Low numbers of repeat units in variable number of tandem repeats (VNTR) regions of white spot syndrome virus are correlated with disease outbreaks.

Science.gov (United States)

Hoa, T T T; Zwart, M P; Phuong, N T; de Jong, M C M; Vlak, J M

2012-11-01

White spot syndrome virus (WSSV) is the most important pathogen in shrimp farming systems worldwide including the Mekong Delta, Vietnam. The genome of WSSV is characterized by the presence of two major 'indel regions' found at ORF14/15 and ORF23/24 (WSSV-Thailand) and three regions with variable number tandem repeats (VNTR) located in ORF75, ORF94 and ORF125. In the current study, we investigated whether or not the number of repeat units in the VNTRs correlates with virus outbreak status and/or shrimp farming practice. We analysed 662 WSSV samples from individual WSSV-infected Penaeus monodon shrimp from 104 ponds collected from two important shrimp farming regions of the Mekong Delta: Ca Mau and Bac Lieu. Using this large data set and statistical analysis, we found that for ORF94 and ORF125, the mean number of repeat units (RUs) in VNTRs was significantly lower in disease outbreak ponds than in non-outbreak ponds. Although a higher mean RU number was observed in the improved-extensive system than in the rice-shrimp or semi-intensive systems, these differences were not significant. VNTR sequences are thus not only useful markers for studying WSSV genotypes and populations, but specific VNTR variants also correlate with disease outbreaks in shrimp farming systems. © 2012 Blackwell Publishing Ltd.

Deletion of intragenic tandem repeats in unit C of FLO1 of Saccharomyces cerevisiae increases the conformational stability of flocculin under acidic and alkaline conditions.

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Ee Li

Full Text Available Flocculation is an attractive property for Saccaromyces cerevisiae, which plays important roles in fermentation industry and environmental remediation. The process of flocculation is mediated by a family of cell surface flocculins. As one member of flocculins, Flo1 is characterized by four families of repeats (designated as repeat units A, B, C and D in the central domain. It is generally accepted that variation of repeat unit A in length in Flo1 influences the degree of flocculation or specificity for sugar recognization. However, no reports were observed for other repeat units. Here, we compared the flocculation ability and its sensitivity to environmental factors between yeast strain YSF1 carrying the intact FLO1 gene and yeast strains carrying the derived forms of FLO1 with partial or complete deletion of repeats in unit C. No obvious differences in flocculation ability and specificity of carbohydrate recognition were observed among these yeast strains, which indicates the truncated flocculins can stride across the cell wall and cluster the N-terminal domain on the surface of yeast cells as the intact Flo1 thereby improving intercellular binding. However, yeast strains with the truncated flocculins required more mannose to inhibit completely the flocculation, displayed broad tolerance of flocculation to pH fluctuation, and the fewer the repeats in unit C, the stronger adaptability of flocculation to pH change, which was not relevant to the position of deletion. This suggests that more stable active conformation is obtained for flocculin by deletion the repeat unit C in the central domain of Flo1, which was validated further by the higher hydrophobicity on the surface of cells of YSF1c with complete deletion of unit C under neutral and alkaline conditions and the stabilization of GFP conformation by fusion with flocculin with complete deletion of unit C in the central domain.

Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation

DEFF Research Database (Denmark)

Hardy, K.J.; Ussery, David; Oppenheim, B.A.

2004-01-01

are similar to those used in the study of the evolution of Mycobacterium tuberculosis clades. Seven VNTRs, termed staphylococcal interspersed repeat units (SIRUs), distributed around the genome are described, occurring in both unique and multiple sites, and varying in length from 48 to 159 bp. Variations...

Structure of filamin A immunoglobulin-like repeat 10 from Homo sapiens

International Nuclear Information System (INIS)

Page, Richard C.; Clark, Jeffrey G.; Misra, Saurav

2011-01-01

The structure of immunoglobulin-like repeat 10 from human filamin A solved at 2.44 Å resolution suggests the potential effects of mutations correlated with otopalatodigital syndrome spectrum disorders. Filamin A (FlnA) plays a critical role in cytoskeletal organization, cell motility and cellular signaling. FlnA utilizes different binding sites on a series of 24 immunoglobulin-like domains (Ig repeats) to interact with diverse cytosolic proteins and with cytoplasmic portions of membrane proteins. Mutations in a specific domain, Ig10 (FlnA-Ig10), are correlated with two severe forms of the otopalatodigital syndrome spectrum disorders Melnick–Needles syndrome and frontometaphyseal dysplasia. The crystal structure of FlnA-Ig10 determined at 2.44 Å resolution provides insight into the perturbations caused by these mutations

Triplet repeat DNA structures and human genetic disease: dynamic ...

Indian Academy of Sciences (India)

Unknown

formed at the loop-outs. [Sinden R R, Potaman V N, Oussatcheva E A, Pearson C E, Lyubchenko Y L and Shlyakhtenko L S 2002 Triplet repeat DNA structures .... 36–39. 40–121 Huntingtin/polyglutamine expansion. Spinocerebellar ataxia 1. SCA1. 6p23. (CAG)n. 6–44. –. 39–82 (pure) Ataxin-1/polyglutamine expansion.

S1 satellite DNA repetitive units display identical structure and overall variability in all Anatolian brown frog taxa.

Science.gov (United States)

Picariello, Orfeo; Feliciello, Isidoro; Chinali, Gianni

2016-02-01

S1 satellite DNA from Palearctic brown frogs has a species-specific structure in all European species. We characterized S1 satellite DNA from the Anatolian brown frogs Rana macrocnemis, R. camerani, and R. holtzi in order to define their taxonomic rank and the structure of this satellite in this frog lineage. Southern blots of genomic DNA digested with KpnI, EcoRV, NdeI, NheI, or StuI produced the same pattern of satellite DNA bands. Moreover, quantitative dot blots showed that this satellite DNA accounts for 0.1 % of the genome in all taxa. Analysis of the overall genomic variability of the S1a repeat sequence in specimens from various populations demonstrated that this repetitive unit also has the same size (476 bp), the same most common sequence (MCS) and the same overall variability in all three taxa, and also in R. macrocnemis tavasensis. The S1a repetitive unit presents three deletions of 9, 8 and 1 bp compared to the 494-bp S1a repeat from European frogs. The S1a MCS has three variable positions (sequence WWTK in positions 183-186), due to the presence of two repeat subpopulations with motifs AATG and WWTT in all taxa. Unlike previously analyzed mitochondrial and nuclear sequences that show considerable variations among these taxa, no difference could be detected in the structure and variability of the S1 satellite repetitive units. This suggests that these taxa should belong to a single species. Our results indicate that this satellite DNA variety probably formed when the Anatolian lineage radiated from common ancestor about 4 mya, and since then has maintained its structure in all four taxa examined.

A Cesium Rare-Earth Silicate Cs3 RESi6 O15 (RE=Dy-Lu, Y, In): The Parent of an Unusual Structural Class Featuring a Remarkable 57 Å Unit Cell Axis.

Science.gov (United States)

Terry, Rylan; Vinton, Daniel; McMillen, Colin D; Kolis, Joseph W

2018-02-19

The structure of Cs 3 RESi 6 O 15 , where RE=Dy-Lu, Y, In, is unusual in that it contains octahedrally coordinated rare-earth ions; their relative orientation dictates the structure, as they rotate about the c-axis supported by the cyclic Si 6 O 15 framework. The repeat unit of the rotation is eight units generating a very long (ca. 57 Å) unit cell axis. This unusual repeat unit is created by the structural flexibility of the hexasilicate ring, which is in turn affected by the size of the rare earth ion as well as the size of alkali ion residing within the silicate layers. Previous work showed for the smaller Sc 3+ ion, the rotation of the octahedra is not sufficient to achieve closure at an integral repeat unit and an incommensurate structure results. The products are prepared as large, high quality single crystals using a high-temperature (650 °C) hydrothermal method with CsOH and F - mineralizers. The presence of fluoride is essential to the formation of the product. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Major Facilitator Superfamily (MFS) Porters, LacY, FucP and XylE of Escherichia coli Appear to have Evolved Positionally Dissimilar Catalytic Residues without Rearrangement of 3-TMS Repeat Units

Science.gov (United States)

Västermark, Åke; Lunt, Bryan; Saier, Milton

2014-01-01

Based on alleged functional residue correspondences between FucP and LacY, a recent study has resulted in a proposed model of 3-TMS unit rearrangements [Madej et al., 2013]. We rebut this theory, using seven different lines of evidence. Our observations suggest that these two transporters are homologous throughout their lengths, having evolved from a common ancestor without repeat unit rearrangements. We exploit the availability of the high resolution XylE crystal structures in multiple conformations including the inward facing state to render possible direct comparisons with LacY. Based on a Δdistance map, we confirm the conclusion of Quistgaard et al. 2013 that the N-terminal 6 TMS halves of these transporters are internally less mobile than the second halves during the conformational transition from the outward occluded state to the inward occluded state and inward occluded state to inward open state. These observations, together with those of Madej et al., 2013, lead to the suggestion that functionally equivalent catalytic residues involved in substrate binding and transport catalysis have evolved in dissimilar positions, but apparently often in similar positions in the putative 3-TMS repeat units, from a single structural scaffold without intragenic rearrangement. PMID:24603210

Revisiting the TALE repeat.

Science.gov (United States)

Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

2014-04-01

Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing

Science.gov (United States)

Stuhlmüller, M.; Schwarz-Finsterle, J.; Fey, E.; Lux, J.; Bach, M.; Cremer, C.; Hinderhofer, K.; Hausmann, M.; Hildenbrand, G.

2015-10-01

Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

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Charlotte Rehm

Full Text Available In prokaryotes simple sequence repeats (SSRs with unit sizes of 1-5 nucleotides (nt are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4 structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc, Xanthomonas axonopodis pv. citri str. 306 (Xac, and Nostoc sp. strain PCC7120 (Ana. In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

Science.gov (United States)

Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT){sub n} {center_dot} (GA){sub n} microsatellite embedded within the U2 repeat unit

Energy Technology Data Exchange (ETDEWEB)

Liao, D.; Weiner, A.M. [Yale Univ., New Haven, CT (United States)

1995-12-10

The RNU2 locus encoding human U2 small nuclear RNA (snRNA) is organized as a nearly perfect tandem array containing 5 to 22 copies of a 5.8-kb repeat unit. Just downstream of the U2 snRNA gene in each 5.8-kb repeat unit lies a large (CT){sub n}{center_dot}(GA){sub n} dinucleotide repeat (n {approx} 70). This form of genomic organization, in which one repeat is embedded within another, provides an unusual opportunity to study the balance of forces maintaining the homogeneity of both kinds of repeats. Using a combination of field inversion gel electrophoresis and polymerase chain reaction, we have been able to study the CT microsatellites within individual U2 tandem arrays. We find that the CT microsatellites within an RNU2 allele exhibit significant length polymorphism, despite the remarkable homogeneity of the surrounding U2 repeat units. Length polymorphism is due primarily to loss or gain of CT dinucleotide repeats, but other types of deletions, insertions, and substitutions are also frequent. Polymorphism is greatly reduced in regions where pure (CT){sub n} tracts are interrupted by occasional G residues, suggesting that irregularities stabilize both the length and the sequence of the dinucleotide repeat. We further show that the RNU2 loci of other catarrhine primates (gorilla, chimpanzee, ogangutan, and baboon) contain orthologous CT microsatellites; these also exhibit length polymorphism, but are highly divergent from each other. Thus, although the CT microsatellite is evolving far more rapidly than the rest of the U2 repeat unit, it has persisted through multiple speciation events spanning >35 Myr. The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion. 70 refs., 5 figs.

Discrete Optimization of Internal Part Structure via SLM Unit Structure-Performance Database

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Li Tang

2018-01-01

Full Text Available The structural optimization of the internal structure of parts based on three-dimensional (3D printing has been recognized as being important in the field of mechanical design. The purpose of this paper is to present a creation of a unit structure-performance database based on the selective laser melting (SLM, which contains various structural units with different functions and records their structure and performance characteristics so that we can optimize the internal structure of parts directly, according to the database. The method of creating the unit structure-performance database was introduced in this paper and several structural units of the unit structure-performance database were introduced. The bow structure unit was used to show how to create the structure-performance database of the unit as an example. Some samples of the bow structure unit were designed and manufactured by SLM. These samples were tested in the WDW-100 compression testing machine to obtain their performance characteristics. After this, the paper collected all data regarding unit structure parameters, weight, performance characteristics, and other data; and, established a complete set of data from the bow structure unit for the unit structure-performance database. Furthermore, an aircraft part was reconstructed conveniently to be more lightweight according to the unit structure-performance database. Its weight was reduced by 36.8% when compared with the original structure, while the strength far exceeded the requirements.

A cesium rare-earth silicate Cs{sub 3}RESi{sub 6}O{sub 15} (RE = Dy-Lu, Y, In). The parent of an unusual structural class featuring a remarkable 57 Aa unit cell axis

Energy Technology Data Exchange (ETDEWEB)

Terry, Rylan; Vinton, Daniel; McMillen, Colin D.; Kolis, Joseph W. [Department of Chemistry and Center for Optical Materials Science and Engineering Technologies (COMSET), Clemson University, H.L. Hunter Laboratories (United States)

2018-02-19

The structure of Cs{sub 3}RESi{sub 6}O{sub 15}, where RE = Dy-Lu, Y, In, is unusual in that it contains octahedrally coordinated rare-earth ions; their relative orientation dictates the structure, as they rotate about the c-axis supported by the cyclic Si{sub 6}O{sub 15} framework. The repeat unit of the rotation is eight units generating a very long (ca. 57 Aa) unit cell axis. This unusual repeat unit is created by the structural flexibility of the hexasilicate ring, which is in turn affected by the size of the rare earth ion as well as the size of alkali ion residing within the silicate layers. Previous work showed for the smaller Sc{sup 3+} ion, the rotation of the octahedra is not sufficient to achieve closure at an integral repeat unit and an incommensurate structure results. The products are prepared as large, high quality single crystals using a high-temperature (650 C) hydrothermal method with CsOH and F{sup -} mineralizers. The presence of fluoride is essential to the formation of the product. (copyright 2018 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

Investigating structural and perfusion deficits due to repeated head trauma in active professional fighters.

Science.gov (United States)

Mishra, Virendra; Sreenivasan, Karthik; Banks, Sarah J; Zhuang, Xiaowei; Yang, Zhengshi; Cordes, Dietmar; Bernick, Charles

2018-01-01

Repeated head trauma experienced by active professional fighters results in various structural, functional and perfusion damage. However, whether there are common regions of structural and perfusion damage due to fighting and whether these structural and perfusion differences are associated with neuropsychological measurements in active professional fighters is still unknown. To that end, T1-weighted and pseudocontinuous arterial spin labeling MRI on a group of healthy controls and active professional fighters were acquired. Voxelwise group comparisons, in a univariate and multivariate sense, were performed to investigate differences in gray and white matter density (GMD, WMD) and cerebral blood flow (CBF) between the two groups. A significantly positive association between global GMD and WMD was obtained with psychomotor speed and reaction time, respectively, in our cohort of active professional fighters. In addition, regional WMD deficit was observed in a cluster encompassing bilateral pons, hippocampus, and thalamus in fighters (0.49 ± 0.04 arbitrary units (a.u.)) as compared to controls (0.51 ± 0.05a.u.). WMD in the cluster of active fighters was also significantly associated with reaction time. Significantly lower CBF was observed in right inferior temporal lobe with both partial volume corrected (46.9 ± 14.93 ml/100 g/min) and non-partial volume corrected CBF maps (25.91 ± 7.99 ml/100 g/min) in professional fighters, as compared to controls (65.45 ± 22.24 ml/100 g/min and 35.22 ± 12.18 ml/100 g/min respectively). A paradoxical increase in CBF accompanying right cerebellum and fusiform gyrus in the active professional fighters (29.52 ± 13.03 ml/100 g/min) as compared to controls (19.43 ± 12.56 ml/100 g/min) was observed with non-partial volume corrected CBF maps. Multivariate analysis with both structural and perfusion measurements found the same clusters as univariate analysis in addition to a cluster in right precuneus

Investigating structural and perfusion deficits due to repeated head trauma in active professional fighters

Directory of Open Access Journals (Sweden)

Virendra Mishra

2018-01-01

Full Text Available Repeated head trauma experienced by active professional fighters results in various structural, functional and perfusion damage. However, whether there are common regions of structural and perfusion damage due to fighting and whether these structural and perfusion differences are associated with neuropsychological measurements in active professional fighters is still unknown. To that end, T1-weighted and pseudocontinuous arterial spin labeling MRI on a group of healthy controls and active professional fighters were acquired. Voxelwise group comparisons, in a univariate and multivariate sense, were performed to investigate differences in gray and white matter density (GMD, WMD and cerebral blood flow (CBF between the two groups. A significantly positive association between global GMD and WMD was obtained with psychomotor speed and reaction time, respectively, in our cohort of active professional fighters. In addition, regional WMD deficit was observed in a cluster encompassing bilateral pons, hippocampus, and thalamus in fighters (0.49 ± 0.04 arbitrary units (a.u. as compared to controls (0.51 ± 0.05a.u.. WMD in the cluster of active fighters was also significantly associated with reaction time. Significantly lower CBF was observed in right inferior temporal lobe with both partial volume corrected (46.9 ± 14.93 ml/100 g/min and non-partial volume corrected CBF maps (25.91 ± 7.99 ml/100 g/min in professional fighters, as compared to controls (65.45 ± 22.24 ml/100 g/min and 35.22 ± 12.18 ml/100 g/min respectively. A paradoxical increase in CBF accompanying right cerebellum and fusiform gyrus in the active professional fighters (29.52 ± 13.03 ml/100 g/min as compared to controls (19.43 ± 12.56 ml/100 g/min was observed with non-partial volume corrected CBF maps. Multivariate analysis with both structural and perfusion measurements found the same clusters as univariate analysis in addition to a cluster in right

Crystal structure and thermal property of polyethylene glycol octadecyl ether

International Nuclear Information System (INIS)

Meng, Jie-yun; Tang, Xiao-fen; Li, Wei; Shi, Hai-feng; Zhang, Xing-xiang

2013-01-01

Highlights: ► The crystal structure of C18En for n ≥ 20 is a monoclinic system. ► Polyethylene glycol octadecyl ether crystallizes perfectly. ► The number of repeat units has significant effect on the melting, crystallizing temperature and enthalpy. ► The thermal stable temperature increases rapidly with increasing the number of repeat unit. - Abstract: The crystal structure, phase change property and thermal stable temperature (T d ) of polyethylene glycol octadecyl ether [HO(CH 2 CH 2 O) n C 18 H 37 , C18En] with various numbers of repeat units (n = 2, 10, 20 and 100) as phase change materials (PCMs) were investigated using temperature variable Fourier transformed infrared spectroscopy (FTIR), wide-angle X-ray diffraction (XRD), differential scanning calorimetry (DSC), and thermogravimetric analysis (TG). C18En crystallizes perfectly at 0 °C; and the crystal structure for n ≥ 20 is a monoclinic system. The number of repeat units has great effect on the phase change properties of C18En. The thermal stable temperature increases rapidly with increasing the number of repeat units. They approach to that of PEG-2000 as the number of repeat units is more than 10. T d increases rapidly with increasing the number of repeat units. C18En are a series of promising polymeric PCMs

The Vertebrate Brain, Evidence of Its Modular Organization and Operating System: Insights into the Brain's Basic Units of Structure, Function, and Operation and How They Influence Neuronal Signaling and Behavior

Science.gov (United States)

Baslow, Morris H.

2011-01-01

The human brain is a complex organ made up of neurons and several other cell types, and whose role is processing information for use in eliciting behaviors. However, the composition of its repeating cellular units for both structure and function are unresolved. Based on recent descriptions of the brain's physiological “operating system”, a function of the tri-cellular metabolism of N-acetylaspartate (NAA) and N-acetylaspartylglutamate (NAAG) for supply of energy, and on the nature of “neuronal words and languages” for intercellular communication, insights into the brain's modular structural and functional units have been gained. In this article, it is proposed that the basic structural unit in brain is defined by its physiological operating system, and that it consists of a single neuron, and one or more astrocytes, oligodendrocytes, and vascular system endothelial cells. It is also proposed that the basic functional unit in the brain is defined by how neurons communicate, and consists of two neurons and their interconnecting dendritic–synaptic–dendritic field. Since a functional unit is composed of two neurons, it requires two structural units to form a functional unit. Thus, the brain can be envisioned as being made up of the three-dimensional stacking and intertwining of myriad structural units which results not only in its gross structure, but also in producing a uniform distribution of binary functional units. Since the physiological NAA–NAAG operating system for supply of energy is repeated in every structural unit, it is positioned to control global brain function. PMID:21720525

The Vertebrate Brain, Evidence of Its Modular Organization and Operating System: Insights into the Brain's Basic Units of Structure, Function, and Operation and How They Influence Neuronal Signaling and Behavior.

Science.gov (United States)

Baslow, Morris H

2011-01-01

The human brain is a complex organ made up of neurons and several other cell types, and whose role is processing information for use in eliciting behaviors. However, the composition of its repeating cellular units for both structure and function are unresolved. Based on recent descriptions of the brain's physiological "operating system", a function of the tri-cellular metabolism of N-acetylaspartate (NAA) and N-acetylaspartylglutamate (NAAG) for supply of energy, and on the nature of "neuronal words and languages" for intercellular communication, insights into the brain's modular structural and functional units have been gained. In this article, it is proposed that the basic structural unit in brain is defined by its physiological operating system, and that it consists of a single neuron, and one or more astrocytes, oligodendrocytes, and vascular system endothelial cells. It is also proposed that the basic functional unit in the brain is defined by how neurons communicate, and consists of two neurons and their interconnecting dendritic-synaptic-dendritic field. Since a functional unit is composed of two neurons, it requires two structural units to form a functional unit. Thus, the brain can be envisioned as being made up of the three-dimensional stacking and intertwining of myriad structural units which results not only in its gross structure, but also in producing a uniform distribution of binary functional units. Since the physiological NAA-NAAG operating system for supply of energy is repeated in every structural unit, it is positioned to control global brain function.

Major facilitator superfamily porters, LacY, FucP and XylE of Escherichia coli appear to have evolved positionally dissimilar catalytic residues without rearrangement of 3-TMS repeat units.

Science.gov (United States)

Västermark, Ake; Lunt, Bryan; Saier, Milton

2014-01-01

Based on alleged functional residue correspondences between FucP and LacY, a recent study has resulted in a proposed model of 3-TMS unit rearrangements [Madej et al.: Proc Natl Acad Sci USA 2013;110:5870-5874]. We rebut this theory, using 7 different lines of evidence. Our observations suggest that these two transporters are homologous throughout their lengths, having evolved from a common ancestor without repeat unit rearrangements. We exploit the availability of the high-resolution XylE crystal structures in multiple conformations including the inward-facing state to render possible direct comparisons with LacY. Based on a Δdistance map, we confirm the conclusion of Quistgaard et al. [Nat Struct Mol Biol 2013;20:766-768] that the N-terminal 6 TMS halves of these transporters are internally less mobile than the second halves during the conformational transition from the outward occluded state to the inward occluded state and inward occluded state to inward open state. These observations, together with those of Madej et al. [2013], lead to the suggestion that functionally equivalent catalytic residues involved in substrate binding and transport catalysis have evolved in dissimilar positions, but apparently often in similar positions in the putative 3-TMS repeat units, from a single structural scaffold without intragenic rearrangement. © 2014 S. Karger AG, Basel.

Electromyographic analysis of repeated bouts of eccentric exercise.

Science.gov (United States)

McHugh, M P; Connolly, D A; Eston, R G; Gartman, E J; Gleim, G W

2001-03-01

The repeated bout effect refers to the protective effect provided by a single bout of eccentric exercise against muscle damage from a similar subsequent bout. The aim of this study was to determine if the repeated bout was associated with an increase in motor unit activation relative to force production, an increased recruitment of slow-twitch motor units or increased motor unit synchronization. Surface electromyographic (EMG) signals were recorded from the hamstring muscles during two bouts of submaximal isokinetic (2.6 rad x s(-1)) eccentric (11 men, 9 women) or concentric (6 men, 4 women) contractions separated by 2 weeks. The EMG per unit torque and median frequency were analysed. The initial bout of eccentric exercise resulted in strength loss, pain and muscle tenderness, while the repeated eccentric bout resulted in a slight increase in strength, no pain and no muscle tenderness (bout x time effects, P exercise. The EMG per unit torque and median frequency were not different between the initial and repeated bouts of eccentric exercise. The EMG per unit torque and median frequency increased during both bouts of eccentric exercise (P < 0.01) but did not change during either concentric bout. In conclusion, there was no evidence that the repeated bout effect was due to a neural adaptation.

A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming.

Science.gov (United States)

Lin, Geng-Ming; Lai, Yu-Heng; Audira, Gilbert; Hsiao, Chung-Der

2017-11-06

Green algae, Chlorella ellipsoidea , Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5-0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

Improving the repeatability of Motor Unit Number Index (MUNIX) by introducing additional epochs at low contraction levels.

Science.gov (United States)

Peng, Yun; Zhang, Yingchun

2017-07-01

To evaluate the repeatability of (Motor Unit Number Index) MUNIX under repeatability conditions, specify the origin of variations and provide strategies for quality control. MUNIX calculations were performed on the bicep brachii muscles of eight healthy subjects. Negative effect of suboptimal electrode positions on MUNIX accuracy was eliminated by employing the high-density surface electromyography technique. MUNIX procedures that utilized a variety of surface interferential pattern (SIP) epoch recruitment strategies (including the original MUNIX procedure, two proposed improvement strategies and their combinations) were described. For each MUNIX procedure, ten thousands of different SIP pools were constructed by randomly recruiting necessary SIP epochs from a large SIP epoch pool (3 datasets, 9 independent electromyography recordings at different contraction levels per dataset and 10 SIP epochs per recording) and implemented for MUNIX calculation. The repeatability of each MUNIX procedure was assessed by summarizing the resulting MUNIX distribution and compared to investigate the effect of SIP epoch selection strategy on repeatability performance. SIP epochs selected at lower contraction levels have a stronger influence on the repeatability of MUNIX than those selected at higher contraction levels. MUNIX under repeatability conditions follows a normal distribution and the standard deviation can be significantly reduced by introducing more epochs near the MUNIX definition line. The MUNIX technique shows an inherent variation attributable to SIP epochs at low contraction levels. It is recommended that more epochs should be sampled at these low contraction levels to improve the repeatability. The present study thoroughly documented the inherent variation of MUNIX and the causes, and offered practical solutions to improve the repeatability of MUNIX. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Vital signs: Repeat births among teens - United States, 2007-2010.

Science.gov (United States)

2013-04-05

Teen childbearing has potential negative health, economic, and social consequences for mother and child. Repeat teen childbearing further constrains the mother's education and employment possibilities. Rates of preterm and low birth weight are higher in teens with a repeat birth, compared with first births. To assess patterns of repeat childbearing and postpartum contraceptive use among teens, CDC analyzed natality data from the National Vital Statistics System (NVSS) and the Pregnancy Risk Assessment Monitoring System (PRAMS) from 2007-2010. Based on 2010 NVSS data from all 50 states and the District of Columbia, of more than 367,000 births to teens aged 15-19 years, 18.3% were repeat births. The percentage of teen births that represented repeat births decreased by 6.2% between 2007 and 2010. Disparities in repeat teen births exist by race/ethnicity, with the highest percentages found among American Indian/Alaska Natives (21.6%), Hispanics (20.9%), and non-Hispanic blacks (20.4%) and lowest among non-Hispanic whites (14.8%). Wide geographic disparities in the percentage of teen births that were repeat births also exist, ranging from 22% in Texas to 10% in New Hampshire. PRAMS data from 16 reporting areas (15 states and New York City) indicate that 91.2% of teen mothers used a contraceptive method 2-6 months after giving birth, but only 22.4% of teen mothers used the most effective methods. Teens with a previous live birth were significantly more likely to use the most effective methods postpartum compared with those with no prior live birth (29.6% versus 20.9%, respectively). Non-Hispanic white and Hispanic teens were significantly more likely to use the most effective methods than non-Hispanic black teens (24.6% and 27.9% versus 14.3%, respectively). The percentage of teens reporting postpartum use of the most effective methods varied greatly geographically across the PRAMS reporting areas, ranging from 50.3% in Colorado to 7.2% in New York State. Although the

Repeated mild traumatic brain injury can cause acute neurologic impairment without overt structural damage in juvenile rats.

Directory of Open Access Journals (Sweden)

Alicia Meconi

Full Text Available Repeated concussion is becoming increasingly recognized as a serious public health concern around the world. Moreover, there is a greater awareness amongst health professionals of the potential for repeated pediatric concussions to detrimentally alter the structure and function of the developing brain. To better study this issue, we developed an awake closed head injury (ACHI model that enabled repeated concussions to be performed reliably and reproducibly in juvenile rats. A neurological assessment protocol (NAP score was generated immediately after each ACHI to help quantify the cumulative effects of repeated injury on level of consciousness, and basic motor and reflexive capacity. Here we show that we can produce a repeated ACHI (4 impacts in two days in both male and female juvenile rats without significant mortality or pain. We show that both single and repeated injuries produce acute neurological deficits resembling clinical concussion symptoms that can be quantified using the NAP score. Behavioural analyses indicate repeated ACHI acutely impaired spatial memory in the Barnes maze, and an interesting sex effect was revealed as memory impairment correlated moderately with poorer NAP score performance in a subset of females. These cognitive impairments occurred in the absence of motor impairments on the Rotarod, or emotional changes in the open field and elevated plus mazes. Cresyl violet histology and structural magnetic resonance imaging (MRI indicated that repeated ACHI did not produce significant structural damage. MRI also confirmed there was no volumetric loss in the cortex, hippocampus, or corpus callosum of animals at 1 or 7 days post-ACHI. Together these data indicate that the ACHI model can provide a reliable, high throughput means to study the effects of concussions in juvenile rats.

Inulin isoforms differ by repeated additions of one crystal unit cell

Science.gov (United States)

Cooper, Peter D.; Barclay, Thomas G.; Ginic-Markovic, Milena; Gerson, Andrea R.; Petrovsky, Nikolai

2014-01-01

Inulin isoforms, especially delta inulin, are important biologically as immune activators and clinically as vaccine adjuvants. In exploring action mechanisms, we previously found regular increments in thermal properties of the seven-member inulin isoform series that suggested regular additions of some energetic structural unit. Because the previous isolates carried additional longer chains that masked defining ranges, these were contrasted with new isoform isolates comprising only inulin chain lengths defining that isoform. The new series began with 19 fructose units per chain (alpha-1 inulin), increasing regularly by 6 fructose units per isoform. Thus the ‘energetic unit’ equates to 6 fructose residues per chain. All isoforms showed indistinguishable X-ray diffraction patterns that were also identical with known inulin crystals. We conclude that an ‘energetic unit’ equates to one helix turn of 6 fructose units per chain as found in one unit cell of the inulin crystal. Each isoform chain comprised progressively more helix turns plus one additional fructose and glucose residues per chain. PMID:24528745

Deployment Repeatability

Science.gov (United States)

2016-04-01

evaluating the deployment repeatability builds upon the testing or analysis of deployment kinematics (Chapter 6) and adds repetition. Introduction...material yield or failure during a test. For the purposes of this chapter, zero shift will refer to permanent changes in the structure, while reversible ...the content of other chapters in this book: Gravity Compensation (Chapter 4) and Deployment Kinematics and Dynamics (Chapter 6). Repeating the

Comparative Geometrical Analysis of Leucine-Rich Repeat Structures in the Nod-Like and Toll-Like Receptors in Vertebrate Innate Immunity

Directory of Open Access Journals (Sweden)

Norio Matsushima

2015-08-01

Full Text Available The NOD-like receptors (NLRs and Toll-like receptors (TLRs are pattern recognition receptors that are involved in the innate, pathogen pattern recognition system. The TLR and NLR receptors contain leucine-rich repeats (LRRs that are responsible for ligand interactions. In LRRs short β-strands stack parallel and then the LRRs form a super helical arrangement of repeating structural units (called a coil of solenoids. The structures of the LRR domains of NLRC4, NLRP1, and NLRX1 in NLRs and of TLR1-5, TLR6, TLR8, TLR9 in TLRs have been determined. Here we report nine geometrical parameters that characterize the LRR domains; these include four helical parameters from HELFIT analysis. These nine parameters characterize well the LRR structures in NLRs and TLRs; the LRRs of NLR adopts a right-handed helix. In contrast, the TLR LRRs adopt either a left-handed helix or are nearly flat; RP105 and CD14 also adopt a left-handed helix. This geometrical analysis subdivides TLRs into four groups consisting of TLR3/TLR8/TLR9, TLR1/TLR2/TRR6, TLR4, and TLR5; these correspond to the phylogenetic tree based on amino acid sequences. In the TLRs an ascending lateral surface that consists of loops connecting the β-strand at the C-terminal side is involved in protein, protein/ligand interactions, but not the descending lateral surface on the opposite side.

Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.

Science.gov (United States)

Chen, Jonathan L; VanEtten, Damian M; Fountain, Matthew A; Yildirim, Ilyas; Disney, Matthew D

2017-07-11

RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 × 1 internal loops of r(3×CAG) are stabilized by one-hydrogen bond (cis Watson-Crick/Watson-Crick) AA pairs, while those of r(3×CUG) prefer one- or two-hydrogen bond (cis Watson-Crick/Watson-Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.

Methodology for repeated load analysis of composite structures with embedded magnetic microwires

Directory of Open Access Journals (Sweden)

K. Semrád

2017-01-01

Full Text Available The article processes issue of strength of cyclically loaded composite structures with the possibility of contactless stress measuring inside a material. For this purpose a contactless tensile stress sensor using improved induction principle based on the magnetic microwires embedded in the composite structure has been developed. The methodology based on the E-N approach was applied for the analysis of the repeated load of the wing hinge connection, including finite element method (FEM fatigue strength analysis. The results proved that composites in comparison with the metal structures offer significant weight reduction of the small aircraft construction, whereas the required strength, stability and lifetime of the components are remained.

Dual market structures and the likelihood of repeated ties - evidence from pharmaceutical biotechnology

NARCIS (Netherlands)

Roijakkers, A.H.W.M.; Hagedoorn, J.; Kranenburg, van H.

2005-01-01

This paper analyses the role of repeated ties in the high-tech pharmaceutical biotechnology industry, a sector that is characterized by a strong dual market structure. Our most important finding is that previous ties in pairs of large pharmaceutical companies and small biotechnology firms have a

Renal Impairment in 79 Pediatric Patients (158 Renal Units) With Repeated Urinary Tract Infection in Relation to Vesicoureteric Reflux

International Nuclear Information System (INIS)

Moustafa, H.; Amin, A.; El-Haddad, Sh.; Moustafa, B.; Wageeh, Sh.; Soliman, N.

1998-01-01

Seventy nine patients with repeated urinary tract infection were evaluated for detection of vesico-ureteric reflux (VUR) by direct (DRC) and indirect (IRC) radionuclide cystography as well as assessment of renal scarring using 99 mTc-DMSA. Positive VUR was evident in 38 patients (59 renal units), 50%, patients had history of recurrent urinary tract infection. Patients kidneys were divided into 2 groups: group A with normal if kidneys (74 renal units), but still they have high grade VUR in 20 renal units (20.6%.Group B with scarred kidneys (84 renal Units) with high grade VUR in 36 renal units (42.9%) with significant difference between both groups (P 99 mTc-DMSA with VUR assessment are essential in pediatric patients with urinary tract infection for detection of high grade VUR which may contribute to renal scarring and damage

Flanking Variation Influences Rates of Stutter in Simple Repeats

Directory of Open Access Journals (Sweden)

August E. Woerner

2017-11-01

Full Text Available It has been posited that the longest uninterrupted stretch (LUS of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL. While there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well. For example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate. To address this, rates of stutter were contrasted against the LUS as well as the PAL on different flanking haplotypic backgrounds. This study shows that rates of stutter can vary substantially depending on the flanking haplotype, and while there are cases where the LUS is a better predictor of stutter than the PAL, examples to the contrary are apparent in commonly assayed forensic markers. Further, flanking variation that is 7 bp from the repeat region can impact rates of stutter. These findings suggest that non-proximal effects, such as DNA secondary structure, may be impacting the rates of stutter in common forensic short tandem repeat markers.

In situ detection of tandem DNA repeat length

Energy Technology Data Exchange (ETDEWEB)

Yaar, R.; Szafranski, P.; Cantor, C.R.; Smith, C.L. [Boston Univ., MA (United States)

1996-11-01

A simple method for scoring short tandem DNA repeats is presented. An oligonucleotide target, containing tandem repeats embedded in a unique sequence, was hybridized to a set of complementary probes, containing tandem repeats of known lengths. Single-stranded loop structures formed on duplexes containing a mismatched (different) number of tandem repeats. No loop structure formed on duplexes containing a matched (identical) number of tandem repeats. The matched and mismatched loop structures were enzymatically distinguished and differentially labeled by treatment with S1 nuclease and the Klenow fragment of DNA polymerase. 7 refs., 4 figs.

Impact of repeated uniaxial mechanical strain on flexible a-IGZO thin film transistors with symmetric and asymmetric structures

Science.gov (United States)

Liao, Po-Yung; Chang, Ting-Chang; Su, Wan-Ching; Chen, Bo-Wei; Chen, Li-Hui; Hsieh, Tien-Yu; Yang, Chung-Yi; Chang, Kuan-Chang; Zhang, Sheng-Dong; Huang, Yen-Yu; Chang, Hsi-Ming; Chiang, Shin-Chuan

2017-06-01

This letter investigates repeated uniaxial mechanical stress-induced degradation behavior in flexible amorphous In-Ga-Zn-O thin-film transistors (TFTs) of different geometric structures. Two types of via-contact structure TFTs are investigated: symmetrical and UI structure (TFTs with I- and U-shaped asymmetric electrodes). After repeated mechanical stress, I-V curves for the symmetrical structure show a significant negative threshold voltage (VT) shift, due to mechanical stress-induced oxygen vacancy generation. However, degradation in the UI structure TFTs after stress is a negative VT shift along with the parasitic transistor characteristic in the forward-operation mode, with this hump not evident in the reverse-operation mode. This asymmetrical degradation is clarified by the mechanical strain simulation of the UI TFTs.

Computational study of the human dystrophin repeats: interaction properties and molecular dynamics.

Directory of Open Access Journals (Sweden)

Baptiste Legrand

Full Text Available Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD. It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.

Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes

DEFF Research Database (Denmark)

Peng, Xu; Brügger, Kim; Shen, Biao

2003-01-01

terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also...... recognizes both main families of repeat sequences in S. solfataricus. The recombinant protein, expressed in Escherichia coli, showed the same binding properties to the SRSR repeat as the native one. The SSO454 protein exhibits a tripartite internal repeat structure which yields a good sequence match...... with a helix-turn-helix DNA-binding motif. Although this putative motif is shared by other archaeal proteins, orthologs of SSO454 were only detected in species within the Sulfolobus genus and in the closely related Acidianus genus. We infer that the genus-specific protein induces an opening of the structure...

Handedness in shearing auxetics creates rigid and compliant structures

Science.gov (United States)

Lipton, Jeffrey Ian; MacCurdy, Robert; Manchester, Zachary; Chin, Lillian; Cellucci, Daniel; Rus, Daniela

2018-05-01

In nature, repeated base units produce handed structures that selectively bond to make rigid or compliant materials. Auxetic tilings are scale-independent frameworks made from repeated unit cells that expand under tension. We discovered how to produce handedness in auxetic unit cells that shear as they expand by changing the symmetries and alignments of auxetic tilings. Using the symmetry and alignment rules that we developed, we made handed shearing auxetics that tile planes, cylinders, and spheres. By compositing the handed shearing auxetics in a manner inspired by keratin and collagen, we produce both compliant structures that expand while twisting and deployable structures that can rigidly lock. This work opens up new possibilities in designing chemical frameworks, medical devices like stents, robotic systems, and deployable engineering structures.

Solution structure of the twelfth cysteine-rich ligand-binding repeat in rat megalin

International Nuclear Information System (INIS)

Wolf, Christian A.; Dancea, Felician; Shi Meichen; Bade-Noskova, Veronika; Rueterjans, Heinz; Kerjaschki, Dontscho; Luecke, Christian

2007-01-01

Megalin, an approx. 600 kDa transmembrane glycoprotein that acts as multi-ligand transporter, is a member of the low density lipoprotein receptor gene family. Several cysteine-rich repeats, each consisting of about 40 residues, are responsible for the multispecific binding of ligands. The solution structure of the twelfth cysteine-rich ligand-binding repeat with class A motif found in megalin features two short β-strands and two helical turns, yielding the typical fold with a I-III, II-V and IV-VI disulfide bridge connectivity pattern and a calcium coordination site at the C-terminal end. The resulting differences in electrostatic surface potential compared to other ligand-binding modules of this gene family, however, may be responsible for the functional divergence

Structure and state of repeatedly rubbed pure iron

Energy Technology Data Exchange (ETDEWEB)

Furuichi, Hiroshi [Dept. of Mechanical System Engineering, Yamanashi Univ., Kofu (Japan); Nakamura, Shoichiro [Dept. of Mechanical System Engineering, Yamanashi Univ., Kofu (Japan); Xuan Junsong [Nippo Precision Ltd., Nirasaki (Japan); Yamazaki, Kunihiro [Dept. of Mechanical System Engineering, Yamanashi Univ., Kofu (Japan)

1995-05-01

Pure iron was repeatedly rubbed under special conditions. The highest and the average hardness near the friction surface were 1431 HV and 1146 HV, respectively. Diffraction patterns near the friction surface showed a broad hexagonal ring corresponding to the (002) plane of {epsilon}-iron (hcp), although the other rings are from {alpha}-iron. Extremely fine imperfectly defined regions were observed from the area of this diffraction pattern. Another diffraction patterns showed an extremely diffuse and faint halo ring indicating an amorphous state, whose average atomic distance equals one of the interplanar spacing of the basal plane of {epsilon}-iron. This amorphous state differs from that by obtained rapid quenching. These results suggest that a structure with only the basal plane of {epsilon}-iron appeared during the rubbing and further destruction resulted in the amorphous state. Extremely high pressure may arise during rubbing: {epsilon}-iron forms above 13 GPa at room temperature and the basal plane consists of the shortest atomic distance of iron. In the latter pattern, a spot arrangement indicating a structure ordered only in one or two directions was observed. Rows of pits and cracks connecting them were observed, on the side surface near the rubbed surface, which shows crack formation during sliding contact fatigue. (orig.)

Topological characteristics of helical repeat proteins

NARCIS (Netherlands)

Groves, M R; Barford, D

The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

Vital Signs: Repeat Births Among Teens — United States, 2007–2010

OpenAIRE

Gavin, Lorrie; Warner, Lee; O’Neil, Mary Elizabeth; Duong, Linh M.; Marshall, Cassondra; Hastings, Philip A.; Harrison, Ayanna T.; Barfield, Wanda

2013-01-01

Background Teen childbearing has potential negative health, economic, and social consequences for mother and child. Repeat teen childbearing further constrains the mother’s education and employment possibilities. Rates of preterm and low birth weight are higher in teens with a repeat birth, compared with first births. Methods To assess patterns of repeat childbearing and postpartum contraceptive use among teens, CDC analyzed natality data from the National Vital Statistics System (NVSS) and t...

[Cross sectional study of structural quality of German intensive care units. A reevaluation of the DIVI register].

Science.gov (United States)

Fölsch, C; Kofahl, N; Waydhas, C; Stiletto, R

2013-09-01

Effectiveness of intensive care treatment is essential to cope with increasing costs. The German national register of intensive care established by the German Interdisciplinary Association for Intensive Care Medicine (DIVI) contains basic data on the structure of intensive care units in Germany. A repeat analysis of data of the DIVI register within 8 years provides information for the development of intensive care units under different economic circumstances. The recent data on the structure of intensive care units were obtained in 2008 and compared with the primary multicenter study from 2000. The hospitals selected were a representative sample for the whole of Germany. Data on the status of the hospital, staff and technical facilities, foundation of the hospital and the statistics of mechanically ventilated patients were analyzed. The technical facilities and the number of staff have improved from 2000 to 2008. A smaller availability of diagnostic procedures and staff remain in hospitals for basic treatment outside normal working hours. The average utilization of intensive care unit beds was not altered. The existence of intermediate care units did not significantly change the proportion of patients with artificial ventilation or ventilation times. The number of beds in intensive care units was unchanged as was the average number of beds in units and the number of patients treated. A relevant number of beds of intensive care units shifted towards hospitals with private foundation without changes in the overall numbers. The structure of the hospitals was comparable at both time points. The introduction of intermediate care units did not alter ventilation parameters of patients in 2008 compared with 2000. There is no obvious medical reason for the shift of intensive care beds towards private hospitals. The number of staff and patients varied considerably between the intensive care units. The average number of patients treated per bed was not different between the

[Clustered regularly interspaced short palindromic repeats: structure, function and application--a review].

Science.gov (United States)

Cui, Yujun; Li, Yanjun; Yan, Yanfeng; Yang, Ruifu

2008-11-01

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats), the basis of spoligotyping technology, can provide prokaryotes with heritable adaptive immunity against phages' invasion. Studies on CRISPR loci and their associated elements, including various CAS (CRISPR-associated) proteins and leader sequences, are still in its infant period. We introduce the brief history', structure, function, bioinformatics research and application of this amazing immunity system in prokaryotic organism for inspiring more scientists to find their interest in this developing topic.

Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

Science.gov (United States)

Waye, J S; Willard, H F

1986-09-01

The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were approximately 98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.

Total synthesis of a Streptococcus pneumoniae serotype 12F CPS repeating unit hexasaccharide

Directory of Open Access Journals (Sweden)

Peter H. Seeberger

2017-01-01

Full Text Available The Gram-positive bacterium Streptococcus pneumoniae causes severe disease globally. Vaccines that prevent S. pneumoniae infections induce antibodies against epitopes within the bacterial capsular polysaccharide (CPS. A better immunological understanding of the epitopes that protect from bacterial infection requires defined oligosaccharides obtained by total synthesis. The key to the synthesis of the S. pneumoniae serotype 12F CPS hexasaccharide repeating unit that is not contained in currently used glycoconjugate vaccines is the assembly of the trisaccharide β-D-GalpNAc-(1→4-[α-D-Glcp-(1→3]-β-D-ManpNAcA, in which the branching points are equipped with orthogonal protecting groups. A linear approach relying on the sequential assembly of monosaccharide building blocks proved superior to a convergent [3 + 3] strategy that was not successful due to steric constraints. The synthetic hexasaccharide is the starting point for further immunological investigations.

Comparative Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) of Streptococcus thermophilus St-I and its Bacteriophage-Insensitive Mutants (BIM) Derivatives.

Science.gov (United States)

Li, Wan; Bian, Xin; Evivie, Smith Etareri; Huo, Gui-Cheng

2016-09-01

The CRISPR-Cas (CRISPR together with CRISPR-associated proteins) modules are the adaptive immune system, acting as an adaptive and heritable immune system in bacteria and archaea. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize, and clear infections. In this study, the homology of CRISPRs sequence in BIMs (bacteriophage-insensitive mutants) of Streptococcus thermophilus St-I were analyzed. Secondary structures of the repeats and the PAMs (protospacer-associated motif) of each CRISPR locus were also predicted. Results showed that CRISPR1 has 27 repeat-spacer units, 5 of them had duplicates; CRISPR2 has one repeat-spacer unit; CRISPR3 has 28 repeat-spacer units. Only BIM1 had a new spacer acquisition in CRISPR3, while BIM2 and BIM3 had no new spacers' insertion, thus indicating that while most CRISPR1 were more active than CRISPR3, new spacer acquisition occurred just in CRSPR3 in some situations. These findings will help establish the foundation for the study of CRSPR-Cas systems in lactic acid bacteria.

Repeated social stress leads to contrasting patterns of structural plasticity in the amygdala and hippocampus.

Science.gov (United States)

Patel, D; Anilkumar, S; Chattarji, S; Buwalda, B

2018-03-23

Previous studies have demonstrated that repeated immobilization and restraint stress cause contrasting patterns of dendritic reorganization as well as alterations in spine density in amygdalar and hippocampal neurons. Whether social and ethologically relevant stressors can induce similar patterns of morphological plasticity remains largely unexplored. Hence, we assessed the effects of repeated social defeat stress on neuronal morphology in basolateral amygdala (BLA), hippocampal CA1 and infralimbic medial prefrontal cortex (mPFC). Male Wistar rats experienced social defeat stress on 5 consecutive days during confrontation in the resident-intruder paradigm with larger and aggressive Wild-type Groningen rats. This resulted in clear social avoidance behavior one day after the last confrontation. To assess the morphological consequences of repeated social defeat, 2 weeks after the last defeat, animals were sacrificed and brains were stained using a Golgi-Cox procedure. Morphometric analyses revealed that, compared to controls, defeated Wistar rats showed apical dendritic decrease in spine density on CA1 but not BLA. Sholl analysis demonstrated a significant dendritic atrophy of CA1 basal dendrites in defeated animals. In contrast, basal dendrites of BLA pyramidal neurons exhibited enhanced dendritic arborization in defeated animals. Social stress failed to induce lasting structural changes in mPFC neurons. Our findings demonstrate for the first time that social defeat stress elicits divergent patterns of structural plasticity in the hippocampus versus amygdala, similar to what has previously been reported with repeated physical stressors. Therefore, brain region specific variations may be a universal feature of stress-induced plasticity that is shared by both physical and social stressors. Copyright © 2018 Elsevier B.V. All rights reserved.

Expression, crystallization and preliminary crystallographic data analysis of filamin A repeats 14–16

International Nuclear Information System (INIS)

Aguda, Adeleke Halilu; Sakwe, Amos Malle; Rask, Lars; Robinson, Robert Charles

2007-01-01

The crystallization and crystallographic data analysis of filamin repeats 14–16 are reported. Human filamin A is a 280 kDa protein involved in actin-filament cross-linking. It is structurally divided into an actin-binding headpiece (ABD) and a rod domain containing 24 immunoglobulin-like (Ig) repeats. A fragment of human filamin A (Ig repeats 14–16) was cloned and expressed in Escherichia coli and the purified protein was crystallized in 1.6 M ammonium sulfate, 2% PEG 1000 and 100 mM HEPES pH 7.5. The crystals diffracted to 1.95 Å and belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 50.63, b = 52.10, c = 98.46 Å, α = β = γ = 90°

Selection pressure on human STR loci and its relevance in repeat expansion disease

KAUST Repository

Shimada, Makoto K.; Sanbonmatsu, Ryoko; Yamaguchi-Kabata, Yumi; Yamasaki, Chisato; Suzuki, Yoshiyuki; Chakraborty, Ranajit; Gojobori, Takashi; Imanishi, Tadashi

2016-01-01

Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat

The 1.7 Å resolution structure of At2g44920, a pentapeptide-repeat protein in the thylakoid lumen of Arabidopsis thaliana

International Nuclear Information System (INIS)

Ni, Shuisong; McGookey, Michael E.; Tinch, Stuart L.; Jones, Alisha N.; Jayaraman, Seetharaman; Tong, Liang; Kennedy, Michael A.

2011-01-01

The crystal structure of At2g44920, a pentapeptide repeat protein (PRP) from Arabidopsis thaliana, has been determined at 1.7 Å resolution. The structure represents the first PRP protein whose subcellular localization has been experimentally confirmed to be the thylakoid lumen of a plant species. At2g44920 belongs to a diverse family (Pfam PF00805) of pentapeptide-repeat proteins (PRPs) that are present in all known organisms except yeast. PRPs contain at least eight tandem-repeating sequences of five amino acids with an approximate consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Recent crystal structures show that PRPs adopt a highly regular four-sided right-handed β-helical structure consisting mainly of type II and type IV β-turns, sometimes referred to as a repeated five-residue (or Rfr) fold. Among sequenced genomes, PRP genes are most abundant in cyanobacteria, leading to speculation that PRPs play an important role in the unique lifestyle of photosynthetic cyanobacteria. Despite the recent structural characterization of several cyanobacterial PRPs, most of their functions remain unknown. Plants, whose chloroplasts are of cyanobacterial origin, have only four PRP genes in their genomes. At2g44920 is one of three PRPs located in the thylakoid lumen. Here, the crystal structure of a double methionine mutant of residues 81–224 of At2g44920, the naturally processed fragment of one of its full-length isoforms, is reported at 1.7 Å resolution. The structure of At2g44920 consists of the characteristic Rfr fold with five uninterrupted coils made up of 25 pentapeptide repeats and α-helical elements capping both termini. A disulfide bridge links the two α-helices with a conserved loop between the helical elements at its C-terminus. This structure represents the first structure of a PRP protein whose subcellular location has been experimentally confirmed to be the thylakoid lumen in a plant species

Chemical synthesis of the tetrasaccharide repeating unit of the O-polysaccharide isolated from Azospirillum brasilense SR80.

Science.gov (United States)

Sarkar, Vikramjit; Mukhopadhyay, Balaram

2015-04-10

A linear strategy has been developed for the synthesis of the tetrasaccharide repeating unit of the O-polysaccharide from Azospirillum brasilense SR80. Stepwise glycosylation of the rationally protected thioglycoside donors activated by NIS in the presence of La(OTf)3 furnished the target tetrasaccharide. The glycosylation reactions resulted in the formation of the desired linkage with absolute stereoselectivity and afforded the required derivatives in good to excellent yields. The phthalimido group has been used as the precursor of the desired acetamido group to meet the requirement of 1,2-trans glycosidic linkage. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparison of the carboxy-terminal DP-repeat region in the co-chaperones Hop and Hip.

Science.gov (United States)

Nelson, Gregory M; Huffman, Holly; Smith, David F

2003-01-01

Functional steroid receptor complexes are assembled and maintained by an ordered pathway of interactions involving multiple components of the cellular chaperone machinery. Two of these components, Hop and Hip, serve as co-chaperones to the major heat shock proteins (Hsps), Hsp70 and Hsp90, and participate in intermediate stages of receptor assembly. In an effort to better understand the functions of Hop and Hip in the assembly process, we focused on a region of similarity located near the C-terminus of each co-chaperone. Contained within this region is a repeated sequence motif we have termed the DP repeat. Earlier mutagenesis studies implicated the DP repeat of either Hop or Hip in Hsp70 binding and in normal assembly of the co-chaperones with progesterone receptor (PR) complexes. We report here that the DP repeat lies within a protease-resistant domain that extends to or is near the C-terminus of both co-chaperones. Point mutations in the DP repeats render the C-terminal regions hypersensitive to proteolysis. In addition, a Hop DP mutant displays altered proteolytic digestion patterns, which suggest that the DP-repeat region influences the folding of other Hop domains. Although the respective DP regions of Hop and Hip share sequence and structural similarities, they are not functionally interchangeable. Moreover, a double-point mutation within the second DP-repeat unit of Hop that converts this to the sequence found in Hip disrupts Hop function; however, the corresponding mutation in Hip does not alter its function. We conclude that the DP repeats are important structural elements within a C-terminal domain, which is important for Hop and Hip function.

Unit cell geometry of 3-D braided structures

Science.gov (United States)

Du, Guang-Wu; Ko, Frank K.

1993-01-01

The traditional approach used in modeling of composites reinforced by three-dimensional (3-D) braids is to assume a simple unit cell geometry of a 3-D braided structure with known fiber volume fraction and orientation. In this article, we first examine 3-D braiding methods in the light of braid structures, followed by the development of geometric models for 3-D braids using a unit cell approach. The unit cell geometry of 3-D braids is identified and the relationship of structural parameters such as yarn orientation angle and fiber volume fraction with the key processing parameters established. The limiting geometry has been computed by establishing the point at which yarns jam against each other. Using this factor makes it possible to identify the complete range of allowable geometric arrangements for 3-D braided preforms. This identified unit cell geometry can be translated to mechanical models which relate the geometrical properties of fabric preforms to the mechanical responses of composite systems.

Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.

Science.gov (United States)

Chen, C M; Wang, C T; Wang, C J; Ho, C H; Kao, Y Y; Chen, C C

1997-12-01

Two tandemly repeated telomere-associated sequences, NP3R and NP4R, have been isolated from Nicotiana plumbaginifolia. The length of a repeating unit for NP3R and NP4R is 165 and 180 nucleotides respectively. The abundance of NP3R, NP4R and telomeric repeats is, respectively, 8.4 x 10(4), 6 x 10(3) and 1.5 x 10(6) copies per haploid genome of N. plumbaginifolia. Fluorescence in situ hybridization revealed that NP3R is located at the ends and/or in interstitial regions of all 10 chromosomes and NP4R on the terminal regions of three chromosomes in the haploid genome of N. plumbaginifolia. Sequence homology search revealed that not only are NP3R and NP4R homologous to HRS60 and GRS, respectively, two tandem repeats isolated from N. tabacum, but that NP3R and NP4R are also related to each other, suggesting that they originated from a common ancestral sequence. The role of these repeated sequences in chromosome healing is discussed based on the observation that two to three copies of a telomere-similar sequence were present in each repeating unit of NP3R and NP4R.

Characterization of α-isopropylmalate synthases containing different copy numbers of tandem repeats in Mycobacterium tuberculosis

Directory of Open Access Journals (Sweden)

Palittapongarnpim Prasit

2009-06-01

Full Text Available Abstract Background Alpha-isopropylmalate synthase (α-IPMS is the key enzyme that catalyzes the first committed step in the leucine biosynthetic pathway. The gene encoding α-IPMS in Mycobacterium tuberculosis, leuA, is polymorphic due to the insertion of 57-bp repeat units referred to as Variable Number of Tandem Repeats (VNTR. The role of the VNTR found within the M. tuberculosis genome is unclear. To investigate the role of the VNTR in leuA, we compared two α-IPMS proteins with different numbers of amino acid repeats, one with two copies and the other with 14 copies. We have cloned leuA with 14 copies of the repeat units into the pET15b expression vector with a His6-tag at the N-terminus, as was previously done for the leuA gene with two copies of the repeat units. Results The recombinant His6-α-IPMS proteins with two and 14 copies (α-IPMS-2CR and α-IPMS-14CR, respectively of the repeat units were purified by immobilized metal ion affinity chromatography and gel filtration. Both enzymes were found to be dimers by gel filtration. Both enzymes work well at pH values of 7–8.5 and temperatures of 37–42°C. However, α-IPMS-14CR tolerates pH values and temperatures outside of this range better than α-IPMS-2CR does. α-IPMS-14CR has higher affinity than α-IPMS-2CR for the two substrates, α-ketoisovalerate and acetyl CoA. Furthermore, α-IPMS-2CR was feedback inhibited by the end product l-leucine, whereas α-IPMS-14CR was not. Conclusion The differences in the kinetic properties and the l-leucine feedback inhibition between the two M. tuberculosis α-IPMS proteins containing low and high numbers of VNTR indicate that a large VNTR insertion affects protein structure and function. Demonstration of l-leucine binding to α-IPMS-14CR would confirm whether or not α-IPMS-14CR responds to end-product feedback inhibition.

Structural analyses of the Ankyrin Repeat Domain of TRPV6 and related TRPV ion channels†‡

OpenAIRE

Phelps, Christopher B.; Huang, Robert J.; Lishko, Polina V.; Wang, Ruiqi R.; Gaudet, Rachelle

2008-01-01

Transient Receptor Potential (TRP) proteins are cation channels composed of a transmembrane domain flanked by large N- and C-terminal cytoplasmic domains. All members of the vanilloid family of TRP channels (TRPV) possess an N-terminal ankyrin repeat domain (ARD). The ARD of mammalian TRPV6, an important regulator of calcium uptake and homeostasis, is essential for channel assembly and regulation. The 1.7 Å crystal structure of the TRPV6-ARD reveals conserved structural elements unique to the...

Effects of Repeated Growing Season Prescribed Fire on the Structure and Composition of Pine–Hardwood Forests in the Southeastern Piedmont, USA

Directory of Open Access Journals (Sweden)

Matthew J. Reilly

2016-12-01

Full Text Available We examined the effects of repeated growing season prescribed fire on the structure and composition of mixed pine–hardwood forests in the southeastern Piedmont region, Georgia, USA. Plots were burned two to four times over an eight-year period with low intensity surface fires during one of four six-week long periods from early April to mid-September. Density of saplings (0.25–11.6 cm diameter at breast height was significantly reduced after one or two fires during the first four-year period. Sapling density declined with additional burning over the next four years, but density of mesic hardwoods including sweetgum (Liquidambar styraciflua and red maple (Acer rubrum remained relatively high (~865 stems ha−1. Repeated burning had little effect on density or basal area of trees (≥11.7 cm dbh and changes in overstory structure were limited to small increases in the quadratic mean diameter of all trees and pines. We found little evidence to suggest differential effects on structure or composition due to timing of burn within the growing season. Although repeated growing season burning alters midstory structure and composition, burning alone is unlikely to result in immediate shifts in overstory composition or structure in mixed pine–hardwood forests of the southeastern Piedmont region.

A novel rat genomic simple repeat DNA with RNA-homology shows triplex (H-DNA)-like structure and tissue-specific RNA expression

International Nuclear Information System (INIS)

Dey, Indranil; Rath, Pramod C.

2005-01-01

Mammalian genome contains a wide variety of repetitive DNA sequences of relatively unknown function. We report a novel 227 bp simple repeat DNA (3.3 DNA) with a d {(GA) 7 A (AG) 7 } dinucleotide mirror repeat from the rat (Rattus norvegicus) genome. 3.3 DNA showed 75-85% homology with several eukaryotic mRNAs due to (GA/CU) n dinucleotide repeats by nBlast search and a dispersed distribution in the rat genome by Southern blot hybridization with [ 32 P]3.3 DNA. The d {(GA) 7 A (AG) 7 } mirror repeat formed a triplex (H-DNA)-like structure in vitro. Two large RNAs of 9.1 and 7.5 kb were detected by [ 32 P]3.3 DNA in rat brain by Northern blot hybridization indicating expression of such simple sequence repeats at RNA level in vivo. Further, several cDNAs were isolated from a rat cDNA library by [ 32 P]3.3 DNA probe. Three such cDNAs showed tissue-specific RNA expression in rat. pRT 4.1 cDNA showed strong expression of a 2.39 kb RNA in brain and spleen, pRT 5.5 cDNA showed strong expression of a 2.8 kb RNA in brain and a 3.9 kb RNA in lungs, and pRT 11.4 cDNA showed weak expression of a 2.4 kb RNA in lungs. Thus, genomic simple sequence repeats containing d (GA/CT) n dinucleotides are transcriptionally expressed and regulated in rat tissues. Such d (GA/CT) n dinucleotide repeats may form structural elements (e.g., triplex) which may be sites for functional regulation of genomic coding sequences as well as RNAs. This may be a general function of such transcriptionally active simple sequence repeats widely dispersed in mammalian genome

The Pentapeptide Repeat Proteins

OpenAIRE

Vetting, Matthew W.; Hegde, Subray S.; Fajardo, J. Eduardo; Fiser, Andras; Roderick, Steven L.; Takiff, Howard E.; Blanchard, John S.

2006-01-01

The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S,T,A,V][D,N][L,F]-[S,T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Myc...

Structural analysis of the exopolysaccharide produced by Streptococcus thermophilus ST1 solely by NMR spectroscopy

International Nuclear Information System (INIS)

Saewen, Elin; Huttunen, Eine; Zhang Xue; Yang Zhennai; Widmalm, Goeran

2010-01-01

The use of lactic acid bacteria in fermentation of milk results in favorable physical and rheological properties due to in situ exopolysaccharide (EPS) production. The EPS from S. thermophilus ST1 produces highly viscous aqueous solutions and its structure has been investigated by NMR spectroscopy. Notably, all aspects of the elucidation of its primary structure including component analysis and absolute configuration of the constituent monosaccharides were carried out by NMR spectroscopy. An array of techniques was utilized including, inter alia, PANSY and NOESY-HSQC TILT experiments. The EPS is composed of hexasaccharide repeating units with the following structure: → 3)[α-d-Glcp-(1 → 4)]-β-d-Galp-(1 → 4)-β-d-Glcp-(1 → 4)[β-d-Galf-(1 → 6)]-β-d-Glcp-(1 → 6)-β-d-Glcp-(1 → , in which the residues in square brackets are terminal groups substituting backbone sugar residues that consequently are branch-points in the repeating unit of the polymer. Thus, the EPS consists of a backbone of four sugar residues with two terminal sugar residues making up two side-chains of the repeating unit. The molecular mass of the polymer was determined using translational diffusion experiments which resulted in M w = 62 kDa, corresponding to 64 repeating units in the EPS.

Creation and structure determination of an artificial protein with three complete sequence repeats

Energy Technology Data Exchange (ETDEWEB)

Adachi, Motoyasu, E-mail: adachi.motoyasu@jaea.go.jp; Shimizu, Rumi; Kuroki, Ryota [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Blaber, Michael [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Florida State University, Tallahassee, FL 32306-4300 (United States)

2013-11-01

An artificial protein with three complete sequence repeats was created and the structure was determined by X-ray crystallography. The structure showed threefold symmetry even though there is an amino- and carboxy-terminal. The artificial protein with threefold symmetry may be useful as a scaffold to capture small materials with C3 symmetry. Symfoil-4P is a de novo protein exhibiting the threefold symmetrical β-trefoil fold designed based on the human acidic fibroblast growth factor. First three asparagine–glycine sequences of Symfoil-4P are replaced with glutamine–glycine (Symfoil-QG) or serine–glycine (Symfoil-SG) sequences protecting from deamidation, and His-Symfoil-II was prepared by introducing a protease digestion site into Symfoil-QG so that Symfoil-II has three complete repeats after removal of the N-terminal histidine tag. The Symfoil-QG and SG and His-Symfoil-II proteins were expressed in Eschericha coli as soluble protein, and purified by nickel affinity chromatography. Symfoil-II was further purified by anion-exchange chromatography after removing the HisTag by proteolysis. Both Symfoil-QG and Symfoil-II were crystallized in 0.1 M Tris-HCl buffer (pH 7.0) containing 1.8 M ammonium sulfate as precipitant at 293 K; several crystal forms were observed for Symfoil-QG and II. The maximum diffraction of Symfoil-QG and II crystals were 1.5 and 1.1 Å resolution, respectively. The Symfoil-II without histidine tag diffracted better than Symfoil-QG with N-terminal histidine tag. Although the crystal packing of Symfoil-II is slightly different from Symfoil-QG and other crystals of Symfoil derivatives having the N-terminal histidine tag, the refined crystal structure of Symfoil-II showed pseudo-threefold symmetry as expected from other Symfoils. Since the removal of the unstructured N-terminal histidine tag did not affect the threefold structure of Symfoil, the improvement of diffraction quality of Symfoil-II may be caused by molecular characteristics of

Confinement and the Glass Transition Temperature in Supported Polymer Films: Molecular Weight, Repeat Unit Modification, and Cooperativity Length Scale Investigations

Science.gov (United States)

Mundra, Manish K.

2005-03-01

It is well known that the glass transition temperatures, Tgs, of supported polystyrene (PS) films decrease dramatically with decreasing film thickness below 60-80 nm. However, a detailed understanding of the cause of this effect is lacking. We have investigated the impact of several parameters, including polymer molecular weight (MW), repeat unit structure, and the length scale of cooperatively rearranging regions in bulk. There is no significant effect of PS MW on the Tg-confinement effect over a range of 5,000 to 3,000,000 g/mol. In contrast, the strength of the Tg reduction and the onset of the confinement effect increase dramatically upon changing the polymer from PS to poly(4-tert-butylstyrene) (PTBS), with PTBS exhibiting a Tg reduction relative to bulk at a thickness of 300-400 nm. PTBS also shows a Tg reduction relative to bulk of 47 K in a 21-nm-thick film, more than twice that observed in a PS film of identical thickness. Characterization of the length scale of cooperatively rearranging regions has been done by differential scanning calorimetry but reveals at best a limited correlation with the confinement effect.

Convergent synthesis of a tetrasaccharide repeating unit of the O-specific polysaccharide from the cell wall lipopolysaccharide of Azospirillum brasilense strain Sp7

Directory of Open Access Journals (Sweden)

Pintu Kumar Mandal

2014-01-01

Full Text Available A straightforward convergent synthesis has been carried out for the tetrasaccharide repeating unit of the O-specific cell wall lipopolysaccharide of the strain Sp7 of Azospirillum brasilense. The target tetrasaccharide has been synthesized from suitably protected monosaccharide intermediates in 42% overall yield in seven steps by using a [2 + 2] block glycosylation approach.

Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms

Energy Technology Data Exchange (ETDEWEB)

Zhu, Haizhong; Lee, Han Youl; Tong, Yufeng; Hong, Bum-Soo; Kim, Kyung-Phil; Shen, Yang; Lim, Kyung Jik; Mackenzie, Farrell; Tempel, Wolfram; Park, Hee-Won (SGC-Toronto); (PPCS); (Toronto)

2012-10-23

Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form 'a carboxylate clamp' with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins.

Parsimonious Structural Equation Models for Repeated Measures Data, with Application to the Study of Consumer Preferences

Science.gov (United States)

Elrod, Terry; Haubl, Gerald; Tipps, Steven W.

2012-01-01

Recent research reflects a growing awareness of the value of using structural equation models to analyze repeated measures data. However, such data, particularly in the presence of covariates, often lead to models that either fit the data poorly, are exceedingly general and hard to interpret, or are specified in a manner that is highly data…

Crystal structure of the Xpo1p nuclear export complex bound to the SxFG/PxFG repeats of the nucleoporin Nup42p.

Science.gov (United States)

Koyama, Masako; Hirano, Hidemi; Shirai, Natsuki; Matsuura, Yoshiyuki

2017-10-01

Xpo1p (yeast CRM1) is the major nuclear export receptor that carries a plethora of proteins and ribonucleoproteins from the nucleus to cytoplasm. The passage of the Xpo1p nuclear export complex through nuclear pore complexes (NPCs) is facilitated by interactions with nucleoporins (Nups) containing extensive repeats of phenylalanine-glycine (so-called FG repeats), although the precise role of each Nup in the nuclear export reaction remains incompletely understood. Here we report structural and biochemical characterization of the interactions between the Xpo1p nuclear export complex and the FG repeats of Nup42p, a nucleoporin localized at the cytoplasmic face of yeast NPCs and has characteristic SxFG/PxFG sequence repeat motif. The crystal structure of Xpo1p-PKI-Nup42p-Gsp1p-GTP complex identified three binding sites for the SxFG/PxFG repeats on HEAT repeats 14-20 of Xpo1p. Mutational analyses of Nup42p showed that the conserved serines and prolines in the SxFG/PxFG repeats contribute to Xpo1p-Nup42p binding. Our structural and biochemical data suggest that SxFG/PxFG-Nups such as Nup42p and Nup159p at the cytoplasmic face of NPCs provide high-affinity docking sites for the Xpo1p nuclear export complex in the terminal stage of NPC passage and that subsequent disassembly of the nuclear export complex facilitates recycling of free Xpo1p back to the nucleus. © 2017 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Spatial and temporal repeatability in parasite community structure of tropical fish hosts.

Science.gov (United States)

Vidal-Martínez, V M; Poulin, R

2003-10-01

An assessment is made of the repeatability of parasite community structure in space for a marine fish, and in space and time for a freshwater fish from south-eastern Mexico. The marine fish species was the red grouper, Epinephelus morio (collected from 9 localities), and the freshwater species was the cichlid, Cichlasoma urophthalmus (collected from 6 localities: including monthly at 2 localities for 1 year, and bimonthly at 1 locality in 1990 and 1999). Pairwise interspecific associations and analyses of nested patterns in the distributions of parasite species among hosts were used in both fish species, with comparisons over time made only with the cichlid. Positive interspecific associations, and nested patterns were noted in some localities for both fish species, and/or at some sampling times for the cichlid fish. However, non-random patterns in the structure of parasite communities in these 2 host species only were observed sporadically. When present, nestedness in both fish species was apparently linked with a positive association between total infection intensities and fish size. Additionally, adjacent localities were more likely to display similar parasite community structure than distant ones. This preliminary result suggests that distance between localities is an important determinant of predictability in parasite community structure.

Disruption of Higher Order DNA Structures in Friedreich's Ataxia (GAA)(n) Repeats by PNA or LNA Targeting

DEFF Research Database (Denmark)

Bergquist, Helen; Rocha, Cristina S. J.; Alvarez-Asencio, Ruben

2016-01-01

Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigen...

Structural Evaluation of the Second Oldest Glued-Laminated Structure in the United States

Science.gov (United States)

Douglas R. Rammer; Jorge de Melo Moura

2013-01-01

The second glued-laminated structure built in the United States was constructed at the USDA Forest Products Laboratory (FPL) in 1934 to demonstrate the performance of wooden arch buildings. After decades of use the structure was decommissioned in 2010. Shortly after construction, researchers structurally evaluated the glued-laminated arch structure for uniform loading...

Molecular analysis of the eTG trinucleotide repeat in South African ...

African Journals Online (AJOL)

-4 When amplified, this trinucleotide repeat is responsible for DNA instability and molecular pathology. A similar mechanism of trinucleotide repeat expansion has been described in fragile X mental retardation syndrome. (CGG):·· spinobulbar muscular atrophy (CAG)' and, more. MRC Human Ecogenetics Research Unit, ...

Structural Performance of the Second Oldest Glued-Laminated Structure in the United States

Science.gov (United States)

Douglas R. Rammer; Jorge de Melo Moura; Robert J. Ross

2014-01-01

The second glued-laminated structure built in the United States was constructed at the USDA Forest Products Laboratory (FPL) in 1934 to demonstrate the performance of wooden arch buildings. After 75 years of use the structure was decommissioned in 2010. Shortly after construction, researchers structurally evaluated the glued-laminated arch structure for uniform loading...

A formalism for scattering of complex composite structures. I. Applications to branched structures of asymmetric sub-units

DEFF Research Database (Denmark)

Svaneborg, Carsten; Pedersen, Jan Skov

2012-01-01

to structural connectivity is completely decoupled from internal structure of the sub-units. This allows sub-units to be replaced by more complex structures. We illustrate the physical interpretation of the formalism diagrammatically. By applying a self-consistency requirement, we derive the pair distributions...

Optimization of sequence alignment for simple sequence repeat regions

Directory of Open Access Journals (Sweden)

Ogbonnaya Francis C

2011-07-01

Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae.

Science.gov (United States)

Albornos, Lucía; Martín, Ignacio; Iglesias, Rebeca; Jiménez, Teresa; Labrador, Emilia; Dopico, Berta

2012-11-07

Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40

Structural analysis of the exopolysaccharide produced by Streptococcus thermophilus ST1 solely by NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Saewen, Elin [Arrhenius Laboratory, Stockholm University, Department of Organic Chemistry (Sweden); Huttunen, Eine; Zhang Xue [University of Helsinki, Department of Food Technology (Finland); Yang Zhennai [Northeast Agricultural Research Center of China, Center of Agro-food Technology (China); Widmalm, Goeran, E-mail: gw@organ.su.s [Arrhenius Laboratory, Stockholm University, Department of Organic Chemistry (Sweden)

2010-06-15

The use of lactic acid bacteria in fermentation of milk results in favorable physical and rheological properties due to in situ exopolysaccharide (EPS) production. The EPS from S. thermophilus ST1 produces highly viscous aqueous solutions and its structure has been investigated by NMR spectroscopy. Notably, all aspects of the elucidation of its primary structure including component analysis and absolute configuration of the constituent monosaccharides were carried out by NMR spectroscopy. An array of techniques was utilized including, inter alia, PANSY and NOESY-HSQC TILT experiments. The EPS is composed of hexasaccharide repeating units with the following structure: {yields} 3)[{alpha}-d-Glcp-(1 {yields} 4)]-{beta}-d-Galp-(1 {yields} 4)-{beta}-d-Glcp-(1 {yields} 4)[{beta}-d-Galf-(1 {yields} 6)]-{beta}-d-Glcp-(1 {yields} 6)-{beta}-d-Glcp-(1 {sup {yields}}, in which the residues in square brackets are terminal groups substituting backbone sugar residues that consequently are branch-points in the repeating unit of the polymer. Thus, the EPS consists of a backbone of four sugar residues with two terminal sugar residues making up two side-chains of the repeating unit. The molecular mass of the polymer was determined using translational diffusion experiments which resulted in M{sub w} = 62 kDa, corresponding to 64 repeating units in the EPS.

Patterns and predictors of repeat fecal immunochemical and occult blood test screening in four large health care systems in the United States.

Science.gov (United States)

Singal, Amit G; Corley, Douglas A; Kamineni, Aruna; Garcia, Michael; Zheng, Yingye; Doria-Rose, Paul V; Quinn, Virginia P; Jensen, Christopher D; Chubak, Jessica; Tiro, Jasmin; Doubeni, Chyke A; Ghai, Nirupa R; Skinner, Celette Sugg; Wernli, Karen; Halm, Ethan A

2018-02-27

Effectiveness of fecal occult blood test (FOBT) for colorectal cancer (CRC) screening depends on annual testing, but little is known about patterns of repeat stool-based screening within different settings. Our study's objective was to characterize screening patterns and identify factors associated with repeat screening among patients who completed an index guaiac FOBT (gFOBT) or fecal immunochemical test (FIT). We performed a multi-center retrospective cohort study among people who completed a FOBT between January 2010 and December 2011 to characterize repeat screening patterns over the subsequent 3 years. We studied at 4 large health care delivery systems in the United States. Logistic regression analyses were used to identify factors associated with repeat screening patterns. We included individuals aged 50-71 years who completed an index FOBT and had at least 3 years of follow-up. We excluded people with a history of CRC, colonoscopy within 10 years or flexible sigmoidoscopy within 5 years before the index test, or positive index stool test. Consistent screening was defined as repeat FOBT within every 15 months and inconsistent screening as repeat testing at least once during follow-up but less than consistent screening. Among 959,857 eligible patients who completed an index FIT or gFOBT, 344,103 had three years of follow-up and met inclusion criteria. Of these, 46.6% had consistent screening, 43.4% inconsistent screening, and 10% had no repeat screening during follow-up. Screening patterns varied substantially across healthcare systems, with consistent screening proportions ranging from 1 to 54.3% and no repeat screening proportions ranging from 6.9 to 42.8%. Higher consistent screening proportions were observed in health systems with screening outreach and in-reach programs, whereas the safety-net health system, which uses opportunistic clinic-based screening, had the lowest consistent screening. Consistent screening increased with older age but was less

Structural racism and myocardial infarction in the United States

OpenAIRE

Lukachko, Alicia; Hatzenbuehler, Mark L.; Keyes, Katherine M.

2014-01-01

There is a growing research literature suggesting that racism is an important risk factor undermining the health of Blacks in the United States. Racism can take many forms, ranging from interpersonal interactions to institutional/structural conditions and practices. Existing research, however, tends to focus on individual forms of racial discrimination using self-report measures. Far less attention has been paid to whether structural racism may disadvantage the health of Blacks in the United ...

R-loops: targets for nuclease cleavage and repeat instability.

Science.gov (United States)

Freudenreich, Catherine H

2018-01-11

R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.

Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase

Energy Technology Data Exchange (ETDEWEB)

Verardi, Raffaello; Kim, Jin-Sik; Ghirlando, Rodolfo; Banerjee, Anirban

2017-09-01

DHHC enzymes catalyze palmitoylation, a major post-translational modification that regulates a number of key cellular processes. There are up to 24 DHHCs in mammals and hundreds of substrate proteins that get palmitoylated. However, how DHHC enzymes engage with their substrates is still poorly understood. There is currently no structural information about the interaction between any DHHC enzyme and protein substrates. In this study we have investigated the structural and thermodynamic bases of interaction between the ankyrin repeat domain of human DHHC17 (ANK17) and Snap25b. We solved a high-resolution crystal structure of the complex between ANK17 and a peptide fragment of Snap25b. Through structure-guided mutagenesis, we discovered key residues in DHHC17 that are critically important for interaction with Snap25b. We further extended our finding by showing that the same residues are also crucial for the interaction of DHHC17 with Huntingtin, one of its most physiologically relevant substrates.

TMPyP4 porphyrin distorts RNA G-quadruplex structures of the disease-associated r(GGGGCC)n repeat of the C9orf72 gene and blocks interaction of RNA-binding proteins.

Science.gov (United States)

Zamiri, Bita; Reddy, Kaalak; Macgregor, Robert B; Pearson, Christopher E

2014-02-21

Certain DNA and RNA sequences can form G-quadruplexes, which can affect genetic instability, promoter activity, RNA splicing, RNA stability, and neurite mRNA localization. Amyotrophic lateral sclerosis and frontotemporal dementia can be caused by expansion of a (GGGGCC)n repeat in the C9orf72 gene. Mutant r(GGGGCC)n- and r(GGCCCC)n-containing transcripts aggregate in nuclear foci, possibly sequestering repeat-binding proteins such as ASF/SF2 and hnRNPA1, suggesting a toxic RNA pathogenesis, as occurs in myotonic dystrophy. Furthermore, the C9orf72 repeat RNA was recently demonstrated to undergo the noncanonical repeat-associated non-AUG translation (RAN translation) into pathologic dipeptide repeats in patient brains, a process that is thought to depend upon RNA structure. We previously demonstrated that the r(GGGGCC)n RNA forms repeat tract length-dependent G-quadruplex structures that bind the ASF/SF2 protein. Here we show that the cationic porphyrin (5,10,15,20-tetra(N-methyl-4-pyridyl) porphyrin (TMPyP4)), which can bind some G-quadruplex-forming sequences, can bind and distort the G-quadruplex formed by r(GGGGCC)8, and this ablates the interaction of either hnRNPA1 or ASF/SF2 with the repeat. These findings provide proof of concept that nucleic acid binding small molecules, such as TMPyP4, can distort the secondary structure of the C9orf72 repeat, which may beneficially disrupt protein interactions, which may ablate either protein sequestration and/or RAN translation into potentially toxic dipeptides. Disruption of secondary structure formation of the C9orf72 RNA repeats may be a viable therapeutic avenue, as well as a means to test the role of RNA structure upon RAN translation.

Identification, variation and transcription of pneumococcal repeat sequences

Science.gov (United States)

2011-01-01

Background Small interspersed repeats are commonly found in many bacterial chromosomes. Two families of repeats (BOX and RUP) have previously been identified in the genome of Streptococcus pneumoniae, a nasopharyngeal commensal and respiratory pathogen of humans. However, little is known about the role they play in pneumococcal genetics. Results Analysis of the genome of S. pneumoniae ATCC 700669 revealed the presence of a third repeat family, which we have named SPRITE. All three repeats are present at a reduced density in the genome of the closely related species S. mitis. However, they are almost entirely absent from all other streptococci, although a set of elements related to the pneumococcal BOX repeat was identified in the zoonotic pathogen S. suis. In conjunction with information regarding their distribution within the pneumococcal chromosome, this suggests that it is unlikely that these repeats are specialised sequences performing a particular role for the host, but rather that they constitute parasitic elements. However, comparing insertion sites between pneumococcal sequences indicates that they appear to transpose at a much lower rate than IS elements. Some large BOX elements in S. pneumoniae were found to encode open reading frames on both strands of the genome, whilst another was found to form a composite RNA structure with two T box riboswitches. In multiple cases, such BOX elements were demonstrated as being expressed using directional RNA-seq and RT-PCR. Conclusions BOX, RUP and SPRITE repeats appear to have proliferated extensively throughout the pneumococcal chromosome during the species' past, but novel insertions are currently occurring at a relatively slow rate. Through their extensive secondary structures, they seem likely to affect the expression of genes with which they are co-transcribed. Software for annotation of these repeats is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/strep_repeats/. PMID:21333003

On balanced minimal repeated measurements designs

Directory of Open Access Journals (Sweden)

Shakeel Ahmad Mir

2014-10-01

Full Text Available Repeated Measurements designs are concerned with scientific experiments in which each experimental unit is assigned more than once to a treatment either different or identical. This class of designs has the property that the unbiased estimators for elementary contrasts among direct and residual effects are obtainable. Afsarinejad (1983 provided a method of constructing balanced Minimal Repeated Measurements designs p < t , when t is an odd or prime power, one or more than one treatment may occur more than once in some sequences and  designs so constructed no longer remain uniform in periods. In this paper an attempt has been made to provide a new method to overcome this drawback. Specifically, two cases have been considered                RM[t,n=t(t-t/(p-1,p], λ2=1 for balanced minimal repeated measurements designs and  RM[t,n=2t(t-t/(p-1,p], λ2=2 for balanced  repeated measurements designs. In addition , a method has been provided for constructing              extra-balanced minimal designs for special case RM[t,n=t2/(p-1,p], λ2=1.

Short consensus repeat domains extend the E-selectin structure in order to grab cells out of flow

KAUST Repository

Aleisa, Fajr A

2017-01-08

Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. They are composed of an N-terminal extracellular C-type lectin like domain, followed by an Endothelial Growth Factor like domain (EGF), a defined number of short consensus repeats SCR (also called “sushi” domains), a transmembrane domain and a C-terminal cytoplasmic tail. The adhesion of cells (expressing ligands) to the endothelium (expressing the selection i.e., E-selectin) occurs through the interaction between the lectin domain of selectins and sLeX presenting ligands. Structural/function studies to date have mainly focused on investigating the influence of the lectin domain of E-selectin on its ability to bind its ligands while other domains received less atention. We prepared a number of different recombinant E-selectin proteins with changes in the SCR units. Specifically we generated wild-type E-selectin proteins as monomeric or dimeric structures, mutant proteins with varied numbers of SCRs as well as proteins where strategic residues were mutated to change the conformation of the selectin. Using a novel real time immunoprecipitation surface plasmon resonance (SPR)-based in vitro binding study developed in our lab, the interaction of recombinant E-selectin proteins with immunoprecipitated endogenous ligands (i.e. CD44) captured on a CM-5 chip was assessed. These studies provided quantitative binding kinetics with on and off rates of selectin-ligand interactions and suggested that robust binding is dependent on the presence of the SCRs and oligomerization. These results provide significant implications on the functional mechanism of E-selectin binding to its ligands.

Short consensus repeat domains extend the E-selectin structure in order to grab cells out of flow

KAUST Repository

Aleisa, Fajr A; Sakashita, Kosuke; Lee, Jaeman; Abu Samra, Dina Bashir Kamil; Habuchi, Satoshi; Kusakabe, Takahiro; Merzaban, Jasmeen

2017-01-01

Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. They are composed of an N-terminal extracellular C-type lectin like domain, followed by an Endothelial Growth Factor like domain (EGF), a defined number of short consensus repeats SCR (also called “sushi” domains), a transmembrane domain and a C-terminal cytoplasmic tail. The adhesion of cells (expressing ligands) to the endothelium (expressing the selection i.e., E-selectin) occurs through the interaction between the lectin domain of selectins and sLeX presenting ligands. Structural/function studies to date have mainly focused on investigating the influence of the lectin domain of E-selectin on its ability to bind its ligands while other domains received less atention. We prepared a number of different recombinant E-selectin proteins with changes in the SCR units. Specifically we generated wild-type E-selectin proteins as monomeric or dimeric structures, mutant proteins with varied numbers of SCRs as well as proteins where strategic residues were mutated to change the conformation of the selectin. Using a novel real time immunoprecipitation surface plasmon resonance (SPR)-based in vitro binding study developed in our lab, the interaction of recombinant E-selectin proteins with immunoprecipitated endogenous ligands (i.e. CD44) captured on a CM-5 chip was assessed. These studies provided quantitative binding kinetics with on and off rates of selectin-ligand interactions and suggested that robust binding is dependent on the presence of the SCRs and oligomerization. These results provide significant implications on the functional mechanism of E-selectin binding to its ligands.

Exploring overlapping functional units with various structure in protein interaction networks.

Directory of Open Access Journals (Sweden)

Xiao-Fei Zhang

Full Text Available Revealing functional units in protein-protein interaction (PPI networks are important for understanding cellular functional organization. Current algorithms for identifying functional units mainly focus on cohesive protein complexes which have more internal interactions than external interactions. Most of these approaches do not handle overlaps among complexes since they usually allow a protein to belong to only one complex. Moreover, recent studies have shown that other non-cohesive structural functional units beyond complexes also exist in PPI networks. Thus previous algorithms that just focus on non-overlapping cohesive complexes are not able to present the biological reality fully. Here, we develop a new regularized sparse random graph model (RSRGM to explore overlapping and various structural functional units in PPI networks. RSRGM is principally dominated by two model parameters. One is used to define the functional units as groups of proteins that have similar patterns of connections to others, which allows RSRGM to detect non-cohesive structural functional units. The other one is used to represent the degree of proteins belonging to the units, which supports a protein belonging to more than one revealed unit. We also propose a regularizer to control the smoothness between the estimators of these two parameters. Experimental results on four S. cerevisiae PPI networks show that the performance of RSRGM on detecting cohesive complexes and overlapping complexes is superior to that of previous competing algorithms. Moreover, RSRGM has the ability to discover biological significant functional units besides complexes.

Repeated Causal Decision Making

Science.gov (United States)

Hagmayer, York; Meder, Bjorn

2013-01-01

Many of our decisions refer to actions that have a causal impact on the external environment. Such actions may not only allow for the mere learning of expected values or utilities but also for acquiring knowledge about the causal structure of our world. We used a repeated decision-making paradigm to examine what kind of knowledge people acquire in…

Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH.

Science.gov (United States)

Kippert, Fred; Gerloff, Dietlind L

2009-09-24

HEAT and ARM repeats occur in a large number of eukaryotic proteins. As these repeats are often highly diverged, the prediction of HEAT or ARM domains can be challenging. Except for the most clear-cut cases, identification at the individual repeat level is indispensable, in particular for determining domain boundaries. However, methods using single sequence queries do not have the sensitivity required to deal with more divergent repeats and, when applied to proteins with known structures, in some cases failed to detect a single repeat. Testing algorithms which use multiple sequence alignments as queries, we found two of them, HHpred and COACH, to detect HEAT and ARM repeats with greatly enhanced sensitivity. Calibration against experimentally determined structures suggests the use of three score classes with increasing confidence in the prediction, and prediction thresholds for each method. When we applied a new protocol using both HHpred and COACH to these structures, it detected 82% of HEAT repeats and 90% of ARM repeats, with the minimum for a given protein of 57% for HEAT repeats and 60% for ARM repeats. Application to bona fide HEAT and ARM proteins or domains indicated that similar numbers can be expected for the full complement of HEAT/ARM proteins. A systematic screen of the Protein Data Bank for false positive hits revealed their number to be low, in particular for ARM repeats. Double false positive hits for a given protein were rare for HEAT and not at all observed for ARM repeats. In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries. A protocol is presented for the identification of individual HEAT or ARM repeats which is straightforward to implement. It provides high

Substantiation of Structure of Adaptive Control Systems for Motor Units

Science.gov (United States)

Ovsyannikov, S. I.

2018-05-01

The article describes the development of new electronic control systems, in particular motor units, for small-sized agricultural equipment. Based on the analysis of traffic control systems, the main course of development of the conceptual designs of motor units has been defined. The systems aimed to control the course motion of the motor unit in automatic mode using the adaptive systems have been developed. The article presents structural models of the conceptual motor units based on electrically controlled systems by the operation of drive motors and adaptive systems that make the motor units completely automated.

Structural racism and myocardial infarction in the United States

Science.gov (United States)

Lukachko, Alicia; Hatzenbuehler, Mark L.; Keyes, Katherine M.

2014-01-01

There is a growing research literature suggesting that racism is an important risk factor undermining the health of Blacks in the United States. Racism can take many forms, ranging from interpersonal interactions to institutional/structural conditions and practices. Existing research, however, tends to focus on individual forms of racial discrimination using self-report measures. Far less attention has been paid to whether structural racism may disadvantage the health of Blacks in the United States. The current study addresses gaps in the existing research by using novel measures of structural racism and by explicitly testing the hypothesis that structural racism is a risk factor for myocardial infarction among Blacks in the United States. State-level indicators of structural racism included four domains: (1) political participation; (2) employment and job status; (3) educational attainment; and (4) judicial treatment. State-level racial disparities across these domains were proposed to represent the systematic exclusion of Blacks from resources and mobility in society. Data on past-year myocardial infarction were obtained from the National Epidemiologic Survey on Alcohol and Related Conditions (non-Hispanic Black: N = 8245; non-Hispanic White: N = 24,507), a nationally representative survey of the U.S. civilian, non-institutionalized population aged 18 and older. Models were adjusted for individual-level confounders (age, sex, education, household income, medical insurance) as well as for state-level disparities in poverty. Results indicated that Blacks living in states with high levels of structural racism were generally more likely to report past-year myocardial infarction than Blacks living in low-structural racism states. Conversely, Whites living in high structural racism states experienced null or lower odds of myocardial infarction compared to Whites living in low-structural racism states. These results raise the provocative possibility that structural

Structural racism and myocardial infarction in the United States.

Science.gov (United States)

Lukachko, Alicia; Hatzenbuehler, Mark L; Keyes, Katherine M

2014-02-01

There is a growing research literature suggesting that racism is an important risk factor undermining the health of Blacks in the United States. Racism can take many forms, ranging from interpersonal interactions to institutional/structural conditions and practices. Existing research, however, tends to focus on individual forms of racial discrimination using self-report measures. Far less attention has been paid to whether structural racism may disadvantage the health of Blacks in the United States. The current study addresses gaps in the existing research by using novel measures of structural racism and by explicitly testing the hypothesis that structural racism is a risk factor for myocardial infarction among Blacks in the United States. State-level indicators of structural racism included four domains: (1) political participation; (2) employment and job status; (3) educational attainment; and (4) judicial treatment. State-level racial disparities across these domains were proposed to represent the systematic exclusion of Blacks from resources and mobility in society. Data on past-year myocardial infarction were obtained from the National Epidemiologic Survey on Alcohol and Related Conditions (non-Hispanic Black: N = 8245; non-Hispanic White: N = 24,507), a nationally representative survey of the U.S. civilian, non-institutionalized population aged 18 and older. Models were adjusted for individual-level confounders (age, sex, education, household income, medical insurance) as well as for state-level disparities in poverty. Results indicated that Blacks living in states with high levels of structural racism were generally more likely to report past-year myocardial infarction than Blacks living in low-structural racism states. Conversely, Whites living in high structural racism states experienced null or lower odds of myocardial infarction compared to Whites living in low-structural racism states. These results raise the provocative possibility that structural

Expression, purification and preliminary biochemical and structural characterization of the leucine rich repeat namesake domain of leucine rich repeat kinase 2.

Science.gov (United States)

Vancraenenbroeck, Renée; Lobbestael, Evy; Weeks, Stephen D; Strelkov, Sergei V; Baekelandt, Veerle; Taymans, Jean-Marc; De Maeyer, Marc

2012-03-01

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease. Much research effort has been directed towards the catalytic core region of LRRK2 composed of GTPase (ROC, Ras of complex proteins) and kinase domains and a connecting COR (C-terminus of ROC) domain. In contrast, the precise functions of the protein-protein interaction domains, such as the leucine-rich repeat (LRR) domain, are not known. In the present study, we modeled the LRRK2 LRR domain (LRR(LRRK2)) using a template assembly approach, revealing the presence of 14 LRRs. Next, we focused on the expression and purification of LRR(LRRK2) in Escherichia coli. Buffer optimization revealed that the protein requires the presence of a zwitterionic detergent, namely Empigen BB, during solubilization and the subsequent purification and characterization steps. This indicates that the detergent captures the hydrophobic surface patches of LRR(LRRK2) thereby suppressing its aggregation. Circular dichroism (CD) spectroscopy measured 18% α-helices and 21% β-sheets, consistent with predictions from the homology model. Size exclusion chromatography (SEC) and dynamic light scattering measurements showed the presence of a single species, with a Stokes radius corresponding to the model dimensions of a protein monomer. Furthermore, no obvious LRR(LRRK2) multimerization was detected via cross-linking studies. Finally, the LRR(LRRK2) clinical mutations did not influence LRR(LRRK2) secondary, tertiary or quaternary structure as determined via SEC and CD spectroscopy. We therefore conclude that these mutations are likely to affect putative LRR(LRRK2) inter- and intramolecular interactions. Copyright © 2011 Elsevier B.V. All rights reserved.

Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

Directory of Open Access Journals (Sweden)

Hua Wan

2016-01-01

Full Text Available TAL effectors (TALEs contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE.

Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

Science.gov (United States)

Pierce, Sarah E.; Wang, Junmei; Jayawickramarajah, Janarthanan; Hamilton, Andrew D.; Brodbelt, Jennifer S.

2010-01-01

Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads. PMID:19746468

Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks.

Science.gov (United States)

Yeh, Chun-Ting; Brunette, T J; Baker, David; McIntosh-Smith, Simon; Parmeggiani, Fabio

2018-02-01

Computational protein design methods have enabled the design of novel protein structures, but they are often still limited to small proteins and symmetric systems. To expand the size of designable proteins while controlling the overall structure, we developed Elfin, a genetic algorithm for the design of novel proteins with custom shapes using structural building blocks derived from experimentally verified repeat proteins. By combining building blocks with compatible interfaces, it is possible to rapidly build non-symmetric large structures (>1000 amino acids) that match three-dimensional geometric descriptions provided by the user. A run time of about 20min on a laptop computer for a 3000 amino acid structure makes Elfin accessible to users with limited computational resources. Protein structures with controlled geometry will allow the systematic study of the effect of spatial arrangement of enzymes and signaling molecules, and provide new scaffolds for functional nanomaterials. Copyright © 2017 Elsevier Inc. All rights reserved.

Interrogating Key Positions of Size-Reduced TALE Repeats Reveals a Programmable Sensor of 5-Carboxylcytosine.

Science.gov (United States)

Maurer, Sara; Giess, Mario; Koch, Oliver; Summerer, Daniel

2016-12-16

Transcription-activator-like effector (TALE) proteins consist of concatenated repeats that recognize consecutive canonical nucleobases of DNA via the major groove in a programmable fashion. Since this groove displays unique chemical information for the four human epigenetic cytosine nucleobases, TALE repeats with epigenetic selectivity can be engineered, with potential to establish receptors for the programmable decoding of all human nucleobases. TALE repeats recognize nucleobases via key amino acids in a structurally conserved loop whose backbone is positioned very close to the cytosine 5-carbon. This complicates the engineering of selectivities for large 5-substituents. To interrogate a more promising structural space, we engineered size-reduced repeat loops, performed saturation mutagenesis of key positions, and screened a total of 200 repeat-nucleobase interactions for new selectivities. This provided insight into the structural requirements of TALE repeats for affinity and selectivity, revealed repeats with improved or relaxed selectivity, and resulted in the first selective sensor of 5-carboxylcytosine.

DNA Replication Dynamics of the GGGGCC Repeat of the C9orf72 Gene.

Science.gov (United States)

Thys, Ryan Griffin; Wang, Yuh-Hwa

2015-11-27

DNA has the ability to form a variety of secondary structures in addition to the normal B-form DNA, including hairpins and quadruplexes. These structures are implicated in a number of neurological diseases and cancer. Expansion of a GGGGCC repeat located at C9orf72 is associated with familial amyotrophic lateral sclerosis and frontotemporal dementia. This repeat expands from two to 24 copies in normal individuals to several hundreds or thousands of repeats in individuals with the disease. Biochemical studies have demonstrated that as little as four repeats have the ability to form a stable DNA secondary structure known as a G-quadruplex. Quadruplex structures have the ability to disrupt normal DNA processes such as DNA replication and transcription. Here we examine the role of GGGGCC repeat length and orientation on DNA replication using an SV40 replication system in human cells. Replication through GGGGCC repeats leads to a decrease in overall replication efficiency and an increase in instability in a length-dependent manner. Both repeat expansions and contractions are observed, and replication orientation is found to influence the propensity for expansions or contractions. The presence of replication stress, such as low-dose aphidicolin, diminishes replication efficiency but has no effect on instability. Two-dimensional gel electrophoresis analysis demonstrates a replication stall with as few as 20 GGGGCC repeats. These results suggest that replication of the GGGGCC repeat at C9orf72 is perturbed by the presence of expanded repeats, which has the potential to result in further expansion, leading to disease. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Repeated wildfires alter forest recovery of mixed-conifer ecosystems.

Science.gov (United States)

Stevens-Rumann, Camille; Morgan, Penelope

2016-09-01

Most models project warmer and drier climates that will contribute to larger and more frequent wildfires. However, it remains unknown how repeated wildfires alter post-fire successional patterns and forest structure. Here, we test the hypothesis that the number of wildfires, as well as the order and severity of wildfire events interact to alter forest structure and vegetation recovery and implications for vegetation management. In 2014, we examined forest structure, composition, and tree regeneration in stands that burned 1-18 yr before a subsequent 2007 wildfire. Three important findings emerged: (1) Repeatedly burned forests had 15% less woody surface fuels and 31% lower tree seedling densities compared with forests that only experienced one recent wildfire. These repeatedly burned areas are recovering differently than sites burned once, which may lead to alternative ecosystem structure. (2) Order of burn severity (high followed by low severity compared with low followed by high severity) did influence forest characteristics. When low burn severity followed high, forests had 60% lower canopy closure and total basal area with 92% fewer tree seedlings than when high burn severity followed low. (3) Time between fires had no effect on most variables measured following the second fire except large woody fuels, canopy closure and tree seedling density. We conclude that repeatedly burned areas meet many vegetation management objectives of reduced fuel loads and moderate tree seedling densities. These differences in forest structure, composition, and tree regeneration have implications not only for the trajectories of these forests, but may reduce fire intensity and burn severity of subsequent wildfires and may be used in conjunction with future fire suppression tactics. © 2016 by the Ecological Society of America.

Repeated treatments of drooling with botulinum toxin B in neurology

DEFF Research Database (Denmark)

Møller, Eigild; Daugaard, Dorthe; Holm, Ole

2015-01-01

OBJECTIVES: To investigate efficacy, saliva flow, and composition in repeated BoNT-B treatments of drooling. MATERIALS AND METHODS: Seventeen neurological patients (median 66 years), referred for treatment of drooling participated in this observational study. Median total doses of 4000 units...

Three-Dimensional Structural Aspects of Protein–Polysaccharide Interactions

Directory of Open Access Journals (Sweden)

Masamichi Nagae

2014-03-01

Full Text Available Linear polysaccharides are typically composed of repeating mono- or disaccharide units and are ubiquitous among living organisms. Polysaccharide diversity arises from chain-length variation, branching, and additional modifications. Structural diversity is associated with various physiological functions, which are often regulated by cognate polysaccharide-binding proteins. Proteins that interact with linear polysaccharides have been identified or developed, such as galectins and polysaccharide-specific antibodies, respectively. Currently, data is accumulating on the three-dimensional structure of polysaccharide-binding proteins. These proteins are classified into two types: exo-type and endo-type. The former group specifically interacts with the terminal units of polysaccharides, whereas the latter with internal units. In this review, we describe the structural aspects of exo-type and endo-type protein-polysaccharide interactions. Further, we discuss the structural basis for affinity and specificity enhancement in the face of inherently weak binding interactions.

75 FR 11936 - Unit Structures LLC, Magnolia, AR; Notice of Termination of Investigation

Science.gov (United States)

2010-03-12

... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-70,367] Unit Structures LLC, Magnolia, AR; Notice of Termination of Investigation Pursuant to Section 223 of the Trade Act of 1974, as... Arkansas Rapid Response Coordinator on behalf of workers of Unit Structures LLC, Magnolia, Arkansas. The...

Electronic Band Structure of Helical Polyisocyanides.

Science.gov (United States)

Champagne, Benoît; Liégeois, Vincent; Fripiat, Joseph G; Harris, Frank E

2017-10-19

Restricted Hartree-Fock computations are reported for a methyl isocyanide polymer (repeating unit -C═N-CH 3 ), whose most stable conformation is expected to be a helical chain. The computations used a standard contracted Gaussian orbital set at the computational levels STO-3G, 3-21G, 6-31G, and 6-31G**, and studies were made for two line-group configurations motivated by earlier work and by studies of space-filling molecular models: (1) A structure of line-group symmetry L9 5 , containing a 9-fold screw axis with atoms displaced in the axial direction by 5/9 times the lattice constant, and (2) a structure of symmetry L4 1 that had been proposed, containing a 4-fold screw axis with translation by 1/4 of the lattice constant. Full use of the line-group symmetry was employed to cause most of the computational complexity to depend only on the size of the asymmetric repeating unit. Data reported include computed bond properties, atomic charge distribution, longitudinal polarizability, band structure, and the convoluted density of states. Most features of the description were found to be insensitive to the level of computational approximation. The work also illustrates the importance of exploiting line-group symmetry to extend the range of polymer structural problems that can be treated computationally.

Prevalence of Huntington's disease gene CAG trinucleotide repeat alleles in patients with bipolar disorder.

Science.gov (United States)

Ramos, Eliana Marisa; Gillis, Tammy; Mysore, Jayalakshmi S; Lee, Jong-Min; Alonso, Isabel; Gusella, James F; Smoller, Jordan W; Sklar, Pamela; MacDonald, Marcy E; Perlis, Roy H

2015-06-01

Huntington's disease is a neurodegenerative disorder characterized by motor, cognitive, and psychiatric symptoms that are caused by huntingtin gene (HTT) CAG trinucleotide repeat alleles of 36 or more units. A greater than expected prevalence of incompletely penetrant HTT CAG repeat alleles observed among individuals diagnosed with major depressive disorder raises the possibility that another mood disorder, bipolar disorder, could likewise be associated with Huntington's disease. We assessed the distribution of HTT CAG repeat alleles in a cohort of individuals with bipolar disorder. HTT CAG allele sizes from 2,229 Caucasian individuals diagnosed with DSM-IV bipolar disorder were compared to allele sizes in 1,828 control individuals from multiple cohorts. We found that HTT CAG repeat alleles > 35 units were observed in only one of 4,458 chromosomes from individuals with bipolar disorder, compared to three of 3,656 chromosomes from control subjects. These findings do not support an association between bipolar disorder and Huntington's disease. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The development of the micro-solid propellant thruster array with improved repeatability

International Nuclear Information System (INIS)

Seo, Daeban; Kwon, Sejin; Lee, Jongkwang

2012-01-01

This paper presents the development of a micro-solid propellant thruster array with improved repeatability. The repeatability and low performance variation of each thruster unit with a high ignition success rate is essential in micro-solid propellant thruster array. To date, the study on the improvement of the repeatability has not yet been reported. As the first step for this study, we propose a new type of micro igniter, using a glass wafer called the heater-contact micro igniter. This igniter is also designed to improve the ignition characteristics of a glass-based micro igniter. The prototype of the igniter array is designed and fabricated to establish its fabrication process and to conduct its performance evaluation. Through the firing test, the performance of the heater-contact micro igniter is verified. The 5 × 5 sized micro-solid propellant thruster array is designed and fabricated applying the developed heater-contact igniter. The measured average thrust of each thruster unit is 2.542 N, and calculated standard deviation is 0.369 N. The calculated average total impulse and its standard deviation are 0.182 and 0.04 mNs, respectively. Based on these results, the improvement of repeatability is verified. Finally, the ignition control system of the micro-thruster array is developed. (paper)

Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

Science.gov (United States)

Zagoskin, Maxim V.; Lazareva, Valentina I.; Grishanin, Andrey K.; Mukha, Dmitry V.

2014-01-01

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals. PMID:25215300

[Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].

Science.gov (United States)

Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian

2009-11-01

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

Analysis of CR1 Repeats in the Zebra Finch Genome

Directory of Open Access Journals (Sweden)

George E. Liu

2013-06-01

Full Text Available Most bird species have smaller genomes and fewer repeats than mammals. Chicken Repeat 1 (CR1 repeat is one of the most abundant families of repeats, ranging from ~133,000 to ~187,000 copies accounting for ~50 to ~80% of the interspersed repeats in the zebra finch and chicken genomes, respectively. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to multiple CR1 subfamilies in the chicken. In this study, we performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the zebra finch genome. We identified and validated 34 CR1 subfamilies and further analyzed the correlation between these subfamilies. We also discovered 4 novel lineage-specific CR1 subfamilies in the zebra finch when compared to the chicken genome. We built various evolutionary trees of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.

[Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella].

Science.gov (United States)

Wang, Pengfei; Wang, Yingfang; Duan, Guangcai; Xue, Zerun; Wang, Linlin; Guo, Xiangjiao; Yang, Haiyan; Xi, Yuanlin

2015-04-01

This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.

Acinetobacter baumannii K27 and K44 capsular polysaccharides have the same K unit but different structures due to the presence of distinct wzy genes in otherwise closely related K gene clusters.

Science.gov (United States)

Shashkov, Alexander S; Kenyon, Johanna J; Senchenkova, Sof'ya N; Shneider, Mikhail M; Popova, Anastasiya V; Arbatsky, Nikolay P; Miroshnikov, Konstantin A; Volozhantsev, Nikolay V; Hall, Ruth M; Knirel, Yuriy A

2016-05-01

Capsular polysaccharides (CPSs), from Acinetobacter baumannii isolates 1432, 4190 and NIPH 70, which have related gene content at the K locus, were examined, and the chemical structures established using 2D(1)H and(13)C NMR spectroscopy. The three isolates produce the same pentasaccharide repeat unit, which consists of 5-N-acetyl-7-N-[(S)-3-hydroxybutanoyl] (major) or 5,7-di-N-acetyl (minor) derivatives of 5,7-diamino-3,5,7,9-tetradeoxy-D-glycero-D-galacto-non-2-ulosonic (legionaminic) acid (Leg5Ac7R), D-galactose, N-acetyl-D-galactosamine and N-acetyl-D-glucosamine. However, the linkage between repeat units in NIPH 70 was different to that in 1432 and 4190, and this significantly alters the CPS structure. The KL27 gene cluster in 4190 and KL44 gene cluster in NIPH 70 are organized identically and contain lga genes for Leg5Ac7R synthesis, genes for the synthesis of the common sugars, as well as anitrA2 initiating transferase and four glycosyltransferases genes. They share high-level nucleotide sequence identity for corresponding genes, but differ in the wzy gene encoding the Wzy polymerase. The Wzy proteins, which have different lengths and share no similarity, would form the unrelated linkages in the K27 and K44 structures. The linkages formed by the four shared glycosyltransferases were predicted by comparison with gene clusters that synthesize related structures. These findings unambiguously identify the linkages formed by WzyK27 and WzyK44, and show that the presence of different wzy genes in otherwise closely related K gene clusters changes the structure of the CPS. This may affect its capacity as a protective barrier for A. baumannii. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

9 CFR 98.16 - The embryo collection unit.

Science.gov (United States)

2010-01-01

... impervious to moisture and constructed of materials that can withstand repeated cleaning and disinfection. If... materials that can withstand repeated cleaning and disinfection. If the outdoor area also has walls or a... withstand repeated cleaning and disinfection. (c) Embryo processing area. The embryo collection unit must...

Thermal stability of chicken brain {alpha}-spectrin repeat 17: a spectroscopic study

Energy Technology Data Exchange (ETDEWEB)

Brenner, Annette K. [University of Bergen, Department of Chemistry (Norway); Kieffer, Bruno [Ecole Superieure de Biotechnologie de Strasbourg, IGBMC Biomolecular NMR Group, CNRS UMR 7104 (France); Trave, Gilles [Ecole Superieure de Biotechnologie de Strasbourg, Equipe Oncoproteines, IREBS, UMR 7242 (France); Froystein, Nils Age [University of Bergen, Department of Chemistry (Norway); Raae, Arnt J., E-mail: arnt.raae@mbi.uib.no [University of Bergen, Department of Molecular Biology (Norway)

2012-06-15

Spectrin is a rod-like multi-modular protein that is mainly composed of triple-helical repeats. These repeats show very similar 3D-structures but variable conformational and thermodynamical stabilities, which may be of great importance for the flexibility and dynamic behaviour of spectrin in the cell. For instance, repeat 17 (R17) of the chicken brain spectrin {alpha}-chain is four times less stable than neighbouring repeat 16 (R16) in terms of Increment G. The structure of spectrin repeats has mainly been investigated by X-ray crystallography, but the structures of a few repeats, e.g. R16, have also been determined by NMR spectroscopy. Here, we undertook a detailed characterization of the neighbouring R17 by NMR spectroscopy. We assigned most backbone resonances and observed NOE restraints, relaxation values and coupling constants that all indicated that the fold of R17 is highly similar to that of R16, in agreement with previous X-ray analysis of a tandem repeat of the two domains. However, {sup 15}N heteronuclear NMR spectra measured at different temperatures revealed particular features of the R17 domain that might contribute to its lower stability. Conformational exchange appeared to alter the linker connecting R17 to R16 as well as the BC-loop in close proximity. In addition, heat-induced splitting was observed for backbone resonances of a few spatially related residues including V99 of helix C, which in R16 is replaced by the larger hydrophobic tryptophan residue that is relatively conserved among other spectrin repeats. These data support the view that the substitution of tryptophan by valine at this position may contribute to the lower stability of R17.

Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.

Science.gov (United States)

Hindle, K Lauren; Bella, Jordi; Lovell, Simon C

2009-11-01

Leucine-rich repeat (LRR) proteins form a large and diverse family. They have a wide range of functions most of which involve the formation of protein-protein interactions. All known LRR structures form curved solenoids, although there is large variation in their curvature. It is this curvature that determines the shape and dimensions of the inner space available for ligand binding. Unfortunately, large-scale parameters such as the overall curvature of a protein domain are extremely difficult to predict. Here, we present a quantitative analysis of determinants of curvature of this family. Individual repeats typically range in length between 20 and 30 residues and have a variety of secondary structures on their convex side. The observed curvature of the LRR domains correlates poorly with the lengths of their individual repeats. We have, therefore, developed a scoring function based on the secondary structure of the convex side of the protein that allows prediction of the overall curvature with a high degree of accuracy. We also demonstrate the effectiveness of this method in selecting a suitable template for comparative modeling. We have developed an automated, quantitative protocol that can be used to predict accurately the curvature of leucine-rich repeat proteins of unknown structure from sequence alone. This protocol is available as an online resource at http://www.bioinf.manchester.ac.uk/curlrr/.

Defining structural and functional dimensions of the extracellular thyrotropin receptor region.

Science.gov (United States)

Kleinau, Gunnar; Mueller, Sandra; Jaeschke, Holger; Grzesik, Paul; Neumann, Susanne; Diehl, Anne; Paschke, Ralf; Krause, Gerd

2011-06-24

The extracellular region of the thyrotropin receptor (TSHR) can be subdivided into the leucine-rich repeat domain (LRRD) and the hinge region. Both the LRRD and the hinge region interact with thyrotropin (TSH) or autoantibodies. Structural data for the TSHR LRRD were previously determined by crystallization (amino acids Glu(30)-Thr(257), 10 repeats), but the structure of the hinge region is still undefined. Of note, the amino acid sequence (Trp(258)-Tyr(279)) following the crystallized LRRD comprises a pattern typical for leucine-rich repeats with conserved hydrophobic side chains stabilizing the repeat fold. Moreover, functional data for amino acids between the LRRD and the transmembrane domain were fragmentary. We therefore investigated systematically these TSHR regions by mutagenesis to reveal insights into their functional contribution and potential structural features. We found that mutations of conserved hydrophobic residues between Thr(257) and Tyr(279) cause TSHR misfold, which supports a structural fold of this peptide, probably as an additional leucine-rich repeat. Furthermore, we identified several new mutations of hydrophilic amino acids in the entire hinge region leading to partial TSHR inactivation, indicating that these positions are important for intramolecular signal transduction. In summary, we provide new information regarding the structural features and functionalities of extracellular TSHR regions. Based on these insights and in context with previous results, we suggest an extracellular activation mechanism that supports an intramolecular agonistic unit as a central switch for activating effects at the extracellular region toward the serpentine domain.

Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup Repeat Specificity

DEFF Research Database (Denmark)

Vognsen, Tina Reinholdt; Möller, Ingvar Rúnar; Kristensen, Ole

2013-01-01

Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat...... peptide. Despite high structural similarity, the FxFG binding site is located between two alpha helices in the G3BP1 NTF2-like domain and not at the dimer interface as observed for nuclear transport factor 2. ITC studies showed specificity towards the FxFG motif but not FG and GLFG motifs. The unliganded...

Adenovirus chromatin structure at different stages of infection

Energy Technology Data Exchange (ETDEWEB)

Daniell, E.; Groff, D.E.; Fedor, M.J.

1981-12-01

The authors investigated the structure of adenovirus deoxyribonecleic acid (DNA)-protein complexes in nuclei of infected cells by using micrococal nuclease. Parental (infecting) DNA was digested into multimers which had a unit fragment size that was indistinguishable from the size of the nucleosomal repeat of cellular chromatin. This pattern was maintained in parental DNA throughout infection. Similar repeating units were detected in hamster cells that were nonpermissive for human adenovirus and in cells pretreated with n-butyrate. Late in infection, the pattern of digestion of viral DNA was determined by two different experimental approaches. Nuclear DNA was electrophoresed, blotted, and hybridized with labeled viral sequences; in this procedure all virus-specific DNA was detected. This technique revealed a diffuse protected band of viral DNA that was smaller than 160 base pairs, but no discrete multimers. All regions of the genome were represented in the protected DNA. To examine the nuclease protection of newly replicated viral DNA, infected cells were labeled with (/sup 3/)thymidine after blocking of cellular DNA synthesis but not viral DNA synthesis. With this procedure they identified a repeating unit which was distinctly different from the cellular nucleosomal repeat. The authors found broad bands with midpoints at 200, 400, and 600 base pairs, as well as the limit digest material revealed by blotting. High-resolution acrylamide gel electrophoresis revealed that the viral species comprised a series of closely spaced bands ranging in size from less than 30 to 250 base pairs.

Investigation on Mechanical Properties’ Anisotropy of Rod Units in Lattice Structures Fabricated by Selective Laser Melting

Directory of Open Access Journals (Sweden)

Jing Chenchen

2017-01-01

Full Text Available Lattice structure with high strength and low mass using selective laser melting (SLM has been a hot topic. However, there are some problems in the fabrication of lattice structure by SLM. Rod unit is the basic component of lattice structure and its performance affects the whole structure. It is necessary to investigate the influence of selective laser melting on rod unit’s mechanical properties. A series of rod units with different inclination angle and diameter were fabricated by SLM in this research. And the mechanical properties of these units were measured by tensile test. The results show that the rod units with different diameters and inclination angles have good mechanical properties and show no difference. It is a good news for lattice structure designing for there is no necessary to consider the mechanical properties’ anisotropy of rod units.

Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae).

Science.gov (United States)

Wang, Q Z; Huang, M; Downie, S R; Chen, Z X

2016-05-23

Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family.

TALEN-Induced Double-Strand Break Repair of CTG Trinucleotide Repeats

Directory of Open Access Journals (Sweden)

Valentine Mosbach

2018-02-01

Full Text Available Trinucleotide repeat expansions involving CTG/CAG triplets are responsible for several neurodegenerative disorders, including myotonic dystrophy and Huntington’s disease. Because expansions trigger the disease, contracting repeat length could be a possible approach to gene therapy for these disorders. Here, we show that a TALEN-induced double-strand break was very efficient at contracting expanded CTG repeats in yeast. We show that RAD51, POL32, and DNL4 are dispensable for double-strand break repair within CTG repeats, the only required genes being RAD50, SAE2, and RAD52. Resection was totally abolished in the absence of RAD50 on both sides of the break, whereas it was reduced in a sae2Δ mutant on the side of the break containing the longest repeat tract, suggesting that secondary structures at double-strand break ends must be removed by the Mre11-Rad50 complex and Sae2. Following the TALEN double-strand break, single-strand annealing occurred between both sides of the repeat tract, leading to repeat contraction.

Structural Vulnerability and Health: Latino Migrant Laborers in the United States

Science.gov (United States)

Quesada, James; Hart, Laurie K.; Bourgois, Philippe

2011-01-01

Latino immigrants in the United States constitute a paradigmatic case of a population group subject to structural violence. Their subordinated location in the global economy and their culturally depreciated status in the United States are exacerbated by legal persecution. Medical Anthropology Volume 30, issues 4 and 5, include a series of ethnographic analyses of the processes that render undocumented Latino immigrants structurally vulnerable to ill-health. We hope to extend the social science concept of ‘structural vulnerability’ to make it a useful tool for health care. Defined as a positionality that imposes physical/emotional suffering on specific population groups and individuals in patterned ways, structural vulnerability is a product of two complementary forces: (1) class-based economic exploitation and cultural, gender/sexual, and racialized discrimination; and (2) processes of symbolic violence and subjectivity formation that have increasingly legitimized punitive neoliberal discourses of individual unworthiness. PMID:21777121

Tandemly repeated sequence in 5'end of mtDNA control region of ...

African Journals Online (AJOL)

STORAGESEVER

2008-12-17

Dec 17, 2008 ... chain reaction (PCR). Japanese Spanish ... mainly covered general ecology and fishery biology. No study concerning the ... Conserved sequence blocks and the repeat units are indicated by boxes. performed using the exact ...

The Disruptive Effect of Lysozyme on the Bacterial Cell Wall Explored by an "In-Silico" Structural Outlook

Science.gov (United States)

Primo, Emiliano D.; Otero, Lisandro H.; Ruiz, Francisco; Klinke, Sebastián; Giordano, Walter

2018-01-01

The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall…

The Role of the Repeat in the Bear Feast in Traditional Khanty Culture

Directory of Open Access Journals (Sweden)

Anna A. Grinevich (Zorkoltseva

2012-09-01

Full Text Available This paper is devoted to a role of repeat in Khanty folklore. Songs of a bear feast have served as the source material for the research. The author traces the role of a repeat at different text levels: structure, lexical level, and plot. The repeat is proposed as a fundamental method of traditional Khanty arts.

The relationship between CA repeat polymorphism of the IGF-1 gene and the structure of motor skills in young athletes.

Science.gov (United States)

Karpowicz, Krzysztof; Krych, Katarzyna; Karpowicz, Małgorzata; Nowak, Witold; Gronek, Piotr

2018-01-01

The map of candidate genes that can potentially affect physical fitness becomes larger every year, and they are associated with such aspects as respiratory and cardiovascular stability; body build and composition - especially muscle mass and strength; carbohydrate and lipid metabolism; response to training; and exercise intolerance.The aim of this study was to analyze the relationship between the CA repeat polymorphism of the P1 promoter of the IGF1 gene and the structure of motor skills in the two groups of Polish young athletes in 2007-2009. In this study, 350 young sportsmen representing different sports disciplines were examined (age = 15.5 ± 0.5 years), by genotyping the IGF1 gene and determining the structure of motor skills using the International Physical Fitness Test (IPFT) battery. The multiple stepwise regression was used to determine the impact of the investigated motor skills on the indicator of the overall physical fitness, measured by the total score of the International Physical Fitness Test (IPFT). The analysis showed some regularity related to the character of the IGF1 gene polymorphism. It can be concluded that the two groups of young boys athletes practicing various sports disciplines (kinds of physical exercise) displayed similar associations between CA repeat polymorphism of the P1 promoter of the IGF1 gene and the level of motor effects. Our results suggest that this polymorphism may be a genetic marker of the physical performance phenotype. We demonstrated that CA repeat polymorphism of the P1 promoter of the IGF1 gene was associated with strength predispositions in the homozygous and non-carriers groups. In the group who were heterozygous it was speed-strength aptitudes.

A TALE-inspired computational screen for proteins that contain approximate tandem repeats.

Science.gov (United States)

Perycz, Malgorzata; Krwawicz, Joanna; Bochtler, Matthias

2017-01-01

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.

RNA structure alignment by a unit-vector approach.

Science.gov (United States)

Capriotti, Emidio; Marti-Renom, Marc A

2008-08-15

The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

Characterization of Dutch Staphylococcus aureus from bovine mastitis using a Multiple Locus Variable Number Tandem Repeat Analysis

NARCIS (Netherlands)

Ikawaty, R.; Brouwer, E.C.; Jansen, M.D.; Duijkeren, van E.; Mevius, D.J.; Verhoef, J.; Fluit, A.C.

2009-01-01

Current typing methods for Staphylococcus aureus have important drawbacks. We evaluated a Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) scheme with 6 loci which lacks most drawbacks on 85 bovine mastitis isolates from The Netherlands. For each locus the number of repeat units (RU) was

Diverticular disease of the colon does not increase risk of repeat C. difficile infection.

Science.gov (United States)

Feuerstadt, Paul; Das, Rohit; Brandt, Lawrence J

2013-01-01

Studies have suggested that colonic diverticulosis might increase the likelihood of repeat Clostridium difficile infection (CDI). Our study was designed to compare rates of repeat infection in patients with and without colon diverticula. Patients who had a positive C. difficile toxin assay and colonoscopic evidence of diverticulosis were classified as CDI and diverticulosis (CDI-D), whereas those with a positive toxin assay but no such colonoscopic evidence were classified as CDI and no diverticulosis (CDI-ND). Various clinical and epidemiologic factors were recorded for each patient. Primary outcomes were "relapse" (repeat CDI within 3 mo of initial infection) and "recurrent" infection (repeat CDI≥3 mo after initial infection). Secondary outcomes 30 days after diagnosis were mortality, intensive care unit transfer, and continuous hospitalization. A total of 128 patients were classified as CDI-D, whereas 137 had CDI-ND. There were no significant differences between CDI-D and CDI-ND when comparing frequencies of repeat infection and its subclassifications, relapse or recurrence. There were, however, statistical associations seen between diverticulosis of the ascending colon and increased recurrence rates [hazard ratio (HR): 1.4±0.38, Pdiverticular disease of the descending (HR: 0.40±0.46, Pcolon (HR: 0.39±0.49, Pcolon association is limited by a small patient population. There were no significant differences in any of the 30-day outcomes including intensive care unit requirement, hospitalization stay, or mortality. Patients with diverticular disease of the colon are not at increased risk of repeat CDI.

Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz

International Nuclear Information System (INIS)

Bundle, D.R.; Cherwonogrodzky, J.W.; Perry, M.B.

1987-01-01

The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-α-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers of the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz 1 H and 125-MHz 13 C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent β-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-lined 4,6-dideoxy-4-formamido-α-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-α-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants

Effects of repeated growing season prescribed fire on the structure and composition of pine-hardwood forests in the southeastern Piedmont, USA

Science.gov (United States)

Matthew Reilly; Kenneth Outcalt; Joseph O’Brien; Dale Wade

2016-01-01

We examined the effects of repeated growing season prescribed fire on the structure and composition of mixed pine–hardwood forests in the southeastern Piedmont region, Georgia, USA. Plots were burned two to four times over an eight-year period with low intensity surface fires during one of four six-week long periods from early April to mid-September. Density...

Additively Manufactured Open-Cell Porous Biomaterials Made from Six Different Space-Filling Unit Cells : The Mechanical and Morphological Properties

NARCIS (Netherlands)

Ahmadi, S.M.; Yavari, S.A.; Wauthle, R.; Pouran, B.; Schrooten, J.; Weinans, H.; Zadpoor, A.A.

2015-01-01

It is known that the mechanical properties of bone-mimicking porous biomaterials are a function of the morphological properties of the porous structure, including the configuration and size of the repeating unit cell from which they are made. However, the literature on this topic is limited,

Structural organization of glycophorin A and B genes: Glycophorin B gene evolved by homologous recombination at Alu repeat sequences

International Nuclear Information System (INIS)

Kudo, Shinichi; Fukuda, Minoru

1989-01-01

Glycophorins A (GPA) and B (GPB) are two major sialoglycoproteins of the human erythrocyte membrane. Here the authors present a comparison of the genomic structures of GPA and GPB developed by analyzing DNA clones isolated from a K562 genomic library. Nucleotide sequences of exon-intron junctions and 5' and 3' flanking sequences revealed that the GPA and GPB genes consist of 7 and 5 exons, respectively, and both genes have >95% identical sequence from the 5' flanking region to the region ∼ 1 kilobase downstream from the exon encoding the transmembrane regions. In this homologous part of the genes, GPB lacks one exon due to a point mutation at the 5' splicing site of the third intron, which inactivates the 5' cleavage event of splicing and leads to ligation of the second to the fourth exon. Following these very homologous sequences, the genomic sequences for GPA and GPB diverge significantly and no homology can be detected in their 3' end sequences. The analysis of the Alu sequences and their flanking direct repeat sequences suggest that an ancestral genomic structure has been maintained in the GPA gene, whereas the GPB gene has arisen from the acquisition of 3' sequences different from those of the GPA gene by homologous recombination at the Alu repeats during or after gene duplication

Structure of long terminal repeats of transcriptionally active and inactive copies of Drosophila mobile dispersed genetic elements mdg3

International Nuclear Information System (INIS)

Dzhumagaliev, E.B.; Mazo, A.N.; Baev, A.A. Jr.; Gorelova, T.V.; Arkhipova, I.R.; Shuppe, N.G.; Il'in, Yu.V.

1986-01-01

The authors have determined the nucleotide sequences of long terminal repeats (LTRS) and adjacent regions in the transcribed and nontranscribed variants of the mobile dispersed gene mdg3. In its main characteristics the mdg3 is similar to other mdg. Its integration into chromosomal DNA brings about duplication of the 4 bp of the host DNA, no specificity of the mdg integration at the nucleotide level being detected. The mdg3 is flanked by a 5 bp inverted repeat. The variations in the length of the LTR in different mdg copies is mainly due to duplication of certain sequences in the U3 and R regions. mdg3 copies with a LTR length of 267 bp are the most abundant and are completely conservative in their primary structure. They are transcribed in the cells of the 67J25D culture, but not transcribed in the K/sub c/ line, where another mdg3 variant with a LTR length of 293 bp is transcriptionally active. The SI mapping of transcription initiation and termination sites has shown that in both mdg3 variants they are localized in the same LTR regions, and that the LTR itself has a characteristic U3-R-U5 structure-like retroviral LTRs. The possible factors involved in the regulation of mdg transcription are discussed

Children's Conceptions of Bullying and Repeated Conventional Transgressions: Moral, Conventional, Structuring and Personal-Choice Reasoning

Science.gov (United States)

Thornberg, Robert; Thornberg, Ulrika Birberg; Alamaa, Rebecca; Daud, Noor

2016-01-01

This study examined 307 elementary school children's judgements and reasoning about bullying and other repeated transgressions when school rules regulating these transgressions have been removed in hypothetical school situations. As expected, children judged bullying (repeated moral transgressions) as wrong independently of rules and as more wrong…

The effect of repeated testing vs repeated practice on skills learning in undergraduate dental education.

Science.gov (United States)

Sennhenn-Kirchner, S; Goerlich, Y; Kirchner, B; Notbohm, M; Schiekirka, S; Simmenroth, A; Raupach, T

2018-02-01

Recent studies in undergraduate medical education have demonstrated the advantage of repeated testing over repeated practice with regard to knowledge and skills retention. The aim of this study was to investigate whether this "testing effect" also applies to skills retention in undergraduate dental education. In this prospective, randomised controlled trial, fourth-year dental students at Göttingen University Medical Centre participated in a training session on surgical suturing in winter term 2014/2015. Following this, they were either assigned to two sessions of additional skills training (group A) or two sessions of skills assessment with feedback (group B). These sessions were spaced over a period of 4 weeks. Skills retention was assessed in a summative objective structured clinical examination (OSCE) at the end of term, that is 6 months after the initial teaching session. A total of 32 students completed the study. With regard to suturing, OSCE performance was significantly better in group B than group A (81.9±13.1% vs 63.0±15.4%; P=0.001; Cohen's d=1.33). There was no significant OSCE performance difference in the two groups with regard to other learning objectives that were addressed in the end-of-term examination. Thus, the group difference was specific to suturing skills. This is the first study to demonstrate that in dental education, repeated testing produces more favourable skills retention than repeated practice. Test-enhanced learning might be a viable concept for skills retention in undergraduate dentistry education. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

How unit level nursing responsibilities are structured in US hospitals.

Science.gov (United States)

Minnick, Ann F; Mion, Lorraine C; Johnson, Mary E; Catrambone, Cathy

2007-10-01

To describe (1) the extent to which acute and intensive care units use the elements of nursing models (team, functional, primary, total patient care, patient-focused care, case management) and (2) the deployment of non-unit-based personnel resources. The lack of current data-based behavioral descriptions of the extent to which elements of nursing models are implemented makes it difficult to determine how work models may influence outcomes. Nurse managers of 56 intensive care units and 80 acute care adult units from 40 randomly selected US hospitals participated in a structured interview regarding (1) day-shift use of patient assignment behaviors associated with nursing models and (2) the availability and consistency of assignment of non-unit-based support personnel. No model was implemented fully. Almost all intensive care units reported similar assignment behaviors except in the consistency of patient assignment. Non-intensive care units demonstrated wide variation in assignment patterns. Patterns differed intra-institutionally. There were large differences in the availability and deployment of non-unit-based supportive resources. Administrators must recognize the differences in work models within their institutions as a part of any quality improvement effort. Attempts to test new work models must be rigorous in the measurement of their implementation.

Structural Characterization of Hexagonal Braiding Architecture Aided by 3D Printing

Directory of Open Access Journals (Sweden)

Li Zhengning

2018-01-01

Full Text Available Hexagonal braiding method has the advantages of high shape compatibility, interlacing density and high volume fraction. Based on hexagonal braiding method, a hexagonal preform was braided. Then, by following the characteristics of repeatability and concentricity of hexagonal braided preform, the printed geometry structure was got in order to understand and optimize geometric structure to make it more compact like the braided geometric structure. Finally, the unit cells were defined with hexagonal prism to analyze the micro-geometric structure of hexagonal braided preform.

Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms.

Science.gov (United States)

Vergara-Jaque, Ariela; Fenollar-Ferrer, Cristina; Kaufmann, Desirée; Forrest, Lucy R

2015-01-01

Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to one or other side of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (a)symmetry of these systems has been successfully used as a bioinformatic tool, called "repeat-swap modeling" to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that nucleoside transport also

Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms

Directory of Open Access Journals (Sweden)

Cristina eFenollar Ferrer

2015-09-01

Full Text Available Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to either the outside or inside of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (asymmetry of these systems has been successfully used as a bioinformatic tool, called repeat-swap modeling to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides

Directory of Open Access Journals (Sweden)

Sarkar Anita

2012-11-01

Full Text Available Abstract Background Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol. Description PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s (when applicable, experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI. It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available. Conclusion PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available

Photographers’ Nomenclature Units: A Structural and Quantitative Analysis

Directory of Open Access Journals (Sweden)

Margarita A. Mihailova

2017-11-01

Full Text Available Addressing the needs of cross and intercultural communication as well as the methodology of contrastive research, the paper presents the results of the complex analysis conducted to describe semantic and pragmatic parameters of nomenclature units denoting photography equipment in the modern Russian informal discourse of professional photographers. The research is exemplified by 34 original nomenclature units and their 34 Russian equivalents used in 6871 comments posted at “Клуб.Foto.ru” web-site in 2015. The structural and quantitative analyses of photographers’ nomenclature demonstrate the users’ morphological and graphic preferences and indirectly reflect their social and professional values. The corpus-based approach developed by Kast-Aigner (2009: 141 was applied in the study with the aim to identify the nomenclature units denoting photography equipment, validate and elaborate the data of the existing corpus. The research also throws light on the problems of professional language development and derivational processes. The perspective of the study lies in the research of the broader context of professional nomenclature.

Characterization of the Unit Tangent Sphere Bundle with $ g $-Natural Metric and Almost Contact B-metric Structure

Directory of Open Access Journals (Sweden)

Farshad Firuzi

2017-06-01

Full Text Available We consider unit tangent sphere bundle of a Riemannian manifold $ (M,g $ as a $ (2n+1 $-dimensional manifold and we equip it with pseudo-Riemannian $ g $-natural almost contact B-metric structure. Then, by computing coefficients of the structure tensor $ F$, we completely characterize the unit tangent sphere bundle equipped to this structure, with respect to the relevant classification of almost contact B-metric structures, and determine a class such that the unit tangent sphere bundle with mentioned structure belongs to it. Also, we find some curvature conditions such that the mentioned structure satisfies each of eleven basic classes.

Two-dimensional quantum repeaters

Science.gov (United States)

Wallnöfer, J.; Zwerger, M.; Muschik, C.; Sangouard, N.; Dür, W.

2016-11-01

The endeavor to develop quantum networks gave rise to a rapidly developing field with far-reaching applications such as secure communication and the realization of distributed computing tasks. This ultimately calls for the creation of flexible multiuser structures that allow for quantum communication between arbitrary pairs of parties in the network and facilitate also multiuser applications. To address this challenge, we propose a two-dimensional quantum repeater architecture to establish long-distance entanglement shared between multiple communication partners in the presence of channel noise and imperfect local control operations. The scheme is based on the creation of self-similar multiqubit entanglement structures at growing scale, where variants of entanglement swapping and multiparty entanglement purification are combined to create high-fidelity entangled states. We show how such networks can be implemented using trapped ions in cavities.

Replication Stalling and Heteroduplex Formation within CAG/CTG Trinucleotide Repeats by Mismatch Repair

KAUST Repository

Viterbo, David; Michoud, Gregoire; Mosbach, Valentine; Dujon, Bernard; Richard, Guy-Franck

2016-01-01

Trinucleotide repeat expansions are responsible for at least two dozen neurological disorders. Mechanisms leading to these large expansions of repeated DNA are still poorly understood. It was proposed that transient stalling of the replication fork by the repeat tract might trigger slippage of the newly-synthesized strand over its template, leading to expansions or contractions of the triplet repeat. However, such mechanism was never formally proven. Here we show that replication fork pausing and CAG/CTG trinucleotide repeat instability are not linked, stable and unstable repeats exhibiting the same propensity to stall replication forks when integrated in a yeast natural chromosome. We found that replication fork stalling was dependent on the integrity of the mismatch-repair system, especially the Msh2p-Msh6p complex, suggesting that direct interaction of MMR proteins with secondary structures formed by trinucleotide repeats in vivo, triggers replication fork pauses. We also show by chromatin immunoprecipitation that Msh2p is enriched at trinucleotide repeat tracts, in both stable and unstable orientations, this enrichment being dependent on MSH3 and MSH6. Finally, we show that overexpressing MSH2 favors the formation of heteroduplex regions, leading to an increase in contractions and expansions of CAG/CTG repeat tracts during replication, these heteroduplexes being dependent on both MSH3 and MSH6. These heteroduplex regions were not detected when a mutant msh2-E768A gene in which the ATPase domain was mutated was overexpressed. Our results unravel two new roles for mismatch-repair proteins: stabilization of heteroduplex regions and transient blocking of replication forks passing through such repeats. Both roles may involve direct interactions between MMR proteins and secondary structures formed by trinucleotide repeat tracts, although indirect interactions may not be formally excluded.

Replication Stalling and Heteroduplex Formation within CAG/CTG Trinucleotide Repeats by Mismatch Repair

KAUST Repository

Viterbo, David

2016-03-16

Trinucleotide repeat expansions are responsible for at least two dozen neurological disorders. Mechanisms leading to these large expansions of repeated DNA are still poorly understood. It was proposed that transient stalling of the replication fork by the repeat tract might trigger slippage of the newly-synthesized strand over its template, leading to expansions or contractions of the triplet repeat. However, such mechanism was never formally proven. Here we show that replication fork pausing and CAG/CTG trinucleotide repeat instability are not linked, stable and unstable repeats exhibiting the same propensity to stall replication forks when integrated in a yeast natural chromosome. We found that replication fork stalling was dependent on the integrity of the mismatch-repair system, especially the Msh2p-Msh6p complex, suggesting that direct interaction of MMR proteins with secondary structures formed by trinucleotide repeats in vivo, triggers replication fork pauses. We also show by chromatin immunoprecipitation that Msh2p is enriched at trinucleotide repeat tracts, in both stable and unstable orientations, this enrichment being dependent on MSH3 and MSH6. Finally, we show that overexpressing MSH2 favors the formation of heteroduplex regions, leading to an increase in contractions and expansions of CAG/CTG repeat tracts during replication, these heteroduplexes being dependent on both MSH3 and MSH6. These heteroduplex regions were not detected when a mutant msh2-E768A gene in which the ATPase domain was mutated was overexpressed. Our results unravel two new roles for mismatch-repair proteins: stabilization of heteroduplex regions and transient blocking of replication forks passing through such repeats. Both roles may involve direct interactions between MMR proteins and secondary structures formed by trinucleotide repeat tracts, although indirect interactions may not be formally excluded.

Structure and method for controlling band offset and alignment at a crystalline oxide-on-semiconductor interface

Science.gov (United States)

McKee, Rodney A.; Walker, Frederick J.

2003-11-25

A crystalline oxide-on-semiconductor structure and a process for constructing the structure involves a substrate of silicon, germanium or a silicon-germanium alloy and an epitaxial thin film overlying the surface of the substrate wherein the thin film consists of a first epitaxial stratum of single atomic plane layers of an alkaline earth oxide designated generally as (AO).sub.n and a second stratum of single unit cell layers of an oxide material designated as (A'BO.sub.3).sub.m so that the multilayer film arranged upon the substrate surface is designated (AO).sub.n (A'BO.sub.3).sub.m wherein n is an integer repeat of single atomic plane layers of the alkaline earth oxide AO and m is an integer repeat of single unit cell layers of the A'BO.sub.3 oxide material. Within the multilayer film, the values of n and m have been selected to provide the structure with a desired electrical structure at the substrate/thin film interface that can be optimized to control band offset and alignment.

DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.

Science.gov (United States)

de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

2015-11-16

Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Repeating and non-repeating fast radio bursts from binary neutron star mergers

Science.gov (United States)

Yamasaki, Shotaro; Totani, Tomonori; Kiuchi, Kenta

2018-04-01

Most fast radio bursts (FRB) do not show evidence of repetition, and such non-repeating FRBs may be produced at the time of a merger of binary neutron stars (BNS), provided that the BNS merger rate is close to the high end of the currently possible range. However, the merger environment is polluted by dynamical ejecta, which may prohibit the radio signal from propagating. We examine this by using a general-relativistic simulation of a BNS merger, and show that the ejecta appears about 1 ms after the rotation speed of the merged star becomes the maximum. Therefore there is a time window in which an FRB signal can reach outside, and the short duration of non-repeating FRBs can be explained by screening after ejecta formation. A fraction of BNS mergers may leave a rapidly rotating and stable neutron star, and such objects may be the origin of repeating FRBs like FRB 121102. We show that a merger remnant would appear as a repeating FRB on a time scale of ˜1-10 yr, and expected properties are consistent with the observations of FRB 121102. We construct an FRB rate evolution model that includes these two populations of repeating and non-repeating FRBs from BNS mergers, and show that the detection rate of repeating FRBs relative to non-repeating ones rapidly increases with improving search sensitivity. This may explain why only the repeating FRB 121102 was discovered by the most sensitive FRB search with Arecibo. Several predictions are made, including the appearance of a repeating FRB 1-10 yr after a BNS merger that is localized by gravitational waves and subsequent electromagnetic radiation.

Improving teamwork: impact of structured interdisciplinary rounds on a hospitalist unit.

Science.gov (United States)

O'Leary, Kevin J; Haviley, Corinne; Slade, Maureen E; Shah, Hiren M; Lee, Jungwha; Williams, Mark V

2011-02-01

Effective collaboration and teamwork is essential in providing safe and effective care. Research reveals deficiencies in teamwork on medical units involving hospitalists. The aim of this study was to assess the impact of an intervention, Structured Inter-Disciplinary Rounds (SIDR), on nurses' ratings of collaboration and teamwork. The study was a controlled trial involving an intervention and control hospitalist unit. The intervention, SIDR, combined a structured format for communication with a forum for regular interdisciplinary meetings. We asked nurses to rate the quality of communication and collaboration with hospitalists using a 5-point ordinal scale. We also assessed teamwork and safety climate using a validated instrument. Multivariable regression analyses were used to assess the impact on length of stay (LOS) and cost using both a concurrent and historic control. A total of 49 of 58 (84%) nurses completed surveys. A larger percentage of nurses rated the quality of communication and collaboration with hospitalists as high or very high on the intervention unit compared to the control unit (80% vs. 54%; P = 0.05). Nurses also rated the teamwork and safety climate significantly higher on the intervention unit (P = 0.008 and P = 0.03 for teamwork and safety climate, respectively). Multivariable analyses demonstrated no difference in the adjusted LOS and an inconsistent effect on cost. SIDR had a positive effect on nurses' ratings of collaboration and teamwork on a hospitalist unit, yet no impact on LOS and cost. Further study is required to assess the impact of SIDR on patient safety measures. Copyright © 2010 Society of Hospital Medicine.

Evolutionary fate of memory-one strategies in repeated prisoner's dilemma game in structured populations

Science.gov (United States)

Liu, Xu-Sheng; Wu, Zhi-Xi; Chen, Michael Z. Q.; Guan, Jian-Yue

2017-07-01

We study evolutionary spatial prisoner's dilemma game involving a one-step memory mechanism of the individuals whenever making strategy updating. In particular, during the process of strategy updating, each individual keeps in mind all the outcome of the action pairs adopted by himself and each of his neighbors in the last interaction, and according to which the individuals decide what actions they will take in the next round. Computer simulation results imply that win-stay-lose-shift like strategy win out of the memory-one strategy set in the stationary state. This result is robust in a large range of the payoff parameter, and does not depend on the initial state of the system. Furthermore, theoretical analysis with mean field and quasi-static approximation predict the same result. Thus, our studies suggest that win-stay-lose-shift like strategy is a stable dominant strategy in repeated prisoner's dilemma game in homogeneous structured populations.

Direct Repeat Unit (dru) Typing of Methicillin-Resistant Staphylococcus pseudintermedius from Dogs and Cats.

Science.gov (United States)

Kadlec, Kristina; Schwarz, Stefan; Goering, Richard V; Weese, J Scott

2015-12-01

Methicillin-resistant Staphylococcus pseudintermedius (MRSP) has emerged in a remarkable manner as an important problem in dogs and cats. However, limited molecular epidemiological information is available. The aims of this study were to apply direct repeat unit (dru) typing in a large collection of well-characterized MRSP isolates and to use dru typing to analyze a collection of previously uncharacterized MRSP isolates. Two collections of MRSP isolates from dogs and cats were included in this study. The first collection comprised 115 well-characterized MRSP isolates from North America and Europe. The data for these isolates included multilocus sequence typing (MLST) and staphylococcal protein A gene (spa) typing results as well as SmaI macrorestriction patterns after pulsed-field gel electrophoresis (PFGE). The second collection was a convenience sample of 360 isolates from North America. The dru region was amplified by PCR, sequenced, and analyzed. For the first collection, the discriminatory indices of the typing methods were calculated. All isolates were successfully dru typed. The discriminatory power for dru typing (D = 0.423) was comparable to that of spa typing (D = 0.445) and of MLST (D = 0.417) in the first collection. Occasionally, dru typing was able to further discriminate between isolates that shared the same spa type. Among all 475 isolates, 26 different dru types were identified, with 2 predominant types (dt9a and dt11a) among 349 (73.4%) isolates. The results of this study underline that dru typing is a useful tool for MRSP typing, being an objective, standardized, sequence-based method that is relatively cost-efficient and easy to perform. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Structures composing protein domains.

Science.gov (United States)

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

2013-08-01

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Identification and characterization of tandem repeats in exon III of dopamine receptor D4 (DRD4) genes from different mammalian species

DEFF Research Database (Denmark)

Larsen, Svend Arild; Mogensen, Line; Dietz, Rune

2005-01-01

repeat being found. In the domestic cow and gray seal we identified tandem repeats composed of 36-bp modules, each consisting of two closely related 18-bp basic units. A tandem repeat consisting of 9-bp modules was identified in sequences from mink and ferret. In the European otter we detected an 18-bp...

Full scale dynamic testing of Kozloduy NPP unit 5 structures

International Nuclear Information System (INIS)

Da Rin, E.M.

1999-01-01

As described in this report, the Kozloduy NPP western site has been subjected to low level earthquake-like ground shaking - through appropriately devised underground explosions - and the resulting dynamic response of the NPP reactor Unit 5 important structures appropriately measured and digitally recorded. In-situ free-field response was measured concurrently more than 100 m aside the main structures of interest. The collected experimental data provide reference information on the actual dynamic characteristics of the Kozloduy NPPs main structures, as well as give some useful indications on the dynamic soil-structure interaction effects for the case of low level excitation. Performing the present full-scale dynamic structural testing activities took advantage of the experience gained by ISMES during similar tests, lately performed in Italy and abroad (in particular, at the Paks NPP in 1994). The IAEA promoted dynamic testing of the Kozloduy NPP Unit 5 by means of pertinently designed buried explosion-induced ground motions which has provided a large amount of data on the dynamic structural response of its major structures. In the present report, the conducted investigation is described and the acquired digital data presented. A series of preliminary analyses were undertaken for examining in detail the ground excitation levels that were produced by these weak earthquake simulation experiments, as well as for inferring some structural characteristics and behaviour information from the collected data. These analyses ascertained the high quality of the collected digital data. Presumably due to soil-structure dynamic interaction effects, reduced excitation levels were observed at the reactor building foundation raft level with respect to the concurrent free-field ground motions. measured at a 140 m distance from the reactor building centre. Further more detailed and systematic analyses are worthwhile to be performed for extracting more complete information about the

SSRscanner: a program for reporting distribution and exact location of simple sequence repeats.

Science.gov (United States)

Anwar, Tamanna; Khan, Asad U

2006-02-20

Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are found in both prokaryotes and eukaryotes. They are distributed almost at random throughout the genome, ranging from mononucleotide to trinucleotide repeats. They are also found at longer lengths (> 6 repeating units) of tracts. Most of the computer programs that find SSRs do not report its exact position. A computer program SSRscanner was written to find out distribution, frequency and exact location of each SSR in the genome. SSRscanner is user friendly. It can search repeats of any length and produce outputs with their exact position on chromosome and their frequency of occurrence in the sequence. This program has been written in PERL and is freely available for non-commercial users by request from the authors. Please contact the authors by E-mail: huzzi99@hotmail.com.

Conservative Sample Size Determination for Repeated Measures Analysis of Covariance.

Science.gov (United States)

Morgan, Timothy M; Case, L Douglas

2013-07-05

In the design of a randomized clinical trial with one pre and multiple post randomized assessments of the outcome variable, one needs to account for the repeated measures in determining the appropriate sample size. Unfortunately, one seldom has a good estimate of the variance of the outcome measure, let alone the correlations among the measurements over time. We show how sample sizes can be calculated by making conservative assumptions regarding the correlations for a variety of covariance structures. The most conservative choice for the correlation depends on the covariance structure and the number of repeated measures. In the absence of good estimates of the correlations, the sample size is often based on a two-sample t-test, making the 'ultra' conservative and unrealistic assumption that there are zero correlations between the baseline and follow-up measures while at the same time assuming there are perfect correlations between the follow-up measures. Compared to the case of taking a single measurement, substantial savings in sample size can be realized by accounting for the repeated measures, even with very conservative assumptions regarding the parameters of the assumed correlation matrix. Assuming compound symmetry, the sample size from the two-sample t-test calculation can be reduced at least 44%, 56%, and 61% for repeated measures analysis of covariance by taking 2, 3, and 4 follow-up measures, respectively. The results offer a rational basis for determining a fairly conservative, yet efficient, sample size for clinical trials with repeated measures and a baseline value.

REPEATABILITY OF FRUIT QUALITY TRAITS OF CACTUS PEAR

Directory of Open Access Journals (Sweden)

VALTÂNIA XAVIER NUNES

2017-12-01

Full Text Available ABSTRACT Repeatability analysis has been used to study traits in several crops, assisting in the definition of the minimum number needed to evaluate genotypes more efficiently and with less time and resource consumption. So far, however, no repeatability studies on cactus pear have been found in the literature. The objective of this study was to determine the coefficient of repeatability for cactus pear fruits traits and the minimum number of evaluations (fruit that can provide acceptable accuracy for the prediction of the true value. The experiment was conducted at the Federal Institute of Bahia/Campus Guanambi, with 150 fruits collected from three municipalities in the state of Bahia. The coefficients of repeatability were estimated by the methods of analysis of variance, principal components based on the covariance (PCCV and correlation (PCC matrices, and structural analysis based on the correlation matrix (SA. The analysis of variance showed that, except for fruit diameter, the effect of the production site (municipality was significant for all traits evaluated. The PCCV method was proven the most suitable for studying the repeatability of quality traits of cactus pear fruits. Seven fruits were required to determine, with 90% confidence, the traits length, diameter, fruit firmness, skin thickness, number of seeds, fruit mass, bark mass, pulp mass, pH, titratable acidity, soluble solids, SS/AT ratio, and pulp yield.

Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome.

Science.gov (United States)

De Nicola, Beatrice; Lech, Christopher J; Heddi, Brahim; Regmi, Sagar; Frasson, Ilaria; Perrone, Rosalba; Richter, Sara N; Phan, Anh Tuân

2016-07-27

The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Analysis of Structural Units and Their Influence on Thermal Degradation of Alkali Lignins

Directory of Open Access Journals (Sweden)

Wen Hua

2016-01-01

Full Text Available The chemical structures of four alkali lignins isolated from poplar, fir, straw, and bagasse were investigated. To explore the relationship between the structural units and the thermal decomposition behavior, the system was tested by elemental analysis, Fourier transform infrared spectrometry, thermogravimetric analysis (TGA, and pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS. The results indicated that the carbon content of poplar lignin (PL was higher than that of others. Fir lignin (FL exhibited the highest guaiacol units, while the other three lignins were abundant in syringol units. The thermal decomposition characteristics and pyrolysis products of the four lignins were influenced by the material structural and composition. The DTG curves showed that the initial temperatures and major degradation temperatures of woody lignins（FL and PL） with complex inherent structures were shifted to the high temperature zoom compared with that of non-woody （BL and SL）lignins. Py-GC/MS analysis showed that guaiacol-type phenolic compounds were predominant pyrolysis products derived from the four lignins. The yield of guaiacol-type phenols could reach 82.87%. Moreover, the BL had selectively on phenol-type compounds with yield of 27.89%.

Estimation of genetic structure of a Mycosphaerella musicola population using inter-simple sequence repeat markers.

Science.gov (United States)

Peixouto, Y S; Dórea Bragança, C A; Andrade, W B; Ferreira, C F; Haddad, F; Oliveira, S A S; Darosci Brito, F S; Miller, R N G; Amorim, E P

2015-07-17

Among the diseases affecting banana (Musa sp), yellow Sigatoka, caused by the fungal pathogen Mycosphaerella musicola Leach, is considered one of the most important in Brazil, causing losses throughout the year. Understanding the genetic structure of pathogen populations will provide insight into the life history of pathogens, including the evolutionary processes occurring in agrosystems. Tools for estimating the possible emergence of pathogen variants with altered pathogenicity, virulence, or aggressiveness, as well as resistance to systemic fungicides, can also be developed from such data. The objective of this study was to analyze the genetic diversity and population genetics of M. musicola in the main banana-producing regions in Brazil. A total of 83 isolates collected from different banana cultivars in the Brazilian states of Bahia, Rio Grande do Norte, and Minas Gerais were evaluated using inter-simple sequence repeat markers. High variability was detected between the isolates, and 85.5% of the haplotypes were singletons in the populations. The highest source of genetic diversity (97.22%) was attributed to variations within populations. Bayesian cluster analysis revealed the presence of 2 probable ancestral groups, however, showed no relationship to population structure in terms of collection site, state of origin, or cultivar. Similarly, we detected noevidence of genetic recombination between individuals within different states, indicating that asexual cycles play a major role in M. musicola reproduction and that long-distance dispersal of the pathogen is the main factor contributing to the lack of population structure in the fungus.

ACCA phosphopeptide recognition by the BRCT repeats of BRCA1.

Science.gov (United States)

Ray, Hind; Moreau, Karen; Dizin, Eva; Callebaut, Isabelle; Venezia, Nicole Dalla

2006-06-16

The tumour suppressor gene BRCA1 encodes a 220 kDa protein that participates in multiple cellular processes. The BRCA1 protein contains a tandem of two BRCT repeats at its carboxy-terminal region. The majority of disease-associated BRCA1 mutations affect this region and provide to the BRCT repeats a central role in the BRCA1 tumour suppressor function. The BRCT repeats have been shown to mediate phospho-dependant protein-protein interactions. They recognize phosphorylated peptides using a recognition groove that spans both BRCT repeats. We previously identified an interaction between the tandem of BRCA1 BRCT repeats and ACCA, which was disrupted by germ line BRCA1 mutations that affect the BRCT repeats. We recently showed that BRCA1 modulates ACCA activity through its phospho-dependent binding to ACCA. To delineate the region of ACCA that is crucial for the regulation of its activity by BRCA1, we searched for potential phosphorylation sites in the ACCA sequence that might be recognized by the BRCA1 BRCT repeats. Using sequence analysis and structure modelling, we proposed the Ser1263 residue as the most favourable candidate among six residues, for recognition by the BRCA1 BRCT repeats. Using experimental approaches, such as GST pull-down assay with Bosc cells, we clearly showed that phosphorylation of only Ser1263 was essential for the interaction of ACCA with the BRCT repeats. We finally demonstrated by immunoprecipitation of ACCA in cells, that the whole BRCA1 protein interacts with ACCA when phosphorylated on Ser1263.

Quality Improvement Process in a Large Intensive Care Unit: Structure and Outcomes.

Science.gov (United States)

Reddy, Anita J; Guzman, Jorge A

2016-11-01

Quality improvement in the health care setting is a complex process, and even more so in the critical care environment. The development of intensive care unit process measures and quality improvement strategies are associated with improved outcomes, but should be individualized to each medical center as structure and culture can differ from institution to institution. The purpose of this report is to describe the structure of quality improvement processes within a large medical intensive care unit while using examples of the study institution's successes and challenges in the areas of stat antibiotic administration, reduction in blood product waste, central line-associated bloodstream infections, and medication errors. © The Author(s) 2015.

A Unified Model for Repeating and Non-repeating Fast Radio Bursts

International Nuclear Information System (INIS)

Bagchi, Manjari

2017-01-01

The model that fast radio bursts (FRBs) are caused by plunges of asteroids onto neutron stars can explain both repeating and non-repeating bursts. If a neutron star passes through an asteroid belt around another star, there would be a series of bursts caused by a series of asteroid impacts. Moreover, the neutron star would cross the same belt repetitively if it were in a binary with the star hosting the asteroid belt, leading to a repeated series of bursts. I explore the properties of neutron star binaries that could lead to the only known repeating FRB so far (FRB121102). In this model, the next two epochs of bursts are expected around 2017 February 27 and 2017 December 18. On the other hand, if the asteroid belt is located around the neutron star itself, then a chance fall of an asteroid from that belt onto the neutron star would lead to a non-repeating burst. Even a neutron star grazing an asteroid belt can lead to a non-repeating burst caused by just one asteroid plunge during the grazing. This is possible even when the neutron star is in a binary with the asteroid-hosting star, if the belt and the neutron star orbit are non-coplanar.

A Unified Model for Repeating and Non-repeating Fast Radio Bursts

Energy Technology Data Exchange (ETDEWEB)

Bagchi, Manjari, E-mail: manjari@imsc.res.in [The Institute of Mathematical Sciences (IMSc-HBNI), 4th Cross Road, CIT Campus, Taramani, Chennai 600113 (India)

2017-04-01

The model that fast radio bursts (FRBs) are caused by plunges of asteroids onto neutron stars can explain both repeating and non-repeating bursts. If a neutron star passes through an asteroid belt around another star, there would be a series of bursts caused by a series of asteroid impacts. Moreover, the neutron star would cross the same belt repetitively if it were in a binary with the star hosting the asteroid belt, leading to a repeated series of bursts. I explore the properties of neutron star binaries that could lead to the only known repeating FRB so far (FRB121102). In this model, the next two epochs of bursts are expected around 2017 February 27 and 2017 December 18. On the other hand, if the asteroid belt is located around the neutron star itself, then a chance fall of an asteroid from that belt onto the neutron star would lead to a non-repeating burst. Even a neutron star grazing an asteroid belt can lead to a non-repeating burst caused by just one asteroid plunge during the grazing. This is possible even when the neutron star is in a binary with the asteroid-hosting star, if the belt and the neutron star orbit are non-coplanar.

Repeatability of Cryogenic Multilayer Insulation

Science.gov (United States)

Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

2017-12-01

Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation (MLI) has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five Glenn Research Center (GRC) provided coupons with 25 layers was shown to be +/- 8.4% whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0%. A second group of 10 coupons has been fabricated by Yetispace and tested by Florida State University, the repeatability between coupons has been shown to be +/- 15-25%. Based on detailed statistical analysis, the data has been shown to be statistically significant.

Transcription arrest by a G quadruplex forming-trinucleotide repeat sequence from the human c-myb gene.

Science.gov (United States)

Broxson, Christopher; Beckett, Joshua; Tornaletti, Silvia

2011-05-17

Non canonical DNA structures correspond to genomic regions particularly susceptible to genetic instability. The transcription process facilitates formation of these structures and plays a major role in generating the instability associated with these genomic sites. However, little is known about how non canonical structures are processed when encountered by an elongating RNA polymerase. Here we have studied the behavior of T7 RNA polymerase (T7RNAP) when encountering a G quadruplex forming-(GGA)(4) repeat located in the human c-myb proto-oncogene. To make direct correlations between formation of the structure and effects on transcription, we have taken advantage of the ability of the T7 polymerase to transcribe single-stranded substrates and of G4 DNA to form in single-stranded G-rich sequences in the presence of potassium ions. Under physiological KCl concentrations, we found that T7 RNAP transcription was arrested at two sites that mapped to the c-myb (GGA)(4) repeat sequence. The extent of arrest did not change with time, indicating that the c-myb repeat represented an absolute block and not a transient pause to T7 RNAP. Consistent with G4 DNA formation, arrest was not observed in the absence of KCl or in the presence of LiCl. Furthermore, mutations in the c-myb (GGA)(4) repeat, expected to prevent transition to G4, also eliminated the transcription block. We show T7 RNAP arrest at the c-myb repeat in double-stranded DNA under conditions mimicking the cellular concentration of biomolecules and potassium ions, suggesting that the G4 structure formed in the c-myb repeat may represent a transcription roadblock in vivo. Our results support a mechanism of transcription-coupled DNA repair initiated by arrest of transcription at G4 structures.

What we have learned about scheduling elective repeat cesarean delivery at term.

Science.gov (United States)

Tita, Alan T N

2016-08-01

The optimal timing of delivery in the setting of various clinical conditions and scenarios remains one of the most common questions for obstetric providers. Over the past 5-10 years, the optimal timing of delivery at term, particularly for elective repeat cesareans, has been the subject of considerable investigation and discussion. There is an increasing consensus that when women opt for an elective repeat cesarean delivery, it should be performed at term rather than preterm. The recent redefinition of the "term" period into early term (37-38 weeks), full-term (39-40 weeks), late term (41 weeks), and post term designations (≥42 weeks) underscores observed heterogeneity in outcomes following delivery at term. The American College of Obstetricians and Gynecologists currently recommends that elective repeat cesarean delivery be performed at full-term. Herein, the available data to support this recommendation regarding timing of elective repeat cesarean delivery are reviewed, including contributions from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Maternal-Fetal Medicine Units (MFMU) Network. Copyright © 2016. Published by Elsevier Inc.

Discontinuous Patterns of Cigarette Smoking From Ages 18 to 50 in the United States: A Repeated-Measures Latent Class Analysis.

Science.gov (United States)

Terry-McElrath, Yvonne M; O'Malley, Patrick M; Johnston, Lloyd D

2017-12-13

Effective cigarette smoking prevention and intervention programming is enhanced by accurate understanding of developmental smoking pathways across the life span. This study investigated within-person patterns of cigarette smoking from ages 18 to 50 among a US national sample of high school graduates, focusing on identifying ages of particular importance for smoking involvement change. Using data from approximately 15,000 individuals participating in the longitudinal Monitoring the Future study, trichotomous measures of past 30-day smoking obtained at 11 time points were modeled using repeated-measures latent class analyses. Sex differences in latent class structure and membership were examined. Twelve latent classes were identified: three characterized by consistent smoking patterns across age (no smoking; smoking developing effective smoking prevention and intervention programming. This study examined cigarette smoking among a national longitudinal US sample of high school graduates from ages 18 to 50 and identified distinct latent classes characterized by patterns of movement between no cigarette use, light-to-moderate smoking, and the conventional definition of heavy smoking at 11 time points via repeated-measures latent class analysis. Membership probabilities for each smoking class were estimated, and critical ages of susceptibility to change in smoking behaviors were identified. © The Author 2017. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Selection pressure on human STR loci and its relevance in repeat expansion disease

KAUST Repository

Shimada, Makoto K.

2016-06-11

Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases. © 2016, Springer-Verlag Berlin Heidelberg.

Reconfigurable multiport EPON repeater

Science.gov (United States)

Oishi, Masayuki; Inohara, Ryo; Agata, Akira; Horiuchi, Yukio

2009-11-01

An extended reach EPON repeater is one of the solutions to effectively expand FTTH service areas. In this paper, we propose a reconfigurable multi-port EPON repeater for effective accommodation of multiple ODNs with a single OLT line card. The proposed repeater, which has multi-ports in both OLT and ODN sides, consists of TRs, BTRs with the CDR function and a reconfigurable electrical matrix switch, can accommodate multiple ODNs to a single OLT line card by controlling the connection of the matrix switch. Although conventional EPON repeaters require full OLT line cards to accommodate subscribers from the initial installation stage, the proposed repeater can dramatically reduce the number of required line cards especially when the number of subscribers is less than a half of the maximum registerable users per OLT. Numerical calculation results show that the extended reach EPON system with the proposed EPON repeater can save 17.5% of the initial installation cost compared with a conventional repeater, and can be less expensive than conventional systems up to the maximum subscribers especially when the percentage of ODNs in lightly-populated areas is higher.

Reliability assessment of Indian Point Unit 3 containment structure under combined loads

International Nuclear Information System (INIS)

Hwang, H.; Shinozuka, M.; Kawakami, J.; Reich, M.

1984-01-01

In the current design criteria, the load combinations specified for design of concrete containment structures are in the deterministic format. However, by applying the probability-based reliability analysis method developed by BNL to the concrete containment structures designed according to the criteria, it is possible to evaluate the reliability levels implied in the current design criteria. For this purpose, the reliability analysis is applied to the Indian Point Unit No. 3 containment. The details of the containment structure such as the geometries and the rebar arrangements, etc., are taken from the working drawings and the Final Safety Analysis Report. Three kinds of loads are considered in the reliability analysis. They are, dead load, accidental pressure due to a large LOCA, and earthquake ground acceleration. This paper presents the reliability analysis results of the Indian Point Unit 3 containment subjected to all combinations of loads

Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

Directory of Open Access Journals (Sweden)

Aparecido R. Silva

2008-05-01

Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

Intensive Care Unit Structure Variation and Implications for Early Mobilization Practices. An International Survey.

Science.gov (United States)

Bakhru, Rita N; McWilliams, David J; Wiebe, Douglas J; Spuhler, Vicki J; Schweickert, William D

2016-09-01

Early mobilization (EM) improves outcomes for mechanically ventilated patients. Variation in structure and organizational characteristics may affect implementation of EM practices. We queried intensive care unit (ICU) environment and standardized ICU practices to evaluate organizational characteristics that enable EM practice. We recruited 151 ICUs in France, 150 in Germany, 150 in the United Kingdom, and 500 in the United States by telephone. Survey domains included respondent characteristics, hospital and ICU characteristics, and ICU practices and protocols. We surveyed 1,484 ICU leaders and received a 64% response rate (951 ICUs). Eighty-eight percent of respondents were in nursing leadership roles; the remainder were physiotherapists. Surveyed ICUs were predominantly mixed medical-surgical units (67%), and 27% were medical ICUs. ICU staffing models differed significantly (P equipment were highly variable among respondents. International ICU structure and practice is quite heterogeneous, and several factors (multidisciplinary rounds, setting daily goals for patients, presence of a dedicated physiotherapist, country, and nurse/patient staffing ratio) are significantly associated with the practice of EM. Practice and barriers may be far different based upon staffing structure. To achieve successful implementation, whether through trials or quality improvement, ICU staffing and practice patterns must be taken into account.

Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2

DEFF Research Database (Denmark)

Kenchappa, Chandra; Heiðarsson, Pétur Orri; Kragelund, Birthe

2013-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) form the basis of diverse adaptive immune systems directed primarily against invading genetic elements of archaea and bacteria. Cbp1 of the crenarchaeal thermoacidophilic order Sulfolobales, carrying three imperfect repeats, binds...... specifically to CRISPR DNA repeats and has been implicated in facilitating production of long transcripts from CRISPR loci. Here, a second related class of CRISPR DNA repeat-binding protein, denoted Cbp2, is characterized that contains two imperfect repeats and is found amongst members of the crenarchaeal...... in facilitating high affinity DNA binding of Cbp2 by tethering the two domains. Structural studies on mutant proteins provide support for Cys(7) and Cys(28) enhancing high thermal stability of Cbp2(Hb) through disulphide bridge formation. Consistent with their proposed CRISPR transcriptional regulatory role, Cbp2...

Interactions between tetrathiafulvalene units in dimeric structures – the influence of cyclic cores

Directory of Open Access Journals (Sweden)

Huixin Jiang

2015-06-01

Full Text Available A selection of cyclic and acyclic acetylenic scaffolds bearing two tetrathiafulvalene (TTF units was prepared by different metal-catalyzed coupling reactions. The bridge separating the two TTF units was systematically changed from linearly conjugated ethyne, butadiyne and tetraethynylethene (trans-substituted units to a cross-conjugated tetraethynylethene unit, placed in either acyclic or cyclic arrangements. The cyclic structures correspond to so-called radiaannulenes having both endo- and exocyclic double bonds. Interactions between two redox-active TTF units in these molecules were investigated by cyclic voltammetry, UV–vis–NIR and EPR absorption spectroscopical methods of the electrochemically generated oxidized species. The electron-accepting properties of the acetylenic cores were also investigated electrochemically.

A Network-Based Algorithm for Clustering Multivariate Repeated Measures Data

Science.gov (United States)

Koslovsky, Matthew; Arellano, John; Schaefer, Caroline; Feiveson, Alan; Young, Millennia; Lee, Stuart

2017-01-01

The National Aeronautics and Space Administration (NASA) Astronaut Corps is a unique occupational cohort for which vast amounts of measures data have been collected repeatedly in research or operational studies pre-, in-, and post-flight, as well as during multiple clinical care visits. In exploratory analyses aimed at generating hypotheses regarding physiological changes associated with spaceflight exposure, such as impaired vision, it is of interest to identify anomalies and trends across these expansive datasets. Multivariate clustering algorithms for repeated measures data may help parse the data to identify homogeneous groups of astronauts that have higher risks for a particular physiological change. However, available clustering methods may not be able to accommodate the complex data structures found in NASA data, since the methods often rely on strict model assumptions, require equally-spaced and balanced assessment times, cannot accommodate missing data or differing time scales across variables, and cannot process continuous and discrete data simultaneously. To fill this gap, we propose a network-based, multivariate clustering algorithm for repeated measures data that can be tailored to fit various research settings. Using simulated data, we demonstrate how our method can be used to identify patterns in complex data structures found in practice.

Alternative Conformations of the Tau Repeat Domain in Complex with an Engineered Binding Protein*

Science.gov (United States)

Grüning, Clara S. R.; Mirecka, Ewa A.; Klein, Antonia N.; Mandelkow, Eckhard; Willbold, Dieter; Marino, Stephen F.; Stoldt, Matthias; Hoyer, Wolfgang

2014-01-01

The aggregation of Tau into paired helical filaments is involved in the pathogenesis of several neurodegenerative diseases, including Alzheimer disease. The aggregation reaction is characterized by conformational conversion of the repeat domain, which partially adopts a cross-β-structure in the resulting amyloid-like fibrils. Here, we report the selection and characterization of an engineered binding protein, β-wrapin TP4, targeting the Tau repeat domain. TP4 was obtained by phage display using the four-repeat Tau construct K18ΔK280 as a target. TP4 binds K18ΔK280 as well as the longest isoform of human Tau, hTau40, with nanomolar affinity. NMR spectroscopy identified two alternative TP4-binding sites in the four-repeat domain, with each including two hexapeptide motifs with high β-sheet propensity. Both binding sites contain the aggregation-determining PHF6 hexapeptide within repeat 3. In addition, one binding site includes the PHF6* hexapeptide within repeat 2, whereas the other includes the corresponding hexapeptide Tau(337–342) within repeat 4, denoted PHF6**. Comparison of TP4-binding with Tau aggregation reveals that the same regions of Tau are involved in both processes. TP4 inhibits Tau aggregation at substoichiometric concentration, demonstrating that it interferes with aggregation nucleation. This study provides residue-level insight into the interaction of Tau with an aggregation inhibitor and highlights the structural flexibility of Tau. PMID:24966331

Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3).

Science.gov (United States)

Mulepati, Sabin; Bailey, Scott

2011-09-09

RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.

A comparison of the structure of radiation oncology in the United States and Japan

International Nuclear Information System (INIS)

Owen, Jean B.; Hanks, Gerald E.; Teshima, Teruki; Sato, Shinichiro; Tsunemoto, Hiroshi; Inoue, Toshihiko

1996-01-01

Purpose: The United States and Japan have very different backgrounds in their medical care systems. In the field of radiation oncology, national surveys on structure have been conducted for both countries and compared to illustrate any similarities and differences present from 1989-1990. Methods and Materials: The Patterns of Care Study Facility Survey conducted in 1989 in the United States and the National Survey of Structure in Japan in 1990 were compared to evaluate the equipment pattern, staffing pattern, compliance rate with the 'blue book' (3) guideline, and the geographic distribution of institutions. Results: In the United States, a total of 598,184 (49% of the total of newly diagnosed) patients were treated with radiation therapy. In Japan, 62,829 (approximately 15% of the total of newly diagnosed) patients were treated. The numbers of external megavoltage treatment machines were 2,397 in the United States and 494 in Japan. The numbers of full time equivalent (FTE) radiation oncologists were 2,335 in the United States and 366 in Japan. Only 15% of United States facilities and 11% of Japan facilities complied with the narrow blue book guideline for the patients per FTE radiation oncologist (200-250), while the most common ratio was 151-200 patients/FTE in the United States and 51-100 in Japan. In Japan, more than 60% of institutions were staffed by a part-time radiation oncologist (FTE < 1.0). Between geographic regions, there was variation in the percentage of cancer patients treated with radiation therapy for both the United States (42-56%) and Japan (6-25%). Conclusion: There is a major difference in the usage of radiation therapy for treating cancer between the United States and Japan with 49% of all new cancer patients treated in the United States and approximately 15% treated in Japan. Equipment structure in the United States is more complete than in Japan with important differences in treatment simulators, treatment planning computers, and support

Potentials and limitations of histone repeat sequences for phylogenetic reconstruction of Sophophora.

Science.gov (United States)

Baldo, A M; Les, D H; Strausbaugh, L D

1999-11-01

Simplified DNA sequence acquisition has provided many new data sets that are useful for phylogenetic reconstruction, including single- and multiple-copy nuclear and organellar genes. Although transcribed regions receive much attention, nontranscribed regions have recently been added to the repertoire of sequences suitable for phylogenetic studies, especially for closely related taxa. We evaluated the efficacy of a small portion of the histone repeat for phylogenetic reconstruction among Drosophila species. Histone repeats in invertebrates offer distinct advantages similar to those of widely used ribosomal repeats. First, the units are tandemly repeated and undergo concerted evolution. Second, histone repeats include both highly conserved coding and variable intergenic regions. This composition facilitates application of "universal" primers spanning potentially informative sites. We examined a small region of the histone repeat, including the intergenic spacer segments of coding regions from the divergently transcribed H2A and H2B histone genes. The spacer (about 230 bp) exists as a mosaic with highly conserved functional motifs interspersed with rapidly diverging regions; the former aid in alignment of the spacer. There are no ambiguities in alignment of coding regions. Coding and noncoding regions were analyzed together and separately for phylogenetic information. Parsimony, distance, and maximum-likelihood methods successfully retrieve the corroborated phylogeny for the taxa examined. This study demonstrates the resolving power of a small histone region which may now be added to the growing collection of phylogenetically useful DNA sequences.

Psychological and physiological responses following repeated peer death.

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Judith Pizarro Andersen

Full Text Available Undergraduates at a university in the United States were exposed - directly and indirectly - to 14 peer deaths during one academic year. We examined how individual and social factors were associated with psychological (e.g., anxiety, depression, somatization and physiological (i.e., cortisol distress responses following this unexpected and repeated experience with loss.Two to three months after the final peer death, respondents (N = 122, 61% female, 18-23 years, M = 20.13, SD = 1.14 reported prior adverse experiences, degree of closeness with the deceased, acute responses to the peer deaths, ongoing distress responses, social support, support seeking, and media viewing. A subset (n = 24 returned hair samples for evaluation of cortisol responses during the previous 3 months.Ongoing psychological distress was associated with a prior interpersonal trauma, b fewer social supports, and c media exposure to news of the deaths (p's25 p/mg compared to individuals with one or two prior bereavement experiences (who were, on average, within the normal range, 10 to 25 p/mg (p<.05. Only 8% of the sample utilized available university psychological or physical health resources and support groups.Limited research has examined the psychological and physiological impact of exposure to chronic, repeated peer loss, despite the fact that there are groups of individuals (e.g., police, military soldiers that routinely face such exposures. Prior adversity appears to play a role in shaping psychological and physiological responses to repeated loss. This topic warrants further research given the health implications of repeated loss for individuals in high-risk occupations and university settings.

Structures of two cell wall-associated polysaccharides of a Streptococcus mitis biovar 1 strain. A unique teichoic acid-like polysaccharide and the group O antigen which is a C-polysaccharide in common with pneumococci

DEFF Research Database (Denmark)

Bergström, N; Jansson, P.-E.; Kilian, Mogens

2000-01-01

The cell wall of Streptococcus mitis biovar 1 strain SK137 contains the C-polysaccharide known as the common antigen of a closely related species Streptococcus pneumoniae, and a teichoic acid-like polysaccharide with a unique structure. The two polysaccharides are different entities and could...... be partially separated by gel chromatography. The structures of the two polysaccharides were determined by chemical methods and by NMR spectroscopy. The teichoic acid-like polymer has a heptasaccharide phosphate repeating unit with the following structure: The structure neither contains ribitol nor glycerol...... phosphate as classical teichoic acids do, thus we have used the expression teichoic acid-like for this polysaccharide. The following structure of the C-polysaccharide repeating unit was established: where AAT is 2-acetamido-4-amino-2,4, 6-trideoxy-D-galactose. It has a carbohydrate backbone identical...

Structure of the Elastin-Contractile Units in the Thoracic Aorta and How Genes That Cause Thoracic Aortic Aneurysms and Dissections Disrupt This Structure.

Science.gov (United States)

Karimi, Ashkan; Milewicz, Dianna M

2016-01-01

The medial layer of the aorta confers elasticity and strength to the aortic wall and is composed of alternating layers of smooth muscle cells (SMCs) and elastic fibres. The SMC elastin-contractile unit is a structural unit that links the elastin fibres to the SMCs and is characterized by the following: (1) layers of elastin fibres that are surrounded by microfibrils; (2) microfibrils that bind to the integrin receptors in focal adhesions on the cell surface of the SMCs; and (3) SMC contractile filaments that are linked to the focal adhesions on the inner side of the membrane. The genes that are altered to cause thoracic aortic aneurysms and aortic dissections encode proteins involved in the structure or function of the SMC elastin-contractile unit. Included in this gene list are the genes encoding protein that are structural components of elastin fibres and microfibrils, FBN1, MFAP5, ELN, and FBLN4. Also included are genes that encode structural proteins in the SMC contractile unit, including ACTA2, which encodes SMC-specific α-actin and MYH11, which encodes SMC-specific myosin heavy chain, along with MYLK and PRKG1, which encode kinases that control SMC contraction. Finally, mutations in the gene encoding the protein linking integrin receptors to the contractile filaments, FLNA, also predispose to thoracic aortic disease. Thus, these data suggest that functional SMC elastin-contractile units are important for maintaining the structural integrity of the aorta. Copyright © 2016 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.

High Regional Variation in Urethroplasty in the United States

Science.gov (United States)

Figler, Bradley D.; Gore, John L.; Holt, Sarah K.; Voelzke, Bryan B.; Wessells, Hunter

2015-01-01

Purpose We identified clinical and regional factors associated with the use of urethroplasty vs repeat endoscopic management for urethral stricture disease. Materials and Methods We analyzed claims for patients 18 to 65 years old in the 2007 to 2011 MarketScan ® Commercial Claims and Encounters Database with a diagnosis of urethral stricture. The primary outcome was treatment with urethroplasty vs repeat endoscopic management, defined as more than 2 dilations or direct vision internal urethrotomies. The likelihood of urethroplasty vs repeat endoscopic management was determined for each major metropolitan area in the United States. Multivariate logistic regression was done to identify factors associated with urethroplasty. Results We identified 41,056 patients with urethral stricture, yielding a diagnosis rate of 296/100,000 men in MarketScan. Repeat endoscopic management and urethroplasty were performed in 2,700 and 1,444 patients, respectively. Compared to patients treated with repeat endoscopic management those with urethroplasty were younger (median age 44 vs 54 years) and more likely to have a Charlson comorbidity score of 0 (84% vs 77%), have traveled out of a metropolitan area for care (34% vs 17%) and have a reconstructive urologist in the treatment metropolitan area (76% and 62%, each p urethroplasty vs repeat endoscopic management. Conclusions Despite the well established benefits of urethroplasty compared to repeat endoscopic management a strong bias for repeat endoscopic management exists in many regions in the United States. PMID:25072180

Clamping characteristics study on different types of clamping unit

Energy Technology Data Exchange (ETDEWEB)

Jiao, Zhiwei; Liu, Haichao; Xie, Pengcheng [College of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing China 100029 (China); Yang, Weimin [College of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing China 100029 (China); State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing China 100029 (China)

2015-05-22

Plastic products are becoming more and more widely used in aerospace, IT, digital electronics and many other fields. With the development of technology, the requirement of product precision is getting higher and higher. However, type and working performance of clamping unit play a decisive role in product precision. Clamping characteristics of different types of clamping unit are discussed in this article, which use finite element numerical analysis method through the software ABAQUS to study the clamping uniformity, and detect the clamping force repeatability precision. The result shows that compared with toggled three-platen clamping unit, clamping characteristics of internal circulation two-platen clamping unit are better, for instance, its mold cavity deformation and force that bars and mold parting surface suffered are more uniform, and its clamping uniformity and repeatability precision is also better.

Formation of integrated structural units using the systematic and integrated method when implementing high-rise construction projects

Science.gov (United States)

Abramov, Ivan

2018-03-01

Development of design documentation for a future construction project gives rise to a number of issues with the main one being selection of manpower for structural units of the project's overall implementation system. Well planned and competently staffed integrated structural construction units will help achieve a high level of reliability and labor productivity and avoid negative (extraordinary) situations during the construction period eventually ensuring improved project performance. Research priorities include the development of theoretical recommendations for enhancing reliability of a structural unit staffed as an integrated construction crew. The author focuses on identification of destabilizing factors affecting formation of an integrated construction crew; assessment of these destabilizing factors; based on the developed mathematical model, highlighting the impact of these factors on the integration criterion with subsequent identification of an efficiency and reliability criterion for the structural unit in general. The purpose of this article is to develop theoretical recommendations and scientific and methodological provisions of an organizational and technological nature in order to identify a reliability criterion for a structural unit based on manpower integration and productivity criteria. With this purpose in mind, complex scientific tasks have been defined requiring special research, development of corresponding provisions and recommendations based on the system analysis findings presented herein.

Magnitude of exercise capacity and quality of life improvement following repeat pulmonary rehabilitation in patients with COPD

Directory of Open Access Journals (Sweden)

Sandoz JS

2017-04-01

Full Text Available Jacqueline S Sandoz,1,2 Mary M Roberts,1,3,4 Jin-Gun Cho,1,3–5 John R Wheatley1,3–5 1Respiratory Ambulatory Care Service, Western Sydney Local Health District, NSW, Australia; 2Canadian Alternatives in Non-invasive Ventilation (CANVent Program, Ottawa Hospital Rehabilitation Centre, Division of Respiratory Medicine, Ottawa Hospital, Ontario, Canada; 3Department of Respiratory and Sleep Medicine, Westmead Hospital, 4Ludwig Engel Centre for Respiratory Research, Westmead Institute for Medical Research, 5Sydney Medical School, University of Sydney, Westmead, NSW, Australia Background: Maintenance and repeated pulmonary rehabilitation programs (PRPs for patients with COPD have attempted to prolong PRP benefits beyond 12–24 months. However, there is limited evidence as to the magnitude of benefit or the ideal interval between repeating the program under “real-world” conditions in which patients are referred based on clinical necessity. Therefore, we reviewed the effects of repeating PRP in a physician-referred cohort of patients with COPD. Methods: A total of 141 individuals with COPD completed PRP twice and 35 completed PRP three times over a 12-year period. We used linear mixed-effects models to quantify the magnitude and change in 6-minute walk distance (6MWD, St George’s Respiratory Questionnaire (SGRQ, and Hospital Anxiety and Depression Scale (HADS for each PRP. One-way analysis of variance with Tukey’s post hoc analysis compared the effects of different time intervals on 6MWD, SGRQ, and HADS between PRPs. Results: Despite 39 mL/year average decrease in forced expiratory volume in 1 second, overall 6MWD improved following each PRP (PRP1=58 m, P<0.0001; PRP2=42 m, P<0.0001; PRP3=32 m, P<0.003. Mean SGRQ decreased after PRP1 (-7.0 units; P<0.001 and PRP2 (-4.9 units;P<0.0001 but not after PRP3 (-3.2 units; P=0.10. HADS decreased after PRP1 (-1.9 units; P<0.0001 and PRP2 (-1.7 units; P=0.0001 but not after PRP3 (-0.4 units

Gene conversion homogenizes the CMT1A paralogous repeats

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Hurles Matthew E

2001-12-01

Full Text Available Abstract Background Non-allelic homologous recombination between paralogous repeats is increasingly being recognized as a major mechanism causing both pathogenic microdeletions and duplications, and structural polymorphism in the human genome. It has recently been shown empirically that gene conversion can homogenize such repeats, resulting in longer stretches of absolute identity that may increase the rate of non-allelic homologous recombination. Results Here, a statistical test to detect gene conversion between pairs of non-coding sequences is presented. It is shown that the 24 kb Charcot-Marie-Tooth type 1A paralogous repeats (CMT1A-REPs exhibit the imprint of gene conversion processes whilst control orthologous sequences do not. In addition, Monte Carlo simulations of the evolutionary divergence of the CMT1A-REPs, incorporating two alternative models for gene conversion, generate repeats that are statistically indistinguishable from the observed repeats. Bounds are placed on the rate of these conversion processes, with central values of 1.3 × 10-4 and 5.1 × 10-5 per generation for the alternative models. Conclusions This evidence presented here suggests that gene conversion may have played an important role in the evolution of the CMT1A-REP paralogous repeats. The rates of these processes are such that it is probable that homogenized CMT1A-REPs are polymorphic within modern populations. Gene conversion processes are similarly likely to play an important role in the evolution of other segmental duplications and may influence the rate of non-allelic homologous recombination between them.

Assessment of teamwork during structured interdisciplinary rounds on medical units.

Science.gov (United States)

O'Leary, Kevin J; Boudreau, Yvonne N; Creden, Amanda J; Slade, Maureen E; Williams, Mark V

2012-01-01

Interdisciplinary rounds (IDR) provide a means to assemble hospital team members and improve collaboration. Little is known about teamwork during IDR. To evaluate and characterize teamwork during IDR. Cross-sectional observational study. Six medical units which had implemented structured interdisciplinary rounds (SIDR). We adapted the Observational Teamwork Assessment for Surgery (OTAS) tool, a behaviorally anchored rating scale shown to be reliable and valid in surgical settings. OTAS provides scores ranging from 0 to 6 (0 = problematic behavior; 6 = exemplary behavior) across 5 domains (communication, coordination, cooperation/backup behavior, leadership, and monitoring/situational awareness) and for prespecified subteams. Two researchers conducted direct observations using the adapted OTAS tool. We conducted 7-8 independent observations for each unit (total = 44) and 20 joint observations. Inter-rater reliability was excellent at the unit level (Spearman's rho = 0.75), and good across domains (rho = 0.53-0.68) and subteams (rho = 0.53-0.76) with the exception of the physician subteam, for which it was poor (rho = 0.35). Though teamwork scores were generally high, we found differences across units, with a median (interquartile range [IQR]) 4.5 (3.9-4.9) for the lowest and 5.4 (5.3-5.5) for the highest performing unit (P teamwork during SIDR across units, domains, and most subteams. Variation in performance suggests a need to improve consistency of teamwork and emphasizes the importance of leadership. Copyright © 2012 Society of Hospital Medicine.

Reliability assessment of Indian Point Unit 3 containment structure

International Nuclear Information System (INIS)

Kawakami, J.; Hwang, H.; Chang, M.T.; Reich, M.

1984-01-01

In the current design criteria, the load combinations specified for design of concrete containment structures are in the deterministic formats. However, by applying the probability-based reliability method developed by BNL to the concrete containment structures designed according to the criteria, it is possible to evaluate the reliability levels implied in the current design criteria. For this purpose, the reliability analysis is applied to the Indian Point Unit No. 3 containment. The details of the containment structure such as the geometries and the rebar arrangements, etc., are taken from the working drawings and the final safety analysis reports. Three kinds of loads are considered in the reliability analysis. They are, dead load (D), accidental pressure due to a large LOCA (P), and earthquake ground acceleration (E). Reliability analysis of the containment subjected to all combinations of loads is performed. Results are presented in this report

Repeat-containing protein effectors of plant-associated organisms

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Carl H. Mesarich

2015-10-01

Full Text Available Many plant-associated organisms, including microbes, nematodes, and insects, deliver effector proteins into the apoplast, vascular tissue, or cell cytoplasm of their prospective hosts. These effectors function to promote colonization, typically by altering host physiology or by modulating host immune responses. The same effectors however, can also trigger host immunity in the presence of cognate host immune receptor proteins, and thus prevent colonization. To circumvent effector-triggered immunity, or to further enhance host colonization, plant-associated organisms often rely on adaptive effector evolution. In recent years, it has become increasingly apparent that several effectors of plant-associated organisms are repeat-containing proteins (RCPs that carry tandem or non-tandem arrays of an amino acid sequence or structural motif. In this review, we highlight the diverse roles that these repeat domains play in RCP effector function. We also draw attention to the potential role of these repeat domains in adaptive evolution with regards to RCP effector function and the evasion of effector-triggered immunity. The aim of this review is to increase the profile of RCP effectors from plant-associated organisms.

Dependence of the polar Kerr angle and coercivity on repeat distance in sequentially prepared Tb/FeCo films

International Nuclear Information System (INIS)

Shin, S.

1991-01-01

Multilayer thin films of Tb and FeCo were prepared by sequential thermal evaporation of Tb and Fe 90 Co 10 alloy on glass substrates at ambient temperature in a vacuum of about 1 x 10 -6 Torr. The repeat distance of the films was varied from 3.5 to 175 A while maintaining the composition constant for all samples. Low-angle x-ray diffraction and Auger electron spectroscopy showed that a multilayer structure was achieved for films fabricated with a repeat distance Λ≥31.5 A. The polar Kerr rotation angle and coercivity of the samples were obtained by measuring the polar Kerr hysteresis loop using a 632.8-nm HeNe laser. It was observed that for the samples having a multilayer structure, the remnant Kerr angle and coercivity monotonically decreased with increasing repeat distance, and eventually disappeared for Λ≥70 A. For the samples showing a nonmultilayer structure, the remnant Kerr angle was independent of repeat distance. However, the coercivity increased with repeat distance until a broad maximum was obtained around Λ congruent 14--21 A

Telomerase Repeated Amplification Protocol (TRAP).

Science.gov (United States)

Mender, Ilgen; Shay, Jerry W

2015-11-20

Telomeres are found at the end of eukaryotic linear chromosomes, and proteins that bind to telomeres protect DNA from being recognized as double-strand breaks thus preventing end-to-end fusions (Griffith et al. , 1999). However, due to the end replication problem and other factors such as oxidative damage, the limited life span of cultured cells (Hayflick limit) results in progressive shortening of these protective structures (Hayflick and Moorhead, 1961; Olovnikov, 1973). The ribonucleoprotein enzyme complex telomerase-consisting of a protein catalytic component hTERT and a functional RNA component hTR or hTERC - counteracts telomere shortening by adding telomeric repeats to the end of chromosomes in ~90% of primary human tumors and in some transiently proliferating stem-like cells (Shay and Wright, 1996; Shay and Wright, 2001). This results in continuous proliferation of cells which is a hallmark of cancer. Therefore, telomere biology has a central role in aging, cancer progression/metastasis as well as targeted cancer therapies. There are commonly used methods in telomere biology such as Telomere Restriction Fragment (TRF) (Mender and Shay, 2015b), Telomere Repeat Amplification Protocol (TRAP) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this detailed protocol we describe Telomere Repeat Amplification Protocol (TRAP). The TRAP assay is a popular method to determine telomerase activity in mammalian cells and tissue samples (Kim et al. , 1994). The TRAP assay includes three steps: extension, amplification, and detection of telomerase products. In the extension step, telomeric repeats are added to the telomerase substrate (which is actually a non telomeric oligonucleotide, TS) by telomerase. In the amplification step, the extension products are amplified by the polymerase chain reaction (PCR) using specific primers (TS upstream primer and ACX downstream primer) and in the detection step, the presence or absence of telomerase is

Hysteresis of magnetostructural transitions: Repeatable and non-repeatable processes

Science.gov (United States)

Provenzano, Virgil; Della Torre, Edward; Bennett, Lawrence H.; ElBidweihy, Hatem

2014-02-01

The Gd5Ge2Si2 alloy and the off-stoichiometric Ni50Mn35In15 Heusler alloy belong to a special class of metallic materials that exhibit first-order magnetostructural transitions near room temperature. The magnetic properties of this class of materials have been extensively studied due to their interesting magnetic behavior and their potential for a number of technological applications such as refrigerants for near-room-temperature magnetic refrigeration. The thermally driven first-order transitions in these materials can be field-induced in the reverse order by applying a strong enough field. The field-induced transitions are typically accompanied by the presence of large magnetic hysteresis, the characteristics of which are a complicated function of temperature, field, and magneto-thermal history. In this study we show that the virgin curve, the major loop, and sequentially measured MH loops are the results of both repeatable and non-repeatable processes, in which the starting magnetostructural state, prior to the cycling of field, plays a major role. Using the Gd5Ge2Si2 and Ni50Mn35In15 alloys, as model materials, we show that a starting single phase state results in fully repeatable processes and large magnetic hysteresis, whereas a mixed phase starting state results in non-repeatable processes and smaller hysteresis.

Hysteresis of magnetostructural transitions: Repeatable and non-repeatable processes

International Nuclear Information System (INIS)

Provenzano, Virgil; Della Torre, Edward; Bennett, Lawrence H.; ElBidweihy, Hatem

2014-01-01

The Gd 5 Ge 2 Si 2 alloy and the off-stoichiometric Ni 50 Mn 35 In 15 Heusler alloy belong to a special class of metallic materials that exhibit first-order magnetostructural transitions near room temperature. The magnetic properties of this class of materials have been extensively studied due to their interesting magnetic behavior and their potential for a number of technological applications such as refrigerants for near-room-temperature magnetic refrigeration. The thermally driven first-order transitions in these materials can be field-induced in the reverse order by applying a strong enough field. The field-induced transitions are typically accompanied by the presence of large magnetic hysteresis, the characteristics of which are a complicated function of temperature, field, and magneto-thermal history. In this study we show that the virgin curve, the major loop, and sequentially measured MH loops are the results of both repeatable and non-repeatable processes, in which the starting magnetostructural state, prior to the cycling of field, plays a major role. Using the Gd 5 Ge 2 Si 2 and Ni 50 Mn 35 In 15 alloys, as model materials, we show that a starting single phase state results in fully repeatable processes and large magnetic hysteresis, whereas a mixed phase starting state results in non-repeatable processes and smaller hysteresis

Clinical validation of an epigenetic assay to predict negative histopathological results in repeat prostate biopsies.

Science.gov (United States)

Partin, Alan W; Van Neste, Leander; Klein, Eric A; Marks, Leonard S; Gee, Jason R; Troyer, Dean A; Rieger-Christ, Kimberly; Jones, J Stephen; Magi-Galluzzi, Cristina; Mangold, Leslie A; Trock, Bruce J; Lance, Raymond S; Bigley, Joseph W; Van Criekinge, Wim; Epstein, Jonathan I

2014-10-01

The DOCUMENT multicenter trial in the United States validated the performance of an epigenetic test as an independent predictor of prostate cancer risk to guide decision making for repeat biopsy. Confirming an increased negative predictive value could help avoid unnecessary repeat biopsies. We evaluated the archived, cancer negative prostate biopsy core tissue samples of 350 subjects from a total of 5 urological centers in the United States. All subjects underwent repeat biopsy within 24 months with a negative (controls) or positive (cases) histopathological result. Centralized blinded pathology evaluation of the 2 biopsy series was performed in all available subjects from each site. Biopsies were epigenetically profiled for GSTP1, APC and RASSF1 relative to the ACTB reference gene using quantitative methylation specific polymerase chain reaction. Predetermined analytical marker cutoffs were used to determine assay performance. Multivariate logistic regression was used to evaluate all risk factors. The epigenetic assay resulted in a negative predictive value of 88% (95% CI 85-91). In multivariate models correcting for age, prostate specific antigen, digital rectal examination, first biopsy histopathological characteristics and race the test proved to be the most significant independent predictor of patient outcome (OR 2.69, 95% CI 1.60-4.51). The DOCUMENT study validated that the epigenetic assay was a significant, independent predictor of prostate cancer detection in a repeat biopsy collected an average of 13 months after an initial negative result. Due to its 88% negative predictive value adding this epigenetic assay to other known risk factors may help decrease unnecessary repeat prostate biopsies. Copyright © 2014 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

All-photonic quantum repeaters

Science.gov (United States)

Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

2015-01-01

Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories. PMID:25873153

Status of Advanced Stitched Unitized Composite Aircraft Structures

Science.gov (United States)

Jegley, Dawn C.; Velicki, Alex

2013-01-01

NASA has created the Environmentally Responsible Aviation (ERA) Project to explore and document the feasibility, benefits and technical risk of advanced vehicle configurations and enabling technologies that will reduce the impact of aviation on the environment. A critical aspect of this pursuit is the development of a lighter, more robust airframe that will enable the introduction of unconventional aircraft configurations that have higher lift-to-drag ratios, reduced drag, and lower community noise levels. The primary structural concept being developed under the ERA project in the Airframe Technology element is the Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) concept. This paper describes how researchers at NASA and The Boeing Company are working together to develop fundamental PRSEUS technologies that could someday be implemented on a transport size aircraft with high aspect ratio wings or unconventional shapes such as a hybrid wing body airplane design.

Constructs for the expression of repeating triple-helical protein domains

International Nuclear Information System (INIS)

Peng, Yong Y; Werkmeister, Jerome A; Vaughan, Paul R; Ramshaw, John A M

2009-01-01

The development of novel scaffolds will be an important aspect in future success of tissue engineering. Scaffolds will preferably contain information that directs the cellular content of constructs so that the new tissue that is formed is closely aligned in structure, composition and function to the target natural tissue. One way of approaching this will be the development of novel protein-based constructs that contain one or more repeats of functional elements derived from various proteins. In the present case, we describe a strategy to make synthetic, recombinant triple-helical constructs that contain repeat segments of biologically relevant domains. Copies of a DNA fragment prepared by PCR from human type III collagen have been inserted in a co-linear contiguous fashion into the yeast expression vector YEpFlag-1, using sequential addition between selected restriction sites. Constructs containing 1, 2 and 3 repeats were designed to maintain the (Gly-X-Y) repeat, which is essential for the formation of an extended triple helix. All constructs gave expressed protein, with the best being the 3-repeat construct which was readily secreted. This material had the expected composition and N-terminal sequence. Incubation of the product at low temperature led to triple-helix formation, shown by reaction with a conformation dependent monoclonal antibody.

Constructs for the expression of repeating triple-helical protein domains

Energy Technology Data Exchange (ETDEWEB)

Peng, Yong Y; Werkmeister, Jerome A; Vaughan, Paul R; Ramshaw, John A M, E-mail: jerome.werkmeister@csiro.a [CSIRO Molecular and Health Technologies, Bag 10, Clayton South, VIC 3169 (Australia)

2009-02-15

The development of novel scaffolds will be an important aspect in future success of tissue engineering. Scaffolds will preferably contain information that directs the cellular content of constructs so that the new tissue that is formed is closely aligned in structure, composition and function to the target natural tissue. One way of approaching this will be the development of novel protein-based constructs that contain one or more repeats of functional elements derived from various proteins. In the present case, we describe a strategy to make synthetic, recombinant triple-helical constructs that contain repeat segments of biologically relevant domains. Copies of a DNA fragment prepared by PCR from human type III collagen have been inserted in a co-linear contiguous fashion into the yeast expression vector YEpFlag-1, using sequential addition between selected restriction sites. Constructs containing 1, 2 and 3 repeats were designed to maintain the (Gly-X-Y) repeat, which is essential for the formation of an extended triple helix. All constructs gave expressed protein, with the best being the 3-repeat construct which was readily secreted. This material had the expected composition and N-terminal sequence. Incubation of the product at low temperature led to triple-helix formation, shown by reaction with a conformation dependent monoclonal antibody.

Acoustic Emission of Large PRSEUS Structures (Pultruded Rod Stitched Efficient Unitized Structure)

Science.gov (United States)

Horne, Michael R.; Juarez, Peter D.

2016-01-01

In the role of structural health monitoring (SHM), Acoustic Emission (AE) analysis is being investigated as an effective method for tracking damage development in large composite structures under load. Structures made using Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) for damage tolerant, light, and economical airframe construction are being pursued by The Boeing Company and NASA under the Environmentally Responsible Aircraft initiative (ERA). The failure tests of two PRSEUS substructures based on the Boeing Hybrid Wing Body fuselage concept were conducted during third quarter 2011 and second quarter 2015. One fundamental concern of these tests was determining the effectiveness of the stitched integral stiffeners to inhibit damage progression. By design, severe degradation of load carrying capability should not occur prior to Design Ultimate Load (DUL). While minor damage prior to DUL was anticipated, the integral stitching should not fail since this would allow a stiffener-skin delamination to progress rapidly and alter the transfer of load into the stiffeners. In addition, the stiffeners should not fracture because they are fundamental to structural integrity. Getting the best information from each AE sensor is a primary consideration because a sparse network of sensors is implemented. Sensitivity to stiffener-contiguous degradation is supported by sensors near the stiffeners, which increases the coverage per sensor via AE waveguide actions. Some sensors are located near potentially critical areas or "critical zones" as identified by numerical analyses. The approach is compared with the damage progression monitored by other techniques (e.g. ultrasonic C-scan).

Comparison of Repeated Measurement Design and Mixed Models in Evaluation of the Entonox Effect on Labor Pain

Directory of Open Access Journals (Sweden)

Nasim Karimi

2017-01-01

Full Text Available Background & objectives: In many medical studies, the response variable is measured repeatedly over time to evaluate the treatment effect that is known as longitudinal study. The analysis method for this type of data is repeated measures ANOVA that uses only one correlation structure and the results are not valid with inappropriate correlation structure. To avoid this problem, a convenient alternative is mixed models. So, the aim of this study was to compare of mixed and repeated measurement models for examination of the Entonox effect on the labor pain. Methods: This experimental study was designed to compare the effect of Entonox and oxygen inhalation on pain relief between two groups. Data were analyzed using repeated measurement and mixed models with different correlation structures. Selection and comparison of proper correlation structures performed using Akaike information criterion, Bayesian information criterion and restricted log-likelihood. Data were analyzed using SPSS-22. Results: Results of our study showed that all variables containing analgesia methods, labor duration of the first and second stages, and time were significant in these tests. In mixed model, heterogeneous first-order autoregressive, first-order autoregressive, heterogeneous Toeplitz and unstructured correlation structures were recognized as the best structures. Also, all variables were significant in these structures. Unstructured variance covariance matrix was recognized as the worst structure and labor duration of the first and second stages was not significant in this structure. Conclusions: This study showed that the Entonox inhalation has a significant effect on pain relief in primiparous and it is confirmed by all of the models.

Structural model for the interaction of a designed Ankyrin Repeat Protein with the human epidermal growth factor receptor 2.

Directory of Open Access Journals (Sweden)

V Chandana Epa

Full Text Available Designed Ankyrin Repeat Proteins are a class of novel binding proteins that can be selected and evolved to bind to targets with high affinity and specificity. We are interested in the DARPin H10-2-G3, which has been evolved to bind with very high affinity to the human epidermal growth factor receptor 2 (HER2. HER2 is found to be over-expressed in 30% of breast cancers, and is the target for the FDA-approved therapeutic monoclonal antibodies trastuzumab and pertuzumab and small molecule tyrosine kinase inhibitors. Here, we use computational macromolecular docking, coupled with several interface metrics such as shape complementarity, interaction energy, and electrostatic complementarity, to model the structure of the complex between the DARPin H10-2-G3 and HER2. We analyzed the interface between the two proteins and then validated the structural model by showing that selected HER2 point mutations at the putative interface with H10-2-G3 reduce the affinity of binding up to 100-fold without affecting the binding of trastuzumab. Comparisons made with a subsequently solved X-ray crystal structure of the complex yielded a backbone atom root mean square deviation of 0.84-1.14 Ångstroms. The study presented here demonstrates the capability of the computational techniques of structural bioinformatics in generating useful structural models of protein-protein interactions.

Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures

Directory of Open Access Journals (Sweden)

Hayes Michael L

2012-05-01

Full Text Available Abstract Background Pentatricopeptide repeat (PPR proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82 and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions. Results All of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3’ UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes. Conclusion PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative

Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures.

Science.gov (United States)

Hayes, Michael L; Giang, Karolyn; Mulligan, R Michael

2012-05-14

Pentatricopeptide repeat (PPR) proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82) and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions. All of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3' UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes. PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative selection even in the absence of an editing site target

The repeatability and reproducibility of the BioRID IIg in a repeatable laboratory seat based on a production car seat.

Science.gov (United States)

Hynd, David; Depinet, Paul; Lorenz, Bernd

2013-01-01

The United Nations Economic Commission for Europe Informal Group on GTR No. 7 Phase 2 are working to define a build level for the BioRID II rear impact (whiplash) crash test dummy that ensures repeatable and reproducible performance in a test procedure that has been proposed for future legislation. This includes the specification of dummy hardware, as well as the development of comprehensive certification procedures for the dummy. This study evaluated whether the dummy build level and certification procedures deliver the desired level of repeatability and reproducibility. A custom-designed laboratory seat was made using the seat base, back, and head restraint from a production car seat to ensure a representative interface with the dummy. The seat back was reinforced for use in multiple tests and the recliner mechanism was replaced by an external spring-damper mechanism. A total of 65 tests were performed with 6 BioRID IIg dummies using the draft GTR No.7 sled pulse and seating procedure. All dummies were subject to the build, maintenance, and certification procedures defined by the Informal Group. The test condition was highly repeatable, with a very repeatable pulse, a well-controlled seat back response, and minimal observed degradation of seat foams. The results showed qualitatively reasonable repeatability and reproducibility for the upper torso and head accelerations, as well as for T1 Fx and upper neck Fx . However, reproducibility was not acceptable for T1 and upper neck Fz or for T1 and upper neck My . The Informal Group has not selected injury or seat assessment criteria for use with BioRID II, so it is not known whether these channels would be used in the regulation. However, the ramping-up behavior of the dummy showed poor reproducibility, which would be expected to affect the reproducibility of dummy measurements in general. Pelvis and spine characteristics were found to significantly influence the dummy measurements for which poor reproducibility was

Accelerating large-scale protein structure alignments with graphics processing units

Directory of Open Access Journals (Sweden)

Pang Bin

2012-02-01

Full Text Available Abstract Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs. As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.

Orthographic units in the absence of visual processing: Evidence from sublexical structure in braille.

Science.gov (United States)

Fischer-Baum, Simon; Englebretson, Robert

2016-08-01

Reading relies on the recognition of units larger than single letters and smaller than whole words. Previous research has linked sublexical structures in reading to properties of the visual system, specifically on the parallel processing of letters that the visual system enables. But whether the visual system is essential for this to happen, or whether the recognition of sublexical structures may emerge by other means, is an open question. To address this question, we investigate braille, a writing system that relies exclusively on the tactile rather than the visual modality. We provide experimental evidence demonstrating that adult readers of (English) braille are sensitive to sublexical units. Contrary to prior assumptions in the braille research literature, we find strong evidence that braille readers do indeed access sublexical structure, namely the processing of multi-cell contractions as single orthographic units and the recognition of morphemes within morphologically-complex words. Therefore, we conclude that the recognition of sublexical structure is not exclusively tied to the visual system. However, our findings also suggest that there are aspects of morphological processing on which braille and print readers differ, and that these differences may, crucially, be related to reading using the tactile rather than the visual sensory modality. Copyright © 2016 Elsevier B.V. All rights reserved.

On Methods of Establishing Design Diagrams for Structural Integrity of Slender Complex Types of Breakwater Armour Units

DEFF Research Database (Denmark)

Burcharth, Hans F.; Howell, Gary J.

1988-01-01

Many of the recent dramatic failures of a number of large rubble mound breakwaters armoured with Dolosse and Tetrapods were caused by breakage of the concrete armour units. Breakage took place before the hydraulic stability of intact units in the armour layers expired. Thus there was not a balance...... between the strength (structural integrity) of the units and the hydraulic stability (resistance to displacements) of the armour layer. Although the relative strength of the units decreases with increasing size (Burcharth 1980) the shape of the units was kept constant and not related to the size...... of the units and the size was not increased beyond the demand dictated by the hydraulic stability.While the hydraulic stability can be roughly estimated by formulae and further evaluated in conventional hydraulic model tests, it is much more complicated to assess the structural integrity of the armour units...

Tube structural integrity evaluation of Palo Verde Unit 1 steam generators for axial upper-bundle cracking

International Nuclear Information System (INIS)

Woodman, B.W.; Begley, J.A.; Brown, S.D.; Sweeney, K.; Radspinner, M.; Melton, M.

1995-01-01

The analysis of the issue of upper bundle axial ODSCC as it apples to steam generator tube structural integrity in Unit 1 at the Palo Verde Nuclear generating Station is presented in this study. Based on past inspection results for Units 2 and 3 at Palo Verde, the detection of secondary side stress corrosion cracks in the upper bundle region of Unit 1 may occur at some future date. The following discussion provides a description and analysis of the probability of axial ODSCC in Unit 1 leading to the exceedance of Regulatory Guide 1.121 structural limits. The probabilities of structural limit exceedance are estimated as function of run time using a conservative approach. The chosen approach models the historical development of cracks, crack growth, detection of cracks and subsequent removal from service and the initiation and growth of new cracks during a given cycle of operation. Past performance of all Palo Verde Units as well as the historical performance of other steam generators was considered in the development of cracking statistics for application to Unit 1. Data in the literature and Unit 2 pulled tube examination results were used to construct probability of detection curves for the detection of axial IGSCC/IGA using an MRPC (multi-frequency rotating panake coil) eddy current probe. Crack growth rates were estimated from Unit 2 eddy current inspection data combined with pulled tube examination results and data in the literature. A Monte-Carlo probabilistic model is developed to provide an overall assessment of the risk of Regulatory Guide exceedance during plant operation

Seismic soil-structure-equipment interaction analysis of unit 5/6, Kozloduy NPP

Energy Technology Data Exchange (ETDEWEB)

Kostov, M [Bulgarian Academy of Sciences, Central Laboratory for Seismic Mechanics and Earthquake Engineering, Sofia (Bulgaria)

1995-07-01

This research project is aimed to analyse problems of soil-structure-equipment interaction under seismic excitation in case of Kozloduy NPP. Reevaluation and upgrading of Kozloduy NPP has started after 1977 Vrancea earthquake. New Safe Shutdown Earthquake (SSE) level was defined, upgrading most of structural equipment was performed, seismic instrumentation was installed. New investigations were initiated after 1990 IAEA mission visited the site. A comprehensive site confirmation project was started with a subsequent structural and equipment reevaluation and upgrading. This work deals with Units 5 and 6 of WWER-1000 type only.

Seismic upgrading of WWER 440-230 structures, units 1/2, Kozloduy NPP

International Nuclear Information System (INIS)

Stafanov, D.; Kostov, M.; Boncheva, H.; Varbanov, G.

1995-01-01

The purpose of this paper is to present final results from a big amount of computational work in connection with the investigations of the possibilities for upgrading of WWER 440-230 structures, units 1/2, Kozloduy NPP. (author)

Molecular structure of basic oligomeric building units of heparan-sulfate glycosaminoglycans

NARCIS (Netherlands)

Remko, Milan; Van Duijnen, Piet Th.; Broer, Ria

2010-01-01

This study reports in detail the results of systematic large-scale theoretical investigations of the acidic dimeric structural units (D-E, E-F, F-G, and G-H) and pentamer D-E-F-G-H (fondaparinux) of the glycosaminoglycan heparin, and their anionic forms. The geometries and energies of these

Hemolysin coregulated protein 1 as a molecular gluing unit for the assembly of nanoparticle hybrid structures

Directory of Open Access Journals (Sweden)

Tuan Anh Pham

2016-03-01

Full Text Available Hybrid nanoparticle (NP structures containing organic building units such as polymers, peptides, DNA and proteins have great potential in biosensor and electronic applications. The nearly free modification of the polymer chain, the variation of the protein and DNA sequence and the implementation of functional moieties provide a great platform to create inorganic structures of different morphology, resulting in different optical and magnetic properties. Nevertheless, the design and modification of a protein structure with functional groups or sequences for the assembly of biohybrid materials is not trivial. This is mainly due to the sensitivity of its secondary, tertiary and quaternary structure to the changes in the interaction (e.g., hydrophobic, hydrophilic, electrostatic, chemical groups between the protein subunits and the inorganic material. Here, we use hemolysin coregulated protein 1 (Hcp1 from Pseudomonas aeruginosa as a building and gluing unit for the formation of biohybrid structures by implementing cysteine anchoring points at defined positions on the protein rim (Hcp1_cys3. We successfully apply the Hcp1_cys3 gluing unit for the assembly of often linear, hybrid structures of plasmonic gold (Au NP, magnetite (Fe3O4 NP, and cobalt ferrite nanoparticles (CoFe2O4 NP. Furthermore, the assembly of Au NPs into linear structures using Hcp1_cys3 is investigated by UV–vis spectroscopy, TEM and cryo-TEM. One key parameter for the formation of Au NP assembly is the specific ionic strength in the mixture. The resulting network-like structure of Au NPs is characterized by Raman spectroscopy, showing surface-enhanced Raman scattering (SERS by a factor of 8·104 and a stable secondary structure of the Hcp1_cys3 unit. In order to prove the catalytic performance of the gold hybrid structures, they are used as a catalyst in the reduction reaction of 4-nitrophenol showing similar catalytic activity as the pure Au NPs. To further extend the

Evidence for a Creative Dilemma Posed by Repeated Collaborations.

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Hiroyasu Inoue

Full Text Available We focused on how repeat collaborations in projects for inventions affect performance. Repeat collaborations have two contradictory aspects. A positive aspect is team development or experience, and a negative aspect is team degeneration or decline. Since both contradicting phenomena are observed, inventors have a dilemma as to whether they should keep collaborating in a team or not. The dilemma has not previously been quantitatively analyzed. We provide quantitative and extensive analyses of the dilemma in creative projects by using patent data from Japan and the United States. We confirm three predictions to quantitatively validate the existence of the dilemma. The first prediction is that the greater the patent a team achieves, the longer the team will work together. The second prediction is that the impact of consecutive patents decreases after a team makes a remarkable invention, which is measured by the impact of patents. The third prediction is that the expectation of impact with new teams is greater than that with the same teams successful in the past. We find these predictions are validated in patents published in Japan and the United States. On the basis of these three predictions, we can quantitatively validate the dilemma in creative projects. We also propose preventive strategies for degeneration. One is developing technological diversity, and another is developing inventor diversity in teams. We find the two strategies are both effective by validating with the data.

A GPU implementation of a track-repeating algorithm for proton radiotherapy dose calculations

International Nuclear Information System (INIS)

Yepes, Pablo P; Mirkovic, Dragan; Taddei, Phillip J

2010-01-01

An essential component in proton radiotherapy is the algorithm to calculate the radiation dose to be delivered to the patient. The most common dose algorithms are fast but they are approximate analytical approaches. However their level of accuracy is not always satisfactory, especially for heterogeneous anatomical areas, like the thorax. Monte Carlo techniques provide superior accuracy; however, they often require large computation resources, which render them impractical for routine clinical use. Track-repeating algorithms, for example the fast dose calculator, have shown promise for achieving the accuracy of Monte Carlo simulations for proton radiotherapy dose calculations in a fraction of the computation time. We report on the implementation of the fast dose calculator for proton radiotherapy on a card equipped with graphics processor units (GPUs) rather than on a central processing unit architecture. This implementation reproduces the full Monte Carlo and CPU-based track-repeating dose calculations within 2%, while achieving a statistical uncertainty of 2% in less than 1 min utilizing one single GPU card, which should allow real-time accurate dose calculations.

Myotonin protein-kinase [AGC]n trinucleotide repeat in seven nonhuman primates

Energy Technology Data Exchange (ETDEWEB)

Novelli, G.; Sineo, L.; Pontieri, E. [Catholic Univ. of Rome (Italy)]|[Univ. of Milan (Italy)]|[Univ. Florence (Italy)] [and others

1994-09-01

Myotonic dystrophy (DM) is due to a genomic instability of a trinucleotide [AGC]n motif, located at the 3{prime} UTR region of a protein-kinase gene (myotonin protein kinase, MT-PK). The [AGC] repeat is meiotically and mitotically unstable, and it is directly related to the manifestations of the disorder. Although a gene dosage effect of the MT-PK has been demonstrated n DM muscle, the mechanism(s) by which the intragenic repeat expansion leads to disease is largely unknown. This non-standard mutational event could reflect an evolutionary mechanism widespread among animal genomes. We have isolated and sequenced the complete 3{prime}UTR region of the MT-PK gene in seven primates (macaque, orangutan, gorilla, chimpanzee, gibbon, owl monkey, saimiri), and examined by comparative sequence nucleotide analysis the [AGC]n intragenic repeat and the surrounding nucleotides. The genomic organization, including the [AGC]n repeat structure, was conserved in all examined species, excluding the gibbon (Hylobates agilis), in which the [AGC]n upstream sequence (GGAA) is replaced by a GA dinucleotide. The number of [AGC]n in the examined species ranged between 7 (gorilla) and 13 repeats (owl monkeys), with a polymorphism informative content (PIC) similar to that observed in humans. These results indicate that the 3{prime}UTR [AGC] repeat within the MT-PK gene is evolutionarily conserved, supporting that this region has important regulatory functions.

Relationship between unit cell type and porosity and the fatigue behavior of selective laser melted meta-biomaterials.

Science.gov (United States)

Amin Yavari, S; Ahmadi, S M; Wauthle, R; Pouran, B; Schrooten, J; Weinans, H; Zadpoor, A A

2015-03-01

Meta-materials are structures when their small-scale properties are considered, but behave as materials when their homogenized macroscopic properties are studied. There is an intimate relationship between the design of the small-scale structure and the homogenized properties of such materials. In this article, we studied that relationship for meta-biomaterials that are aimed for biomedical applications, otherwise known as meta-biomaterials. Selective laser melted porous titanium (Ti6Al4V ELI) structures were manufactured based on three different types of repeating unit cells, namely cube, diamond, and truncated cuboctahedron, and with different porosities. The morphological features, static mechanical properties, and fatigue behavior of the porous biomaterials were studied with a focus on their fatigue behavior. It was observed that, in addition to static mechanical properties, the fatigue properties of the porous biomaterials are highly dependent on the type of unit cell as well as on porosity. None of the porous structures based on the cube unit cell failed after 10(6) loading cycles even when the applied stress reached 80% of their yield strengths. For both other unit cells, higher porosities resulted in shorter fatigue lives for the same level of applied stress. When normalized with respect to their yield stresses, the S-N data points of structures with different porosities very well (R(2)>0.8) conformed to one single power law specific to the type of the unit cell. For the same level of normalized applied stress, the truncated cuboctahedron unit cell resulted in a longer fatigue life as compared to the diamond unit cell. In a similar comparison, the fatigue lives of the porous structures based on both truncated cuboctahedron and diamond unit cells were longer than that of the porous structures based on the rhombic dodecahedron unit cell (determined in a previous study). The data presented in this study could serve as a basis for design of porous biomaterials

78 FR 65594 - Vehicular Repeaters

Science.gov (United States)

2013-11-01

... coordinators estimate the effect on coordination fees? Does the supposed benefit that mobile repeater stations... allow the licensing and operation of vehicular repeater systems and other mobile repeaters by public... email: [email protected] or phone: 202-418- 0530 or TTY: 202-418-0432. For detailed instructions for...

Three-dimensional structure of the Trypanosome flagellum suggests that the paraflagellar rod functions as a biomechanical spring.

Directory of Open Access Journals (Sweden)

Louise C Hughes

Full Text Available Flagellum motility is critical for normal human development and for transmission of pathogenic protozoa that cause tremendous human suffering worldwide. Biophysical principles underlying motility of eukaryotic flagella are conserved from protists to vertebrates. However, individual cells exhibit diverse waveforms that depend on cell-specific elaborations on basic flagellum architecture. Trypanosoma brucei is a uniflagellated protozoan parasite that causes African sleeping sickness. The T. brucei flagellum is comprised of a 9+2 axoneme and an extra-axonemal paraflagellar rod (PFR, but the three-dimensional (3D arrangement of the underlying structural units is poorly defined. Here, we use dual-axis electron tomography to determine the 3D architecture of the T. brucei flagellum. We define the T. brucei axonemal repeating unit. We observe direct connections between the PFR and axonemal dyneins, suggesting a mechanism by which mechanochemical signals may be transmitted from the PFR to axonemal dyneins. We find that the PFR itself is comprised of overlapping laths organized into distinct zones that are connected through twisting elements at the zonal interfaces. The overall structure has an underlying 57 nm repeating unit. Biomechanical properties inferred from PFR structure lead us to propose that the PFR functions as a biomechanical spring that may store and transmit energy derived from axonemal beating. These findings provide insight into the structural foundations that underlie the distinctive flagellar waveform that is a hallmark of T. brucei cell motility.

Tevatron serial data repeater system

International Nuclear Information System (INIS)

Ducar, R.J.

1981-01-01

A ten megabit per second serial data repeater system has been developed for the 6.28km Tevatron accelerator. The repeaters are positioned at each of the thirty service buildings and accommodate control and abort system communications as well as distribution of the Tevatron time and energy clocks. The repeaters are transparent to the particular protocol of the transmissions. Serial data are encoded locally as unipolar two volt signals employing the self-clocking Manchester Bi-Phase code. The repeaters modulate the local signals to low-power bursts of 50 MHz rf carrier for the 260m transmission between service buildings. The repeaters also demodulate the transmission and restructure the data for local utilization. The employment of frequency discrimination techniques yields high immunity to the characteristic noise spectrum

Twisting right to left: A…A mismatch in a CAG trinucleotide repeat overexpansion provokes left-handed Z-DNA conformation.

Directory of Open Access Journals (Sweden)

Noorain Khan

2015-04-01

Full Text Available Conformational polymorphism of DNA is a major causative factor behind several incurable trinucleotide repeat expansion disorders that arise from overexpansion of trinucleotide repeats located in coding/non-coding regions of specific genes. Hairpin DNA structures that are formed due to overexpansion of CAG repeat lead to Huntington's disorder and spinocerebellar ataxias. Nonetheless, DNA hairpin stem structure that generally embraces B-form with canonical base pairs is poorly understood in the context of periodic noncanonical A…A mismatch as found in CAG repeat overexpansion. Molecular dynamics simulations on DNA hairpin stems containing A…A mismatches in a CAG repeat overexpansion show that A…A dictates local Z-form irrespective of starting glycosyl conformation, in sharp contrast to canonical DNA duplex. Transition from B-to-Z is due to the mechanistic effect that originates from its pronounced nonisostericity with flanking canonical base pairs facilitated by base extrusion, backbone and/or base flipping. Based on these structural insights we envisage that such an unusual DNA structure of the CAG hairpin stem may have a role in disease pathogenesis. As this is the first study that delineates the influence of a single A…A mismatch in reversing DNA helicity, it would further have an impact on understanding DNA mismatch repair.

Rapid-Response or Repeat-Mode Topography from Aerial Structure from Motion

Science.gov (United States)

Nissen, E.; Johnson, K. L.; Fitzgerald, F. S.; Morgan, M.; White, J.

2014-12-01

This decade has seen a surge of interest in Structure-from-Motion (SfM) as a means of generating high-resolution topography and coregistered texture maps from stereo digital photographs. Using an unstructured set of overlapping photographs captured from multiple viewpoints and minimal GPS ground control, SfM solves simultaneously for scene topography and camera positions, orientations and lens parameters. The use of cheap unmanned aerial vehicles or tethered helium balloons as camera platforms expedites data collection and overcomes many of the cost, time and logistical limitations of LiDAR surveying, making it a potentially valuable tool for rapid response mapping and repeat monitoring applications. We begin this presentation by assessing what data resolutions and precisions are achievable using a simple aerial camera platform and commercial SfM software (we use the popular Agisoft Photoscan package). SfM point clouds generated at two small (~0.1 km2), sparsely-vegetated field sites in California compare favorably with overlapping airborne and terrestrial LiDAR surveys, with closest point distances of a few centimeters between the independent datasets. Next, we go on to explore the method in more challenging conditions, in response to a major landslide in Mesa County, Colorado, on 25th May 2014. Photographs collected from a small UAV were used to generate a high-resolution model of the 4.5 x 1 km landslide several days before an airborne LiDAR survey could be organized and flown. An initial estimate of the mass balance of the landslide could quickly be made by differencing this model against pre-event topography generated using stereo photographs collected in 2009 as part of the National Agricultural Imagery Program (NAIP). This case study therefore demonstrates the rich potential offered by this technique, as well as some of the challenges, particularly with respect to the treatment of vegetation.

Poly(phenylsesquioxane) base silicon resins: synthesis, characterization and structural study by SAXS; Resinas de silicona a base de poli(fenilsilsesquioxano): sintese, caracterizacao e estudo estrutural por SAXS

Energy Technology Data Exchange (ETDEWEB)

Prado, Luis Antonio Sanchez de Almeida; Yoshida, Inez Valeria Pagotto [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Inst. de Quimica], e-mail: valeria@iqm.unicamp.br

2000-07-01

T{sup Ph}, T{sup Ph}D{sup L} and T{sup Ph}D{sup C} silicone resins were prepared by sol-gel method, using phenyltriethoxysilane as a source of T{sup Ph} repeating units, and poly(dimethylsiloxane), D{sup L}, or tetramethyldiethoxydissiloxane, D{sup C}, as sources of D segments. The molecular structure of these resins were characterized by FT-IR and {sup 29}Si MAS NMR spectra. SAXS traces of T{sup Ph}D{sup L} resins presented a halo associated to a high concentration of scattering units with spatial correlation. The behavior of the SAXS traces for T{sup Ph}D{sup C} were an indication of a random distribution of scattering centers. The nano structure of these materials cannot be described as a system of isolated scattering centers. The electron density contrast was attributed to the presence of regions richer in T{sup Ph} repeating units. TGA curves evidenced good thermal stability for all resins obtained. (author)

Identification of infusion strategy for achieving repeatable nanoparticle distribution and quantification of thermal dosage using micro-CT Hounsfield unit in magnetic nanoparticle hyperthermia.

Science.gov (United States)

LeBrun, Alexander; Joglekar, Tejashree; Bieberich, Charles; Ma, Ronghui; Zhu, Liang

2016-01-01

The objective of this study was to identify an injection strategy leading to repeatable nanoparticle deposition patterns in tumours and to quantify volumetric heat generation rate distribution based on micro-CT Hounsfield unit (HU) in magnetic nanoparticle hyperthermia. In vivo animal experiments were performed on graft prostatic cancer (PC3) tumours in immunodeficient mice to investigate whether lowering ferrofluid infusion rate improves control of the distribution of magnetic nanoparticles in tumour tissue. Nanoparticle distribution volume obtained from micro-CT scan was used to evaluate spreading of the nanoparticles from the injection site in tumours. Heating experiments were performed to quantify relationships among micro-CT HU values, local nanoparticle concentrations in the tumours, and the ferrofluid-induced volumetric heat generation rate (q(MNH)) when nanoparticles were subject to an alternating magnetic field. An infusion rate of 3 µL/min was identified to result in the most repeatable nanoparticle distribution in PC3 tumours. Linear relationships have been obtained to first convert micro-CT greyscale values to HU values, then to local nanoparticle concentrations, and finally to nanoparticle-induced q(MNH) values. The total energy deposition rate in tumours was calculated and the observed similarity in total energy deposition rates in all three infusion rate groups suggests improvement in minimising nanoparticle leakage from the tumours. The results of this study demonstrate that micro-CT generated q(MNH) distribution and tumour physical models improve predicting capability of heat transfer simulation for designing reliable treatment protocols using magnetic nanoparticle hyperthermia.

Repeat Customer Success in Extension

Science.gov (United States)

Bess, Melissa M.; Traub, Sarah M.

2013-01-01

Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

Film repeats in radiology department

International Nuclear Information System (INIS)

Suwan, A. Z.; Al-Shakharah, A. I

1997-01-01

During a one year period, 4910 radiographs of 55780 films were repeated. The objective of our study was to analyse and to classify the causes in order to minimize the repeats, cut the expenses and to provide optimal radiographs for accurate diagnosis. Analysis of the different factors revealed that, 43.6% of film repeats in our service were due to faults in exposure factors, centering comprises 15.9% of the repeats, while too much collimation was responsible for 7.6% of these repeats. All of which can be decreased by awareness and programmed training of technicians. Film blurring caused by patient motion was also responsible for 4.9% for radiographs reexamination, which can be minimized by detailed explanation to the patient and providing the necessary privacy. Fogging of X-Ray films by improper storage or inadequate handling or processing faults were responsible for 14.5% in repeats in our study. Methods and criteria for proper storage and handling of films were discussed. Recommendation for using modern day-light and laser processor has been high lighted. Artefacts are noticeably high in our cases, due to spinal dresses and frequent usage of precious metals for c osmotic purposes in this part of the world. The repeated films comprise 8.8% of all films We conclude that, the main factor responsible for repeats of up to 81.6% of cases was the technologists, thus emphasizing the importance of adequate training of the technologists. (authors). 15 refs., 9 figs., 1 table

The breathing of webs under repeated partial edge loading

Czech Academy of Sciences Publication Activity Database

Škaloud, Miroslav; Zörnerová, Marie; Urushadze, Shota

2012-01-01

Roč. 40, č. 1 (2012), s. 463-468 E-ISSN 1877-7058. [Steel structures and bridges. Podbanske, 26.09.2012-28.09.2012] R&D Projects: GA ČR GA103/08/1340 Institutional support: RVO:68378297 Keywords : slender webs * breathing * fatigue limit state * design * repeated partial edge loading Subject RIV: JM - Building Engineering

Repeat migration and disappointment.

Science.gov (United States)

Grant, E K; Vanderkamp, J

1986-01-01

This article investigates the determinants of repeat migration among the 44 regions of Canada, using information from a large micro-database which spans the period 1968 to 1971. The explanation of repeat migration probabilities is a difficult task, and this attempt is only partly successful. May of the explanatory variables are not significant, and the overall explanatory power of the equations is not high. In the area of personal characteristics, the variables related to age, sex, and marital status are generally significant and with expected signs. The distance variable has a strongly positive effect on onward move probabilities. Variables related to prior migration experience have an important impact that differs between return and onward probabilities. In particular, the occurrence of prior moves has a striking effect on the probability of onward migration. The variable representing disappointment, or relative success of the initial move, plays a significant role in explaining repeat migration probabilities. The disappointment variable represents the ratio of actural versus expected wage income in the year after the initial move, and its effect on both repeat migration probabilities is always negative and almost always highly significant. The repeat probabilities diminish after a year's stay in the destination region, but disappointment in the most recent year still has a bearing on the delayed repeat probabilities. While the quantitative impact of the disappointment variable is not large, it is difficult to draw comparisons since similar estimates are not available elsewhere.

Quantum repeated games revisited

International Nuclear Information System (INIS)

Frąckiewicz, Piotr

2012-01-01

We present a scheme for playing quantum repeated 2 × 2 games based on Marinatto and Weber’s approach to quantum games. As a potential application, we study the twice repeated Prisoner’s Dilemma game. We show that results not available in the classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games proposed by Iqbal and Toor. We point out the drawbacks that make their results unacceptable. (paper)

Computer-aided polymer design using group contribution plus property models

DEFF Research Database (Denmark)

Satyanarayana, Kavitha Chelakara; Abildskov, Jens; Gani, Rafiqul

2009-01-01

. Polymer repeat unit property prediction models are required to calculate the properties of the generated repeat units. A systematic framework incorporating recently developed group contribution plus (GC(+)) models and an extended CAMD technique to include design of polymer repeat units is highlighted...... in this paper. The advantage of a GC(+) model in CAMD applications is that a very large number of polymer structures can be considered even though some of the group parameters may not be available. A number of case studies involving different polymer design problems have been solved through the developed......The preliminary step for polymer product design is to identify the basic repeat unit structure of the polymer that matches the target properties. Computer-aided molecular design (CAMD) approaches can be applied for generating the polymer repeat unit structures that match the required constraints...

Centre-containing spiral-geometric structure of the space-time and nonrelativistic relativity of the unit time

International Nuclear Information System (INIS)

Shakhazizyan, S.R.

1987-01-01

The problem of nonrelativistic dependence of unit length and unit time on the position in the space is considered on the basis of centre-containing spiral-geometric structure of the space-time. The experimental results of variation of the unit time are analyzed which well agree with the requirements of the model proposed. 13 refs.; 12 figs

Genetic instability associated with loop or stem–loop structures within transcription units can be independent of nucleotide excision repair

Science.gov (United States)

Burns, John A; Chowdhury, Moinuddin A; Cartularo, Laura; Berens, Christian; Scicchitano, David A

2018-01-01

Abstract Simple sequence repeats (SSRs) are found throughout the genome, and under some conditions can change in length over time. Germline and somatic expansions of trinucleotide repeats are associated with a series of severely disabling illnesses, including Huntington's disease. The underlying mechanisms that effect SSR expansions and contractions have been experimentally elusive, but models suggesting a role for DNA repair have been proposed, in particular the involvement of transcription-coupled nucleotide excision repair (TCNER) that removes transcription-blocking DNA damage from the transcribed strand of actively expressed genes. If the formation of secondary DNA structures that are associated with SSRs were to block RNA polymerase progression, TCNER could be activated, resulting in the removal of the aberrant structure and a concomitant change in the region's length. To test this, TCNER activity in primary human fibroblasts was assessed on defined DNA substrates containing extrahelical DNA loops that lack discernible internal base pairs or DNA stem–loops that contain base pairs within the stem. The results show that both structures impede transcription elongation, but there is no corresponding evidence that nucleotide excision repair (NER) or TCNER operates to remove them. PMID:29474673

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

Directory of Open Access Journals (Sweden)

Glass John I

2010-07-01

Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

Breaks in the 45S rDNA Lead to Recombination-Mediated Loss of Repeats

Directory of Open Access Journals (Sweden)

Daniël O. Warmerdam

2016-03-01

Full Text Available rDNA repeats constitute the most heavily transcribed region in the human genome. Tumors frequently display elevated levels of recombination in rDNA, indicating that the repeats are a liability to the genomic integrity of a cell. However, little is known about how cells deal with DNA double-stranded breaks in rDNA. Using selective endonucleases, we show that human cells are highly sensitive to breaks in 45S but not the 5S rDNA repeats. We find that homologous recombination inhibits repair of breaks in 45S rDNA, and this results in repeat loss. We identify the structural maintenance of chromosomes protein 5 (SMC5 as contributing to recombination-mediated repair of rDNA breaks. Together, our data demonstrate that SMC5-mediated recombination can lead to error-prone repair of 45S rDNA repeats, resulting in their loss and thereby reducing cellular viability.

Dynamical simulation of structural multiplicity in grain boundaries

International Nuclear Information System (INIS)

Majid, I.; Bristowe, P.D.

1987-06-01

Work on a computer simulation study of a low-energy high-angle boundary structure which is not periodic have been recently reported. This result is of interest since grain boundary structures are usually assumed to have a periodicity corresponding to the appropriate coincidence site lattice (CSL) and many experimental observations of the structure of grain boundaries performed using conventional and high-resolution electron microscopy, electron diffraction and x-ray diffraction appear to support this work. However, this work, using empirical interatomic pair potentials and the relaxation method of molecular statics, have simulated a Σ = 5 36.87 0 (001) twist boundary and found a low energy structure having a larger repeat cell than the CSL and is composed of two different types of structural unit that are randomly distributed in the boundary plane. This result, which has been termed the multiplicity of grain boundary structures, has also been found in the simulation of tilt boundaries. The multiplicity phenomenon is of special interest in twist boundaries since it is used as a structural model to explain the x-ray scattering from a Σ = 5 boundary in gold. These scattering patterns had previously remained unexplained using stable structures that had simple CSL periodicity. Also, the effect of having a multiple number of low energy structural units coexisting in the grain boundary is of more general interest since it implies that the boundary structures may be quasi-periodic and, in some circumstances, may even result in a roughening of the boundary plane. This paper extends this work by showing, using molecular dynamics, that a multiplicity of structural units can actually nucleate spontaneously in a high-angle grain boundary at finite temperatures

Extra-regulatory impact tests and analyses of the structural evaluation test unit

International Nuclear Information System (INIS)

Ludwigsen, J.S.; Ammerman, D.J.

1995-01-01

The structural evaluation test unit is roughly equivalent to a 1/3 scale model of a high level waste rail cask. The test unit was designed to just meet the requirements of NRC Regulatory Guide 7.6 when subjected to a 9 m (30 ft) free drop resulting in an impact velocity of 13.4 m/s (30 mph) onto an unyielding target in the end-on orientation. The test unit was then subjected to impacts with higher velocities to determine the amount of built-in conservatism in this design approach. Test impacts of 13.4, 20.1 and 26.8 m/s (30, 45, and 60 mph) were performed. This paper will describe the design, testing, and comparison of measured strains and deformations to the equivalent analytical predictions

Repeated episodes of ozone inhalation amplifies the effects of allergen sensitization and inhalation on airway immune and structural development in Rhesus monkeys.

Science.gov (United States)

Schelegle, Edward S; Miller, Lisa A; Gershwin, Laurel J; Fanucchi, Michelle V; Van Winkle, Laura S; Gerriets, Joan E; Walby, William F; Mitchell, Valerie; Tarkington, Brian K; Wong, Viviana J; Baker, Gregory L; Pantle, Lorraine M; Joad, Jesse P; Pinkerton, Kent E; Wu, Reen; Evans, Michael J; Hyde, Dallas M; Plopper, Charles G

2003-08-15

Twenty-four infant rhesus monkeys (30 days old) were exposed to 11 episodes of filtered air (FA), house dust mite allergen aerosol (HDMA), ozone (O3), or HDMA + O3 (5 days each followed by 9 days of FA). Ozone was delivered for 8 h/day at 0.5 ppm. Twelve of the monkeys were sensitized to house dust mite allergen (Dermatophagoides farinae) at ages 14 and 28 days by subcutaneous inoculation (SQ) of HDMA in alum and intraperitoneal injection of heat-killed Bordetella pertussis cells. Sensitized monkeys were exposed to HDMA aerosol for 2 h/day on days 3-5 of either FA (n = 6) or O3 (n = 6) exposure. Nonsensitized monkeys were exposed to either FA (n = 6) or O3 (n = 6). During the exposure regimen, parameters of allergy (i.e., serum IgE, histamine, and eosinophilia), airways resistance, reactivity, and structural remodeling were evaluated. Eleven repeated 5-day cycles of inhaling 0.5 ppm ozone over a 6-month period had only mild effects on the airways of nonsensitized infant rhesus monkeys. Similarly, the repeated inhalation of HDMA by HDMA-sensitized infant monkeys resulted in only mild airway effects, with the exception of a marked increase in proximal airway and terminal bronchiole content of eosinophils. In contrast, the combined cyclic inhalation of ozone and HDMA by HDMA sensitized infants monkeys resulted in a marked increase in serum IgE, serum histamine, and airways eosinophilia. Furthermore, combined cyclic inhalation of ozone and HDMA resulted in even greater alterations in airway structure and content that were associated with a significant elevation in baseline airways resistance and reactivity. These results suggest that ozone can amplify the allergic and structural remodeling effects of HDMA sensitization and inhalation.

Repeatability of visual acuity measurement.

Science.gov (United States)

Raasch, T W; Bailey, I L; Bullimore, M A

1998-05-01

This study investigates features of visual acuity chart design and acuity testing scoring methods which affect the validity and repeatability of visual acuity measurements. Visual acuity was measured using the Sloan and British Standard letter series, and Landolt rings. Identifiability of the different letters as a function of size was estimated, and expressed in the form of frequency-of-seeing curves. These functions were then used to simulate acuity measurements with a variety of chart designs and scoring criteria. Systematic relationships exist between chart design parameters and acuity score, and acuity score repeatability. In particular, an important feature of a chart, that largely determines the repeatability of visual acuity measurement, is the amount of size change attributed to each letter. The methods used to score visual acuity performance also affect repeatability. It is possible to evaluate acuity score validity and repeatability using the statistical principles discussed here.

Molecular structure and chromosome distribution of three repetitive DNA families in Anemone hortensis L. (Ranunculaceae).

Science.gov (United States)

Mlinarec, Jelena; Chester, Mike; Siljak-Yakovlev, Sonja; Papes, Drazena; Leitch, Andrew R; Besendorfer, Visnja

2009-01-01

The structure, abundance and location of repetitive DNA sequences on chromosomes can characterize the nature of higher plant genomes. Here we report on three new repeat DNA families isolated from Anemone hortensis L.; (i) AhTR1, a family of satellite DNA (stDNA) composed of a 554-561 bp long EcoRV monomer; (ii) AhTR2, a stDNA family composed of a 743 bp long HindIII monomer and; (iii) AhDR, a repeat family composed of a 945 bp long HindIII fragment that exhibits some sequence similarity to Ty3/gypsy-like retroelements. Fluorescence in-situ hybridization (FISH) to metaphase chromosomes of A. hortensis (2n = 16) revealed that both AhTR1 and AhTR2 sequences co-localized with DAPI-positive AT-rich heterochromatic regions. AhTR1 sequences occur at intercalary DAPI bands while AhTR2 sequences occur at 8-10 terminally located heterochromatic blocks. In contrast AhDR sequences are dispersed over all chromosomes as expected of a Ty3/gypsy-like element. AhTR2 and AhTR1 repeat families include polyA- and polyT-tracks, AT/TA-motifs and a pentanucleotide sequence (CAAAA) that may have consequences for chromatin packing and sequence homogeneity. AhTR2 repeats also contain TTTAGGG motifs and degenerate variants. We suggest that they arose by interspersion of telomeric repeats with subtelomeric repeats, before hybrid unit(s) amplified through the heterochromatic domain. The three repetitive DNA families together occupy approximately 10% of the A. hortensis genome. Comparative analyses of eight Anemone species revealed that the divergence of the A. hortensis genome was accompanied by considerable modification and/or amplification of repeats.

Magnetoresistance oscillations of two-dimensional electron systems in lateral superlattices with structured unit cells

Science.gov (United States)

Gerhardts, Rolf R.

2015-11-01

Model calculations for commensurability oscillations of the low-field magnetoresistance of two-dimensional electron systems (2DES) in lateral superlattices, consisting of unit cells with an internal structure, are compared with recent experiments. The relevant harmonics of the effective modulation potential depend not only on the geometrical structure of the modulated unit cell, but also strongly on the nature of the modulation. While higher harmonics of an electrostatically generated surface modulation are exponentially damped at the position of the 2DES about 90 nm below the surface, no such damping appears for strain-induced modulation generated, e.g., by the deposition of stripes of calixarene resist on the surface before cooling down the sample.

Changes in the state of heat-resistant steel induced by repeated hot deformation

Science.gov (United States)

Lyubimova, Lyudmila L.; Fisenko, Roman N.; Tashlykov, Alexander A.; Tabakaev, Roman B.

2018-01-01

This work deals with the problems of structural regeneration by thermal restoration treatment (TRT). These include the lack of a structural sign showing that TRT is possible, a consensus on TRT modes, the data on the necessary relaxation depth of residual stresses, or criteria of structural restoration. Performing a TRT without solving these problems may deteriorate the properties of steel or even accelerate its destruction. With this in view, the purpose of this work is to determine experimentally how the residual stress state changes under thermal and mechanical loads in order to specify the signs of the restoration of structure and structural stability. The object of this research is unused 12Cr1MoV steel that has been aged naturally for 13 years. Using X-ray dosimetry with X-ray spectral analysis, we study the distribution of internal residual stresses of the first kind during the repeated hot deformation. After repeated thermal deformation, the sample under study transforms from a viscoelastic Maxwell material into a Kelvin-Voigt material, which facilitates structural stabilization. A sign of this is the relaxation limit increase, prevention of continuous decay of an α-solid solution of iron and restoration of the lattice parameter.

Structural empowerment and patient safety culture among registered nurses working in adult critical care units.

Science.gov (United States)

Armellino, Donna; Quinn Griffin, Mary T; Fitzpatrick, Joyce J

2010-10-01

The aim of the present study was to examine the relationship between structural empowerment and patient safety culture among staff level Registered Nurses (RNs) within adult critical care units (ACCU). There is literature to support the value of RNs' structurally empowered work environments and emerging literature towards patient safety culture; the link between empowerment and patient safety culture is being discovered. A sample of 257 RNs, working within adult critical care of a tertiary hospital in the United States, was surveyed. Instruments included a background data sheet, the Conditions of Workplace Effectiveness and the Hospital Survey on Patient Safety Culture. Structural empowerment and patient safety culture were significantly correlated. As structural empowerment increased so did the RNs' perception of patient safety culture. To foster patient safety culture, nurse leaders should consider providing structurally empowering work environments for RNs. This study contributes to the body of knowledge linking structural empowerment and patient safety culture. Results link structurally empowered RNs and increased patient safety culture, essential elements in delivering efficient, competent, quality care. They inform nursing management of key factors in the nurses' environment that promote safe patient care environments. © 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd.

Crystal structure of LGR4-Rspo1 complex: insights into the divergent mechanisms of ligand recognition by leucine-rich repeat G-protein-coupled receptors (LGRs).

Science.gov (United States)

Xu, Jin-Gen; Huang, Chunfeng; Yang, Zhengfeng; Jin, Mengmeng; Fu, Panhan; Zhang, Ni; Luo, Jian; Li, Dali; Liu, Mingyao; Zhou, Yan; Zhu, Yongqun

2015-01-23

Leucine-rich repeat G-protein-coupled receptors (LGRs) are a unique class of G-protein-coupled receptors characterized by a large extracellular domain to recognize ligands and regulate many important developmental processes. Among the three groups of LGRs, group B members (LGR4-6) recognize R-spondin family proteins (Rspo1-4) to stimulate Wnt signaling. In this study, we successfully utilized the "hybrid leucine-rich repeat technique," which fused LGR4 with the hagfish VLR protein, to obtain two recombinant human LGR4 proteins, LGR415 and LGR49. We determined the crystal structures of ligand-free LGR415 and the LGR49-Rspo1 complex. LGR4 exhibits a twisted horseshoe-like structure. Rspo1 adopts a flat and β-fold architecture and is bound in the concave surface of LGR4 in the complex through electrostatic and hydrophobic interactions. All the Rspo1-binding residues are conserved in LGR4-6, suggesting that LGR4-6 bind R-spondins through an identical surface. Structural analysis of our LGR4-Rspo1 complex with the previously determined LGR4 and LGR5 structures revealed that the concave surface of LGR4 is the sole binding site for R-spondins, suggesting a one-site binding model of LGR4-6 in ligand recognition. The molecular mechanism of LGR4-6 is distinct from the two-step mechanism of group A receptors LGR1-3 and the multiple-interface binding model of group C receptors LGR7-8, suggesting LGRs utilize the divergent mechanisms for ligand recognition. Our structures, together with previous reports, provide a comprehensive understanding of the ligand recognition by LGRs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

CGG repeats associated with fragile X chromosome form left-handed Z-DNA structure

Czech Academy of Sciences Publication Activity Database

Renčiuk, Daniel; Kypr, Jaroslav; Vorlíčková, Michaela

2011-01-01

Roč. 95, č. 3 (2011), s. 174-181 ISSN 0006-3525 R&D Projects: GA ČR(CZ) GA202/07/0094; GA AV ČR(CZ) IAA100040701 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : fragile X chromosome syndrome * Z-DNA * trinucleotide repeats Subject RIV: BO - Biophysics Impact factor: 2.870, year: 2011

Dispersion Measure Variation of Repeating Fast Radio Burst Sources

Energy Technology Data Exchange (ETDEWEB)

Yang, Yuan-Pei; Zhang, Bing, E-mail: yypspore@gmail.com, E-mail: zhang@physics.unlv.edu [Kavli Institute for Astronomy and Astrophysics, Peking University, Beijing 100871 (China)

2017-09-20

The repeating fast radio burst (FRB) 121102 was recently localized in a dwarf galaxy at a cosmological distance. The dispersion measure (DM) derived for each burst from FRB 121102 so far has not shown significant evolution, even though an apparent increase was recently seen with newly detected VLA bursts. It is expected that more repeating FRB sources may be detected in the future. In this work, we investigate a list of possible astrophysical processes that might cause DM variation of a particular FRB source. The processes include (1) cosmological scale effects such as Hubble expansion and large-scale structure fluctuations; (2) FRB local effects such as gas density fluctuation, expansion of a supernova remnant (SNR), a pulsar wind nebula, and an H ii region; and (3) the propagation effect due to plasma lensing. We find that the DM variations contributed by the large-scale structure are extremely small, and any observable DM variation is likely caused by the plasma local to the FRB source. In addition to mechanisms that decrease DM over time, we suggest that an FRB source in an expanding SNR around a nearly neutral ambient medium during the deceleration (Sedov–Taylor and snowplow) phases or in a growing H ii region can increase DM. Some effects (e.g., an FRB source moving in an H ii region or plasma lensing) can produce either positive or negative DM variations. Future observations of DM variations of FRB 121102 and other repeating FRB sources can provide important clues regarding the physical origin of these sources.

Dispersion Measure Variation of Repeating Fast Radio Burst Sources

International Nuclear Information System (INIS)

Yang, Yuan-Pei; Zhang, Bing

2017-01-01

The repeating fast radio burst (FRB) 121102 was recently localized in a dwarf galaxy at a cosmological distance. The dispersion measure (DM) derived for each burst from FRB 121102 so far has not shown significant evolution, even though an apparent increase was recently seen with newly detected VLA bursts. It is expected that more repeating FRB sources may be detected in the future. In this work, we investigate a list of possible astrophysical processes that might cause DM variation of a particular FRB source. The processes include (1) cosmological scale effects such as Hubble expansion and large-scale structure fluctuations; (2) FRB local effects such as gas density fluctuation, expansion of a supernova remnant (SNR), a pulsar wind nebula, and an H ii region; and (3) the propagation effect due to plasma lensing. We find that the DM variations contributed by the large-scale structure are extremely small, and any observable DM variation is likely caused by the plasma local to the FRB source. In addition to mechanisms that decrease DM over time, we suggest that an FRB source in an expanding SNR around a nearly neutral ambient medium during the deceleration (Sedov–Taylor and snowplow) phases or in a growing H ii region can increase DM. Some effects (e.g., an FRB source moving in an H ii region or plasma lensing) can produce either positive or negative DM variations. Future observations of DM variations of FRB 121102 and other repeating FRB sources can provide important clues regarding the physical origin of these sources.

A case study examination of structure and function in a state health department chronic disease unit.

Science.gov (United States)

Alongi, Jeanne

2015-04-01

I explored the structural and operational practices of the chronic disease prevention and control unit of a state health department and proposed a conceptual model of structure, function, and effectiveness for future study. My exploratory case study examined 7 elements of organizational structure and practice. My interviews with staff and external stakeholders of a single chronic disease unit yielded quantitative and qualitative data that I coded by perspective, process, relationship, and activity. I analyzed these for patterns and emerging themes. Chi-square analysis revealed significant correlations among collaboration with goal ambiguity, political support, and responsiveness, and evidence-based decisions with goal ambiguity and responsiveness. Although my study design did not permit conclusions about causality, my findings suggested that some elements of the model might facilitate effectiveness for chronic disease units and should be studied further. My findings might have important implications for identifying levers around which capacity can be built that may strengthen effectiveness.

Breaks in the 45S rDNA Lead to Recombination-Mediated Loss of Repeats.

Science.gov (United States)

Warmerdam, Daniël O; van den Berg, Jeroen; Medema, René H

2016-03-22

rDNA repeats constitute the most heavily transcribed region in the human genome. Tumors frequently display elevated levels of recombination in rDNA, indicating that the repeats are a liability to the genomic integrity of a cell. However, little is known about how cells deal with DNA double-stranded breaks in rDNA. Using selective endonucleases, we show that human cells are highly sensitive to breaks in 45S but not the 5S rDNA repeats. We find that homologous recombination inhibits repair of breaks in 45S rDNA, and this results in repeat loss. We identify the structural maintenance of chromosomes protein 5 (SMC5) as contributing to recombination-mediated repair of rDNA breaks. Together, our data demonstrate that SMC5-mediated recombination can lead to error-prone repair of 45S rDNA repeats, resulting in their loss and thereby reducing cellular viability. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Structural review of the Palisades Nuclear Power Plant Unit 1 containment structure under combined loads for the Systematic Evaluation Program

International Nuclear Information System (INIS)

Liaw, C.Y.; Debeling, A.; Tsai, N.C.

1981-12-01

A structural reassessment of the containment structure of the Palisades Nuclear Power Plant Unit 1 was performed for the Nuclear Regulatory Commission as part of the Systematic Evaluation Program. Conclusions about the ability of the containment structure to withstand the Abnormal/Extreme Environment are presented. The reassessment focused mainly on the overall structural integrity of the containment building for the Abnormal/Extreme Environment. In this case, the Abnormal Environmental condition is caused by the worst case of either a Loss-of-Coolant Accident or a main steam line break. The Extreme Environmental condition is the Safe Shutdown Earthquake

Preservice science teachers' experiences with repeated, guided inquiry

Science.gov (United States)

Slack, Amy B.

The purpose of this study was to examine preservice science teachers' experiences with repeated scientific inquiry (SI) activities. The National Science Education Standards (National Research Council, 1996) stress students should understand and possess the abilities to do SI. For students to meet these standards, science teachers must understand and be able to perform SI; however, previous research demonstrated that many teachers have naive understandings in this area. Teacher preparation programs provide an opportunity to facilitate the development of inquiry understandings and abilities. In this study, preservice science teachers had experiences with two inquiry activities that were repeated three times each. The research questions for this study were (a) How do preservice science teachers' describe their experiences with repeated, guided inquiry activities? (b) What are preservice science teachers' understandings and abilities of SI? This study was conducted at a large, urban university in the southeastern United States. The 5 participants had bachelor's degrees in science and were enrolled in a graduate science education methods course. The researcher was one of the course instructors but did not lead the activities. Case study methodology was used. Data was collected from a demographic survey, an open-ended questionnaire with follow-up interviews, the researcher's observations, participants' lab notes, personal interviews, and participants' journals. Data were coded and analyzed through chronological data matrices to identify patterns in participants' experiences. The five domains identified in this study were understandings of SI, abilities to conduct SI, personal feelings about the experience, science content knowledge, and classroom implications. Through analysis of themes identified within each domain, the four conclusions made about these preservice teachers' experiences with SI were that the experience increased their abilities to conduct inquiry

Structural Insights into the Quadruplex-Duplex 3' Interface Formed from a Telomeric Repeat: A Potential Molecular Target.

Science.gov (United States)

Russo Krauss, Irene; Ramaswamy, Sneha; Neidle, Stephen; Haider, Shozeb; Parkinson, Gary N

2016-02-03

We report here on an X-ray crystallographic and molecular modeling investigation into the complex 3' interface formed between putative parallel stranded G-quadruplexes and a duplex DNA sequence constructed from the human telomeric repeat sequence TTAGGG. Our crystallographic approach provides a detailed snapshot of a telomeric 3' quadruplex-duplex junction: a junction that appears to have the potential to form a unique molecular target for small molecule binding and interference with telomere-related functions. This unique target is particularly relevant as current high-affinity compounds that bind putative G-quadruplex forming sequences only rarely have a high degree of selectivity for a particular quadruplex. Here DNA junctions were assembled using different putative quadruplex-forming scaffolds linked at the 3' end to a telomeric duplex sequence and annealed to a complementary strand. We successfully generated a series of G-quadruplex-duplex containing crystals, both alone and in the presence of ligands. The structures demonstrate the formation of a parallel folded G-quadruplex and a B-form duplex DNA stacked coaxially. Most strikingly, structural data reveals the consistent formation of a TAT triad platform between the two motifs. This triad allows for a continuous stack of bases to link the quadruplex motif with the duplex region. For these crystal structures formed in the absence of ligands, the TAT triad interface occludes ligand binding at the 3' quadruplex-duplex interface, in agreement with in silico docking predictions. However, with the rearrangement of a single nucleotide, a stable pocket can be produced, thus providing an opportunity for the binding of selective molecules at the interface.

Obstetrical correlates of the first time cesarean section, compared with the repeated cesarean section

International Nuclear Information System (INIS)

Rukh, G.; Akhtar, S.

2007-01-01

To determine the clinical and epidemiological characteristics in patients having their first cesarean section (FCS) and compare it with findings in patients with repeated cesarean section (RCS). This study included all the women who gave birth by cesarean sections, 817 of the total 5992 deliveries, at this unit during the study period. Data on potential risk factors for the first cesarean section (FCS) and repeated cesarean section (RCS were extracted from medical records, which were reviewed and compared between these two groups of women. Data were statistically analyzed with student t-test for comparison between means and Chi-square test for comparison between percentages. Crude odds ratio (OR) with 95% confidence interval (95% CI) were calculated. Significance was taken at p 0.05). The frequency of first cesarean section and repeat cesarean section is high in our setup. Adequate following of the programs to diminish the percentage of FCS by curtailing its predisposing factors is needed. (author)

Repeated causal decision making.

Science.gov (United States)

Hagmayer, York; Meder, Björn

2013-01-01

Many of our decisions refer to actions that have a causal impact on the external environment. Such actions may not only allow for the mere learning of expected values or utilities but also for acquiring knowledge about the causal structure of our world. We used a repeated decision-making paradigm to examine what kind of knowledge people acquire in such situations and how they use their knowledge to adapt to changes in the decision context. Our studies show that decision makers' behavior is strongly contingent on their causal beliefs and that people exploit their causal knowledge to assess the consequences of changes in the decision problem. A high consistency between hypotheses about causal structure, causally expected values, and actual choices was observed. The experiments show that (a) existing causal hypotheses guide the interpretation of decision feedback, (b) consequences of decisions are used to revise existing causal beliefs, and (c) decision makers use the experienced feedback to induce a causal model of the choice situation even when they have no initial causal hypotheses, which (d) enables them to adapt their choices to changes of the decision problem. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Fostering repeat donations in Ghana.

Science.gov (United States)

Owusu-Ofori, S; Asenso-Mensah, K; Boateng, P; Sarkodie, F; Allain, J-P

2010-01-01

Most African countries are challenged in recruiting and retaining voluntary blood donors by cost and other complexities and in establishing and implementing national blood policies. The availability of replacement donors who are a cheaper source of blood has not enhanced repeat voluntary donor initiatives. An overview of activities for recruiting and retaining voluntary blood donors was carried out. Donor records from mobile sessions were reviewed from 2002 to 2008. A total of 71,701 blood donations; 45,515 (63.5%) being voluntary donations with 11,680 (25%) repeat donations were collected during the study period. Donations from schools and colleges contributed a steady 60% of total voluntary whilst radio station blood drives increased contribution from 10 to 27%. Though Muslim population is less than 20%, blood collection was above the 30-donation cost-effectiveness threshold with a repeat donation trend reaching 60%. In contrast Christian worshippers provided donations. Repeat donation trends amongst school donors and radio blood drives were 20% and 70% respectively. Repeat donations rates have been variable amongst different blood donor groups in Kumasi, Ghana. The impact of community leaders in propagating altruism cannot be overemphasized. Programs aiming at motivating replacement donors to be repeat donors should be developed and assessed. Copyright 2009 The International Association for Biologicals. All rights reserved.

Structural investigation of cell wall polysaccharides of Lactobacillus delbrueckii subsp. bulgaricus 17.

Science.gov (United States)

Vinogradov, E; Sadovskaya, I; Cornelissen, A; van Sinderen, D

2015-09-02

Lactobacilli are valuable strains for commercial (functional) food fermentations. Their cell surface-associated polysaccharides (sPSs) possess important functional properties, such as acting as receptors for bacteriophages (bacterial viruses), influencing autolytic characteristics and providing protection against antimicrobial peptides. The current report provides an elaborate molecular description of several surface carbohydrates of Lactobacillus delbrueckii subsp. bulgaricus strain 17. The cell surface of this strain was shown to contain short chain poly(glycerophosphate) teichoic acids and at least two different sPSs, designated here as sPS1 and sPS2, whose chemical structures were examined by 2D nuclear magnetic resonance spectroscopy and methylation analysis. Neutral branched sPS1, extracted with n-butanol, was shown to be composed of hexasaccharide repeating units (-[α-d-Glcp-(1-3)-]-4-β-l-Rhap2OAc-4-β-d-Glcp-[α-d-Galp-(1-3)]-4-α-Rhap-3-α-d-Galp-), while the major component of the TCA-extracted sPS2 was demonstrated to be a linear d-galactan with the repeating unit structure being (-[Gro-3P-(1-6)-]-3-β-Galf-3-α-Galp-2-β-Galf-6-β-Galf-3-β-Galp-). Copyright © 2015 Elsevier Ltd. All rights reserved.

Multivariate linear models and repeated measurements revisited

DEFF Research Database (Denmark)

Dalgaard, Peter

2009-01-01

Methods for generalized analysis of variance based on multivariate normal theory have been known for many years. In a repeated measurements context, it is most often of interest to consider transformed responses, typically within-subject contrasts or averages. Efficiency considerations leads...... to sphericity assumptions, use of F tests and the Greenhouse-Geisser and Huynh-Feldt adjustments to compensate for deviations from sphericity. During a recent implementation of such methods in the R language, the general structure of such transformations was reconsidered, leading to a flexible specification...

Factors influencing repeated teenage pregnancy: a review and meta-analysis.

Science.gov (United States)

Maravilla, Joemer C; Betts, Kim S; Couto E Cruz, Camila; Alati, Rosa

2017-11-01

Existing evidence of predictors of repeated teenage pregnancy has not been assessed rigorously. This systematic review provides a comprehensive evaluation of protective and risk factors that are associated with repeated teenage pregnancy through a metaanalytical consensus. We used PubMed, EMBASE, CINAHL, ProQuest, PsychINFO, ScienceDirect, Scopus, and Web of Science databases from 1997-2015 and the reference list of other relevant research papers and related reviews. Eligibility criteria included (1) epidemiologic studies that analyzed factors associated with repeated pregnancy or birth among adolescents pregnancy, and (2) experimental studies with an observational component that was adjusted for the intervention. We performed narrative synthesis of study characteristics, participant characteristics, study results, and quality assessment. We also conducted random-effects and quality-effects metaanalyses with meta-regression to obtain pooled odds ratios of identified factors and to determine sources of between-study heterogeneity. Twenty-six eligible epidemiologic studies, most from the United States (n=24), showed >47 factors with no evidence of publication bias for each metaanalysis. Use of contraception (pooled odds ratio, 0.60; 95% confidence interval, 0.35-1.02), particularly long-acting reversible contraceptives (pooled odds ratio, 0.19; 95% confidence interval, 0.08-0.45), considerably reduced repeated teenage pregnancy risk. Among studies about contraception, the number of follow-up visits (adjusted coefficient, 0.72; P=.102) and country of study (unadjusted coefficient, 2.57; permuted P=.071) explained between-study heterogeneity. Education-related factors, which included higher level of education (pooled odds ratio, 0.74; 95% confidence interval, 0.60-0.91) and school continuation (pooled odds ratio, 0.53; 95% confidence interval, 0.33-0.84), were found to be protective. Conversely, depression (pooled odds ratio, 1.46; 95% confidence interval, 1

Plasmid P1 replication: negative control by repeated DNA sequences.

OpenAIRE

Chattoraj, D; Cordes, K; Abeles, A

1984-01-01

The incompatibility locus, incA, of the unit-copy plasmid P1 is contained within a fragment that is essentially a set of nine 19-base-pair repeats. One or more copies of the fragment destabilizes the plasmid when present in trans. Here we show that extra copies of incA interfere with plasmid DNA replication and that a deletion of most of incA increases plasmid copy number. Thus, incA is not essential for replication but is required for its control. When cloned in a high-copy-number vector, pi...

Repeated DNA sequences in fungi

Energy Technology Data Exchange (ETDEWEB)

Dutta, S K

1974-11-01

Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

Development and static testing of the 18x6 m SSU-TTMBF spatial structural unit

Science.gov (United States)

Deordiev, S.; Frolovskaia, A.; Krasiev, M.

2018-03-01

The aim of this work is the development of a fragment of the structural covering, consisting of a triangular block of frames, the choice of step size (width) of the structural unit and a study of its mode of deformation by comparing experimental and theoretical results of research.

Meteorite Unit Models for Structural Properties

Science.gov (United States)

Agrawal, Parul; Carlozzi, Alexander A.; Karajeh, Zaid S.; Bryson, Kathryn L.

2017-10-01

To assess the threat posed by an asteroid entering Earth’s atmosphere, one must predict if, when, and how it fragments during entry. A comprehensive understanding of the asteroid material properties is needed to achieve this objective. At present, the meteorite material found on earth are the only objects from an entering asteroid that can be used as representative material and be tested inside a laboratory. Due to complex composition, it is challenging and expensive to obtain reliable material properties by means of laboratory test for a family of meteorites. In order to circumvent this challenge, meteorite unit models are developed to determine the effective material properties including Young’s modulus, compressive and tensile strengths and Poisson’s ratio, that in turn would help deduce the properties of asteroids. The meteorite unit model is a representative volume that accounts for diverse minerals, porosity, cracks and matrix composition.The Young’s Modulus and Poisson’s Ratio in the meteorite units are calculated by performing several hundreds of Monte Carlo simulations by randomly distributing the various phases inside these units. Once these values are obtained, cracks are introduced in these units. The size, orientation and distribution of cracks are derived by CT-scans and visual scans of various meteorites. Subsequently, simulations are performed to attain stress-strain relations, strength and effective modulus values in the presence of these cracks. The meteorite unit models are presented for H, L and LL ordinary chondrites, as well as for terrestrial basalt. In the case of the latter, data from the simulations is compared with experimental data to validate the methodology. These meteorite unit models will be subsequently used in fragmentation modeling of full scale asteroids.

Imperfect DNA mirror repeats in the gag gene of HIV-1 (HXB2 identify key functional domains and coincide with protein structural elements in each of the mature proteins

Directory of Open Access Journals (Sweden)

Lang Dorothy M

2007-10-01

Full Text Available Abstract Background A DNA mirror repeat is a sequence segment delimited on the basis of its containing a center of symmetry on a single strand, e.g. 5'-GCATGGTACG-3'. It is most frequently described in association with a functionally significant site in a genomic sequence, and its occurrence is regarded as noteworthy, if not unusual. However, imperfect mirror repeats (IMRs having ≥ 50% symmetry are common in the protein coding DNA of monomeric proteins and their distribution has been found to coincide with protein structural elements – helices, β sheets and turns. In this study, the distribution of IMRs is evaluated in a polyprotein – to determine whether IMRs may be related to the position or order of protein cleavage or other hierarchal aspects of protein function. The gag gene of HIV-1 [GenBank:K03455] was selected for the study because its protein motifs and structural components are well documented. Results There is a highly specific relationship between IMRs and structural and functional aspects of the Gag polyprotein. The five longest IMRs in the polyprotein translate a key functional segment in each of the five cleavage products. Throughout the protein, IMRs coincide with functionally significant segments of the protein. A detailed annotation of the protein, which combines structural, functional and IMR data illustrates these associations. There is a significant statistical correlation between the ends of IMRs and the ends of PSEs in each of the mature proteins. Weakly symmetric IMRs (≥ 33% are related to cleavage positions and processes. Conclusion The frequency and distribution of IMRs in HIV-1 Gag indicates that DNA symmetry is a fundamental property of protein coding DNA and that different levels of symmetry are associated with different functional aspects of the gene and its protein. The interaction between IMRs and protein structure and function is precise and interwoven over the entire length of the polyprotein. The

An approach for evaluating the repeatability of rapid wetland assessment methods: The effects of training and experience

Science.gov (United States)

We sampled 92 wetlands from four different basins in the United States to quantify observer repeatability in rapid wetland condition assessment using the Delaware Rapid Assessment Protocol (DERAP). In the Inland Bays basin of Delaware, 58 wetland sites were sampled by multiple ob...

Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription

NARCIS (Netherlands)

Berkhout, B.; Vastenhouw, N. L.; Klasens, B. I.; Huthoff, H.

2001-01-01

Two obligatory DNA strand transfers take place during reverse transcription of a retroviral RNA genome. The first strand transfer is facilitated by terminal repeat (R) elements in the viral genome. This strand-transfer reaction depends on base pairing between the cDNA of the 5'R and the 3'R. There

Experimental broadband absorption enhancement in silicon nanohole structures with optimized complex unit cells.

Science.gov (United States)

Lin, Chenxi; Martínez, Luis Javier; Povinelli, Michelle L

2013-09-09

We design silicon membranes with nanohole structures with optimized complex unit cells that maximize broadband absorption. We fabricate the optimized design and measure the optical absorption. We demonstrate an experimental broadband absorption about 3.5 times higher than an equally-thick thin film.

REPEATABILITY OF THE FRENCH HIGHER VEGETATION TYPES ACCORDING

Directory of Open Access Journals (Sweden)

H. BRISSE

1998-04-01

Full Text Available Higher vegetation types are generally determined by successive approximations and defined by a common consent. Instead, they might be statistically determined and repeated, according to a numerical method called ‘socio-ecology’. This method deals only with floristical data, but gives them an ecological meaning by a previous calibration of the relations between plants, computed as ecological indices. It is applied to a pair of two homologous samples, each having 2.000 relevés and coming from the 60.000 relevés stored in the French data bank ‘Sophy’. Each sample covers the main ecological gradients of the bank, it defines a hierarchy of vegetation types and it explains half the peculiarity of a type with only 10 to 30 discriminant plants, out of the 5.000 plants observed in the relevés. Results : 1 The discriminant plants may characterize the vegetation types, including the higher ones, in a coherent and readable form. 2 In the two independent classifications, having different structures, the same vegetation types are repeated. They are the reciprocal nearest types, in the socio-ecological space. Though the two classifications have no one relevé in common, the repeated types have nearly the same discriminant plants. 3 At the highest level, two clear-cut main types show the difference between light and shadow. The same herbaceous discriminant plants, for a type, and the ligneous or sciaphilous ones, for the other, have similar fidelities and constancies in the two classifications. 4 Such a numerical agreement, instead of common consent, appears again in the sub-types, which remind the classical ones, but which are repeatable.

UK 2009-2010 repeat station report

Directory of Open Access Journals (Sweden)

Thomas J.G. Shanahan

2013-03-01

Full Text Available The British Geological Survey is responsible for conducting the UK geomagnetic repeat station programme. Measurements made at the UK repeat station sites are used in conjunction with the three UK magnetic observatories: Hartland, Eskdalemuir and Lerwick, to produce a regional model of the local field each year. The UK network of repeat stations comprises 41 stations which are occupied at approximately 3-4 year intervals. Practices for conducting repeat station measurements continue to evolve as advances are made in survey instrumentation and as the usage of the data continues to change. Here, a summary of the 2009 and 2010 UK repeat station surveys is presented, highlighting the measurement process and techniques, density of network, reduction process and recent results.

Primary blast survival and injury risk assessment for repeated blast exposures.

Science.gov (United States)

Panzer, Matthew B; Bass, Cameron R Dale; Rafaels, Karin A; Shridharani, Jay; Capehart, Bruce P

2012-02-01

The widespread use of explosives by modern insurgents and terrorists has increased the potential frequency of blast exposure in soldiers and civilians. This growing threat highlights the importance of understanding and evaluating blast injury risk and the increase of injury risk from exposure to repeated blast effects. Data from more than 3,250 large animal experiments were collected from studies focusing on the effects of blast exposure. The current study uses 2,349 experiments from the data collection for analysis of the primary blast injury and survival risk for both long- and short-duration blasts, including the effects from repeated exposures. A piecewise linear logistic regression was performed on the data to develop survival and injury risk assessment curves. New injury risk assessment curves uniting long- and short-duration blasts were developed for incident and reflected pressure measures and were used to evaluate the risk of injury based on blast over pressure, positive-phase duration, and the number of repeated exposures. The risk assessments were derived for three levels of injury severity: nonauditory, pulmonary, and fatality. The analysis showed a marked initial decrease in injury tolerance with each subsequent blast exposure. This effect decreases with increasing number of blast exposures. The new injury risk functions showed good agreement with the existing experimental data and provided a simplified model for primary blast injury risk. This model can be used to predict blast injury or fatality risk for single exposure and repeated exposure cases and has application in modern combat scenarios or in setting occupational health limits. .Copyright © 2012 by Lippincott Williams & Wilkins

Structure of a streptococcal adhesion carbohydrate receptor

International Nuclear Information System (INIS)

Cassels, F.J.; Fales, H.M.; London, J.; Carlson, R.W.; van Halbeek, H.

1990-01-01

Interactions between complementary protein and carbohydrate structures on different genera of human oral bacteria have been implicated in the formation of dental plaque. The carbohydrate receptor on Streptococcus sanguis H1 that is specific for the adhesion on Capnocytophaga ochracea ATCC 33596 has been isolated from the streptococcal cell wall, purified, and structurally characterized. The hexasaccharide repeating unit of the polysaccharide was purified by reverse-phase, amino-bonded silica, and gel permeation high performance liquid chromatography. Earlier studies established that the repeating unit was a hexasaccharide composed of rhamnose, galactose, and glucose in the ration of 2:3:1, respectively. In the present study, determination of absolute configuration by gas chromatography of the trimethylsilyl (+)-2-butyl glycosides revealed that the rhamnose residues were of the L configuration while the hexoses were all D. 252Californium plasma desorption mass spectrometry of the native, the acetylated and the reduced and acetylated hexasaccharide determined that the molecular mass of the native hexasaccharide was 959, and that the 2 rhamnose residues were linked to each other at the nonreducing terminus of the linear molecule. Methylation analysis revealed the positions of the glycosidic linkages in the hexasaccharide and showed that a galactose residue was present at the reducing end. The structural characterization of the hexasaccharide was completed by one and two dimensional 1H and 13C NMR spectroscopy. Complete 1H and 13C assignments for each glycosyl residue were established by two-dimensional (1H,1H) correlation spectroscopy, homonuclear Hartmann-Hahn, and (13C,1H) correlation experiments. The configurations of the glycosidic linkages were inferred from the chemical shifts and coupling constants of the anomeric 1H and 13C resonances

Structural characterization and condition for measurement statistics preservation of a unital quantum operation

International Nuclear Information System (INIS)

Lee, Kai-Yan; Fung, Chi-Hang Fred; Chau, H F

2013-01-01

We investigate the necessary and sufficient condition for a convex cone of positive semidefinite operators to be fixed by a unital quantum operation ϕ acting on finite-dimensional quantum states. By reducing this problem to the problem of simultaneous diagonalization of the Kraus operators associated with ϕ, we can completely characterize the kinds of quantum states that are fixed by ϕ. Our work has several applications. It gives a simple proof of the structural characterization of a unital quantum operation that acts on finite-dimensional quantum states—a result not explicitly mentioned in earlier studies. It also provides a necessary and sufficient condition for determining what kind of measurement statistics is preserved by a unital quantum operation. Finally, our result clarifies and extends the work of Størmer by giving a proof of a reduction theorem on the unassisted and entanglement-assisted classical capacities, coherent information, and minimal output Renyi entropy of a unital channel acting on a finite-dimensional quantum state. (paper)

Reject/repeat analysis and the effect prior film viewing has on a department's reject/repeat rate

International Nuclear Information System (INIS)

Clark, P.A.; Hogg, P.

2003-01-01

Purpose: Achieving cost-effectiveness within the NHS is an old initiative but one that has again been highlighted by recent government policies (The New NHS-Modern and Dependable, Stationary Office, London, 1997). It has been reiterated that it is the responsibility of individual Trusts to devise means to provide such a service. Reject/repeat analyses have long been the primary tool used to assess the cost-effectiveness of radiography departments (Quality Assurance in Diagnostic Radiology, WHO, Geneva, 1982). This research paper examines an in-house initiative (viewing patients' previous films) commonly employed in other Health Trusts in order to reduce departmental repeat/reject rates. Method: Three hundred orthopaedic patients with hip, knee and ankle prostheses were included in a reject/repeat analysis. The aim was to investigate whether or not viewing patient's previous relevant radiographs would be advantageous to the practicing radiographer. This was done through an audit cycle consisting of two audit periods each lasting for 3 months. The primary audit period recorded the baseline repeat/reject rate, with the secondary audit period recording the repeat/reject rate under an experimental condition of viewing the relevant radiographs. Results: The baseline audit revealed repeat rates of 33% in orthopaedic patients with hip, knee and ankle prostheses. The availability of prior film viewing to the radiographer reduced this repeat rate to 10.6%. Conclusion: Prior film viewing dramatically reduced the department's repeat/reject rate by 22.4%. This provides scope for significant patient dose reductions as well as reducing departmental film expenses. This is an underestimated initiative and should be used appropriately in routine clinical practice

Structure of an extracellular polysaccharide produced by Lactobacillus rhamnosus strain C83

Energy Technology Data Exchange (ETDEWEB)

Vanhaverbeke, C.; Bosso, C.; Colin-Morel, P.; Gey, C.; Heyraud, A. [Centre de Recherches sur les Macromolecules Vegetales, CNRS and Universite Joseph Fourier, B.P.53, F-38041 Grenoble (France); Gamar-Nourani, L.; Blondeau, K.; Simonet, J.-M. [Institut de Genetique et Microbiologie, Laboratoire de Genetique Moleculaire des Bacteries d' Interet Industriel, CNRS URA 2225, Batiment 360, Universite de Paris Sud, F-91405 Orsay (France)

1998-12-31

The extracellular polysaccharide produced by Lactobacillus rhamnosus strain C83 was found to be composed of d-glucose and d-galactose in a molar ratio of 2:3. The primary structure of the polysaccharide was shown by sugar analysis, methylation analysis, FABMS, partial acid hydrolysis and nuclear magnetic resonance (NMR) spectroscopy to consist of a pentasaccharide repeating unit having the following structure:-3)-{alpha}-d-Glcp-(1-2)-{beta}-d-Galf-(1-6)-{alpha}-d-Galp-(1-6) -{alpha}-d-Glcp-(1-3)-{beta}-d-Galf-(1-. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

Structure of an extracellular polysaccharide produced by Lactobacillus rhamnosus strain C83

International Nuclear Information System (INIS)

Vanhaverbeke, C.; Bosso, C.; Colin-Morel, P.; Gey, C.; Heyraud, A.; Gamar-Nourani, L.; Blondeau, K.; Simonet, J.-M.

1998-01-01

The extracellular polysaccharide produced by Lactobacillus rhamnosus strain C83 was found to be composed of d-glucose and d-galactose in a molar ratio of 2:3. The primary structure of the polysaccharide was shown by sugar analysis, methylation analysis, FABMS, partial acid hydrolysis and nuclear magnetic resonance (NMR) spectroscopy to consist of a pentasaccharide repeating unit having the following structure:-3)-α-d-Glcp-(1-2)-β-d-Galf-(1-6)-α-d-Galp-(1-6) -α-d-Glcp-(1-3)-β-d-Galf-(1-. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

Repeat Purchase Intention of Starbucks Consumers in Indonesia: A Green Brand Approach

Directory of Open Access Journals (Sweden)

Naili Farida

2015-12-01

Full Text Available This study develops and tests the repeat purchase intention model (with a green brand approach. The model considers four determinants; perceived image, satisfaction, trust, and attitude. The model is tested using data and a survey of 203 Starbucks customers in Indonesia. The analysis was carried out by employing Structural Equation Modeling. The data was processed with AMOS 21. The results confirm that the company’s green brand image is positively and significantly related to consumer satisfaction, trust, and attitude. On the other hand, consumer satisfaction and trust are shown to have insignificant influence on repeat purchase intention.

Use of the Primitive Unit Cell in Understanding Subtle Features of the Cubic Closest-Packed Structure

Science.gov (United States)

Hawkins, John A.; Rittenhouse, Jeffrey L.; Soper, Linda M.; Rittenhouse, Robert C.

2008-01-01

One of the most important crystal structures adopted by metals is characterized by the "abcabc"...stacking of close-packed layers. This structure is commonly referred to in textbooks as the cubic close-packed (ccp) or face-centered cubic (fcc) structure, since the entire lattice can be generated by replication of a face-centered cubic unit cell…

Additively Manufactured Open-Cell Porous Biomaterials Made from Six Different Space-Filling Unit Cells: The Mechanical and Morphological Properties

Directory of Open Access Journals (Sweden)

Seyed Mohammad Ahmadi

2015-04-01

Full Text Available It is known that the mechanical properties of bone-mimicking porous biomaterials are a function of the morphological properties of the porous structure, including the configuration and size of the repeating unit cell from which they are made. However, the literature on this topic is limited, primarily because of the challenge in fabricating porous biomaterials with arbitrarily complex morphological designs. In the present work, we studied the relationship between relative density (RD of porous Ti6Al4V EFI alloy and five compressive properties of the material, namely elastic gradient or modulus (Es20–70, first maximum stress, plateau stress, yield stress, and energy absorption. Porous structures with different RD and six different unit cell configurations (cubic (C, diamond (D, truncated cube (TC, truncated cuboctahedron (TCO, rhombic dodecahedron (RD, and rhombicuboctahedron (RCO were fabricated using selective laser melting. Each of the compressive properties increased with increase in RD, the relationship being of a power law type. Clear trends were seen in the influence of unit cell configuration and porosity on each of the compressive properties. For example, in terms of Es20–70, the structures may be divided into two groups: those that are stiff (comprising those made using C, TC, TCO, and RCO unit cell and those that are compliant (comprising those made using D and RD unit cell.

A taxonomy of state public health preparedness units: an empirical examination of organizational structure.

Science.gov (United States)

Menachemi, Nir; Yeager, Valerie A; Duncan, W Jack; Katholi, Charles R; Ginter, Peter M

2012-01-01

State public health preparedness units (SPHPUs) were developed in response to federal funding to improve response to disasters: a responsibility that had not traditionally been within the purview of public health. The SPHPUs were created within the existing public health organizational structure, and their placement may have implications for how the unit functions, how communication takes place, and ultimately how well the key responsibilities are performed. This study empirically identifies a taxonomy of similarly structured SPHPUs and examines whether this structure is associated with state geographic, demographic, and threat-vulnerability characteristics. Data representing each SPHPU were extracted from publically available sources, including organizational charts and emergency preparedness plans for 2009. A cross-sectional segmentation analysis was conducted of variables representing structural attributes. Fifty state public health departments. Variables representing "span of control" and "hierarchal levels" were extracted from organizational charts. Structural "complexity" and "centralization" were extracted from state emergency preparedness documents and other secondary sources. On average, 6.6 people report to the same manager as the SPHPU director; 2.1 levels separate the SPHPU director from the state health officer; and a mean of 13.5 agencies collaborate with SPHPU during a disaster. Despite considerable variability in how SPHPUs had been structured, results of the cluster and principal component analysis identified 7 similarly structured groups. Neither the taxonomic groups nor the individual variables representing structure were found to be associated with state characteristics, including threat vulnerabilities. Our finding supports the hypothesis that SPHPUs are seemingly inadvertently (eg, not strategically) organized. This taxonomy provides the basis for which future research can examine how SPHPU structure relates to performance measures and

Unit roots, nonlinearities and structural breaks

DEFF Research Database (Denmark)

Haldrup, Niels; Kruse, Robinson; Teräsvirta, Timo

One of the most influential research fields in econometrics over the past decades concerns unit root testing in economic time series. In macro-economics much of the interest in the area originate from the fact that when unit roots are present, then shocks to the time series processes have...

A comparative analysis of business structures suitable for farmer-owned wind power projects in the United States

International Nuclear Information System (INIS)

Bolinger, Mark; Wiser, Ryan

2006-01-01

For years, farmers in the United States have looked with envy on their European counterparts' ability to profitably farm the wind through ownership of distributed, utility-scale wind projects. Only within the past few years, however, has farmer- or community-owned wind power development become a reality in the United States. The primary hurdle to this type of development in the United States has been devising and implementing suitable business and legal structures that enable such projects to take advantage of tax-based federal incentives for wind power. This article discusses the limitations of such incentives in supporting farmer- or community-owned wind projects, describes four ownership structures that potentially overcome such limitations, and finally conducts comparative financial analysis on those four structures, using as an example a hypothetical 1.5 MW farmer-owned project located in the state of Oregon. We find that material differences in the competitiveness of each structure do exist, but that choosing the best structure for a given project will largely depend on the conditions at hand; e.g., the ability of the farmer(s) to utilize tax credits, preference for individual versus 'cooperative' ownership, and the state and utility service territory in which the project will be located

Electron transfer reactions in structural units of copper proteins

International Nuclear Information System (INIS)

Faraggi, M.

1975-01-01

In previous pulse radiolysis studies it was suggested that the reduction of the Cu(II) ions in copper proteins by the hydrated electron is a multi-step electron migration process. The technique has been extended to investigate the reduction of some structural units of these proteins. These studies include: the reaction of the hydrated electron with peptides, the reaction of the disulphide bridge with formate radical ion and radicals produced by the reduction of peptides, and the reaction of Cu(II)-peptide complex with esub(aq)sup(-) and CO 2 - . Using these results the reduction mechanism of copper and other proteins will be discussed. (author)

Longleaf pine site response to repeated fertilization and forest floor removal by raking and prescribed burning

Science.gov (United States)

Kim Ludovici; Robert Eaton; Stanley Zarnoch

2018-01-01

Removal of forest floor litter by pine needle raking and prescribed burning is a common practice in longleaf pine (Pinus palustris Mill.) stands on Coastal Plain sites in the Southeastern United States. Repeated removal of litter by raking and the loss of surface organic matter from controlled burns can affect the...

Repeating Marx

DEFF Research Database (Denmark)

Fuchs, Christian; Monticelli, Lara

2018-01-01

This introduction sets out the context of the special issue “Karl Marx @ 200: Debating Capitalism & Perspectives for the Future of Radical Theory”, which was published on the occasion of Marx’s bicentenary on 5 May 2018. First, we give a brief overview of contemporary capitalism’s development...... and its crises. Second, we argue that it is important to repeat Marx today. Third, we reflect on lessons learned from 200 years of struggles for alternatives to capitalism. Fourth, we give an overview of the contributions in this special issue. Taken together, the contributions in this special issue show...... that Marx’s theory and politics remain key inspirations for understanding exploitation and domination in 21st-century society and for struggles that aim to overcome these phenomena and establishing a just and fair society. We need to repeat Marx today....

Basidiomycete fungal communities in Australian sclerophyll forest soil are altered by repeated prescribed burning.

Science.gov (United States)

Anderson, Ian C; Bastias, Brigitte A; Genney, David R; Parkin, Pamela I; Cairney, John W G

2007-04-01

Soil basidiomycetes play key roles in forest nutrient and carbon cycling processes, yet the diversity and structure of below ground basidiomycete communities remain poorly understood. Prescribed burning is a commonly used forest management practice and there is evidence that single fire events can have an impact on soil fungal communities but little is known about the effects of repeated prescribed burning. We have used internal transcribed spacer (ITS) terminal restriction fragment length polymorphism (T-RFLP) analysis to investigate the impacts of repeated prescribed burning every two or four years over a period of 30 years on soil basidiomycete communities in an Australian wet sclerophyll forest. Detrended correspondence analysis of ITS T-RFLP profiles separated basidiomycete communities in unburned control plots from those in burned plots, with those burned every two years being the most different from controls. Burning had no effect on basidiomycete species richness, thus these differences appear to be due to changes in community structure. Basidiomycete communities in the unburned control plots were vertically stratified in the upper 20 cm of soil, but no evidence was found for stratification in the burned plots, suggesting that repeated prescribed burning results in more uniform basidiomycete communities. Overall, the results demonstrate that repeated prescribed burning alters soil basidiomycete communities, with the effect being greater with more frequent burning.

Electronic structures and band gaps of chains and sheets based on phenylacetylene units

International Nuclear Information System (INIS)

Kondo, Masakazu; Nozaki, Daijiro; Tachibana, Masamitsu; Yumura, Takashi; Yoshizawa, Kazunari

2005-01-01

We investigate the electronic structures of polymers composed of π-conjugated phenylacetylene (PA) units, m-PA-based and p-PA-based wires, at the extended Hueckel level of theory. It is demonstrated that these conjugated systems should have a variety of electric conductance. All of the one-dimensional (1D) chains and the two-dimensional (2D) sheet based on the m-PA unit are insulators with large band gaps of 2.56 eV because there is no effective orbital interaction with neighboring chains. On the other hand, p-PA-based 1D chains have relatively small band gaps that decrease with an increase in chain width (1.17-1.74 eV) and are semiconductive. The p-PA-based sheet called 'graphyne', a 2D-limit of the p-PA-based 1D chains, shows a small band gap of 0.89 eV. The variety of band electronic structures is discussed in terms of frontier crystal orbitals

Comparison of the degree of homology of DNA and quantity of repeated sequences in an intact plant and cell structure

International Nuclear Information System (INIS)

Solov'yan, V.T.; Kunaleh, V.A.; Shumnyl, V.K.; Vershinin, A.V.

1986-01-01

This paper attempts to assess the quantity of repeated sequences and degree of homology of DNA in the intact plant and two lines of callus tissue of Rauwolfia serpentina Benth maintained for 20 years, which differ among themselves in the level of biosynthesis of the pharmacologically valuable alkaloid ajmaline. The tritium-labeled repeats of plants and calli were used in direct and reverse hybridization on nitrocellulose filters. Hybridization of H 3-labeled repeats with phage 17 DNA was used as control. The radioactivity of filters after washing was measured in a liquid scintillation counter

Insertion device and method for accurate and repeatable target insertion

Science.gov (United States)

Gubeli, III, Joseph F.; Shinn, Michelle D.; Bevins, Michael E.; Dillon-Townes, Lawrence; Neil, George R.

2017-07-04

The present invention discloses a device and a method for inserting and positioning a target within a free electron laser, particle accelerator, or other such device that generates or utilizes a beam of energy or particles. The system includes a three-point registration mechanism that insures angular and translational accuracy and repeatability of positioning upon multiple insertions within the same structure.

Structural design of the turbine building of Angra Nuclear Power Station, Unit 1

International Nuclear Information System (INIS)

Varella, L.N.; Reis, F.J.C.; Jurkiewicz, W.J.

1978-01-01

The Turbine Building of the Angra Nuclear Power Plant, Unit 1, and particularly its structure and structural design are described. The Turbine Building, as far as its structure is concerned, deviates from the standard structure of any turbine building due to the fact that huge ducts are provided in the foundation mat as to accomodate the circulating water system. This aspect and the fact that the building is founded upon a very deep strata of compacted and controlled fill, makes out of the building structure 'a concrete ship floating in the sea of sand', and by the same reason presents by itself an interesting structure, worth to be known to all engineers involved in design of power plants. This pape, suplemented by a few slides shown during presentation of the paper at the conference, covers the subject mainly from the designers' point of view. (Author)

Analysis of repeated measures data

CERN Document Server

Islam, M Ataharul

2017-01-01

This book presents a broad range of statistical techniques to address emerging needs in the field of repeated measures. It also provides a comprehensive overview of extensions of generalized linear models for the bivariate exponential family of distributions, which represent a new development in analysing repeated measures data. The demand for statistical models for correlated outcomes has grown rapidly recently, mainly due to presence of two types of underlying associations: associations between outcomes, and associations between explanatory variables and outcomes. The book systematically addresses key problems arising in the modelling of repeated measures data, bearing in mind those factors that play a major role in estimating the underlying relationships between covariates and outcome variables for correlated outcome data. In addition, it presents new approaches to addressing current challenges in the field of repeated measures and models based on conditional and joint probabilities. Markov models of first...

Adaptive cellular structures and devices with internal features for enhanced structural performance

Science.gov (United States)

Pontecorvo, Michael Eugene

and force inputs are contrasted in relation to these metrics. The key innovation to the early structural elements presented here is the combination of the VMT with the pin-jointed hexagonal cell. Chapter 3 explores several prototypes of repeatable structural elements for simultaneous load-carrying capability and energy dissipation that are based on this innovation. The final demonstration prototype presented in this chapter is a column-like element that is based on a hexagonal cell containing two horizontal springs and one vertical damper. The unit is enclosed by a pair of buckling plates that serve to give the prototype a high initial stiffness and load carrying capability. The prototype is tested in both displacement and force input and its behavior is compared to simulation. Chapter 4 builds on the conceptual designs of Chapter 3 with the introduction of a plate-like element, that contains two compact VMTs connected by a horizontally oriented damper. Pre-loaded springs are used in the prototype to perform the same load carrying function as the buckling plates in the column-like prototype with increased predictability. The plate-like prototype is studied under impact to demonstrate its effectiveness as a protective layer. It is shown to reduce peak impact loads transmitted to the base of the device by over 60%. In most cases, the prototype compares well with a conventional protective rubber layer, and in cases of extreme impact loads, it exceeds the performance of the rubber layer. In addition to impact testing, the prototype is also experimentally tested under harmonic displacement input, and is simulated under both harmonic displacement and force input. The experiments illustrate that while the VMT parameters of a single layer can be optimized to a particular harmonic load amplitude, having two layers with softer and stiffer VMTs allows the system to show good energy dissipation characteristics at different harmonic load amplitude levels. Chapter 5 examines using

Structure-Function Analysis of Cf-9, a Receptor-Like Protein with Extracytoplasmic Leucine-Rich Repeats

NARCIS (Netherlands)

Hoorn, van der R.A.L.; Wulff, B.B.H.; Rivas, S.; Durrant, M.C.; Ploeg, van der A.; Wit, de P.J.G.M.; Jones, J.D.G.

2005-01-01

The tomato (Lycopersicon pimpinellifolium) resistance protein Cf-9 belongs to a large class of plant proteins with extracytoplasmic Leu-rich repeats (eLRRs). eLRR proteins play key roles in plant defense and development, mainly as receptor-like proteins or receptor-like kinases, conferring

Revisiting the structure of the anti-neoplastic glucans of Mycobacterium bovis Bacille Calmette-Guerin. Structural analysis of the extracellular and boiling water extract-derived glucans of the vaccine substrains.

Science.gov (United States)

Dinadayala, Premkumar; Lemassu, Anne; Granovski, Pierre; Cérantola, Stéphane; Winter, Nathalie; Daffé, Mamadou

2004-03-26

The attenuated strain of Mycobacterium bovis Bacille Calmette-Guérin (BCG), used worldwide to prevent tuberculosis and leprosy, is also clinically used as an immunotherapeutic agent against superficial bladder cancer. An anti-tumor polysaccharide has been isolated from the boiling water extract of the Tice substrain of BCG and tentatively characterized as consisting primarily of repeating units of 6-linked-glucosyl residues. Mycobacterium tuberculosis and other mycobacterial species produce a glycogen-like alpha-glucan composed of repeating units of 4-linked glucosyl residues substituted at some 6 positions by short oligoglucosyl units that also exhibits an anti-tumor activity. Therefore, the impression prevails that mycobacteria synthesize different types of anti-neoplastic glucans or, alternatively, the BCG substrains are singular in producing a unique type of glucan that may confer to them their immunotherapeutic property. The present study addresses this question through the comparative analysis of alpha-glucans purified from the extracellular materials and boiling water extracts of three vaccine substrains. The polysaccharides were purified, and their structural features were established by mono- and two-dimensional NMR spectroscopy and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of the enzymatic and chemical degradation products of the purified compounds. The glucans isolated by the two methods from the three substrains of BCG were shown to exhibit identical structural features shared with the glycogen-like alpha-glucan of M. tuberculosis and other mycobacteria. Incidentally, we observed an occasional release of dextrans from Sephadex columns that may explain the reported occurrence of 6-substituted alpha-glucans in mycobacteria.

Liver cirrhosis is a risk factor of repeat acute hemorrhagic rectal ulcer in intensive care unit patients

Directory of Open Access Journals (Sweden)

Pi-Kai Chang

2014-01-01

Full Text Available Background: Acute hemorrhagic rectal ulcer (AHRU can be found in patients with severe comorbid illness, who are bedridden for a long time. Per anal suturing is a quick and feasible treatment. However, recurrent bleeding occurs frequently after suture ligation of a bleeder and can be life-threatening. However, the risk factor for recurrent bleeding is not well known. Our study tries to clarify the risk factor of repeat AHRU in Intensive Care Unit (ICU patients. Materials and Methods: From January 2004 to December 2009, the medical records of 32 patients, who were admitted to the ICU of the Tri-Service General Hospital, a tertiary referral center in Taiwan, and who underwent per anal suturing of acute hemorrhagic rectal ulcer were retrospectively reviewed. Results: Of the 96 patients who received emergency treatment for acute massive hematochezia, 32 patients were diagnosed with AHRU. Eight (25% patients had recurrent bleeding following suture ligation of AHRU and underwent a reoperation; no patient had recurrent bleeding after the second operation. The duration from the first hematochezia attack to surgery (P = 0.04, liver cirrhosis (P = 0.002, and coagulopathy (P = 0.01 were the risk factors of recurrent bleeding after suture ligation of a bleeder. Multivariate logistic regression analysis indicated that liver cirrhosis (OR = 37.77, P = 0.014 was an independent risk factor for recurrent bleeding. Conclusion: AHRU could be a major cause of acute massive hematochezia in patients with severe illness. Our data showed that per anal suturing could quickly and effectively control bleeding. We found that liver cirrhosis was an independent risk factor for recurrent bleeding. Therefore, treatment of a liver cirrhosis patient with AHUR should be more aggressive, such as, early detection and proper suture ligation.

Design loads, loading combinations and structural acceptance criteria for BWR containments in the United States

International Nuclear Information System (INIS)

Edwards, N.W.

1979-01-01

The definition of loads, loading combinations, and structural acceptance criteria used for the design and evaluation of BWR containments in the Unites States has become much more comprehensive over the past decade. The Mark I pressure suppression containment vessels were designed for a static design pressure, a design temperature, dead load and static equivalent earthquake. The current Mark III containments are being designed to accommodate many more loads such as safety relief valve discharge loads, and suppression pool hydrodynamic loadings associated with the steam condensation phenomena as well as pressure and temperature transients for a range of pipe break sizes. Consistent with the more comprehensive definition of loads and loading combinations, the ASME Code presently establishes structural acceptance criteria with different margins of safety by the definition of Service Level Assignments A, B, C and D. Acting in a responsible manner, United States utilities are currently evaluating and modifying existing containment vessels to account for the more detailed load definition and structural acceptance criteria. (orig.)

Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness.

Science.gov (United States)

Reiter, Johannes G; Hilbe, Christian; Rand, David G; Chatterjee, Krishnendu; Nowak, Martin A

2018-02-07

Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze "crosstalk" between a player's concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person's decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games.

Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods.

Science.gov (United States)

Nakazawa, Yasumoto; Asakura, Tetsuo

2003-06-18

Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.

PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae.

Science.gov (United States)

Zucchini, Laure; Mercy, Chryslène; Garcia, Pierre Simon; Cluzel, Caroline; Gueguen-Chaignon, Virginie; Galisson, Frédéric; Freton, Céline; Guiral, Sébastien; Brochier-Armanet, Céline; Gouet, Patrice; Grangeasse, Christophe

2018-02-01

Eukaryotic-like serine/threonine kinases (eSTKs) with extracellular PASTA repeats are key membrane regulators of bacterial cell division. How PASTA repeats govern eSTK activation and function remains elusive. Using evolution- and structural-guided approaches combined with cell imaging, we disentangle the role of each PASTA repeat of the eSTK StkP from Streptococcus pneumoniae. While the three membrane-proximal PASTA repeats behave as interchangeable modules required for the activation of StkP independently of cell wall binding, they also control the septal cell wall thickness. In contrast, the fourth and membrane-distal PASTA repeat directs StkP localization at the division septum and encompasses a specific motif that is critical for final cell separation through interaction with the cell wall hydrolase LytB. We propose a model in which the extracellular four-PASTA domain of StkP plays a dual function in interconnecting the phosphorylation of StkP endogenous targets along with septal cell wall remodelling to allow cell division of the pneumococcus.

Ethical Leadership, Leader-Member Exchange and Feedback Seeking: A Double-Moderated Mediation Model of Emotional Intelligence and Work-Unit Structure

Science.gov (United States)

Qian, Jing; Wang, Bin; Han, Zhuo; Song, Baihe

2017-01-01

This research elucidates the role of ethical leadership in employee feedback seeking by examining how and when ethical leadership may exert a positive influence on feedback seeking. Using matched reports from 64 supervisors and 265 of their immediate employees from a hotel group located in a major city in China, we proposed and tested a moderated mediation model that examines leader-member exchange (LMX) as the mediator and emotional intelligence as well as work-unit structure as double moderators in the relationships between ethical leadership and followers’ feedback-seeking behavior from supervisors and coworkers. Our findings indicated that (1) LMX mediated the positive relationship between ethical leadership and feedback seeking from both ethical leaders and coworkers, and (2) emotional intelligence and work-unit structure served as joint moderators on the mediated positive relationship in such a way that the relationship was strongest when the emotional intelligence was high and work-unit structure was more of an organic structure rather than a mechanistic structure. PMID:28744251

Genetic diversity and population structure analysis in Perilla frutescens from Northern areas of China based on simple sequence repeats.

Science.gov (United States)

Ma, S J; Sa, K J; Hong, T K; Lee, J K

2017-09-21

In this study, 21 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population structure among 77 Perilla accessions from high-latitude and middle-latitude areas of China. Ninety-five alleles were identified with an average of 4.52 alleles per locus. The average polymorphic information content (PIC) and genetic diversity values were 0.346 and 0.372, respectively. The level of genetic diversity and PIC value for cultivated accessions of Perilla frutescens var. frutescens from middle-latitude areas were higher than accessions from high-latitude areas. Based on the dendrogram of unweighted pair group method with arithmetic mean (UPGMA), all accessions were classified into four major groups with a genetic similarity of 46%. All accessions of the cultivated var. frutescens were discriminated from the cultivated P. frutescens var. crispa. Furthermore, most accessions of the cultivated var. frutescens collected in high-latitude and middle-latitude areas were distinguished depending on their geographical location. However, the geographical locations of several accessions of the cultivated var. frutescens have no relation with their positions in the UPGMA dendrogram and population structure. This result implies that the diffusion of accessions of the cultivated Perilla crop in the northern areas of China might be through multiple routes. On the population structure analysis, 77 Perilla accessions were divided into Group I, Group II, and an admixed group based on a membership probability threshold of 0.8. Finally, the findings in this study can provide useful theoretical knowledge for further study on the population structure and genetic diversity of Perilla and benefit for Perilla crop breeding and germplasm conservation.

simple sequence repeats (EST-SSR)

African Journals Online (AJOL)

Yomi

2012-01-19

Jan 19, 2012 ... 212 primer pairs selected, based on repeat patterns of n≥8 for di-, tri-, tetra- and penta-nucleotide repeat ... Cluster analysis revealed a high genetic similarity among the sugarcane (Saccharum spp.) breeding lines which could reduce the genetic gain in ..... The multiple allele characteristic of SSR com-.

Nifty Nines and Repeating Decimals

Science.gov (United States)

Brown, Scott A.

2016-01-01

The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

Repeated Prescribed Burning in Aspen

Science.gov (United States)

Donald A. Perala

1974-01-01

Infrequent burning weather, low flammability of the aspen-hardwood association, and prolific sprouting and seeding of shrubs and hardwoods made repeated dormant season burning a poor tool to convert good site aspen to conifers. Repeat fall burns for wildlife habitat maintenance is workable if species composition changes are not important.

Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE).

Science.gov (United States)

Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K; Graham, Shirley; Liu, Huanting; Naismith, James H; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J; White, Malcolm F; Lawrence, C Martin

2011-06-17

In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.

Interconnection between the geometry and the structure of unit cells of substances in inorganic chemistry

International Nuclear Information System (INIS)

Eliseev, A.A.; Kuz'micheva, G.M.

1979-01-01

Regularity of interconnection between the geometry and the structure of elementary cells of inorganic compounds is investigated. Structural motives on the basis of NaCl structure for all phases of rare earth chalcogenides are built. It is shown that compounds (phases of variable content), detected on 23 (out of 48 possible) state diagrams of rare earths chalcogen binary systems are closely bound both from the viewpoint of geometric dimensions of elementary cells and structural motives. It is shown that using ion representations the number of formula units in the cell of a new rare earth chalcogenide can be calculated and its structural motif can be built

Inferring repeat-protein energetics from evolutionary information.

Directory of Open Access Journals (Sweden)

Rocío Espada

2017-06-01

Full Text Available Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing covariations in extant sequences. Still, many natural proteins that fold into the same structural topology show different stabilization energies, and these are often related to their physiological behavior. We propose a description for the energetic variation given by sequence modifications in repeat proteins, systems for which the overall problem is simplified by their inherent symmetry. We explicitly account for single amino acid and pair-wise interactions and treat higher order correlations with a single term. We show that the resulting evolutionary field can be interpreted with structural detail. We trace the variations in the energetic scores of natural proteins and relate them to their experimental characterization. The resulting energetic evolutionary field allows the prediction of the folding free energy change for several mutants, and can be used to generate synthetic sequences that are statistically indistinguishable from the natural counterparts.

Pickering unit 1 containment leakage characterization

International Nuclear Information System (INIS)

Zakaib, G.D.

1994-01-01

Results of the design pressure test carried out on Pickering Reactor Building number 1 during late 1992 showed that the leakage rate of the building was close to the safety analysis value of 2.7% contained mass per hour at the design pressure of 41.4 kPa(g) and was significantly higher than that reported after the previous test conducted in the spring of 1987. This unexpected finding initiated the longest and the most comprehensive containment leakage investigation ever undertaken by Ontario Hydro. A thorough investigation of leakage behaviour by repeated testing, inspections, leak search and analysis was launched. The extensive leak search effort included items such as: leak source detection by soap solution application, use of ultrasonic detectors, fogging and tracer gas techniques, systematic systems isolation, thermal imaging of the exterior, and quantification of leak sites by flowmeter and bagging. Using a specially designed volumetric technique, the root cause of the problem was finally confirmed as being due to 'pressure dependent laminar leakage' through the hairline cracks in the dome concrete. Structural analysis indicated that the thermal gradients and pressure loading combined to cause the cracking early in the structure's operating history and that overall structural integrity has not been compromised. Leakage rate analysis using a new fluid mechanics model augmented by the effect of thermal strains indicated that the leakage could be significantly less under certain transient temperature gradient conditions. Several options for repairing the dome were considered by a multidisciplinary team and it was finally decided to apply a specially engineered multilayer elastomeric coating to the exterior concrete surface. When the unit was re-tested in October 1993, a dramatic ten-fold improvement in leakage rate (down to 0.25%/h at design pressure) was observed. This is lower than even the commissioning results and comparable to the performance of newer units

Medial temporal lobe-dependent repetition suppression and enhancement due to implicit versus explicit processing of individual repeated search displays

Directory of Open Access Journals (Sweden)

Thomas eGeyer

2012-10-01

Full Text Available Using visual search, functional magnetic resonance imaging (fMRI and patient studies have demonstrated that medial temporal lobe (MTL structures differentiate repeated from novel displays – even when observers are unaware of display repetitions. This suggests a role for MTL in both explicit and, importantly, implicit learning of repeated sensory information (Greene et al., 2007. However, recent behavioral studies suggest, by examining visual search and recognition performance concurrently, that observers have explicit knowledge of at least some of the repeated displays (Geyer et al., 2010. The aim of the present fMRI study was thus to contribute new evidence regarding the contribution of MTL structures to explicit versus implicit learning in visual search. It was found that MTL activation was increased for explicit and, respectively, decreased for implicit relative to baseline displays. These activation differences were most pronounced in left anterior parahippocampal cortex, especially when observers were highly trained on the repeated displays. The data are taken to suggest that explicit and implicit memory processes are linked within MTL structures, but expressed via functionally separable mechanisms (repetition enhancement vs. -suppression. They further show that repetition effects in visual search would have to be investigated at the display level.

Polyacrolein with microspherical structure obtained by radiation-Initiation and base catalysis

International Nuclear Information System (INIS)

Usanmaz, A.; Dogan, R.D.

1990-01-01

Acrolein was polymerized by radiation and base catalyzed condensation. Radiation polymerization was carried in bulk form under vacuum and air atmosphere at several temperatures. The conversion reached close to 100 %, and polymers were free flowing white powders up to 5 % conversion at -15degC, up to 80 % at higher temperatures and up to 10 % in air atmosphere polymerization. Radiation polymerization from aqueous solutions of various pH and from acetone solutions gave white powder polymers with limiting conversions ranging from 10 to 18 % depending on the solution type or pH. The conversion at pH between 1, 5 to 8 gave minimum pH of 5 to 6. The base catalyzed polymerization at pH of 9 to 12 gave white powdered polymers changing to a yellowish colour with increase of pH. The limiting conversion was about 14 %. The nature of repeating units in the polymer chains was studied by IR and thermogravimetry. The polymers contained different repeating units randomly, and the aldehyde content was higher for radiation polymerization than base catalyzed polymerization. A scanning electron microscope investigation showed the powder polymers to have microspherical structures of various size depending on polymerization conditions. (author)

The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures.

Directory of Open Access Journals (Sweden)

Diego U Ferreiro

2008-05-01

Full Text Available Repeat-proteins are made up of near repetitions of 20- to 40-amino acid stretches. These polypeptides usually fold up into non-globular, elongated architectures that are stabilized by the interactions within each repeat and those between adjacent repeats, but that lack contacts between residues distant in sequence. The inherent symmetries both in primary sequence and three-dimensional structure are reflected in a folding landscape that may be analyzed as a quasi-one-dimensional problem. We present a general description of repeat-protein energy landscapes based on a formal Ising-like treatment of the elementary interaction energetics in and between foldons, whose collective ensemble are treated as spin variables. The overall folding properties of a complete "domain" (the stability and cooperativity of the repeating array can be derived from this microscopic description. The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (DeltaG(water and the cooperativity of denaturation (m-value, which do not ordinarily apply for globular proteins. We show how the parameters for the "coarse-grained" description in terms of foldon spin variables can be extracted from more detailed folding simulations on perfectly funneled landscapes. To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR repeat proteins and quantitatively relate the results to the experimentally observed folding transitions. Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are "poised" at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions.

Repeat Colonoscopy within 6 Months after Initial Outpatient Colonoscopy in Ontario: A Population-Based Cross-Sectional Study

Directory of Open Access Journals (Sweden)

Lawrence Paszat

2017-01-01

Full Text Available Background. The goal of this study is to examine utilization of early repeat colonoscopy ≤ 6 months after an index procedure. Methods. We identified persons having repeat colonoscopy ≤ 6 months following outpatient colonoscopy without prior colonoscopy ≤ 5 years or prior diagnosis of colorectal cancer (CRC. We modeled repeat colonoscopy using a generalized estimating equation with an exchangeable correlation structure to account for clustering of patients by endoscopist. Results. The population included 334,663 persons, 7,892 (2.36% of whom had an early repeat colonoscopy within 6 months. Overall, endoscopist prior year colonoscopy volume was inversely related to repeat ≤ 6 months. Repeat colonoscopy ≤ 6 months varied by the clinical setting of the index colonoscopy (adjusted OR = 1.41 (95% CI 1.29–1.55 at nonhospital facilities compared to teaching or community hospitals. Among those who had polypectomy or biopsy, the adjusted OR for early repeat ≤ 6 months was elevated among those whose index colonoscopy was at a nonhospital facility (OR 1.44, 95% CI 1.30–1.60, compared to those at a teaching hospital or community hospital. Conclusions. Repeat colonoscopy ≤ 6 months after an index procedure is associated with the clinical setting of the index colonoscopy.

Drought-induced changes in Amazon forest structure from repeat airborne lidar

Science.gov (United States)

Morton, D. C.; Leitold, V.; Longo, M.; Keller, M.; dos-Santos, M. N.; Scaranello, M. A., Sr.

2017-12-01

Drought events in tropical forests, including the 2015-2016 El Niño, may reduce net primary productivity and increase canopy tree mortality, thereby altering the short and long-term net carbon balance of tropical forests. Given the broad extent of drought impacts, forest inventory plots or eddy flux towers may not capture regional variability in forest response to drought. Here, we analyzed repeat airborne lidar data to evaluate canopy turnover from branch and tree fall before (2013-2014) and during (2014-2016) the recent El Niño drought in the eastern and central Brazilian Amazon. Coincident field surveys for a 16-ha subset of the lidar coverage provided complementary information to classify turnover areas by mechanism (branch, multiple branch, tree fall, multiple tree fall) and estimate the total coarse woody debris volume from canopy and understory tree mortality. Annualized rates of canopy turnover increased by 50%, on average, during the drought period in both intact and fragmented forests near Santarém, Pará. Turnover increased uniformly across all size classes, and there was limited evidence that taller trees contributed a greater proportion of turnover events in any size class in 2014-2016 compared to 2013-2014. This short-term increase in canopy turnover differs from findings in multi-year rainfall exclusion experiments that large trees were more sensitive to drought impacts. Field measurements confirmed the separability of the smallest (single branch) and largest damage classes (multiple tree falls), but single tree and multiple branch fall events generated similar coarse woody debris production and lidar-derived changes in canopy volume. Large-scale sampling possible with repeat airborne lidar data also captured strong local and regional gradients in canopy turnover. Differences in slope partially explained the north-south gradient in canopy turnover dynamics near Santarém, with larger increases in turnover on flatter terrain. Regional variability

Structure of the neutral capsular polysaccharide of Acinetobacter baumannii NIPH146 that carries the KL37 capsule gene cluster.

Science.gov (United States)

Arbatsky, Nikolay P; Shneider, Mikhail M; Kenyon, Johanna J; Shashkov, Alexander S; Popova, Anastasiya V; Miroshnikov, Konstantin A; Volozhantsev, Nikolay V; Knirel, Yuriy A

2015-09-02

Capsular polysaccharide (CPS) was isolated from Acinetobacter baumannii NIPH146, and the following structure of branched pentasaccharide repeating unit was established by sugar analyses along with 1D and 2D NMR spectroscopy: In comparison to most other known capsular polysaccharides of A. baumannii, the CPS studied is neutral and lacks any specific monosaccharide component. The synthesis, assembly and export of this structure could be attributed to genes in a novel capsule biosynthesis gene cluster, designated KL37, which was found in the NIPH146 genome. The CPS of A. baumannii NIPH146 shares the α-d-Galp-(1→6)-β-d-Glcp-(1→3)-d-GalpNAc-(1→ trisaccharide fragment with the CPS units of several A. baumannii strains, including ATCC 17978 and LUH 5537 that carry the KL3 and KL22 gene clusters, respectively. KL37 contains two genes for glycosyltransferases that are related to two glycosyltransferase genes present in both KL3 and KL22, and the encoded proteins could be tentatively assigned to linkages between sugars in the CPS repeat. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dedicated education unit: student perspectives.

Science.gov (United States)

Nishioka, Vicki M; Coe, Michael T; Hanita, Makoto; Moscato, Susan R

2014-01-01

The study compared students' perceptions of their clinical learning experiences in a dedicated education unit (DEU) with their experiences in traditional clinical education. Unlike traditional academic-instructor models, expert nurses in the DEU provide clinical education to students with faculty support. This repeated measures design used student surveys, supplemented by focus group data. Students were more likely to agree that their clinical learning experience was high quality and they had a consistent mentoring relationship during DEU rotations. Students also reported the quality of the unit's learning environment, the leadership style of the nurse manager, and the nursing care on the unit was more favorable in DEUs than traditional units. Consistent with their changed role in DEUs, faculty members were less active in helping students integrate theory and practice. These findings provide additional evidence of the value that the DEU model contributes to high-quality clinical education.

Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)

DEFF Research Database (Denmark)

Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K

2011-01-01

In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA....... The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5......a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2...

Amino acid sequence analysis of the annexin super-gene family of proteins.

Science.gov (United States)

Barton, G J; Newman, R H; Freemont, P S; Crumpton, M J

1991-06-15

The annexins are a widespread family of calcium-dependent membrane-binding proteins. No common function has been identified for the family and, until recently, no crystallographic data existed for an annexin. In this paper we draw together 22 available annexin sequences consisting of 88 similar repeat units, and apply the techniques of multiple sequence alignment, pattern matching, secondary structure prediction and conservation analysis to the characterisation of the molecules. The analysis clearly shows that the repeats cluster into four distinct families and that greatest variation occurs within the repeat 3 units. Multiple alignment of the 88 repeats shows amino acids with conserved physicochemical properties at 22 positions, with only Gly at position 23 being absolutely conserved in all repeats. Secondary structure prediction techniques identify five conserved helices in each repeat unit and patterns of conserved hydrophobic amino acids are consistent with one face of a helix packing against the protein core in predicted helices a, c, d, e. Helix b is generally hydrophobic in all repeats, but contains a striking pattern of repeat-specific residue conservation at position 31, with Arg in repeats 4 and Glu in repeats 2, but unconserved amino acids in repeats 1 and 3. This suggests repeats 2 and 4 may interact via a buried saltbridge. The loop between predicted helices a and b of repeat 3 shows features distinct from the equivalent loop in repeats 1, 2 and 4, suggesting an important structural and/or functional role for this region. No compelling evidence emerges from this study for uteroglobin and the annexins sharing similar tertiary structures, or for uteroglobin representing a derivative of a primordial one-repeat structure that underwent duplication to give the present day annexins. The analyses performed in this paper are re-evaluated in the Appendix, in the light of the recently published X-ray structure for human annexin V. The structure confirms most of

The polymorphic integumentary mucin B.1 from Xenopus laevis contains the short consensus repeat.

Science.gov (United States)

Probst, J C; Hauser, F; Joba, W; Hoffmann, W

1992-03-25

The frog integumentary mucin B.1 (FIM-B.1), discovered by molecular cloning, contains a cysteine-rich C-terminal domain which is homologous with von Willebrand factor. With the help of the polymerase chain reaction, we now characterize a contiguous region 5' to the von Willebrand factor domain containing the short consensus repeat typical of many proteins from the complement system. Multiple transcripts have been cloned, which originate from a single animal and differ by a variable number of tandem repeats (rep-33 sequences). These different transcripts probably originate solely from two genes and are generated presumably by alternative splicing of an huge array of functional cassettes. This model is supported by analysis of genomic FIM-B.1 sequences from Xenopus laevis. Here, rep-33 sequences are arranged in an interrupted array of individual units. Additionally, results of Southern analysis revealed genetic polymorphism between different animals which is predicted to be within the tandem repeats. A first investigation of the predicted mucins with the help of a specific antibody against a synthetic peptide determined the molecular mass of FIM-B.1 to greater than 200 kDa. Here again, genetic polymorphism between different animals is detected.

The Impact of the Demand for Integration in the Large Multi-Business Unit Firm on the IT Organization Structure

Science.gov (United States)

Larson, Eric Christopher

2012-01-01

Large, multi-business unit firms are decentralizing their overall corporate structures. At the same time, the structures of their IT organizations are becoming more centralized. This is contrary to current wisdom that the IT organization structure will mimic the structure of the corporation, all else being equal. Because the general business…

Triplet repeat DNA structures and human genetic disease

Indian Academy of Sciences (India)

Laboratory of DNA Structure and Mutagenesis, Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University System Health Sciences Center, 2121 West Holcombe Blvd., Houston, TX 77030-3303, USA; Hospital for Sick Children, Department of Genetics, 555 University Avenue, Elm Wing, ...

Genetic variability in maned wolf based on heterologous short-tandem repeat markers from domestic dog.

Science.gov (United States)

Salim, D C; Akimoto, A A; Carvalho, C B; Oliveira, S F; Grisolia, C K; Moreira, J R; Klautau-Guimarães, M N

2007-06-20

The maned wolf (Chrysocyon brachyurus) is the largest South American canid. Habitat loss and fragmentation, due to agricultural expansion and predatory hunting, are the main threats to this species. It is included in the official list of threatened wildlife species in Brazil, and is also protected by IUCN and CITES. Highly variable genetic markers such as microsatellites have the potential to resolve genetic relationships at all levels of the population structure (among individuals, demes or metapopulations) and also to identify the evolutionary unit for strategies for the conservation of the species. Tests were carried out to verify whether a class of highly polymorphic tetranucleotide repeats described for the domestic dog effectively amplifies DNA in the maned wolf. All five loci studied were amplified; however, one of these, was shown to be monomorphic in 69 maned wolf samples. The average allele number and estimated heterozygosity per polymorphic locus were 4.3 and 67%, respectively. The genetic variability found for this species, which is considered threatened with extinction, showed similar results when compared to studies of other canids.

Fabrication of silicon strip detectors using a step-and-repeat lithography system

International Nuclear Information System (INIS)

Holland, S.

1991-11-01

In this work we describe the use of a step-and-repeat lithography system (stepper) for the fabrication of silicon strip detectors. Although the field size of the stepper is only 20 mm in diameter, we have fabricated much larger detectors by printing a repetitive strip detector pattern in a step-and-repeat fashion. The basic unit cell is 7 mm in length. The stepper employs a laser interferometer for stage placement, and the resulting high precision allows one to accurately place the repetitive patterns on the wafer. A small overlap between the patterns ensures a continuous strip. A detector consisting of 512 strips on a 50 μm pitch has been fabricated using this technique. The dimensions of the detector are 6.3 cm by 2.56 cm. Yields of over 99% have been achieved, where yield is defined as the percentage of strips with reverse leakage current below 1 nA. In addition to the inherent advantages of a step-and-repeat system, this technique offers great flexibility in the fabrication of large-area strip detectors since the length and width of the detector can be changed by simply reprogramming the stepper computer. Hence various geometry strip detectors can be fabricated with only one set of masks, as opposed to a separate set of masks for each geometry as would be required with a contact or proximity aligner

Dislocation structures of Σ3 {112} twin boundaries in face centered cubic metals

Science.gov (United States)

Wang, J.; Anderoglu, O.; Hirth, J. P.; Misra, A.; Zhang, X.

2009-07-01

High resolution transmission electron microscopy of nanotwinned Cu films revealed Σ3 {112} incoherent twin boundaries (ITBs), with a repeatable pattern involving units of three {111} atomic planes. Topological analysis shows that Σ3 {112} ITBs adopt two types of atomic structure with differing arrangements of Shockley partial dislocations. Atomistic simulations were performed for Cu and Al. These studies revealed the structure of the two types of ITBs, the formation mechanism and stability of the associated 9R phase, and the influence of stacking fault energies on them. The results suggest that Σ3 {112} ITBs may migrate through the collective glide of partial dislocations.

Automated genotyping of dinucleotide repeat markers

Energy Technology Data Exchange (ETDEWEB)

Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

1994-09-01

The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

Quantum and Information Thermodynamics: A Unifying Framework Based on Repeated Interactions

Science.gov (United States)

Strasberg, Philipp; Schaller, Gernot; Brandes, Tobias; Esposito, Massimiliano

2017-04-01

We expand the standard thermodynamic framework of a system coupled to a thermal reservoir by considering a stream of independently prepared units repeatedly put into contact with the system. These units can be in any nonequilibrium state and interact with the system with an arbitrary strength and duration. We show that this stream constitutes an effective resource of nonequilibrium free energy, and we identify the conditions under which it behaves as a heat, work, or information reservoir. We also show that this setup provides a natural framework to analyze information erasure ("Landauer's principle") and feedback-controlled systems ("Maxwell's demon"). In the limit of a short system-unit interaction time, we further demonstrate that this setup can be used to provide a thermodynamically sound interpretation to many effective master equations. We discuss how nonautonomously driven systems, micromasers, lasing without inversion and the electronic Maxwell demon can be thermodynamically analyzed within our framework. While the present framework accounts for quantum features (e.g., squeezing, entanglement, coherence), we also show that quantum resources do not offer any advantage compared to classical ones in terms of the maximum extractable work.

Material Units, Structures/Landforms, and Stratigraphy for the Global Geologic Map of Ganymede (1:15M)

Science.gov (United States)

Patterson, G. Wesley; Head, James W.; Collins, Geoffrey C.; Pappalardo, Robert T.; Prockter, Louis M.; Lucchitta, Baerbel K.

2008-01-01

In the coming year a global geological map of Ganymede will be completed that represents the most recent understanding of the satellite on the basis of Galileo mission results. This contribution builds on important previous accomplishments in the study of Ganymede utilizing Voyager data and incorporates the many new discoveries that were brought about by examination of Galileo data. Material units have been defined, structural landforms have been identified, and an approximate stratigraphy has been determined utilizing a global mosaic of the surface with a nominal resolution of 1 km/pixel assembled by the USGS. This mosaic incorporates the best available Voyager and Galileo regional coverage and high resolution imagery (100-200 m/pixel) of characteristic features and terrain types obtained by the Galileo spacecraft. This map has given us a more complete understanding of: 1) the major geological processes operating on Ganymede, 2) the characteristics of the geological units making up its surface, 3) the stratigraphic relationships of geological units and structures, and 4) the geological history inferred from these relationships. A summary of these efforts is provided here.

Crystal structure representations for machine learning models of formation energies

Energy Technology Data Exchange (ETDEWEB)

Faber, Felix [Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel Switzerland; Lindmaa, Alexander [Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping Sweden; von Lilienfeld, O. Anatole [Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel Switzerland; Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass Avenue Lemont Illinois 60439; Armiento, Rickard [Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping Sweden

2015-04-20

We introduce and evaluate a set of feature vector representations of crystal structures for machine learning (ML) models of formation energies of solids. ML models of atomization energies of organic molecules have been successful using a Coulomb matrix representation of the molecule. We consider three ways to generalize such representations to periodic systems: (i) a matrix where each element is related to the Ewald sum of the electrostatic interaction between two different atoms in the unit cell repeated over the lattice; (ii) an extended Coulomb-like matrix that takes into account a number of neighboring unit cells; and (iii) an ansatz that mimics the periodicity and the basic features of the elements in the Ewald sum matrix using a sine function of the crystal coordinates of the atoms. The representations are compared for a Laplacian kernel with Manhattan norm, trained to reproduce formation energies using a dataset of 3938 crystal structures obtained from the Materials Project. For training sets consisting of 3000 crystals, the generalization error in predicting formation energies of new structures corresponds to (i) 0.49, (ii) 0.64, and (iii) 0.37eV/atom for the respective representations.

Failure mechanisms of additively manufactured porous biomaterials: Effects of porosity and type of unit cell.

Science.gov (United States)

Kadkhodapour, J; Montazerian, H; Darabi, A Ch; Anaraki, A P; Ahmadi, S M; Zadpoor, A A; Schmauder, S

2015-10-01

Since the advent of additive manufacturing techniques, regular porous biomaterials have emerged as promising candidates for tissue engineering scaffolds owing to their controllable pore architecture and feasibility in producing scaffolds from a variety of biomaterials. The architecture of scaffolds could be designed to achieve similar mechanical properties as in the host bone tissue, thereby avoiding issues such as stress shielding in bone replacement procedure. In this paper, the deformation and failure mechanisms of porous titanium (Ti6Al4V) biomaterials manufactured by selective laser melting from two different types of repeating unit cells, namely cubic and diamond lattice structures, with four different porosities are studied. The mechanical behavior of the above-mentioned porous biomaterials was studied using finite element models. The computational results were compared with the experimental findings from a previous study of ours. The Johnson-Cook plasticity and damage model was implemented in the finite element models to simulate the failure of the additively manufactured scaffolds under compression. The computationally predicted stress-strain curves were compared with the experimental ones. The computational models incorporating the Johnson-Cook damage model could predict the plateau stress and maximum stress at the first peak with less than 18% error. Moreover, the computationally predicted deformation modes were in good agreement with the results of scaling law analysis. A layer-by-layer failure mechanism was found for the stretch-dominated structures, i.e. structures made from the cubic unit cell, while the failure of the bending-dominated structures, i.e. structures made from the diamond unit cells, was accompanied by the shearing bands of 45°. Copyright © 2015 Elsevier Ltd. All rights reserved.

Decree 190/997 Industry, Energy and Mining Ministry: it approve the project of the organize structure reformulation of the respective executant Units

International Nuclear Information System (INIS)

1997-01-01

In Ordinance 190 are about the approval of the reformulate of the organizational structure of the parenthesis 08 Ministry of Industry Energy and Mining that it will be integrated by the following Units executory:001 General Direction of Secretary,002 National Direction of Industrias,004 National Direction of the Property Industrial,007 National Direction of Mining and Geology,008Direction of Energy,009 National Direction of Handicrafts,Small and Medium Enterprises,011 National Direction of Technology Nuclear,del Parenthesis 08. The strategic objective ,organizational structure, structure of positions of work installation ,plan settles down in the whole Ministry.Special stress it is made to the sub paragraph 011 National Direction of Nuclear Technology being established their strategic objective support substantive to the nouns that Units Executory,organizational structure activities remains in the unit in execution in charge of third, structural of positions of work installation ,plan and flowchart of the new structure [es

WD-repeat instability and diversification of the Podospora anserina hnwd non-self recognition gene family.

Science.gov (United States)

Chevanne, Damien; Saupe, Sven J; Clavé, Corinne; Paoletti, Mathieu

2010-05-06

Genes involved in non-self recognition and host defence are typically capable of rapid diversification and exploit specialized genetic mechanism to that end. Fungi display a non-self recognition phenomenon termed heterokaryon incompatibility that operates when cells of unlike genotype fuse and leads to the cell death of the fusion cell. In the fungus Podospora anserina, three genes controlling this allorecognition process het-d, het-e and het-r are paralogs belonging to the same hnwd gene family. HNWD proteins are STAND proteins (signal transduction NTPase with multiple domains) that display a WD-repeat domain controlling recognition specificity. Based on genomic sequence analysis of different P. anserina isolates, it was established that repeat regions of all members of the gene family are extremely polymorphic and undergoing concerted evolution arguing for frequent recombination within and between family members. Herein, we directly analyzed the genetic instability and diversification of this allorecognition gene family. We have constituted a collection of 143 spontaneous mutants of the het-R (HNWD2) and het-E (hnwd5) genes with altered recognition specificities. The vast majority of the mutants present rearrangements in the repeat arrays with deletions, duplications and other modifications as well as creation of novel repeat unit variants. We investigate the extreme genetic instability of these genes and provide a direct illustration of the diversification strategy of this eukaryotic allorecognition gene family.

A comparative study on pathological features of transgenic rat lines expressing either three or four repeat misfolded tau.

Science.gov (United States)

Valachova, Bernadeta; Brezovakova, Veronika; Bugos, Ondrej; Jadhav, Santosh; Smolek, Tomas; Novak, Petr; Zilka, Norbert

2018-08-01

Human tauopathies represent a heterogeneous group of neurodegenerative disorders characterized by distinct clinical features, typical histopathological structures, and defined ratio(s) of three-repeat and four-repeat tau isoforms within pathological aggregates. How the optional microtubule-binding repeat of tau influences this differentiation of pathologies is understudied. We have previously generated and characterized transgenic rodent models expressing human truncated tau aa151-391 with either three (SHR24) or four microtubule-binding repeats (SHR72). Here, we compare the behavioral and neuropathological hallmarks of these two transgenic lines using a battery of tests for sensorimotor, cognitive, and neurological functions over the age range of 3.5-15 months. Progression of sensorimotor and neurological deficits was similar in both transgenic lines; however, the lifespan of transgenic line SHR72 expressing truncated four-repeat tau was markedly shorter than SHR24. Moreover, the expression of three or four-repeat tau induced distinct neurofibrillary pathology in these lines. Transgenic lines displayed different distribution of tau pathology and different type of neurofibrillary tangles. Our results suggest that three- and four-repeat isoforms of tau may display different modes of action in the diseased brain. © 2018 Wiley Periodicals, Inc.

Digital repeat analysis; setup and operation.

Science.gov (United States)

Nol, J; Isouard, G; Mirecki, J

2006-06-01

Since the emergence of digital imaging, there have been questions about the necessity of continuing reject analysis programs in imaging departments to evaluate performance and quality. As a marketing strategy, most suppliers of digital technology focus on the supremacy of the technology and its ability to reduce the number of repeats, resulting in less radiation doses given to patients and increased productivity in the department. On the other hand, quality assurance radiographers and radiologists believe that repeats are mainly related to positioning skills, and repeat analysis is the main tool to plan training needs to up-skill radiographers. A comparative study between conventional and digital imaging was undertaken to compare outcomes and evaluate the need for reject analysis. However, digital technology still being at its early development stages, setting a credible reject analysis program became the major task of the study. It took the department, with the help of the suppliers of the computed radiography reader and the picture archiving and communication system, over 2 years of software enhancement to build a reliable digital repeat analysis system. The results were supportive of both philosophies; the number of repeats as a result of exposure factors was reduced dramatically; however, the percentage of repeats as a result of positioning skills was slightly on the increase for the simple reason that some rejects in the conventional system qualifying for both exposure and positioning errors were classified as exposure error. The ability of digitally adjusting dark or light images reclassified some of those images as positioning errors.

Use of multiple-locus variable-number tandem-repeats analysis (MLVA) typing to characterize Salmonella Typhimurium DT41 broiler breeder infections

DEFF Research Database (Denmark)

Litrup, E.; Christensen, H.; Nordentoft, Steen

2010-01-01

To characterize isolates of Salmonella Typhimurium DT41 obtained from infected flocks of broiler breeders by multiple-locus variable-number tandem-repeats analysis (MLVA) and compare results with a diverse strain collection from Germany and United Kingdom and isolates from Danish patients. A total...

Interrelated chemical-microstructural-nanomechanical variations in the structural units of the cuttlebone of Sepia officinalis

Science.gov (United States)

North, L.; Labonte, D.; Oyen, M. L.; Coleman, M. P.; Caliskan, H. B.; Johnston, R. E.

2017-11-01

"Cuttlebone," the internalized shell found in all members of the cephalopod family Sepiidae, is a sophisticated buoyancy device combining high porosity with considerable strength. Using a complementary suite of characterization tools, we identified significant structural, chemical, and mechanical variations across the different structural units of the cuttlebone: the dorsal shield consists of two stiff and hard layers with prismatic mineral organization which encapsulate a more ductile and compliant layer with a lamellar structure, enriched with organic matter. A similar organization is found in the chambers, which are separated by septa, and supported by meandering plates ("pillars"). Like the dorsal shield, septa contain two layers with lamellar and prismatic organization, respectively, which differ significantly in their mechanical properties: layers with prismatic organization are a factor of three stiffer and up to a factor of ten harder than those with lamellar organization. The combination of stiff and hard, and compliant and ductile components may serve to reduce the risk of catastrophic failure, and reflect the role of organic matter for the growth process of the cuttlebone. Mechanically "weaker" units may function as sacrificial structures, ensuring a stepwise failure of the individual chambers in cases of overloading, allowing the animals to retain near-neutral buoyancy even with partially damaged cuttlebones. Our findings have implications for our understanding of the structure-property-function relationship of cuttlebone, and may help to identify novel bioinspired design strategies for light-weight yet high-strength foams.

Repeatability of apparent diffusion coefficient and intravoxel incoherent motion parameters at 3.0 Tesla in orbital lesions

Energy Technology Data Exchange (ETDEWEB)

Lecler, Augustin [Fondation Ophtalmologique Adolphe de Rothschild, Department of Radiology, Paris (France); Cardiovascular Research Centre - PARCC, Universite Paris Descartes Sorbonne Paris Cite, INSERM UMR-S970, Paris (France); Savatovsky, Julien; Sadik, Jean-Claude; Charbonneau, Frederique; Berges, Olivier [Fondation Ophtalmologique Adolphe de Rothschild, Department of Radiology, Paris (France); Balvay, Daniel [Cardiovascular Research Centre - PARCC, Universite Paris Descartes Sorbonne Paris Cite, INSERM UMR-S970, Paris (France); Zmuda, Mathieu; Galatoire, Olivier [Fondation Ophtalmologique Adolphe de Rothschild, Department of Orbitopalpebral Surgery, Paris (France); Picard, Herve [Fondation Ophtalmologique Adolphe de Rothschild, Clinical Research Unit, Paris (France); Fournier, Laure [Cardiovascular Research Centre - PARCC, Universite Paris Descartes Sorbonne Paris Cite, INSERM UMR-S970, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Assistance Publique-Hopitaux de Paris, Hopital Europeen Georges Pompidou, Radiology Department, Paris (France)

2017-12-15

To evaluate repeatability of intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) parameters in the orbit. From December 2015 to March 2016, 22 patients were scanned twice using an IVIM sequence with 15b values (0-2,000 s/mm{sup 2}) at 3.0T. Two readers independently delineated regions of interest in an orbital mass and in different intra-orbital and extra-orbital structures. Short-term test-retest repeatability and inter-observer agreement were assessed using the intra-class correlation coefficient (ICC), the coefficient of variation (CV) and Bland-Altman limits of agreements (BA-LA). Test-retest repeatability of IVIM parameters in the orbital mass was satisfactory for ADC and D (mean CV 12% and 14%, ICC 95% and 93%), poor for f and D*(means CV 43% and 110%, ICC 90% and 65%). Inter-observer repeatability agreement was almost perfect in the orbital mass for all the IVIM parameters (ICC = 95%, 93%, 94% and 90% for ADC, D, f and D*, respectively). IVIM appeared to be a robust tool to measure D in orbital lesions with good repeatability, but this approach showed a poor repeatability of f and D*. (orig.)

Repeatability of apparent diffusion coefficient and intravoxel incoherent motion parameters at 3.0 Tesla in orbital lesions

International Nuclear Information System (INIS)

Lecler, Augustin; Savatovsky, Julien; Sadik, Jean-Claude; Charbonneau, Frederique; Berges, Olivier; Balvay, Daniel; Zmuda, Mathieu; Galatoire, Olivier; Picard, Herve; Fournier, Laure

2017-01-01

To evaluate repeatability of intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) parameters in the orbit. From December 2015 to March 2016, 22 patients were scanned twice using an IVIM sequence with 15b values (0-2,000 s/mm 2 ) at 3.0T. Two readers independently delineated regions of interest in an orbital mass and in different intra-orbital and extra-orbital structures. Short-term test-retest repeatability and inter-observer agreement were assessed using the intra-class correlation coefficient (ICC), the coefficient of variation (CV) and Bland-Altman limits of agreements (BA-LA). Test-retest repeatability of IVIM parameters in the orbital mass was satisfactory for ADC and D (mean CV 12% and 14%, ICC 95% and 93%), poor for f and D*(means CV 43% and 110%, ICC 90% and 65%). Inter-observer repeatability agreement was almost perfect in the orbital mass for all the IVIM parameters (ICC = 95%, 93%, 94% and 90% for ADC, D, f and D*, respectively). IVIM appeared to be a robust tool to measure D in orbital lesions with good repeatability, but this approach showed a poor repeatability of f and D*. (orig.)

Low Density Lipoprotein Receptor Class A Repeats Are O-Glycosylated in Linker Regions

DEFF Research Database (Denmark)

Pedersen, Nis Borbye; Wang, Shengjun; Narimatsu, Yoshiki

2014-01-01

, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. The glycosites in linker regions of LDLR class A repeats are conserved in LDLR from man to Xenopus and found in other homologous receptors. O-Glycosylation is controlled by a large family of polypeptide Gal...

Coexistence of 3G repeaters with LTE base stations.

Science.gov (United States)

Yeo, Woon-Young; Lee, Sang-Min; Hwang, Gyung-Ho; Kim, Jae-Hoon

2013-01-01

Repeaters have been an attractive solution for mobile operators to upgrade their wireless networks at low cost and to extend network coverage effectively. Since the first LTE commercial deployment in 2009, many mobile operators have launched LTE networks by upgrading their 3G and legacy networks. Because all 3G frequency bands are shared with the frequency bands for LTE deployment and 3G mobile operators have an enormous number of repeaters, reusing 3G repeaters in LTE networks is definitely a practical and cost-efficient solution. However, 3G repeaters usually do not support spatial multiplexing with multiple antennas, and thus it is difficult to reuse them directly in LTE networks. In order to support spatial multiplexing of LTE, the role of 3G repeaters should be replaced with small LTE base stations or MIMO-capable repeaters. In this paper, a repeater network is proposed to reuse 3G repeaters in LTE deployment while still supporting multilayer transmission of LTE. Interestingly, the proposed network has a higher cluster throughput than an LTE network with MIMO-capable repeaters.

Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates

Energy Technology Data Exchange (ETDEWEB)

Jackson, P.J.; Walthers, E.A.; Richmond, K.L. [Los Alamos National Lab., NM (United States)] [and others

1997-04-01

PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five Polymorphisms differed by the presence Of two to six copies of the 12-bp tandem repeat 5{prime}-CAATATCAACAA-3{prime}. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats are generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations. 22 refs., 4 figs., 3 tabs.

Repeatability & Workability Evaluation of SIGMOD 2009

KAUST Repository

Manegold, Stefan

2010-12-15

SIGMOD 2008 was the first database conference that offered to test submitters\\' programs against their data to verify the repeatability of the experiments published [1]. Given the positive feedback concerning the SIGMOD 2008 repeatability initiative, SIGMOD 2009 modified and expanded the initiative with a workability assessment.

Repeatability & Workability Evaluation of SIGMOD 2009

KAUST Repository

Manegold, Stefan; Manolescu, Ioana; Afanasiev, Loredana; Feng, Jieling; Gou, G.; Hadjieleftheriou, Marios; Harizopoulos, Stavros; Kalnis, Panos; Karanasos, Konstantinos; Laurent, Dominique; Lupu, M.; Onose, N.; Ré , C.; Sans, Virginie; Senellart, Pierre; Wu, T.; Shasha, Dennis E.

2010-01-01

SIGMOD 2008 was the first database conference that offered to test submitters' programs against their data to verify the repeatability of the experiments published [1]. Given the positive feedback concerning the SIGMOD 2008 repeatability initiative, SIGMOD 2009 modified and expanded the initiative with a workability assessment.

HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment

NARCIS (Netherlands)

Kappei, D.; Butter, F.; Benda, C.; Scheibe, M.; Draskovic, Irena; Stevense, M.; Novo, C.L.; Basquin, C.; Araki, M.; Araki, K.; Krastev, D.B.; Kittler, R.; Jessberger, R.; Londono-Vallejo, J.A.; Mann, M.; Buchholz, F.

2013-01-01

Telomeres are repetitive DNA structures that, together with the shelterin and the CST complex, protect the ends of chromosomes. Telomere shortening is mitigated in stem and cancer cells through the de novo addition of telomeric repeats by telomerase. Telomere elongation requires the delivery of the

FRB 121102: A Starquake-induced Repeater?

Science.gov (United States)

Wang, Weiyang; Luo, Rui; Yue, Han; Chen, Xuelei; Lee, Kejia; Xu, Renxin

2018-01-01

Since its initial discovery, the fast radio burst (FRB) FRB 121102 has been found to be repeating with millisecond-duration pulses. Very recently, 14 new bursts were detected by the Green Bank Telescope during its continuous monitoring observations. In this paper, we show that the burst energy distribution has a power-law form which is very similar to the Gutenberg–Richter law of earthquakes. In addition, the distribution of burst waiting time can be described as a Poissonian or Gaussian distribution, which is consistent with earthquakes, while the aftershock sequence exhibits some local correlations. These findings suggest that the repeating FRB pulses may originate from the starquakes of a pulsar. Noting that the soft gamma-ray repeaters (SGRs) also exhibit such distributions, the FRB could be powered by some starquake mechanisms associated with the SGRs, including the crustal activity of a magnetar or solidification-induced stress of a newborn strangeon star. These conjectures could be tested with more repeating samples.

Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

Directory of Open Access Journals (Sweden)

Harvey Steven P

2007-03-01

Full Text Available Abstract Background The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations. Results B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10-5 per locus per generation to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were

Theoretical analysis of the spatio-temporal structure of bone multicellular units

International Nuclear Information System (INIS)

Buenzli, P R; Pivonka, P; Gardiner, B S; Smith, D W; Dunstan, C R; Mundy, G R

2010-01-01

Bone multicellular units (BMUs) maintain the viability of the skeletal tissue by coordinating locally the sequence of bone resorption and bone formation performed by cells of the osteoclastic and osteoblastic lineage. Understanding the emergence and the net bone balance of such structured microsystems out of the complex network of biochemical interactions between bone cells is fundamental for many bone-related diseases and the evaluation of fracture risk. Based on current experimental knowledge, we propose a spatio-temporal continuum model describing the interactions of osteoblastic and osteoclastic cells. We show that this model admits travelling-wave-like solutions with well-confined cell profiles upon specifying external conditions mimicking the environment encountered in cortical bone remodelling. The shapes of the various cell concentration profiles within this travelling structure are intrinsically linked to the parameters of the model such as differentiation, proliferation, and apoptosis rates of bone cells. The internal structure of BMUs is reproduced, allowing for experimental calibration. The spatial distribution of the key regulatory factors can also be exhibited, which in diseased states could give hints as to the biochemical agent most accountable for the disorder.

Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers

KAUST Repository

Kandeel, Mahmoud; Al-Taher, Abdulla; Li, Huifang; Schwingenschlö gl, Udo; Alnazawi, Mohamed

2018-01-01

Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulation was carried out to unravel changes in the MERS CoV heptad repeat domains (HRs

Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures

OpenAIRE

Schloss, Patrick D.; Handelsman, Jo

2006-01-01

The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furt...

High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation

Science.gov (United States)

Dimzon, Ian Ken; Trier, Xenia; Frömel, Tobias; Helmus, Rick; Knepper, Thomas P.; de Voogt, Pim

2016-02-01

High resolution mass spectrometry (HRMS) was successfully applied to elucidate the structure of a polyfluorinated polyether (PFPE)-based formulation. The mass spectrum generated from direct injection into the MS was examined by identifying the different repeating units manually and with the aid of an instrument data processor. Highly accurate mass spectral data enabled the calculation of higher-order mass defects. The different plots of MW and the nth-order mass defects (up to n = 3) could aid in assessing the structure of the different repeating units and estimating their absolute and relative number per molecule. The three major repeating units were -C2H4O-, -C2F4O-, and -CF2O-. Tandem MS was used to identify the end groups that appeared to be phosphates, as well as the possible distribution of the repeating units. Reversed-phase HPLC separated of the polymer molecules on the basis of number of nonpolar repeating units. The elucidated structure resembles the structure in the published manufacturer technical data. This analytical approach to the characterization of a PFPE-based formulation can serve as a guide in analyzing not just other PFPE-based formulations but also other fluorinated and non-fluorinated polymers. The information from MS is essential in studying the physico-chemical properties of PFPEs and can help in assessing the risks they pose to the environment and to human health.

Occupational structure and socioeconomic inequality: a comparative study between Brazil and the United States

Directory of Open Access Journals (Sweden)

Alexandre Gori Maia

2015-08-01

Full Text Available ABSTRACTThis paper explores how occupational structure is associated with economic inequality in Brazil in comparison to the United States. Changes in the Brazilian and American occupational structures between 1983 and 2011 are investigated in order to assess how closely they generate high socioeconomic inequalities. The effects of education, age, gender and race on occupational attainment are taken into account. Highlights of the results include: (1 a higher level of socioeconomic development in the American occupational structure, reflecting huge socioeconomic differences between these countries; (2 a tenuous convergence between the Brazilian and American occupational structures; (3 a significant decrease in the net impacts of education, age, gender and race on occupational attainment (i.e., reduced social stratification in both countries. These results suggest the analytical worth of considering occupational structure as a significant intermediate variable affecting the level of socioeconomic inequality within a country over time, as well as between two countries at a given point in time.

Childhood Family Structure and Intergenerational Income Mobility in the United States.

Science.gov (United States)

Bloome, Deirdre

2017-04-01

The declining prevalence of two-parent families helped increase income inequality over recent decades. Does family structure also condition how economic (dis)advantages pass from parents to children? If so, shifts in the organization of family life may contribute to enduring inequality between groups defined by childhood family structure. Using National Longitudinal Survey of Youth data, I combine parametric and nonparametric methods to reveal how family structure moderates intergenerational income mobility in the United States. I find that individuals raised outside stable two-parent homes are much more mobile than individuals from stable two-parent families. Mobility increases with the number of family transitions but does not vary with children's time spent coresiding with both parents or stepparents conditional on a transition. However, this mobility indicates insecurity, not opportunity. Difficulties maintaining middle-class incomes create downward mobility among people raised outside stable two-parent homes. Regardless of parental income, these people are relatively likely to become low-income adults, reflecting a new form of perverse equality. People raised outside stable two-parent families are also less likely to become high-income adults than people from stable two-parent homes. Mobility differences account for about one-quarter of family-structure inequalities in income at the bottom of the income distribution and more than one-third of these inequalities at the top.

Preservice and inservice requirements for containment structures in the United States - a status report

International Nuclear Information System (INIS)

Sammataro, R.F.

1987-01-01

Assuring the lifetime integrity of containment structures for nuclear power plants is becoming increasingly important as existing design criteria are reexamined, as new requirements for containment inspection and testing are formulated, and as today's operating nuclear plants are growing older. Section XI of the ASME Code contains separate rules for metal (Class MC) and concrete (Class CC) containments. Requirements for Class MC containments have been published in Subsection IWE, Requirements for Class MC Components of Light-Water Cooled Power Plants, of Section XI. Rules for Class CC containments are currently being developed and will be published in Subsection IWL, Requirements for Class CC Components of Light-Water Cooled Power Plants, of Section XI. First published in 1981, Subsection IWE has been adopted by a number of state jurisdictions in the United States and is presently being reviewed by the United States Nuclear Regulatory Commission. Federal regulations that will require mandatory compliance by nuclear plant owners are forthcoming. When implemented, the requirements in Subsection IWE and Subsection IWL will provide a reasonable and systematic basis for assuring the integrity of metal and concrete containment structures during their service lifetime. This paper presents an overview of the preservice and inservice requirements for containment structures in Section XI of the ASME Code with consideration of the practical factors that should accompany user compliance. (orig./GL)

Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti.

Science.gov (United States)

Godreuil, S; Renaud, F; Choisy, M; Depina, J J; Garnotel, E; Morillon, M; Van de Perre, P; Bañuls, A L

2010-07-01

Djibouti is an East African country with a high tuberculosis incidence. This study was conducted over a 2-month period in Djibouti, during which 62 consecutive patients with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using mycobacterial interspersed repetitive-unit variable-number tandem-repeat typing and spoligotyping, was performed. The genetic and phylogenetic analysis revealed only three major families (Central Asian, East African Indian and T). The high diversity and linkage disequilibrium within each family suggest a long period of clonal evolution. A Bayesian approach shows that the phylogenetic structure observed in our sample of 62 isolates is very likely to be representative of the phylogenetic structure of the M. tuberculosis population in the total number of TB cases.

Integrative structure and functional anatomy of a nuclear pore complex

Science.gov (United States)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

2018-03-01

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Integrative structure and functional anatomy of a nuclear pore complex.

Science.gov (United States)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

2018-03-22

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Novel expressed sequence tag- simple sequence repeats (EST ...

African Journals Online (AJOL)

Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

United States Armed Forces Celebrating 60 Years of Integration: 1948-2008

National Research Council Canada - National Science Library

Ledesma, Michael; Marcum, Rebecca; Moeser, Erin

2008-01-01

.... Despite repeated resistance, the U.S. military has throughout its history created cohesive and effective fighting units out of a fractious and diverse collection of civilians, integrating service members with vast differences in cultural...

Role of memory errors in quantum repeaters

International Nuclear Information System (INIS)

Hartmann, L.; Kraus, B.; Briegel, H.-J.; Duer, W.

2007-01-01

We investigate the influence of memory errors in the quantum repeater scheme for long-range quantum communication. We show that the communication distance is limited in standard operation mode due to memory errors resulting from unavoidable waiting times for classical signals. We show how to overcome these limitations by (i) improving local memory and (ii) introducing two operational modes of the quantum repeater. In both operational modes, the repeater is run blindly, i.e., without waiting for classical signals to arrive. In the first scheme, entanglement purification protocols based on one-way classical communication are used allowing to communicate over arbitrary distances. However, the error thresholds for noise in local control operations are very stringent. The second scheme makes use of entanglement purification protocols with two-way classical communication and inherits the favorable error thresholds of the repeater run in standard mode. One can increase the possible communication distance by an order of magnitude with reasonable overhead in physical resources. We outline the architecture of a quantum repeater that can possibly ensure intercontinental quantum communication

Hydrothermal syntheses and characterization of uranyl tungstates with electro-neutral structural units

Energy Technology Data Exchange (ETDEWEB)

Balboni, Enrica; Burns, Peter C. [Univ. of Notre Dame, IN (United States). Dept. of Civil and Enviromental Engineering and Earth Sciences; Univ. of Notre Dame, IN (United States). Dept. of Chemistry and Biochemistry

2015-11-01

Two uranyl tungstates, (UO{sub 2})(W{sub 2}O{sub 7})(H{sub 2}O){sub 3} (1) and (UO{sub 2}){sub 3}(W{sub 2}O{sub 8})F{sub 2}(H{sub 2}O){sub 3} (2), were synthesized under hydrothermal conditions at 220 C and were structurally, chemically, and spectroscopically characterized. 1 Crystallizes in space group Pbcm, a = 6.673(5) Aa, b = 12.601(11) Aa, c = 11.552 Aa; 2 is in C2/m, a = 13.648(1) Aa, b = 16.852(1) Aa, c = 9.832(1) Aa, β = 125.980(1) {sup circle}. In 1 the U(VI) cations are present as (UO{sub 2}){sup 2+} uranyl ions that are coordinated by five oxygen atoms to give pentagonal bipyramids. These share two edges with two tungstate octahedra and single vertices with four additional octahedra, resulting in a sheet with the iriginite-type anion topology. Only water molecules are located in the interlayer. The structural units of 2 consist of (UO{sub 2}){sup 2+} uranyl oxy-fluoride pentagonal bipyramids present as either [UO{sub 2}F{sub 2}O{sub 3}]{sup -6} or [UO{sub 2}FO{sub 4}]{sup -5}, and strongly distorted tungstate octahedra. The linkage of uranyl pentagonal bipyramids and tungstate octahedra gives a unique sheet anion topology consisting of pentagons, squares and triangles. In 2, the uranyl tungstates sheets are connected into a novel electro-neutral three-dimensional framework through dimers of uranyl pentagonal bipyramids. These dimers connecting the sheets share an edge defined by F anions. 2 is the first example of a uranyl tungstate oxy-fluoride, and 1 and 2 are rare examples of uranyl compounds containing electro-neutral structural units.

Organization of Control Units with Operational Addressing

OpenAIRE

Alexander A. Barkalov; Roman M. Babakov; Larysa A. Titarenko

2012-01-01

The using of operational addressing unit as the block of control unit is proposed. The new structure model of Moore finite-state machine with reduced hardware amount is developed. The generalized structure of operational addressing unit is suggested. An example of synthesis process for Moore finite-state machine with operational addressing unit is given. The analytical researches of proposed structure of control unit are executed.

Ocular surface sensitivity repeatability with Cochet-Bonnet esthesiometer.

Science.gov (United States)

Chao, Cecilia; Stapleton, Fiona; Badarudin, Ezailina; Golebiowski, Blanka

2015-02-01

To determine the repeatability of ocular surface threshold measurements using the Cochet-Bonnet esthesiometer on the same day and 3 months apart. Two separate studies were conducted to determine the repeatability of ocular surface threshold measurements made on the same day (n = 20 subjects) and 3 months apart (n = 29 subjects). The Cochet-Bonnet esthesiometer was used to measure corneal and inferior conjunctival thresholds using the ascending method of limits. The pressure exerted by the Cochet-Bonnet esthesiometer was determined using an analytical balance, for both the 0.08- and 0.12-mm-diameter filaments. This calibration was then used to convert filament length measurements to pressure. Repeatability was determined using a Bland and Altman analysis. The pressure exerted at each filament length differed between the two filament diameters. The measured pressure also differed from values provided by the manufacturer. Repeatability of threshold measurements at the central cornea was shown to be good, with better repeatability for same-day measurements (coefficient of repeatability [CoR] = ±0.23 g/mm²) than for those 3 months apart (CoR = ±0.52 g/mm²). Threshold measurements at the inferior conjunctiva, in contrast, were poorly repeatable (CoR = ±12.78 g/mm²). Cochet-Bonnet esthesiometry is repeatable when performed on the central cornea on the same day and 3 months apart, but this instrument is not recommended for conjunctival threshold measurements.

Safety of Repeated Yttrium-90 Radioembolization

International Nuclear Information System (INIS)

Lam, Marnix G. E. H.; Louie, John D.; Iagaru, Andrei H.; Goris, Michael L.; Sze, Daniel Y.

2013-01-01

Purpose: Repeated radioembolization (RE) treatments carry theoretically higher risk of radiation-induced hepatic injury because of the liver’s cumulative memory of previous exposure. We performed a retrospective safety analysis on patients who underwent repeated RE. Methods: From 2004 to 2011, a total of 247 patients were treated by RE. Eight patients (5 men, 3 women, age range 51–71 years) underwent repeated treatment of a targeted territory, all with resin microspheres (SIR-Spheres; Sirtex, Lane Cove, Australia). Adverse events were graded during a standardized follow-up. In addition, the correlation between the occurrence of RE-induced liver disease (REILD) and multiple variables was investigated in univariate and multivariate analyses in all 247 patients who received RE. Results: Two patients died shortly after the second treatment (at 84 and 107 days) with signs and symptoms of REILD. Both patients underwent whole liver treatment twice (cumulative doses 3.08 and 2.66 GBq). The other 6 patients demonstrated only minor toxicities after receiving cumulative doses ranging from 2.41 to 3.88 GBq. All patients experienced objective tumor responses. In the whole population, multifactorial analysis identified three risk factors associated with REILD: repeated RE (p = 0.036), baseline serum total bilirubin (p = 0.048), and baseline serum aspartate aminotransferase (p = 0.043). Repeated RE proved to be the only independent risk factor for REILD in multivariate analysis (odds ratio 9.6; p = 0.002). Additionally, the administered activity per target volume (in GBq/L) was found to be an independent risk factor for REILD, but only in whole liver treatments (p = 0.033). Conclusion: The risk of REILD appears to be elevated for repeated RE. Objective tumor responses were observed, but establishment of safety limits will require improvement in dosimetric measurement and prediction

Safety of Repeated Yttrium-90 Radioembolization

Energy Technology Data Exchange (ETDEWEB)

Lam, Marnix G. E. H.; Louie, John D. [Stanford University School of Medicine, Division of Interventional Radiology (United States); Iagaru, Andrei H.; Goris, Michael L. [Stanford University School of Medicine, Division of Nuclear Medicine (United States); Sze, Daniel Y., E-mail: dansze@stanford.edu [Stanford University School of Medicine, Division of Interventional Radiology (United States)

2013-10-15

Purpose: Repeated radioembolization (RE) treatments carry theoretically higher risk of radiation-induced hepatic injury because of the liver's cumulative memory of previous exposure. We performed a retrospective safety analysis on patients who underwent repeated RE. Methods: From 2004 to 2011, a total of 247 patients were treated by RE. Eight patients (5 men, 3 women, age range 51-71 years) underwent repeated treatment of a targeted territory, all with resin microspheres (SIR-Spheres; Sirtex, Lane Cove, Australia). Adverse events were graded during a standardized follow-up. In addition, the correlation between the occurrence of RE-induced liver disease (REILD) and multiple variables was investigated in univariate and multivariate analyses in all 247 patients who received RE. Results: Two patients died shortly after the second treatment (at 84 and 107 days) with signs and symptoms of REILD. Both patients underwent whole liver treatment twice (cumulative doses 3.08 and 2.66 GBq). The other 6 patients demonstrated only minor toxicities after receiving cumulative doses ranging from 2.41 to 3.88 GBq. All patients experienced objective tumor responses. In the whole population, multifactorial analysis identified three risk factors associated with REILD: repeated RE (p = 0.036), baseline serum total bilirubin (p = 0.048), and baseline serum aspartate aminotransferase (p = 0.043). Repeated RE proved to be the only independent risk factor for REILD in multivariate analysis (odds ratio 9.6; p = 0.002). Additionally, the administered activity per target volume (in GBq/L) was found to be an independent risk factor for REILD, but only in whole liver treatments (p = 0.033). Conclusion: The risk of REILD appears to be elevated for repeated RE. Objective tumor responses were observed, but establishment of safety limits will require improvement in dosimetric measurement and prediction.

Dependence of the paired motor unit analysis on motor unit discharge characteristics in the human tibialis anterior muscle

Science.gov (United States)

Stephenson, Jennifer L.; Maluf, Katrina S.

2011-01-01

The paired motor unit analysis provides in vivo estimates of the magnitude of persistent inward currents (PIC) in human motoneurons by quantifying changes in the firing rate (ΔF) of an earlier recruited (reference) motor unit at the time of recruitment and derecruitment of a later recruited (test) motor unit. This study assessed the variability of ΔF estimates, and quantified the dependence of ΔF on the discharge characteristics of the motor units selected for analysis. ΔF was calculated for 158 pairs of motor units recorded from nine healthy individuals during repeated submaximal contractions of the tibialis anterior muscle. The mean (SD) ΔF was 3.7 (2.5) pps (range −4.2 to 8.9 pps). The median absolute difference in ΔF for the same motor unit pair across trials was 1.8 pps, and the minimal detectable change in ΔF required to exceed measurement error was 4.8 pps. ΔF was positively related to the amount of discharge rate modulation in the reference motor unit (r2=0.335; Precruitment of the reference and test motor units (r2=0.229, Pmotor unit activity (r2=0.110, Precruitment threshold of the test motor unit (r2=0.237, Pmotor unit analysis. PMID:21459110

Structure and anticoagulant activity of a sulfated galactan from the red alga, Gelidium crinale. Is there a specific structural requirement for the anticoagulant action?

Science.gov (United States)

Pereira, Maria G; Benevides, Norma M B; Melo, Marcia R S; Valente, Ana Paula; Melo, Fábio R; Mourão, Paulo A S

2005-09-05

Marine red algae are an abundant source of sulfated galactans with potent anticoagulant activity. However, the specific structural motifs that confer biological activity remain to be elucidated. We have now isolated and purified a sulfated galactan from the marine red alga, Gellidium crinale. The structure of this polysaccharide was determined using NMR spectroscopy. It is composed of the repeating structure -4-alpha-Galp-(1-->3)-beta-Galp1--> but with a variable sulfation pattern. Clearly 15% of the total alpha-units are 2,3-di-sulfated and another 55% are 2-sulfated. No evidence for the occurrence of 3,6-anhydro alpha-galactose units was observed in the NMR spectra. We also compared the anticoagulant activity of this sulfated galactan with a polysaccharide from the species, Botryocladia occidentalis, with a similar saccharide chain but with higher amounts of 2,3-di-sulfated alpha-units. The sulfated galactan from G. crinale has a lower anticoagulant activity on a clotting assay when compared with the polysaccharide from B. occidentalis. When tested in assays using specific proteases and coagulation inhibitors, these two galactans showed significant differences in their activity. They do not differ in thrombin inhibition mediated by antithrombin, but in assays where heparin cofactor II replaces antithrombin, the sulfated galactan from G. crinale requires a significantly higher concentration to achieve the same inhibitory effect as the polysaccharide from B. occidentalis. In contrast, when factor Xa instead of thrombin is used as the target protease, the sulfated galactan from G. crinale is a more potent anticoagulant. These observations suggest that the proportion and/or the distribution of 2,3-di-sulfated alpha-units along the galactan chain may be a critical structural motif to promote the interaction of the protease with specific protease and coagulation inhibitors.

Effect of repeat unit structure and molecular mass of lactic acid bacteria hetero-exopolysaccharides on binding to milk proteins

DEFF Research Database (Denmark)

Birch, Johnny; HarÐarson, HörÐur Kári; Khan, Sanaullah

2017-01-01

-exopolysaccharides (HePSs) of 0.14–4.9 MDa from lactic acid bacteria to different milk proteins (β-casein, κ-casein, native and heat-treated β-lactoglobulin) at pH 4.0–5.0. Maximum binding capacity (RUmax) and apparent affinity (KA,app) were HePS- and protein-dependent and varied for example 10- and 600-fold......, respectively, in the complexation with native β-lactoglobulin at pH 4.0. Highest RUmax and KA,app were obtained with heat-treated β-lactoglobulin and β-casein, respectively. Overall, RUmax and KA,app decreased 6- and 20-fold, respectively, with increasing pH from 4.0 to 5.0. KA,app was influenced by ionic......Interactions of exopolysaccharides and proteins are of great importance in food science, but complicated to analyze and quantify at the molecular level. A surface plasmon resonance procedure was established to characterize binding of seven structure-determined, branched hetero...

Dental Fear in Children with Repeated Tooth Injuries.

Science.gov (United States)

Negovetić Vranić, Dubravka; Ivančić Jokić, Nataša; Bakarčić, Danko; Carek, Andreja; Rotim, Željko; Verzak, Željko

2016-06-01

Tooth injuries are serious clinical conditions. Some children experience dental trauma only once, while others are more prone to repeated tooth injuries. Repeated dental trauma occurs in 19.4% to 30% of patients. Pain and dental trauma are the most common reasons for fear and anxiety. The main objective of this study was to investigate how dental trauma, as well as repeated dental trauma affects the occurrence and development of dental fear in children. The study was conducted on a random sample of 147 subjects (88 boys and 59 girls) aged 5-8 and 9-12 years. Subjects in both age groups were divided into subroups without dental trauma, with one dental trauma and with repeated dental trauma. The validated Children’s Fear Survey Schedule – Dental Subscale was used on fear assessment. Results showed that only 12.2% of children without trauma, 33.3% with one trauma and 51.7% with repeated trauma were not afraid of injection. Older children had a significantly lower fear of injections, touch of an unknown person, choking, going to the hospital and people in white uniforms. Dentist was not the cause of fear in 65.5% of patients with repeated trauma. With each repeated injury of teeth, the degree of their fear of dental treatment was lower.

Human mismatch repair protein hMutLα is required to repair short slipped-DNAs of trinucleotide repeats.

Science.gov (United States)

Panigrahi, Gagan B; Slean, Meghan M; Simard, Jodie P; Pearson, Christopher E

2012-12-07

Mismatch repair (MMR) is required for proper maintenance of the genome by protecting against mutations. The mismatch repair system has also been implicated as a driver of certain mutations, including disease-associated trinucleotide repeat instability. We recently revealed a requirement of hMutSβ in the repair of short slip-outs containing a single CTG repeat unit (1). The involvement of other MMR proteins in short trinucleotide repeat slip-out repair is unknown. Here we show that hMutLα is required for the highly efficient in vitro repair of single CTG repeat slip-outs, to the same degree as hMutSβ. HEK293T cell extracts, deficient in hMLH1, are unable to process single-repeat slip-outs, but are functional when complemented with hMutLα. The MMR-deficient hMLH1 mutant, T117M, which has a point mutation proximal to the ATP-binding domain, is defective in slip-out repair, further supporting a requirement for hMLH1 in the processing of short slip-outs and possibly the involvement of hMHL1 ATPase activity. Extracts of hPMS2-deficient HEC-1-A cells, which express hMLH1, hMLH3, and hPMS1, are only functional when complemented with hMutLα, indicating that neither hMutLβ nor hMutLγ is sufficient to repair short slip-outs. The resolution of clustered short slip-outs, which are poorly repaired, was partially dependent upon a functional hMutLα. The joint involvement of hMutSβ and hMutLα suggests that repeat instability may be the result of aberrant outcomes of repair attempts.

Erroneous Memories Arising from Repeated Attempts to Remember

Science.gov (United States)

Henkel, Linda A.

2004-01-01

The impact of repeated and prolonged attempts at remembering on false memory rates was assessed in three experiments. Participants saw and imagined pictures and then made repeated recall attempts before taking a source memory test. Although the number of items recalled increased with repeated tests, the net gains were associated with more source…

Structure and Function of the Ankyrin Repeats in the Sw14/Sw16 Transcription Complex of Budding Yeast

National Research Council Canada - National Science Library

Breeden, Linda

1998-01-01

ANK repeats were first found in the Swi6 transcription factor of Saccharomyces cerevisiae and since then were identified in many proteins, including oncogenes and tumor suppressors We have previously...

Hydrogeologic framework of the uppermost principal aquifer systems in the Williston and Powder River structural basins, United States and Canada

Science.gov (United States)

Thamke, Joanna N.; LeCain, Gary D.; Ryter, Derek W.; Sando, Roy; Long, Andrew J.

2014-01-01

The glacial, lower Tertiary, and Upper Cretaceous aquifer systems in the Williston and Powder River structural basins within the United States and Canada are the uppermost principal aquifer systems and most accessible sources of groundwater for these energy-producing basins. The glacial aquifer system covers the northeastern part of the Williston structural basin. The lower Tertiary and Upper Cretaceous aquifer systems are present in about 91,300 square miles (mi2) of the Williston structural basin and about 25,500 mi2 of the Powder River structural basin. Directly under these aquifer systems are 800 to more than 3,000 feet (ft) of relatively impermeable marine shale that serves as a basal confining unit. The aquifer systems in the Williston structural basin have a shallow (less than 2,900 ft deep), wide, and generally symmetrical bowl shape. The aquifer systems in the Powder River structural basin have a very deep (as much as 8,500 ft deep), narrow, and asymmetrical shape.

[Active miniature inverted-repeat transposable elements transposon in plants: a review].

Science.gov (United States)

Hu, Bingjie; Zhou, Mingbing

2018-02-25

Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

Multi-band microwave photonic satellite repeater scheme employing intensity Mach-Zehnder modulators

Institute of Scientific and Technical Information of China (English)

Yin Jie; Dong Tao; Zhang Bin; Hao Yan; Cao Guixing; Cheng Zijing; Xu Kun; Zhou Yue; Dai Jian

2017-01-01

To solve the satellite repeater's flexible and wideband frequency conversion problem,we propose a novel microwave photonic repeater system,which can convert the upload signal's carrier to six different frequencies.The scheme employs one 20 GHz bandwidth dual-drive Mach-Zehnder modulator (MZM) and two 10 GHz bandwidth MZMs.The basic principle of this scheme is filtering out two optical sidebands after the optical carrier suppression (OCS) modulation and combining two sidebands modulated by the input radio frequency (RF) signal.This structure can realize simultaneous multi-band frequency conversion with only one frequency-fixed microwave source and prevent generating harmful interference sidebands by using two corresponding optical filters after optical modulation.In the simulation,one C-band signal of 6 GHz carrier can be successfully converted to 12 GHz (Ku-band),28 GHz,34 GHz,40 GHz,46 GHz (Ka-band) and 52 GHz (V-band),which can be an attractive method to realize multi-band microwave photonic satellite repeater.Alternatively,the scheme can be configured to generate multi-band local oscillators (LOs) for widely satellite onboard clock distribution when the input RF signal is replaced by the internal clock source.

Second unit scheduling concerns on a dual-unit nuclear project

International Nuclear Information System (INIS)

Block, H.R.; Mazzini, R.A.

1978-01-01

This paper explores the planning and scheduling problems of Unit 2 of the Susquehanna steam electric station. The causes of these problems and methods to avoid or mitigate their consequences are discussed. The Susquehanna steam electric station has two boiling water reactors rated at 1,100 MW each. Topics considered include cost factors, structures, equipment, engineering and home office, construction services, completion data phasing, work sequencing, structural dependences, and segregation. Substatial cost and schedule benefits can result if two nuclear units are designed and constructed as one integral station, and if maximum sharing of facilities and services between the units occurs. It is concluded that the cost benefits of highly integrated dual unit construction outweigh the schedule and logistical problems caused by that approach

Structure and genetics of the O-specific polysaccharide of Escherichia coli O27.

Science.gov (United States)

Perepelov, Andrei V; Chen, Tingting; Senchenkova, Sofya N; Filatov, Andrei V; Song, Jingjie; Shashkov, Alexander S; Liu, Bin; Knirel, Yuriy A

2018-02-01

The O-specific polysaccharide (O-antigen) is a part of the lipopolysaccharide on the cell surface of Gram-negative bacteria. The O-polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide of Escherichia coli O27 and studied by sugar analysis and Smith degradation along with 1 H and 13 C NMR spectroscopy. The following structure of the branched hexasaccharide repeating unit was established, which is unique among known structures of bacterial polysaccharides:where GlcA is non-stoichiometrically O-acetylated at position 3 (∼22%) or 4 (∼37%). Functions of genes in the O-antigen gene cluster of E. coli O27 were tentatively assigned by comparison with sequences in the available databases and found to be consistent with the O-polysaccharide structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

Deciphering structural and temporal interplays during the architectural development of mango trees.

Science.gov (United States)

Dambreville, Anaëlle; Lauri, Pierre-Éric; Trottier, Catherine; Guédon, Yann; Normand, Frédéric

2013-05-01

Plant architecture is commonly defined by the adjacency of organs within the structure and their properties. Few studies consider the effect of endogenous temporal factors, namely phenological factors, on the establishment of plant architecture. This study hypothesized that, in addition to the effect of environmental factors, the observed plant architecture results from both endogenous structural and temporal components, and their interplays. Mango tree, which is characterized by strong phenological asynchronisms within and between trees and by repeated vegetative and reproductive flushes during a growing cycle, was chosen as a plant model. During two consecutive growing cycles, this study described vegetative and reproductive development of 20 trees submitted to the same environmental conditions. Four mango cultivars were considered to assess possible cultivar-specific patterns. Integrative vegetative and reproductive development models incorporating generalized linear models as components were built. These models described the occurrence, intensity, and timing of vegetative and reproductive development at the growth unit scale. This study showed significant interplays between structural and temporal components of plant architectural development at two temporal scales. Within a growing cycle, earliness of bud burst was highly and positively related to earliness of vegetative development and flowering. Between growing cycles, flowering growth units delayed vegetative development compared to growth units that did not flower. These interplays explained how vegetative and reproductive phenological asynchronisms within and between trees were generated and maintained. It is suggested that causation networks involving structural and temporal components may give rise to contrasted tree architectures.

Nonparametric additive regression for repeatedly measured data

KAUST Repository

Carroll, R. J.; Maity, A.; Mammen, E.; Yu, K.

2009-01-01

We develop an easily computed smooth backfitting algorithm for additive model fitting in repeated measures problems. Our methodology easily copes with various settings, such as when some covariates are the same over repeated response measurements

Quantum key distribution with two-segment quantum repeaters

Energy Technology Data Exchange (ETDEWEB)

Kampermann, Hermann; Abruzzo, Silvestre; Bruss, Dagmar [Theoretische Physik III, Heinrich-Heine-Universitaet Duesseldorf (Germany)

2014-07-01

Quantum repeaters represent one possible way to achieve long-distance quantum key distribution. One way of improving the repeater rate and decreasing the memory coherence time is the usage of multiplexing. Motivated by the experimental fact that long-range connections are practically demanding, we extend the analysis of the quantum repeater multiplexing protocol to the case of short-range connections. We derive formulas for the repeater rate and we show that short-range connections lead to most of the benefits of a full-range multiplexing protocol. A less demanding QKD-protocol without quantum memories was recently introduced by Lo et al. We generalize this measurement-device-independent quantum key Distribution protocol to the scenario where the repeater Station contains also heralded quantum memories. We assume either single-photon sources or weak coherent pulse sources plus decay states. We show that it is possible to significantly outperform the original proposal, even in presence of decoherence of the quantum memory. We give formulas in terms of device imperfections i.e., the quantum bit error rate and the repeater rate.

Structure-guided investigation of lipopolysaccharide O-antigen chain length regulators reveals regions critical for modal length control.

Science.gov (United States)

Kalynych, Sergei; Ruan, Xiang; Valvano, Miguel A; Cygler, Miroslaw

2011-08-01

The O-antigen component of the lipopolysaccharide (LPS) represents a population of polysaccharide molecules with nonrandom (modal) chain length distribution. The number of the repeat O units in each individual O-antigen polymer depends on the Wzz chain length regulator, an inner membrane protein belonging to the polysaccharide copolymerase (PCP) family. Different Wzz proteins confer vastly different ranges of modal lengths (4 to >100 repeat units), despite having remarkably conserved structural folds. The molecular mechanism responsible for the selective preference for a certain number of O units is unknown. Guided by the three-dimensional structures of PCPs, we constructed a panel of chimeric molecules containing parts of two closely related Wzz proteins from Salmonella enterica and Shigella flexneri which confer different O-antigen chain length distributions. Analysis of the O-antigen length distribution imparted by each chimera revealed the region spanning amino acids 67 to 95 (region 67 to 95), region 200 to 255, and region 269 to 274 as primarily affecting the length distribution. We also showed that there is no synergy between these regions. In particular, region 269 to 274 also influenced chain length distribution mediated by two distantly related PCPs, WzzB and FepE. Furthermore, from the 3 regions uncovered in this study, region 269 to 274 appeared to be critical for the stability of the oligomeric form of Wzz, as determined by cross-linking experiments. Together, our data suggest that chain length determination depends on regions that likely contribute to stabilize a supramolecular complex.

Asymmetry of inverted-topology repeats in the AE1 anion exchanger suggests an elevator-like mechanism

Science.gov (United States)

Faraldo-Gómez, José D.

2017-01-01

The membrane transporter anion exchanger 1 (AE1), or band 3, is a key component in the processes of carbon-dioxide transport in the blood and urinary acidification in the renal collecting duct. In both erythrocytes and the basolateral membrane of the collecting-duct α-intercalated cells, the role of AE1 is to catalyze a one-for-one exchange of chloride for bicarbonate. After decades of biochemical and functional studies, the structure of the transmembrane region of AE1, which catalyzes the anion-exchange reaction, has finally been determined. Each protomer of the AE1 dimer comprises two repeats with inverted transmembrane topologies, but the structures of these repeats differ. This asymmetry causes the putative substrate-binding site to be exposed only to the extracellular space, consistent with the expectation that anion exchange occurs via an alternating-access mechanism. Here, we hypothesize that the unknown, inward-facing conformation results from inversion of this asymmetry, and we propose a model of this state constructed using repeat-swap homology modeling. By comparing this inward-facing model with the outward-facing experimental structure, we predict that the mechanism of AE1 involves an elevator-like motion of the substrate-binding domain relative to the nearly stationary dimerization domain and to the membrane plane. This hypothesis is in qualitative agreement with a wide range of biochemical and functional data, which we review in detail, and suggests new avenues of experimentation. PMID:29167180

Asymmetry of inverted-topology repeats in the AE1 anion exchanger suggests an elevator-like mechanism.

Science.gov (United States)

Ficici, Emel; Faraldo-Gómez, José D; Jennings, Michael L; Forrest, Lucy R

2017-12-04

The membrane transporter anion exchanger 1 (AE1), or band 3, is a key component in the processes of carbon-dioxide transport in the blood and urinary acidification in the renal collecting duct. In both erythrocytes and the basolateral membrane of the collecting-duct α-intercalated cells, the role of AE1 is to catalyze a one-for-one exchange of chloride for bicarbonate. After decades of biochemical and functional studies, the structure of the transmembrane region of AE1, which catalyzes the anion-exchange reaction, has finally been determined. Each protomer of the AE1 dimer comprises two repeats with inverted transmembrane topologies, but the structures of these repeats differ. This asymmetry causes the putative substrate-binding site to be exposed only to the extracellular space, consistent with the expectation that anion exchange occurs via an alternating-access mechanism. Here, we hypothesize that the unknown, inward-facing conformation results from inversion of this asymmetry, and we propose a model of this state constructed using repeat-swap homology modeling. By comparing this inward-facing model with the outward-facing experimental structure, we predict that the mechanism of AE1 involves an elevator-like motion of the substrate-binding domain relative to the nearly stationary dimerization domain and to the membrane plane. This hypothesis is in qualitative agreement with a wide range of biochemical and functional data, which we review in detail, and suggests new avenues of experimentation. © 2017 Ficici et al.

Deployment Repeatability

Science.gov (United States)

2016-08-31

large cohort of trials to spot unusual cases. However, deployment repeatability is inherently a nonlinear phenomenon, which makes modeling difficult...and GEMS tip position were both tracked during ground testing by a laser target tracking system. Earlier SAILMAST testing in 2005 [8] used...recalls the strategy used by SRTM, where a constellation of lights was installed at the tip of the boom and a modified star tracker was used to track tip

Analysis of the Local Budget’s Expenditures Structure at Different Types of Administrative Units in Romania

Directory of Open Access Journals (Sweden)

Dan-Constantin Danuletiu

2016-01-01

Full Text Available Financial decentralization process affected the expenditure part of the local budgets in Romania by imposing new destinations for own revenues, but also by limiting the decision autonomy because of the equalization system design or the transfer of responsibilities without establishing new sources of revenues. But the effects on the local budgets are not the same for every administrative unit. The article highlights the structure of expenditures of local budgets for different types of administrative unit, for identifying variations in and potential causes of the financial autonomy regarding local expenditures.

Repeat profile analysis in an x-ray department

International Nuclear Information System (INIS)

Bassey, C.E.; Ojo, O.O.; Akpabio, I.

1991-01-01

The repeat profile of an x-ray department in a developing country was analysed monthly between July 1989 and June 1990. Results showed an average repeat rate of 3.7% for the period of study. The main causes of film repetition were: equipment fault, 33.9%; radiographer's fault, 27.4%; film fault, 19.3%; processing fault, 10.8% and patient's fault, 8.6%. The average repeat rate in the first 6 months of study reduced by 50% in the last 6 months. This was due to the effectiveness of implementation of corrective actions. The overall repeat rate was found to correlate well with both the equipment fault and radiographer's fault with correlation coefficients, r, of 0.94 and 0.91, respectively. It is expected that a further reduction in the repeat rate will be obtained after the introduction of quality assurance programmes. (author)

A structural and thermal packaging approach for power processing units for 30-cm ion thrusters

Science.gov (United States)

Maloy, J. E.; Sharp, G. R.

1975-01-01

Solar Electric Propulsion (SEP) is currently being studied for possible use in a number of near earth and planetary missions. The thruster subsystem for these missions would consist of 30 centimeter ion thrusters with Power Processor Units (PPU) clustered in assemblies of from two to ten units. A preliminary design study of the electronic packaging of the PPU has been completed at Lewis Research Center of NASA. This study evaluates designs meeting the competing requirements of low system weight and overall mission flexibility. These requirements are evaluated regarding structural and thermal design, electrical efficiency, and integration of the electrical circuits into a functional PPU layout.

Electronic structure description of the cis-MoOS unit in models for molybdenum hydroxylases.

Science.gov (United States)

Doonan, Christian J; Rubie, Nick D; Peariso, Katrina; Harris, Hugh H; Knottenbelt, Sushilla Z; George, Graham N; Young, Charles G; Kirk, Martin L

2008-01-09

The molybdenum hydroxylases catalyze the oxidation of numerous aromatic heterocycles and simple organics and, unlike other hydroxylases, utilize water as the source of oxygen incorporated into the product. The electronic structures of the cis-MoOS units in CoCp2[TpiPrMoVOS(OPh)] and TpiPrMoVIOS(OPh) (TpiPr = hydrotris(3-isopropylpyrazol-1-yl)borate), new models for molybdenum hydroxylases, have been studied in detail using S K-edge X-ray absorption spectroscopy, vibrational spectroscopy, and detailed bonding calculations. The results show a highly delocalized Mo=S pi* LUMO redox orbital that is formally Mo(dxy) with approximately 35% sulfido ligand character. Vibrational spectroscopy has been used to quantitate Mo-Ssulfido bond order changes in the cis-MoOS units as a function of redox state. Results support a redox active molecular orbital that has a profound influence on MoOS bonding through changes to the relative electro/nucleophilicity of the terminal sulfido ligand accompanying oxidation state changes. The bonding description for these model cis-MoOS systems supports enzyme mechanisms that are under orbital control and dominantly influenced by the unique electronic structure of the cis-MoOS site. The electronic structure of the oxidized enzyme site is postulated to play a role in polarizing a substrate carbon center for nucleophilic attack by metal activated water and acting as an electron sink in the two-electron oxidation of substrates.

Plant Growth and Development: An Outline for a Unit Structured Around the Life Cycle of Rapid-Cycling Brassica Rapa.

Science.gov (United States)

Becker, Wayne M.

This outline is intended for use in a unit of 10-12 lectures on plant growth and development at the introductory undergraduate level as part of a course on organismal biology. The series of lecture outlines is structured around the life cycle of rapid-cycling Brassica rapa (RCBr). The unit begins with three introductory lectures on general plant…

D20S16 is a complex interspersed repeated sequence: Genetic and physical analysis of the locus

Energy Technology Data Exchange (ETDEWEB)

Bowden, D.W.; Krawchuk, M.D.; Howard, T.D. [Wake Forest Univ., Winston-Salem, NC (United States)] [and others

1995-01-20

The genomic structure of the D20S16 locus has been evaluated using genetic and physical methods. D20S16, originally detected with the probe CRI-L1214, is a highly informative, complex restriction fragment length polymorphism consisting of two separate allelic systems. The allelic systems have the characteristics of conventional VNTR polymorphisms and are separated by recombination ({theta} = 0.02, Z{sub max} = 74.82), as demonstrated in family studies. Most of these recombination events are meiotic crossovers and are maternal in origin, but two, including deletion of the locus in a cell line from a CEPH family member, occur without evidence for exchange of flanking markers. DNA sequence analysis suggests that the basis of the polymorphism is variable numbers of a 98-bp sequence tandemly repeated with 87 to 90% sequence similarity between repeats. The 98-bp repeat is a dimer of 49 bp sequence with 45 to 98% identity between the elements. In addition, nonpolymorphic genomic sequences adjacent to the polymorphic 98-bp repeat tracts are also repeated but are not polymorphic, i.e., show no individual to individual variation. Restriction enzyme mapping of cosmids containing the CRI-L1214 sequence suggests that there are multiple interspersed repeats of the CRI-L1214 sequence on chromosome 20. The results of dual-color fluorescence in situ hybridization experiments with interphase nuclei are also consistent with multiple repeats of an interspersed sequence on chromosome 20. 23 refs., 6 figs.

High-Pressure NMR and SAXS Reveals How Capping Modulates Folding Cooperativity of the pp32 Leucine-rich Repeat Protein.

Science.gov (United States)

Zhang, Yi; Berghaus, Melanie; Klein, Sean; Jenkins, Kelly; Zhang, Siwen; McCallum, Scott A; Morgan, Joel E; Winter, Roland; Barrick, Doug; Royer, Catherine A

2018-04-27

Many repeat proteins contain capping motifs, which serve to shield the hydrophobic core from solvent and maintain structural integrity. While the role of capping motifs in enhancing the stability and structural integrity of repeat proteins is well documented, their contribution to folding cooperativity is not. Here we examined the role of capping motifs in defining the folding cooperativity of the leucine-rich repeat protein, pp32, by monitoring the pressure- and urea-induced unfolding of an N-terminal capping motif (N-cap) deletion mutant, pp32-∆N-cap, and a C-terminal capping motif destabilization mutant pp32-Y131F/D146L, using residue-specific NMR and small-angle X-ray scattering. Destabilization of the C-terminal capping motif resulted in higher cooperativity for the unfolding transition compared to wild-type pp32, as these mutations render the stability of the C-terminus similar to that of the rest of the protein. In contrast, deletion of the N-cap led to strong deviation from two-state unfolding. In both urea- and pressure-induced unfolding, residues in repeats 1-3 of pp32-ΔN-cap lost their native structure first, while the C-terminal half was more stable. The residue-specific free energy changes in all regions of pp32-ΔN-cap were larger in urea compared to high pressure, indicating a less cooperative destabilization by pressure. Moreover, in contrast to complete structural disruption of pp32-ΔN-cap at high urea concentration, its pressure unfolded state remained compact. The contrasting effects of the capping motifs on folding cooperativity arise from the differential local stabilities of pp32, whereas the contrasting effects of pressure and urea on the pp32-ΔN-cap variant arise from their distinct mechanisms of action. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of repeated burning on woody vegetation structure and composition in a semi-arid southern African savanna

NARCIS (Netherlands)

Gandiwa, E.

2011-01-01

The objective of this study was to investigate the effects of repeated dry season annual hot fires on woody plants in a semiarid southern African savanna in Zimbabwe. Parts of the National University of Science and Technology (NUST) research fields in Bulawayo, Zimbabwe have been burnt annually in

Variable presence of the inverted repeat and plastome stability in Erodium

OpenAIRE

Blazier, John C.; Jansen, Robert K.; Mower, Jeffrey P.; Govindu, Madhu; Zhang, Jin; Weng, Mao-Lun; Ruhlman, Tracey A.

2016-01-01

Background and Aims Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stabili...

Firefighting and mental health: Experiences of repeated exposure to trauma.

Science.gov (United States)

Jahnke, Sara A; Poston, Walker S Carlos; Haddock, Christopher K; Murphy, Beth

2016-02-15

Firefighters must be ready to respond to a broad range of emergencies every duty day. In the course of many of these emergencies, firefighters witness events which have the potential to induce emotional trauma, such as badly injured people, deceased children, and individuals who are highly distraught. Previous research suggests that repeated exposure to these traumas (RET) may have negative impacts on the emotional and mental health of fire service personnel. Research on the mental health of firefighters has been limited to small surveys reporting the prevalence of specific mental health problems such as depression and post-traumatic stress disorder among firefighters. Despite the likelihood that RET leads to negative outcomes in firefighters, data is lacking on how exposure impacts fire service personnel. The current study examines the experiences of firefighters related to RET. Using formative research methods, we examined the beliefs and experiences of firefighters and administrators from across the United States regarding the impact of RET on firefighter health. Study findings highlight the cumulative psychological toll of repeated exposure to traumatic events including desensitization, flashbacks, and irritability. Results of the current study suggest that RET is a significant concern for emergency responders that warrants additional research and attention. It is likely that the long term consequences of RET are closely intertwined with other mental health outcomes and general well-being of this important occupational group.

A description of the ABCD organizational structure and communication framework.

Science.gov (United States)

Auchter, Allison M; Hernandez Mejia, Margie; Heyser, Charles J; Shilling, Paul D; Jernigan, Terry L; Brown, Sandra A; Tapert, Susan F; Dowling, Gayathri J

2018-04-16

The Adolescent Brain Cognitive Development (ABCD) study is designed to be the largest study of brain development and child health in the United States, performing comprehensive assessments of 11,500 children repeatedly for 10 years. An endeavor of this magnitude requires an organized framework of governance and communication that promotes collaborative decision-making and dissemination of information. The ABCD consortium structure, built upon the Matrix Management approach of organizational theory, facilitates the integration of input from all institutions, numerous internal workgroups and committees, federal partners, and external advisory groups to make use of a broad range of expertise to ensure the study's success. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fine-resolution repeat topographic surveying of dryland landscapes using UAS-based structure-from-motion photogrammetry: Assessing accuracy and precision against traditional ground-based erosion measurements

Science.gov (United States)

Gillian, Jeffrey K.; Karl, Jason W.; Elaksher, Ahmed; Duniway, Michael C.

2017-01-01

Structure-from-motion (SfM) photogrammetry from unmanned aerial system (UAS) imagery is an emerging tool for repeat topographic surveying of dryland erosion. These methods are particularly appealing due to the ability to cover large landscapes compared to field methods and at reduced costs and finer spatial resolution compared to airborne laser scanning. Accuracy and precision of high-resolution digital terrain models (DTMs) derived from UAS imagery have been explored in many studies, typically by comparing image coordinates to surveyed check points or LiDAR datasets. In addition to traditional check points, this study compared 5 cm resolution DTMs derived from fixed-wing UAS imagery with a traditional ground-based method of measuring soil surface change called erosion bridges. We assessed accuracy by comparing the elevation values between DTMs and erosion bridges along thirty topographic transects each 6.1 m long. Comparisons occurred at two points in time (June 2014, February 2015) which enabled us to assess vertical accuracy with 3314 data points and vertical precision (i.e., repeatability) with 1657 data points. We found strong vertical agreement (accuracy) between the methods (RMSE 2.9 and 3.2 cm in June 2014 and February 2015, respectively) and high vertical precision for the DTMs (RMSE 2.8 cm). Our results from comparing SfM-generated DTMs to check points, and strong agreement with erosion bridge measurements suggests repeat UAS imagery and SfM processing could replace erosion bridges for a more synoptic landscape assessment of shifting soil surfaces for some studies. However, while collecting the UAS imagery and generating the SfM DTMs for this study was faster than collecting erosion bridge measurements, technical challenges related to the need for ground control networks and image processing requirements must be addressed before this technique could be applied effectively to large landscapes.

The influence of sampling unit size and spatial arrangement patterns on neighborhood-based spatial structure analyses of forest stands

Energy Technology Data Exchange (ETDEWEB)

Wang, H.; Zhang, G.; Hui, G.; Li, Y.; Hu, Y.; Zhao, Z.

2016-07-01

Aim of study: Neighborhood-based stand spatial structure parameters can quantify and characterize forest spatial structure effectively. How these neighborhood-based structure parameters are influenced by the selection of different numbers of nearest-neighbor trees is unclear, and there is some disagreement in the literature regarding the appropriate number of nearest-neighbor trees to sample around reference trees. Understanding how to efficiently characterize forest structure is critical for forest management. Area of study: Multi-species uneven-aged forests of Northern China. Material and methods: We simulated stands with different spatial structural characteristics and systematically compared their structure parameters when two to eight neighboring trees were selected. Main results: Results showed that values of uniform angle index calculated in the same stand were different with different sizes of structure unit. When tree species and sizes were completely randomly interspersed, different numbers of neighbors had little influence on mingling and dominance indices. Changes of mingling or dominance indices caused by different numbers of neighbors occurred when the tree species or size classes were not randomly interspersed and their changing characteristics can be detected according to the spatial arrangement patterns of tree species and sizes. Research highlights: The number of neighboring trees selected for analyzing stand spatial structure parameters should be fixed. We proposed that the four-tree structure unit is the best compromise between sampling accuracy and costs for practical forest management. (Author)

Recursion Of Binary Space As A Foundation Of Repeatable Programs

Directory of Open Access Journals (Sweden)

Jeremy Horne

2006-10-01

Full Text Available Every computation, including recursion, is based on natural philosophy. Our world may be expressed in terms of a binary logical space that contains functions that act simultaneously as objects and processes (operands and operators. This paper presents an outline of the results of research about that space and suggests routes for further inquiry. Binary logical space is generated sequentially from an origin in a standard coordinate system. At least one method exists to show that each of the resulting 16 functions repeats itself by repeatedly forward-feeding outputs of a function operating over two others as new operands of the original function until the original function appears as an output, thus behaving as an apparent homeostatic automaton. As any space of any dimension is composed of one or more of these functions, so the space is recursive, as well. Semantics gives meaning to recursive structures, computer programs and fundamental constituents of our universe being two examples. Such thoughts open inquiry into larger philosophical issues as free will and determinism.

Accelerating VASP electronic structure calculations using graphic processing units

KAUST Repository

Hacene, Mohamed

2012-08-20

We present a way to improve the performance of the electronic structure Vienna Ab initio Simulation Package (VASP) program. We show that high-performance computers equipped with graphics processing units (GPUs) as accelerators may reduce drastically the computation time when offloading these sections to the graphic chips. The procedure consists of (i) profiling the performance of the code to isolate the time-consuming parts, (ii) rewriting these so that the algorithms become better-suited for the chosen graphic accelerator, and (iii) optimizing memory traffic between the host computer and the GPU accelerator. We chose to accelerate VASP with NVIDIA GPU using CUDA. We compare the GPU and original versions of VASP by evaluating the Davidson and RMM-DIIS algorithms on chemical systems of up to 1100 atoms. In these tests, the total time is reduced by a factor between 3 and 8 when running on n (CPU core + GPU) compared to n CPU cores only, without any accuracy loss. © 2012 Wiley Periodicals, Inc.

Accelerating VASP electronic structure calculations using graphic processing units

KAUST Repository

Hacene, Mohamed; Anciaux-Sedrakian, Ani; Rozanska, Xavier; Klahr, Diego; Guignon, Thomas; Fleurat-Lessard, Paul

2012-01-01

We present a way to improve the performance of the electronic structure Vienna Ab initio Simulation Package (VASP) program. We show that high-performance computers equipped with graphics processing units (GPUs) as accelerators may reduce drastically the computation time when offloading these sections to the graphic chips. The procedure consists of (i) profiling the performance of the code to isolate the time-consuming parts, (ii) rewriting these so that the algorithms become better-suited for the chosen graphic accelerator, and (iii) optimizing memory traffic between the host computer and the GPU accelerator. We chose to accelerate VASP with NVIDIA GPU using CUDA. We compare the GPU and original versions of VASP by evaluating the Davidson and RMM-DIIS algorithms on chemical systems of up to 1100 atoms. In these tests, the total time is reduced by a factor between 3 and 8 when running on n (CPU core + GPU) compared to n CPU cores only, without any accuracy loss. © 2012 Wiley Periodicals, Inc.

Analyzing Repeated Measures Marginal Models on Sample Surveys with Resampling Methods

Directory of Open Access Journals (Sweden)

James D. Knoke

2005-12-01

Full Text Available Packaged statistical software for analyzing categorical, repeated measures marginal models on sample survey data with binary covariates does not appear to be available. Consequently, this report describes a customized SAS program which accomplishes such an analysis on survey data with jackknifed replicate weights for which the primary sampling unit information has been suppressed for respondent confidentiality. First, the program employs the Macro Language and the Output Delivery System (ODS to estimate the means and covariances of indicator variables for the response variables, taking the design into account. Then, it uses PROC CATMOD and ODS, ignoring the survey design, to obtain the design matrix and hypothesis test specifications. Finally, it enters these results into another run of CATMOD, which performs automated direct input of the survey design specifications and accomplishes the appropriate analysis. This customized SAS program can be employed, with minor editing, to analyze general categorical, repeated measures marginal models on sample surveys with replicate weights. Finally, the results of our analysis accounting for the survey design are compared to the results of two alternate analyses of the same data. This comparison confirms that such alternate analyses, which do not properly account for the design, do not produce useful results.

Pentapeptide-repeat proteins that act as topoisomerase poison resistance factors have a common dimer interface

International Nuclear Information System (INIS)

Vetting, Matthew W.; Hegde, Subray S.; Zhang, Yong; Blanchard, John S.

2011-01-01

The pentapeptide repeat protein AlbG, provides self-resistance to the nonribosomally encoded hybrid polyketide-peptide termed albicidin. Analysis of the AlbG three-dimensional structure and the sequences of other pentapeptide repeat proteins that confer resistance to topiosomerase poisons suggests they have a similar dimer interface which may be critical to their interaction with topoisomerases. The protein AlbG is a self-resistance factor against albicidin, a nonribosomally encoded hybrid polyketide-peptide with antibiotic and phytotoxic properties produced by Xanthomonas albilineans. Primary-sequence analysis indicates that AlbG is a member of the pentapeptide-repeat family of proteins (PRP). The structure of AlbG from X. albilineans was determined at 2.0 Å resolution by SAD phasing using data collected from a single trimethyllead acetate derivative on a home source. AlbG folds into a right-handed quadrilateral β-helix composed of approximately eight semi-regular coils. The regularity of the β-helix is blemished by a large loop/deviation in the β-helix between coils 4 and 5. The C-terminus of the β-helix is capped by a dimerization module, yielding a dimer with a 110 Å semi-collinear β-helical axis. This method of dimer formation appears to be common to all PRP proteins that confer resistance to topoisomerase poisons and contrasts with most PRP proteins, which are typically monomeric

Development of analog watch with minute repeater

Science.gov (United States)

Okigami, Tomio; Aoyama, Shigeru; Osa, Takashi; Igarashi, Kiyotaka; Ikegami, Tomomi

A complementary metal oxide semiconductor with large scale integration was developed for an electronic minute repeater. It is equipped with the synthetic struck sound circuit to generate natural struck sound necessary for the minute repeater. This circuit consists of an envelope curve drawing circuit, frequency mixer, polyphonic mixer, and booster circuit made by using analog circuit technology. This large scale integration is a single chip microcomputer with motor drivers and input ports in addition to the synthetic struck sound circuit, and it is possible to make an electronic system of minute repeater at a very low cost in comparison with the conventional type.

Geodynamic movements and deformations of the Sudetic structural unit of the Bohemian Massif

Science.gov (United States)

Schenk, V.; Jechumtálová, Z.; Schenková, Z.; Kottnauer, P.

2003-04-01

The African plate pushes to European orogenic Alpine structures that transfer the compression further to Variscan structural units, including the Bohemian Massif. Central parts of the Bohemian Massif are relatively deep-seated and, therefore, some of marginal parts of the Massif and its border geological structures should be affected intensively and moved distinctly with respect to the central parts. The geodynamical GPS network EAST SUDETEN is located just over the area mentioned above, i.e. it covers both kinetically quasi-effected and quasi-non-effected structural blocks. GPS data observed already for six annual campaigns (1997-2002) were processed and movement vectors of individual network sites were assessed. Applied data processing did not allow errors in the horizontal direction 2 mm and in the vertical direction 5-6 mm to be exceeded. Since time series of coordinate changes for several network sites gave rather pronounce movement trends, preliminary deformations among individual structural blocks were evaluated and compared to other geological, geophysical and geodetic materials. The investigation has been supported by the Grant Agency of the Czech Republic, projects 205/97/0679 and 205/01/0480, and by the research programme of the Ministry of Education, Youth and Sport of the Czech Republic, project LN00A005 "Dynamics of the Earth".

RTEL1 Inhibits Trinucleotide Repeat Expansions and Fragility

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Aisling Frizzell

2014-03-01

Full Text Available Human RTEL1 is an essential, multifunctional helicase that maintains telomeres, regulates homologous recombination, and helps prevent bone marrow failure. Here, we show that RTEL1 also blocks trinucleotide repeat expansions, the causal mutation for 17 neurological diseases. Increased expansion frequencies of (CTG⋅CAG repeats occurred in human cells following knockdown of RTEL1, but not the alternative helicase Fbh1, and purified RTEL1 efficiently unwound triplet repeat hairpins in vitro. The expansion-blocking activity of RTEL1 also required Rad18 and HLTF, homologs of yeast Rad18 and Rad5. These findings are reminiscent of budding yeast Srs2, which inhibits expansions, unwinds hairpins, and prevents triplet-repeat-induced chromosome fragility. Accordingly, we found expansions and fragility were suppressed in yeast srs2 mutants expressing RTEL1, but not Fbh1. We propose that RTEL1 serves as a human analog of Srs2 to inhibit (CTG⋅CAG repeat expansions and fragility, likely by unwinding problematic hairpins.