the ability to induce tumors in syngeneic newborn animals or in adult nude mice. One particular transformed line, which had received the HpaII/BamHIA (59 per cent) fragment, was found to contain about 3 integrated copies of this fragment per cell and no significant amount of the HpaII/BamHIB (41 per cent fragment). This line which grew to high saturatio densities and efficiently formed clones in low serum on plastic, produced tumors in both syngeneic rats and nude mice. Thus the HpaII/BamHIA fragment, which mainly includes early viral information, was sufficient to impart these properties to rat epithelioid lung cells. (author)

IL-27 Receptor Signalling Restricts the Formation of Pathogenic, Terminally Differentiated Th1 Cells during Malaria Infection by Repressing IL-12 Dependent Signals

Science.gov (United States)

Villegas-Mendez, Ana; de Souza, J. Brian; Lavelle, Seen-Wai; Gwyer Findlay, Emily; Shaw, Tovah N.; van Rooijen, Nico; Saris, Christiaan J.; Hunter, Christopher A.; Riley, Eleanor M.; Couper, Kevin N.

2013-01-01

The IL-27R, WSX-1, is required to limit IFN-γ production by effector CD4+ T cells in a number of different inflammatory conditions but the molecular basis of WSX-1-mediated regulation of Th1 responses in vivo during infection has not been investigated in detail. In this study we demonstrate that WSX-1 signalling suppresses the development of pathogenic, terminally differentiated (KLRG-1+) Th1 cells during malaria infection and establishes a restrictive threshold to constrain the emergent Th1 response. Importantly, we show that WSX-1 regulates cell-intrinsic responsiveness to IL-12 and IL-2, but the fate of the effector CD4+ T cell pool during malaria infection is controlled primarily through IL-12 dependent signals. Finally, we show that WSX-1 regulates Th1 cell terminal differentiation during malaria infection through IL-10 and Foxp3 independent mechanisms; the kinetics and magnitude of the Th1 response, and the degree of Th1 cell terminal differentiation, were comparable in WT, IL-10R1−/− and IL-10−/− mice and the numbers and phenotype of Foxp3+ cells were largely unaltered in WSX-1−/− mice during infection. As expected, depletion of Foxp3+ cells did not enhance Th1 cell polarisation or terminal differentiation during malaria infection. Our results significantly expand our understanding of how IL-27 regulates Th1 responses in vivo during inflammatory conditions and establishes WSX-1 as a critical and non-redundant regulator of the emergent Th1 effector response during malaria infection. PMID:23593003

Properties, production and applications of camelid single-domain antibody fragments

NARCIS (Netherlands)

Harmsen, M.M.; Haard, de H.J.

2007-01-01

Camelids produce functional antibodies devoid of light chains of which the single N-terminal domain is fully capable of antigen binding. These single-domain antibody fragments (VHHs or Nanobodies®) have several advantages for biotechnological applications. They are well expressed in microorganisms

Anti-retroviral therapy-induced status epilepticus in "pseudo-HIV serodeconversion".

Science.gov (United States)

Etgen, Thorleif; Eberl, Bernhard; Freudenberger, Thomas

2010-01-01

Diligence in the interpretation of results is essential as information gained from the psychiatric patient's history might often be restricted. Nonobservance of established guidelines may lead to a wrong diagnosis, induce a false therapy and result in life-threatening situations. Communication errors between hospitals and doctors and uncritical acceptance of prior diagnoses add substantially to this problem. We present a patient with alcohol-related dementia who received anti-retroviral therapy that promoted a non-convulsive status epilepticus. HIV serodeconversion was considered after our laboratory result yielded a HIV-negative status. Critical review of previous diagnostic investigations revealed several errors in the diagnosis of HIV infection leading to a "pseudo-serodeconversion." Finally, anti-retroviral therapy could be discontinued. Copyright © 2010 Elsevier Inc. All rights reserved.

Decompositions, partitions, and coverings with convex polygons and pseudo-triangles

NARCIS (Netherlands)

Aichholzer, O.; Huemer, C.; Kappes, S.; Speckmann, B.; Tóth, Cs.D.

2007-01-01

We propose a novel subdivision of the plane that consists of both convex polygons and pseudo-triangles. This pseudo-convex decomposition is significantly sparser than either convex decompositions or pseudo-triangulations for planar point sets and simple polygons. We also introduce pseudo-convex

Restriction fragment polymorphism (RFLP) of a "new" HLA-DP specificity, CDP-HEI

DEFF Research Database (Denmark)

Hyldig-Nielsen, J J; Ødum, Niels; Morling, Niels

1988-01-01

Southern blotting with a DP beta cDNA probe of MspI digested DNA from 83 healthy unrelated individuals revealed a 1.8 kb fragment present in all four individuals (and no others) possessing the newly determined DP specificity, CDP-HEI....

A novel tandem reporter quantifies RNA polymerase II termination in mammalian cells.

Directory of Open Access Journals (Sweden)

Ayan Banerjee

2009-07-01

Full Text Available Making the correct choice between transcription elongation and transcription termination is essential to the function of RNA polymerase II, and fundamental to gene expression. This choice can be influenced by factors modifying the transcription complex, factors modifying chromatin, or signals mediated by the template or transcript. To aid in the study of transcription elongation and termination we have developed a transcription elongation reporter system that consists of tandem luciferase reporters flanking a test sequence of interest. The ratio of expression from the reporters provides a measure of the relative rates of successful elongation through the intervening sequence.Size matched fragments containing the polyadenylation signal of the human beta-actin gene (ACTB and the human beta-globin gene (HBB were evaluated for transcription termination using this new ratiometric tandem reporter assay. Constructs bearing just 200 base pairs on either side of the consensus poly(A addition site terminated 98% and 86% of transcription for ACTB and HBB sequences, respectively. The nearly 10-fold difference in read-through transcription between the two short poly(A regions was eclipsed when additional downstream poly(A sequence was included for each gene. Both poly(A regions proved very effective at termination when 1100 base pairs were included, stopping 99.6% of transcription. To determine if part of the increased termination was simply due to the increased template length, we inserted several kilobases of heterologous coding sequence downstream of each poly(A region test fragment. Unexpectedly, the additional length reduced the effectiveness of termination of HBB sequences 2-fold and of ACTB sequences 3- to 5-fold.The tandem construct provides a sensitive measure of transcription termination in human cells. Decreased Xrn2 or Senataxin levels produced only a modest release from termination. Our data support overlap in allosteric and torpedo mechanisms

Pseudo random signal processing theory and application

CERN Document Server

Zepernick, Hans-Jurgen

2013-01-01

In recent years, pseudo random signal processing has proven to be a critical enabler of modern communication, information, security and measurement systems. The signal's pseudo random, noise-like properties make it vitally important as a tool for protecting against interference, alleviating multipath propagation and allowing the potential of sharing bandwidth with other users. Taking a practical approach to the topic, this text provides a comprehensive and systematic guide to understanding and using pseudo random signals. Covering theoretical principles, design methodologies and applications

Population dynamics of Pseudo-nitzschia species ...

African Journals Online (AJOL)

The genus Pseudo-nitzschia is a chain-forming diatom comprising about 30 species some of which are known to produce domoic acid (DA) that causes amnesic shellfish poisoning (ASP). The current study aimed at assessing the population dynamics of Pseudo-nitzschia in the near shore waters of Dar es Salaam. Samples ...

Pseudo-differential operators groups, geometry and applications

CERN Document Server

Zhu, Hongmei

2017-01-01

This volume consists of papers inspired by the special session on pseudo-differential operators at the 10th ISAAC Congress held at the University of Macau, August 3-8, 2015 and the mini-symposium on pseudo-differential operators in industries and technologies at the 8th ICIAM held at the National Convention Center in Beijing, August 10-14, 2015. The twelve papers included present cutting-edge trends in pseudo-differential operators and applications from the perspectives of Lie groups (Chapters 1-2), geometry (Chapters 3-5) and applications (Chapters 6-12). Many contributions cover applications in probability, differential equations and time-frequency analysis. A focus on the synergies of pseudo-differential operators with applications, especially real-life applications, enhances understanding of the analysis and the usefulness of these operators.

Pseudo-populations a basic concept in statistical surveys

CERN Document Server

Quatember, Andreas

2015-01-01

This book emphasizes that artificial or pseudo-populations play an important role in statistical surveys from finite universes in two manners: firstly, the concept of pseudo-populations may substantially improve users’ understanding of various aspects in the sampling theory and survey methodology; an example of this scenario is the Horvitz-Thompson estimator. Secondly, statistical procedures exist in which pseudo-populations actually have to be generated. An example of such a scenario can be found in simulation studies in the field of survey sampling, where close-to-reality pseudo-populations are generated from known sample and population data to form the basis for the simulation process. The chapters focus on estimation methods, sampling techniques, nonresponse, questioning designs and statistical disclosure control.This book is a valuable reference in understanding the importance of the pseudo-population concept and applying it in teaching and research.

Plasmon response in K, Na and Li clusters: systematics using the separable random-phase approximation with pseudo-Hamiltonians

International Nuclear Information System (INIS)

Kleinig, W.; Nesterenko, V.O.; Reinhard, P.-G.; Serra, Ll.

1998-01-01

The systematics of the plasmon response in spherical K, Na and Li clusters in a wide size region (8≤N≤440) is studied. We have considered two simplifying approximations whose validity has been established previously. First, a separable approach to the random-phase approximation is used. This involves an expansion of the residual interaction into a sum of separable terms until convergence is reached. Second, the electron-ion interaction is modelled by using the pseudo-Hamiltonian jellium model (MHJM) which includes nonlocal effects by means of realistic atomic pseudo-Hamiltonians. In cases where nonlocal effects are negligible the Structure Averaged Jellium Model (SAJM) has been used. Good agreement with available experimental data is achieved for K, Na (using the SAJM) and small Li clusters (invoking the PHJM). The trends for peak position and width are generally well reproduced, even up to details of the Landau fragmentation in several clusters. Less good agreement, however, is found for large Li clusters. This remains an open question

Abstracts of papers presented at the 8th workshop of the Virology Section of the Deutsche Gesellschaft für Hygiene und Mikro-biologie, Würzburg, March 17-19, 1983.

Science.gov (United States)

1983-09-01

17 adenovirus strains were found to be antigenically related to prototype Ad 15 by neutralization. No relationship to Ad 15, but to Ad 9 could be detected by hemagglutination-inhibition; we therefore named them Ad 15/H9 intermediate strains. After analysis of the genome by five different restriction enzymes, the fragment patterns obtained deviated widely from the prototype Ad 15, but only slightly from Ad 9. Differences could also be observed among the variants. After digestion by five restriction enzymes, altogether six genome types could be established among the 17 intermediate strains. To map the variations on the genome of the 15/H9 strains, two methods were employed: the double digestion of the DNA and DNA fragments together with the determination of the terminal fragments made it possible to construct a physical map. The second method depends on a particularity of adenoviruses: the DNA is covalently linked with a 55 kD protein at the 5' terminus. After digestion of the DNA, which does contain this protein, the terminal DNA fragments do not migrate into the agarose gel; after an additional digestion with pronase B, they do migrate into the gel. Thus the terminal fragments were determined by comparing the fragment patterns with and without previous pronase B treatment.

Investigation of the surface terminations of icosahedral AlPdMn quasicrystal based on a modified non-spherical model

International Nuclear Information System (INIS)

Yu Fengmei; Zou Huamin; Wang Jianbo; Wang Renhui

2004-01-01

The atomic positions are obtained from a modified non-spherical model of icosahedral AlPdMn quasicrystal (Fang et al 2003 J. Phys.: Condens. Matter 15 4947) by the cut method. The four-shell pseudo-Mackay clusters (PMCs) were searched for in a box of 400 A x 400 A x 400 A. The results show that the number of atoms in the fourth shell, an icosidodecahedron, of the pseudo-Mackay cluster can vary from 15 to 30 because of the cluster overlap, and about 99.96% of the total atoms are included in such incomplete pseudo-Mackay clusters. The characteristics of the atom distribution in the planes perpendicular to a fivefold axis indicate that the planes, which are 1.56 A apart from their neighbouring planes, are expected to be the terminal surfaces. If one such a plane and its closest neighbouring plane, between which the spacing is 0.48 A, are considered as a thin layer or a corrugated surface, these layers are also the layers with the maximum density. The pair of corrugated surfaces that are 1.56 A apart have almost identical chemical composition. These planes form terraces that follow the rule of the Fibonacci sequence with two step heights, 6.60 and 4.08 A. On the corrugated surfaces perpendicular to a fivefold axis the pentagonal holes arise from the interspaces of adjacent incomplete PMCs. For the atomic planes normal to a twofold axis, the planes with spacing of 1.48 A from their adjacent planes might be expected to be the terminal surfaces, which form terraces with step heights of 6.28 and 3.88 A following the rule of the Fibonacci sequence. For the atomic planes normal to a threefold axis, the planes with spacing of 0.86 A from their adjacent planes might be expected to be the terminal surfaces. No similar results were found for the atomic layers perpendicular to a pseudo-twofold axis

Comparison of renal and osseous binding of parathyroid hormone and hormonal fragments

International Nuclear Information System (INIS)

Demay, M.; Mitchell, J.; Goltzman, D.

1985-01-01

The authors compared receptor binding and adenylate cyclase stimulation of intact bovine parathyroid hormone (bPTH)-(1-84) and the synthetic amino-terminal fragments, bPTH-(1-34) and rat PTH (rPTH)-(1-34). In both canine renal membranes and cloned rat osteosarcoma cells the amino-terminal fragments bound to a single order of sites; the affinity of rPTH-(1-34) exceeded that of bPTH-(1-34), correlating with its higher potency in stimulating adenylate cyclase. In studies with oxidized bPTH-(1--84), the middle and carboxyl regions of intact PTH were found to bind to both tissues but with higher affinity to osteosarcoma cells than to renal membranes. Our results demonstrate that rPTH-(1--34) is the most favorable probe of amino-terminal PTH binding and the most potent of the PTH peptides in stimulating renal and osseous adenylate cyclase. The results also show that midregion and carboxyl determinants within intact PTH contribute to hormone binding, which does not correlate with adenylate cyclase activation and appears more significant for skeletal than for renal binding

A novel pseudo-complementary PNA G-C base pair

DEFF Research Database (Denmark)

Olsen, Anne G.; Dahl, Otto; Petersen, Asger Bjørn

2011-01-01

Pseudo-complementary oligonucleotide analogues and mimics provide novel opportunities for targeting duplex structures in RNA and DNA. Previously, a pseudo-complementary A-T base pair has been introduced. Towards sequence unrestricted targeting, a pseudo-complementary G-C base pair consisting...

Circulating forms of immunoreactive parathyroid hormone-related protein for identifying patients with humoral hypercalcemia of malignancy. A comparative study with C-terminal (109-141)- and N-terminal (1-86)-region-specific PTHrP radioassay

International Nuclear Information System (INIS)

Suehiro, Mitsuko; Murakami, Minoru; Fukuchi, Minoru

1994-01-01

We evaluated the circulating forms of immunoreactive parathyroid hormone-related protein(PTHrP) in 115 healthy subjects and 122 patients with malignant diseases by using radioassay systems (RAS) specific for the C-terminal (109-141) fragment of PTHrP (C-RAS) and for the N-terminal(1-86) (N-RAS). PTHrP levels in healthy controls ranged from 1.5 to 38.2 (mean: 24.5) pmol/L with the C-RAS and from 0.9 to 2.5 (mean: 1.7) pmol/L with the N-RAS. The ratio of circulating N-terminal fragment (N) to C-terminal fragment (C) of PTHrP was calculated to be about 1 : 14.4 in the healthy subjects. Of the 122 patients with malignant diseases, 40 (32.8%) had circulating PTHrP levels undetectable with the N-RAS, but only 11 (9.0%) patients had levels undetectable with the C-RAS. Of the former 122 patients, 41 (33.6%) had high PTHrP as determined with the C-RAS, and 10 (8.2%) had high PTHrP as determined with the N-RAS. The former of these included only 8 (19.5%) humoral hypercalcemia malignancy(HHM) patients, while the latter included 8 (80.0%) HHM patients. The circulating N to C ratio was about 1 : 70.7 in the HHM patients. The N and C obtained with the different RASs showed a close correlation (r=0.86). The values also showed a close correlation with serum Ca; r=0.75 for C-RAS and r=0.81 for N-RAS. In addition, the correlation between the PTHrP reading obtained with the different RASs and serum Cr were: r=0.42 with C-RAS and r=0.26 with N-RAS. The circulating form of immunoreactive PTHrP fragments is therefore comprised mainly of PTHrP (109-141). In contrast, circulating concentrations of the PTHrP (1-86) fragment are very low, but detection of the PTHrP (1-86) fragment with the N-RAS is a more useful indicator of HHM with fewer false positive results and is less likely to be influenced by renal function than the detection of the PHPrP (109-141) fragment with C-RAS. (author)

Linearized pseudo-Einstein equations on the Heisenberg group

Science.gov (United States)

Barletta, Elisabetta; Dragomir, Sorin; Jacobowitz, Howard

2017-02-01

We study the pseudo-Einstein equation R11bar = 0 on the Heisenberg group H1 = C × R. We consider first order perturbations θɛ =θ0 + ɛ θ and linearize the pseudo-Einstein equation about θ0 (the canonical Tanaka-Webster flat contact form on H1 thought of as a strictly pseudoconvex CR manifold). If θ =e2uθ0 the linearized pseudo-Einstein equation is Δb u - 4 | Lu|2 = 0 where Δb is the sublaplacian of (H1 ,θ0) and L bar is the Lewy operator. We solve the linearized pseudo-Einstein equation on a bounded domain Ω ⊂H1 by applying subelliptic theory i.e. existence and regularity results for weak subelliptic harmonic maps. We determine a solution u to the linearized pseudo-Einstein equation, possessing Heisenberg spherical symmetry, and such that u(x) → - ∞ as | x | → + ∞.

Fragmentation in rotating isothermal protostellar clouds

International Nuclear Information System (INIS)

Bodenheimer, P.; Black, D.C.

1980-01-01

In this paper we report briefly the results of an extensive set of 3-D hydrodynamic calculations that have been performed during the past two and one-half years to investigate the susceptibility of rotating clouds to gravitational fragmentation. Because of the immensity of parameter space and the expense of computations, we have chosen to restrict this investigation to strictly isothermal collapse sequences. (orig./WL)

Pseudo-Riemannian VSI spaces

International Nuclear Information System (INIS)

Hervik, Sigbjoern; Coley, Alan

2011-01-01

In this paper we consider pseudo-Riemannian spaces of arbitrary signature for which all of the polynomial curvature invariants vanish (VSI spaces). We discuss an algebraic classification of pseudo-Riemannian spaces in terms of the boost weight decomposition and define the S i - and N-properties, and show that if the curvature tensors of the space possess the N-property, then it is a VSI space. We then use this result to construct a set of metrics that are VSI. All of the VSI spaces constructed possess a geodesic, expansion-free, shear-free, and twist-free null congruence. We also discuss the related Walker metrics.

Pseudo-Riemannian VSI spaces

Energy Technology Data Exchange (ETDEWEB)

Hervik, Sigbjoern [Faculty of Science and Technology, University of Stavanger, N-4036 Stavanger (Norway); Coley, Alan, E-mail: sigbjorn.hervik@uis.no, E-mail: aac@mathstat.dal.ca [Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 3J5 (Canada)

2011-01-07

In this paper we consider pseudo-Riemannian spaces of arbitrary signature for which all of the polynomial curvature invariants vanish (VSI spaces). We discuss an algebraic classification of pseudo-Riemannian spaces in terms of the boost weight decomposition and define the S{sub i}- and N-properties, and show that if the curvature tensors of the space possess the N-property, then it is a VSI space. We then use this result to construct a set of metrics that are VSI. All of the VSI spaces constructed possess a geodesic, expansion-free, shear-free, and twist-free null congruence. We also discuss the related Walker metrics.

Pseudo-differential operators on manifolds with singularities

CERN Document Server

Schulze, B-W

1991-01-01

The analysis of differential equations in domains and on manifolds with singularities belongs to the main streams of recent developments in applied and pure mathematics. The applications and concrete models from engineering and physics are often classical but the modern structure calculus was only possible since the achievements of pseudo-differential operators. This led to deep connections with index theory, topology and mathematical physics. The present book is devoted to elliptic partial differential equations in the framework of pseudo-differential operators. The first chapter contains the Mellin pseudo-differential calculus on R+ and the functional analysis of weighted Sobolev spaces with discrete and continuous asymptotics. Chapter 2 is devoted to the analogous theory on manifolds with conical singularities, Chapter 3 to manifolds with edges. Employed are pseudo-differential operators along edges with cone-operator-valued symbols.

Ninety-five- and 25-kDa fragments of the human immunodeficiency virus envelope glycoprotein gp120 bind to the CD4 receptor

International Nuclear Information System (INIS)

Nygren, A.; Bergman, T.; Matthews, T.; Joernvall, H.; Wigzell, H.

1988-01-01

Iodine-125-labeled gp120 (120-kDa envelope glycoprotein) from the BH10 isolate of human immunodeficiency virus is cleaved to a limited extend with the glutamate-specific protease from Staphylococcus aureus. After disulfide bond reduction, fragments with approximate molecular masses of 95, 60, 50, and 25 kDa are produced. Tests for binding to CD4-positive cells show that only two fragments, the 95- and 25- kDa peptides, are observed in cleavage products that retain the selective binding capacity of gp120. Radiosequence analysis of the fragments after sodium dodecyl sulfate/polyacrylamide gel electrophoresis and electroblotting demonstrates that the 95-kDa fragment lacks the N-terminal region of gp120 and starts at position 143 of the mature envelope protein. The 50-kDa fragment starts at the same position. The 25-kDa binding fragment was similarly deduced to be generated as a small fragment from a cleavage site in the C-terminal part of gp120. The identifications of these fragments demonstrate that radiosequence analysis utilizing 125 I-labeled tyrosine residues can function as a useful and reliable method for small-scale determination of cleavage sites in proteins. Combined, the data suggest domain-like subdivisions of gp120, define at least two intervening segments especially sensitive to proteolytic cleavage, and demonstrate the presence of a functional region for receptor binding in the C-terminal part of the molecule

The Fermi pseudo-potential in one dimension

International Nuclear Information System (INIS)

Coutinho, F A B; Nogami, Y; Tomio, Lauro; Toyama, F M

2004-01-01

Wu and Yu recently examined point interactions in one dimension in the form of the Fermi pseudo-potential. On the other hand there are point interactions in the form of self-adjoint extensions (SAEs) of the kinetic energy operator. We examine the relationship between the point interactions in these two forms in the one-channel and two-channel cases. In the one-channel case the pseudo-potential leads to the standard three-parameter family of SAEs. In the two-channel case the pseudo-potential furnishes a ten-parameter family of SAEs

Anticoagulant and calcium-binding properties of high molecular weight derivatives of human fibrinogen, produced by plasmin (fragments X)

NARCIS (Netherlands)

Nieuwenhuizen, W.; Gravesen, M.

1981-01-01

Early plasmin degradation products (X fragments) of human fibrinogen were prepared in the presence of calcium-ions or EGTA, and purified on Sepharose 6B-CL. X fragments were characterized with respect to amino-terminal amino acids, polypeptide-chain composition, anticlotting properties and

Lactobacillus strain diversity based on partial hsp60 gene sequences and design of PCR-restriction fragment length polymorphism assays for species identification and differentiation.

Science.gov (United States)

Blaiotta, Giuseppe; Fusco, Vincenzina; Ercolini, Danilo; Aponte, Maria; Pepe, Olimpia; Villani, Francesco

2008-01-01

A phylogenetic tree showing diversities among 116 partial (499-bp) Lactobacillus hsp60 (groEL, encoding a 60-kDa heat shock protein) nucleotide sequences was obtained and compared to those previously described for 16S rRNA and tuf gene sequences. The topology of the tree produced in this study showed a Lactobacillus species distribution similar, but not identical, to those previously reported. However, according to the most recent systematic studies, a clear differentiation of 43 single-species clusters was detected/identified among the sequences analyzed. The slightly higher variability of the hsp60 nucleotide sequences than of the 16S rRNA sequences offers better opportunities to design or develop molecular assays allowing identification and differentiation of either distant or very closely related Lactobacillus species. Therefore, our results suggest that hsp60 can be considered an excellent molecular marker for inferring the taxonomy and phylogeny of members of the genus Lactobacillus and that the chosen primers can be used in a simple PCR procedure allowing the direct sequencing of the hsp60 fragments. Moreover, in this study we performed a computer-aided restriction endonuclease analysis of all 499-bp hsp60 partial sequences and we showed that the PCR-restriction fragment length polymorphism (RFLP) patterns obtainable by using both endonucleases AluI and TacI (in separate reactions) can allow identification and differentiation of all 43 Lactobacillus species considered, with the exception of the pair L. plantarum/L. pentosus. However, the latter species can be differentiated by further analysis with Sau3AI or MseI. The hsp60 PCR-RFLP approach was efficiently applied to identify and to differentiate a total of 110 wild Lactobacillus strains (including closely related species, such as L. casei and L. rhamnosus or L. plantarum and L. pentosus) isolated from cheese and dry-fermented sausages.

Mutant DNA quantification by digital PCR can be confounded by heating during DNA fragmentation.

Science.gov (United States)

Kang, Qing; Parkin, Brian; Giraldez, Maria D; Tewari, Muneesh

2016-04-01

Digital PCR (dPCR) is gaining popularity as a DNA mutation quantification method for clinical specimens. Fragmentation prior to dPCR is required for non-fragmented genomic DNA samples; however, the effect of fragmentation on DNA analysis has not been well-studied. Here we evaluated three fragmentation methods for their effects on dPCR point mutation assay performance. Wild-type (WT) human genomic DNA was fragmented by heating, restriction digestion, or acoustic shearing using a Covaris focused-ultrasonicator. dPCR was then used to determine the limit of blank (LoB) by quantifying observed WT and mutant allele counts of the proto-oncogenes KRAS and BRAF in the WT DNA sample. DNA fragmentation by heating to 95°C, while the simplest and least expensive method, produced a high background mutation frequency for certain KRAS mutations relative to the other methods. This was due to heat-induced mutations, specifically affecting dPCR assays designed to interrogate guanine to adenine (G>A) mutations. Moreover, heat-induced fragmentation overestimated gene copy number, potentially due to denaturation and partition of single-stranded DNA into different droplets. Covaris acoustic shearing and restriction enzyme digestion showed similar LoBs and gene copy number estimates to one another. It should be noted that moderate heating, commonly used in genomic DNA extraction protocols, did not significantly increase observed KRAS mutation counts.

Prenatal diagnosis of metatropic dysplasia: beware of the pseudo-bowing sign

International Nuclear Information System (INIS)

Garel, Catherine; Dhouib, Amira; Sileo, Chiara; Ducou le Pointe, Hubert; Cormier-Daire, Valerie

2014-01-01

Metatropic dysplasia is a very rare form of osteochondrodysplasia with only one case of prenatal diagnosis described in the literature. It is characterized by marked shortening of the long bones with severe platyspondyly and dumbbell-shape metaphyses. We report a case of metatropic dysplasia that was diagnosed prenatally and describe the findings on US and CT. The pregnancy was terminated and the post-mortem radiographs are shown. The woman had been referred for short and bowed long bones. Severe metaphyseal enlargement was a misleading finding because it had been misinterpreted as limb bowing. Thus when abnormal curvature of the long bones is observed at prenatal US, attention should be drawn not only to the diaphyses but also to the metaphyses because severe metaphyseal enlargement might be responsible for pseudo-bowing. (orig.)

Prenatal diagnosis of metatropic dysplasia: beware of the pseudo-bowing sign

Energy Technology Data Exchange (ETDEWEB)

Garel, Catherine [Trousseau Hospital, University Hospitals of the East of Paris, Department of Radiology, Paris (France); Hopital d' Enfants Armand-Trousseau, Department of Radiology, Paris (France); Dhouib, Amira; Sileo, Chiara; Ducou le Pointe, Hubert [Trousseau Hospital, University Hospitals of the East of Paris, Department of Radiology, Paris (France); Cormier-Daire, Valerie [Paris Descartes University, Sorbonne Paris Cite, Necker-Enfants-Malades Hospital, Department of Genetics, Paris (France)

2014-03-15

Metatropic dysplasia is a very rare form of osteochondrodysplasia with only one case of prenatal diagnosis described in the literature. It is characterized by marked shortening of the long bones with severe platyspondyly and dumbbell-shape metaphyses. We report a case of metatropic dysplasia that was diagnosed prenatally and describe the findings on US and CT. The pregnancy was terminated and the post-mortem radiographs are shown. The woman had been referred for short and bowed long bones. Severe metaphyseal enlargement was a misleading finding because it had been misinterpreted as limb bowing. Thus when abnormal curvature of the long bones is observed at prenatal US, attention should be drawn not only to the diaphyses but also to the metaphyses because severe metaphyseal enlargement might be responsible for pseudo-bowing. (orig.)

Pseudo-capacitor device for aqueous electrolytes

Science.gov (United States)

Prakash, Jai; Thackeray, Michael M.; Dees, Dennis W.; Vissers, Donald R.; Myles, Kevin M.

1998-01-01

A pseudo-capacitor having a high energy storage capacity develops a double layer capacitance as well as a Faradaic or battery-like redox reaction, also referred to as pseudo-capacitance. The Faradaic reaction gives rise to a capacitance much greater than that of the typical ruthenate oxide ultracapacitor which develops only charge separation-based double layer capacitance. The capacitor employs a lead and/or bismuth/ruthenate and/or iridium system having the formula A.sub.2 ›B.sub.2-x Pb.sub.x !O.sub.7-y, where A=Pb, Bi, and B=Ru, Ir, and Ocapacitor. The amount of expensive ruthenate and iridium can be substantially reduced in the pseudo-capacitor by increasing the lead content while improving energy storage capacity.

The N-terminal neurotensin fragment, NT1-11, inhibits cortisol secretion by human adrenocortical cells.

Science.gov (United States)

Sicard, Flavie; Contesse, Vincent; Lefebvre, Hervé; Ait-Ali, Djida; Gras, Marjorie; Cartier, Dorthe; Decker, Annick; Chartrel, Nicolas; Anouar, Youssef; Vaudry, Hubert; Delarue, Catherine

2006-08-01

Neurotensin (NT) modulates corticosteroid secretion from the mammalian adrenal gland. The objective of this study was to investigate the possible involvement of NT in the control of cortisol secretion in the human adrenal gland. In vitro studies were conducted on cultured human adrenocortical cells. This study was conducted in a university research laboratory. Adrenal explants from patients undergoing expanded nephrectomy for kidney cancer were studied. Cortisol secretion from cultured adrenocortical cells was measured. NT1-11, the N-terminal fragment of NT, dose-dependently inhibited basal and ACTH-stimulated cortisol production by human adrenocortical cells in primary culture. In contrast, NT had no influence on cortisol output at concentrations up to 10(-6) m. HPLC and RT-PCR analyses failed to detect any significant amounts of NT and NT mRNA, respectively, in adrenal extracts. Molecular and pharmacological studies were performed to determine the type of NT receptor involved in the corticostatic effect of NT1-11. RT-PCR analysis revealed the expression of NT receptor type (NTR) 3 mRNA but not NTR1 and NTR2 mRNAs in the human adrenal tissue. However, the pharmacological profile of the adrenal NT1-11 receptor was different from that of NTR3, indicating that this receptor type is not involved in the action of NT1-11 on corticosteroidogenesis. Our results indicate that NT1-11 may act as an endocrine factor to inhibit cortisol secretion through activation of a receptor distinct from the classical NTR1, NTR2, and NTR3.

Papain cleavage of the 38,000-dalton fragment inhibits the binding of 4, 4'-diisothiocyanostilbene-2, 2'-disulfonate to lys-539 on the 60,000-dalton fragment in human band 3.

Science.gov (United States)

Yamaguchi, Takeo; Kojima, Hideaki; Kawaguchi, Shiori; Shimada, Maiko; Aso, Haruka

2017-08-01

Human band 3 is a 98-kDa transmembrane (TM) protein comprising 14 TM segments. Papain cleavages band 3 into 38- and 60-kDa fragments. Under vigorous conditions, the cleavage of the loop region between the TM 7 of gate domain and the TM 8 of core domain in the 38-kDa fragment produces 7- and 31-kDa fragments. Conformational changes of the TM 5 segment containing Lys-539 by cleavage of the 38-kDa fragment remain unclear. Pressure-induced haemolysis of erythrocytes was suppressed by binding of 4, 4'-diisothiocyanostilbene-2, 2'-disulfonate (DIDS) to Lys-539. Such effect of DIDS was not observed upon cleavage of the 38-kDa fragment, because of inhibition of DIDS binding to Lys-539. Using fluorescence of DIDS labelled to Lys-539, conformational changes of band 3 were examined. Fluorescence spectra demonstrated that the molecular motion of DIDS is more restricted upon digestion of the 38-kDa fragment. Interestingly, the quenching of DIDS fluorescence showed that Hg2+ is less accessible to DIDS upon digestion of the 38-kDa fragment. Taken together, we propose that the conformational changes of the TM 5 segment characterized by the sequestration and restricted motion of Lys-539 are induced by the cleavage of the loop region between the TM 7 and the TM 8. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Three-dimensional vectorial multifocal arrays created by pseudo-period encoding

Science.gov (United States)

Zeng, Tingting; Chang, Chenliang; Chen, Zhaozhong; Wang, Hui-Tian; Ding, Jianping

2018-06-01

Multifocal arrays have been attracting considerable attention recently owing to their potential applications in parallel optical tweezers, parallel single-molecule orientation determination, parallel recording and multifocal multiphoton microscopy. However, the generation of vectorial multifocal arrays with a tailorable structure and polarization state remains a great challenge, and reports on multifocal arrays have hitherto been restricted either to scalar focal spots without polarization versatility or to regular arrays with fixed spacing. In this work, we propose a specific pseudo-period encoding technique to create three-dimensional (3D) vectorial multifocal arrays with the ability to manipulate the position, polarization state and intensity of each focal spot. We experimentally validated the flexibility of our approach in the generation of 3D vectorial multiple spots with polarization multiplicity and position tunability.

Gene flow and effective population sizes of the butterfly Maculinea alcon in a highly fragmented, anthropogenic landscape

DEFF Research Database (Denmark)

Vanden Broeck, An; Maes, Dirk; Kelager, Andreas

2017-01-01

fragmentation as they occupy narrow niches or restricted habitat ranges. Here, we assess contemporary interpopulation connectedness of the threatened, myrmecophilous butterfly,Maculinea alcon, in a highly fragmented landscape.Weinferred dispersal, effective population sizes, genetic diversity and structure...

Morphological and Molecular Characterization of Dietary-Induced Pseudo-Albinism during Post-Embryonic Development of Solea senegalensis (Kaup, 1858)

Science.gov (United States)

Darias, Maria J.; Andree, Karl B.; Boglino, Anaïs; Rotllant, Josep; Cerdá-Reverter, José Miguel; Estévez, Alicia; Gisbert, Enric

2013-01-01

The appearance of the pseudo-albino phenotype was investigated in developing Senegalese sole (Solea senegalensis, Kaup 1858) larvae at morphological and molecular levels. In order to induce the development of pseudo-albinos, Senegalese sole larvae were fed Artemia enriched with high levels of arachidonic acid (ARA). The development of their skin pigmentation was compared to that of a control group fed Artemia enriched with a reference commercial product. The relative amount of skin melanophores, xanthophores and iridophores revealed that larval pigmentation developed similarly in both groups. However, results from different relative proportions, allocation patterns, shapes and sizes of skin chromatophores revealed changes in the pigmentation pattern between ARA and control groups from 33 days post hatching onwards. The new populations of chromatophores that should appear at post-metamorphosis were not formed in the ARA group. Further, spatial patterns of distribution between the already present larval xanthophores and melanophores were suggestive of short-range interaction that seemed to be implicated in the degradation of these chromatophores, leading to the appearance of the pseudo-albino phenotype. The expression profile of several key pigmentation-related genes revealed that melanophore development was promoted in pseudo-albinos without a sufficient degree of terminal differentiation, thus preventing melanogenesis. Present results suggest the potential roles of asip1 and slc24a5 genes on the down-regulation of trp1 expression, leading to defects in melanin production. Moreover, gene expression data supports the involvement of pax3, mitf and asip1 genes in the developmental disruption of the new post-metamorphic populations of melanophores, xanthophores and iridophores. PMID:23874785

Pseudo-supersymmetry and the domain-wall/cosmology correspondence

International Nuclear Information System (INIS)

Skenderis, Kostas; Townsend, Paul K

2007-01-01

The correspondence between domain-wall and cosmological solutions of gravity coupled to scalar fields is explained. Any domain-wall solutions that admit a Killing spinor are shown to correspond to a cosmology that admits a pseudo-Killing spinor; whereas the Killing spinor obeys a Dirac-type equation with Hermitian 'mass'-matrix, the corresponding pseudo-Killing spinor obeys a Dirac-type equation with a anti-Hermitian 'mass'-matrix. We comment on some implications of (pseudo)supersymmetry

Identification of Echinococcus granulosus strains using polymerase chain reaction-restriction fragment length polymorphism amongst livestock in Moroto district, Uganda.

Science.gov (United States)

Chamai, Martin; Omadang, Leonard; Erume, Joseph; Ocaido, Michael; Oba, Peter; Othieno, Emmanuel; Bonaventure, Straton; Kitibwa, Annah

2016-07-29

A descriptive study was conducted to identify the different strains of Echinococcus granulosus occurring in livestock in Moroto district, Uganda. Echinococcus cysts from 104 domestic animals, including cattle, sheep, goats and camels, were taken and examined by microscopy, polymerase chain reaction with restriction fragment length polymorphism and Sanger DNA sequencing. Echinococcus granulosus genotypes or strains were identified through use of Bioinformatics tools: BioEdit, BLAST and MEGA6. The major finding of this study was the existence of a limited number of E. granulosus genotypes from cattle, goats, sheep and camels. The most predominant genotype was G1 (96.05%), corresponding to the common sheep strain. To a limited extent (3.95%), the study revealed the existence of Echinococcus canadensis G6/7 in three (n = 3) of the E. granulosus-positive samples. No other strains of E. granulosus were identified. It was concluded that the common sheep strain of Echinococcus sensu stricto and G6/7 of E. canadensis were responsible for echinococcal disease in Moroto district, Uganda.

Lyme disease with facial nerve palsy: rapid diagnosis using a nested polymerase chain reaction-restriction fragment length polymorphism analysis.

Science.gov (United States)

Hashimoto, Y; Takahashi, H; Kishiyama, K; Sato, Y; Nakao, M; Miyamoto, K; Iizuka, H

1998-02-01

A 64-year-old woman with Lyme disease and manifesting facial nerve palsy had been bitten by a tick on the left frontal scalp 4 weeks previously. Erythema migrans appeared on the left forehead, accompanied by left facial paralysis. Nested polymerase chain reaction-restriction fragment length polymorphism analysis (nested PCR-RFLP) was performed on DNA extracted from a skin biopsy of the erythema on the left forehead. Borrelia flagellin gene DNA was detected and its RFLP pattern indicated that the organism was B. garinii, Five weeks later, B. garinii was isolated by conventional culture from the erythematous skin lesion, but not from the cerebrospinal fluid. After treatment with ceftriaxone intravenously for 10 days and oral administration of minocycline for 7 days, both the erythema and facial nerve palsy improved significantly. Nested PCR and culture taken after the lesion subsided, using skin samples obtained from a site adjacent to the original biopsy, were both negative. We suggest that nested PCR-RFLP analysis might be useful for the rapid diagnosis of Lyme disease and for evaluating therapy.

The simultaneous use of several pseudo-random binary sequences in the identification of linear multivariable dynamic systems

International Nuclear Information System (INIS)

Cummins, J.D.

1965-02-01

With several white noise sources the various transmission paths of a linear multivariable system may be determined simultaneously. This memorandum considers the restrictions on pseudo-random two state sequences to effect simultaneous identification of several transmission paths and the consequential rejection of cross-coupled signals in linear multivariable systems. The conditions for simultaneous identification are established by an example, which shows that the integration time required is large i.e. tends to infinity, as it does when white noise sources are used. (author)

Systemic N-terminal fragments of adrenocorticotropin reduce inflammation- and stress-induced anhedonia in rats.

Science.gov (United States)

Markov, Dmitrii D; Yatsenko, Ksenia A; Inozemtseva, Lyudmila S; Grivennikov, Igor A; Myasoedov, Nikolai F; Dolotov, Oleg V

2017-08-01

Emerging evidence implicates impaired self-regulation of the hypothalamic-pituitary-adrenal (HPA) axis and inflammation as important and closely related components of the pathophysiology of major depression. Antidepressants show anti-inflammatory effects and are suggested to enhance glucocorticoid feedback inhibition of the HPA axis. HPA axis activity is also negatively self-regulated by the adrenocorticotropic hormone (ACTH), a potent anti-inflammatory peptide activating five subtypes of melanocortin receptors (MCRs). There are indications that ACTH-mediated feedback can be activated by noncorticotropic N-terminal ACTH fragments such as a potent anti-inflammatory MC1/3/4/5R agonist α-melanocyte-stimulating hormone (α-MSH), corresponding to ACTH(1-13), and a MC3/5R agonist ACTH(4-10). We investigated whether intraperitoneal administration of rats with these peptides affects anhedonia, which is a core symptom of depression. Inflammation-related anhedonia was induced by a single intraperitoneal administration of a low dose (0.025mg/kg) of lipopolysaccharide (LPS). Stress-related anhedonia was induced by the chronic unpredictable stress (CUS) procedure. The sucrose preference test was used to detect anhedonia. We found that ACTH(4-10) pretreatment decreased LPS-induced increase in serum corticosterone and tumor necrosis factor (TNF)-α, and a MC3/4R antagonist SHU9119 blocked this effect. Both α-MSH and ACTH(4-10) alleviated LPS-induced anhedonia. In the CUS model, these peptides reduced anhedonia and normalized body weight gain. The data indicate that systemic α-MSH and ACTH(4-10) produce an antidepressant-like effect on anhedonia induced by stress or inflammation, the stimuli that trigger the release of ACTH and α-MSH into the bloodstream. The results suggest a counterbalancing role of circulating melanocortins in depression and point to a new approach for antidepressant treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Allelopathic potential of Robinia pseudo-acacia L.

Science.gov (United States)

Nasir, Habib; Iqbal, Zahida; Hiradate, Syuntaro; Fujii, Yoshiharu

2005-09-01

Robinia pseudo-acacia L. (black locust) is a nonindigenous species currently invading the central part of Japanese grasslands. Several allelochemicals were identified and characterized from the leaf tissue. The growth of both radicle and hypocotyl in the tested species (barnyard grass, white clover, lettuce, and Chinese cabbage) was reduced when grown in soil mixed with the leaves of R. pseudo-acacia at various concentrations. Aqueous leaf extracts, when bioassayed, exhibited a significant suppression of radicle growth. Chromatographic separation of an ethanolic extract of R. pseudo-acacia leaves resulted in isolation of three compounds, identified as robinetin (1), myricetin (2), and quercetin (3) by nuclear magnetic resonance and mass spectroscopy. All inhibited root and shoot growth of lettuce. Robinetin, found in a large amount, caused 50% suppression of the root and shoot growth of lettuce at 100 ppm. The presence of these bioactive substances in leaf tissue suggests a potential role for flavonoids in R. pseudo-acacia invasion in introduced habitats.

Primary palpebral and orbital ossification in pseudo-pseudohypoparathyroidism

DEFF Research Database (Denmark)

Klauber, S.; Heegaard, S.; Prause, J.U.

2002-01-01

ophthalmology, Albright's heriditary osteodystrophy, ossification, pseudo-pseudohypoparathyroidism, pseodohypoparathyroidism, hypothyroidism, GNAS1 gene, history, eyelid, orbit......ophthalmology, Albright's heriditary osteodystrophy, ossification, pseudo-pseudohypoparathyroidism, pseodohypoparathyroidism, hypothyroidism, GNAS1 gene, history, eyelid, orbit...

Generation of biologically active endostatin fragments from human collagen XVIII by distinct matrix metalloproteases

International Nuclear Information System (INIS)

Heljasvaara, Ritva; Nyberg, Pia; Luostarinen, Jani; Parikka, Mataleena; Heikkilae, Pia; Rehn, Marko; Sorsa, Timo; Salo, Tuula; Pihlajaniemi, Taina

2005-01-01

Endostatin, a potent inhibitor of endothelial cell proliferation, migration, angiogenesis and tumor growth, is proteolytically cleaved from the C-terminal noncollagenous NC1 domain of type XVIII collagen. We investigated the endostatin formation from human collagen XVIII by several MMPs in vitro. The generation of endostatin fragments differing in molecular size (24-30 kDa) and in N-terminal sequences was identified in the cases of MMP-3, -7, -9, -13 and -20. The cleavage sites were located in the protease-sensitive hinge region between the trimerization and endostatin domains of NC1. MMP-1, -2, -8 and -12 did not show any significant activity against the C-terminus of collagen XVIII. The anti-proliferative effect of the 20-kDa endostatin, three longer endostatin-containing fragments generated in vitro by distinct MMPs and the entire NC1 domain, on bFGF-stimulated human umbilical vein endothelial cells was established. The anti-migratory potential of some of these fragments was also studied. In addition, production of endostatin fragments between 24-30 kDa by human hepatoblastoma cells was shown to be due to MMP action on type XVIII collagen. Our results indicate that certain, especially cancer-related, MMP family members can generate biologically active endostatin-containing polypeptides from collagen XVIII and thus, by releasing endostatin fragments, may participate in the inhibition of endothelial cell proliferation, migration and angiogenesis

Pseudo LRM waveforms from CryoSat SARin acquisition

Science.gov (United States)

Scagliola, Michele; Fornari, Marco; Bouffard, Jerome; Parrinello, Tommaso; Féménias, Pierre

2016-04-01

CryoSat was launched on the 8th April 2010 and is the first European ice mission dedicated to the monitoring of precise changes in the thickness of polar ice sheets and floating sea ice. The main payload of CryoSat is a Ku-band pulsewidth limited radar altimeter, called SIRAL (Synthetic interferometric radar altimeter). When commanded in SARIn (synthetic aperture radar interferometry) mode, through coherent along-track processing of the returns received from two antennas, the interferometric phase related to the first arrival of the echo is used to retrieve the angle of arrival of the scattering in the across-track direction. When SIRAL operates in SAR or SARin mode, the obtained waveforms have an along-track resolution and a speckle reduction which is increased with respect to the pulse-limited waveforms. Anyway, in order to analyze the continuity of the geophysical retrieved parameters among different acquisition modes, techniques to transform SARin mode data to pseudo-LRM mode data are welcome. The transformation process is known as SAR reduction and it is worth recalling here that only approximate pseudo-LRM waveforms can be obtained in case of closed burst acquisitions, as SIRAL operates. A SAR reduction processing scheme has been developed to obtain pseudo-LRM waveforms from CryoSat SARin acquisition. As a trade-off between the along-track length on Earth surface contributing to one SARin pseudo-LRM waveform and the noisiness of the waveform itself, it has been chosen a SAR reduction approach based on the averaging of all the SARin echoes received each 20Hz, resulting in one pseudo-LRM waveform for each SARin burst given the SARin burst repetition period. SARin pseudo-LRM waveforms have been produced for CryoSat acquisition both on ice and sea surfaces, aiming at verifying the continuity of the retracked surface height over the ellipsoid between genuine LRM products and pseudo-LRM products. Moreover, the retracked height from the SARin pseudo-LRM has been

Transmission of tuberculosis in Havana, Cuba: a molecular epidemiological study by IS6110 restriction fragment length polymorphism typing

Directory of Open Access Journals (Sweden)

Diaz R

2001-01-01

Full Text Available The combination of molecular and conventional epidemiological methods has improved the knowledge about the transmission of tuberculosis in urban populations. To examine transmission of tuberculosis in Havana, Cuba, with DNA fingerprinting, we studied 51 out of 92 Mycobacterium tuberculosis strains isolated from tuberculosis patients who resided in Havana and whose infection was culture-confirmed in the period from September 1997 to March 1998. Isolates from 28 patients (55% had unique IS6110 restriction fragment length polymorphism (RFLP patterns, while isolates from 23 others (45% had identical patterns and belonged to 7 clusters. Three clusters consisting of six, five and two cases were each related to small outbreaks that occurred in a closed setting. Three other clustered cases were linked to a large outbreak that occurred in another institution. Younger patients were more correlated to clustering than older ones. The finding that 45% of the isolates had clustered RFLP patterns suggests that recent transmission is a key factor in the tuberculosis cases in Havana. The IS6110 RFLP typing made it possible to define the occurrence of outbreaks in two closed institutions.

MEMS-LSI Integrated Microchip using Pseudo-SoC Technology

Science.gov (United States)

Funaki, Hideyuki; Itaya, Kazuhiko; Yamada, Hiroshi; Onozuka, Yutaka; Iida, Atsuko

The authors have developed pseudo-SoC technology to realize MEMS-LSI integrated micro-chip. The pseudo-SoC technology consists of three technologies which are wafer reconfiguration technology, inter-chip redistribution layer technology, and pseudo-SoC thinning technology. In the wafer reconfiguration technology, the filling of resin and surface step between heterogeneous chips were improved through the optimization of vacuum printing process and resin material. These improvements reduced the warpage of reconfiguration wafer, leading to achievement of the reconfiguration wafer with 5 inch in diameter. In the inter-chip redistribution layer technology, the interface adherence between planar layer and inter-chip redistribution layer was improved, leading to the inter-chip redistribution layer with 1μm/1μm in line/space on reconfiguration wafer. In the pseudo-SoC thinning technology, thin pseudo-SoC device with 100μm in thickness was achieved through developing mechanical backside grinding process technology. Furthermore, ultra-thin pseudo-SoC which integrated electrostatic MEMS light valve and PWM driver IC was prototyped through developing the ultra-thin MEMS encapsulation technology.

Pseudo-classical theory of Majorana-Weyl particle

International Nuclear Information System (INIS)

Grigoryan, G.V.; Grigoryan, R.P.; Tyutin, I.V.

1996-01-01

A pseudo-classical theory of Weyl particle in the space-time dimensions D = 2 n is constructed. The canonical quantization of that pseudo-classical theory is carried out and it results in the theory of the D = 2 n dimensional Weyl particle in the Foldy-Wouthuysen representation. 28 refs

Molecular mechanism of the intramembrane cleavage of the β-carboxyl terminal fragment of amyloid precursor protein by γ-secretase

Directory of Open Access Journals (Sweden)

Maho eMorishima-Kawashima

2014-11-01

Full Text Available Amyloid β-protein (Aβ plays a central role in the pathogenesis of Alzheimer’s disease, the most common age-associated neurodegenerative disorder. Aβ is generated through intramembrane proteolysis of the β-carboxyl terminal fragment (βCTF of β-amyloid precursor protein (APP by γ-secretase. The initial cleavage by γ-secretase occurs in the membrane/cytoplasm boundary of the βCTF, liberating the APP intracellular domain (AICD. The remaining βCTFs, which are truncated at the C-terminus (longer Aβs, are then cropped sequentially in a stepwise manner, predominantly at three residue intervals, to generate Aβ. There are two major Aβ product lines which generate Aβ40 and Aβ42 with concomitant release of three and two tripeptides, respectively. Additionally, many alternative cleavages occur, releasing peptides with three to six residues. These modulate the Aβ product lines and define the species and quantity of Aβ generated. Here, we review our current understanding of the intramembrane cleavage of the βCTF by γ-secretase, which may contribute to the future goal of developing an efficient therapeutic strategy for Alzheimer’s disease.

Intermittency in 197Au fragmentation

International Nuclear Information System (INIS)

Dabrowska, A.; Holynski, R.; Olszewski, A.; Szarska, M.; Wilczynska, B.; Wolter, W.; Wosiek, B.; Cherry, M.L.; Deines-Jones, P.; Jones, W.V.; Sengupta, K.; Wefel, B.

1995-07-01

The concept of factorial moments was applied to an analysis of the dynamical fluctuations in the charge distributions of the fragments emitted from gold nuclei with energies 10.6 and < 1.0 GeV/n interacting with emulsion nuclei. Clear evidence for intermittent fluctuations has been found in an analysis using all the particles released from the gold projectile, with a stronger effect observed below 1 GeV/n than at 10.6 GeV/n. For the full data sets, however, the intermittency effect was found to be very sensitive to the singly charged particles, and neglecting these particles strongly reduces the intermittency signal. When the analysis is restricted to the multiply charged fragments, an intermittency effect is revealed only for multifragmentation events, although one that is enhanced as compared to the analysis of all, singly and multiply charged, particles. The properties of the anomalous fractal dimensions suggest a sequential decay mechanism, rather than the existence of possible critical behaviour in the process of nuclear fragmentation. The likely influence of the charge conservation effects and the finite size of decaying systems on the observed intermittency signals was pointed out. (author). 37 refs, 9 figs, 5 tabs

Investigation of the fate and effects of acetyl cedrene on Capitella teleta and sediment bacterial community

DEFF Research Database (Denmark)

Ellegaard-Jensen, Lea; Selck, Henriette; Priemé, Anders

2010-01-01

/without Capitella teleta (formerly Capitella sp. I)). Furthermore effects of AC on microbial respiration in the system were determined by examining CO(2) flux. T-RFLP (terminal restriction fragment length polymorphism) was used to analyze PCR (polymerase chain reaction) amplified 16S DNA gene fragments from...

Coherent control of indirect photofragmentation in the weak-field limit: Control of transient fragment distributions

DEFF Research Database (Denmark)

Shu, Chuan-Cun; Henriksen, Niels Engholm

2011-01-01

I molecule, where it is shown that the probability of observing atomic fragments as well as the distribution of their relative momenta can be changed by a phase modulated pulse with a fixed bandwidth. This type of control is restricted to finite times during the indirect fragmentation. (C) 2011 American...

Anatomical etiology of “pseudo-sciatica” from superior cluneal nerve entrapment: a laboratory investigation

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Konno T

2017-11-01

Full Text Available Tomoyuki Konno,1 Yoichi Aota,2 Hiroshi Kuniya,1 Tomoyuki Saito,1 Ning Qu,3 Shogo Hayashi,3 Shinichi Kawata,3 Masahiro Itoh3 1Department of Orthopaedic Surgery, Yokohama City University Graduate School of Medicine, 2Department of Spine & Spinal Cord Surgery, Yokohama Brain and Spine Center, Yokohama, 3Department of Anatomy, Tokyo Medical University, Tokyo, Japan Objective: The superior cluneal nerve (SCN may become entrapped where it pierces the thoracolumbar fascia over the iliac crest; this can cause low back pain (LBP and referred pain radiating into the posterior thigh, calf, and occasionally the foot, producing the condition known as “pseudo-sciatica.” Because the SCN was thought to be a cutaneous branch of the lumbar dorsal rami, originating from the dorsal roots of L1–L3, previous anatomical studies failed to explain why SCN causes “pseudo-sciatica”. The purpose of the present anatomical study was to better elucidate the anatomy and improve the understanding of “pseudo-sciatica” from SCN entrapment. Materials and methods: SCN branches were dissected from their origin to termination in subcutaneous tissue in 16 cadavers (5 male and 11 female with a mean death age of 88 years (range 81–101 years. Special attention was paid to identify SCNs from their emergence from nerve roots and passage through the fascial attachment to the iliac crest. Results: Eighty-one SCN branches were identified originating from T12 to L5 nerve roots with 13 branches passing through the osteofibrous tunnel. These 13 branches originated from L3 (two sides, L4 (six sides, and L5 (five sides. Ten of the 13 branches showed macroscopic entrapment in the tunnel. Conclusion: The majority of SCNs at risk of nerve entrapment originated from the lower lumbar nerve. These anatomical results may explain why patients with SCN entrapment often evince leg pain or tingling that mimics sciatica. Keywords: superior cluneal nerve, entrapment neuropathy, dorsal rami

The N-end rule pathway counteracts cell death by destroying proapoptotic protein fragments.

Science.gov (United States)

Piatkov, Konstantin I; Brower, Christopher S; Varshavsky, Alexander

2012-07-03

In the course of apoptosis, activated caspases cleave ∼500 to ∼1,000 different proteins in a mammalian cell. The dynamics of apoptosis involve a number of previously identified, caspase-generated proapoptotic protein fragments, defined as those that increase the probability of apoptosis. In contrast to activated caspases, which can be counteracted by inhibitor of apoptosis proteins, there is little understanding of antiapoptotic responses to proapoptotic protein fragments. One possibility is the regulation of proapoptotic fragments through their selective degradation. The previously identified proapoptotic fragments Cys-RIPK1, Cys-TRAF1, Asp-BRCA1, Leu-LIMK1, Tyr-NEDD9, Arg-BID, Asp-BCL(XL), Arg-BIM(EL), Asp-EPHA4, and Tyr-MET bear destabilizing N-terminal residues. Tellingly, the destabilizing nature (but not necessarily the actual identity) of N-terminal residues of proapoptotic fragments was invariably conserved in evolution. Here, we show that these proapoptotic fragments are short-lived substrates of the Arg/N-end rule pathway. Metabolic stabilization of at least one such fragment, Cys-RIPK1, greatly augmented the activation of the apoptosis-inducing effector caspase-3. In agreement with this understanding, even a partial ablation of the Arg/N-end rule pathway in two specific N-end rule mutants is shown to sensitize cells to apoptosis. We also found that caspases can inactivate components of the Arg/N-end rule pathway, suggesting a mutual suppression between this pathway and proapoptotic signaling. Together, these results identify a mechanistically specific and functionally broad antiapoptotic role of the Arg/N-end rule pathway. In conjunction with other apoptosis-suppressing circuits, the Arg/N-end rule pathway contributes to thresholds that prevent a transient or otherwise weak proapoptotic signal from reaching the point of commitment to apoptosis.

A Semester-Long Project for Teaching Basic Techniques in Molecular Biology Such as Restriction Fragment Length Polymorphism Analysis to Undergraduate and Graduate Students

Science.gov (United States)

DiBartolomeis, Susan M.

2011-01-01

Several reports on science education suggest that students at all levels learn better if they are immersed in a project that is long term, yielding results that require analysis and interpretation. I describe a 12-wk laboratory project suitable for upper-level undergraduates and first-year graduate students, in which the students molecularly locate and map a gene from Drosophila melanogaster called dusky and one of dusky's mutant alleles. The mapping strategy uses restriction fragment length polymorphism analysis; hence, students perform most of the basic techniques of molecular biology (DNA isolation, restriction enzyme digestion and mapping, plasmid vector subcloning, agarose and polyacrylamide gel electrophoresis, DNA labeling, and Southern hybridization) toward the single goal of characterizing dusky and the mutant allele dusky73. Students work as individuals, pairs, or in groups of up to four students. Some exercises require multitasking and collaboration between groups. Finally, results from everyone in the class are required for the final analysis. Results of pre- and postquizzes and surveys indicate that student knowledge of appropriate topics and skills increased significantly, students felt more confident in the laboratory, and students found the laboratory project interesting and challenging. Former students report that the lab was useful in their careers. PMID:21364104

10.23  Mcps laser pseudo-code ranging system with 0.33  mm (1σ) pseudo-range measurement precision.

Science.gov (United States)

Yu, Xiaonan; Tong, Shoufeng; Zhang, Lei; Dong, Yan; Zhao, Xin; Qiao, Yue

2017-07-01

The inter-satellite laser link is the backbone of the next inter-satellite information network, and ranging and communication are the main functions of the inter-satellite laser link. This study focuses on the inter-satellite laser ranging based on the pseudo-code correlation technology. In this paper, several typical laser-ranging methods have been compared and we determined that the laser pseudo-code ranging architecture is more suitable for the inter-satellite laser communication link. The pseudo-code ranging system is easy to combine with a digital communication system, and we used it to calculate integer ambiguity by modulating the time information. The main challenge of the ranging system is range precision, which is the main focus of this paper. First, the framework of the pseudo-code ranging system is introduced; the ranging architecture of dual one-way ranging is used to eliminate the clock error between the two transceivers, and then the uncertainty of the phase detector is analyzed. In the analysis, the carrier to noise ratio and the ranging code rate are constrained by the laser communication link margin and the electronic hardware limitation. Therefore, the relationship between the sampling depth and the phase detector uncertainty is verified. A series of optical fiber channel laser pseudo-code ranging experiments demonstrated the effects of sampling depth on the ranging precision. By adjusting the depth of storage, such as the depth of 1.6 Mb, we obtained a pseudo-range measurement precision of 0.33 mm (1σ), which is equivalent to 0.0001 times code subdivision of 10.23 Mcps pseudo-code. This paper has achieved high precision in a pseudo-range measurements, which is the foundation of the inter-satellite laser link.

Gene Flow of a Forest-Dependent Bird across a Fragmented Landscape.

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Rachael V Adams

Full Text Available Habitat loss and fragmentation can affect the persistence of populations by reducing connectivity and restricting the ability of individuals to disperse across landscapes. Dispersal corridors promote population connectivity and therefore play important roles in maintaining gene flow in natural populations inhabiting fragmented landscapes. In the prairies, forests are restricted to riparian areas along river systems which act as important dispersal corridors for forest dependent species across large expanses of unsuitable grassland habitat. However, natural and anthropogenic barriers within riparian systems have fragmented these forested habitats. In this study, we used microsatellite markers to assess the fine-scale genetic structure of a forest-dependent species, the black-capped chickadee (Poecile atricapillus, along 10 different river systems in Southern Alberta. Using a landscape genetic approach, landscape features (e.g., land cover were found to have a significant effect on patterns of genetic differentiation. Populations are genetically structured as a result of natural breaks in continuous habitat at small spatial scales, but the artificial barriers we tested do not appear to restrict gene flow. Dispersal between rivers is impeded by grasslands, evident from isolation of nearby populations (~ 50 km apart, but also within river systems by large treeless canyons (>100 km. Significant population genetic differentiation within some rivers corresponded with zones of different cottonwood (riparian poplar tree species and their hybrids. This study illustrates the importance of considering the impacts of habitat fragmentation at small spatial scales as well as other ecological processes to gain a better understanding of how organisms respond to their environmental connectivity. Here, even in a common and widespread songbird with high dispersal potential, small breaks in continuous habitats strongly influenced the spatial patterns of genetic

Higher-order Jordan Osserman pseudo-Riemannian manifolds

International Nuclear Information System (INIS)

Gilkey, Peter B; Ivanova, Raina; Zhang Tan

2002-01-01

We study the higher-order Jacobi operator in pseudo-Riemannian geometry. We exhibit a family of manifolds so that this operator has constant Jordan normal form on the Grassmannian of subspaces of signature (r, s) for certain values of (r, s). These pseudo-Riemannian manifolds are new and non-trivial examples of higher-order Osserman manifolds

Higher-order Jordan Osserman pseudo-Riemannian manifolds

Energy Technology Data Exchange (ETDEWEB)

Gilkey, Peter B [Mathematics Department, University of Oregon, Eugene, OR 97403 (United States); Ivanova, Raina [Mathematics Department, University of Hawaii - Hilo, 200 W Kawili St, Hilo, HI 96720 (United States); Zhang Tan [Department of Mathematics and Statistics, Murray State University, Murray, KY 42071 (United States)

2002-09-07

We study the higher-order Jacobi operator in pseudo-Riemannian geometry. We exhibit a family of manifolds so that this operator has constant Jordan normal form on the Grassmannian of subspaces of signature (r, s) for certain values of (r, s). These pseudo-Riemannian manifolds are new and non-trivial examples of higher-order Osserman manifolds.

Pseudo-Glassification Material for G-Demption

Energy Technology Data Exchange (ETDEWEB)

Casella, Andrew M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Buck, Edgar C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Gates, Robert O. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Riley, Brian J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2014-09-01

G-Demption, LLC has requested that PPNL provide design input for a “pseudo-glassification” process associated with their proposed technology for generating gamma irradiation stations from used nuclear fuel. The irradiation design currently consists of an aluminum enclosure designed to allow for proper encapsulation of and heat flow from a used fuel rod while minimally impacting the streaming of gamma rays from the fuel. In order to make their design more robust, G-Demption is investigating the benefits of backfilling this aluminum enclosure with a setting material once the used fuel rod is properly placed. This process has been initially referred to as “pseudo-glassification”, and strives not to impact heat transport or gamma streaming from the used fuel rod while providing increased fuel rod protection and fission gas retention. PNNL has compiled an internal material evaluation and discussion for the “pseudo-glassification” process in this report.

Pseudo-entanglement evaluated in noninertial frames

International Nuclear Information System (INIS)

Mehri-Dehnavi, Hossein; Mirza, Behrouz; Mohammadzadeh, Hosein; Rahimi, Robabeh

2011-01-01

Research highlights: → We study pseudo-entanglement in noninertial frames. → We examine different measures of entanglement and nonclassical correlation for the state. → We find the threshold for entanglement is changed in noninertial frames. → We also describe the behavior of local unitary classes of states in noninertial frames. - Abstract: We study quantum discord, in addition to entanglement, of bipartite pseudo-entanglement in noninertial frames. It is shown that the entanglement degrades from its maximum value in a stationary frame to a minimum value in an infinite accelerating frame. There is a critical region found in which, for particular cases, entanglement of states vanishes for certain accelerations. The quantum discord of pseudo-entanglement decreases by increasing the acceleration. Also, for a physically inaccessible region, entanglement and nonclassical correlation are evaluated and shown to match the corresponding values of the physically accessible region for an infinite acceleration.

Morphological and molecular characterization of dietary-induced pseudo-albinism during post-embryonic development of Solea senegalensis (Kaup, 1858.

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Maria J Darias

Full Text Available The appearance of the pseudo-albino phenotype was investigated in developing Senegalese sole (Solea senegalensis, Kaup 1858 larvae at morphological and molecular levels. In order to induce the development of pseudo-albinos, Senegalese sole larvae were fed Artemia enriched with high levels of arachidonic acid (ARA. The development of their skin pigmentation was compared to that of a control group fed Artemia enriched with a reference commercial product. The relative amount of skin melanophores, xanthophores and iridophores revealed that larval pigmentation developed similarly in both groups. However, results from different relative proportions, allocation patterns, shapes and sizes of skin chromatophores revealed changes in the pigmentation pattern between ARA and control groups from 33 days post hatching onwards. The new populations of chromatophores that should appear at post-metamorphosis were not formed in the ARA group. Further, spatial patterns of distribution between the already present larval xanthophores and melanophores were suggestive of short-range interaction that seemed to be implicated in the degradation of these chromatophores, leading to the appearance of the pseudo-albino phenotype. The expression profile of several key pigmentation-related genes revealed that melanophore development was promoted in pseudo-albinos without a sufficient degree of terminal differentiation, thus preventing melanogenesis. Present results suggest the potential roles of asip1 and slc24a5 genes on the down-regulation of trp1 expression, leading to defects in melanin production. Moreover, gene expression data supports the involvement of pax3, mitf and asip1 genes in the developmental disruption of the new post-metamorphic populations of melanophores, xanthophores and iridophores.

Theory of pseudo-differential operators over C*-Algebras

International Nuclear Information System (INIS)

Mohammad, N.

1987-06-01

In this article the behaviour of adjoints and composition of pseudo-differential operators in the framework of a C*-algebra is studied. It results that the class of pseudo-differential operators of order zero is a C*-algebra. 8 refs

Pseudo-nitzschia species on the Catalan coast: characterization and contribution to the current knowledge of the distribution of this genus in the Mediterranean Sea

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Sonia Quijano-Scheggia

2010-04-01

Full Text Available Proliferations of the genus Pseudo-nitzschia recur along the Catalan coast (NW Mediterranean throughout the year. The establishment of 58 clonal cultures facilitated morphological studies with scanning electron microscopy (SEM and ITS 5.8S rDNA sequence characterization. Moreover, strains of each species were examined with respect to sexual compatibility and toxicity. The results of the morphological and phylogenetic studies confirmed nine species of the genus Pseudo-nitzschia: P. brasiliana, P. calliantha, P. delicatissima clade A/del 2, P. arenysensis, P. fraudulenta, P. galaxiae, P. linea, P. multistriata and P. pungens clade I. Moreover, two Pseudo-nitzschia species, P. caciantha and P. cf mannii, could only be identified following SEM analysis of their morphology. None of the cultured strains of Pseudo-nitzschia analyzed produced domoic acid in amounts above the limit of detection. The current distributions of the Pseudo-nitzschia species in the Mediterranean Sea were plotted on maps, which led to the following observations: i diversity within this genus is much greater than previously considered, ii some species have a broad distribution (e.g. P. calliantha, iii whereas the distribution of others is narrowly restricted (e.g. P. pungens clade I. Moreover, this study reports the first detection of P. linea in the Mediterranean Sea and is the first description of P. galaxiae and P. cf mannii along the Catalan coast. Morphological studies coupled with molecular biological characterization, mating tests and biogeographic distribution analyses provide a critical theoretical basis for testing and/or implementing the current phylogenetic framework in the genus Pseudo-nitzschia.

Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis

International Nuclear Information System (INIS)

Mohr, Stephan; Masella, Michel; Ratcliff, Laura E.; Genovese, Luigi

2017-01-01

We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then introduce a simple and efficient formalism (which can be written as generalization of other well-known population analyses) to extract, from first principles, electrostatic multipoles for these fragments. The corresponding fragment multipoles can in this way be seen as reliable (pseudo-) observables. By applying our formalism within the code BigDFT, we show that the usage of a minimal set of in-situ optimized basis functions is of utmost importance for having at the same time a proper fragment definition and an accurate description of the electronic structure. With this approach it becomes possible to simplify the modeling of environmental fragments by a set of multipoles, without notable loss of precision in the description of the active quantum mechanical region. Furthermore, this leads to a considerable reduction of the degrees of freedom by an effective coarsegraining approach, eventually also paving the way towards efficient QM/QM and QM/MM methods coupling together different levels of accuracy.

Structure of the N-terminal Gyrase B fragment in complex with ADP⋅Pi reveals rigid-body motion induced by ATP hydrolysis.

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Frédéric V Stanger

Full Text Available Type II DNA topoisomerases are essential enzymes that catalyze topological rearrangement of double-stranded DNA using the free energy generated by ATP hydrolysis. Bacterial DNA gyrase is a prototype of this family and is composed of two subunits (GyrA, GyrB that form a GyrA2GyrB2 heterotetramer. The N-terminal 43-kDa fragment of GyrB (GyrB43 from E. coli comprising the ATPase and the transducer domains has been studied extensively. The dimeric fragment is competent for ATP hydrolysis and its structure in complex with the substrate analog AMPPNP is known. Here, we have determined the remaining conformational states of the enzyme along the ATP hydrolysis reaction path by solving crystal structures of GyrB43 in complex with ADP⋅BeF3, ADP⋅Pi, and ADP. Upon hydrolysis, the enzyme undergoes an obligatory 12° domain rearrangement to accommodate the 1.5 Å increase in distance between the γ- and β-phosphate of the nucleotide within the sealed binding site at the domain interface. Conserved residues from the QTK loop of the transducer domain (also part of the domain interface couple the small structural change within the binding site with the rigid body motion. The domain reorientation is reflected in a significant 7 Å increase in the separation of the two transducer domains of the dimer that would embrace one of the DNA segments in full-length gyrase. The observed conformational change is likely to be relevant for the allosteric coordination of ATP hydrolysis with DNA binding, cleavage/re-ligation and/or strand passage.

Differentiation of canine distemper virus isolates in fur animals from various vaccine strains by reverse transcription-polymerase chain reaction-restriction fragment length polymorphism according to phylogenetic relations in china

Directory of Open Access Journals (Sweden)

Zhao Jianjun

2011-02-01

Full Text Available Abstract In order to effectively identify the vaccine and field strains of Canine distemper virus (CDV, a new differential diagnostic test has been developed based on reverse transcription-polymerase chain reaction (RT-PCR and restriction fragment length polymorphism (RFLP. We selected an 829 bp fragment of the nucleoprotein (N gene of CDV. By RFLP analysis using BamHI, field isolates were distinguishable from the vaccine strains. Two fragments were obtained from the vaccine strains by RT-PCR-RFLP analysis while three were observed in the field strains. An 829 nucleotide region of the CDV N gene was analyzed in 19 CDV field strains isolated from minks, raccoon dogs and foxes in China between 2005 and 2007. The results suggest this method is precise, accurate and efficient. It was also determined that three different genotypes exist in CDV field strains in fur animal herds of the north of China, most of which belong to Asian type. Mutated field strains, JSY06-R1, JSY06-R2 and JDH07-F1 also exist in Northern China, but are most closely related to the standard virulent strain A75/17, designated in Arctic and America-2 genetype in the present study, respectively.

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion.

Science.gov (United States)

Santillán, Orlando; Ramírez-Romero, Miguel A; Dávila, Guillermo

2017-06-25

Here, we present chimera assembly by plasmid recovery and restriction enzyme site insertion (CAPRRESI). CAPRRESI benefits from many strengths of the original plasmid recovery method and introduces restriction enzyme digestion to ease DNA ligation reactions (required for chimera assembly). For this protocol, users clone wildtype genes into the same plasmid (pUC18 or pUC19). After the in silico selection of amino acid sequence regions where chimeras should be assembled, users obtain all the synonym DNA sequences that encode them. Ad hoc Perl scripts enable users to determine all synonym DNA sequences. After this step, another Perl script searches for restriction enzyme sites on all synonym DNA sequences. This in silico analysis is also performed using the ampicillin resistance gene (ampR) found on pUC18/19 plasmids. Users design oligonucleotides inside synonym regions to disrupt wildtype and ampR genes by PCR. After obtaining and purifying complementary DNA fragments, restriction enzyme digestion is accomplished. Chimera assembly is achieved by ligating appropriate complementary DNA fragments. pUC18/19 vectors are selected for CAPRRESI because they offer technical advantages, such as small size (2,686 base pairs), high copy number, advantageous sequencing reaction features, and commercial availability. The usage of restriction enzymes for chimera assembly eliminates the need for DNA polymerases yielding blunt-ended products. CAPRRESI is a fast and low-cost method for fusing protein-coding genes.

Pseudo harmonic morphisms on Riemannian polyhedra

International Nuclear Information System (INIS)

Aprodu, M.A.; Bouziane, T.

2004-10-01

The aim of this paper is to extend the notion of pseudo harmonic morphism (introduced by Loubeau) to the case when the source manifold is an admissible Riemannian polyhedron. We define these maps to be harmonic in the sense of Eells-Fuglede and pseudo-horizontally weakly conformal in our sense. We characterize them by means of germs of harmonic functions on the source polyhedron, in the sense of Korevaar-Schoen, and germs of holomorphic functions on the Kaehler target manifold. (author)

IS1245 restriction fragment length polymorphism typing of Mycobacterium avium from patients admitted to a reference hospital in Campinas, Brazil

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A.C. Panunto

2003-10-01

Full Text Available Mycobacterium avium is an important pathogen among immunodeficient patients, especially patients with AIDS. The natural history of this disease is unclear. Several environmental sources have been implicated as the origin of this infection. Polyclonal infection with this species is observed, challenging the understanding of its pathogenesis and treatment. In the present study 45 M. avium strains were recovered from 39 patients admitted to a reference hospital between 1996 and 1998. Species identification was performed using a species-specific nucleic acid hybridization test (AccuProbe® from Gen-Probe®. Strains were genotyped using IS1245 restriction fragment length polymorphism typing. Blood was the main source of the organism. In one patient with disseminated disease, M. avium could be recovered more than once from potentially sterile sites. Strains isolated from this patient had different genotypes, indicating that the infection was polyclonal. Four patient clones were characterized in this population, the largest clone being detected in eight patients. This finding points to a common-source transmission of the organism.

Radiation-induced recurrent intestinal pseudo-obstruction

International Nuclear Information System (INIS)

Conklin, J.L.; Anuras, S.

1981-01-01

The syndrome of intestinal pseudo-obstruction is a complex of signs and symptoms of intestinal obstruction without evidence of mechanical obstruction of the intestinal lumen. A patient with radiation-induced intestinal pseudoobstruction is described. The patient is a 74-year old woman with a history of chronic diarrhea, recurrent episodes of crampy abdominal pain, nausea and vomiting since receiving a 13,000 rad radiation dose to the pelvis in 1954. She has been hospitalized on many occasions for symptoms and signs of bowel obstruction. Upper gastrointestinal contrast roentgenograms with small bowel follow-through done during these episodes revealed multiple dilated loops of small bowel with no obstructing lesion. Barium enemas revealed no obstructing lesion. Each episode resolved with conservative therapy. Other secondary causes for intestinal pseudo-obstruction were ruled out in our patient. She gave no history of familial gastrointestinal disorders. Although postirradiation motility abnormalities have been demonstrated experimentally this is the first report of radiation induced intestinal pseudo-obstruction

Kinematics of current region fragmentation in semi-inclusive deeply inelastic scattering

Energy Technology Data Exchange (ETDEWEB)

Boglione, M., E-mail: elena.boglione@to.infn.it [Dipartimento di Fisica, Università di Torino, INFN - Sezione Torino, Via P. Giuria 1, 10125 Torino (Italy); Collins, J., E-mail: jcc8@psu.edu [Department of Physics, Penn State University, University Park, PA 16802 (United States); Gamberg, L., E-mail: lpg10@psu.edu [Science Division, Penn State University Berks, Reading, PA 19610 (United States); Gonzalez-Hernandez, J.O., E-mail: jogh@jlab.org [Department of Physics, Old Dominion University, Norfolk, VA 23529 (United States); Theory Center, Jefferson Lab, 12000 Jefferson Avenue, Newport News, VA 23606 (United States); Rogers, T.C., E-mail: trogers@odu.edu [Department of Physics, Old Dominion University, Norfolk, VA 23529 (United States); Theory Center, Jefferson Lab, 12000 Jefferson Avenue, Newport News, VA 23606 (United States); Sato, N., E-mail: nsato@jlab.org [Theory Center, Jefferson Lab, 12000 Jefferson Avenue, Newport News, VA 23606 (United States)

2017-03-10

Different kinematical regions of semi-inclusive deeply inelastic scattering (SIDIS) processes correspond to different underlying partonic pictures, and it is important to understand the transition between them. We find criteria in semi-inclusive deeply inelastic scattering (SIDIS) for identifying the current fragmentation region — the kinematical region where a factorization picture with fragmentation functions is appropriate, especially for studies of transverse-momentum-dependent (TMD) functions. This region is distinguished from the central (soft) and target fragmentation regions. The basis of our argument is in the errors in approximations used in deriving factorization. As compared with previous work, we show that it is essential to take account of the transverse momentum of the detected hadron, and we find a much more restricted range for genuine current fragmentation. We show that it is important to develop an extended factorization formulation to treat hadronization in the central region, as well as the current and target fragmentation regions, and to obtain a unified formalism spanning all rapidities for the detected hadron.

PSEUDO-CODEWORD LANDSCAPE

Energy Technology Data Exchange (ETDEWEB)

CHERTKOV, MICHAEL [Los Alamos National Laboratory; STEPANOV, MIKHAIL [Los Alamos National Laboratory

2007-01-10

The authors discuss performance of Low-Density-Parity-Check (LDPC) codes decoded by Linear Programming (LP) decoding at moderate and large Signal-to-Noise-Ratios (SNR). Frame-Error-Rate (FER) dependence on SNR and the noise space landscape of the coding/decoding scheme are analyzed by a combination of the previously introduced instanton/pseudo-codeword-search method and a new 'dendro' trick. To reduce complexity of the LP decoding for a code with high-degree checks, {ge} 5, they introduce its dendro-LDPC counterpart, that is the code performing identifically to the original one under Maximum-A-Posteriori (MAP) decoding but having reduced (down to three) check connectivity degree. Analyzing number of popular LDPC codes and their dendro versions performing over the Additive-White-Gaussian-Noise (AWGN) channel, they observed two qualitatively different regimes: (i) error-floor sets early, at relatively low SNR, and (ii) FER decays with SNR increase faster at moderate SNR than at the largest SNR. They explain these regimes in terms of the pseudo-codeword spectra of the codes.

Pseudo-affinity chromatography of rumen microbial cellulase on ...

African Journals Online (AJOL)

Pseudo-affinity chromatography of rumen microbial cellulase on Sepharose- Cibacron Blue F3GA. ... African Journal of Biotechnology ... Pseudo affinity adsorption of bioproducts on Sepharose-cibacron blue F3-GA was subjected to rumen microbial enzyme evaluation through batch binding and column chromatography of ...

Sperm DNA fragmentation, recurrent implantation failure and recurrent miscarriage

Directory of Open Access Journals (Sweden)

Carol Coughlan

2015-01-01

Full Text Available Evidence is increasing that the integrity of sperm DNA may also be related to implantation failure and recurrent miscarriage (RM. To investigate this, the sperm DNA fragmentation in partners of 35 women with recurrent implantation failure (RIF following in vitro fertilization, 16 women diagnosed with RM and seven recent fathers (control were examined. Sperm were examined pre- and post-density centrifugation by the sperm chromatin dispersion (SCD test and the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL assay. There were no significant differences in the age of either partner or sperm concentration, motility or morphology between three groups. Moreover, there were no obvious differences in sperm DNA fragmentation measured by either test. However, whilst on average sperm DNA fragmentation in all groups was statistically lower in prepared sperm when measured by the SCD test, this was not seen with the results from the TUNEL assay. These results do not support the hypothesis that sperm DNA fragmentation is an important cause of RIF or RM, or that sperm DNA integrity testing has value in such patients. It also highlights significant differences between test methodologies and sperm preparation methods in interpreting the data from sperm DNA fragmentation tests.

Radioimmunoassays of parathyroid hormone: Clinical value of the midregion and c-terminal assay

International Nuclear Information System (INIS)

Hengst, K.; Raidt, H.; Hoegemann, B.; Wagner, H.

1984-01-01

PTH was measured by midregion and carboxy-terminal assay in 20 patients suffering from primary hyperparathyroidism, 30 patients with secondary hyperparathyroidism, 10 persons with tertiary hyperparathyroidism, 50 patients who underwent transplantation of the kidney, 10 patients with hypoparathyroidism and 10 patients with other hypocalcemia as well as in 50 normal persons. Diagnosing hyperparathyroidism both assays were successful, when serum kreatinine was within the normal range. Especially midregion fragments became elevated, when serum kreatinine was above 2,0 mg. During renal failure diagnosis of hyperparathyroidism and hypoparathyroidism is more difficult. In normal renal function, however, the midregion assay is more sensitive for diagnosis of hypoparathyroidism compared to the carboxy-terminal assay. After kidney transplantation midregion levels of PTH are elevated, perhaps because of a failure of the transplanted kidney to eliminate the midregion fragment. (orig.) [de

Inter-terminal transfer between port terminals. A continuous mathematical programming model to optimize scheduling and deployment of transport units

Energy Technology Data Exchange (ETDEWEB)

Morales Fusco, P.; Pedrielli, G.; Zhou, C.; Hay Lee, L.; Peng Chew, E.

2016-07-01

In most large port cities, the challenge of inter-terminal transfers (ITT) prevails due to the long distance between multiple terminals. The quantity of containers requiring movement between terminals as they connect from pre-carrier to on-carrier is increasing with the formation of the mega-alliances. The paper proposes a continuous time mathematical programming model to optimize the deployment and schedule of trucks and barges to minimize the number of operating transporters, their makespan, costs and the distance travelled by the containers by choosing the right combination of transporters and container movements while fulfilling time window restrictions imposed on reception of the containers. A multi-step routing problem is developed where transporters can travel from one terminal to another and/or load or unload containers from a specific batch at each step. The model proves successful in identifying the costless schedule and means of transportation. And a sensibility analysis over the parameters used is provided. (Author)

Global patterns of fragmentation and connectivity of mammalian carnivore habitat.

Science.gov (United States)

Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; Rondinini, Carlo; Boitani, Luigi

2011-09-27

Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges, a greater proportion of habitat within their range, greater habitat connectivity and a lower risk of extinction. Species with higher connectivity (i.e. less habitat isolation) also had a greater proportion of high-quality habitat, but had smaller, not larger, ranges, probably reflecting shorter distances between habitat patches for species with restricted distributions; such species were also more threatened, as would be expected given the negative relationship between range size and extinction risk. Fragmentation and connectivity did not differ among Carnivora families, and body mass was associated with connectivity but not fragmentation. On average, only 54.3 per cent of a species' geographical range comprised high-quality habitat, and more troubling, only 5.2 per cent of the range comprised such habitat within protected areas. Identification of global hotspots of fragmentation and connectivity will help guide strategic priorities for carnivore conservation.

Comparison of tool feed influence in CNC polishing between a novel circular-random path and other pseudo-random paths.

Science.gov (United States)

Takizawa, Ken; Beaucamp, Anthony

2017-09-18

A new category of circular pseudo-random paths is proposed in order to suppress repetitive patterns and improve surface waviness on ultra-precision polished surfaces. Random paths in prior research had many corners, therefore deceleration of the polishing tool affected the surface waviness. The new random path can suppress velocity changes of the polishing tool and thus restrict degradation of the surface waviness, making it suitable for applications with stringent mid-spatial-frequency requirements such as photomask blanks for EUV lithography.

a Pseudo-Random Number Generator Employing Multiple RÉNYI Maps

Science.gov (United States)

Lui, Oi-Yan; Yuen, Ching-Hung; Wong, Kwok-Wo

2013-11-01

The increasing risk along with the drastic development of multimedia data transmission has raised a big concern on data security. A good pseudo-random number generator is an essential tool in cryptography. In this paper, we propose a novel pseudo-random number generator based on the controlled combination of the outputs of several digitized chaotic Rényi maps. The generated pseudo-random sequences have passed both the NIST 800-22 Revision 1a and the DIEHARD tests. Moreover, simulation results show that the proposed pseudo-random number generator requires less operation time than existing generators and is highly sensitive to the seed.

Introduction to fractional and pseudo-differential equations with singular symbols

CERN Document Server

Umarov, Sabir

2015-01-01

The book systematically presents the theories of pseudo-differential operators with symbols singular in dual variables, fractional order derivatives, distributed and variable order fractional derivatives, random walk approximants, and applications of these theories to various initial and multi-point boundary value problems for pseudo-differential equations. Fractional Fokker-Planck-Kolmogorov equations associated with a large class of stochastic processes are presented. A complex version of the theory of pseudo-differential operators with meromorphic symbols based on the recently introduced complex Fourier transform is developed and applied for initial and boundary value problems for systems of complex differential and pseudo-differential equations.

Intermittency in {sup 197}Au fragmentation

Energy Technology Data Exchange (ETDEWEB)

Dabrowska, A; Holynski, R; Olszewski, A; Szarska, M; Wilczynska, B; Wolter, W; Wosiek, B [Institute of Nuclear Physics, Cracow (Poland); Cherry, M L; Deines-Jones, P; Jones, W V; Sengupta, K; Wefel, B [Louisiana State Univ., Baton Rouge, LA (United States). Dept. of Physics and Astronomy; Waddington, C J [Minnesota Univ., Minneapolis, MN (United States). School of Physics and Astronomy; Pozharova, E A; Skorodko, T Yu [Inst. of Theoretical and Experimental Physics, Moscow (Russian Federation); KLMM Collaboration

1995-07-01

The concept of factorial moments was applied to an analysis of the dynamical fluctuations in the charge distributions of the fragments emitted from gold nuclei with energies 10.6 and < 1.0 GeV/n interacting with emulsion nuclei. Clear evidence for intermittent fluctuations has been found in an analysis using all the particles released from the gold projectile, with a stronger effect observed below 1 GeV/n than at 10.6 GeV/n. For the full data sets, however, the intermittency effect was found to be very sensitive to the singly charged particles, and neglecting these particles strongly reduces the intermittency signal. When the analysis is restricted to the multiply charged fragments, an intermittency effect is revealed only for multifragmentation events, although one that is enhanced as compared to the analysis of all, singly and multiply charged, particles. The properties of the anomalous fractal dimensions suggest a sequential decay mechanism, rather than the existence of possible critical behaviour in the process of nuclear fragmentation. The likely influence of the charge conservation effects and the finite size of decaying systems on the observed intermittency signals was pointed out. (author). 37 refs, 9 figs, 5 tabs.

Generalized Heisenberg algebra and (non linear) pseudo-bosons

Science.gov (United States)

Bagarello, F.; Curado, E. M. F.; Gazeau, J. P.

2018-04-01

We propose a deformed version of the generalized Heisenberg algebra by using techniques borrowed from the theory of pseudo-bosons. In particular, this analysis is relevant when non self-adjoint Hamiltonians are needed to describe a given physical system. We also discuss relations with nonlinear pseudo-bosons. Several examples are discussed.

Commissioning the A1900 projectile fragment separator

CERN Document Server

Morrissey, D J; Steiner, M; Stolz, A; Wiedenhöver, I

2003-01-01

An important part of the recent upgrade of the NSCL facility is the replacement of the A1200 fragment separator with a new high acceptance device called the A1900. The design of the A1900 device represents a third generation projectile fragment separator (relative to the early work at LBL) as it is situated immediately after the primary accelerator, has a very large acceptance, a bending power significantly larger than that of the cyclotron and is constructed from large superconducting magnets (quadrupoles with 20 and 40 cm diameter warm bores). The A1900 can accept over 90% of a large range of projectile fragmentation products produced at the NSCL, leading to large gains in the intensity of the secondary beams. The results of initial tests of the system with a restricted momentum acceptance (+-0.5%) indicate that the A1900 is performing up to specifications. Further large gains in the intensities of primary beams, typically two or three orders of magnitude, will be possible as the many facets of high current...

Site-specific DNA transesterification catalyzed by a restriction enzyme

OpenAIRE

Sasnauskas, Giedrius; Connolly, Bernard A.; Halford, Stephen E.; Siksnys, Virginijus

2007-01-01

Most restriction endonucleases use Mg2+ to hydrolyze phosphodiester bonds at specific DNA sites. We show here that BfiI, a metal-independent restriction enzyme from the phospholipase D superfamily, catalyzes both DNA hydrolysis and transesterification reactions at its recognition site. In the presence of alcohols such as ethanol or glycerol, it attaches the alcohol covalently to the 5′ terminus of the cleaved DNA. Under certain conditions, the terminal 3′-OH of one DNA strand can attack the t...

Wavefield Extrapolation in Pseudo-depth Domain

KAUST Repository

Ma, Xuxin

2011-12-11

Wave-equation based seismic migration and inversion tools are widely used by the energy industry to explore hydrocarbon and mineral resources. By design, most of these techniques simulate wave propagation in a space domain with the vertical axis being depth measured from the surface. Vertical depth is popular because it is a straightforward mapping of the subsurface space. It is, however, not computationally cost-effective because the wavelength changes with local elastic wave velocity, which in general increases with depth in the Earth. As a result, the sampling per wavelength also increases with depth. To avoid spatial aliasing in deep fast media, the seismic wave is oversampled in shallow slow media and therefore increase the total computation cost. This issue is effectively tackled by using the vertical time axis instead of vertical depth. This is because in a vertical time representation, the "wavelength" is essentially time period for vertical rays. This thesis extends the vertical time axis to the pseudo-depth axis, which features distance unit while preserving the properties of the vertical time representation. To explore the potentials of doing wave-equation based imaging in the pseudo-depth domain, a Partial Differential Equation (PDE) is derived to describe acoustic wave in this new domain. This new PDE is inherently anisotropic because the use of a constant vertical velocity to convert between depth and vertical time. Such anisotropy results in lower reflection coefficients compared with conventional space domain modeling results. This feature is helpful to suppress the low wavenumber artifacts in reverse-time migration images, which are caused by the widely used cross-correlation imaging condition. This thesis illustrates modeling acoustic waves in both conventional space domain and pseudo-depth domain. The numerical tool used to model acoustic waves is built based on the lowrank approximation of Fourier integral operators. To investigate the potential

Reexamination of fission fragment angular distributions and the fission process: Formalism

International Nuclear Information System (INIS)

Bond, P.D.

1985-01-01

The theory of fission fragment angular distributions is examined and the universally used expression is found to be valid only under restrictive assumptions. A more general angular distribution formula is derived and applied to recent data of high spin systems. At the same time it is shown that the strong anisotropies observed from such systems can be understood without changing the essential basis of standard fission theory. The effects of reaction mechanisms other than complete fusion on fission fragment angular distributions are discussed and possible angular distribution signatures of noncompound nucleus formation are mentioned

A novel pseudo resistor structure for biomedical front-end amplifiers.

Science.gov (United States)

Yu-Chieh Huang; Tzu-Sen Yang; Shun-Hsi Hsu; Xin-Zhuang Chen; Jin-Chern Chiou

2015-08-01

This study proposes a novel pseudo resistor structure with a tunable DC bias voltage for biomedical front-end amplifiers (FEAs). In the proposed FEA, the high-pass filter composed of differential difference amplifier and a pseudo resistor is implemented. The FEA is manufactured by using a standard TSMC 0.35 μm CMOS process. In this study, three types FEAs included three different pseudo resistor are simulated, fabricated and measured for comparison and electrocorticography (ECoG) measurement, and all the results show the proposed pseudo resistor is superior to other two types in bandwidth. In chip implementation, the lower and upper cutoff frequencies of the high-pass filter with the proposed pseudo resistor are 0.15 Hz and 4.98 KHz, respectively. It also demonstrates lower total harmonic distortion performance of -58 dB at 1 kHz and higher stability with wide supply range (1.8 V and 3.3 V) and control voltage range (0.9 V and 1.65 V) than others. Moreover, the FEA with the proposed pseudo successfully recorded spike-and-wave discharges of ECoG signal in in vivo experiment on rat with pentylenetetrazol-induced seizures.

Discrete Weighted Pseudo-Almost Automorphy and Applications

Directory of Open Access Journals (Sweden)

Zhinan Xia

2014-01-01

Full Text Available We deal with discrete weighted pseudo almost automorphy which extends some classical concepts and systematically explore its properties in Banach space including a composition result. As an application, we establish some sufficient criteria for the existence and uniqueness of the discrete weighted pseudo almost automorphic solutions to the Volterra difference equations of convolution type and also to nonautonomous semilinear difference equations. Some examples are presented to illustrate the main findings.

Brain MR image segmentation using NAMS in pseudo-color.

Science.gov (United States)

Li, Hua; Chen, Chuanbo; Fang, Shaohong; Zhao, Shengrong

2017-12-01

Image segmentation plays a crucial role in various biomedical applications. In general, the segmentation of brain Magnetic Resonance (MR) images is mainly used to represent the image with several homogeneous regions instead of pixels for surgical analyzing and planning. This paper proposes a new approach for segmenting MR brain images by using pseudo-color based segmentation with Non-symmetry and Anti-packing Model with Squares (NAMS). First of all, the NAMS model is presented. The model can represent the image with sub-patterns to keep the image content and largely reduce the data redundancy. Second, the key idea is proposed that convert the original gray-scale brain MR image into a pseudo-colored image and then segment the pseudo-colored image with NAMS model. The pseudo-colored image can enhance the color contrast in different tissues in brain MR images, which can improve the precision of segmentation as well as directly visual perceptional distinction. Experimental results indicate that compared with other brain MR image segmentation methods, the proposed NAMS based pseudo-color segmentation method performs more excellent in not only segmenting precisely but also saving storage.

Episodic seasonal Pseudo-Bartter syndrome in cystic fibrosis.

Science.gov (United States)

Kintu, Brett; Brightwell, Alex

2014-06-01

Pseudo-Bartter syndrome (PBS) describes an uncommon but well recognised complication of cystic fibrosis leading to hypochloraemic, hypokalaemic metabolic alkalosis. Pseudo-Bartter syndrome is usually seen at initial presentation or within the first two years of life in children with cystic fibrosis. Risk factors for development of PBS include warm weather conditions, severe respiratory or pancreatic disease and gastrointestinal losses (e.g. vomiting and diarrhoea). PBS is rare in older children and adolescents although epidemics have been associated with heat wave conditions in warmer climates. In this era of climate change, it is crucial that clinicians consider Pseudo-Bartter syndrome when patients with cystic fibrosis present unwell during summer. Copyright © 2014 Elsevier Ltd. All rights reserved.

The recombinant C-terminal fragment of tetanus toxin protects against cholinotoxicity by intraseptal injection of β-amyloid peptide (25-35) in rats.

Science.gov (United States)

Patricio-Martínez, A; Mendieta, L; Martínez, I; Aguilera, J; Limón, I D

2016-02-19

The recombinant C-terminal domain of tetanus toxin (Hc-TeTx) is a new non-toxic peptide of the tetanus toxin that exerts a protective action against glutamate excitotoxicity in motoneurons. Moreover, its efficacy as a neuroprotective agent has been demonstrated in several animal models of neurodegeneration. The eleven amino acids in the β amyloid peptide (Aβ25-35) mimic the toxic effects of the full β amyloid peptide (Aβ1-42), causing the impairment of the cholinergic system in the medial septum (MS) which, in turn, alters the septo-hippocampal pathway and leads to learning and memory impairments. The aim of this study was to examine the neuroprotective effects of the Hc-TeTx fragment against cholinotoxicity. The Hc-TeTx fragment (100 ng) was injected into the rats intercranially, with the Aβ(25-35) (2 μg) then injected into their MS. The animals were tested for spatial learning and memory in the eight-arm radial maze. The brains were removed to assess cholinergic markers, such as choline acetyltransferase (ChAT) and acetylcholinesterase (AChE), and to explore neurodegeneration in the MS and hippocampus, using amino-cupric silver and H&E staining. Finally, capase-3, a marker of apoptosis, was examined in the MS. Our results clearly demonstrate that the application of Hc-TeTx prevents the loss of cholinergic markers (ChAT and AChE), the activation of capase-3, and neurodegeneration in the MS and the CA1 and CA3 subfields of the hippocampus. All these improvements were reflected in spatial learning and memory performance, and were significantly higher compared with animals treated with Aβ(25-35). Interestingly, the single administration of Hc-TeTx into the MS modified the ChAT and AChE expression that affect cognitive processes, without inducing neurodegeneration or an increase in capase-3 expression in the MS and hippocampus. In summary, our findings suggest that the recombinant Hc-TeTx fragment offers effective protection for the septo-hippocampal pathway

Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain - A fragment based approach.

Science.gov (United States)

Upadhyay, Anup K; Judge, Russell A; Li, Leiming; Pithawalla, Ron; Simanis, Justin; Bodelle, Pierre M; Marin, Violeta L; Henry, Rodger F; Petros, Andrew M; Sun, Chaohong

2018-06-01

The tandem TUDOR domains present in the non-catalytic C-terminal half of the KDM4A, 4B and 4C enzymes play important roles in regulating their chromatin localizations and substrate specificities. They achieve this regulatory role by binding to different tri-methylated lysine residues on histone H3 (H3-K4me3, H3-K23me3) and histone H4 (H4-K20me3) depending upon the specific chromatin environment. In this work, we have used a 2D-NMR based fragment screening approach to identify a novel fragment (1a), which binds to the KDM4A-TUDOR domain and shows modest competition with H3-K4me3 binding in biochemical as well as in vitro cell based assays. A co-crystal structure of KDM4A TUDOR domain in complex with 1a shows that the fragment binds stereo-specifically to the methyl lysine binding pocket forming a network of strong hydrogen bonds and hydrophobic interactions. We anticipate that the fragment 1a can be further developed into a novel allosteric inhibitor of the KDM4 family of enzymes through targeting their C-terminal tandem TUDOR domain. Copyright © 2018 Elsevier Ltd. All rights reserved.

KERAGAMAN GENETIK BENIH IKAN KERAPU SUNU, Plectrophomus leopardus TURUNAN PERTAMA (F1 DENGAN ANALISIS RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP MT-DNA

Directory of Open Access Journals (Sweden)

Gusti Ngurah Permana

2016-11-01

The variability of differences size was occurred on every culture period of coral trout. The aimed of this study was to know genetics variability and evaluated of which are expressed on large, medium, and small size fry on total of length sizes and different weight. Amplification of single fragment using set primer 16 SrDNA (F5’CGCCTG TTTAACAAAAACAT-3’ and reverse (R: 5’-CCGGTCTGAACTCAGATCATGT-3’. Result showed that PCR amplification of mt-DNA was 625 bp. Restriction digestion processed with Mnl I enzyme showed that polymorphism in large size and monomorphic in both medium and small sizes. Two types of haplotype were found in large size (ABABB and ABAAB while one haplotype observed in medium and small sizes ABABB. The heterozygosities value of large, medium and small sizes from Bali location were 0.480, 0.000, and 0.000 restectively. Heterozygosities value of samples from East Java were 0.211, 0.000, and 0.000 restectively. Samples from Lampung were monomorphic (0.000.

The prevalence of cryptosporidiosis in Turkish children, and geno typing of isolates by nested polymerase chain reaction-restriction fragment length polymorphism

International Nuclear Information System (INIS)

Tamer, Gulden S.; Turk, M.; Dagci, H.; Pektas, B.; Guruz, Adnan Y.; Uner, A.; Guy, E.C.

2007-01-01

Objective was to verify the incidence of cryptosporidiosis among Turkish elementary school students. The study was conducted in the Dept. of Parasitology, Faculty of Medicine, Ege University, Turkey during a 3-month period in 2006. We assessed the fecal samples of 707 children using modified acid-fast and phenol-auramine staining followed by modified Ritchie concentration method. All cryptosporidium species isolates were analysed by nested polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) to differentiate genotypes of the isolates. After the coprological examination, 4 samples were found to be positive for cryptosporidium species oocysts. In the present study, all 4 oocysts were of zoonotic origin and belonged to cryptoporodium parvum genotype 2 indicating that in Turkey the potential sources of human cryptosporidiosis is from animals. The application of genotyping to clinical isolates of cryptosporidium has significantly increased our knowledge and understanding of the distribution and epidemiology of this parasite. The PCR and RFLP techniques represent a more rapid and simple method of genotyping to support epidemiological and clinical investigations than conventional analytical DNA techniques. (author)

Biharmonic Submanifolds with Parallel Mean Curvature Vector in Pseudo-Euclidean Spaces

Energy Technology Data Exchange (ETDEWEB)

Fu, Yu, E-mail: yufudufe@gmail.com [Dongbei University of Finance and Economics, School of Mathematics and Quantitative Economics (China)

2013-12-15

In this paper, we investigate biharmonic submanifolds in pseudo-Euclidean spaces with arbitrary index and dimension. We give a complete classification of biharmonic spacelike submanifolds with parallel mean curvature vector in pseudo-Euclidean spaces. We also determine all biharmonic Lorentzian surfaces with parallel mean curvature vector field in pseudo-Euclidean spaces.

Biharmonic Submanifolds with Parallel Mean Curvature Vector in Pseudo-Euclidean Spaces

International Nuclear Information System (INIS)

Fu, Yu

2013-01-01

In this paper, we investigate biharmonic submanifolds in pseudo-Euclidean spaces with arbitrary index and dimension. We give a complete classification of biharmonic spacelike submanifolds with parallel mean curvature vector in pseudo-Euclidean spaces. We also determine all biharmonic Lorentzian surfaces with parallel mean curvature vector field in pseudo-Euclidean spaces

Pseudo Steady-State Free Precession for MR-Fingerprinting.

Science.gov (United States)

Assländer, Jakob; Glaser, Steffen J; Hennig, Jürgen

2017-03-01

This article discusses the signal behavior in the case the flip angle in steady-state free precession sequences is continuously varied as suggested for MR-fingerprinting sequences. Flip angle variations prevent the establishment of a steady state and introduce instabilities regarding to magnetic field inhomogeneities and intravoxel dephasing. We show how a pseudo steady state can be achieved, which restores the spin echo nature of steady-state free precession. Based on geometrical considerations, relationships between the flip angle, repetition and echo time are derived that suffice to the establishment of a pseudo steady state. The theory is tested with Bloch simulations as well as phantom and in vivo experiments. A typical steady-state free precession passband can be restored with the proposed conditions. The stability of the pseudo steady state is demonstrated by comparing the evolution of the signal of a single isochromat to one resulting from a spin ensemble. As confirmed by experiments, magnetization in a pseudo steady state can be described with fewer degrees of freedom compared to the original fingerprinting and the pseudo steady state results in more reliable parameter maps. The proposed conditions restore the spin-echo-like signal behavior typical for steady-state free precession in fingerprinting sequences, making this approach more robust to B 0 variations. Magn Reson Med 77:1151-1161, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Inflammatory pseudo tumor (pseudo sarcoma) of the urinary bladder: clinical aspects and computed tomography images

International Nuclear Information System (INIS)

Romero, A.; Bueno, A.; Trigo, J.E.; Torres, A.

1998-01-01

Inflammatory pseudo tumor (pseudosarcoma) of the urinary bladder is an uncommon lesion with benign histopathological features. It consists of large cell proliferation, spindle-cell morphology (myofibroblasts) deriving from the bladder sub mucosa. It can present in patients of either sex and of any age; on occasion, it has been related to a history of surgery or previous bladder injury. Both the clinical and radiological features are nonspecific in that they do not differentiate this lesion from malignant disease; its diagnosis can only be definitively established by histopathological study. We present a case of inflammatory bladder pseudo tumor in a young girl, describing the clinical and radiological features of this lesion, which only rarely has been dealt with in the literature, particularly that concerning radiology. (Author) 13 refs

Mapping of the human APOB gene to chromosome 2p and demonstration of a two-allele restriction fragment length polymorphism

International Nuclear Information System (INIS)

Huang, L.; Miller, D.A.; Bruns, G.A.P.; Breslow, J.L.

1986-01-01

ApoB is a large glycoprotein with an apparent molecular mass of 550 kDa on NaDodSO 4 /PAGE. Recently, apoB cDNA clones have been isolated from an expression library made with mRNA from a human hepatoma cell line. These clones, which were all 1.5-1.6 kilobases (kb) long and corresponded to the 3' end of apoB mRNA, were used to demonstrate that hepatic apoB mRNA is ≅ 22 kb long. In the current report, a probe derived from one of these cDNA clones, pB8, was used for in situ hybridization experiments to map the human gene for apoB, APOB, to the distal half of the short arm of chromosome 2. This probe was also used to analyze somatic cell hybrids and, in agreement with the in situ hybridization studies, concordancy was demonstrated with chromosome 2. In addition, two hybrids with chromosome 2 translocations that contain only the short arm reacted with the pB8 probe. A third hybrid with a complex rearrangement of chromosome 2, which deleted an interstitial region and the tip of the short arm of chromosome 2, did not react. These data indicate that APOB maps to either 2p21-p23 or 2p24-pter. In further studies, DNA from normal individuals, digested with the restriction endonuclease EcoRI and subjected to Southern blot analysis with the pB8 probe, revealed a two-allele restriction fragment length polymorphism (RFLP). The mapping studies provide the means for understanding the relationship of the APOB locus to others in the human genome, whereas the demonstration of an APOB RFLP increases their ability to assess the role of this locus in determining plasma lipoprotein levels

Gamma-carboxylation and fragmentation of osteocalcin in human serum defined by mass spectrometry

Science.gov (United States)

Serum osteocalcin (Oc) concentration is a highly specific measure of bone turnover, but its circulating proteoform(s) have not been well defined. Based on immunological methods, the major forms are thought to be the intact polypeptide and a large N-terminal-mid molecule fragment for which there is n...

Post-irradiation studies on knock-out and pseudo-recoil releases of fission products from fissioning UO2

International Nuclear Information System (INIS)

Yamagishi, S.; Tanifuji, T.

1976-01-01

By using post-irradiation techniques, in-pile releases of 133 Xe, sup(85m)Kr, 88 Kr, 87 Kr and 138 Xe from UO 2 fissioning at low temperatures below about 200 0 C are studied: these are analyzed into a time-dependent knock-out and time-independent pseudo-recoil releases. For the latter, a 'self knock-out' mechanism is proposed: when a fission fragment loses thoroughly its energy near the UO 2 surface and stops there, it will knock out the surface substances and accordingly the fragment (i.e. the fission product) will be released. The effective thickness of the layer where the self knock-out occurs is found to be approximately 7A. As for the knock-out release, the following is estimated from its dependence on various factors: the knock-out release of fission products occurs from the surface layer with the effective thickness of approximately 20A: the shape of UO 2 matrix knocked out by one fission fragment passing through the surface is equivalent to a cylinder approximately 32A diameter by approximately 27A thick, (i.e. the knock-out coefficient for UO 2 is approximately 660 uranium atoms per knock-out event). On the basis of the above estimations, the conclusions derived from the past in-pile studies of fission gas releases are evaluated. (Auth.)

Molecular identification of Candida species isolated from cases of neonatal candidemia using polymerase chain reaction-restriction fragment length polymorphism in a tertiary care hospital

Directory of Open Access Journals (Sweden)

Akeela Fatima

2017-01-01

Full Text Available Context: Candida spp. is an emerging cause of bloodstream infections worldwide. Delay in speciation of Candida isolates by conventional methods and resistance to antifungal drugs in various Candida species are responsible for the increase in morbidity and mortality due to candidemia. Hence, the rapid identification of Candida isolates is very important for the proper management of patients with candidemia. Aims: The aim was to re-evaluate the identification of various Candida spp. by polymerase chain reaction (PCR-restriction fragment length polymorphism (RFLP and to evaluate the accuracy, speed, and cost of phenotypic methodology versus PCR-RFLP. Settings and Design: Hospital-based cross-sectional study. Materials and Methods: Ninety consecutive clinical isolates of seven Candida species, isolated from blood of neonates and identified by routine phenotypic methods, were re-evaluated using universal primers internal transcribed spacer 1 (ITS1 and ITS4 for PCR amplification and Msp I restriction enzyme for RFLP. Statistical Analysis Used: Kappa test for agreement. Results: The results of PCR-RFLP were 100% in agreement with those obtained using conventional phenotypic methods. Identification could be achieved within 3 work days by both the methods. Our routine methods proved to be cost effective than PCR-RFLP. Conclusions: We can continue with our routine phenotypic methods and PCR-RFLP can be used for periodic quality control or when conventional methods fail to identify a species.

IMRT optimization with pseudo-biologic objective function

International Nuclear Information System (INIS)

Yi, B. Y.; Ahn, S. D.; Kim, J. H.; Lee, S. W.; Choi, E. K.

2002-01-01

The pseudo-biologic objective function has been proposed for the IMRT optimization. It is similar to the biological objective function in mathematical shape, but uses physical parameters. The pseudo-biologic objective function concept is consisted of the target coverage index (TCI) and the organ score index (OSI), was introduced. The TCI was expressed as the sum of all of the weighted bins of target dose volume histogram (DVH). The weights were given as the normal distribution of which the average is 100 % and the standard deviation is ±. The OSI was expressed as similar way. The average of the normal distribution was 0% of the dose and that of standard deviation was selected as a function of limiting dose and its importance. The objective function could be calculated as the product of the TCI and OSI's. The RTP Tool Box (RTB) was used for this study. The constraints applied in the optimization was intuitively clinical experience based numbers, while the physical objective function asks just numbers which are not necessarily based on the clinic, and the parameters for the biologic objective functions are uncertain. The OSI's from the pseudo-biological function showed better results than from the physical functions, while TCI's showed similar tendency. We could show that the pseudo-biologic function can be used for an IMRT objective function on behalf of the biological objective function

Degeneracy of energy levels of pseudo-Gaussian oscillators

International Nuclear Information System (INIS)

Iacob, Theodor-Felix; Iacob, Felix; Lute, Marina

2015-01-01

We study the main features of the isotropic radial pseudo-Gaussian oscillators spectral properties. This study is made upon the energy levels degeneracy with respect to orbital angular momentum quantum number. In a previous work [6] we have shown that the pseudo-Gaussian oscillators belong to the class of quasi-exactly solvable models and an exact solution has been found

Comparative analysis of human cytomegalovirus a-sequence in multiple clinical isolates by using polymerase chain reaction and restriction fragment length polymorphism assays.

Science.gov (United States)

Zaia, J A; Gallez-Hawkins, G; Churchill, M A; Morton-Blackshere, A; Pande, H; Adler, S P; Schmidt, G M; Forman, S J

1990-01-01

The human cytomegalovirus (HCMV) a-sequence (a-seq) is located in the joining region between the long (L) and short (S) unique sequences of the virus (L-S junction), and this hypervariable junction has been used to differentiate HCMV strains. The purpose of this study was to investigate whether there are differences among strains of human cytomegalovirus which could be characterized by polymerase chain reaction (PCR) amplification of the a-seq of HCMV DNA and to compare a PCR method of strain differentiation with conventional restriction fragment length polymorphism (RFLP) methodology by using HCMV junction probes. Laboratory strains of HCMV and viral isolates from individuals with HCMV infection were characterized by using both RFLPs and PCR. The PCR assay amplified regions in the major immediate-early gene (IE-1), the 64/65-kDa matrix phosphoprotein (pp65), and the a-seq of the L-S junction region. HCMV laboratory strains Towne, AD169, and Davis were distinguishable, in terms of size of the amplified product, when analyzed by PCR with primers specific for the a-seq but were indistinguishable by using PCR targeted to IE-1 and pp65 sequences. When this technique was applied to a characterization of isolates from individuals with HCMV infection, selected isolates could be readily distinguished. In addition, when the a-seq PCR product was analyzed with restriction enzyme digestion for the presence of specific sequences, these DNA differences were confirmed. PCR analysis across the variable a-seq of HCMV demonstrated differences among strains which were confirmed by RFLP in 38 of 40 isolates analyzed. The most informative restriction enzyme sites in the a-seq for distinguishing HCMV isolates were those of MnlI and BssHII. This indicates that the a-seq of HCMV is heterogeneous among wild strains, and PCR of the a-seq of HCMV is a practical way to characterize differences in strains of HCMV. Images PMID:1980680

Pseudo-random bit generator based on lag time series

Science.gov (United States)

García-Martínez, M.; Campos-Cantón, E.

2014-12-01

In this paper, we present a pseudo-random bit generator (PRBG) based on two lag time series of the logistic map using positive and negative values in the bifurcation parameter. In order to hidden the map used to build the pseudo-random series we have used a delay in the generation of time series. These new series when they are mapped xn against xn+1 present a cloud of points unrelated to the logistic map. Finally, the pseudo-random sequences have been tested with the suite of NIST giving satisfactory results for use in stream ciphers.

Age bimodality in the central region of pseudo-bulges in S0 galaxies

Science.gov (United States)

Mishra, Preetish K.; Barway, Sudhanshu; Wadadekar, Yogesh

2017-11-01

We present evidence for bimodal stellar age distribution of pseudo-bulges of S0 galaxies as probed by the Dn(4000) index. We do not observe any bimodality in age distribution for pseudo-bulges in spiral galaxies. Our sample is flux limited and contains 2067 S0 and 2630 spiral galaxies drawn from the Sloan Digital Sky Survey. We identify pseudo-bulges in S0 and spiral galaxies, based on the position of the bulge on the Kormendy diagram and their central velocity dispersion. Dividing the pseudo-bulges of S0 galaxies into those containing old and young stellar populations, we study the connection between global star formation and pseudo-bulge age on the u - r colour-mass diagram. We find that most old pseudo-bulges are hosted by passive galaxies while majority of young bulges are hosted by galaxies that are star forming. Dividing our sample of S0 galaxies into early-type S0s and S0/a galaxies, we find that old pseudo-bulges are mainly hosted by early-type S0 galaxies while most of the pseudo-bulges in S0/a galaxies are young. We speculate that morphology plays a strong role in quenching of star formation in the disc of these S0 galaxies, which stops the growth of pseudo-bulges, giving rise to old pseudo-bulges and the observed age bimodality.

N-terminal pro-atrial natriuretic peptide measurement in plasma suggests covalent modification

DEFF Research Database (Denmark)

Hunter, Ingrid; Alehagen, Urban; Dahlström, Ulf

2011-01-01

different proANP assays on clinical outcome. METHODS: We examined 474 elderly patients with symptoms of heart failure presenting in a primary healthcare setting. Samples were analyzed with an automated immunoluminometric midregion proANP (MR-proANP) assay and a new processing-independent assay (PIA.......74 (95% CI, 0.66–0.81); P = 0.32]. The prognostic ability to report cardiovascular mortality during a 10-year follow-up revealed AUC values of 0.66 (95% CI, 0.60–0.71) for the proANP PIA and 0.69 (95% CI, 0.63–0.74) for the MR-proANP assay (P = 0.08, for comparing the 2 assays). CONCLUSIONS: Our data......BACKGROUND: The N-terminal fragment of cardiac-derived pro–B-type natriuretic peptide is a glycosylated polypeptide. It is unknown whether N-terminal pro–atrial natriuretic peptide (proANP) fragments are also covalently modified. We therefore evaluated the clinical performance of 2 distinctly...

Genotyping of the fish rhabdovirus, viral haemorrhagic septicaemia virus, by restriction fragment length polymorphisms

DEFF Research Database (Denmark)

Einer-Jensen, Katja; Winton, J.; Lorenzen, Niels

2005-01-01

The aim of this study was to develop a standardized molecular assay that used limited resources and equipment for routine genotyping of isolates of the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV). Computer generated restriction maps, based on 62 unique full-length (1524 nt....... Experimental evaluation of the method consisted of three steps: (i) RT-PCR amplification of the G-gene of VHSV isolates using purified viral RNA as template, (ii) digestion of the PCR products with a panel of restriction endonucleases and (iii) interpretation of the resulting RFLP profiles. The RFLP analysis...

The role of the spectator assumption in models for projectile fragmentation

International Nuclear Information System (INIS)

Mc Voy, K.W.

1984-01-01

This review is restricted to direct-reaction models for the production of projectile fragments in nuclear collisions, at beam energies of 10 or more MeV/nucleon. Projectile fragments are normally identified as those which have near-beam velocities, and there seem to be two principal mechanisms for the production of these fast particles: 1. Direct breakup, 2. Sequential breakup. Of the two, the authors exclude from their discussion the ''sequential breakup'' process, in which the projectile is excited by the initial collision (either via inelastic scattering or transfer to unbound states) and then subsequently decays, outside the range of interaction

A case of Pseudo-Bartter syndrome

International Nuclear Information System (INIS)

Yang, Ik; Choi, Bo Whan; Lee, Yul; Chung, Soo Young

1994-01-01

Pseudo-Bartter Syndrome is a rare medical disease of the kidney characterized by normal blood pressure, hypokalemic metabolic alkalosis, hyperreninemia and hyperaldosteronism with drug history of diuretics. We report US, CT and MRI findings of a patients with clinically proved Pseudo-Bartter syndrome. The patient was a 37 year old woman with a history of long term ingestion of the diuretics(furosemide) for 20 years. Renal US revealed hyperechoic renal medulla at both kidneys. The resistive index(RI), calculated from the duplex doppler waveform is 0.61. Unenhanced CT revealed faint high attenuation along the medulla. T1-weighted MRI revealed indistinct corticomedullary differentiation

A case of Pseudo-Bartter syndrome

Energy Technology Data Exchange (ETDEWEB)

Yang, Ik; Choi, Bo Whan; Lee, Yul; Chung, Soo Young [College of Medicine, Hallym University, Seoul (Korea, Republic of)

1994-10-15

Pseudo-Bartter Syndrome is a rare medical disease of the kidney characterized by normal blood pressure, hypokalemic metabolic alkalosis, hyperreninemia and hyperaldosteronism with drug history of diuretics. We report US, CT and MRI findings of a patients with clinically proved Pseudo-Bartter syndrome. The patient was a 37 year old woman with a history of long term ingestion of the diuretics(furosemide) for 20 years. Renal US revealed hyperechoic renal medulla at both kidneys. The resistive index(RI), calculated from the duplex doppler waveform is 0.61. Unenhanced CT revealed faint high attenuation along the medulla. T1-weighted MRI revealed indistinct corticomedullary differentiation.

A Restriction Fragment Length Polymorphism Map and Electrophoretic Karyotype of the Fungal Maize Pathogen Cochliobolus Heterostrophus

Science.gov (United States)

Tzeng, T. H.; Lyngholm, L. K.; Ford, C. F.; Bronson, C. R.

1992-01-01

A restriction fragment length polymorphism (RFLP) map has been constructed of the nuclear genome of the plant pathogenic ascomycete Cochliobolus heterostrophus. The segregation of 128 RFLP and 4 phenotypic markers was analyzed among 91 random progeny of a single cross; linkages were detected among 126 of the markers. The intact chromosomal DNAs of the parents and certain progeny were separated using pulsed field gel electrophoresis and hybridized with probes used to detect the RFLPs. In this way, 125 markers were assigned to specific chromosomes and linkages among 120 of the markers were confirmed. These linkages totalled 941 centimorgans (cM). Several RFLPs and a reciprocal translocation were identified tightly linked to Tox1, a locus controlling host-specific virulence. Other differences in chromosome arrangement between the parents were also detected. Fourteen gaps of at least 40 cM were identified between linkage groups on the same chromosomes; the total map length was therefore estimated to be, at a minimum, 1501 cM. Fifteen A chromosomes ranging from about 1.3 megabases (Mb) to about 3.7 Mb were identified; one of the strains also has an apparent B chromosome. This chromosome appears to be completely dispensable; in some progeny, all of 15 markers that mapped to this chromosome were absent. The total genome size was estimated to be roughly 35 Mb. Based on these estimates of map length and physical genome size, the average kb/cM ratio in this cross was calculated to be approximately 23. This low ratio of physical to map distance should make this RFLP map a useful tool for cloning genes. PMID:1346261

Intestinal sclerosis with pseudo-obstruction in three dogs.

Science.gov (United States)

Moore, R; Carpenter, J

1984-04-01

Intestinal sclerosis causing chronic intestinal pseudo-obstruction was diagnosed in 3 dogs. The pseudo-obstruction was characterized by vomiting and weight loss of 2 weeks' to 3 months' duration. A patent intestinal lumen was determined by contrast radiography and verified at surgery. Intestinal biopsy revealed diffuse atrophy, fibrosis, and mononuclear cell infiltration of the tunica muscularis. Each dog was euthanatized because of a progressive, deteriorating clinical course.

Pseudo-interactive monitoring in distributed computing

International Nuclear Information System (INIS)

Sfiligoi, I.; Bradley, D.; Livny, M.

2009-01-01

Distributed computing, and in particular Grid computing, enables physicists to use thousands of CPU days worth of computing every day, by submitting thousands of compute jobs. Unfortunately, a small fraction of such jobs regularly fail; the reasons vary from disk and network problems to bugs in the user code. A subset of these failures result in jobs being stuck for long periods of time. In order to debug such failures, interactive monitoring is highly desirable; users need to browse through the job log files and check the status of the running processes. Batch systems typically don't provide such services; at best, users get job logs at job termination, and even this may not be possible if the job is stuck in an infinite loop. In this paper we present a novel approach of using regular batch system capabilities of Condor to enable users to access the logs and processes of any running job. This does not provide true interactive access, so commands like vi are not viable, but it does allow operations like ls, cat, top, ps, lsof, netstat and dumping the stack of any process owned by the user; we call this pseudo-interactive monitoring. It is worth noting that the same method can be used to monitor Grid jobs in a glidein-based environment. We further believe that the same mechanism could be applied to many other batch systems.

Pseudo-interactive monitoring in distributed computing

International Nuclear Information System (INIS)

Sfiligoi, I; Bradley, D; Livny, M

2010-01-01

Distributed computing, and in particular Grid computing, enables physicists to use thousands of CPU days worth of computing every day, by submitting thousands of compute jobs. Unfortunately, a small fraction of such jobs regularly fail; the reasons vary from disk and network problems to bugs in the user code. A subset of these failures result in jobs being stuck for long periods of time. In order to debug such failures, interactive monitoring is highly desirable; users need to browse through the job log files and check the status of the running processes. Batch systems typically don't provide such services; at best, users get job logs at job termination, and even this may not be possible if the job is stuck in an infinite loop. In this paper we present a novel approach of using regular batch system capabilities of Condor to enable users to access the logs and processes of any running job. This does not provide true interactive access, so commands like vi are not viable, but it does allow operations like ls, cat, top, ps, lsof, netstat and dumping the stack of any process owned by the user; we call this pseudo-interactive monitoring. It is worth noting that the same method can be used to monitor Grid jobs in a glidein-based environment. We further believe that the same mechanism could be applied to many other batch systems.

Pseudo-interactive monitoring in distributed computing

Energy Technology Data Exchange (ETDEWEB)

Sfiligoi, I.; /Fermilab; Bradley, D.; Livny, M.; /Wisconsin U., Madison

2009-05-01

Distributed computing, and in particular Grid computing, enables physicists to use thousands of CPU days worth of computing every day, by submitting thousands of compute jobs. Unfortunately, a small fraction of such jobs regularly fail; the reasons vary from disk and network problems to bugs in the user code. A subset of these failures result in jobs being stuck for long periods of time. In order to debug such failures, interactive monitoring is highly desirable; users need to browse through the job log files and check the status of the running processes. Batch systems typically don't provide such services; at best, users get job logs at job termination, and even this may not be possible if the job is stuck in an infinite loop. In this paper we present a novel approach of using regular batch system capabilities of Condor to enable users to access the logs and processes of any running job. This does not provide true interactive access, so commands like vi are not viable, but it does allow operations like ls, cat, top, ps, lsof, netstat and dumping the stack of any process owned by the user; we call this pseudo-interactive monitoring. It is worth noting that the same method can be used to monitor Grid jobs in a glidein-based environment. We further believe that the same mechanism could be applied to many other batch systems.

Neutrosophic Regular Filters and Fuzzy Regular Filters in Pseudo-BCI Algebras

Directory of Open Access Journals (Sweden)

Xiaohong Zhang

2017-09-01

Full Text Available Neutrosophic set is a new mathematical tool for handling problems involving imprecise, indeterminacy and inconsistent data. Pseudo-BCI algebra is a kind of non-classical logic algebra in close connection with various non-commutative fuzzy logics. Recently, we applied neutrosophic set theory to pseudo-BCI algebras. In this paper, we study neutrosophic filters in pseudo-BCI algebras.

Application of dynamic pseudo fission products and actinides for accurate burnup calculations

Energy Technology Data Exchange (ETDEWEB)

Hoogenboom, J.E.; Leege, P.F.A. de [Technische Univ. Delft (Netherlands). Interfacultair Reactor Inst.; Kloosterman, J.L.

1996-09-01

The introduction of pseudo fission products for accurate fine-group spectrum calculations during burnup is discussed. The calculation of the density of the pseudo nuclides is done before each spectrum calculation from the actual densities and their cross sections of all nuclides to be lumped into a pseudo fission product. As there are also many actinides formed in the fuel during its life cycle, a pseudo actinide with fission cross section is also introduced. From a realistic burnup calculation it is demonstrated that only a few fission products and actinides need to be included explicitly in a spectrum calculation. All other fission products and actinides can be accurately represented in the pseudo nuclides. (author)

Electron with arbitrary pseudo-spins in multilayer graphene

Institute of Scientific and Technical Information of China (English)

Worasak Prarokijjak; Bumned Soodchomshom

2015-01-01

Using the low-energy effective Hamiltonian of the ABC-stacked multilayer graphene, the pseudo-spin coupling to real orbital angular momentum of electrons in multilayer graphene is investigated. We show that the electron wave function in N-layer graphene mimics the behavior of a particle with a spin of N × (}/2), where N={1, 2, 3, . . .}. It is said that for N>1 the low-energy effective Hamiltonian for ABC-stacked graphene cannot be used to describe pseudo-spin-1/2 particles. The wave function of electrons in multilayer graphene may behave like fermionic (or bosonic) particle for N being odd (or even). In this paper, we propose a theory of graphene serving as a host material of electrons with arbitrary pseudo-spins tunable by changing the number of graphene layers.

Electron with arbitrary pseudo-spins in multilayer graphene

International Nuclear Information System (INIS)

Prarokijjak Worasak; Soodchomshom Bumned

2015-01-01

Using the low-energy effective Hamiltonian of the ABC-stacked multilayer graphene, the pseudo-spin coupling to real orbital angular momentum of electrons in multilayer graphene is investigated. We show that the electron wave function in N-layer graphene mimics the behavior of a particle with a spin of N × (ħ/2), where N = {1, 2, 3,…}. It is said that for N > 1 the low-energy effective Hamiltonian for ABC-stacked graphene cannot be used to describe pseudo-spin-1/2 particles. The wave function of electrons in multilayer graphene may behave like fermionic (or bosonic) particle for N being odd (or even). In this paper, we propose a theory of graphene serving as a host material of electrons with arbitrary pseudo-spins tunable by changing the number of graphene layers. (paper)

Pseudo-periodic maps and degeneration of Riemann surfaces

CERN Document Server

Matsumoto, Yukio

2011-01-01

The first part of the book studies pseudo-periodic maps of a closed surface of genus greater than or equal to two. This class of homeomorphisms was originally introduced by J. Nielsen in 1944 as an extension of periodic maps. In this book, the conjugacy classes of the (chiral) pseudo-periodic mapping classes are completely classified, and Nielsen’s incomplete classification is corrected. The second part applies the results of the first part to the topology of degeneration of Riemann surfaces. It is shown that the set of topological types of all the singular fibers appearing in one-parameter holomorphic families of Riemann surfaces is in a bijective correspondence with the set of conjugacy classes of the pseudo-periodic maps of negative twists. The correspondence is given by the topological monodromy.

Amplified-fragment length polymorphism fingerprinting of Mycoplasma species

DEFF Research Database (Denmark)

Kokotovic, Branko; Friis, N.F.; Jensen, J.S.

1999-01-01

Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including...... Mycoplasma genitalium (n = 11), Mycoplasma pneumoniae (n = 5), Mycoplasma hominis (n = 5), Mycoplasma hyopneunmoniae (n = 9), Myco plasma flocculare (n = 5), Mycoplasma hyosynoviae (n = 10), and Mycoplasma dispar (n = 5), AFLP templates were prepared by the digestion of mycoplasmal DNA with BglII and Mfe...... to discriminate the analyzed strains at species and intraspecies levels as well, Each of the tested Mycoplasma species developed a banding pattern entirely different from those obtained from other species under analysis, Subtle intraspecies genomic differences were detected among strains of all of the Mycoplasma...

A 17-kDa Fragment of Lactoferrin Associates With the Termination of Inflammation and Peptides Within Promote Resolution

Directory of Open Access Journals (Sweden)

Aviv Lutaty

2018-03-01

Full Text Available During the resolution of inflammation, macrophages engulf apoptotic polymorphonuclear cells (PMN and can accumulate large numbers of their corpses. Here, we report that resolution phase macrophages acquire the neutrophil-derived glycoprotein lactoferrin (Lf and fragments thereof in vivo and ex vivo. During the onset and resolving phases of inflammation in murine peritonitis and bovine mastitis, Lf fragments of 15 and 17 kDa occurred in various body fluids, and the murine fragmentation, accumulation, and release were mediated initially by neutrophils and later by efferocytic macrophages. The 17-kDa fragment contained two bioactive tripeptides, FKD and FKE that promoted resolution phase macrophage conversion to a pro-resolving phenotype. This resulted in a reduction in peritoneal macrophage numbers and an increase in the CD11blow subset of these cells. Moreover, FKE, but not FKD, peptides enhanced efferocytosis of apoptotic PMN, reduced TNFα and interleukin (IL-6, and increased IL-10 secretion by lipopolysaccharide-stimulated macrophages ex vivo. In addition, FKE promoted neutrophil-mediated resolution at high concentrations (100 µM by enhancing the formation of cytokine-scavenging aggregated NETs (tophi at a low cellular density. Thus, PMN Lf is processed, acquired, and “recycled” by neutrophils and macrophages during inflammation resolution to generate fragments and peptides with paramount pro-resolving activities.

22 CFR 513.225 - Failure to adhere to restrictions.

Science.gov (United States)

2010-04-01

... shall not knowingly do business under a covered transaction with a person who is— (1) Debarred or... excluded from the covered transaction. (b) Violation of the restriction under paragraph (a) of this section may result in disallowance of costs, annulment or termination of award, issuance of a stop work order...

Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors.

Science.gov (United States)

Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

2017-06-01

The molecular interactions of inhibitors of bromodomains (BRDs) were investigated. BRDs are protein interaction modules that recognizing ε-N-acetyl-lysine (εAc-Lys) motifs found in histone tails and are promising protein-protein interaction (PPI) targets. First, we analyzed a peptide ligand containing εAc-Lys to evaluate native PPIs. We then analyzed tetrahydroquinazoline-6-yl-benzensulfonamide derivatives found by fragment-based drug design (FBDD) and examined their interactions with the protein compared with the peptide ligand in terms of the inter-fragment interaction energy. In addition, we analyzed benzodiazepine derivatives that are high-affinity ligands for BRDs and examined differences in the CH/π interactions of the amino acid residues. We further surveyed changes in the charges of the amino acid residues among individual ligands, performed pair interaction energy decomposition analysis and estimated the water profile within the ligand binding site. Thus, useful insights for drug design were provided. Through these analyses and considerations, we show that the FMO method is a useful drug design tool to evaluate the process of FBDD and to explore PPI inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

Pseudo-deterministic Algorithms

OpenAIRE

Goldwasser , Shafi

2012-01-01

International audience; In this talk we describe a new type of probabilistic algorithm which we call Bellagio Algorithms: a randomized algorithm which is guaranteed to run in expected polynomial time, and to produce a correct and unique solution with high probability. These algorithms are pseudo-deterministic: they can not be distinguished from deterministic algorithms in polynomial time by a probabilistic polynomial time observer with black box access to the algorithm. We show a necessary an...

Interactions of $^{16}$O Projectile and its Fragments in Nuclear Emulsion at about 60 and 200 GeV/nucleon

CERN Multimedia

2002-01-01

The aim of the experiment is to measure the multiplicity ``$ n _{s} $'' and pseudo-rapidity ``$\\eta$'' of the shower particles ($\\beta$~$\\geq$~0.7) produced in different types of collisions (peripheral, semi-central and central), of $^{16}$O and $^{32}$S in nuclear emulsions. The multiplicities and angular distributions of both the grey ``$ n _{g} $'' (mainly due to knock- on and recoil protons), and black ``$ n _{b} $'' (slow evaporated target fragments) particles, and the inter-correlation between them are studied. \\\\ \\\\ The yield, charge and angular distributions of produced relativistic projectile fragments P.F.S., for $ Z _{P} . _{F} . $ $\\geq$~2 are measured and their interactions in emulsions are investigated. \\\\ \\\\ The study of the mean free paths for the projectile fragments with Z $\\geq$ 3 produced from 200~A~GeV $^{16}$ 0 interactions were performed, which show the absence of the anomalous phenomena. \\\\ \\\\ The possible production of zero-spin light neutral scaler bosons and pseudoscaler bosons from...

Investigation of Pseudo-Active State in Z-Source Inverter

DEFF Research Database (Denmark)

Schaltz, Erik; Oprea, Octavian; Larsen, Lasse

2005-01-01

This paper introduces a new operating state of the Z-source inverter denoted the pseudo-active state. The pseudoactive state is a state that may boost the output voltage of the Zsource inverter to a level higher than expected. The influence of the pseudo-active state is investigated and an equation...

Abortion as empowerment: reproductive rights activism in a legally restricted context.

Science.gov (United States)

McReynolds-Pérez, Julia

2017-11-08

This paper analyzes the strategies used by activist health professionals in Argentina who justify providing abortion despite legal restrictions on the procedure. These "insider activists" make a case for abortion rights by linking pregnancy termination to a woman's ability to exert agency at a key point in her reproductive life, and argue that refusing women access to the procedure constitutes a grievous health risk. This argument frames pregnancy termination as an issue of empowerment and also as a medical necessity. This article is based on ethnographic research conducted in Argentina in 2013 and 2015, which includes in-depth interviews with abortion activists and health professionals and ethnographic observation at activist events and in clinics. During the period of my field research, the medical staff in one clinic shifted from abortion counseling, based on a harm reduction model, to legal pregnancy termination, a new mode of abortion provision where they directly provided abortions based on the legal health exception. These insider activists formalized the latter approach by creating a diagnostic instrument that frames women's "bio-psycho-social" reasons for wishing to terminate a pregnancy as medically justified. The clinical practice analyzed in this article raises important questions about the potential for health professionals to take on an activist role by making safe abortion accessible, even in a context where the procedure is highly restricted.

Genetic analysis of autoimmune gld mice. I. Identification of a restriction fragment length polymorphism closely linked to the gld mutation within a conserved linkage group

Science.gov (United States)

1988-01-01

A linkage map of distal mouse chromosome 1 was generated using restriction fragment length polymorphism (RFLP) analysis of DNA prepared from 95 [C3H-gld/gld X Mus spretus)F1 X C3H-gld/gld] backcross mice. The gene order was: (centromere) C4bp, Ren-1,2, Ly-5, [At-3/gld], Apoa-2/Ly-17, Spna-1 (telomere). All mice expressing the phenotype of gld homozygotes were homozygous for the At-3 RFLP characteristic of C3H mice and none of the mice heterozygous for At-3 RFLPs had characteristics of gld homozygotes, demonstrating close linkage between these genes. The identification of an RFLP closely linked to the gld gene provides a starting point for the identification of a genetic defect that results in abnormal T cells and autoimmune disease. PMID:2894402

Lower sperm DNA fragmentation after r-FSH administration in functional hypogonadotropic hypogonadism.

Science.gov (United States)

Ruvolo, Giovanni; Roccheri, Maria Carmela; Brucculeri, Anna Maria; Longobardi, Salvatore; Cittadini, Ettore; Bosco, Liana

2013-04-01

An observational clinical and molecular study was designed to evaluate the effects of the administration of recombinant human FSH on sperm DNA fragmentation in men with a non-classical form of hypogonadotropic hypogonadism and idiopathic oligoasthenoteratozoospermia. In the study were included 53 men with a non-classical form of hypogonadotropic hypogonadism and idiopathic oligoasthenoteratozoospermia. In all patients, sperm DNA fragmentation index (DFI), assessed by terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate (dUTP) in situ DNA nick end-labelling (TUNEL) assay, was evaluated before starting the treatment with 150 IU of recombinant human FSH, given three times a week for at least 3 months. Patients' semen analysis and DNA fragmentation index were re-evaluated after the 3-month treatment period. After recombinant human FSH therapy, we did not find any differences in terms of sperm count, motility and morphology. The average DNA fragmentation index was significantly reduced (21.15 vs 15.2, p15 %), while no significant variation occurred in the patients with DFI values ≤ 15 %. Recombinant human FSH administration improves sperm DNA integrity in hypogonadotropic hypogonadism and idiopathic oligoasthenoteratozoospermia men with DNA fragmentation index value >15 % .

Photo-crosslinking induced geometric restriction controls the self-assembly of diphenylalanine based peptides

International Nuclear Information System (INIS)

Tie Zuoxiu; Qin Meng; Zou Dawei; Cao Yi; Wang Wei

2011-01-01

The diphenylalanine (FF) motif has been widely used in the design of peptides that are capable of forming various ordered structures, such as nanotubes, nanospheres and hydrogels. In these assemblies, FF based peptides adopt an antiparallel structure and are stabilized by π-π stacking among the phenyl groups. Here we show that assembly of FF-based peptides can be controlled by their geometric restrictions. Using tripeptide FFY (L-Phe-L-Phe-L-Tyr) as an example, we demonstrate that photo-crosslinking of C-terminal tyrosine can impose a geometric restriction to the formation of an antiparallel structure, leading to a structural change of the assemblies from nanosphere to amorphous. This finding is confirmed using far-UV circular dichroism, Fourier transform infrared spectroscopy and atomic force microscopy. Based on such a mechanism, we are able to control the gel-sol transition of Fmoc-FFY using the geometric restriction induced by photo-crosslinking of C-terminal tyrosine groups. We believe that geometric restriction should be considered as an important factor in the design of peptide-based materials. It can also be implemented as a useful strategy for the construction of environment-responsive 'smart' materials. (authors)

Leonardo and the Pseudo-RCO

OpenAIRE

Wills, Joerg M.

2013-01-01

There are two hypotheses on Leonardo's polyhedron based on the Pseudo-RCO and drawn for Luca Pacioli's book: Leonardo made an error, or: Leonardo draw it with intention, as it is. We give arguments, which support the Intention-hypothesis.

Molecular characterization of Mycobacterium tuberculosis isolates from Tehran, Iran by restriction fragment length polymorphism analysis and spoligotyping

Directory of Open Access Journals (Sweden)

Seifu Gizaw Feyisa

2016-04-01

Full Text Available Abstract: INTRODUCTION Characterization of Mycobacterium tuberculosis (MTB isolates by DNA fingerprinting has contributed to tuberculosis (TB control. The aim of this study was to determine the genetic diversity of MTB isolates from Tehran province in Iran. METHODS MTB isolates from 60 Iranian and 10 Afghan TB patients were fingerprinted by standard IS6110-restriction fragment length polymorphism (RFLP analysis and spoligotyping. RESULTS The copy number of IS6110 ranged from 10-24 per isolate. The isolates were classified into 22 clusters showing ≥ 80% similarity by RFLP analysis. Fourteen multidrug-resistant (MDR isolates were grouped into 4 IS6110-RFLP clusters, with 10 isolates [71% (95% CI: 45-89%] in 1 cluster, suggesting a possible epidemiological linkage. Eighteen Iranian isolates showed ≥ 80% similarity with Afghan isolates. There were no strains with identical fingerprints. Spoligotyping of 70 isolates produced 23 distinct patterns. Sixty (85.7% isolates were grouped into 13 clusters, while the remaining 10 isolates (14.2% were not clustered. Ural (formerly Haarlem4 (n = 22, 31.4% was the most common family followed by Central Asian strain (CAS (n = 18, 25.7% and T (n = 9, 12.8% families. Only 1strain was characterized as having the Beijing genotype. Among 60 Iranian and 10 Afghan MTB isolates, 25% (95% CI: 16-37 and 70% (95% CI: 39-89 were categorized as Ural lineage, respectively. CONCLUSIONS A higher prevalence of Ural family MTB isolates among Afghan patients than among Iranian patients suggests the possible transmission of this lineage following the immigration of Afghans to Iran.

Preliminary studies on fragmentation in tissue-equivalent material produced by 55 MeV/u 40Ar17+ ion beam

International Nuclear Information System (INIS)

Dang Bingrong; Wei Zengquan; Duan Limin; Zhang Baoguo; Li Songlin; Yin Xu; Zhu Yongtai; Li Wenjian; Li Qiang; Yuan Shibin

2002-01-01

By using a 55 MeV/u 40 Ar 17+ beam produced by HIRFL, the distribution of fragments in 1.5 mm lucite on three different directions were measured at the radiobiology terminal. Feasibilities of the phoswich detector composed of fast plastic scintillator and CsI(Tl) detectors for determination of angular distribution of fragments in tissue-equivalent materials were investigated. The results obtained were satisfactory

N-terminal nesprin-2 variants regulate β-catenin signalling

Energy Technology Data Exchange (ETDEWEB)

Zhang, Qiuping; Minaisah, Rose-Marie; Ferraro, Elisa; Li, Chen; Porter, Lauren J.; Zhou, Can; Gao, Fang; Zhang, Junyi; Rajgor, Dipen; Autore, Flavia; Shanahan, Catherine M.; Warren, Derek T., E-mail: derek.warren@kcl.ac.uk

2016-07-15

The spatial compartmentalisation of biochemical signalling pathways is essential for cell function. Nesprins are a multi-isomeric family of proteins that have emerged as signalling scaffolds, herein, we investigate the localisation and function of novel nesprin-2 N-terminal variants. We show that these nesprin-2 variants display cell specific distribution and reside in both the cytoplasm and nucleus. Immunofluorescence microscopy revealed that nesprin-2 N-terminal variants colocalised with β-catenin at cell-cell junctions in U2OS cells. Calcium switch assays demonstrated that nesprin-2 and β-catenin are lost from cell-cell junctions in low calcium conditions whereas emerin localisation at the NE remained unaltered, furthermore, an N-terminal fragment of nesprin-2 was sufficient for cell-cell junction localisation and interacted with β-catenin. Disruption of these N-terminal nesprin-2 variants, using siRNA depletion resulted in loss of β-catenin from cell-cell junctions, nuclear accumulation of active β-catenin and augmented β-catenin transcriptional activity. Importantly, we show that U2OS cells lack nesprin-2 giant, suggesting that the N-terminal nesprin-2 variants regulate β-catenin signalling independently of the NE. Together, these data identify N-terminal nesprin-2 variants as novel regulators of β-catenin signalling that tether β-catenin to cell-cell contacts to inhibit β-catenin transcriptional activity. - Highlights: • N-terminal nesprin-2 variants display cell specific expression patterns. • N-terminal spectrin repeats of nesprin-2 interact with β-catenin. • N-terminal nesprin-2 variants scaffold β-catenin at cell-cell junctions.. • Nesprin-2 variants play multiple roles in β-catenin signalling.

Nonsingular Terminal Sliding Mode Control of Uncertain Second-Order Nonlinear Systems

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Minh-Duc Tran

2015-01-01

Full Text Available This paper presents a high-performance nonsingular terminal sliding mode control method for uncertain second-order nonlinear systems. First, a nonsingular terminal sliding mode surface is introduced to eliminate the singularity problem that exists in conventional terminal sliding mode control. By using this method, the system not only can guarantee that the tracking errors reach the reference value in a finite time with high-precision tracking performance but also can overcome the complex-value and the restrictions of the exponent (the exponent should be fractional number with an odd numerator and an odd denominator in traditional terminal sliding mode. Then, in order to eliminate the chattering phenomenon, a super-twisting higher-order nonsingular terminal sliding mode control method is proposed. The stability of the closed-loop system is established using the Lyapunov theory. Finally, simulation results are presented to illustrate the effectiveness of the proposed method.

Graphical analysis of some pseudo-random number generators

OpenAIRE

Lewis, Peter A. W.

1986-01-01

There exist today many 'good' pseudo-random number generators; the problem is to retrieve them. This document discusses three commonly used pseudo- random number generators, the first being RANDU, a notoriously bad generator, but one which is still occasionally used. The next is the widely used prime modulus, multiplicative congruential generator used in LL-RANDOMII, the Naval Postgraduate School random number package, and the last is the random number generator provided for microcomputers wi...

Pseudo-tumoral hepatic tuberculosis discovered after surgical resection

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Miloudi Nizar

2012-02-01

Full Text Available Pseudo-tumoral hepatic tuberculosis is rare. It is characterized by non-specific symptoms and radiological polymorphism. Diagnosis is problematic. This article presents three cases, each clinically different from each other, that illustrate how difficult diagnosis can be. The definitive diagnosis of pseudo-tumoral hepatic tuberculosis was reached on the basis of histological examination of surgical samples. Treatment of the disease based on appropriate anti-tubercular therapy generally gives a positive outcome.

5 CFR 2641.207 - One-year restriction on any former private sector assignee under the Information Technology...

Science.gov (United States)

2010-01-01

... private sector assignee under the Information Technology Exchange Program representing, aiding, counseling... CONFLICT OF INTEREST RESTRICTIONS Prohibitions § 2641.207 One-year restriction on any former private sector... one year after the termination of his assignment from a private sector organization to an agency under...

A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity.

Science.gov (United States)

Freemont, P S; Ollis, D L; Steitz, T A; Joyce, C M

1986-09-01

The Klenow fragment of DNA polymerase I from Escherichia coli has two enzymatic activities: DNA polymerase and 3'-5' exonuclease. The crystal structure showed that the fragment is folded into two distinct domains. The smaller domain has a binding site for deoxynucleoside monophosphate and a divalent metal ion that is thought to identify the 3'-5' exonuclease active site. The larger C-terminal domain contains a deep cleft that is believed to bind duplex DNA. Several lines of evidence suggested that the large domain also contains the polymerase active site. To test this hypothesis, we have cloned the DNA coding for the large domain into an expression system and purified the protein product. We find that the C-terminal domain has polymerase activity (albeit at a lower specific activity than the native Klenow fragment) but no measurable 3'-5' exonuclease activity. These data are consistent with the hypothesis that each of the three enzymatic activities of DNA polymerase I from E. coli resides on a separate protein structural domain.

Molecular cloning and restriction analysis of EcoRI-fragments of Vicia faba rDNA

International Nuclear Information System (INIS)

Yakura, Kimitaka; Tanifuji, Shigeyuki.

1983-01-01

EcoRI-fragments of Vicia faba rDNA were cloned in plasmid pBR325. Southern blot hybridization of BamHI-digests of these cloned plasmids and Vicia genomic DNA led to the determination of relative positions of BamHI sites in the rDNA and the physical map that had been tentatively made is corrected. (author)

Pseudo-communication vs Quasi-communication

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Елена Константиновна Черничкина

2016-12-01

Full Text Available The article is devoted to the analysis of such specific forms of human interaction as quasi- and pseudo-communication. The authors specify the terms which sometimes are used interchangeably. The aim of the conducted research is to find out and demonstrate existing differences and similarities of these communicative phenomena on the basis of theoretical and empirical analysis of the research material in the Russian and English languages. The authors describe communicative features of these phenomena and consider the reasons for such forms of communication and their increased use at present. The research material is represented fiction extracts, film scripts, jokes, print media, a collection of oral speech records both in Russian and English. The authors make use of the following research methods: definitional analysis (to define the terminology of the research, the method of linguistic observation and introspection (to select the communicative situations, the descriptive-analytical method and the method of comparative analysis (to identify similarities and differences of the target phenomena, and the conversational analysis method (to view productivity and effectiveness of a dialogue, etc. The classification of possible forms of their existence in different discourses is suggested. The authors assume that both pseudo- and quasi-communication are characterized as fictitious forms of human interaction with some noticeable violation of the basic communicative model. Pseudo-communication suffers from the discrepancy of the meaning of a coded and decoded message. The authors put forward the main parameters of scientific classification of it as follows: adequate understanding, intentionality, and the stage of communicative action where the failure takes place. At the same time they stress the necessity to distinguish the cases of pseudo talks from phatic and indirect communication. Quasi-communcation is marked by the lack of a real partner and hence

A note on Lorentz transformation and pseudo-rapidity distributions

International Nuclear Information System (INIS)

Hama, Y.

1980-07-01

It is shown that although rapidity and pseudo-rapidity are almost equivalent variables, their difference may in pratice become quite remarkable. Non Lorentz invariance of pseudo-rapidity distributions may cause appearance of strange effects at first sight, such as deformation of a perfectly symmetric particle distribution into an asymmetric one when going to another frame. (Author) [pt

Identification of two invasive Cacopsylla chinensis (Hemiptera: Psyllidae) lineages based on two mitochondrial sequences and restriction fragment length polymorphism of cytochrome oxidase I amplicon.

Science.gov (United States)

Lee, Hsien-Chung; Yang, Man-Miao; Yeh, Wen-Bin

2008-08-01

The occurrence of pear decline, a disease found in some pear (Pyrus spp.) orchards of Taiwan in recent years, is accompanied by an outbreak of Cacopsylla chinensis (Yang & Li). Two major morphological forms (summer and winter forms) with a variety of intermediate body color and two phylogenetic lineages of this psyllid have been described. The work herein used sequences of mitochondrial cytochrome oxidase I (COI) and 16S rDNA regions to delineate the genetic differentiation of this color-variable insect and to elucidate their relationship. Sequence divergence and phylogenetic analysis have shown that C. chinensis individuals could be divided into two lineages with 3.3 and 2.3% divergence of COI and 16S rDNA, respectively. All specimens from China were found to belong to lineage I. Restriction fragment length polymorphism analysis of COI with restriction enzymes AcuI, AseI, BccI, and FokI on 263 specimens of six populations from Taiwan produced two digestion patterns, which are in agreement with the two lineages described above. Both patterns could be found in each population, with most individuals belonging to lineage I and 5-21% of the individuals belonging to lineage II. Because these two lineages included summer as well as winter morphological forms, the lineage differentiation is apparently not related to morphological characters of this psyllid. Because the invasive records are not in favor of a sympatric differentiation, this psyllid is more likely introduced as different populations from countries in temperate regions.

Pseudo-Goldstino in Field Theory

International Nuclear Information System (INIS)

Argurio, Riccardo; Komargodski, Zohar; Mariotti, Alberto

2011-01-01

We consider two SUSY-breaking hidden sectors which decouple when their respective couplings to the visible particles are switched off. In such a scenario one expects to find two light fermions: the Goldstino and the pseudo-Goldstino. While the former remains massless in the rigid limit, the latter becomes massive due to radiative effects which we analyze from several different points of view. This analysis is greatly facilitated by a version of the Goldberger-Treiman relation, which allows us to write a universal nonperturbative formula for the mass. We carry out the analysis in detail in the context of gauge mediation, where we find that the pseudo-Goldstino mass is at least around the GeV scale and can be easily at the electroweak range, even in low scale models. This leads to interesting and unconventional possibilities in collider physics and it also has potential applications in cosmology.

Detonation and fragmentation modeling for the description of large scale vapor explosions

International Nuclear Information System (INIS)

Buerger, M.; Carachalios, C.; Unger, H.

1985-01-01

The thermal detonation modeling of large-scale vapor explosions is shown to be indispensable for realistic safety evaluations. A steady-state as well as transient detonation model have been developed including detailed descriptions of the dynamics as well as the fragmentation processes inside a detonation wave. Strong restrictions for large-scale vapor explosions are obtained from this modeling and they indicate that the reactor pressure vessel would even withstand explosions with unrealistically high masses of corium involved. The modeling is supported by comparisons with a detonation experiment and - concerning its key part - hydronamic fragmentation experiments. (orig.) [de

M protein typing of Thai group A streptococcal isolates by PCR-Restriction fragment length polymorphism analysis

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Good Michael F

2005-10-01

Full Text Available Abstract Background Group A streptococcal (GAS infections can lead to the development of severe post-infectious sequelae, such as rheumatic fever (RF and rheumatic heart disease (RHD. RF and RHD are a major health concern in developing countries, and in indigenous populations of developed nations. The majority of GAS isolates are M protein-nontypeable (MNT by standard serotyping. However, GAS typing is a necessary tool in the epidemiologically analysis of GAS and provides useful information for vaccine development. Although DNA sequencing is the most conclusive method for M protein typing, this is not a feasible approach especially in developing countries. To overcome this problem, we have developed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP-based assay for molecular typing the M protein gene (emm of GAS. Results Using one pair of primers, 13 known GAS M types showed one to four bands of PCR products and after digestion with Alu I, they gave different RFLP patterns. Of 106 GAS isolates examined from the normal Thai population and from patients with GAS-associated complications including RHD, 95 isolates gave RFLP patterns that corresponded to the 13 known M types. Only 11 isolates gave RFLP patterns that differed from the 13 known M types. These were then analyzed by DNA sequencing and six additional M types were identified. In addition, we found that M93 GAS was the most common M type in the population studied, and is consistent with a previous study of Thai GAS isolates. Conclusion PCR-RFLP analysis has the potential for the rapid screening of different GAS M types and is therefore considerably advantageous as an alternative M typing approach in developing countries in which GAS is endemic.

A Repetition Test for Pseudo-Random Number Generators

OpenAIRE

Gil, Manuel; Gonnet, Gaston H.; Petersen, Wesley P.

2017-01-01

A new statistical test for uniform pseudo-random number generators (PRNGs) is presented. The idea is that a sequence of pseudo-random numbers should have numbers reappear with a certain probability. The expectation time that a repetition occurs provides the metric for the test. For linear congruential generators (LCGs) failure can be shown theoretically. Empirical test results for a number of commonly used PRNGs are reported, showing that some PRNGs considered to have good statistical propert...

Zero-Shot Learning by Generating Pseudo Feature Representations

OpenAIRE

Lu, Jiang; Li, Jin; Yan, Ziang; Zhang, Changshui

2017-01-01

Zero-shot learning (ZSL) is a challenging task aiming at recognizing novel classes without any training instances. In this paper we present a simple but high-performance ZSL approach by generating pseudo feature representations (GPFR). Given the dataset of seen classes and side information of unseen classes (e.g. attributes), we synthesize feature-level pseudo representations for novel concepts, which allows us access to the formulation of unseen class predictor. Firstly we design a Joint Att...

Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology

Science.gov (United States)

Neumann, Lars; Ritscher, Allegra; Müller, Gerhard; Hafenbradl, Doris

2009-08-01

For the detection of the precise and unambiguous binding of fragments to a specific binding site on the target protein, we have developed a novel reporter displacement binding assay technology. The application of this technology for the fragment screening as well as the fragment evolution process with a specific modelling based design strategy is demonstrated for inhibitors of the protein kinase p38alpha. In a fragment screening approach seed fragments were identified which were then used to build compounds from the deep-pocket towards the hinge binding area of the protein kinase p38alpha based on a modelling approach. BIRB796 was used as a blueprint for the alignment of the fragments. The fragment evolution of these deep-pocket binding fragments towards the fully optimized inhibitor BIRB796 included the modulation of the residence time as well as the affinity. The goal of our study was to evaluate the robustness and efficiency of our novel fragment screening technology at high fragment concentrations, compare the screening data with biochemical activity data and to demonstrate the evolution of the hit fragments with fast kinetics, into slow kinetic inhibitors in an in silico approach.

[Elaboration of Pseudo-natural Products Using Artificial In Vitro Biosynthesis Systems].

Science.gov (United States)

Goto, Yuki

2018-01-01

 Peptidic natural products often consist of not only proteinogenic building blocks but also unique non-proteinogenic structures such as macrocyclic scaffolds and N-methylated backbones. Since such non-proteinogenic structures are important structural motifs that contribute to diverse bioactivity, we have proposed that peptides with non-proteinogenic structures should be attractive candidates as artificial bioactive peptides mimicking natural products, or so-called pseudo-natural products. We previously devised an engineered translation system for pseudo-natural peptides, referred to as the flexible in vitro translation (FIT) system. This system enabled "one-pot" synthesis of highly diverse pseudo-natural peptide libraries, which can be rapidly screened by mRNA display technology for the discovery of pseudo-natural peptides with diverse bioactivities.

Pseudo-observations in survival analysis

DEFF Research Database (Denmark)

Andersen, Per Kragh; Perme, Maja Pohar

2010-01-01

-state models, e.g. the competing risks cumulative incidence function. Graphical and numerical methods for assessing goodness-of-fit for hazard regression models and for the Fine-Gray model in competing risks studies based on pseudo-observations are also reviewed. Sensitivity to covariate-dependent censoring...

Generating pseudo test collections for learning to rank scientific articles

NARCIS (Netherlands)

Berendsen, R.; Tsagkias, M.; de Rijke, M.; Meij, E.

2012-01-01

Pseudo test collections are automatically generated to provide training material for learning to rank methods. We propose a method for generating pseudo test collections in the domain of digital libraries, where data is relatively sparse, but comes with rich annotations. Our intuition is that

Properties making a chaotic system a good Pseudo Random Number Generator

OpenAIRE

Falcioni, Massimo; Palatella, Luigi; Pigolotti, Simone; Vulpiani, Angelo

2005-01-01

We discuss two properties making a deterministic algorithm suitable to generate a pseudo random sequence of numbers: high value of Kolmogorov-Sinai entropy and high-dimensionality. We propose the multi dimensional Anosov symplectic (cat) map as a Pseudo Random Number Generator. We show what chaotic features of this map are useful for generating Pseudo Random Numbers and investigate numerically which of them survive in the discrete version of the map. Testing and comparisons with other generat...

Uterine bacterial flora in postpartum Danish Holstein dairy cows determined using DNA-based fingerprinting: Correlation to uterine condition and calving management

DEFF Research Database (Denmark)

Elkjær, K.; Ancker, M.-L.; Gustafsson, H.

2013-01-01

The overall aim of this study was to describe uterine bacterial flora during the postpartum period in Danish Holstein cows using the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method. This method produces a pattern of nucleic acid fragments from the microorganisms present, reflect......The overall aim of this study was to describe uterine bacterial flora during the postpartum period in Danish Holstein cows using the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method. This method produces a pattern of nucleic acid fragments from the microorganisms present......, reflecting the “fingerprint” of the actual microbial flora. As well as characterizing changes in flora with time from calving and between herds, data were examined for strong relations between uterine bacterial flora, calving management and uterine condition. In total 125 Holstein cows from five herds were...... included, and for each cow calving management was recorded. Cows were clinically examined on average 8 (range 0–19) and 28 (range 22–38) days after calving, and a uterine sample was taken for bacterial identification using T-RFLP. Milk samples were taken weekly for progesterone analysis. Bacteria were...

Deciding Security for a Fragment of ASLan

DEFF Research Database (Denmark)

Mödersheim, Sebastian Alexander

situations in security such as the interaction between the work ow of a system with its access control policies. While even the transition relation is undecidable for ASLan in general, we show the security problem is decidable for a large and useful fragment that we call TASLan, as long as we bound...... the number of steps of honest participants. The restriction of TASLan is that all messages and predicates must be in a certain sense unambiguous in their interpretation, excluding \\type-confusions" similar to some tagging results for security protocols....

Magnetic bead purification of labeled DNA fragments forhigh-throughput capillary electrophoresis sequencing

Energy Technology Data Exchange (ETDEWEB)

Elkin, Christopher; Kapur, Hitesh; Smith, Troy; Humphries, David; Pollard, Martin; Hammon, Nancy; Hawkins, Trevor

2001-09-15

We have developed an automated purification method for terminator sequencing products based on a magnetic bead technology. This 384-well protocol generates labeled DNA fragments that are essentially free of contaminates for less than $0.005 per reaction. In comparison to laborious ethanol precipitation protocols, this method increases the phred20 read length by forty bases with various DNA templates such as PCR fragments, Plasmids, Cosmids and RCA products. Our method eliminates centrifugation and is compatible with both the MegaBACE 1000 and ABIPrism 3700 capillary instruments. As of September 2001, this method has produced over 1.6 million samples with 93 percent averaging 620 phred20 bases as part of Joint Genome Institutes Production Process.

On pseudo-values for regression analysis in competing risks models

DEFF Research Database (Denmark)

Graw, F; Gerds, Thomas Alexander; Schumacher, M

2009-01-01

For regression on state and transition probabilities in multi-state models Andersen et al. (Biometrika 90:15-27, 2003) propose a technique based on jackknife pseudo-values. In this article we analyze the pseudo-values suggested for competing risks models and prove some conjectures regarding their...

Detection of titin fragments in urine in response to exercise-induced muscle damage.

Directory of Open Access Journals (Sweden)

Kazue Kanda

Full Text Available Many studies have attempted to determine the associations between blood biomarkers and exercise-induced muscle damage. However, poor correlations between the changes in biomarker levels and the magnitude of muscle symptoms have been reported. Recent advances in proteomic tools offer a strategy for the comprehensive analysis of protein expression, which can be used to identify biomarkers. Here, we used a proteomic analysis to identify urinary proteins that appear in response to a calf-raise exercise, including repetitive eccentric muscle contractions, and found that a titin (also known as connectin N-terminal fragment molecule appears in the urine after eccentric exercise. We measured the titin fragment in urine samples from nine individuals before and after eccentric exercise using a newly-established enzyme-linked immunosorbent assay and found that the titin fragment excretion rate increased 96 h after the exercise (5.1 to 77.6 pg/min, p <0.01. The changes in the titin fragment excretion rate were correlated strongly with blood markers of muscle damage and with muscle symptoms. These findings suggest that the urinary titin fragment is potentially a noninvasive biomarker of muscle damage.

Brane-worlds pseudo-Goldstinos

International Nuclear Information System (INIS)

Benakli, Karim; Moura, Cesar

2008-01-01

We consider a space-time with extra dimensions containing sectors, branes and bulk, that communicate only through gravitational interactions. In each sector, if considered separately, supersymmetry could be spontaneously broken, leading to the appearance of Goldstinos. However, when taken all together, only certain combinations of the latter states turn out to be true 'would-be-Goldstinos', eaten by the gravitinos. The other (orthogonal) combinations, we call pseudo-Goldstinos, remain in the low energy spectrum. We discuss explicitly how this happen in the simplest set-up of five-dimensional space compactified on S 1 /Z 2 . Our results divide into two parts that can be considered separately. First, we build an extension of the bulk five-dimensional supergravity, by a set of new auxiliary fields, that allows coupling it to branes where supersymmetry is spontaneously broken. Second, we discuss in details the super-Higgs mechanism in the R ξ and unitary gauges, in the presence of both of a bulk Scherk-Schwarz mechanism and brane localized F-terms. This leads us to compute the gravitino mass and provide explicit formulae for the pseudo-Goldstinos spectrum

Molecular determinants of interactions between the N-terminal domain and the transmembrane core that modulate hERG K+ channel gating.

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Jorge Fernández-Trillo

Full Text Available A conserved eag domain in the cytoplasmic amino terminus of the human ether-a-go-go-related gene (hERG potassium channel is critical for its slow deactivation gating. Introduction of gene fragments encoding the eag domain are able to restore normal deactivation properties of channels from which most of the amino terminus has been deleted, and also those lacking exclusively the eag domain or carrying a single point mutation in the initial residues of the N-terminus. Deactivation slowing in the presence of the recombinant domain is not observed with channels carrying a specific Y542C point mutation in the S4-S5 linker. On the other hand, mutations in some initial positions of the recombinant fragment also impair its ability to restore normal deactivation. Fluorescence resonance energy transfer (FRET analysis of fluorophore-tagged proteins under total internal reflection fluorescence (TIRF conditions revealed a substantial level of FRET between the introduced N-terminal eag fragments and the eag domain-deleted channels expressed at the membrane, but not between the recombinant eag domain and full-length channels with an intact amino terminus. The FRET signals were also minimized when the recombinant eag fragments carried single point mutations in the initial portion of their amino end, and when Y542C mutated channels were used. These data suggest that the restoration of normal deactivation gating by the N-terminal recombinant eag fragment is an intrinsic effect of this domain directed by the interaction of its N-terminal segment with the gating machinery, likely at the level of the S4-S5 linker.

Pseudo-Scientific Information: Reasons of Spread and Premises of Vitality

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Valdas Pruskus

2011-04-01

Full Text Available The phenomenon of pseudo-scientific information, the reasons of its spread and premises of its vitality are discussed in the paper. Pseudo-scientific information is understandable as an attempt to suit a demand, which exists in society, while providing a simple answer to a question, which an individual or society is concerned about, and that answer is not sustained by scientific research. It is showed that the rise and spread of pseudo-scientific information in society are conditioned by objective reasons. Firstly, the lack of information concerning a subject which is significant for society. Secondly, the lack of information for a particular individual (social group concerning a substantial subject. Thirdly, fast spread of scientific and technical inventions and penetration of technological innovations into various spheres of life the understanding of which demands an appropriate informal “processing”, i e it demands provision in an appropriate form, which is partly provided by pseudo-scientific knowledge.The existence of pseudo-scientific information is determined by the fact that it performs important social functions in society. The existence of pseudo-scientific information by official certified scientific information and the fact, that all social groups are affected to a larger or lesser extent, show its ambivalent power and vitality. On the one part, the roots of its vitality lie in the duality of this phenomenon, where opposite things coexist in a strange way – the truth (scientifically verified propositions and speculations which are based on intuition rather than on scientifically verified facts. On the other part, it is maintained by our permanent wish to get an additional and fresher information, though not totally reliable, while seeking to know universally and better the world around us and its phenomena. While meeting this requirement, a pseudo-scientific information stimulates researchers both to enhance their attempts to

Production of bioethanol using agricultural waste: banana pseudo stem

Directory of Open Access Journals (Sweden)

Snehal Ingale

2014-09-01

Full Text Available India is amongst the largest banana (Musa acuminata producing countries and thus banana pseudo stem is commonly available agricultural waste to be used as lignocellulosic substrate. Present study focuses on exploitation of banana pseudo stem as a source for bioethanol production from the sugars released due to different chemical and biological pretreatments. Two fungal strains Aspergillus ellipticus and Aspergillus fumigatus reported to be producing cellulolytic enzymes on sugarcane bagasse were used under co-culture fermentation on banana pseudo stem to degrade holocellulose and facilitate maximum release of reducing sugars. The hydrolysate obtained after alkali and microbial treatments was fermented by Saccharomyces cerevisiae NCIM 3570 to produce ethanol. Fermentation of cellulosic hydrolysate (4.1 g% gave maximum ethanol (17.1 g/L with yield (84% and productivity (0.024 g%/h after 72 h. Some critical aspects of fungal pretreatment for saccharification of cellulosic substrate using A. ellipticus and A. fumigatus for ethanol production by S. cerevisiae NCIM 3570 have been explored in this study. It was observed that pretreated banana pseudo stem can be economically utilized as a cheaper substrate for ethanol production.

MRI-based treatment planning with pseudo CT generated through atlas registration.

Science.gov (United States)

Uh, Jinsoo; Merchant, Thomas E; Li, Yimei; Li, Xingyu; Hua, Chiaho

2014-05-01

To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787-0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%-98.7%) satisfied the criteria of chi-evaluation (pediatric brain tumor patients. The doses calculated from pseudo CTs agreed well with those from real CTs

A model for pseudo-Dirac neutrinos: leptogenesis and ultra-high energy neutrinos

Energy Technology Data Exchange (ETDEWEB)

Ahn, Y.H. [Center for Theoretical Physics of the Universe, Institute for Basic Science (IBS),Daejeon, 34051 (Korea, Republic of); Kang, Sin Kyu [Insitute for Convergence Fundamental Study, School of Liberal Arts, Seoul-Tech.,Seoul, 01811 (Korea, Republic of); Kim, C.S. [Dept. of Physics and IPAP, Yonsei University,Seoul, 120-749 (Korea, Republic of)

2016-10-18

We propose a model where sterile neutrinos are introduced to make light neutrinos to be pseudo-Dirac particles. It is shown how tiny mass splitting necessary for realizing pseudo-Dirac neutrinos can be achieved. Within the model, we show how leptogenesis can be successfully generated. Motivated by the recent observation of very high energy neutrino events at IceCube, we study a possibility to observe the effects of the pseudo-Dirac property of neutrinos by performing astronomical-scale baseline experiments to uncover the oscillation effects of very tiny mass splitting. We also discuss future prospect to observe the effects of the pseudo-Dirac property of neutrinos at high energy neutrino experiments.

Inflammatory pseudo tumor of the spleen. Radiologic findings

International Nuclear Information System (INIS)

Folgueral, M.; Naranjo, G.; Grasa, J.

1998-01-01

The inflammatory splenic pseudo tumor is an uncommon benign lesion of unknown etiology that usually is detected incidentally in patients being examined for other disorders. We present the ultrasound, computed tomography (CT) and magnetic resonance (MR) findings in two patients (a 56-year-old woman and 67-year-old man) with inflammatory pseudo tumor of the spleen. Ultrasound images of the inflammatory splenic pseudo tumor show a hypoechoic mass with or without calcifications. In CT, the mass presents a low attenuation that is slightly enhanced by intravenous injection of an iodinated contrast medium. MR images show an isointense spleen in T1-weighted spin-echo sequences that is hypointense in T2-weighted sequences. The differential diagnosis should consider other more common splenic masses. but the definitive diagnosis can not be based on imaging methods alone. In the both cases, the final diagnosis was reached after splenectomy and pathological study. (Author) 8 refs

Algebra of pseudo-differential operators over C*-algebra

International Nuclear Information System (INIS)

Mohammad, N.

1982-08-01

Algebras of pseudo-differential operators over C*-algebras are studied for the special case when in Hormander class Ssub(rho,delta)sup(m)(Ω) Ω = Rsup(n); rho = 1, delta = 0, m any real number, and the C*-algebra is infinite dimensional non-commutative. The space B, i.e. the set of A-valued C*-functions in Rsup(n) (or Rsup(n) x Rsup(n)) whose derivatives are all bounded, plays an important role. A denotes C*-algebra. First the operator class Ssub(phi,0)sup(m) is defined, and through it, the class Lsub(1,0)sup(m) of pseudo-differential operators. Then the basic asymptotic expansion theorems concerning adjoint and product of operators of class Ssub(1,0)sup(m) are stated. Finally, proofs are given of L 2 -continuity theorem and the main theorem, which states that algebra of all pseudo-differential operators over C*-algebras is itself C*-algebra

Photo-Crosslinking Induced Geometric Restriction Controls the Self-Assembly of Diphenylalanine Based Peptides

International Nuclear Information System (INIS)

Tie Zuo-Xiu; Qin Meng; Zou Da-Wei; Cao Yi; Wang Wei

2011-01-01

The diphenylalanine (FF) motif has been widely used in the design of peptides that are capable of forming various ordered structures, such as nanotubes, nanospheres and hydrogels. In these assemblies, FF based peptides adopt an antiparallel structure and are stabilized by π — π stacking among the phenyl groups. Here we show that assembly of FF-based peptides can be controlled by their geometric restrictions. Using tripeptide FFY (L-Phe-L-Phe-L-Tyr) as an example, we demonstrate that photo-crosslinking of C-terminal tyrosine can impose a geometric restriction to the formation of an antiparallel structure, leading to a structural change of the assemblies from nanosphere to amorphous. This finding is confirmed using far-UV circular dichroism, Fourier transform infrared spectroscopy and atomic force microscopy. Based on such a mechanism, we are able to control the gel-sol transition of Fmoc-FFY using the geometric restriction induced by photo-crosslinking of C-terminal tyrosine groups. We believe that geometric restriction should be considered as an important factor in the design of peptide-based materials. It can also be implemented as a useful strategy for the construction of environment-responsive 'smart' materials. (cross-disciplinary physics and related areas of science and technology)

Radioimmunological assay of the biologically active fragment of the human parathyroid hormone

International Nuclear Information System (INIS)

Desplan, C.; Jullienne, A.; Raulais, D.; Rivaille, P.; Barlet, J.P.; Moukthar, M.S.; Milhaud, G.

1977-01-01

The authors describe a RIA of the biologically active fraction (N-terminal) of human parathyroid hormone. This homologous test uses antibodies obtained in goats against a N-terminal 1-34 fragment of hPTH synthetised according to the method of Niall and Coll. In this system, natural hPTH of different origin (extracts from parathyroid adenomas, adenomal culture medium, hyperparathyroid plasma, adsorption chromatography extract of normal human plasma) behaved in the same manner as the synthetic reference hormone 1-34 hPTHN. The RIA detected PTH in 65% of the normal subjects and distinguished the normal values from the values of hyperparathyroid patients, which makes it suitable for clinical practice. (AJ) [de

[Pseudo-continent perineal colostomy. Results and techniques].

Science.gov (United States)

Lasser, P; Dubé, P; Guillot, J M; Elias, D

1997-09-01

This prospective study was conducted to assess functional results obtained after pseudo-continent perineal colostomy using the Schmidt procedure. Functional outcome was assessed in 40 patients who had undergone amputation of the rectum for cancer and pseudo-continent perineal colostomy reconstruction between 1989 and 1995 in our institution. The cancer pathology, operative procedure and post-operative care were noted. Morbidity, functional outcome and degree of patient satisfaction were recorded. Mean follow-up was 45 months (18-87) in 100% of the patients. There were no operative deaths. Twenty patients had post-operative complications and 2 patients required early conversion to definitive abdominal colostomy due to severe perineal complications. Function outcome showed normal continence in 4 patients, air incontinence in 23, occasional minimal leakage in 9 and incontinence requiring iliac colostomy in 2. Eighty-six percent of the patients were highly satisfied or satisfied with their continence capacity. Pseudo-continent perineal colostomy is a reliable technique which can be proposed as an alternative to left iliac colostomy after amputation of the rectum for cancer if a rigorous procedure is applied: careful patient selection, informed consent, rigorous surgical procedure, daily life-long irrigation of the colon.

POPULATION DYNAMICS OF PSEUDO-NITZSCHIA SPECIES ...

African Journals Online (AJOL)

nb

current study aimed at assessing the population dynamics of Pseudo-nitzschia ... and to the developing aquaculture industry ... B. Hotel. Pangani Island. Bongoyo Island. Mbudya Island. Msasani Bay ... Salinity values did not show clear trends.

Variability of Pseudo-Nitzschia and Domoic Acid Along the U.S. West Coast

Science.gov (United States)

Wood, S.; Bill, B. D.; Trainer, V. L.

2017-12-01

A massive, destructive harmful algal bloom (HAB) along the U.S. West Coast in 2015 illustrated the threat posed to fisheries, marine mammal survival, and public health by toxigenic diatom Pseudo-nitzschia. Certain species of the genus Pseudo-nitzschia produce the neurotoxin domoic acid (DA), which can cause amnesic shellfish poisoning (ASP) in humans who consume shellfish contaminated with DA. The specific environmental conditions producing toxic algal blooms remain largely unclear. The continued assessment of the abundance and toxicity of Pseudo-nitzschia is used to identify emerging hotspots, investigate the occurrence of Pseudo-nitzschia and DA relative to environmental phenomena such as El Niño and the Blob, and make more robust the data that are incorporated into the HAB early-warning system. Seawater samples collected on NOAA research vessel Bell M. Shimada in May 2017 were analyzed in the laboratory using the following methods: 1. indirect cBASI Enzyme-linked Immunosorbent Assays (ELISAs) to determine DA concentration; 2. light microscopy to determine abundance of Pseudo-nitzschia; and 3. scanning electron microscopy to determine Pseudo-nitzschia species composition at select locations. Results indicated that freshwater plumes can affect the location and abundance of Pseudo-nitzschia at HAB hotspots near Heceta Bank. Future analysis will examine the potential connection between the abundance of toxic species of Pseudo-nitzschia with nutrient and chlorophyll data. This research adds to the time series data needed to determine the relative influence of various drivers of Pseudo-nitzschia blooms, including local factors such as macronutrient concentrations, and climatic influences such as El Niño, La Niña, and the Pacific Decadal Oscillation.

Pseudo Random Coins Show More Heads Than Tails

OpenAIRE

Bauke, Heiko; Mertens, Stephan

2003-01-01

Tossing a coin is the most elementary Monte Carlo experiment. In a computer the coin is replaced by a pseudo random number generator. It can be shown analytically and by exact enumerations that popular random number generators are not capable of imitating a fair coin: pseudo random coins show more heads than tails. This bias explains the empirically observed failure of some random number generators in random walk experiments. It can be traced down to the special role of the value zero in the ...

T cell telomere length in HIV-1 infection: no evidence for increased CD4+ T cell turnover

NARCIS (Netherlands)

Wolthers, K. C.; Bea, G.; Wisman, A.; Otto, S. A.; de Roda Husman, A. M.; Schaft, N.; de Wolf, F.; Goudsmit, J.; Coutinho, R. A.; van der Zee, A. G.; Meyaard, L.; Miedema, F.

1996-01-01

Progression to acquired immunodeficiency syndrome (AIDS) has been related to exhaustion of the regenerative capacity of the immune system resulting from high T cell turnover. Analysis of telomeric terminal restriction fragment (TRF) length, a marker for cellular replicative history, showed that

Efficient production of Trastuzumab Fab antibody fragments in Brevibacillus choshinensis expression system.

Science.gov (United States)

Mizukami, Makoto; Onishi, Hiromasa; Hanagata, Hiroshi; Miyauchi, Akira; Ito, Yuji; Tokunaga, Hiroko; Ishibashi, Matsujiro; Arakawa, Tsutomu; Tokunaga, Masao

2018-10-01

The Brevibacillus expression system has been successfully employed for the efficient productions of a variety of recombinant proteins, including enzymes, cytokines, antigens and antibody fragments. Here, we succeeded in secretory expression of Trastuzumab Fab antibody fragments using B. choshinensis/BIC (Brevibacillus in vivocloning) expression system. In the fed-batch high-density cell culture, recombinant Trastuzumab Fab with amino-terminal His-tag (His-BcFab) was secreted at high level, 1.25 g/liter, and Fab without His-tag (BcFab) at ∼145 mg/L of culture supernatant. His-BcFab and BcFab were purified to homogeneity using combination of conventional column chromatographies with a yield of 10-13%. This BcFab preparation exhibited native structure and functions evaluated by enzyme-linked immunosorbent assay, surface plasmon resonance, circular dichroism measurements and size exclusion chromatography. To our knowledge, this is the highest production of Fab antibody fragments in gram-positive bacterial expression/secretion systems. Copyright © 2018 Elsevier Inc. All rights reserved.

A Pseudo Fractional-N Clock Generator with 50% Duty Cycle Output

Science.gov (United States)

Yang, Wei-Bin; Lo, Yu-Lung; Chao, Ting-Sheng

A proposed pseudo fractional-N clock generator with 50% duty cycle output is presented by using the pseudo fractional-N controller for SoC chips and the dynamic frequency scaling applications. The different clock frequencies can be generated with the particular phase combinations of a four-stage voltage-controlled oscillator (VCO). It has been fabricated in a 0.13µm CMOS technology, and work with a supply voltage of 1.2V. According to measured results, the frequency range of the proposed pseudo fractional-N clock generator is from 71.4MHz to 1GHz and the peak-to-peak jitter is less than 5% of the output period. Duty cycle error rates of the output clock frequencies are from 0.8% to 2% and the measured power dissipation of the pseudo fractional-N controller is 146µW at 304MHz.

The terminal portion of leptospiral immunoglobulin-like protein LigA confers protective immunity against lethal infection in the hamster model of leptospirosis.

Science.gov (United States)

Silva, Everton F; Medeiros, Marco A; McBride, Alan J A; Matsunaga, Jim; Esteves, Gabriela S; Ramos, João G R; Santos, Cleiton S; Croda, Júlio; Homma, Akira; Dellagostin, Odir A; Haake, David A; Reis, Mitermayer G; Ko, Albert I

2007-08-14

Subunit vaccines are a potential intervention strategy against leptospirosis, which is a major public health problem in developing countries and a veterinary disease in livestock and companion animals worldwide. Leptospiral immunoglobulin-like (Lig) proteins are a family of surface-exposed determinants that have Ig-like repeat domains found in virulence factors such as intimin and invasin. We expressed fragments of the repeat domain regions of LigA and LigB from Leptospira interrogans serovar Copenhageni. Immunization of Golden Syrian hamsters with Lig fragments in Freund's adjuvant induced robust antibody responses against recombinant protein and native protein, as detected by ELISA and immunoblot, respectively. A single fragment, LigANI, which corresponds to the six carboxy-terminal Ig-like repeat domains of the LigA molecule, conferred immunoprotection against mortality (67-100%, P<0.05) in hamsters which received a lethal inoculum of L. interrogans serovar Copenhageni. However, immunization with this fragment did not confer sterilizing immunity. These findings indicate that the carboxy-terminal portion of LigA is an immunoprotective domain and may serve as a vaccine candidate for human and veterinary leptospirosis.

The X chromosome shows less genetic variation at restriction sites than the autosomes

NARCIS (Netherlands)

Hofker, M. H.; Skraastad, M. I.; Bergen, A. A.; Wapenaar, M. C.; Bakker, E.; Millington-Ward, A.; van Ommen, G. J.; Pearson, P. L.

1986-01-01

Using a standard technique, 122 single-copy probes were screened for their ability to detect restriction fragment length polymorphisms (RFLPs) in the human genome. The use of a standardized RFLP screening enables the introduction of statistical methods in the analysis of differences in RFLP content

Influencia del Pseudo Dionisio en Nicolás de Cusa

Directory of Open Access Journals (Sweden)

Andrés Hubert R

2007-01-01

Full Text Available Nicolás de Cusa (1401-1464 reconoce la influencia del Pseudo Dionisio en su propio pensamiento, especialmente en su teología negativa. Este trabajo busca mostrar esta influencia en el libro referencia del Cusano: el De Docta Ignorantia (la Docta Ignorancia. Esta obra consta de 3 partes. Solo en la primera parte, Nicolás sigue de cerca las ideas del Pseudo Dionisio y solo en ella lo cita. En las demás, aunque se nota la influencia, nuestro autor se siente más libre: las fundaciones están firmes, el constructor puede construir libremente. Para probar esta tesis, se toman dos ejemplos: el tema de las tinieblas y la coincidencia de los opuestos. Este ejercicio permite conocer cómo y por qué se recibió al Pseudo Dionisio en la historia de la teología. Permite también profundizar el sentido de la teología de Nicolás de CusaThe reflections of Nicolas of Cusa (1401-1464 recognise the influence of Pseudo Dyonisius, particularly in his negative theology. The present study shows this influence on Nicolas' most important book: the De Docta Ignorantia (the Learned Ignorance. The book is divided into three parts and it is in the first part that Nicolas directly pursues the ideas of Pseudo Dyonisius and it is only here that he quotes them. In the other parts of the book although the influence is noted, the foundations have been set and are solid and the author or builder can construct with freedom. To prove this thesis, 2 examples are presented: the theme of darkness and the coincidence of opposites. This exercise shows how and why Pseudo Dyonisius has been accepted into the history of the theology. It also deepens the meaning of the Nicolas of Cusa's theology

Enhancing Pseudo-Telepathy in the Magic Square Game

Science.gov (United States)

Pawela, Łukasz; Gawron, Piotr; Puchała, Zbigniew; Sładkowski, Jan

2013-01-01

We study the possibility of reversing an action of a quantum channel. Our principal objective is to find a specific channel that reverses as accurately as possible an action of a given quantum channel. To achieve this goal we use semidefinite programming. We show the benefits of our method using the quantum pseudo-telepathy Magic Square game with noise. Our strategy is to move the pseudo-telepathy region to higher noise values. We show that it is possible to reverse the action of a noise channel using semidefinite programming. PMID:23762246

The characteristics of failure among students who experienced pseudo thinking

Science.gov (United States)

Anggraini, D.; Kusmayadi, T. A.; Pramudya, I.

2018-04-01

The purpose of this research is to describe the thinking process of students who experienced pseudo thinking when solving the straight line equation. The result of this study shows the characteristics of error that caused students to experience pseudo thinking when solving the problem and their relation with students’ metacognition skill. This qualitative research was conducted in State 16 Junior High School in Surakarta, Indonesia during the odd semester of 2017/2018 academic year. The subjects of the study were students Junior High School students of 8th grade chosen using purposive sampling technique. Data were collected through the administration of think aloud method. The result showed that the characteristics of errors among the subjects are: 1) the answers resulted from pseudo thinking when solving the problem were obtained from the spontaneous, fast, unconscious and uncontrolled thinking process; 2) students had misconception; 3) students had tendency to memorize the formula and imitate the completion procedure; 4) students experienced fuzzy memory when solving the problem. From the mistakes among students who experienced pseudo thinking, their metacognition ability could be inferred.

Virtual fragment preparation for computational fragment-based drug design.

Science.gov (United States)

Ludington, Jennifer L

2015-01-01

Fragment-based drug design (FBDD) has become an important component of the drug discovery process. The use of fragments can accelerate both the search for a hit molecule and the development of that hit into a lead molecule for clinical testing. In addition to experimental methodologies for FBDD such as NMR and X-ray Crystallography screens, computational techniques are playing an increasingly important role. The success of the computational simulations is due in large part to how the database of virtual fragments is prepared. In order to prepare the fragments appropriately it is necessary to understand how FBDD differs from other approaches and the issues inherent in building up molecules from smaller fragment pieces. The ultimate goal of these calculations is to link two or more simulated fragments into a molecule that has an experimental binding affinity consistent with the additive predicted binding affinities of the virtual fragments. Computationally predicting binding affinities is a complex process, with many opportunities for introducing error. Therefore, care should be taken with the fragment preparation procedure to avoid introducing additional inaccuracies.This chapter is focused on the preparation process used to create a virtual fragment database. Several key issues of fragment preparation which affect the accuracy of binding affinity predictions are discussed. The first issue is the selection of the two-dimensional atomic structure of the virtual fragment. Although the particular usage of the fragment can affect this choice (i.e., whether the fragment will be used for calibration, binding site characterization, hit identification, or lead optimization), general factors such as synthetic accessibility, size, and flexibility are major considerations in selecting the 2D structure. Other aspects of preparing the virtual fragments for simulation are the generation of three-dimensional conformations and the assignment of the associated atomic point charges.

Orbit classification in an equal-mass non-spinning binary black hole pseudo-Newtonian system

Science.gov (United States)

Zotos, Euaggelos E.; Dubeibe, F. L.; González, Guillermo A.

2018-04-01

The dynamics of a test particle in a non-spinning binary black hole system of equal masses is numerically investigated. The binary system is modeled in the context of the pseudo-Newtonian circular restricted three-body problem, such that the primaries are separated by a fixed distance and move in a circular orbit around each other. In particular, the Paczyński-Wiita potential is used for describing the gravitational field of the two non-Newtonian primaries. The orbital properties of the test particle are determined through the classification of the initial conditions of the orbits, using several values of the Jacobi constant, in the Hill's regions of possible motion. The initial conditions are classified into three main categories: (i) bounded, (ii) escaping and (iii) displaying close encounters. Using the smaller alignment index (SALI) chaos indicator, we further classify bounded orbits into regular, sticky or chaotic. To gain a complete view of the dynamics of the system, we define grids of initial conditions on different types of two-dimensional planes. The orbital structure of the configuration plane, along with the corresponding distributions of the escape and collision/close encounter times, allow us to observe the transition from the classical Newtonian to the pseudo-Newtonian regime. Our numerical results reveal a strong dependence of the properties of the considered basins with the Jacobi constant as well as with the Schwarzschild radius of the black holes.

Characterization of crystals of an antibody-recognition fragment of the cancer differentiation antigen mesothelin in complex with the therapeutic antibody MORAb-009

International Nuclear Information System (INIS)

Ma, Jichun; Tang, Wai Kwan; Esser, Lothar; Pastan, Ira; Xia, Di

2012-01-01

The therapeutic antibody MORAb-009 disrupts the interaction of mesothelin and the ovarian cancer antigen CA-125. Crystals have been grown of the Fab fragment derived from MORAb-009 and of its complex with an N-terminal fragment of mesothelin. The mesothelin-specific monoclonal antibody MORAb-009 is capable of blocking the binding of mesothelin to CA-125 and displays promising anticancer potential. It is currently undergoing clinical trials. In order to understand the basis of the interaction between MORAb-009 and mesothelin at atomic resolution, both the Fab fragment of MORAb-009 and the complex between the Fab and an N-terminal fragment of mesothelin (residues 7–64) were crystallized. The crystals of the Fab diffracted X-rays to 1.75 Å resolution and had the symmetry of space group P4 1 2 1 2, with unit-cell parameters a = b = 140.6, c = 282.0 Å. The crystals of the mesothelin–Fab complex diffracted to 2.6 Å resolution and belonged to the hexagonal space group P6 4 , with unit-cell parameters a = b = 146.2, c = 80.9 Å. Structural analyses of these molecules are in progress

On the Relativistic Origin of Pseudo spin Symmetry in Nuclei

International Nuclear Information System (INIS)

Leviatan, A.

1998-01-01

We review the concept of pseudo spin symmetry and its role in nuclear spectroscopy. We survey the attempts to arrive at a microscopic understanding of this symmetry. In particular, we show that pseudo spin symmetry in nuclei could arise from nucleons moving in a relativistic mean field which has an attractive scalar (Vs) and repulsive vector (Vv) potential nearly equal in magnitude but opposite in sign. We show that the generators of pseudo spin symmetry are the non-relativistic limit of the generators of an SU(2) symmetry which leaves invariant the Dirac Hamiltonian with Vs 2= -Vv. Furthermore within this framework, we demonstrate that this symmetry may be approximately conserved for realistic scalar and vector potentials

Role of mTOR, Bad, and Survivin in RasGAP Fragment N-Mediated Cell Protection

Science.gov (United States)

Yang, Jiang-Yan; Widmann, Christian

2013-01-01

Partial cleavage of p120 RasGAP by caspase-3 in stressed cells generates an N-terminal fragment, called fragment N, which activates an anti-apoptotic Akt-dependent survival response. Akt regulates several effectors but which of these mediate fragment N-dependent cell protection has not been defined yet. Here we have investigated the role of mTORC1, Bad, and survivin in the capacity of fragment N to protect cells from apoptosis. Neither rapamycin, an inhibitor of mTORC1, nor silencing of raptor, a subunit of the mTORC1 complex, altered the ability of fragment N from inhibiting cisplatin- and Fas ligand-induced death. Cells lacking Bad, despite displaying a stronger resistance to apoptosis, were still protected by fragment N against cisplatin-induced death. Fragment N was also able to protect cells from Fas ligand-induced death in conditions where Bad plays no role in apoptosis regulation. Fragment N expression in cells did neither modulate survivin mRNA nor its protein expression. Moreover, the expression of cytoplasmic survivin, known to exert anti-apoptotic actions in cells, still occurred in UV-B-irradiated epidermis of mouse expressing a caspase-3-resistant RasGAP mutant that cannot produce fragment N. Additionally, survivin function in cell cycle progression was not affected by fragment N. These results indicate that, taken individually, mTOR, Bad, or Survivin are not required for fragment N to protect cells from cell death. We conclude that downstream targets of Akt other than mTORC1, Bad, or survivin mediate fragment N-induced protection or that several Akt effectors can compensate for each other to induce the pro-survival fragment N-dependent response. PMID:23826368

Mycobacterium avium restriction fragment lenght polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains

Directory of Open Access Journals (Sweden)

Patrícia Carvalho de Sequeira

2005-11-01

Full Text Available Simple double repetitive element polymerase chain reaction (MaDRE-PCR and Pvu II-IS1245 restriction fragment length polymorphism (RFLP typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 Aids inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

Pseudo-BINPUT, a free formal input package for Fortran programmes

International Nuclear Information System (INIS)

Gubbins, M.E.

1977-11-01

Pseudo - BINPUT is an input package for reading free format data in codeword control in a FORTRAN programme. To a large degree it mimics in function the Winfrith Subroutine Library routine BINPUT. By using calls of the data input package DECIN to mimic the input routine BINPUT, Pseudo - BINPUT combines some of the advantages of both systems. (U.K.)

Pseudo-differential operators and generalized functions

CERN Document Server

Toft, Joachim

2015-01-01

This book gathers peer-reviewed contributions representing modern trends in the theory of generalized functions and pseudo-differential operators. It is dedicated to Professor Michael Oberguggenberger (Innsbruck University, Austria) in honour of his 60th birthday. The topics covered were suggested by the ISAAC Group in Generalized Functions (GF) and the ISAAC Group in Pseudo-Differential Operators (IGPDO), which met at the 9th ISAAC congress in Krakow, Poland in August 2013. Topics include Columbeau algebras, ultra-distributions, partial differential equations, micro-local analysis, harmonic analysis, global analysis, geometry, quantization, mathematical physics, and time-frequency analysis. Featuring both essays and research articles, the book will be of great interest to graduate students and researchers working in analysis, PDE and mathematical physics, while also offering a valuable complement to the volumes on this topic previously published in the OT series.

SPERM MORPHOLOGICAL ABNORMALITIES AS INDICATORS OF DNA FRAGMENTATION AND FERTILIZATION IN ASSISTED REPRODUCTION

Directory of Open Access Journals (Sweden)

Barbara Dariš

2018-02-01

Full Text Available Background. To determine the relationship between sperm morphological abnormalities, DNA fragmentation and fertilization rate in IVF and ICSI. Methods. Sperm samples from 10 IVF and 20 ICSI cycles were analyzed. Morphology was assessed according to strict criteria, and DNA fragmentation was measured by terminal deoxynucleotidyl transferase (TdT-mediated fluorescein-dUTP nick end labelling (TUNEL using a flow cytometry. Results. There was a significant difference in the amount of morphological abnormalities between sperm samples with low (< 20 % and high (≥ 20 % degree of DNA fragmentation. The percentages of amorphous heads (10 vs. 4 % and overall head abnormalities (42 vs. 30 % were significantly higher in sperm samples with elevated degree of DNA fragmentation. No correlation was found between sperm DNA fragmentation and fertilization rate after IVF and ICSI. When the predominant morphological abnormality in sperm samples was determined, a negative correlation was found between the percentage of spermatozoa with elongated heads and fertilization rate in ICSI (r = –0.45, P < 0.05. The fertilization rate after IVF was lower in the case of acrosomal abnormalities (35.3 %, compared to the cases of other predominant morphological abnormalities. Conclusions. Head abnormalities, especially amorphous heads, are related to elevated degree of DNA fragmentation. Predominant abnormal form in sperm samples, such as elongated heads and acrosomal abnormalities, may affect fertilization in ART.

High hardness and superlative oxidation resistance in a pseudo-icosahehdral Cr-Al binary

Science.gov (United States)

Simonson, J. W.; Rosa, R.; Antonacci, A. K.; He, H.; Bender, A. D.; Pabla, J.; Adrip, W.; McNally, D. E.; Zebro, A.; Kamenov, P.; Geschwind, G.; Ghose, S.; Dooryhee, E.; Ibrahim, A.; Aronson, M. C.

Improving the efficiency of fossil fuel plants is a practical option for decreasing carbon dioxide emissions from electrical power generation. Present limits on the operating temperatures of exposed steel components, however, restrict steam temperatures and therefore energy efficiency. Even as a new generation of creep-resistant, high strength steels retain long term structural stability to temperatures as high as ~ 973 K, the low Cr-content of these alloys hinders their oxidation resistance, necessitating the development of new corrosion resistant coatings. We report here the nearly ideal properties of potential coating material Cr55Al229, which exhibits high hardness at room temperature as well as low thermal conductivity and superlative oxidation resistance at 973 K, with an oxidation rate at least three times smaller than those of benchmark materials. These properties originate from a pseudo-icosahedral crystal structure, suggesting new criteria for future research.

Structure of the RBD-PRDI fragment of the antiterminator protein GlcT

International Nuclear Information System (INIS)

Himmel, Sebastian; Grosse, Christian; Wolff, Sebastian; Schwiegk, Claudia; Becker, Stefan

2012-01-01

The crystal structure of the RBD-PRDI fragment of the antiterminator protein GlcT from Bacillus subtilis has been solved at 2 Å resolution. The structure represents an inactive state of the protein. GlcT is a transcriptional antiterminator protein that is involved in regulation of glucose metabolism in Bacillus subtilis. Antiterminator proteins bind specific RNA sequences, thus preventing the formation of overlapping terminator stem-loops. The structure of a fragment (residues 3–170) comprising the RNA-binding domain (RBD) and the first regulatory domain (PRDI) of GlcT was solved at 2.0 Å resolution with one molecule in the asymmetric unit. The two domains are connected by a helical linker. Their interface is mostly constituted by hydrophobic interactions

Localized extinction of an arboreal desert lizard caused by habitat fragmentation

Science.gov (United States)

Munguia-Vega, Adrian; Rodriguez-Estrella, Ricardo; Shaw, William W.; Culver, Melanie

2013-01-01

We adopted a species’ perspective for predicting extinction risk in a small, endemic, and strictly scansorial lizard (Urosaurus nigricaudus), in an old (∼60 year) and highly fragmented (8% habitat remaining) agricultural landscape from the Sonoran Desert, Mexico. We genotyped 10 microsatellite loci in 280 individuals from 11 populations in fragmented and continuous habitat. Individual dispersal was restricted to less than 400 m, according to analyses of spatial autocorrelation and spatially explicit Bayesian assignment methods. Within this scale, continuous areas and narrow washes with native vegetation allowed high levels of gene flow over tens of kilometers. In the absence of the native vegetation, cleared areas and highways were identified as partial barriers. In contrast, outside the scale of dispersal, cleared areas behaved as complete barriers, and surveys corroborated the species went extinct after a few decades in all small (less than 45 ha), isolated habitat fragments. No evidence for significant loss of genetic diversity was found, but results suggested fragmentation increased the spatial scale of movements, relatedness, genetic structure, and potentially affected sex-biased dispersal. A plausible threshold of individual dispersal predicted only 23% of all fragments in the landscape were linked with migration from continuous habitat, while complete barriers isolated the majority of fragments. Our study suggested limited dispersal, coupled with an inability to use a homogeneous and hostile matrix without vegetation and shade, could result in frequent time-delayed extinctions of small ectotherms in highly fragmented desert landscapes, particularly considering an increase in the risk of overheating and a decrease in dispersal potential induced by global warming.

Pseudo-Kaehler quantization on flag manifolds

International Nuclear Information System (INIS)

Karabegov, A.V.

1997-07-01

A unified approach to geometric, symbol and deformation quantizations on a generalized flag manifold endowed with an invariant pseudo-Kaehler structure is proposed. In particular cases we arrive at Berezin's quantization via covariant and contravariant symbols. (author). 16 refs

Solution and crystal structures of a C-terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB

Directory of Open Access Journals (Sweden)

Amar Joshi

2014-03-01

Full Text Available The eukaryotic polypyrimidine tract binding protein (PTB serves primarily as a regulator of alternative splicing of messenger RNA, but is also co-opted to other roles such as RNA localisation and translation initiation from internal ribosome entry sites. The neuronal paralogue of PTB (nPTB is 75% identical in amino acid sequence with PTB. Although the two proteins have broadly similar RNA binding specificities and effects on RNA splicing, differential expression of PTB and nPTB can lead to the generation of alternatively spliced mRNAs. RNA binding by PTB and nPTB is mediated by four RNA recognition motifs (RRMs. We present here the crystal and solution structures of the C-terminal domain of nPTB (nPTB34 which contains RRMs 3 and 4. As expected the structures are similar to each other and to the solution structure of the equivalent fragment from PTB (PTB34. The result confirms that, as found for PTB, RRMs 3 and 4 of nPTB interact with one another to form a stable unit that presents the RNA-binding surfaces of the component RRMs on opposite sides that face away from each other. The major differences between PTB34 and nPTB34 arise from amino acid side chain substitutions on the exposed β-sheet surfaces and adjoining loops of each RRM, which are likely to modulate interactions with RNA.

Pseudo Landau levels and quantum oscillations in strained Weyl semimetals

Science.gov (United States)

Alisultanov, Z. Z.

2018-05-01

The crystal lattice deformation in Weyl materials where the two chiralities are separated in momentum space leads to the appearance of gauge pseudo-fields. We investigated the pseudo-magnetic field induced quantum oscillations in strained Weyl semimetal (WSM). In contrast to all previous works on this problem, we use here a more general tilted Hamiltonian. Such Hamiltonian, seems to be is more suitable for a strained WSMs. We have shown that a pseudo-magnetic field induced magnetization of strained WSM is nonzero due to the fact that electric field (gradient of the deformation potential) is induced simultaneously with the pseudo-magnetic field. This related with fact that the pseudo Landau levels (LLs) in strained WSM are differ in vicinities of different WPs due to the presence of tilt in spectrum. Such violation of the equivalence between Weyl points (WPs) leads to modulation of quantum oscillations. We also showed that magnetization magnitude can be changed by application of an external electric field. In particular, it can be reduced to zero. The possibility of controlling of the magnetization by an electric field is interesting both from a fundamental point of view (a new type of magneto-electric effect) and application point of view (additional possibility to control diamagnetism of deformed WSMs). Finally, a coexistence of type-I and type-II Weyl fermions is possible in the system under investigation. Such phase is absolutely new for physics of topological systems.

Genetics Home Reference: intestinal pseudo-obstruction

Science.gov (United States)

... A characteristic of X-linked inheritance is that fathers cannot pass X-linked traits to their sons. Intestinal pseudo-obstruction caused by ACTG2 gene mutations is inherited in an autosomal dominant pattern , which means one copy of the altered ...

Spin dynamics in the pseudo-gap state of a high-temperature superconductor

Energy Technology Data Exchange (ETDEWEB)

Hinkov, V; Lin, C T; Chen, D P; Keimer, B [Max Planck Inst Solid State Res, D-70569 Stuttgart, (Germany); Bourges, P; Pailhes, S; Sidis, Y [CEA, CNRS, CE Saclay, Lab Leon Brillouin, F-91191 Gif Sur Yvette, (France); Ivanov, A [Inst Max Von Laue Paul Langevin, F-38042 Grenoble, (France); Frost, C D; Perring, T G [Rutherford Appleton Lab, ISIS Facil, Didcot OX11 0QX, Oxon, (United Kingdom)

2007-07-01

The pseudo-gap is one of the most pervasive phenomena of high-temperature superconductors. It is attributed either to incoherent Cooper pairing setting in above the superconducting transition temperature, Tc, or to a hidden order parameter competing with superconductivity. Here, we use inelastic neutron scattering from under-doped YBa{sub 2}Cu{sub 3}O{sub 6.6} to show that the dispersion relations of spin excitations in the superconducting and pseudo-gap states are qualitatively different. Specifically, the extensively studied 'hour glass' shape of the magnetic dispersions in the superconducting state is no longer discernible in the pseudo-gap state and we observe an unusual 'vertical' dispersion with pronounced in-plane anisotropy. The differences between superconducting and pseudo-gap states are thus more profound than generally believed, suggesting a competition between these two states. Whereas the high-energy excitations are common to both states and obey the symmetry of the copper oxide square lattice, the low-energy excitations in the pseudo-gap state may be indicative of collective fluctuations towards a state with broken orientational symmetry predicted in theoretical work. (authors)

A domain decomposition method for pseudo-spectral electromagnetic simulations of plasmas

International Nuclear Information System (INIS)

Vay, Jean-Luc; Haber, Irving; Godfrey, Brendan B.

2013-01-01

Pseudo-spectral electromagnetic solvers (i.e. representing the fields in Fourier space) have extraordinary precision. In particular, Haber et al. presented in 1973 a pseudo-spectral solver that integrates analytically the solution over a finite time step, under the usual assumption that the source is constant over that time step. Yet, pseudo-spectral solvers have not been widely used, due in part to the difficulty for efficient parallelization owing to global communications associated with global FFTs on the entire computational domains. A method for the parallelization of electromagnetic pseudo-spectral solvers is proposed and tested on single electromagnetic pulses, and on Particle-In-Cell simulations of the wakefield formation in a laser plasma accelerator. The method takes advantage of the properties of the Discrete Fourier Transform, the linearity of Maxwell’s equations and the finite speed of light for limiting the communications of data within guard regions between neighboring computational domains. Although this requires a small approximation, test results show that no significant error is made on the test cases that have been presented. The proposed method opens the way to solvers combining the favorable parallel scaling of standard finite-difference methods with the accuracy advantages of pseudo-spectral methods

The theory of pseudo-differential operators on the noncommutative n-torus

Science.gov (United States)

Tao, J.

2018-02-01

The methods of spectral geometry are useful for investigating the metric aspects of noncommutative geometry and in these contexts require extensive use of pseudo-differential operators. In a foundational paper, Connes showed that, by direct analogy with the theory of pseudo-differential operators on finite-dimensional real vector spaces, one may derive a similar pseudo-differential calculus on noncommutative n-tori, and with the development of this calculus came many results concerning the local differential geometry of noncommutative tori for n=2,4, as shown in the groundbreaking paper in which the Gauss-Bonnet theorem on the noncommutative two-torus is proved and later papers. Certain details of the proofs in the original derivation of the calculus were omitted, such as the evaluation of oscillatory integrals, so we make it the objective of this paper to fill in all the details. After reproving in more detail the formula for the symbol of the adjoint of a pseudo-differential operator and the formula for the symbol of a product of two pseudo-differential operators, we extend these results to finitely generated projective right modules over the noncommutative n-torus. Then we define the corresponding analog of Sobolev spaces and prove equivalents of the Sobolev and Rellich lemmas.

Pseudo-Cl estimators which do not mix E and B modes

International Nuclear Information System (INIS)

Smith, Kendrick M.

2006-01-01

Pseudo-C l quadratic estimators for CMB temperature and polarization power spectra have been used in the analysis pipelines of many CMB experiments, such as WMAP and Boomerang. In the polarization case, these estimators mix E and B modes, in the sense that the estimated B-mode power is nonzero for a noiseless CMB realization which contains only E modes. Recently, Challinor, and Chon showed that for moderately sized surveys (f sky ∼0.01), this mixing limits the gravity wave B-mode signal which can be detected using pseudo-C l estimators to T/S∼0.05. We modify the pseudo-C l construction, defining pure pseudo-C l estimators, which do not mix E and B modes in this sense. We study these estimators in detail for a survey geometry similar to that which has been proposed for the QUIET experiment, for a variety of noise levels, and both homogeneous and inhomogeneous noise. For noise levels l estimators. In the homogeneous case, we compute optimal power spectrum errors using a Fisher matrix approach, and show that our pure pseudo-C l estimators are roughly 80% of optimal, across a wide range of noise levels. There is no limit, imposed by the estimators alone, to the value of T/S which can be detected

Use of Full-Length Recombinant Calflagin and Its C Fragment for Improvement of Diagnosis of Trypanosoma cruzi Infection†

Science.gov (United States)

Marcipar, Iván S.; Roodveldt, Cintia; Corradi, Gerardo; Cabeza, María L.; Brito, Maria Edileuza F.; Winter, Lucile M. Floeter; Marcipar, Alberto J.; Silber, Ariel M.

2005-01-01

Serological diagnosis of Trypanosoma cruzi infection is hampered by issues related to test specificity due to the cross-reactivity of most antigens with proteins of related parasites such as Leishmania spp. The recombinant calflagins are considered relevant antigens for the diagnosis of infection by Trypanosoma cruzi. In the present work, we describe two genes coding for putative calflagins in Leishmania major with the N-terminal moieties presenting high similarity with T. cruzi genes. This fact raised questions about their role in some cross-recognition of this antigen by sera from Leishmania spp.-infected individuals. The complete T. cruzi calflagin and two fragments of the protein, consisting of 146 amino acids of the N-terminal and 65 amino acids of the C-terminal regions, were expressed and evaluated against a panel of sera, which included well-characterized samples from T. cruzi, and Leishmania-infected patients. We were able to show that sera from Leishmania (Viannia) braziliensis-infected individuals recognized the recombinant full-length calflagin. Both the N-terminal and the complete protein presented the same high sensitivity (98.5% of sera from T. cruzi-infected patients was detected) but different specificities (94% and 98%, respectively, when evaluated against sera from people not infected by T. cruzi, including 15 sera from people infected with L. braziliensis). The C-terminal fragment presented low sensitivity (70%) but 100% specificity. We propose the use of these antigens in two sequential assays to optimize the serological diagnosis of T. cruzi infection in humans in geographic areas where Leishmania spp. infection is coendemic. PMID:16272476

Political fragmentation and widening disparities in African-American and white mortality, 1972-1988.

Science.gov (United States)

Kim, Yonsu; Bruckner, Tim A

2016-12-01

During the 1970s and 1980s in the U.S., population movement, urban sprawl and urban governance reform led to a proliferation of local, autonomous jurisdictions. Prior literature examines how this creation of local governments, also referred to as political fragmentation, contributes to economic growth and social inequality. We examine the impact of political fragmentation on health equity by testing the hypothesis that the mortality disparity between whites and African-Americans varies positively with political fragmentation. We retrieved mortality data from the multiple cause-of-death file and calculated total number of local governments per 1000 residents in a county to measure the degree of political fragmentation. We focused on 226 U.S. counties with population size greater than 200,000 and restricted the analysis to four distinct periods with overlapping government and mortality data (1972-73, 1977-78, 1982-83, and 1987-88). We applied generalized estimating equation methods that permit analysis of clustered data over time. Methods also controlled for the age structure of the population, reductions in mortality over time, and confounding by county-level sociodemographic variables. Adjusted coefficients of fragmentation are positive and statistically significant for both whites (coef: 2.60, SE: 0.60, p politically fragmented urban counties and/or time periods. From 1972 to 1988, political fragmentation in large urban counties moves positively with the racial/ethnic gap in mortality between whites and African-Americans. We discuss intervening mechanisms through which political fragmentation may disproportionately affect mortality among African-Americans.

Phenomenology of a pseudo-scalar inflaton: naturally large nongaussianity

International Nuclear Information System (INIS)

Barnaby, Neil; Namba, Ryo; Peloso, Marco

2011-01-01

Many controlled realizations of chaotic inflation employ pseudo-scalar axions. Pseudo-scalars φ are naturally coupled to gauge fields through cφF F-tilde . In the presence of this coupling, gauge field quanta are copiously produced by the rolling inflaton. The produced gauge quanta, in turn, source inflaton fluctuations via inverse decay. These new cosmological perturbations add incoherently with the ''vacuum'' perturbations, and are highly nongaussian. This provides a natural mechanism to generate large nongaussianity in single or multi field slow-roll inflation. The resulting phenomenological signatures are highly distinctive: large nongaussianity of (nearly) equilateral shape, in addition to detectably large values of both the scalar spectral tilt and tensor-to-scalar ratio (both being typical of large field inflation). The WMAP bound on nongaussianity implies that the coupling c of the pseudo-scalar inflaton to any gauge field must be smaller than about 10 2 M p −1

"Fooling fido"--chemical and behavioral studies of pseudo-explosive canine training aids.

Science.gov (United States)

Kranz, William D; Strange, Nicholas A; Goodpaster, John V

2014-12-01

Genuine explosive materials are traditionally employed in the training and testing of explosive-detecting canines so that they will respond reliably to these substances. However, challenges arising from the acquisition, storage, handling, and transportation of explosives have given rise to the development of "pseudo-explosive" training aids. These products attempt to emulate the odor of real explosives while remaining inert. Therefore, a canine trained on a pseudo-explosive should respond to its real-life analog. Similarly, a canine trained on an actual explosive should respond to the pseudo-explosive as if it was real. This research tested those assumptions with a focus on three explosives: single-base smokeless powder, 2,4,6-trinitrotoluene (TNT), and a RDX-based plastic explosive (Composition C-4). Using gas chromatography-mass spectrometry with solid phase microextraction as a pre-concentration technique, we determined that the volatile compounds given off by pseudo-explosive products consisted of various solvents, known additives from explosive formulations, and common impurities present in authentic explosives. For example, simulated smokeless powders emitted terpenes, 2,4-dinitrotoluene, diphenylamine, and ethyl centralite. Simulated TNT products emitted 2,4- and 2,6-dinitrotoluene. Simulated C-4 products emitted cyclohexanone, 2-ethyl-1-hexanol, and dimethyldinitrobutane. We also conducted tests to determine whether canines trained on pseudo-explosives are capable of alerting to genuine explosives and vice versa. The results show that canines trained on pseudo-explosives performed poorly at detecting all but the pseudo-explosives they are trained on. Similarly, canines trained on actual explosives performed poorly at detecting all but the actual explosives on which they were trained.

Ionic interaction of myosin loop 2 with residues located beyond the N-terminal part of actin probed by chemical cross-linking.

Science.gov (United States)

Pliszka, Barbara; Martin, Brian M; Karczewska, Emilia

2008-02-01

To probe ionic contacts of skeletal muscle myosin with negatively charged residues located beyond the N-terminal part of actin, myosin subfragment 1 (S1) and actin split by ECP32 protease (ECP-actin) were cross-linked with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). We have found that unmodified S1 can be cross-linked not only to the N-terminal part, but also to the C-terminal 36 kDa fragment of ECP-actin. Subsequent experiments performed on S1 cleaved by elastase or trypsin indicate that the cross-linking site in S1 is located within loop 2. This site is composed of Lys-636 and Lys-637 and can interact with negatively charged residues of the 36 kDa actin fragment, most probably with Glu-99 and Glu-100. Cross-links are formed both in the absence and presence of MgATP.P(i) analog, although the addition of nucleotide decreases the efficiency of the cross-linking reaction.

Computer systems for annotation of single molecule fragments

Science.gov (United States)

Schwartz, David Charles; Severin, Jessica

2016-07-19

There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

Optimizing the Number of Cooperating Terminals for Energy Aware Task Computing in Wireless Networks

DEFF Research Database (Denmark)

Olsen, Anders Brødløs; Fitzek, Frank H. P.; Koch, Peter

2005-01-01

It is generally accepted that energy consumption is a significant design constraint for mobile handheld systems, therefore motivations for methods optimizing the energy consumption making better use of the restricted battery resources are evident. A novel concept of distributed task computing...... is previously proposed (D2VS), where the overall idea of selective distribution of tasks among terminals is made. In this paper the optimal number of terminals for cooperative task computing in a wireless network will be investigated. The paper presents an energy model for the proposed scheme. Energy...... consumption of the terminals with respect to their workload and the overhead of distributing tasks among terminals are taken into account. The paper shows, that the number of cooperating terminals is in general limited to a few, though alternating with respect to the various system parameters....

Evolutionary Pseudo-Relaxation Learning Algorithm for Bidirectional Associative Memory

Institute of Scientific and Technical Information of China (English)

Sheng-Zhi Du; Zeng-Qiang Chen; Zhu-Zhi Yuan

2005-01-01

This paper analyzes the sensitivity to noise in BAM (Bidirectional Associative Memory), and then proves the noise immunity of BAM relates not only to the minimum absolute value of net inputs (MAV) but also to the variance of weights associated with synapse connections. In fact, it is a positive monotonically increasing function of the quotient of MAV divided by the variance of weights. Besides, the performance of pseudo-relaxation method depends on learning parameters (λ and ζ), but the relation of them is not linear. So it is hard to find a best combination of λ and ζ which leads to the best BAM performance. And it is obvious that pseudo-relaxation is a kind of local optimization method, so it cannot guarantee to get the global optimal solution. In this paper, a novel learning algorithm EPRBAM (evolutionary psendo-relaxation learning algorithm for bidirectional association memory) employing genetic algorithm and pseudo-relaxation method is proposed to get feasible solution of BAM weight matrix. This algorithm uses the quotient as the fitness of each individual and employs pseudo-relaxation method to adjust individual solution when it does not satisfy constraining condition any more after genetic operation. Experimental results show this algorithm improves noise immunity of BAM greatly. At the same time, EPRBAM does not depend on learning parameters and can get global optimal solution.

Chaos-based Pseudo-random Number Generation

KAUST Repository

Barakat, Mohamed L.

2014-04-10

Various methods and systems related to chaos-based pseudo-random number generation are presented. In one example, among others, a system includes a pseudo-random number generator (PRNG) to generate a series of digital outputs and a nonlinear post processing circuit to perform an exclusive OR (XOR) operation on a first portion of a current digital output of the PRNG and a permutated version of a corresponding first portion of a previous post processed output to generate a corresponding first portion of a current post processed output. In another example, a method includes receiving at least a first portion of a current output from a PRNG and performing an XOR operation on the first portion of the current PRNG output with a permutated version of a corresponding first portion of a previous post processed output to generate a corresponding first portion of a current post processed output.

Wavefield extrapolation in pseudo-depth domain

KAUST Repository

Ma, Xuxin; Alkhalifah, Tariq Ali

2012-01-01

Extrapolating seismic waves in Cartesian coordinate is prone to uneven spatial sampling, because the seismic wavelength tends to grow with depth, as velocity increase. We transform the vertical depth axis to a pseudo one using a velocity weighted mapping, which can effectively mitigate this wavelength variation. We derive acoustic wave equations in this new domain based on the direct transformation of the Laplacian derivatives, which admits solutions that are more accurate and stable than those derived from the kinematic transformation. The anisotropic versions of these equations allow us to isolate the vertical velocity influence and reduce its impact on modeling and imaging. The major benefit of extrapolating wavefields in pseudo-depth space is its near uniform wavelength as opposed to the normally dramatic change of wavelength with the conventional approach. Time wavefield extrapolation on a complex velocity shows some of the features of this approach.

[Hysterical pseudo-coma: A case report].

Science.gov (United States)

Chouaib, N; Chouaib, H; Belyamani, L; Otheman, Y; Bichra, M Z

2015-09-01

Hysterical pseudo-coma corresponds to a state of clinical sleep with contrasting waking electroencephalogram. It can last several hours or even several days in the absence of an underlying organic disease. In psychiatry, this disorder is currently part of the "dissociative disorder not otherwise specified". Through this case report, we describe the evolution of a hysterical pseudo-coma that lasted four days in a 28-year-old man. The normality of biological, radiological and electroencephalographic assessments, and responsiveness of the patient during the implementation of a nasogastric tube, led us to suspect a mental origin. An adapted psychiatric care allowed the patient to recover his autonomy after three days of hospitalization. This had prevented the escalation of explorations and invasive treatments. However, the search for organic comorbidity and its management remains a priority. Copyright © 2014 L’Encéphale, Paris. Published by Elsevier Masson SAS. All rights reserved.

Chaos-based Pseudo-random Number Generation

KAUST Repository

Barakat, Mohamed L.; Mansingka, Abhinav S.; Radwan, Ahmed Gomaa Ahmed; Salama, Khaled N.

2014-01-01

Various methods and systems related to chaos-based pseudo-random number generation are presented. In one example, among others, a system includes a pseudo-random number generator (PRNG) to generate a series of digital outputs and a nonlinear post processing circuit to perform an exclusive OR (XOR) operation on a first portion of a current digital output of the PRNG and a permutated version of a corresponding first portion of a previous post processed output to generate a corresponding first portion of a current post processed output. In another example, a method includes receiving at least a first portion of a current output from a PRNG and performing an XOR operation on the first portion of the current PRNG output with a permutated version of a corresponding first portion of a previous post processed output to generate a corresponding first portion of a current post processed output.

Pseudo ribbon metal ion beam source

International Nuclear Information System (INIS)

Stepanov, Igor B.; Ryabchikov, Alexander I.; Sivin, Denis O.; Verigin, Dan A.

2014-01-01

The paper describes high broad metal ion source based on dc macroparticle filtered vacuum arc plasma generation with the dc ion-beam extraction. The possibility of formation of pseudo ribbon beam of metal ions with the parameters: ion beam length 0.6 m, ion current up to 0.2 A, accelerating voltage 40 kV, and ion energy up to 160 kV has been demonstrated. The pseudo ribbon ion beam is formed from dc vacuum arc plasma. The results of investigation of the vacuum arc evaporator ion-emission properties are presented. The influence of magnetic field strength near the cathode surface on the arc spot movement and ion-emission properties of vacuum-arc discharge for different cathode materials are determined. It was shown that vacuum-arc discharge stability can be reached when the magnetic field strength ranges from 40 to 70 G on the cathode surface

Pseudo ribbon metal ion beam source.

Science.gov (United States)

Stepanov, Igor B; Ryabchikov, Alexander I; Sivin, Denis O; Verigin, Dan A

2014-02-01

The paper describes high broad metal ion source based on dc macroparticle filtered vacuum arc plasma generation with the dc ion-beam extraction. The possibility of formation of pseudo ribbon beam of metal ions with the parameters: ion beam length 0.6 m, ion current up to 0.2 A, accelerating voltage 40 kV, and ion energy up to 160 kV has been demonstrated. The pseudo ribbon ion beam is formed from dc vacuum arc plasma. The results of investigation of the vacuum arc evaporator ion-emission properties are presented. The influence of magnetic field strength near the cathode surface on the arc spot movement and ion-emission properties of vacuum-arc discharge for different cathode materials are determined. It was shown that vacuum-arc discharge stability can be reached when the magnetic field strength ranges from 40 to 70 G on the cathode surface.

Recurrent chronic histiocytic intervillositis with intrauterine growth restriction, osteopenia, and fractures.

Science.gov (United States)

Crawford, April; Moore, Lynette; Bennett, Gregory; Savarirayan, Ravi; Manton, Nicholas; Khong, Yee; Barnett, Christopher P; Haan, Eric

2016-11-01

Chronic histiocytic intervillositis (CHI) is characterized by the presence of histiocytes within the intervillous space of the placenta. The pathogenesis is unclear but available evidence supports an alloimmune mechanism on the basis of the presence in maternal blood of HLA antibodies directed against paternal HLA antigens. CHI has a high risk of recurrence and of abnormal perinatal outcomes. Little is known about the effects of CHI on the developing fetus, in particular on the growth and development of the skeleton. We have studied a woman whose third pregnancy was terminated after ultrasonography showed severe intrauterine growth restriction, raising the possibility of a lethal skeletal dysplasia. Postmortem radiographs showed multiple fractures and other signs of osteogenesis imperfecta (OI). However, bone histology was not typical of OI and no abnormalities were identified by sequencing OI genes. The subsequent pregnancy was also severely growth restricted and was terminated. The placenta showed chronic histiocytic intervillositis, which, on retrospective review, had also been present in her second and third pregnancies. Her fifth pregnancy was again associated with intrauterine growth restriction and CHI but resulted in a premature birth. CHI can be associated with radiographic features that mimic OI and should be considered when fetal fractures occur in the context of recurrent miscarriage, fetal death in utero, and intrauterine growth restriction. The correct diagnosis can be made by histopathology of the placenta, supported by bone histology and normal results of molecular studies for OI. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Basic Characteristics and Spatial Patterns of Pseudo-Settlements--Taking Dalian as An Example.

Science.gov (United States)

Gao, Jiaji; Zhang, Yingjia; Li, Xueming

2016-01-20

A person's living behavior patterns are closely related to three types of settlements: real-life settlements, imagined settlements, and pseudo-settlements. The term "pseudo-settlement" (PS) refers to the places that are selectively recorded and represented after the mass media chose and restructure the residence information. As the mass media rapidly develops and people's way of obtaining information gradually change, PS has already become one of the main ways for people to recognize and understand real-life settlements, as well as describe their impressions of imagined settlements. PS also has a profound impact on tourism, employment, investment, migration, real estate development, etc. Thus, the study of PSs has important theoretical and practical significance. This paper proposes to put forward residential quarters where the mass media is displayed as the object of study and establishes the pseudo-settlement index system of Dalian in and elaborate analysis of the concept of PSs. From three aspects, including pseudo-buildings, pseudo-districts and pseudo-culture, this paper uses the ArcGIS 10.0 kernel density (spacial analyst) to analyze and interpret the basic characteristics and spatial patterns of 14 elements of the PS in Dalian. Through systemic clustering analysis, it identifies eight major types of PSs in Dalian. Then it systematically elaborates current situations and characteristics of the spatial pattern of PSs in Dalian, namely: regionally concentrated, widely scattered and blank spaces without pseudo-settlements. Finally, this paper discusses the mechanism of formation of PSs in Dalian.

Expression and Purification of BmrI Restriction Endonuclease and Its N-terminal Cleavage Domain Variants

OpenAIRE

Bao, Yongming; Higgins, Lauren; Zhang, Penghua; Chan, Siu-hong; Laget, Sophie; Sweeney, Suzanne; Lunnen, Keith; Xu, Shuang-yong

2007-01-01

BmrI (ACTGGG N5/N4) is one of the few metal-independent restriction endonucleases (REases) found in bacteria. The BmrI restriction-modification system was cloned by the methylase selection method, inverse PCR, and PCR. BmrI REase shows significant amino acid sequence identity to BfiI and a putative endonuclease MspBNCORF3798 from the sequenced Mesorhizobium sp. BNC1 genome. The EDTA-resistant BmrI REase was successfully over-expressed in a pre-modified E. coli strain from pET21a or pBAC-expIQ...

Global climate change and fragmentation of native brook trout distribution in the southern Appalachian Mountains

Science.gov (United States)

Patricia A. Flebbe

1997-01-01

Current distributions of native brook trout (Salvelinus fontinalis) in the Southern Appalachians are restricted to upper elevations by multiple factors, including habitat requirements, introduced rainbow (Oncorhynchus mykiss) and brown (Salmo trutta) trout, and other human activities. Present-day distribution of brook trout habitat is already fragmented. Increased...

Pseudo-Random Number Generator Based on Coupled Map Lattices

Science.gov (United States)

Lü, Huaping; Wang, Shihong; Hu, Gang

A one-way coupled chaotic map lattice is used for generating pseudo-random numbers. It is shown that with suitable cooperative applications of both chaotic and conventional approaches, the output of the spatiotemporally chaotic system can easily meet the practical requirements of random numbers, i.e., excellent random statistical properties, long periodicity of computer realizations, and fast speed of random number generations. This pseudo-random number generator system can be used as ideal synchronous and self-synchronizing stream cipher systems for secure communications.

Time-of-flight experiments using a pseudo-statistical chopper

International Nuclear Information System (INIS)

Aizawa, Otohiko; Kanda, Keiji

1975-01-01

A ''pseudo-statistical'' chopper was manufactured and used for the experiments on neutron transmission and scattering. The characteristics of the chopper and the experimental results are discussed in comparison with those in the time-of-flight technique using a conventional chopper. Which of the two methods is superior depends on the form of the time-of-flight distribution to be measured. Pseudo-statistical pulsing may be especially advantageous for scattering experiments with single or a few-line time-of-flight spectrum. (auth.)

The technique of «Subliminal verbal suggestion for the treatment of [pseudo]obsessions»

Directory of Open Access Journals (Sweden)

N. V. Danilevska

2016-03-01

Full Text Available [Pseudo]obsessions therapy in patients with endogenous diseases of schizophrenic round accompanied with difficulties, caused by both psycho etio pathogenetic features of the disease. Disadvantages of the existing methods of therapy are associated with therapeutic conflict between two nosologies. Aim: to develop and test etiopsychopathogenetic technique "Subliminal verbal suggestion for the treatment of [pseudo]obsessions" as a subsidiary method of treatment of schizophrenia patients with [pseudo] obsessions in the structure of the disease. Methods and results. 137 patients who underwent hospital treatment 65 schizophrenia patients (F20 with the [pseudo]obsessive symptoms in the structure of the disease were examined on the basis of Public Health Institution «Regional clinical mental hospital» of the Zaporizhzhian regional council. 30 patients received standard pharmacotherapy (antipsychotic drugs according to clinical protocols that was combined with proposed technique "Subliminal verbal suggestion for the treatment of [pseudo]obsessions". The comparison group consisted of 35 patients treated with the use of standard pharmacotherapy: antipsychotic drugs. The next methods were used: medical history assessment, follow-up, clinical-psychopathological, psychodiagnostic. "Subliminal verbal suggestion for the treatment of [pseudo]obsessions" technique was developed. This technique is a combination of suggestion in the waking state and neurolinguistic programming, implemented with specially compiled auditory complex listening. The main therapeutic component s realized through the subthreshold perception of the verbal formulas that are unavailable to awareness. The technique consists of two components – primary and secondary, and three stages. The methodology was tested, its therapeutic efficacy was confirmed. Conclusion. "Subliminal verbal suggestion for the treatment of [pseudo]obsessions" technique was developed as a subsidiary method of the

Nicked apomyoglobin: a noncovalent complex of two polypeptide fragments comprising the entire protein chain.

Science.gov (United States)

Musi, Valeria; Spolaore, Barbara; Picotti, Paola; Zambonin, Marcello; De Filippis, Vincenzo; Fontana, Angelo

2004-05-25

Limited proteolysis of the 153-residue chain of horse apomyoglobin (apoMb) by thermolysin results in the selective cleavage of the peptide bond Pro88-Leu89. The N-terminal (residues 1-88) and C-terminal (residues 89-153) fragments of apoMb were isolated to homogeneity and their conformational and association properties investigated in detail. Far-UV circular dichroism (CD) measurements revealed that both fragments in isolation acquire a high content of helical secondary structure, while near-UV CD indicated the absence of tertiary structure. A 1:1 mixture of the fragments leads to a tight noncovalent protein complex (1-88/89-153, nicked apoMb), characterized by secondary and tertiary structures similar to those of intact apoMb. The apoMb complex binds heme in a nativelike manner, as given by CD measurements in the Soret region. Second-derivative absorption spectra in the 250-300 nm region provided evidence that the degree of exposure of Tyr residues in the nicked species is similar to that of the intact protein at neutral pH. Also, the microenvironment of Trp residues, located in positions 7 and 14 of the 153-residue chain of the protein, is similar in both protein species, as given by fluorescence emission data. Moreover, in analogy to intact apoMb, the nicked protein binds the hydrophobic dye 1-anilinonaphthalene-8-sulfonate (ANS). Taken together, our results indicate that the two proteolytic fragments 1-88 and 89-153 of apoMb adopt partly folded states characterized by sufficiently nativelike conformational features that promote their specific association and mutual stabilization into a nicked protein species much resembling in its structural features intact apoMb. It is suggested that the formation of a noncovalent complex upon fragment complementation can mimic the protein folding process of the entire protein chain, with the difference that the folding of the complementary fragments is an intermolecular process. In particular, this study emphasizes the

Discrete Weighted Pseudo Asymptotic Periodicity of Second Order Difference Equations

Directory of Open Access Journals (Sweden)

Zhinan Xia

2014-01-01

Full Text Available We define the concept of discrete weighted pseudo-S-asymptotically periodic function and prove some basic results including composition theorem. We investigate the existence, and uniqueness of discrete weighted pseudo-S-asymptotically periodic solution to nonautonomous semilinear difference equations. Furthermore, an application to scalar second order difference equations is given. The working tools are based on the exponential dichotomy theory and fixed point theorem.

Pseudo-aneurisma post-traumático de tronco de arteria coronaria izquierda Post-traumatic false (pseudo aneurysm of the left main coronary artery

Directory of Open Access Journals (Sweden)

Melina M. Gallo

2011-08-01

Full Text Available El pseudo-aneurisma de arteria coronaria es extremadamente raro. Su historia natural es poco conocida y su tratamiento discutido. Se presenta el caso de un paciente con pseudo-aneurisma de tronco de la coronaria izquierda e infarto antero-apical del ventrículo izquierdo cinco años después de un paro cardíaco secundario a un traumatismo no penetrante de tórax. Se consideró entonces que la lesión no era pasible de corrección percutánea o quirúrgica por lo que se optó por tratamiento médico conservador. Una angiografía coronaria por tomografía computarizada multicorte realizada 10 años después del evento inicial mostró ausencia de progresión de la lesión.Coronary pseudo-aneurysm is an extremely rare entity. Its natural history is scarcely known and its treatment is controversial. We report a case of pseudo-aneurysm of the left main coronary artery associated with an antero-apical infarct of the left ventricle diagnosed five years after a cardiac arrest following a non-penetrating thoracic trauma. The patient was treated conservatively because percutaneous or surgical correction were not considered suitable for this lesion. A multidetector computed tomography coronary angiogram performed 10 years after the initial event showed no evidence of progression.

Pseudo-diode based on protonic/electronic hybrid oxide transistor

Science.gov (United States)

Fu, Yang Ming; Liu, Yang Hui; Zhu, Li Qiang; Xiao, Hui; Song, An Ran

2018-01-01

Current rectification behavior has been proved to be essential in modern electronics. Here, a pseudo-diode is proposed based on protonic/electronic hybrid indium-gallium-zinc oxide electric-double-layer (EDL) transistor. The oxide EDL transistors are fabricated by using phosphorous silicate glass (PSG) based proton conducting electrolyte as gate dielectric. A diode operation mode is established on the transistor, originating from field configurable proton fluxes within the PSG electrolyte. Current rectification ratios have been modulated to values ranged between ˜4 and ˜50 000 with gate electrode biased at voltages ranged between -0.7 V and 0.1 V. Interestingly, the proposed pseudo-diode also exhibits field reconfigurable threshold voltages. When the gate is biased at -0.5 V and 0.3 V, threshold voltages are set to ˜-1.3 V and -0.55 V, respectively. The proposed pseudo-diode may find potential applications in brain-inspired platforms and low-power portable systems.

„Pseudo-yat“ in Dalmato-Romance and Balkan Latin (On Balkan Latin VIII

Directory of Open Access Journals (Sweden)

Ligorio Orsat L.

2015-01-01

Full Text Available Article discusses the origins and the development of the so-called pseudo-yat in Dalmatian Romance and Balkan Latin. (E.g. SCr. mrčela-murtila-murtela from Lat. *MYRTICELLA or tovijerna-tovirna-toverna from TABERNA. Pseudo-yat is derived from -ECC-, in short syllables, and in long syllables from -ERR-, -ERC-. This suggestion is tried on 58 Dalmatian loans in Serbo-Croatian. The fact that pseudo-yat is found only in a part of these is of particular significance for the stratification of Dalmatian loans in Serbo-Croatian since loans with pseudo-yat are ostensibly older than the ones without it. [Projekat Ministarstva nauke Republike Srbije, br. 178007

Mapping of the antigenic and allergenic epitopes of Lol p VB using gene fragmentation.

Science.gov (United States)

Ong, E K; Knox, R B; Singh, M B

1995-03-01

The recombinant proteins of Lol p VA and Lol p VB expressed in E. coli reacted with IgE antibodies from sera of allergic patients and mAbs FMC A7 and PpV1. Cross-absorption analyses using these recombinant proteins showed that Lol p VA and Lol p VB possess both similar and unique IgE binding determinants. Gene fragmentation was utilized to localize the antigenic and allergenic determinants of Lol p VB. When full-length cDNA of Lol p VB was digested into three fragments and expressed as the fusions from the glutathione transferase of pGEX vectors, fragments Met1-Val196 and Asp197-Val339 bound IgE while fragment Met1-Pro96 did not. The data suggest that there are at least two IgE binding determinants in Lol p VB. In addition, only fragment Met1-Val196 reacted with mAb PpV1. The localization of these determinants was further resolved using random fragment expression libraries. The mAb PpV1 determinant was near the N-terminal region of Lol p VB molecule. The IgE binding determinants were distributed in the central region: region I (amino acids 111-195) and II (199-254). These IgE binding determinants are conserved in Lol p VA.

Structure of non-(1-84) PTH fragments secreted by parathyroid glands in primary and secondary hyperparathyroidism.

Science.gov (United States)

D'Amour, Pierre; Brossard, Jean-Hugues; Rousseau, Louise; Nguyen-Yamamoto, Loan; Nassif, Edgard; Lazure, Claude; Gauthier, Dany; Lavigne, Jeffrey R; Zahradnik, Richard J

2005-09-01

Non-(1-84) parathyroid hormone (PTH) fragments are large circulating carboxyl-terminal (C) fragments with a partially preserved amino-terminal (N) structure. hPTH (7-84), a synthetic surrogate, has been demonstrated to exert biologic effects in vivo and in vitro which are opposite to those of hPTH (1-34) on the PTH/PTHrP type I receptor through a C-PTH receptor. We wanted to determine the N structure of non-(1-84) PTH fragments. Parathyroid cells isolated from glands obtained at surgery from three patients with primary hyperparathyroidism and three patients with secondary hyperparathyroidism were incubated with 35S-methionine to internally label their secretion products. Incubations were performed for 8 hours at the patient-ionized calcium concentration and in the presence of various protease inhibitors. The supernatant was fractionated by high-performance liquid chromatography (HPLC) and fractions were analyzed with PTH assays having (1 to 4) and (12 to 23) epitopes, respectively. The serum of each patient was similarly analyzed. Peaks of immunoreactivity identified were submitted to sequence analysis to recover the 35S-methionine residues in positions 8 and 18. Three regions of interest were identified with PTH assays. They corresponded to non-(1-84) PTH fragments (further divided in regions 3 and 4), a peak of N-PTH migrating in front of hPTH (1-84) (region 2) and a peak of immunoreactivity corresponding to the elution position of hPTH (1-84) (region 1). The last corresponded to a single sequence starting at position 1. Region 2 gave similar results in all cases (a major signal starting at position 1) but also sometimes minor sequences starting at position 4 or 7. Regions 3 and 4 always identified a major sequence starting at positions 7 and minor sequences starting at positions 8, 10, and 15. Surprisingly, a major signal starting at position 1 was also present in region 3. The HPLC profile obtained from a given patient's parathyroid cells was qualitatively

MRI-based treatment planning with pseudo CT generated through atlas registration

International Nuclear Information System (INIS)

Uh, Jinsoo; Merchant, Thomas E.; Hua, Chiaho; Li, Yimei; Li, Xingyu

2014-01-01

Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. Results: The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787–0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%–98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the

MRI-based treatment planning with pseudo CT generated through atlas registration

Energy Technology Data Exchange (ETDEWEB)

Uh, Jinsoo, E-mail: jinsoo.uh@stjude.org; Merchant, Thomas E.; Hua, Chiaho [Department of Radiological Sciences, St. Jude Children' s Research Hospital, Memphis, Tennessee 38105 (United States); Li, Yimei; Li, Xingyu [Department of Biostatistics, St. Jude Children' s Research Hospital, Memphis, Tennessee 38105 (United States)

2014-05-15

Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. Results: The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787–0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%–98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the

Hypokalaemia: Bartter's syndrome or pseudo-Bartter's syndrome?

OpenAIRE

Robb, J D; Delargy, M A; Nolan, M; Tomkin, G H

1984-01-01

The difficulties in the diagnosis of hypokalaemia are often considerable. This paper reports three patients who presented with hypokalaemia. Investigations are described which may help to distinguish Bartter's syndrome from pseudo-Bartter's syndrome.

Electrostatic field of the large fragment of Escherichia coli DNA polymerase I.

Science.gov (United States)

Warwicker, J; Ollis, D; Richards, F M; Steitz, T A

1985-12-05

The electrostatic field of the large fragment of Escherichia coli DNA polymerase I (Klenow fragment) has been calculated by the finite difference procedure on a 2 A grid. The potential field is substantially negative at physiological pH (reflecting the net negative charge at this pH). The largest regions of positive potential are in the deep crevice of the C-terminal domain, which is the proposed binding site for the DNA substrate. Within the crevice, the electrostatic potential has a partly helical form. If the DNA is positioned to fulfil stereochemical requirements, then the positive potential generally follows the major groove and (to a lesser extent) the negative potential is in the minor groove. Such an arrangement could stabilize DNA configurations related by screw symmetry. The histidine residues of the Klenow fragment give the positive field of the groove a sensitivity to relatively small pH changes around neutrality. We suggest that the histidine residues could change their ionization states in response to DNA binding, and that this effect could contribute to the protein-DNA binding energy.

El Pseudo-Hiepes es Bernardo Polo

Directory of Open Access Journals (Sweden)

Jordan, William B.

2009-12-01

Full Text Available Nearly fifteen years ago, the author proposed the name Pseudo-Hiepes to refer to a then anonymous painter whom certain Italian art historians had called the Master of the Lombard Fruit Bowl. At the time, he argued for an Aragonese origin in the later part of the century. A signed work has finally been discovered and is published here. The artist was indeed from Zaragoza, and his name is Bernardo Polo.

Hace unos quince años, el autor propuso el apodo Pseudo-Hiepes para identificar al pintor anónimo a quien algunos entendidos italianos habían bautizado como Maestro del Frutero lombardo. En aquel entonces, argumentó que debía tratarse de un artista aragonés, de la segunda mitad de siglo. Por fin ha aparecido una obra firmada que se presenta aquí. Efectivamente, el artista era zaragozano y su nombre es Bernardo Polo.

Pseudo-random number generation using a 3-state cellular automaton

Science.gov (United States)

Bhattacharjee, Kamalika; Paul, Dipanjyoti; Das, Sukanta

This paper investigates the potentiality of pseudo-random number generation of a 3-neighborhood 3-state cellular automaton (CA) under periodic boundary condition. Theoretical and empirical tests are performed on the numbers, generated by the CA, to observe the quality of it as pseudo-random number generator (PRNG). We analyze the strength and weakness of the proposed PRNG and conclude that the selected CA is a good random number generator.

Pollicisation: The Myth about Creating a Pseudo-Trapezium.

Science.gov (United States)

Mennen, Ulrich

2018-06-01

We have performed 14 pollicisations without creating a "pseudo-trapezium" from the metacarpal head. The entire metacarpal of the intended finger to be pollicised is removed and the proximal phalanx of the finger is inserted into the space left by the base of the excised metacarpal. The results are good to excellent in all 14 cases followed for 2-9 years. The advantages are that the operation is much simpler, thus also much quicker. The new thumb looks more like a thumb (not too long) and is more stable (ball-and-socket joint), with no long term complications often seen with the pseudo-trapezium.

Basic Characteristics and Spatial Patterns of Pseudo-Settlements—Taking Dalian as An Example

Directory of Open Access Journals (Sweden)

Jiaji Gao

2016-01-01

Full Text Available A person’s living behavior patterns are closely related to three types of settlements: real-life settlements, imagined settlements, and pseudo-settlements. The term “pseudo-settlement” (PS refers to the places that are selectively recorded and represented after the mass media chose and restructure the residence information. As the mass media rapidly develops and people’s way of obtaining information gradually change, PS has already become one of the main ways for people to recognize and understand real-life settlements, as well as describe their impressions of imagined settlements. PS also has a profound impact on tourism, employment, investment, migration, real estate development, etc. Thus, the study of PSs has important theoretical and practical significance. This paper proposes to put forward residential quarters where the mass media is displayed as the object of study and establishes the pseudo-settlement index system of Dalian in and elaborate analysis of the concept of PSs. From three aspects, including pseudo-buildings, pseudo-districts and pseudo-culture, this paper uses the ArcGIS 10.0 kernel density (spacial analyst to analyze and interpret the basic characteristics and spatial patterns of 14 elements of the PS in Dalian. Through systemic clustering analysis, it identifies eight major types of PSs in Dalian. Then it systematically elaborates current situations and characteristics of the spatial pattern of PSs in Dalian, namely: regionally concentrated, widely scattered and blank spaces without pseudo-settlements. Finally, this paper discusses the mechanism of formation of PSs in Dalian.

Basic Characteristics and Spatial Patterns of Pseudo-Settlements—Taking Dalian as An Example

Science.gov (United States)

Gao, Jiaji; Zhang, Yingjia; Li, Xueming

2016-01-01

A person’s living behavior patterns are closely related to three types of settlements: real-life settlements, imagined settlements, and pseudo-settlements. The term “pseudo-settlement” (PS) refers to the places that are selectively recorded and represented after the mass media chose and restructure the residence information. As the mass media rapidly develops and people’s way of obtaining information gradually change, PS has already become one of the main ways for people to recognize and understand real-life settlements, as well as describe their impressions of imagined settlements. PS also has a profound impact on tourism, employment, investment, migration, real estate development, etc. Thus, the study of PSs has important theoretical and practical significance. This paper proposes to put forward residential quarters where the mass media is displayed as the object of study and establishes the pseudo-settlement index system of Dalian in and elaborate analysis of the concept of PSs. From three aspects, including pseudo-buildings, pseudo-districts and pseudo-culture, this paper uses the ArcGIS 10.0 kernel density (spacial analyst) to analyze and interpret the basic characteristics and spatial patterns of 14 elements of the PS in Dalian. Through systemic clustering analysis, it identifies eight major types of PSs in Dalian. Then it systematically elaborates current situations and characteristics of the spatial pattern of PSs in Dalian, namely: regionally concentrated, widely scattered and blank spaces without pseudo-settlements. Finally, this paper discusses the mechanism of formation of PSs in Dalian. PMID:26805859

Evaluation of Pseudo-Haptic Interactions with Soft Objects in Virtual Environments.

Directory of Open Access Journals (Sweden)

Min Li

Full Text Available This paper proposes a pseudo-haptic feedback method conveying simulated soft surface stiffness information through a visual interface. The method exploits a combination of two feedback techniques, namely visual feedback of soft surface deformation and control of the indenter avatar speed, to convey stiffness information of a simulated surface of a soft object in virtual environments. The proposed method was effective in distinguishing different sizes of virtual hard nodules integrated into the simulated soft bodies. To further improve the interactive experience, the approach was extended creating a multi-point pseudo-haptic feedback system. A comparison with regards to (a nodule detection sensitivity and (b elapsed time as performance indicators in hard nodule detection experiments to a tablet computer incorporating vibration feedback was conducted. The multi-point pseudo-haptic interaction is shown to be more time-efficient than the single-point pseudo-haptic interaction. It is noted that multi-point pseudo-haptic feedback performs similarly well when compared to a vibration-based feedback method based on both performance measures elapsed time and nodule detection sensitivity. This proves that the proposed method can be used to convey detailed haptic information for virtual environmental tasks, even subtle ones, using either a computer mouse or a pressure sensitive device as an input device. This pseudo-haptic feedback method provides an opportunity for low-cost simulation of objects with soft surfaces and hard inclusions, as, for example, occurring in ever more realistic video games with increasing emphasis on interaction with the physical environment and minimally invasive surgery in the form of soft tissue organs with embedded cancer nodules. Hence, the method can be used in many low-budget applications where haptic sensation is required, such as surgeon training or video games, either using desktop computers or portable devices, showing

N-terminal Pro-B-type natriuretic peptide: a measure of significant patent cuctus arteriosus

LENUS (Irish Health Repository)

OFarombi-Oghuvbu, IO

2008-01-24

Background: B type natriuretic peptide (BNP) is a marker for ventricular dysfunction secreted as a pre-prohormone, Pro-B-type natriuretic peptide (ProBNP), and cleaved into BNP and a biologically inactive fragment, N-terminal pro-B-type natriuretic peptide (NT-proBNP). Little is known about the clinical usefulness of NT-proBNP in preterm infants.\\r\

Transformations of solutions for equations and hierarchies of pseudo-spherical type

CERN Document Server

Reyes, E G

2003-01-01

It is known that if an equation describes non-trivial one-parameter families of pseudo-spherical surfaces, its conservation laws, (generalized, nonlocal) symmetries and Baecklund transformations can be studied by geometrical means [4, 10]. In this letter it is pointed out that there exist correspondences, or 'generalized Baecklund transformations', between arbitrary solutions (satisfying some genericity conditions) of any two single equations describing pseudo-spherical surfaces. Then, the notion of a hierarchy of equations of pseudo-spherical type is introduced, and a theorem stating that there also exist correspondences between arbitrary solutions of any two such hierarchies is presented. A full account of these results appears elsewhere [12, 13]. (letter to the editor)

A role for galanin N-terminal fragment (1-15) in anxiety- and depression-related behaviors in rats.

Science.gov (United States)

Millón, Carmelo; Flores-Burgess, Antonio; Narváez, Manuel; Borroto-Escuela, Dasiel O; Santín, Luis; Parrado, Concepción; Narváez, José Angel; Fuxe, Kjell; Díaz-Cabiale, Zaida

2014-10-31

Galanin (GAL) plays a role in mood regulation. In this study we analyzed the action of the active N-terminal fragment [GAL(1-15)] in anxiety- and depression-related behavioral tests in rats. The effect of GAL(1-15) was analyzed in the forced swimming test, tail suspension test, open field test, and light/dark test. The proximity of GAL1 and GAL2 receptors was examined with the proximity ligation assay (PLA). We tested the GAL receptors involved in GAL(1-15) effects with the GAL2 receptor antagonist M871 and with an in vivo model of siRNA GAL2 receptor knockdown or siRNA GAL1 receptor knockdown rats. The effects of GAL(1-15) were also studied in the cell line RN33B. GAL(1-15) induced strong depression-like and anxiogenic-like effects in all the tests. These effects were stronger than the ones induced by GAL. The involvement of the GAL2 receptor was demonstrated with M871 and with the siRNA GAL2 receptor knockdown rats. The PLA indicated the possible existence of GAL1 and GAL2 heteroreceptor complexes in the dorsal hippocampus and especially in the dorsal raphe nucleus. In the siRNA GAL1 receptor knockdown rats the behavioral actions of GAL(1-15) disappeared, and in the siRNA GAL2 receptor knockdown rats the reductions of the behavioral actions of GAL(1-15) was linked to a disappearance of PLA. In the cell line RN33B, GAL(1-15) decreased 5-HT immunoreactivity more strongly than GAL. Our results indicate that GAL(1-15) exerts strong depression-related and anxiogenic-like effects and may give the basis for the development of drugs targeting GAL1 and GAL2 heteroreceptor complexes in the raphe-limbic system for the treatment of depression and anxiety. © The Author 2015. Published by Oxford University Press on behalf of CINP.

Intelligent Design, A Young Universe, Astrology, UFO's, and More: Tackling Astronomical Pseudo-science

Science.gov (United States)

Fraknoi, A.

2008-11-01

During IYA educators and scientists will interact with the public in many ways. There will likely be public questions at IYA events about pseudo-scientific topics. While the particular pseudo-sciences that are in vogue change with time, these days popular astronomical pseudo-science includes creationism and intelligent design (and their denial of the age of the universe), astrology, UFO's as extra-terrestrial spaceships, selling star names, the ``face'' on Mars, the claim that the moon landings were a hoax, etc. We discuss some of the recent surveys of belief in pseudo-science and some ways to respond to questions about these topics. A separate resource guide to help answer questions about astronomical pseudoscience is also included in this volume.

NLO corrections to differential cross sections for pseudo-scalar Higgs boson production

International Nuclear Information System (INIS)

Field, B.; Smith, J.; Tejeda-Yeomans, M.E.; Neerven, W.L. van

2003-01-01

We have computed the full next-to-leading (NLO) QCD corrections to the differential distributions d 2 σ/(dp T dy) for pseudo-scalar Higgs (A) production at large hadron colliders. This calculation has been carried out using the effective Lagrangian approach which is valid as long as the mass of the pseudo-scalar Higgs boson m A and its transverse momentum p T do not exceed the top-quark mass m t . The shape of the distributions hardly differ from those obtained for scalar Higgs (H) production because, apart from the overall coupling constant and mass, there are only small differences between the partonic differential distributions for scalar and pseudo-scalar production. Therefore, there are only differences in the magnitudes of the hadronic differential distributions which can be mainly attributed to the unknown mixing angle β describing the pseudo-scalar Higgs coupling to the top quarks

Transcriptional response after exposure to domoic acid-producing Pseudo-nitzschia in the digestive gland of the mussel Mytilus galloprovincialis.

Science.gov (United States)

Pazos, Antonio J; Ventoso, Pablo; Martínez-Escauriaza, Roi; Pérez-Parallé, M Luz; Blanco, Juan; Triviño, Juan C; Sánchez, José L

2017-12-15

Bivalve molluscs are filter feeding species that can accumulate biotoxins in their body tissues during harmful algal blooms. Amnesic Shellfish Poisoning (ASP) is caused by species of the diatom genus Pseudo-nitzschia, which produces the toxin domoic acid. The Mytilus galloprovincialis digestive gland transcriptome was de novo assembled based on the sequencing of 12 cDNA libraries, six obtained from control mussels and six from mussels naturally exposed to domoic acid-producing diatom Pseudo-nitzschia australis. After de novo assembly 94,727 transcripts were obtained, with an average length of 1015 bp and a N50 length of 761 bp. The assembled transcripts were clustered (homology > 90%) into 69,294 unigenes. Differential gene expression analysis was performed (DESeq2 algorithm) in the digestive gland following exposure to the toxic algae. A total of 1158 differentially expressed unigenes (absolute fold change > 1.5 and p-value < 0.05) were detected: 686 up-regulated and 472 down-regulated. Several membrane transporters belonging to the family of the SLC (solute carriers) were over-expressed in exposed mussels. Functional enrichment was performed using Pfam annotations obtained from the genes differentially expressed, 37 Pfam families were found to be significantly (FDR adjusted p-value < 0.1) enriched. Some of these families (sulfotransferases, aldo/keto reductases, carboxylesterases, C1q domain and fibrinogen C-terminal globular domain) could be putatively involved in detoxification processes, in the response against of the oxidative stress and in immunological processes. Protein network analysis with STRING algorithm found alteration of the Notch signaling pathway under the action of domoic acid-producing Pseudo-nitzschia. In conclusion, this study provides a high quality reference transcriptome of M. galloprovincialis digestive gland and identifies potential genes involved in the response to domoic acid. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat.

Science.gov (United States)

Finger, Aline; Kaiser-Bunbury, Christopher N; Kettle, Chris J; Valentin, Terence; Ghazoul, Jaboury

2014-01-01

Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow.

Genetic connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat.

Directory of Open Access Journals (Sweden)

Aline Finger

Full Text Available Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow.

High-Performance Pseudo-Random Number Generation on Graphics Processing Units

OpenAIRE

Nandapalan, Nimalan; Brent, Richard P.; Murray, Lawrence M.; Rendell, Alistair

2011-01-01

This work considers the deployment of pseudo-random number generators (PRNGs) on graphics processing units (GPUs), developing an approach based on the xorgens generator to rapidly produce pseudo-random numbers of high statistical quality. The chosen algorithm has configurable state size and period, making it ideal for tuning to the GPU architecture. We present a comparison of both speed and statistical quality with other common parallel, GPU-based PRNGs, demonstrating favourable performance o...

Design of CMOS CFOA Based on Pseudo Operational Transconductance Amplifier

OpenAIRE

Hassan Jassim Motlak

2015-01-01

A novel design technique employing CMOS Current Feedback Operational Amplifier (CFOA) is presented. The feature of consumption very low power in designing pseudo-OTA is used to decreasing the total power consumption of the proposed CFOA. This design approach applies pseudo-OTA as input stage cascaded with buffer stage. Moreover, the DC input offset voltage and harmonic distortion (HD) of the proposed CFOA are very low values compared with the conventional CMOS CFOA due to...

EDF fragment relocation model based on the displacement of rigid bodies

International Nuclear Information System (INIS)

Callu, C.; Baron, D.; Ruck, J.M.

1997-01-01

In order to release the restricting conditions imposed to the reactor operations with regards to PCMI (Pellet-Cladding Mechanical Interaction), the simulation of a fuel rod thermomechanical behavior has to be improved. The computer programming has to cope with the more and more sophisticated mathematical modellings induced by the complexity and the interdependence of the phenomena. Therefore EDF is developing a new code - CYRANO3 - since 1990 putting emphasis on its evolution capacities. Concerning more precisely the PCMI simulation, the pellet fragmentation and the fragments relocation is one of the major aspect one must account for. Thanks to recent analytical experiments, EDF developed a new modelling based on the displacement of rigid bodies and on the calculation of the interaction efforts between the fragments. This paper presents the basis of the model, its introduction within the CYRANO3 code and its calibration on a specific analytical experiment. The modelling is then tested against PWR fuel rods deformations from the EDF data base. The results are presented and discussed. (author)

Analysis of the bacterial diversity existing on animal hide and wool: development of a preliminary PCR-restriction fragment length polymorphism fingerprint database for identifying isolates.

Science.gov (United States)

Chen, Yu; Gao, Hongwei; Zhang, Yanming; Deng, Mingjun; Wu, Zhenxing; Zhu, Laihua; Duan, Qing; Xu, Biao; Liang, Chengzhu; Yue, Zhiqin; Xiao, Xizhi

2012-01-01

Twenty-one bacterial strains were isolated from imported cattle hide and rabbit wool using two types of media, nutrient broth, and nutrient broth with serum. The bacteria identified were Brevibacillus laterosporus, Leclercia adecarboxylata, Peptococcus niger, Bacillus circulans, Raoultella ornithinolytica, Bacillus subtilis, Bacillus cereus, Bacillus thermobacillus, Bacillus choshinensis, Bacillus sphaericus, Acinetobacter haemolyticus, Sphingomonas paucimobilis, Bacillus thuringiensis, Staphylococcus intermedius, Mycobacteria, Moraxella, Klebsiella pneumoniae, Ralstonia pickettii, Staphylococcus chromogenes, Comamonas testosteroni, and Cupriavidus pauculus. The 16s rDNA gene of each bacterium was amplified using the universal primers 27f and 1492r. The amplicons were digested with AvaI, BamHI, BgII, DraI, EcoRI, EcoRV, HindIII, HinfI, HpaI, PstI, SmaI, TaqII, XbaI, XmaI, AluI, XhoI, and PvuI individually. A specific fingerprint from the PCR-restriction fragment length polymorphism method based on 16s rDNA was obtained for each bacterium. The results showed that the method developed was useful not only for bacterial identification but also for the etiological investigation of pathogens in imported animal hair and wool.

Covalent Bonding of Pyrrolobenzodiazepines (PBDs) to Terminal Guanine Residues within Duplex and Hairpin DNA Fragments

Science.gov (United States)

Mantaj, Julia; Jackson, Paul J. M.; Karu, Kersti; Rahman, Khondaker M.; Thurston, David E.

2016-01-01

Pyrrolobenzodiazepines (PBDs) are covalent-binding DNA-interactive agents with growing importance as payloads in Antibody Drug Conjugates (ADCs). Until now, PBDs were thought to covalently bond to C2-NH2 groups of guanines in the DNA-minor groove across a three-base-pair recognition sequence. Using HPLC/MS methodology with designed hairpin and duplex oligonucleotides, we have now demonstrated that the PBD Dimer SJG-136 and the C8-conjugated PBD Monomer GWL-78 can covalently bond to a terminal guanine of DNA, with the PBD skeleton spanning only two base pairs. Control experiments with the non-C8-conjugated anthramycin along with molecular dynamics simulations suggest that the C8-substituent of a PBD Monomer, or one-half of a PBD Dimer, may provide stability for the adduct. This observation highlights the importance of PBD C8-substituents, and also suggests that PBDs may bind to terminal guanines within stretches of DNA in cells, thus representing a potentially novel mechanism of action at the end of DNA strand breaks. PMID:27055050

Generalised linear models for correlated pseudo-observations, with applications to multi-state models

DEFF Research Database (Denmark)

Andersen, Per Kragh; Klein, John P.; Rosthøj, Susanne

2003-01-01

Generalised estimating equation; Generalised linear model; Jackknife pseudo-value; Logistic regression; Markov Model; Multi-state model......Generalised estimating equation; Generalised linear model; Jackknife pseudo-value; Logistic regression; Markov Model; Multi-state model...

HLA-DPB1 typing with polymerase chain reaction and restriction fragment length polymorphism technique in Danes

DEFF Research Database (Denmark)

Hviid, T V; Madsen, H O; Morling, N

1992-01-01

endonucleases: RsaI, FokI, ApaI, SacI, BstUI, EcoNI, and DdeI, and the DNA fragments were separated by electrophoresis in agarose gels. Altogether, 71 individuals were investigated and 16 different HLA-DPB1 types were observed in 26 different heterozygotic combinations, as well as five possible homozygotes...

Nonaneurysmal "Pseudo-Subarachnoid Hemorrhage" Computed Tomography Patterns: Challenges in an Acute Decision-Making Heuristics.

Science.gov (United States)

Hasan, Tasneem F; Duarte, Walter; Akinduro, Oluwaseun O; Goldstein, Eric D; Hurst, Rebecca; Haranhalli, Neil; Miller, David A; Wharen, Robert E; Tawk, Rabih G; Freeman, William D

2018-06-05

Acute aneurysmal subarachnoid hemorrhage (SAH) is a medical and neurosurgical emergency from ruptured brain aneurysm. Aneurysmal SAH is identified on brain computed tomography (CT) as increased density of basal cisterns and subarachnoid spaces from acute blood products. Aneurysmal SAH-like pattern on CT appears as an optical illusion effect of hypodense brain parenchyma and/or hyperdense surrounding cerebral cisterns and blood vessels termed as "pseudo-subarachnoid hemorrhage" (pseudo-SAH). We reviewed clinical, laboratory, and radiographic data of all SAH diagnoses between January 2013 and January 2018, and found subsets of nonaneurysmal SAH, originally suspected to be aneurysmal in origin. We performed a National Library of Medicine search methodology using terms "subarachnoid hemorrhage," "pseudo," and "non-aneurysmal subarachnoid hemorrhage" singly and in combination to understand the sensitivity, specificity, and precision of pseudo-SAH. Over 5 years, 230 SAH cases were referred to our tertiary academic center and only 7 (3%) met the definition of pseudo-SAH. Searching the National Library of Medicine using subarachnoid hemorrhage yielded 27,402 results. When subarachnoid hemorrhage and pseudo were combined, this yielded 70 results and sensitivity was 50% (n = 35). Similarly, search precision was relatively low (26%) as only 18 results fit the clinical description similar to the 7 cases discussed in our series. Aneurysmal SAH pattern on CT is distinct from nonaneurysmal and pseudo-SAH patterns. The origin of pseudo-SAH terminology appears mostly tied to comatose cardiac arrest patients with diffuse dark brain Hounsfield units and cerebral edema, and is a potential imaging pitfall in acute medical decision-making. Copyright © 2018 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Radioimmunoassay of Pro-. gamma. -melanotropin, the amino-terminal fragment of proopiolipomelanocortin. [Swine

Energy Technology Data Exchange (ETDEWEB)

Ekman, R.; Hakanson, R.; Larsson, I.; Sundler, F.; Thorell, J.I.

1982-08-01

A RIA has been developed for natural porcine pro-..gamma..-MSH, the 103-amino acid peptide that represents the amino-terminal part of proopiolipomelanocortin. Rabbits were immunized with the purified peptide polymerized with glutaraldehyde. The antiserum is directed against the amino-terminial end of the antigen and does not cross-react with corticotropin, ..beta..-lipotropin, ..beta..-endorphin, ..gamma../sub 3/MSH, or ..gamma../sub 2/MSH. The minimum detectable concentration is 0.15 ng/ml standard pro-..gamma..MSH (15 pg/tube). Pro-..gamma..MSH-like immunoreactivity was detected in plasma and extracts of the hypothalamus and pituitary of pigs. Gel chromatography of these extracts revealed at least three immunoreactive peaks in the anterior and neurointermediate lobes of the pituitary, wheras two immunoreactive peaks were found in extracts of the hypothalalmus. (Endocrinology 111:578,1982)

On holography for (pseudo-)conformal cosmology

CERN Document Server

Libanov, M.; Sibiryakov, S.

2015-01-01

We propose a holographic dual for (pseudo-)conformal cosmological scenario, with a scalar field that forms a moving domain wall in adS_5. The domain wall separates two vacua with unequal energy densities. Unlike in the existing construction, the 5d solution is regular in the relevant space-time domain.

Jet fragmentation

International Nuclear Information System (INIS)

Saxon, D.H.

1985-10-01

The paper reviews studies on jet fragmentation. The subject is discussed under the topic headings: fragmentation models, charged particle multiplicity, bose-einstein correlations, identified hadrons in jets, heavy quark fragmentation, baryon production, gluon and quark jets compared, the string effect, and two successful models. (U.K.)

Pseudo-Kähler Quantization on Flag Manifolds

Science.gov (United States)

Karabegov, Alexander V.

A unified approach to geometric, symbol and deformation quantizations on a generalized flag manifold endowed with an invariant pseudo-Kähler structure is proposed. In particular cases we arrive at Berezin's quantization via covariant and contravariant symbols.

Existence of pseudo almost periodic solutions for a class of partial functional differential equations

Directory of Open Access Journals (Sweden)

Hui-Sheng Ding

2013-04-01

Full Text Available In this paper, we first introduce a new class of pseudo almost periodic type functions and investigate some properties of pseudo almost periodic type functions; and then we discuss the existence of pseudo almost periodic solutions to the class of abstract partial functional differential equations $x'(t=Ax(t+f(t,x_t$ with finite delay in a Banach space X.

Genetic polymorphism of toll-like receptors 4 gene by polymerase chain reaction-restriction fragment length polymorphisms, polymerase chain reaction-single-strand conformational polymorphism to correlate with mastitic cows

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Pooja H. Gupta

2015-05-01

Full Text Available Aim: An attempt has been made to study the toll-like receptors 4 (TLR4 gene polymorphism from cattle DNA to correlate with mastitis cows. Materials and Methods: In present investigation, two fragments of TLR4 gene named T4CRBR1 and T4CRBR2 of a 316 bp and 382 bp were amplified by polymerase chain reaction (PCR, respectively from Kankrej (22 and Triple cross (24 cattle. The genetic polymorphisms in the two populations were detected by a single-strand conformational polymorphism in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one. Results: Results showed that both alleles (A and B of two loci were found in all the two populations and the value of polymorphism information content indicated that these were highly polymorphic. Statistical results of χ2 test indicated that two polymorphism sites in the two populations fit with Hardy–Weinberg equilibrium (p˂0.05. Meanwhile, the effect of polymorphism of TLR4 gene on the somatic cell score (SCS indicated the cattle with allele a in T4CRBR1 showed lower SCS than that of allele B (p<0.05. Thus, the allele A might play an important role in mastitis resistance in cows. Conclusion: The relationship between the bovine mastitis trait and the polymorphism of TLR4 gene indicated that the bovine TLR4 gene may play an important role in mastitis resistance.

International conference Fourier Analysis and Pseudo-Differential Operators

CERN Document Server

Turunen, Ville; Fourier Analysis : Pseudo-differential Operators, Time-Frequency Analysis and Partial Differential Equations

2014-01-01

This book is devoted to the broad field of Fourier analysis and its applications to several areas of mathematics, including problems in the theory of pseudo-differential operators, partial differential equations, and time-frequency analysis. This collection of 20 refereed articles is based on selected talks given at the international conference “Fourier Analysis and Pseudo-Differential Operators,” June 25–30, 2012, at Aalto University, Finland, and presents the latest advances in the field. The conference was a satellite meeting of the 6th European Congress of Mathematics, which took place in Krakow in July 2012; it was also the 6th meeting in the series “Fourier Analysis and Partial Differential Equations.”

Anaesthetic Management of a Patient with Pseudo-TORCH Syndrome.

Science.gov (United States)

Berk, Derya; Kuş, Alparslan; Sahin, Tülay; Solak, Mine; Toker, Kamil

2013-09-01

Pseudo-TORCH syndrome is a rare, chronic disorder that is characterised by dimorphic features such as microcephaly, intracranial calcification, seizures, mental retardation, hepatosplenomegaly and coagulation disorders. We present the anaesthetic management of a forty day-old boy with Pseudo-TORCH syndrome during magnetic resonance imaging. Microcephaly, growth failure, high palate and bilateral rales in the lungs were detected in pre-anaesthetic physical examination. The peripheral oxygen saturation was 88-89% in room-air and was 95% in a hood with 5 L/min oxygen. We planned general anaesthesia to ensure immobility during magnetic resonance imaging. After standard monitoring, general anaesthesia was induced with 8% sevoflurane in 100% O2. After an adequate depth of anaesthesia was reached, we inserted a supraglottic airway device to avoid intubation without the use of a muscle relaxant. In patients with Pseudo-TORCH syndrome, the perioperative anaesthetic risk was increased. We believe that using a supraglottic airway device to secure the airway is less invasive than intubation, and can be performed without the need of muscle relaxants.

Anaesthetic Management of a Patient with Pseudo-TORCH Syndrome

Directory of Open Access Journals (Sweden)

Derya Berk

2013-09-01

Full Text Available Background: Pseudo-TORCH syndrome is a rare, chronic disorder that is characterised by dimorphic features such as microcephaly, intracranial calcification, seizures, mental retardation, hepatosplenomegaly and coagulation disorders. Case Report: We present the anaesthetic management of a forty day-old boy with Pseudo-TORCH syndrome during magnetic resonance imaging. Microcephaly, growth failure, high palate and bilateral rales in the lungs were detected in pre-anaesthetic physical examination. The peripheral oxygen saturation was 88-89% in room-air and was 95% in a hood with 5 L/min oxygen. We planned general anaesthesia to ensure immobility during magnetic resonance imaging. After standard monitoring, general anaesthesia was induced with 8% sevoflurane in 100% O2. After an adequate depth of anaesthesia was reached, we inserted a supraglottic airway device to avoid intubation without the use of a muscle relaxant. Conclusion: In patients with Pseudo-TORCH syndrome, the perioperative anaesthetic risk was increased. We believe that using a supraglottic airway device to secure the airway is less invasive than intubation, and can be performed without the need of muscle relaxants.

Pseudo-Meigs' syndrome secondary to metachronous ovarian metastases from transverse colon cancer.

Science.gov (United States)

Kyo, Kennoki; Maema, Atsushi; Shirakawa, Motoaki; Nakamura, Toshio; Koda, Kenji; Yokoyama, Hidetaro

2016-05-14

Pseudo-Meigs' syndrome associated with colorectal cancer is extremely rare. We report here a case of pseudo-Meigs' syndrome secondary to metachronous ovarian metastases from colon cancer. A 65-year-old female with a history of surgery for transverse colon cancer and peritoneal dissemination suffered from metachronous ovarian metastases during treatment with systemic chemotherapy. At first, neither ascites nor pleural effusion was observed, but she later complained of progressive abdominal distention and dyspnea caused by rapidly increasing ascites and pleural effusion and rapidly enlarging ovarian metastases. Abdominocenteses were repeated, and cytological examinations of the fluids were all negative for malignant cells. We suspected pseudo-Meigs' syndrome, and bilateral oophorectomies were performed after thorough informed consent. The patient's postoperative condition improved rapidly after surgery. We conclude that pseudo-Meigs' syndrome should be included in the differential diagnosis of massive or rapidly increasing ascites and pleural effusion associated with large or rapidly enlarging ovarian tumors.

Missing Fragments: Detecting Cooperative Binding in Fragment-Based Drug Design

Science.gov (United States)

2012-01-01

The aim of fragment-based drug design (FBDD) is to identify molecular fragments that bind to alternate subsites within a given binding pocket leading to cooperative binding when linked. In this study, the binding of fragments to human phenylethanolamine N-methyltransferase is used to illustrate how (a) current protocols may fail to detect fragments that bind cooperatively, (b) theoretical approaches can be used to validate potential hits, and (c) apparent false positives obtained when screening against cocktails of fragments may in fact indicate promising leads. PMID:24900472