Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

PubMed

Beauparlant, Marc A; Drouin, Guy

2014-02-01

Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liao, D.; Weiner, A.M.

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 studymore » 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.« less

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.

PubMed

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.

Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

PubMed Central

Lee, Tong Geon; Kumar, Indrajit; Diers, Brian W; Hudson, Matthew E

2015-01-01

The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess Rhg1 alleles. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at Rhg1. PMID:25735447

Length and sequence heterogeneity in 5S rDNA of Populus deltoides.

PubMed

Negi, Madan S; Rajagopal, Jyothi; Chauhan, Neeti; Cronn, Richard; Lakshmikumaran, Malathi

2002-12-01

The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (pi) estimates that are less than 0.15% of those obtained for class 2 spacers (pi = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.

An exploration of risk for recurrent falls in two geriatric care settings

PubMed Central

2013-01-01

Background Fall events were examined in two distinct geriatric populations to identify factors associated with repeat fallers, and to examine whether patients who use gait aids, specifically a walker, were more likely to experience repeat falls. Each unit already had a generic program for falls prevention in place. Methods Secondary data analysis was conducted on information collected during the pilot testing of a new quality assurance Incident Reporting Tool between October 2006 and September 2008. The study settings included an in-patient geriatric rehabilitation unit (GRU) and a long stay veterans’ unit (LSVU) in a rehabilitation and long-stay hospital in Ontario. Participants were two hundred and twenty three individuals, aged 65 years or older on these two units, who experienced one or more fall incidents during the study period. Results Logistic regression analyses showed that on the GRU age was significantly associated with repeat falls. On the LSVU first falls in the morning or late evening were associated with repeat falling. Walker as a gait aid listed at time of first fall was not associated with repeat falls. Conclusions This study suggests that different intervention may be necessary in different geriatric settings to identify, for secondary prevention, certain individuals for which the generic programs prove inadequate. Information collection with a specific focus on the issue of repeat falls may be necessary for greater insight. PMID:24106879

High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation

NASA Astrophysics Data System (ADS)

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.

High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation.

PubMed

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. Graphical Abstract ᅟ.

Itaca2 - Twin 76-ilat auroral monitors.

NASA Astrophysics Data System (ADS)

Massetti, S.; Candidi, M.; Cerulli-Irelli, P.; Sparapani, R.; Maggiore, M.; Philipsen, H.; Baldetti, P.; Morbidini, A.

2003-04-01

In August 2002, the Italian Research Council (CNR) set up a new automatic auroral monitor in Daneborg, on the North-East coast of Greenland, thanks to the support of the Progetto Nazionale Ricerche in Antartide (PNRA), and to the logistical support of the Danish Polar Center (DPC) and the Sirus-patrol (PNG). The new station is equipped with a digital all-sky camera, and it is intended to operate in conjunction with the other Italian station located in Ny-Ålesund, Svalbard: the two observatories constitute a system of twin auroral monitors, owing almost the same invariant latitude of 76°, which is mainly devoted to the observation of the dayside red aurora connected to the cusp/LLBL magnetospheric region. When observing the high altitude dayside auroras, the field-of-views of the two stations are contiguous and allow the monitoring of the dayside auroral activity over about 80° of magnetic longitude (about 5/6 hours MLT). Since many years ago, Svalbard Islands have been an ideal place for polar researches due to its scientific facilities, the easy access during all the year and the frequent flight connections. In Greenland, on the contrary, the set up and maintenance of a high-latitude station that has to operate during the winter season, needs more logistical efforts, and it would be impossible without the precious support of people residing in-situ.

Organometallic macromolecules with piano stool coordination repeating units: chain configuration and stimulated solution behaviour.

PubMed

Cao, Kai; Ward, Jonathan; Amos, Ryan C; Jeong, Moon Gon; Kim, Kyoung Taek; Gauthier, Mario; Foucher, Daniel; Wang, Xiaosong

2014-09-11

Theoretical calculations illustrate that organometallic macromolecules with piano stool coordination repeating units (Fe-acyl complex) adopt linear chain configuration with a P-Fe-C backbone surrounded by aromatic groups. The macromolecules show molecular weight-dependent and temperature stimulated solution behaviour in DMSO.

Designing occupancy studies: general advice and allocating survey effort

USGS Publications Warehouse

MacKenzie, D.I.; Royle, J. Andrew

2005-01-01

1. The fraction of sampling units in a landscape where a target species is present (occupancy) is an extensively used concept in ecology. Yet in many applications the species will not always be detected in a sampling unit even when present, resulting in biased estimates of occupancy. Given that sampling units are surveyed repeatedly within a relatively short timeframe, a number of similar methods have now been developed to provide unbiased occupancy estimates. However, practical guidance on the efficient design of occupancy studies has been lacking. 2. In this paper we comment on a number of general issues related to designing occupancy studies, including the need for clear objectives that are explicitly linked to science or management, selection of sampling units, timing of repeat surveys and allocation of survey effort. Advice on the number of repeat surveys per sampling unit is considered in terms of the variance of the occupancy estimator, for three possible study designs. 3. We recommend that sampling units should be surveyed a minimum of three times when detection probability is high (> 0.5 survey-1), unless a removal design is used. 4. We found that an optimal removal design will generally be the most efficient, but we suggest it may be less robust to assumption violations than a standard design. 5. Our results suggest that for a rare species it is more efficient to survey more sampling units less intensively, while for a common species fewer sampling units should be surveyed more intensively. 6. Synthesis and applications. Reliable inferences can only result from quality data. To make the best use of logistical resources, study objectives must be clearly defined; sampling units must be selected, and repeated surveys timed appropriately; and a sufficient number of repeated surveys must be conducted. Failure to do so may compromise the integrity of the study. The guidance given here on study design issues is particularly applicable to studies of species occurrence and distribution, habitat selection and modelling, metapopulation studies and monitoring programmes.

Topological characteristics of helical repeat proteins.

PubMed

Groves, M R; Barford, D

1999-06-01

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 repeats of an alpha-helical structural unit, creating extended superhelical structures that are ideally suited to create a protein recognition interface.

Effects of electronics, aromaticity, and solvent polarity on the rate of azaquinone-methide-mediated depolymerization of aromatic carbamate oligomers.

PubMed

Robbins, Jessica S; Schmid, Kyle M; Phillips, Scott T

2013-04-05

This paper uses physical-organic studies on well-defined oligomers to establish design principles for creating aromatic poly(carbamates) that depolymerize from head-to-tail in low dielectric constant environments when exposed to specific applied signals. We show that either increasing electron density or decreasing the aromaticity of aromatic repeating units in poly(carbamates) increase the overall depolymerization rate. For example, a methoxybenzene-based repeating unit provides depolymerization rates that are 143× faster than oligomers that contain a benzene-based repeating unit. Furthermore, the rate of depolymerization in the methoxybenzene-based system is tolerant to low dielectric environments, whereas the benzene-based oligomers are not.

Structural investigation of the exopolysaccharide produced by Pseudomonas flavescens strain B62--degradation by a fungal cellulase and isolation of the oligosaccharide repeating unit.

PubMed

Cescutti, P; Toffanin, R; Fett, W F; Osman, S F; Pollesello, P; Paoletti, S

1998-02-01

Pseudomonas flavescens strain B62 (NCPPB 3063) is a recently described bacterium isolated from walnut blight cankers. This strain has been designated as the type strain of a Pseudomonas rRNA group-I species. Strain B62 produced a mixture of two exopolysaccharides, differing in weight average relative molecular mass and composition. Only the most abundant exopolysaccharide (90% by mass), corresponding to the one with the lower molecular mass, was investigated by use of methylation analysis, partial acid hydrolysis, and NMR spectroscopy. The polysaccharide was depolymerised by the action of the cellulase produced by Penicillum funiculosum and the oligosaccharide obtained, corresponding to the repeating unit, was characterised by NMR spectroscopy and ion-spray mass spectrometry. The repeating unit of the B62 exopolysaccharide is [structure in text] where X is glucose (75%) or mannose (25%), and Lac is lactate. The O-acetyl groups are present only on 75% of the repeating units, and they are linked to the C6 of the hexose residues in non-stoichiometric amounts.

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

PubMed

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 predictions and shows the power of techniques for the determination of tertiary structural information from the amino acid sequences of an aligned protein family.

Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population.

PubMed

Hirata, Satoshi; Kojima, Kaname; Misawa, Kazuharu; Gervais, Olivier; Kawai, Yosuke; Nagasaki, Masao

2018-05-01

Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

Concise chemical synthesis of a tetrasaccharide repeating unit of the O-antigen of Hafnia alvei 10457.

PubMed

Kumar, Rishi; Maulik, Prakas R; Misra, Anup Kumar

2008-08-01

Concise chemical synthesis of a tetrasaccharide repeating unit of the O-antigen of Hafnia alvei 10457 is reported. Construction of the tetrasaccharide as its 4-methoxyphenyl glycoside was achieved by condensation of less abundant monosaccharide units such as, D-galactofuranose, N-acetyl-D-galactosamine and N-acetylneuraminic acid. The synthetic strategy consists of the preparation of suitably protected required monosaccharide intermediates from the commercially available reducing sugars and high yielding glycosylation reactions.

Genetic Studies of the Prp17 Gene of Saccharomyces Cerevisiae: A Domain Essential for Function Maps to a Nonconserved Region of the Protein

PubMed Central

Seshadri, V.; Vaidya, V. C.; Vijayraghavan, U.

1996-01-01

The PRP17 gene product is required for the second step of pre-mRNA splicing reactions. The C-terminal half of this protein bears four repeat units with homology to the β transducin repeat. Missense mutations in three temperature-sensitive prp17 mutants map to a region in the N-terminal half of the protein. We have generated, in vitro, 11 missense alleles at the β transducin repeat units and find that only one affects function in vivo. A phenotypically silent missense allele at the fourth repeat unit enhances the slow-growing phenotype conferred by an allele at the third repeat, suggesting an interaction between these domains. Although many missense mutations in highly conserved amino acids lack phenotypic effects, deletion analysis suggests an essential role for these units. Only mutations in the N-terminal nonconserved domain of PRP17 are synthetically lethal in combination with mutations in PRP16 and PRP18, two other gene products required for the second splicing reaction. A mutually allele-specific interaction between prp17 and snr7, with mutations in U5 snRNA, was observed. We therefore suggest that the functional region of Prp17p that interacts with Prp18p, Prp16p, and U5 snRNA is in the N terminal region of the protein. PMID:8722761

Plant chromosomes from end to end: telomeres, heterochromatin and centromeres.

PubMed

Lamb, Jonathan C; Yu, Weichang; Han, Fangpu; Birchler, James A

2007-04-01

Recent evidence indicates that heterochromatin in plants is composed of heterogeneous sequences, which are usually composed of transposable elements or tandem repeat arrays. These arrays are associated with chromatin modifications that produce a closed configuration that limits transcription. Centromere sequences in plants are usually composed of tandem repeat arrays that are homogenized across the genome. Analysis of such arrays in closely related taxa suggests a rapid turnover of the repeat unit that is typical of a particular species. In addition, two lines of evidence for an epigenetic component of centromere specification have been reported, namely an example of a neocentromere formed over sequences without the typical repeat array and examples of centromere inactivation. Although the telomere repeat unit is quite prevalent in the plant kingdom, unusual repeats have been found in some families. Recently, it was demonstrated that the introduction of telomere sequences into plants cells causes truncation of the chromosomes, and that this technique can be used to produce artificial chromosome platforms.

The structure of the exopolysaccharide of Pseudomonas fluorescens strain H13.

PubMed

Osman, S F; Fett, W F; Irwin, P; Cescutti, P; Brouillette, J N; O'Connor, J V

1997-05-19

An acidic exopolysaccharide was isolated from P. fluorescens strain H13. The structure of the polysaccharide repeating unit was determined using chemical methods and 1D and 2D NMR techniques. The repeating unit was characterized as a trisaccharide composed of D-glucose, 2-acetamido-2-deoxy-D-glucose and 4-O-acetyl-2-acetamido-2-deoxy-D-mannuronic acid.

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

PubMed

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.

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

PubMed

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.

47 CFR 90.247 - Mobile repeater stations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... of the mobile unit and an automatic time-delay device that de-activates the transmitter after any... 47 Telecommunication 5 2010-10-01 2010-10-01 false Mobile repeater stations. 90.247 Section 90.247... MOBILE RADIO SERVICES Non-Voice and Other Specialized Operations § 90.247 Mobile repeater stations. A...

Effects of electrical stimulation on the histological properties of wounds in diabetic mice.

PubMed

Thawer, H A; Houghton, P E

2001-01-01

The purpose of this study was to identify mechanisms underlying electrically stimulated wound closure in diabetic mice. Adult male mice (n = 58) with full-thickness excisional wounds were treated five times using negative polarity over the wound site for 15 minutes each over a 16-day period with sham (0 Volts) or 5.0, 10.0, 12.5 Volts. In addition, animals (diabetic (n = 33) and nondiabetic (n = 22)) received treatments of electrical stimulation (12.5 V), or sham treatment (0 V) at wound sites which were then harvested and prepared for histological analysis at 2, 8, and 16 days postwounding. Using computerized image analysis of sections stained with a picro sirus red-fast green staining technique, we found that increasing doses of electrical stimulation reduced collagen/noncollagenous protein ratios measured in the superficial scar of nondiabetic animals, with no effect in diabetic animals. In the deep scar, lower doses of electrical stimulation (5.0 V) produced significantly (p < 0.01) increased collagen deposition in wounds of nondiabetic animals compared with sham controls. Higher doses of electrical stimulation (12.5 V) were required to produce changes in diabetic animals than were observed in nondiabetic animals. These results suggest that electrical stimulation altered collagen deposition in excisional wounds of diabetic and nondiabetic animals. Electrical stimulation had a differential effect on wound healing in diabetic compared with nondiabetic animals. These data speak to the need to study the effects of electrical stimulation on healing in disease-specific models.

Discordant expression and variable numbers of neighboring GGA- and GAA-rich triplet repeats in the 3' untranslated regions of two groups of messenger RNAs encoded by the rat polymeric immunoglobulin receptor gene.

PubMed Central

Koch, K S; Gleiberman, A S; Aoki, T; Leffert, H L; Feren, A; Jones, A L; Fodor, E J

1995-01-01

An unusual S1-nuclease sensitive microsatellite (STMS) has been found in the single copy, rat polymeric immunoglobulin receptor gene (PIGR) terminal exon. In Fisher rats, elements within or beyond the STMS are expressed variably in the 3' untranslated regions (3'UTRs) of two 'Groups' of PIGR-encoded hepatic mRNAs (pIg-R) during liver regeneration. STMS elements include neighboring constant regions (a 60-bp d[GA]-rich tract with a chi-like octamer, followed by 15 tandem d[GGA] repeats) that merge directly with 36 or 39 tandem d[GAA] repeats (Fisher or Wistar strains, respectively) interrupted by d[AA] between their 5th-6th repeat units. The Wistar STMS is flanked upstream by two regions of nearly contiguous d[CA] or d[CT] repeats in the 3' end of intron 8; and downstream, by a 283 bp 'unit' containing several inversions at its 5' end, and two polyadenylation signals at its 3' end. The 283 nt unit is expressed in Group 1 pIg-R mRNAs; but it is absent in the Group 2 family so that their GAA repeats merge with their poly A tails. In contrast to genomic sequence, GGA triplet repeats are amplified (n > or = 24-26), whereas GAA triplet repeats are truncated variably (n < or = 9-37) and expressed uninterruptedly in both mRNA Groups. These results suggest that 3' end processing of the rat PIGR gene may involve misalignment, slippage and premature termination of RNA polymerase II. The function of this unusual processing and possible roles of chi-like octamers in quiescent or extrahepatic tissues are discussed. Images PMID:7739889

High Regional Variation in Urethroplasty in the United States

PubMed Central

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 < 0.001). When controlling for age and Charlson comorbidity score, travel out of a metropolitan area (OR 2.7, 95% CI 2.2–3.3) and a reconstructive urologist in the treatment metropolitan area (OR 2.0, 95% CI 1.7–2.5) were associated with a greater likelihood of 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

Solid polymeric electrolytes for lithium batteries

DOEpatents

Angell, Charles A.; Xu, Wu; Sun, Xiaoguang

2006-03-14

Novel conductive polyanionic polymers and methods for their preparion are provided. The polyanionic polymers comprise repeating units of weakly-coordinating anionic groups chemically linked to polymer chains. The polymer chains in turn comprise repeating spacer groups. Spacer groups can be chosen to be of length and structure to impart desired electrochemical and physical properties to the polymers. Preferred embodiments are prepared from precursor polymers comprising the Lewis acid borate tri-coordinated to a selected ligand and repeating spacer groups to form repeating polymer chain units. These precursor polymers are reacted with a chosen Lewis base to form a polyanionic polymer comprising weakly coordinating anionic groups spaced at chosen intervals along the polymer chain. The polyanionic polymers exhibit high conductivity and physical properties which make them suitable as solid polymeric electrolytes in lithium batteries, especially secondary lithium batteries.

Novel variants of the 5S rRNA genes in Eruca sativa.

PubMed

Singh, K; Bhatia, S; Lakshmikumaran, M

1994-02-01

The 5S ribosomal RNA (rRNA) genes of Eruca sativa were cloned and characterized. They are organized into clusters of tandemly repeated units. Each repeat unit consists of a 119-bp coding region followed by a noncoding spacer region that separates it from the coding region of the next repeat unit. Our study reports novel gene variants of the 5S rRNA genes in plants. Two families of the 5S rDNA, the 0.5-kb size family and the 1-kb size family, coexist in the E. sativa genome. The 0.5-kb size family consists of the 5S rRNA genes (S4) that have coding regions similar to those of other reported plant 5S rDNA sequences, whereas the 1-kb size family consists of the 5S rRNA gene variants (S1) that exist as 1-kb BamHI tandem repeats. S1 is made up of two variant units (V1 and V2) of 5S rDNA where the BamHI site between the two units is mutated. Sequence heterogeneity among S4, V1, and V2 units exists throughout the sequence and is not limited to the noncoding spacer region only. The coding regions of V1 and V2 show approximately 20% dissimilarity to the coding regions of S4 and other reported plant 5S rDNA sequences. Such a large variation in the coding regions of the 5S rDNA units within the same plant species has been observed for the first time. Restriction site variation is observed between the two size classes of 5S rDNA in E. sativa.(ABSTRACT TRUNCATED AT 250 WORDS)

Repeating Patterns in Kindergarten: Findings from Children's Enactments of Two Activities

ERIC Educational Resources Information Center

Tsamir, Pessia; Tirosh, Dina; Levenson, Esther S.; Barkai, Ruthi; Tabach, Michal

2017-01-01

This paper describes kindergarten children's engagement with two patterning activities. The first activity includes two tasks in which children are asked to choose possible ways for extending two different repeating patterns and the second activity calls for comparing different pairs of repeating patterns. Children's recognition of the unit of…

Lessons that Bear Repeating and Repeating that Bears Lessons: An Interdisciplinary Unit on Principles of Minimalism in Modern Music, Art, and Poetry (Grades 4-8)

ERIC Educational Resources Information Center

Smigel, Eric; McDonald, Nan L.

2012-01-01

This theory-to-practice article focuses on interdisciplinary classroom activities based on principles of minimalism in modern music, art, and poetry. A lesson sequence was designed for an inner-city Grades 4 and 5 general classroom of English language learners, where the unit was taught, assessed, and documented by the authors. Included in the…

Tempered mlo broad-spectrum resistance to barley powdery mildew in an Ethiopian landrace

PubMed Central

Ge, Xintian; Deng, Weiwei; Lee, Zheng Zhou; Lopez-Ruiz, Francisco J.; Schweizer, Patrick; Ellwood, Simon R.

2016-01-01

Recessive mutations in the Mlo gene confer broad spectrum resistance in barley (Hordeum vulgare) to powdery mildew (Blumeria graminis f. sp. hordei), a widespread and damaging disease. However, all alleles discovered to date also display deleterious pleiotropic effects, including the naturally occurring mlo-11 mutant which is widely deployed in Europe. Recessive resistance was discovered in Eth295, an Ethiopian landrace, which was developmentally controlled and quantitative without spontaneous cell wall appositions or extensive necrosis and loss of photosynthetic tissue. This resistance is determined by two copies of the mlo-11 repeat units, that occur upstream to the wild-type Mlo gene, compared to 11–12 in commonly grown cultivars and was designated mlo-11 (cnv2). mlo-11 repeat unit copy number-dependent DNA methylation corresponded with cytological and macroscopic phenotypic differences between copy number variants. Sequence data indicated mlo-11 (cnv2) formed via recombination between progenitor mlo-11 repeat units and the 3′ end of an adjacent stowaway MITE containing region. mlo-11 (cnv2) is the only example of a moderated mlo variant discovered to date and may have arisen by natural selection against the deleterious effects of the progenitor mlo-11 repeat unit configuration. PMID:27404990

Testing the Predictive Capability of the High-Fidelity Generalized Method of Cells Using an Efficient Reformulation

NASA Technical Reports Server (NTRS)

Arnold, Steven M. (Technical Monitor); Bansal, Yogesh; Pindera, Marek-Jerzy

2004-01-01

The High-Fidelity Generalized Method of Cells is a new micromechanics model for unidirectionally reinforced periodic multiphase materials that was developed to overcome the original model's shortcomings. The high-fidelity version predicts the local stress and strain fields with dramatically greater accuracy relative to the original model through the use of a better displacement field representation. Herein, we test the high-fidelity model's predictive capability in estimating the elastic moduli of periodic composites characterized by repeating unit cells obtained by rotation of an infinite square fiber array through an angle about the fiber axis. Such repeating unit cells may contain a few or many fibers, depending on the rotation angle. In order to analyze such multi-inclusion repeating unit cells efficiently, the high-fidelity micromechanics model's framework is reformulated using the local/global stiffness matrix approach. The excellent agreement with the corresponding results obtained from the standard transformation equations confirms the new model's predictive capability for periodic composites characterized by multi-inclusion repeating unit cells lacking planes of material symmetry. Comparison of the effective moduli and local stress fields with the corresponding results obtained from the original Generalized Method of Cells dramatically highlights the original model's shortcomings for certain classes of unidirectional composites.

Mechanical properties of regular porous biomaterials made from truncated cube repeating unit cells: Analytical solutions and computational models.

PubMed

Hedayati, R; Sadighi, M; Mohammadi-Aghdam, M; Zadpoor, A A

2016-03-01

Additive manufacturing (AM) has enabled fabrication of open-cell porous biomaterials based on repeating unit cells. The micro-architecture of the porous biomaterials and, thus, their physical properties could then be precisely controlled. Due to their many favorable properties, porous biomaterials manufactured using AM are considered as promising candidates for bone substitution as well as for several other applications in orthopedic surgery. The mechanical properties of such porous structures including static and fatigue properties are shown to be strongly dependent on the type of the repeating unit cell based on which the porous biomaterial is built. In this paper, we study the mechanical properties of porous biomaterials made from a relatively new unit cell, namely truncated cube. We present analytical solutions that relate the dimensions of the repeating unit cell to the elastic modulus, Poisson's ratio, yield stress, and buckling load of those porous structures. We also performed finite element modeling to predict the mechanical properties of the porous structures. The analytical solution and computational results were found to be in agreement with each other. The mechanical properties estimated using both the analytical and computational techniques were somewhat higher than the experimental data reported in one of our recent studies on selective laser melted Ti-6Al-4V porous biomaterials. In addition to porosity, the elastic modulus and Poisson's ratio of the porous structures were found to be strongly dependent on the ratio of the length of the inclined struts to that of the uninclined (i.e. vertical or horizontal) struts, α, in the truncated cube unit cell. The geometry of the truncated cube unit cell approaches the octahedral and cube unit cells when α respectively approaches zero and infinity. Consistent with those geometrical observations, the analytical solutions presented in this study approached those of the octahedral and cube unit cells when α approached respectively 0 and infinity. Copyright © 2015 Elsevier B.V. All rights reserved.

A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences.

PubMed

Kapila, R; Das, S; Srivastava, P S; Lakshmikumaran, M

1996-08-01

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5'-TTTAGGG-3'. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31 digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature.

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

PubMed

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 organization of repeating units in mitochondrial DNA from yeast petite mutants.

PubMed

Bos, J L; Heyting, C; Van der Horst, G; Borst, P

1980-04-01

We have reinvestigated the linkage orientation of repeating units in mtDNAs of yeast ρ(-) petite mutants containing an inverted duplication. All five petite mtDNAs studied contain a continuous segment of wild-type mtDNA, part of which is duplicated and present in inverted form in the repeat. We show by restriction enzyme analysis that the non-duplicated segments between the inverted duplications are present in random orientation in all five petite mtDNAs. There is no segregation of sub-types with unique orientation. We attribute this to the high rate of intramolecular recombination between the inverted duplications. The results provide additional evidence for the high rate of recombination of yeast mtDNA even in haploid ρ(-) petite cells.We conclude that only two types of stable sequence organization exist in petite mtDNA: petites without an inverted duplication have repeats linked in straight head-to-tail arrangement (abcabc); petites with an inverted duplication have repeats in which the non-duplicated segments are present in random orientation.

Structural study of the exopolysaccharide produced by a clinical isolate of Burkholderia cepacia.

PubMed

Cescutti, P; Bosco, M; Picotti, F; Impallomeni, G; Leitão, J H; Richau, J A; Sá-Correia, I

2000-07-14

The primary structure of the exopolysaccharide produced by a clinical isolate of the bacterium Burkholderia cepacia was studied by means of methylation analysis, selective degradation, NMR spectroscopy, and electrospray mass spectrometry. The resulting data showed that the parent repeating unit of the exopolysaccharide is a highly branched heptasaccharide with the following structure: Two acetyl groups are present per repeating unit, as noncarbohydrate substituents. Copyright 2000 Academic Press.

Intratypic variability of a tandem repeat locus within the DNA polymerase gene of human herpes simplex virus type 2.

PubMed

Sun, Yongjiang; Chan, Roy Kum Wah; Tan, Suat Hoon

2004-01-01

In this study, the irntratypic variability of a tandem repeat locus within the DNA polymerase (pol) gene of human herpes simplex virus type 2 (HSV2) was uncovered. The locus contained variable numbers of tandem dodecanucleotide (5'-GAC GAG GAC GGG-3') repetitive units. Our result showed that approximately 95% of analyzed HSV2 clinical isolates and the current GenBank HSV2 strains contained two copies of the repetitive units. From genital herpes specimens, three new HSV2 strains, which respectively contained 1, 3, and 4 copies of the repetitive units, were identified. This variable number of tandem repeat (VNTR) locus is absent in HSV1, and thus it also contributes to the intertypic variability of HSV1 and HSV2. The intratypic variability of the locus may be useful for HSV2 strain genotyping and this application is discussed.

The evolution and function of protein tandem repeats in plants.

PubMed

Schaper, Elke; Anisimova, Maria

2015-04-01

Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

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.

PubMed

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.

Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.

PubMed

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.

Leishmania infantum: Lipophosphoglycan intraspecific variation and interaction with vertebrate and invertebrate hosts.

PubMed

Coelho-Finamore, J M; Freitas, V C; Assis, R R; Melo, M N; Novozhilova, N; Secundino, N F; Pimenta, P F; Turco, S J; Soares, R P

2011-03-01

Interspecies variations in lipophosphoglycan (LPG) have been the focus of intense study over the years due its role in specificity during sand fly-Leishmania interaction. This cell surface glycoconjugate is highly polymorphic among species with variations in sugars that branch off the conserved Gal(β1,4)Man(α1)-PO(4) backbone of repeat units. However, the degree of intraspecies polymorphism in LPG of Leishmania infantum (syn. Leishmania chagasi) is not known. In this study, intraspecific variation in the repeat units of LPG was evaluated in 16 strains of L. infantum from Brazil, France, Algeria and Tunisia. The structural polymorphism in the L. infantum LPG repeat units was relatively slight and consisted of three types: type I does not have side chains; type II has one β-glucose residue that branches off the disaccharide-phosphate repeat units and type III has up to three glucose residues (oligo-glucosylated). The significance of these modifications was investigated during in vivo interaction of L. infantum with Lutzomyia longipalpis, and in vitro interaction of the parasites and respective LPGs with murine macrophages. There were no consequential differences in the parasite densities in sand fly midguts infected with Leishmania strains exhibiting type I, II and III LPGs. However, higher nitric oxide production was observed in macrophages exposed to glucosylated type II LPG. Copyright © 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Synthesis and study of the vibrational spectra of a first generation phosphorus-containing dendrimer with pyridyl functional groups

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Tripathi, V.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2018-06-01

A new phosphorus-containing dendrimer of the first-generation with potential pharmacological activity was synthesized and studied by spectral methods. The FTIR, FT Raman, 1H and 31P NMR spectra of the first generation dendrimer G1 with a cyclotriphosphazene core, six branches sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd P(S) < and twelve 4-oxyphenethylamidopyridyl end groups sbnd Osbnd C6H4sbnd (CH2)2sbnd NHsbnd COsbnd C5NH4 were recorded. Amide groups of the dendrimer participate in the formation of an intermolecular hydrogen bond. Structure, geometric parameters, the frequency and intensity of the bands in the vibrational spectra were calculated using DFT with PBE functional and TZ2P basis set. Spectral characteristics, charge distribution and reactivity of the core, repeating units and terminal groups of the dendrimer were determined. The first-generation dendrimer molecule has the shape of a concave lens with a slightly non-planar cyclotriphosphazene core and flat repeating units. Repeating units are arranged symmetrically on three on each side of the core, there are no steric hindrances in it and the end groups are able to enter into subsequent reactions and dendrimer has a sufficiently large cavity for accommodating guest molecules. The HOMO covers the repeating units with a noticeable conjugation and the LUMO belongs to the terminal groups.

Ligand-Binding Properties and Conformational Dynamics of Autolysin Repeat Domains in Staphylococcal Cell Wall Recognition

PubMed Central

Zoll, Sebastian; Schlag, Martin; Shkumatov, Alexander V.; Rautenberg, Maren; Svergun, Dmitri I.; Götz, Friedrich

2012-01-01

The bifunctional major autolysin Atl plays a key role in staphylococcal cell separation. Processing of Atl yields catalytically active amidase (AM) and glucosaminidase (GL) domains that are each fused to repeating units. The two repeats of AM (R1 and R2) target the enzyme to the septum, where it cleaves murein between dividing cells. We have determined the crystal structure of R2, which reveals that each repeat folds into two half-open β-barrel subunits. We further demonstrate that lipoteichoic acid serves as a receptor for the repeats and that this interaction depends on conserved surfaces in each subunit. Small-angle X-ray scattering of the mature amidase reveals the presence of flexible linkers separating the AM, R1, and R2 units. Different levels of flexibility for each linker provide mechanistic insights into the conformational dynamics of the full-length protein and the roles of its components in cell wall association and catalysis. Our analysis supports a model in which the repeats direct the catalytic AM domain to the septum, where it can optimally perform the final step of cell division. PMID:22609916

The minisatellite of the GPI/AMF/NLK/MF gene: interspecies conservation and transcriptional activity.

PubMed

Williams, R R; Hassan-Walker, A F; Lavender, F L; Morgan, M; Faik, P; Ragoussis, J

2001-05-16

Minisatellites are tandemly repeated DNA sequences found throughout the genomes of all eukaryotes. They are regions often prone to instability and hence hypervariability; thus repeat unit sequence is generally not conserved beyond closely related species. We have studied the minisatellite located in intron 9 of the human glucose phosphate isomerase (GPI) gene (also known as neuroleukin, autocrine motility factor, maturation and differentiation factor) and have found, by Zoo blotting coupled with PCR amplification and DNA sequencing, that similar repeat units are present in seven other species of mammal. There is also evidence for the presence of the minisatellite in chicken. The repeat unit does not appear to be present at any other locus in these genomes. Minisatellite DNA has been reported to be involved in recombination activity, control of gene expression of nearby gene(s) (both transcriptional and translational), whilst others form protein coding regions. The high level of conservation exhibited by the GPI minisatellite, coupled with the unique location, strongly suggests a functional role. Our results from transient and stable transfections using luciferase reporter constructs have shown that the GPI minisatellite region can act to increase transcription from the SV40 promoter, CMV promoter and the human GPI promoter.

Clamping characteristics study on different types of clamping unit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiao, Zhiwei; Liu, Haichao; Xie, Pengcheng

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-platenmore » 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.« less

Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins

PubMed Central

Hu, Yueming; Huang, He; Hui, Xinjie; Cheng, Xi; White, Aaron P.

2016-01-01

Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia. PMID:27217422

A Legionella pneumophila collagen-like protein encoded by a gene with a variable number of tandem repeats is involved in the adherence and invasion of host cells.

PubMed

Vandersmissen, Liesbeth; De Buck, Emmy; Saels, Veerle; Coil, David A; Anné, Jozef

2010-05-01

Legionella pneumophila is a Gram-negative, facultative intracellular pathogen and the causative agent of Legionnaires' disease, a severe pneumonia in humans. Analysis of the Legionella sequenced genomes revealed a gene with a variable number of tandem repeats (VNTRs), whose number varies between strains. We examined the strain distribution of this gene among a collection of 108 clinical, environmental and hot spring serotype I strains. Twelve variants were identified, but no correlation was observed between the number of repeat units and clinical and environmental strains. The encoded protein contains the C-terminal consensus motif of outer membrane proteins and has a large region of collagen-like repeats that is encoded by the VNTR region. We have therefore annotated this protein Lcl for Legionella collagen-like protein. Lcl was shown to contribute to the adherence and invasion of host cells and it was demonstrated that the number of repeat units present in lcl had an influence on these adhesion characteristics.

Continuous Removal of Coal-Gasification Residue

NASA Technical Reports Server (NTRS)

Collins, Earl R., Jr.; Suitor, J.; Dubis, D.

1986-01-01

Continuous-flow hopper processes solid residue from coal gasification, converting it from ashes, cinders, and clinkers to particles size of sand granules. Unit does not require repeated depressurization of lockhopper to admit and release materials. Therefore consumes less energy. Because unit has no airlock valves opened and closed repeatedly on hot, abrasive particles, subjected to lesser wear. Coal-gasification residue flows slowly through pressure-letdown device. Material enters and leaves continuously. Cleanout door on each pressure-letdown chamber allows access for maintenance and emergencies.

Structure of chromatin and the linking number of DNA.

PubMed Central

Worcel, A; Strogatz, S; Riley, D

1981-01-01

Recent observations suggest that the basic supranucleosomal structure of chromatin is a zigzag helical ribbon with a repeat unit made of two nucleosomes connected by a relaxed spacer DNA. A remarkable feature of one particular ribbon is that it solves the apparent paradox between the number of DNA turns per nucleosome and the total linking number of a nucleosome-containing closed circular DNA molecule. We show here that the repeat unit of the proposed structure, which contains two nucleosomes with -1 3/4 DNA turns per nucleosome and one spacer crossover per repeat, contributes -2 to the linking number of closed circular DNA. Space-filling models show that the cylindrical 250-A chromatin fiber can be generated by twisting the ribbon. Images PMID:6940168

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

PubMed

Larsen, Svend Arild; Mogensen, Line; Dietz, Rune; Baagøe, Hans Jørgen; Andersen, Mogens; Werge, Thomas; Rasmussen, Henrik Berg

2005-12-01

In this study we have identified and characterized dopamine receptor D4 (DRD4) exon III tandem repeats in 33 public available nucleotide sequences from different mammalian species. We found that the tandem repeat in canids could be described in a novel and simple way, namely, as a structure composed of 15- and 12- bp modules. Tandem repeats composed of 18-bp modules were found in sequences from the horse, zebra, onager, and donkey, Asiatic bear, polar bear, common raccoon, dolphin, harbor porpoise, and domestic cat. Several of these sequences have been analyzed previously without a tandem 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 tandem repeat, while a tandem repeat consisting of 27-bp modules was identified in a sequence from European badger. Both these tandem repeats were composed of 9-bp basic units, which were closely related with the 9-bp repeat modules identified in the mink and ferret. Tandem repeats could not be identified in sequences from rodents. All tandem repeats possessed a high GC content with a strong bias for C. On phylogenetic analysis of the tandem repeats evolutionary related species were clustered into the same groups. The degree of conservation of the tandem repeats varied significantly between species. The deduced amino acid sequences of most of the tandem repeats exhibited a high propensity for disorder. This was also the case with an amino acid sequence of the human DRD4 exon III tandem repeat, which was included in the study for comparative purposes. We identified proline-containing motifs for SH3 and WW domain binding proteins, potential phosphorylation sites, PDZ domain binding motifs, and FHA domain binding motifs in the amino acid sequences of the tandem repeats. The numbers of potential functional sites varied pronouncedly between species. Our observations provide a platform for future studies of the architecture and evolution of the DRD4 exon III tandem repeat, and they suggest that differences in the structure of this tandem repeat contribute to specialization and generation of diversity in receptor function.

Hollow cathode heater development for the Space Station plasma contactor

NASA Technical Reports Server (NTRS)

Soulas, George C.

1993-01-01

A hollow cathode-based plasma contactor has been selected for use on the Space Station. During the operation of the plasma contactor, the hollow cathode heater will endure approximately 12000 thermal cycles. Since a hollow cathode heater failure would result in a plasma contactor failure, a hollow cathode heater development program was established to produce a reliable heater design. The development program includes the heater design, process documents for both heater fabrication and assembly, and heater testing. The heater design was a modification of a sheathed ion thruster cathode heater. Three heaters have been tested to date using direct current power supplies. Performance testing was conducted to determine input current and power requirements for achieving activation and ignition temperatures, single unit operational repeatability, and unit-to-unit operational repeatability. Comparisons of performance testing data at the ignition input current level for the three heaters show the unit-to-unit repeatability of input power and tube temperature near the cathode tip to be within 3.5 W and 44 degrees C, respectively. Cyclic testing was then conducted to evaluate reliability under thermal cycling. The first heater, although damaged during assembly, completed 5985 ignition cycles before failing. Two additional heaters were subsequently fabricated and have completed 3178 cycles to date in an on-going test.

O-Acetyl location on cepacian, the principal exopolysaccharide of Burkholderia cepacia complex bacteria.

PubMed

Cescutti, Paola; Impallomeni, Giuseppe; Garozzo, Domenico; Rizzo, Roberto

2011-12-27

Cepacian is an exopolysaccharide produced by the majority of the isolates belonging to the Burkholderia cepacia complex bacteria, a group of 17 species, some of which infect cystic fibrosis patients, sometime with fatal outcome. The repeating unit of cepacian consists of a backbone having a trisaccharidic repeating unit with three side chains, as reported in the formula below. The exopolysaccharide is also acetylated, carrying from one to three acetyl esters per repeating unit, depending on the strain examined. The consequences of O-acetyl substitution in a polysaccharide are important both for its biological functions and for industrial applications, including the preparation of conjugated vaccines, since O-acetyl groups are important immunogenic determinants. The location of acetyl groups was achieved by NMR spectroscopy and ESI mass spectrometry and revealed that these substituents are scattered in non-stoichiometric ratio on many sugar residues in different positions, a feature which adds to the already unique carbohydrate structure of the polysaccharide. Copyright © 2011 Elsevier Ltd. All rights reserved.

Duration of the speech disfluencies of beginning stutterers.

PubMed

Zebrowski, P M

1991-06-01

This study compared the duration of within-word disfluencies and the number of repeated units per instance of sound/syllable and whole-word repetitions of beginning stutterers to those produced by age- and sex-matched nonstuttering children. Subjects were 10 stuttering children [9 males and 1 female; mean age 4:1 (years:months); age range 3:2-5:1), and 10 nonstuttering children (9 males and 1 female; mean age 4:0; age range: 2:10-5:1). Mothers of the stuttering children reported that their children had been stuttering for 1 year or less. One 300-word conversational speech sample from each of the stuttering and nonstuttering children was analyzed for (a) mean duration of sound/syllable repetition and sound prolongation, (b) mean number of repeated units per instance of sound/syllable and whole-word repetition, and (c) various related measures of the frequency of all between- and within-word speech disfluencies. There were no significant between-group differences for either the duration of acoustically measured sound/syllable repetitions and sound prolongations or the number of repeated units per instance of sound/syllable and whole-word repetition. Unlike frequency and type of speech disfluency produced, average duration of within-word disfluencies and number of repeated units per repetition do not differentiate the disfluent speech of beginning stutterers and their nonstuttering peers. Additional analyses support findings from previous perceptual work that type and frequency of speech disfluency, not duration, are the principal characteristics listeners use in distinguishing these two talker groups.

Structural elucidation of the O-antigen of the Shigella flexneri provisional serotype 88-893: structural and serological similarities with S. flexneri provisional serotype Y394 (1c).

PubMed

Foster, R A; Carlin, N I A; Majcher, M; Tabor, H; Ng, L-K; Widmalm, G

2011-05-01

The structure of the repeating unit of the O-antigen polysaccharide from Shigella flexneri provisional serotype 88-893 has been determined. (1)H and (13)C NMR spectroscopy as well as 2D NMR experiments were employed to elucidate the structure. The carbohydrate part of the hexasaccharide repeating unit is identical to the previously elucidated structure of the O-polysaccharide from S. flexneri prov. serotype Y394. The O-antigen of S. flexneri prov. serotype 88-893 carries 0.7 mol O-acetyl group per repeating unit located at O-2 of the 3-substituted rhamnosyl residue, as identified by H2BC and BS-CT-HMBC NMR experiments. The O-antigen polysaccharide is composed of hexasaccharide repeating units with the following structure: →2)-α-L-Rhap-(1→2)-α-L-Rhap-(1→3)-α-L-Rhap2Ac-(1→3)[α-D-Glcp-(1→2)-α-D-Glcp-(1→4)]-β-D-GlcpNAc-(1→. Serological studies showed that type antigens for the two provisional serotypes are identical; in addition 88-893 expresses S. flexneri group factor 6 antigen. We propose that provisional serotypes Y394 and 88-893 be designated as two new serotypes 7a and 7b, respectively, in the S. flexneri typing scheme. Copyright © 2011 Elsevier Ltd. All rights reserved.

Optimization of sequence alignment for simple sequence repeat regions.

PubMed

Jighly, Abdulqader; Hamwieh, Aladdin; Ogbonnaya, Francis C

2011-07-20

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. 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. 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 phylogenic relationship.

A novel tandem repeat sequence located on human chromosome 4p: isolation and characterization.

PubMed

Kogi, M; Fukushige, S; Lefevre, C; Hadano, S; Ikeda, J E

1997-06-01

In an effort to analyze the genomic region of the distal half of human chromosome 4p, to where Huntington disease and other diseases have been mapped, we have isolated the cosmid clone (CRS447) that was likely to contain a region with specific repeat sequences. Clone CRS447 was subjected to detailed analysis, including chromosome mapping, restriction mapping, and DNA sequencing. Chromosome mapping by both a human-CHO hybrid cell panel and FISH revealed that CRS447 was predominantly located in the 4p15.1-15.3 region. CRS447 was shown to consist of tandem repeats of 4.7-kb units present on chromosome 4p. A single EcoRI unit was subcloned (pRS447), and the complete sequence was determined as 4752 nucleotides. When pRS447 was used as a probe, the number of copies of this repeat per haploid genome was estimated to be 50-70. Sequence analysis revealed that it contained two internal CA repeats and one putative ORF. Database search established that this sequence was unreported. However, two homologous STS markers were found in the database. We concluded that CRS447/pRS447 is a novel tandem repeat sequence that is mainly specific to human chromosome 4p.

Unit Mastery Learning in an Introductory Geography Course

ERIC Educational Resources Information Center

Healy, John R.; Stephenson, Larry K.

1975-01-01

The unit mastery learning system is a method of individualized, self-paced learning which, through repeatable testing, enables students to attain a mastery of the content of one unit before proceeding to the next in the program. This article describes the unit mastery learning system and its application in an introductory geography course at Hilo…

42 CFR 84.307 - Environmental treatments.

Code of Federal Regulations, 2013 CFR

2013-10-01

... environmental treatments simulating extreme storage temperatures, shock, and vibration. (b) The units will be...) The units will be subjected to vibration according to the following procedure: (1) The unit will be...; and (3) The vibration frequency regimen applied to each axis will be cyclical, repeating the sequence...

42 CFR 84.307 - Environmental treatments.

Code of Federal Regulations, 2012 CFR

2012-10-01

... environmental treatments simulating extreme storage temperatures, shock, and vibration. (b) The units will be...) The units will be subjected to vibration according to the following procedure: (1) The unit will be...; and (3) The vibration frequency regimen applied to each axis will be cyclical, repeating the sequence...

42 CFR 84.307 - Environmental treatments.

Code of Federal Regulations, 2014 CFR

2014-10-01

... environmental treatments simulating extreme storage temperatures, shock, and vibration. (b) The units will be...) The units will be subjected to vibration according to the following procedure: (1) The unit will be...; and (3) The vibration frequency regimen applied to each axis will be cyclical, repeating the sequence...

Slipped-strand mispairing at noncontiguous repeats in Poecilia reticulata: a model for minisatellite birth.

PubMed Central

Taylor, J S; Breden, F

2000-01-01

The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the "raw material" for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the "imperfect" or "short direct" repeats frequently observed adjacent to both mtDNA and nuclear VNTRs. PMID:10880490

GFP-based fluorescence assay for CAG repeat instability in cultured human cells.

PubMed

Santillan, Beatriz A; Moye, Christopher; Mittelman, David; Wilson, John H

2014-01-01

Trinucleotide repeats can be highly unstable, mutating far more frequently than point mutations. Repeats typically mutate by addition or loss of units of the repeat. CAG repeat expansions in humans trigger neurological diseases that include myotonic dystrophy, Huntington disease, and several spinocerebellar ataxias. In human cells, diverse mechanisms promote CAG repeat instability, and in mice, the mechanisms of instability are varied and tissue-dependent. Dissection of mechanistic complexity and discovery of potential therapeutics necessitates quantitative and scalable screens for repeat mutation. We describe a GFP-based assay for screening modifiers of CAG repeat instability in human cells. The assay exploits an engineered intronic CAG repeat tract that interferes with expression of an inducible GFP minigene. Like the phenotypes of many trinucleotide repeat disorders, we find that GFP function is impaired by repeat expansion, in a length-dependent manner. The intensity of fluorescence varies inversely with repeat length, allowing estimates of repeat tract changes in live cells. We validate the assay using transcription through the repeat and engineered CAG-specific nucleases, which have previously been reported to induce CAG repeat instability. The assay is relatively fast and should be adaptable to large-scale screens of chemical and shRNA libraries.

GFP-Based Fluorescence Assay for CAG Repeat Instability in Cultured Human Cells

PubMed Central

Santillan, Beatriz A.; Moye, Christopher; Mittelman, David; Wilson, John H.

2014-01-01

Trinucleotide repeats can be highly unstable, mutating far more frequently than point mutations. Repeats typically mutate by addition or loss of units of the repeat. CAG repeat expansions in humans trigger neurological diseases that include myotonic dystrophy, Huntington disease, and several spinocerebellar ataxias. In human cells, diverse mechanisms promote CAG repeat instability, and in mice, the mechanisms of instability are varied and tissue-dependent. Dissection of mechanistic complexity and discovery of potential therapeutics necessitates quantitative and scalable screens for repeat mutation. We describe a GFP-based assay for screening modifiers of CAG repeat instability in human cells. The assay exploits an engineered intronic CAG repeat tract that interferes with expression of an inducible GFP minigene. Like the phenotypes of many trinucleotide repeat disorders, we find that GFP function is impaired by repeat expansion, in a length-dependent manner. The intensity of fluorescence varies inversely with repeat length, allowing estimates of repeat tract changes in live cells. We validate the assay using transcription through the repeat and engineered CAG-specific nucleases, which have previously been reported to induce CAG repeat instability. The assay is relatively fast and should be adaptable to large-scale screens of chemical and shRNA libraries. PMID:25423602

A prospective evaluation of the repeatability of left ventricular ejection fraction measurement by gated SPECT.

PubMed

Kliner, Dustin; Wang, Li; Winger, Daniel; Follansbee, William P; Soman, Prem

2015-12-01

Gated single-photon emission computed tomography (SPECT) is widely used for myocardial perfusion imaging and provides an automated assessment of left ventricular ejection fraction (LVEF). We prospectively tested the repeatability of serial SPECT-derived LVEF. This information is essential in order to inform the interpretation of a change in LV function on serial testing. Consenting patients (n = 50) from among those referred for clinically indicated gated myocardial perfusion SPECT (MPs) were recruited. Following the clinical rest-stress study, patients were repositioned on the camera table for a second acquisition using identical parameters. Patient positioning, image acquisition and processing for the second scan were independently performed by a technologist blinded to the clinical scan. Quantitative LVEF was generated by Quantitative Gated SPECT and recorded as EF1 and EF2, respectively. Repeatability of serial results was assessed using the Bland-Altman method. The limits of repeatability and repeatability coefficients were generated to determine the maximum variation in LVEF that can be expected to result from test variability. Repeatability was tested across a broad range of LV systolic function and myocardial perfusion. The mean difference between EF1 and EF2 was 1.6% (EF units), with 95% limits of repeatability of +9.1% to -6.0% (repeatability coefficient 7.5%). Correlation between serial EF measurements was excellent (r = 0.9809). Similar results were obtained in subgroups based on normal or abnormal EF and myocardial perfusion. The largest repeatability coefficient of 8.1% was seen in patients with abnormal LV systolic function. When test protocol and acquisition parameters are kept constant, a difference of >8% EF units on serial MPs is indicative of a true change 95% of the time.

Human minisatellite alleles detectable only after PCR amplification.

PubMed

Armour, J A; Crosier, M; Jeffreys, A J

1992-01-01

We present evidence that a proportion of alleles at two human minisatellite loci is undetected by standard Southern blot hybridization. In each case the missing allele(s) can be identified after PCR amplification and correspond to tandem arrays too short to detect by hybridization. At one locus, there is only one undetected allele (population frequency 0.3), which contains just three repeat units. At the second locus, there are at least five undetected alleles (total population frequency 0.9) containing 60-120 repeats; they are not detected because these tandem repeats give very poor signals when used as a probe in standard Southern blot hybridization, and also cross-hybridize with other sequences in the genome. Under these circumstances only signals from the longest tandemly repeated alleles are detectable above the nonspecific background. The structures of these loci have been compared in human and primate DNA, and at one locus the short human allele containing three repeat units is shown to be an intermediate state in the expansion of a monomeric precursor allele in primates to high copy number in the longer human arrays. We discuss the implications of such loci for studies of human populations, minisatellite isolation by cloning, and the evolution of highly variable tandem arrays.

Validity and repeatability of inertial measurement units for measuring gait parameters.

PubMed

Washabaugh, Edward P; Kalyanaraman, Tarun; Adamczyk, Peter G; Claflin, Edward S; Krishnan, Chandramouli

2017-06-01

Inertial measurement units (IMUs) are small wearable sensors that have tremendous potential to be applied to clinical gait analysis. They allow objective evaluation of gait and movement disorders outside the clinic and research laboratory, and permit evaluation on large numbers of steps. However, repeatability and validity data of these systems are sparse for gait metrics. The purpose of this study was to determine the validity and between-day repeatability of spatiotemporal metrics (gait speed, stance percent, swing percent, gait cycle time, stride length, cadence, and step duration) as measured with the APDM Opal IMUs and Mobility Lab system. We collected data on 39 healthy subjects. Subjects were tested over two days while walking on a standard treadmill, split-belt treadmill, or overground, with IMUs placed in two locations: both feet and both ankles. The spatiotemporal measurements taken with the IMU system were validated against data from an instrumented treadmill, or using standard clinical procedures. Repeatability and minimally detectable change (MDC) of the system was calculated between days. IMUs displayed high to moderate validity when measuring most of the gait metrics tested. Additionally, these measurements appear to be repeatable when used on the treadmill and overground. The foot configuration of the IMUs appeared to better measure gait parameters; however, both the foot and ankle configurations demonstrated good repeatability. In conclusion, the IMU system in this study appears to be both accurate and repeatable for measuring spatiotemporal gait parameters in healthy young adults. Copyright © 2017 Elsevier B.V. All rights reserved.

19 CFR 10.619 - Repeated false or unsupported preference claims.

Code of Federal Regulations, 2010 CFR

2010-04-01

... Republic-Central America-United States Free Trade Agreement Origin Verifications and Determinations § 10... 19 Customs Duties 1 2010-04-01 2010-04-01 false Repeated false or unsupported preference claims. 10.619 Section 10.619 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND...

40 CFR 1066.20 - Units of measure and overview of calculations.

Code of Federal Regulations, 2014 CFR

2014-07-01

... POLLUTION CONTROLS VEHICLE-TESTING PROCEDURES Applicability and General Provisions § 1066.20 Units of..., repeatability, linearity, or noise specification. See 40 CFR 1065.1001 for the definition of tolerance. In this...

Handedness in shearing auxetics creates rigid and compliant structures

NASA Astrophysics Data System (ADS)

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.

Variable Number Of Tandem Repeats (VNTR) and its application in bacterial epidemiology.

PubMed

Ramazanzadeh, Rashid; McNerney, Ruth

2007-08-15

Molecular epidemiology is the using of molecular techniques to study bacterial distribution in human populations. Recently molecular epidemiologist benefit from several techniques such as Variable Number Tandem Repeat (VNTR) typing method to typing bacterial strains. Variable Number Tandem Repeat (VNTR) typing is a tool for genotyping and provides data in a simple and numeric format based on the number of repetitive sequences. VNTR for first time identified in M. tuberculosis as Mycobacterial Interspersed Repeat Units (MIRUs). General terms of VNTR have now been reported in Bacillus anthracis, Legionella pneumophila, Pseudomonas aeruginosa, Salmonella enterica and Escherichia coli O157.

Thymidylate synthase repeat polymorphisms and risk of neural tube defects in a population from the northern United Kingdom.

PubMed

Wilding, Craig S; Relton, Caroline L; Sutton, Matthew J; Jonas, Pat A; Lynch, Sally-Ann; Tawn, E Janet; Burn, John

2004-07-01

A 28-bp repeat polymorphism in the 5'UTR of the thymidylate synthase (TYMS) gene represents a candidate risk factor for neural tube defects (NTDs) due to involvement in folate-dependent homocysteine metabolism. Non-Hispanic, white, U.S. citizens carrying at least one 2x 28-bp repeat allele have recently been shown to be at a four-fold increased risk of spina bifida (SB). We investigated the association between this polymorphism and risk of NTD in families affected by NTDs and controls from the northern United Kingdom (UK). PCR was performed on genomic DNA extracted from blood or mouth swabs of family members affected by NTDs (mothers, fathers, and cases), and unaffected controls (mothers and infants) to determine the number of 28-bp repeat units within the promoter region of TYMS. Case-control and TDT analyses of the influence of TYMS genotype on risk of NTD, or NTD pregnancy, were conducted. Odds ratio (OR) analysis indicated that individuals carrying the 2x 28-bp repeat allele either in homozygous or heterozygous form, are not at increased risk of NTDs, or of having an NTD affected pregnancy. Control population allele frequencies are seen to be markedly different between the U.S. controls and those in this study. TYMS polymorphism appears to be not universally associated with NTD risk across Caucasian samples. The elevated risk of spina bifida in U.S. samples appears to be driven by an unusually low risk allele (2x 28 bp) frequency in control samples. Family based (TDT) testing of U.S. samples is therefore advocated.

Distribution and sequence homogeneity of an abundant satellite DNA in the beetle, Tenebrio molitor.

PubMed Central

Davis, C A; Wyatt, G R

1989-01-01

The mealworm beetle, Tenebrio molitor, contains an unusually abundant and homogeneous satellite DNA which constitutes up to 60% of its genome. The satellite DNA is shown to be present in all of the chromosomes by in situ hybridization. 18 dimers of the repeat unit were cloned and sequenced. The consensus sequence is 142 nt long and lacks any internal repeat structure. Monomers of the sequence are very similar, showing on average a 2% divergence from the calculated consensus. Variant nucleotides are scattered randomly throughout the sequence although some variants are more common than others. Neighboring repeat units are no more alike than randomly chosen ones. The results suggest that some mechanism, perhaps gene conversion, is acting to maintain the homogeneity of the satellite DNA despite its abundance and distribution on all of the chromosomes. Images PMID:2762148

Implementation of a Smeared Crack Band Model in a Micromechanics Framework

NASA Technical Reports Server (NTRS)

Pineda, Evan J.; Bednarcyk, Brett A.; Waas, Anthony M.; Arnold, Steven M.

2012-01-01

The smeared crack band theory is implemented within the generalized method of cells and high-fidelity generalized method of cells micromechanics models to capture progressive failure within the constituents of a composite material while retaining objectivity with respect to the size of the discretization elements used in the model. An repeating unit cell containing 13 randomly arranged fibers is modeled and subjected to a combination of transverse tension/compression and transverse shear loading. The implementation is verified against experimental data (where available), and an equivalent finite element model utilizing the same implementation of the crack band theory. To evaluate the performance of the crack band theory within a repeating unit cell that is more amenable to a multiscale implementation, a single fiber is modeled with generalized method of cells and high-fidelity generalized method of cells using a relatively coarse subcell mesh which is subjected to the same loading scenarios as the multiple fiber repeating unit cell. The generalized method of cells and high-fidelity generalized method of cells models are validated against a very refined finite element model.

Progressive Failure of a Unidirectional Fiber-Reinforced Composite Using the Method of Cells: Discretization Objective Computational Results

NASA Technical Reports Server (NTRS)

Pineda, Evan J.; Bednarcyk, Brett A.; Waas, Anthony M.; Arnold, Steven M.

2012-01-01

The smeared crack band theory is implemented within the generalized method of cells and high-fidelity generalized method of cells micromechanics models to capture progressive failure within the constituents of a composite material while retaining objectivity with respect to the size of the discretization elements used in the model. An repeating unit cell containing 13 randomly arranged fibers is modeled and subjected to a combination of transverse tension/compression and transverse shear loading. The implementation is verified against experimental data (where available), and an equivalent finite element model utilizing the same implementation of the crack band theory. To evaluate the performance of the crack band theory within a repeating unit cell that is more amenable to a multiscale implementation, a single fiber is modeled with generalized method of cells and high-fidelity generalized method of cells using a relatively coarse subcell mesh which is subjected to the same loading scenarios as the multiple fiber repeating unit cell. The generalized method of cells and high-fidelity generalized method of cells models are validated against a very refined finite element model.

Identification of a highly sulfated fucoidan from sea cucumber Pearsonothuria graeffei with well-repeated tetrasaccharides units.

PubMed

Hu, Yaqin; Li, Shan; Li, Junhui; Ye, Xingqian; Ding, Tian; Liu, Donghong; Chen, Jianchu; Ge, Zhiwei; Chen, Shiguo

2015-12-10

Sea cucumber fucoidan is a major bioactive component of sea cucumber. The structures of fucoidans have significant influences on their biological activities. The present study clarified the delicate structure of a fucoidan from Pearsonothuria graeffei. Fucoidan was obtained after papain digestion and purified by ion chromatography. The carbohydrate sequence of fucoidan was firstly determined by negative-ion electrospray tandem mass spectrometry (ES-MS) with collision-induced dissociation of the oligosaccharide fragments, which were obtained by mild acid hydrolysis, and completed by NMR for assignment of the anomeric conformation. It was unambiguously identified as a tetrasaccharide repeating unit with a backbone of [ → 3Fuc (2S, 4S) α1 → 3Fucα1→ 3Fuc (4S) α1 → 3Fuc#7 × 10#]n. The glycosidic bonds between the non-sulfated and 2,4-O-disulfated fucose residues were selectively cleaved, and highly ordered oligosaccharide fragments with a tetrasaccharide repeating unit were obtained. The highly 4-O- and 2, 4-di-O-sulfated polysaccharide deserves further developments for Pharmacia use. Copyright © 2015 Elsevier Ltd. All rights reserved.

The temporal characteristics of humpback whale songs

NASA Astrophysics Data System (ADS)

Au, Whitlow W. L.; Lammers, Marc O.; Stimpert, Alison; Schotten, Michiel

2005-09-01

Songs sung by male humpback whales consist of distinct, pulsed sounds that are designated as units. Units are produced in some sequence to form a phrase, a repeated set of phrases forms a theme, and repeated themes form a song. A song can last from minutes to hours. The songs of eight humpback whales were recorded with a vertical array of five hydrophones spaced 7 m apart with the array located within 100 m of the whales. At least seven distinct units were identified aurally from this data set obtained during the 2002 winter humpback whale session in Hawaii. Four distinct recurring themes were found in the songs, and for each whale at least two themes were recorded. The average duration of each unit sampled and the silent interval following the unit were determined in order to describe the temporal characteristics of the songs. From the data the temporal consistency and cadence control of unit production by each humpback whale and between whales were determined. Understanding the temporal and spectral characteristics of units within songs and how these units vary between whales could ultimately help in the design of computer algorithms to automatically identify individual whales.

Complete structure of the cell surface polysaccharide of Streptococcus oralis C104: A 600-MHz NMR study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abeygunawardana, C.; Bush, C.A.; Cisar, J.O.

1991-09-03

Specific lectin-carbohydrate interactions between certain oral streptococci and actinomyces contribute to the microbial colonization of teeth. The receptor molecules of Streptococcus oralis, 34, ATCC 10557, and Streptococcus mitis J22 for the galactose and N-acetylgalactosamine reactive fimbrial lectins of Actinomyces viscosus and Actinomyces naeslundii are antigenically distinct polysaccharides, each formed by a different phosphodiester-linked oligosaccharide repeating unit. Receptor polysaccharide was isolated form S. oralis C104 cells and was shown to contain galactose, N-acetylgalactosamine, ribitol, and phosphate with molar ratios of 4:1:1:1. The {sup 1}H NMR spectrum of the polysaccharide shows that it contains a repeating structure. The individual sugars in themore » repeating unit were identified by {sup 1}H coupling constants observed in E-COSY and DQF-COSY spectra. NMR methods included complete resonance assignments ({sup 1}H and {sup 13}C) by various homonuclear and heteronuclear correlation experiments that utilize scalar couplings. Sequence and linkage assignments were obtained from the heteronuclear multiple-bond correlation (HMBC) spectrum. This analysis shows that the receptor polysaccharide of S. oralis C104 is a ribitol teichoic acid polymer composed of a linear hexasaccharide repeating unit containing two residues each of galactopyranose and galactofuranose and a residue each of GalNAc and ribitol joined end to end by phosphodiester linkages.« less

A Dynamic Tandem Repeat in Monocotyledons Inferred from a Comparative Analysis of Chloroplast Genomes in Melanthiaceae.

PubMed

Do, Hoang Dang Khoa; Kim, Joo-Hwan

2017-01-01

Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore "hot spots" for genomic events in Melanthiaceae. Comparative analysis of 23 complete cpDNA sequences revealed that there were different stages of deletion in the rps16 region across the Melanthiaceae. Based on the partial or complete loss of rps16 gene in cpDNA, we have firstly reported potential molecular markers for recognizing two sections ( Veratrum and Fuscoveratrum ) of Veratrum . Melathiaceae exhibits a significant change in the junction between large single copy and inverted repeat regions, ranging from trnH_GUG to a part of rps3 . Our results show an accumulation of tandem repeats in the rpl23-ycf2 regions of cpDNAs. Small conserved sequences exist and flank tandem repeats in further observation of this region across most of the examined taxa of Liliales. Therefore, we propose three scenarios in which different small repeated sequences were used during SSM events to generate newly distinct types of repeats. Occasionally, prior to the SSM process, point mutation event and double strand break repair occurred and induced the formation of initial repeat units which are indispensable in the SSM process. SSM may have likely occurred more frequently for short repeats than for long repeat sequences in tribe Parideae (Melanthiaceae, Liliales). Collectively, these findings add new evidence of dynamic results from SSM in chloroplast genomes which can be useful for further evolutionary studies in angiosperms. Additionally, genomics events in cpDNA are potential resources for mining molecular markers in Liliales.

Ionic strength and temperature induced conformational changes in mononucleosomes and oligonucleosomes. [Chromatin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmitz, K.S.; Kent, J.C.; Parthasarathy, N.

1980-10-01

Chromatin is a nucleohistone complex which exhibits a repeat unit structure as inferred from nuclease digestion studies. The repeat unit, or nucleosome, is defined as approx. 200 base pairs of DNA wrapped about the surface of an octameric histone complex (two copies each of the histones H2A, H2B, H3, and H4). We report in this communication preliminary studies on the conformation of chromatin mononucleosomes and oligonucleosomes as a function of temperature and ionic strength. The methods used were conductivity, fluorescence of bound proflavine, and quasielastic light scattering.

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

EPA Science Inventory

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...

Repeatability estimates for oleoresin yield measurements in three species of the southern pines

Treesearch

James H. Roberds; Brain L. Strom

2006-01-01

Repeatability was estimated for constitutive oleoresin yield measurements in 10 stands of three species of pines native to southeastern United States. Trees of these species that discharge large quantities of oleoresin upon wounding are considered to be most resistant to attack by southern pine beetle (Dendroctonus frontalis Zimmermann). Oleoresin...

Independence of motor unit recruitment and rate modulation during precision force control.

PubMed

Kamen, G; Du, D C

1999-01-01

The vertebrate motor system chiefly employs motor unit recruitment and rate coding to modulate muscle force output. In this paper, we studied how the recruitment of new motor units altered the firing rate of already-active motor units during precision force production in the first dorsal interosseous muscle. Six healthy adults performed linearly increasing isometric voluntary contractions while motor unit activity and force output were recorded. After motor unit discharges were identified, motor unit firing rates were calculated before and after the instances of new motor unit recruitment. Three procedures were applied to compute motor unit firing rate, including the mean of a fixed number of inter-spike intervals and the constant width weighted Hanning window filter method, as well as a modified boxcar technique. In contrast to previous reports, the analysis of the firing rates of over 200 motor units revealed that reduction of the active firing rates was not a common mechanism used to accommodate the twitch force produced by the recruitment of a new motor unit. Similarly, during de-recruitment there was no tendency for motor unit firing rates to increase immediately following the cessation of activity in other motor units. Considerable consistency in recruitment behavior was observed during repeated contractions. However, firing rates during repeated contractions demonstrated considerably more fluctuation. It is concluded that the neuromuscular system does not use short-term preferential motor unit disfacilitation to effect precise regulation of muscular force output.

Identification of Simple Sequence Repeats in Chloroplast Genomes of Magnoliids Through Bioinformatics Approach.

PubMed

Srivastava, Deepika; Shanker, Asheesh

2016-12-01

Basal angiosperms or Magnoliids is an important clade of commercially important plants which mainly include spices and edible fruits. In this study, 17 chloroplast genome sequences belonging to clade Magnoliids were screened for the identification of chloroplast simple sequence repeats (cpSSRs). Simple sequence repeats or microsatellites are short stretches of DNA up to 1-6 base pair in length. These repeats are ubiquitous and play important role in the development of molecular markers and to study the mapping of traits of economic, medical or ecological interest. A total of 479 SSRs were detected, showing average density of 1 SSR/6.91 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 24 bp for mono-, 12 to 18 bp for di-, 12 to 26 bp for tri-, 12 to 24 bp for tetra-, 15 bp for penta- and 18 bp for hexanucleotide repeats. Mononucleotide repeats were the most frequent (207, 43.21 %) followed by tetranucleotide repeats (130, 27.13 %). Penta- and hexanucleotide repeats were least frequent or absent in these chloroplast genomes.

Engineering customized TALE nucleases (TALENs) and TALE transcription factors by fast ligation-based automatable solid-phase high-throughput (FLASH) assembly.

PubMed

Reyon, Deepak; Maeder, Morgan L; Khayter, Cyd; Tsai, Shengdar Q; Foley, Jonathan E; Sander, Jeffry D; Joung, J Keith

2013-07-01

Customized DNA-binding domains made using transcription activator-like effector (TALE) repeats are rapidly growing in importance as widely applicable research tools. TALE nucleases (TALENs), composed of an engineered array of TALE repeats fused to the FokI nuclease domain, have been used successfully for directed genome editing in various organisms and cell types. TALE transcription factors (TALE-TFs), consisting of engineered TALE repeat arrays linked to a transcriptional regulatory domain, have been used to up- or downregulate expression of endogenous genes in human cells and plants. This unit describes a detailed protocol for the recently described fast ligation-based automatable solid-phase high-throughput (FLASH) assembly method. FLASH enables automated high-throughput construction of engineered TALE repeats using an automated liquid handling robot or manually using a multichannel pipet. Using the automated approach, a single researcher can construct up to 96 DNA fragments encoding TALE repeat arrays of various lengths in a single day, and then clone these to construct sequence-verified TALEN or TALE-TF expression plasmids in a week or less. Plasmids required for FLASH are available by request from the Joung lab (http://eGenome.org). This unit also describes improvements to the Zinc Finger and TALE Targeter (ZiFiT Targeter) web server (http://ZiFiT.partners.org) that facilitate the design and construction of FLASH TALE repeat arrays in high throughput. © 2013 by John Wiley & Sons, Inc.

3 CFR 8589 - Proclamation 8589 of October 22, 2010. United Nations Day, 2010

Code of Federal Regulations, 2011 CFR

2011-01-01

... devastating wars to rededicate themselves to peace, justice, and progress. The founders of the United Nations vowed to work together to ensure that the horrors seen in World War II would never be repeated. On... 3 The President 1 2011-01-01 2011-01-01 false Proclamation 8589 of October 22, 2010. United...

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

Treesearch

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...

Effects of repeated burning on snag abundance in shortleaf pine woodlands

Treesearch

Roger W. Perry; Phillip N. Jordan; Virginia L. McDaniel

2017-01-01

Forest managers are restoring and maintaining forest woodlands across substantial areas of the United States, and these efforts typically require the use of frequent prescribed fire. The effects of frequent prescribed fire on important habitat components such as snags remain unknown. We conducted a study to determine how snag densities are affected by repeated...

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

PubMed Central

Glunčić, Matko; Paar, Vladimir

2013-01-01

The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012.exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of α-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of ‘magnifying glass’ effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes). PMID:22977183

Rapid and accurate synthesis of TALE genes from synthetic oligonucleotides.

PubMed

Wang, Fenghua; Zhang, Hefei; Gao, Jingxia; Chen, Fengjiao; Chen, Sijie; Zhang, Cuizhen; Peng, Gang

2016-01-01

Custom synthesis of transcription activator-like effector (TALE) genes has relied upon plasmid libraries of pre-fabricated TALE-repeat monomers or oligomers. Here we describe a novel synthesis method that directly incorporates annealed synthetic oligonucleotides into the TALE-repeat units. Our approach utilizes iterative sets of oligonucleotides and a translational frame check strategy to ensure the high efficiency and accuracy of TALE-gene synthesis. TALE arrays of more than 20 repeats can be constructed, and the majority of the synthesized constructs have perfect sequences. In addition, this novel oligonucleotide-based method can readily accommodate design changes to the TALE repeats. We demonstrated an increased gene targeting efficiency against a genomic site containing a potentially methylated cytosine by incorporating non-conventional repeat variable di-residue (RVD) sequences.

Depressive Symptoms and Violence Exposure: Contributors to Repeat Pregnancies Among Adolescents

PubMed Central

Anderson, Cheryl A.; Pierce, Lisa

2015-01-01

ABSTRACT Depressive symptoms and violence exposure (VE) often cooccur and have been recognized to influence childbearing; contribution to repeat pregnancy is unclear and examined in this article. This cross-sectional, descriptive, study screened for depressive symptoms and VE among 193 adolescent mothers at a large county hospital in Southwestern United States. Repeat pregnancy and depressive symptoms characterized one-third and one-quarter of adolescents, respectively. Despite minimal disclosure of VE, repeat pregnancy was significantly influenced by child abuse and past traumatic life experiences. Assessments and interventions with adolescents should focus on frequency of repeat pregnancies and symptoms of depression and VE. Nurses and childbirth educators are poised to offer birth control information and education, support, and resources highlighting depression and VE to adolescents. PMID:26834444

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

PubMed

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.

Iron balance in the red blood cell donor.

PubMed

Brittenham, G M

2005-01-01

Phlebotomy of a unit of blood produces a loss of 200 to 250 mg of iron in haemoglobin. Because of physiological differences in iron balance between women of childbearing age and men, the loss of similar amounts of iron at donation has divergent consequences for committed donors. Women of childbearing age have an increased risk of iron deficiency if they donate more than one unit per year while men are usually able to maintain iron balance while donating four or more units of blood per year. Lack of iron is the most important medical reason for deferral from repeat donation and primarily affects women of childbearing age. Deferral of these women discourages them from further donation and may lead to their loss as donors. Provisions for blood donation should protect those who give blood from adverse consequences of their altruism. Safe and effective approaches to iron replacement after donation have been developed that can prevent iron deficiency in women who give blood repeatedly. Blood centres should consider incorporating programmes of iron replacement for women of childbearing age who give blood repeatedly to protect these donors against iron deficiency and to enhance their retention and commitment as dedicated donors.

A model of high-affinity antibody binding to type III group B Streptococcus capsular polysaccharide.

PubMed

Wessels, M R; Muñoz, A; Kasper, D L

1987-12-01

We recently reported that the single repeating-unit pentasaccharide of type III group B Streptococcus (GBS) capsular polysaccharide is only weakly reactive with type III GBS antiserum. To further elucidate the relationship between antigen-chain length and antigenicity, tritiated oligosaccharides derived from type III capsular polysaccharide were used to generate detailed saturation binding curves with a fixed concentration of rabbit antiserum in a radioactive antigen-binding assay. A graded increase in affinity of antigen-antibody binding was seen as oligosaccharide size increased from 2.6 repeating units to 92 repeating units. These differences in affinity of antibody binding to oligosaccharides of different molecular size were confirmed by immunoprecipitation and competitive ELISA, two independent assays of antigen-antibody binding. Analysis of the saturation binding experiment indicated a difference of 300-fold in antibody-binding affinity for the largest versus the smallest tested oligosaccharides. Unexpectedly, the saturation binding values approached by the individual curves were inversely related to oligosaccharide chain length on a molar basis but equivalent on a weight basis. This observation is compatible with a model in which binding of an immunoglobulin molecule to an antigenic site on the polysaccharide facilitates subsequent binding of antibody to that antigen.

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

PubMed

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, P<0.05] and decreased rates of relapse in diverticular disease of the descending (HR: 0.40±0.46, P<0.05), and sigmoid colon (HR: 0.39±0.49, P<0.05). The ascending colon 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.

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

PubMed

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.

Microevolution of Pandemic Vibrio parahaemolyticus Assessed by the Number of Repeat Units in Short Sequence Tandem Repeat Regions

PubMed Central

García, Katherine; Gavilán, Ronnie G.; Höfle, Manfred G.; Martínez-Urtaza, Jaime; Espejo, Romilio T.

2012-01-01

The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by comparison of their variable number tandem repeats (VNTRs). The differentiation of the isolates by the differences in VNTRs will allow inferring the population dynamics and microevolution of this strain but this requires knowing the rate and mechanism of VNTRs' variation. Our study of mutants obtained after serial cultivation of clones showed that mutation rates of the six VNTRs examined are on the order of 10−4 mutant per generation and that difference increases by stepwise addition of single mutations. The single stepwise mutation (SSM) was deduced because mutants with 1, 2, 3, or more repeat unit deletions or insertions follow a geometric distribution. Plausible phylogenetic trees are obtained when, according to SSM, the genetic distance between clusters with different number of repeats is assessed by the absolute differences in repeats. Using this approach, mutants originated from different isolates of pandemic V. parahaemolyticus after serial cultivation are clustered with their parental isolates. Additionally, isolates of pandemic V. parahaemolyticus from Southeast Asia, Tokyo, and northern and southern Chile are clustered according their geographical origin. The deepest split in these four populations is observed between the Tokyo and southern Chile populations. We conclude that proper phylogenetic relations and successful tracing of pandemic V. parahaemolyticus requires measuring the differences between isolates by the absolute number of repeats in the VNTRs considered. PMID:22292049

Tandemly repeated sequences in mtDNA control region of whitefish, Coregonus lavaretus.

PubMed

Brzuzan, P

2000-06-01

Length variation of the mitochondrial DNA control region was observed with PCR amplification of a sample of 138 whitefish (Coregonus lavaretus). Nucleotide sequences of representative PCR products showed that the variation was due to the presence of an approximately 100-bp motif tandemly repeated two, three, or five times in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA. This is the first report on the tandem array composed of long repeat units in mitochondrial DNA of salmonids.

History Repeats Itself at Yorktown Middle.

ERIC Educational Resources Information Center

Haskin, Teresa T.

1999-01-01

Describes two interdisciplinary units that can be used in most middle school classrooms, one on the sinking of the "Titanic" and one on Pickett's charge at Gettysburg during the Civil War. Describes how each unit involves English, math, social studies, and science classes and activities. (SR)

Comprehensive analysis of all triple helical repeats in beta-spectrins reveals patterns of selective evolutionary conservation.

PubMed

Baines, Anthony J

2003-01-01

The spectrin superfamily (spectrin, alpha-actinin, utrophin and dystrophin) has in common a triple helical repeating unit of ~106 amino acid residues. In spectrin, alpha and beta chains contain multiple copies of this repeat. beta-spectrin chains contain the majority of binding activities in spectrin and are essential for animal life. Canonical beta-spectrins have 17 repeats; beta-heavy spectrins have 30. Here, the repeats of five human beta-spectrins, plus beta-spectrins from several other vertebrates and invertebrates, have been analysed. Repeats 1, 2, 14 and 17 in canonical beta are highly conserved between invertebrates and vertebrates, and repeat 8 in some isoforms. This is consistent with conservation of critical functions, since repeats 1, 2 and 17 bind alpha-spectrin. Repeats 1 of beta-spectrins are not always detected by SMART or Pfam tools. A profile hidden Markov model of beta-spectrin repeat 1 detects alpha-actinins, but not utrophin or dystrophin. Novel examples of repeat 1 were detected in the spectraplakins MACF1, BPAG1 and plectin close to the actin-binding domain. Ankyrin binds to the C-terminal portion of repeat 14; the high conservation of this entire repeat may point to additional, undiscovered ligand-binding activities. This analysis indicates that the basic triple helical repeat pattern was adapted early in the evolution of the spectrin superfamily to encompass essential binding activities, which characterise individual repeats in proteins extant today.

Structural analysis of two length variants of the rDNA intergenic spacer from Eruca sativa.

PubMed

Lakshmikumaran, M; Negi, M S

1994-03-01

Restriction enzyme analysis of the rRNA genes of Eruca sativa indicated the presence of many length variants within a single plant and also between different cultivars which is unusual for most crucifers studied so far. Two length variants of the rDNA intergenic spacer (IGS) from a single individual E. sativa (cv. Itsa) plant were cloned and characterized. The complete nucleotide sequences of both the variants (3 kb and 4 kb) were determined. The intergenic spacer contains three families of tandemly repeated DNA sequences denoted as A, B and C. However, the long (4 kb) variant shows the presence of an additional repeat, denoted as D, which is a duplication of a 224 bp sequence just upstream of the putative transcription initiation site. Repeat units belonging to the three different families (A, B and C) were in the size range of 22 to 30 bp. Such short repeat elements are present in the IGS of most of the crucifers analysed so far. Sequence analysis of the variants (3 kb and 4 kb) revealed that the length heterogeneity of the spacer is located at three different regions and is due to the varying copy numbers of repeat units belonging to families A and B. Length variation of the spacer is also due to the presence of a large duplication (D repeats) in the 4 kb variant which is absent in the 3 kb variant. The putative transcription initiation site was identified by comparisons with the rDNA sequences from other plant species.

Development of Electrochemical Supercapacitors for EMA Applications

NASA Technical Reports Server (NTRS)

Kosek, John A.; Dunning, Thomas; LaConti, Anthony B.

1996-01-01

A limitation of the typical electrochemical capacitor is the maximum available power and energy density, and an improvement in capacitance per unit weight and volume is needed. A solid-ionomer electrochemical capacitor having a unit cell capacitance greater than 2 F/sq cm and a repeating element thickness of 6 mils has been developed. This capacitor could provide high-current pulses for electromechanical actuation (EMA). Primary project objectives were to develop high-capacitance particulates, to increase capacitor gravimetric and volumetric energy densities above baseline and to fabricate a 10-V capacitor with a repeating element thickness of 6 mils or less. Specific EMA applications were identified and capacitor weight and volume projections made.

The United States Army’s Full-Spectrum Training Strategy Challenge

DTIC Science & Technology

2012-05-17

the high operational tempo for deployed and deploying units. Soldiers and units conducted repeat deployments to both Iraq and Afghanistan with little...prevalent in Strategic Operational Design and associated variations of design. Further complicating Israeli ideas of warfare was the notion that...Army to develop an overarching operational framework that finally replaces Airland Battle, like EBO or some variation of operational design. But one

Understanding the new HbA1c units for the diagnosis of Type 2 diabetes.

PubMed

Braatvedt, Geoff D; Cundy, Tim; Crooke, Michael; Florkowski, Chris; Mann, Jim I; Lunt, Helen; Jackson, Rod; Orr-Walker, Brandon; Kenealy, Timothy; Drury, Paul L

2012-09-21

In New Zealand laboratories the measurement of glycated haemoglobin (HbA1c) for diagnosis of diabetes is now only reported in SI units of mmol/mol. HbA1c is now recommended as the preferred test to diagnose diabetes in most circumstances. The requirement for a second positive test in asymptomatic individuals is retained. An HbA1c greater than and equal to 50 mmol/mol (repeated on a second occasion in asymptomatic patients) is diagnostic of diabetes and a value less than and equal to 40 mmol/mol represents normal glucose tolerance. For patients with an initial HbA1c result of 41-49 mmol/mol, cardiovascular risk assessment and lifestyle interventions are recommended with repeat HbA1c screening in 6-12 months. For patients whose HbA1c is less than and equal to 40 mmol/mol, repeat screening (including for CVD risk) at intermittent intervals is recommended as per published guidelines.

Response of soricid populations to repeated fire and fuel reduction treatments in the southern Appalachain Mountains

Treesearch

Charlotte E Matthews; Christopher E Moorman; Cathryn H Greenberg

2009-01-01

Fuel hazards have increased in forests across the United States because offire exclusion during the 20th century. Treatments used to reduce fuel buildup Illay affect wildlife. such as shrews. living 011 the forest floor. especially when treatments are applied repeatedly. From mid-May to mid-August 2006 and 2007.  we used drift fences...

Certificates Count: An Analysis of Sub-Baccalaureate Certificates

ERIC Educational Resources Information Center

Bosworth, Brian

2010-01-01

Since President Obama took office, he has repeatedly called for the United States to significantly improve its postsecondary education performance. One goal in particular has gained wide attention: the President's declaration that in an ever more competitive global marketplace, the United States must once again lead the world in college…

Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes.

PubMed

Ohno, S

1984-01-01

Three outstanding properties uniquely qualify repeats of base oligomers as the primordial coding sequences of all polypeptide chains. First, when compared with randomly generated base sequences in general, they are more likely to have long open reading frames. Second, periodical polypeptide chains specified by such repeats are more likely to assume either alpha-helical or beta-sheet secondary structures than are polypeptide chains of random sequence. Third, provided that the number of bases in the oligomeric unit is not a multiple of 3, these internally repetitious coding sequences are impervious to randomly sustained base substitutions, deletions, and insertions. This is because the recurring periodicity of their polypeptide chains is given by three consecutive copies of the oligomeric unit translated in three different reading frames. Accordingly, when one reading frame is open, the other two are automatically open as well, all three being capable of coding for polypeptide chains of identical periodicity. Under this circumstance, a frame shift due to the deletion or insertion of a number of bases that is not a multiple of 3 fails to alter the down-stream amino acid sequence, and even a base change causing premature chain-termination can silence only one of the three potential coding units. Newly arisen coding sequences in modern organisms are oligomeric repeats, and most of the older genes retain various vestiges of their original internal repetitions. Some of the genes (e.g., oncogenes) have even inherited the property of being impervious to randomly sustained base changes.

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

PubMed

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.

Single-Chain Folding of Synthetic Polymers: A Critical Update.

PubMed

Altintas, Ozcan; Barner-Kowollik, Christopher

2015-11-23

The current contribution serves as a critical update to a previous feature article from us (Macromol. Rapid Commun. 2012, 33, 958-971), and highlights the latest advances in the preparation of single chain polymeric nanoparticles and initial-yet promising-attempts towards mimicking the structure of natural biomacromolecules via single-chain folding of well-defined linear polymers via so-called single chain selective point folding and repeat unit folding. The contribution covers selected examples from the literature published up to ca. September 2015. Our aim is not to provide an exhaustive review but rather highlight a selection of new and exciting examples for single-chain folding based on advanced macromolecular precision chemistry. Initially, the discussion focuses on the synthesis and characterization of single-chain folded structures via selective point folding. The second part of the feature article addresses the folding of well-defined single-chain polymers by means of repeat unit folding. The current state of the art in the field of single-chain folding indicates that repeat unit folding-driven nanoparticle preparation is well-advanced, while initial encouraging steps towards building selective point folding systems have been taken. In addition, a summary of the-in our view-open key questions is provided that may guide future biomimetic design efforts. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fine typing of methicillin-resistant Staphylococcus aureus isolates using direct repeat unit and staphylococcal interspersed repeat unit typing methods.

PubMed

Ho, Cheng-Mao; Ho, Mao-Wang; Li, Chi-Yuan; Lu, Jang-Jih

2015-08-01

Methicillin-resistant Staphylococcus aureus (MRSA) typing is an important epidemiologic tool for monitoring trends and preventing outbreaks. However, the efficiency of various MRSA typing methods for each SCCmec MRSA isolate is rarely evaluated. A total of 157 MRSA isolates from four different regions in Taiwan were typed with five different molecular methods, including SCCmec typing, multilocus sequence typing (MLST), spa typing, mec-associated direct repeat unit (dru) copy number determination, and staphylococcal interspersed repeat unit (SIRU) profiling. There were four SCCmec types, eight MLST types, 15 spa types, 11 dru types, and 31 SIRU profiles. The most common type determined by each molecular typing method was SCCmec III (115 isolates, 73.2%), ST239 (99 isolates, 63.1%), t037 (107 isolates, 68.2%), 14 dru copies (76 isolates, 48.4%), and SIRU profile 3013722 (102 isolates, 65%), respectively. When using the combination of MLST, spa typing, and dru copy number, ST5-t002-4 (n = 8), ST239-t037-14 (n = 68), ST59-t437-9 (n = 9), and ST59-t437-11 (n = 6) were found to be the most common types of SCCmec types II (n = 9), III (n = 115), IV (n = 21), and VT (n = 11) isolates, respectively. SCCmec type III isolates were further classified into 11 dru types. Of the 21 SCCmec type IV isolates, 14 SIRU profiles were found. Seven SIRU patterns were observed in the 11 SCCmec type VT isolates. Different typing methods showed a similar Hunter-Gaston discrimination index among the 157 MRSA isolates. However, dru and SIRU typing methods had a better discriminatory power for SCCmec type III and SCCmec types IV and VT isolates, respectively, suggesting that dru and SIRU can be used to further type these isolates. Copyright © 2013. Published by Elsevier B.V.

Genetic Transfer of Salmonella typhimurium and Escherichia coli Lipopolysaccharide Antigens to Escherichia coli K-12

PubMed Central

Jones, Randall T.; Koeltzow, Donald E.; Stocker, B. A. D.

1972-01-01

Escherichia coli K-12 ϰ971 was crossed with a smooth Salmonella typhimurium donor, HfrK6, which transfers early the ilv-linked rfa region determining lipopolysaccharide (LPS) core structure. Two ilv+ hybrids differing in their response to the LPS-specific phages FO and C21 were then crossed with S. typhimurium HfrK9, which transfers early the rfb gene cluster determining O repeat unit structure. Most recombinants selected for his+ (near rfb) were agglutinated by Salmonella factor 4 antiserum. Transfer of an F′ factor (FS400) carrying the rfb–his region of S. typhimurium to the same two ilv+ hybrids gave similar results. LPS extracted from two ilv+,his+, factor 4-positive hybrids contained abequose, the immunodominant sugar for factor 4 specificity. By contrast, his+ hybrids obtained from ϰ971 itself by similar HfrK9 and F′FS400 crosses were not agglutinated by factor 4 antiserum, indicating that the parental E. coli ϰ971 does not have the capacity to attach Salmonella O repeat units to its LPS core. It is concluded that the Salmonella rfb genes are expressed only in E. coli ϰ971 hybrids which have also acquired ilv-linked genes (presumably rfa genes affecting core structure or O-translocase ability, or both) from a S. typhimurium donor. When E. coli ϰ971 was crossed with a smooth E. coli donor, Hfr59, of serotype O8, which transfers his early, most his+ recombinants were agglutinated by E. coli O8 antiserum and lysed by the O8-specific phage, Ω8. This suggests that, although the parental E. coli K-12 strain ϰ971 cannot attach Salmonella-specific repeat units to its LPS core, it does have the capacity to attach E. coli O8-specific repeat units. PMID:4559827

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.

PubMed

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.

Effects of repeated prescribed fires on the structure, composition, and regeneration of mixed-oak forests in Ohio

Treesearch

Todd F. Hutchinson; Elaine Kennedy Sutherland; Daniel A. Yaussy

2005-01-01

This study quantifies prescribed fire effects at four sites in southern Ohio, from 1995 to 2002. Each site had three treatment units: an unburned control, a unit burned 2x (1996 and 1999), and a unit burned 4 x (1996-1999). Vegetation plots were stratified by an integrated moisture index (IMI) into xeric, intermediate, and mesic classes. Prior to treatments, oak (...

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

PubMed

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.

Opinions on Suicide and Perceived Barriers to Care in a Sample of United States Marine Non-Commissioned Officers: Implications for Future Frontline Supervisors’ Suicide Prevention Training Programs

DTIC Science & Technology

2013-11-06

the Scree plot (Figure 3) and the analysis was repeated saving these four factors. The Kaiser - Meyer - Olkin measure of sampling adequacy was .95...the Scree plot (Figure 4) and the analysis was repeated saving these three factors. The Kaiser - Meyer - Olkin measure of sampling adequacy was .90, above

Protocol for multiple node network

NASA Technical Reports Server (NTRS)

Kirkham, Harold (Inventor)

1995-01-01

The invention is a multiple interconnected network of intelligent message-repeating remote nodes which employs an antibody recognition message termination process performed by all remote nodes and a remote node polling process performed by other nodes which are master units controlling remote nodes in respective zones of the network assigned to respective master nodes. Each remote node repeats only those messages originated in the local zone, to provide isolation among the master nodes.

Protocol for multiple node network

NASA Technical Reports Server (NTRS)

Kirkham, Harold (Inventor)

1994-01-01

The invention is a multiple interconnected network of intelligent message-repeating remote nodes which employs an antibody recognition message termination process performed by all remote nodes and a remote node polling process performed by other nodes which are master units controlling remote nodes in respective zones of the network assigned to respective master nodes. Each remote node repeats only those messages originated in the local zone, to provide isolation among the master nodes.

Intergenic Variable-Number Tandem-Repeat Polymorphism Upstream of rocA Alters Toxin Production and Enhances Virulence in Streptococcus pyogenes.

PubMed

Zhu, Luchang; Olsen, Randall J; Horstmann, Nicola; Shelburne, Samuel A; Fan, Jia; Hu, Ye; Musser, James M

2016-07-01

Variable-number tandem-repeat (VNTR) polymorphisms are ubiquitous in bacteria. However, only a small fraction of them has been functionally studied. Here, we report an intergenic VNTR polymorphism that confers an altered level of toxin production and increased virulence in Streptococcus pyogenes The nature of the polymorphism is a one-unit deletion in a three-tandem-repeat locus upstream of the rocA gene encoding a sensor kinase. S. pyogenes strains with this type of polymorphism cause human infection and produce significantly larger amounts of the secreted cytotoxins S. pyogenes NADase (SPN) and streptolysin O (SLO). Using isogenic mutant strains, we demonstrate that deleting one or more units of the tandem repeats abolished RocA production, reduced CovR phosphorylation, derepressed multiple CovR-regulated virulence factors (such as SPN and SLO), and increased virulence in a mouse model of necrotizing fasciitis. The phenotypic effect of the VNTR polymorphism was nearly the same as that of inactivating the rocA gene. In summary, we identified and characterized an intergenic VNTR polymorphism in S. pyogenes that affects toxin production and virulence. These new findings enhance understanding of rocA biology and the function of VNTR polymorphisms in S. pyogenes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Complete mitochondrial genome of the Asian pencil halfbeak Hyporhamphus intermedius (Beloniformes, Hemirhamphidae).

PubMed

Song, Chao; Hu, Gengdong; Qiu, Liping; Fan, Limin; Meng, Shunlong; Chen, Jiazhang

2016-11-01

The complete mitochondrial genome of Hyporhamphus intermedius was determined to be 16,720 bp in length with (A + T) content of 56.3%, and it consists of 13 protein-coding genes, 22 tRNAs, two ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the H. intermedius complete mtDNA were identical to most of the other vertebrates. Interestingly, two tandem repeat units were identified across tRNA-Pro and control region (2*41 bp), while in most of the fishes the tandem repeat units are located in the control region. The molecular data we presented here could play a useful role to study the evolutionary relationships and population genetics of Hemirhamphidae fish.

Mitochondrial genome of the tomato clownfish Amphiprion frenatus (Pomacentridae, Amphiprioninae).

PubMed

Ye, Le; Hu, Jing; Wu, Kaichang; Wang, Yu; Li, Jianlong

2016-01-01

The complete mitochondrial (mt) genome of the tomato clownfish Amphiprion frenatus was obtained in this study. The circular mtDNA molecule was 16,774 bp in size and the overall nucleotide composition of the H-strand was 29.72% A, 25.81% T, 15.38% G and 29.09% C, with an A + T bias. The complete mitogenome encoded 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region (D-loop), with the gene arrangement and translation direction basically identical to other typical vertebrate mitogenomes. The D-loop included termination associated sequence (TAS), central conserved domain (CCD) and conserved sequence block (CSB), and was composed of 6 complete continuity tandem repeat units and an imperfect tandem repeat unit.

Isolation and characterization of microsatellite loci in the intertidal sponge Halichondria panicea

USGS Publications Warehouse

Knowlton, Anne L.; Pierson, Barbara J.; Talbot, S.L.; Highsmith, Ray C.

2003-01-01

GA- and CA-enriched genomic libraries were constructed for the intertidal sponge Halichondria panicea. Unique repeat motifs identified varied from the expected simple dinucleotide repeats to more complex repeat units. All sequences tended to be highly repetitive but did not necessarily contain the targeted motifs. Seven microsatellite loci were evaluated on sponges from the clone source population. All seven were polymorphic with 5.43 ± 0.92 mean number of alleles. Six of the seven loci that could be resolved had mean heterozygosities of 0.14–0.68. The loci identified here will be useful for population studies.

Novel structure of cockroach allergen Bla g 1 has implications for allergenicity and exposure assessment

PubMed Central

Mueller, Geoffrey A.; Pedersen, Lars C.; Lih, Fred B.; Glesner, Jill; Moon, Andrea F.; Chapman, Martin D.; Tomer, Kenneth B.; London, Robert E.; Pomés, Anna

2013-01-01

Background Sensitization to cockroach allergens is a major risk factor for asthma. The cockroach allergen Bla g 1 has multiple repeats of ~100 amino acids, but the fold of the protein and the biological function are unknown. Objective To determine the structure of Bla g 1, investigate the implications for allergic disease, and standardize cockroach exposure assays. Methods Natural Bla g 1 and recombinant constructs were compared by ELISA using specific murine IgG and human IgE. The structure of Bla g 1 was determined by X-ray crystallography. Mass spectrometry and NMR were utilized to examine ligand-binding properties of the allergen. Results The structure of a recombinant Bla g 1 construct with comparable IgE and IgG reactivity to the natural allergen was solved by X-ray crystallography. The Bla g 1 repeat forms a novel fold with 6 helices. Two repeats encapsulate a large and nearly spherical hydrophobic cavity, defining the basic structural unit. Lipids in the cavity varied depending on the allergen origin. Palmitic, oleic and stearic acids were associated with nBla g 1 from cockroach frass. One Unit of Bla g 1 was equivalent to 104 ng of allergen. Conclusions Bla g 1 has a novel fold with a capacity to bind various lipids, which suggests a digestive function associated with non-specific transport of lipid molecules in cockroaches. Defining the basic structural unit of Bla g 1 facilitates the standardization of assays in absolute units for the assessment of environmental allergen exposure. PMID:23915714

Gross rearrangements within the 5'-untranslated region of the picornaviral genomes.

PubMed

Pilipenko, E V; Blinov, V M; Agol, V I

1990-06-11

An analysis of reported nucleotide sequences revealed several cases of gross rearrangements in the 5'-untranslated region (5-UTR) of picornaviral genomes. A large (greater than 100 nt) duplication was discovered in a downstream region of poliovirus 5-UTR involved in the translational control. Properties of the poliovirus mutants with large deletions [Kuge and Nomoto (1987) J. Virol. 61, 1478-1487] show that a single copy of the appropriate repeating unit is compatible with a wild type phenotype of the virus. In contrast to poliovirus and another enterovirus genomes, human rhinovirus RNAs contain only a single copy of this repeating unit. Another similarly large repeat was found in an upstream segment of the bovine enterovirus 5-UTR. A comparison of the primary and secondary structures of cardio- and aphthovirus 5-UTRs demonstrated the existence of a large (ca. 250 nucleotides) insertion/deletion in a region preceding the poly(C) tract. The two latter rearrangements appear to involve elements of the viral genome replication machinery. Possible origin as well as evolutionary and functional implications of these structural peculiarities are discussed.

Technologist-Directed Repeat Musculoskeletal and Chest Radiographs: How Often Do They Impact Diagnosis?

PubMed

Rosenkrantz, Andrew B; Jacobs, Jill E; Jain, Nidhi; Brusca-Augello, Geraldine; Mechlin, Michael; Parente, Marc; Recht, Michael P

2017-12-01

Radiologic technologists may repeat images within a radiographic examination because of perceived suboptimal image quality, excluding these original images from submission to a PACS. This study assesses the appropriateness of technologists' decisions to repeat musculoskeletal and chest radiographs as well as the utility of repeat radiographs in addressing examinations' clinical indication. We included 95 musculoskeletal and 87 chest radiographic examinations in which the technologist repeated one or more images because of perceived image quality issues, rejecting original images from PACS submission. Rejected images were retrieved from the radiograph unit and uploaded for viewing on a dedicated server. Musculoskeletal and chest radiologists reviewed rejected and repeat images in their timed sequence, in addition to the studies' remaining images. Radiologists answered questions regarding the added value of repeat images. The reviewing radiologist agreed with the reason for rejection for 64.2% of musculoskeletal and 60.9% of chest radiographs. For 77.9% and 93.1% of rejected radiographs, the clinical inquiry could have been satisfied without repeating the image. For 75.8% and 64.4%, the repeated images showed improved image quality. Only 28.4% and 3.4% of repeated images were considered to provide additional information that was helpful in addressing the clinical question. Most repeated radiographs (chest more so than musculoskeletal radiographs) did not add significant clinical information or alter diagnosis, although they did increase radiation exposure. The decision to repeat images should be made after viewing the questionable image in context with all images in a study and might best be made by a radiologist rather than the performing technologist.

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

PubMed Central

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

Using a Virtual Manipulative Environment to Support Students' Organizational Structuring of Volume Units

ERIC Educational Resources Information Center

O'Dell, Jenna R.; Barrett, Jeffrey E.; Cullen, Craig J.; Rupnow, Theodore J.; Clements, Douglas H.; Sarama, Julie; Rutherford, George; Beck, Pamela S.

2017-01-01

In this study, we investigated how Grade 3 and 4 students' organizational structure for volume units develops through repeated experiences with a virtual manipulative for building prisms. Our data consist of taped clinical interviews within a micro-genetic experiment. We report on student strategy development using a virtual manipulative for…

Asian Longhorned Beetle - A New Introduction, Pest Alert

Treesearch

USDA Forest Service, State and Private Forestry, Northeastern Area; Animal and Plant Health Inspection Service

2008-01-01

The Asian longhorned beetle (ALB) has been discovered attacking trees in the United States. Tunneling by beetle larvae girdles tree stems and branches. Repeated attacks lead to dieback of the tree crown and, eventually, death of the tree. ALB probably traveled to the United States inside solid wood packing material from China. The beetle has been intercepted at ports...

Exploring the repeat protein universe through computational protein design

DOE PAGES

Brunette, TJ; Parmeggiani, Fabio; Huang, Po-Ssu; ...

2015-12-16

A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. In this paper, we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix–loop–helix–loop structural motif. Eighty-three designs with sequences unrelatedmore » to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Finally, our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.« less

Fostering repeat donations in Ghana.

PubMed

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 <25 unit/session and 30% repeat 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.

Cellular computational platform and neurally inspired elements thereof

DOEpatents

Okandan, Murat

2016-11-22

A cellular computational platform is disclosed that includes a multiplicity of functionally identical, repeating computational hardware units that are interconnected electrically and optically. Each computational hardware unit includes a reprogrammable local memory and has interconnections to other such units that have reconfigurable weights. Each computational hardware unit is configured to transmit signals into the network for broadcast in a protocol-less manner to other such units in the network, and to respond to protocol-less broadcast messages that it receives from the network. Each computational hardware unit is further configured to reprogram the local memory in response to incoming electrical and/or optical signals.

Characterization of natural photonic crystals in iridescent wings of damselfly Chalcopteryx rutilans by FIB/SEM, TEM, and TOF-SIMS.

PubMed

Carr, David M; Ellsworth, Ashley A; Fisher, Gregory L; Valeriano, Wescley W; Vasco, Juan P; Guimarães, Paulo S S; de Andrade, Rodrigo R; da Silva, Elizabeth R; Rodrigues, Wagner N

2018-02-05

The iridescent wings of the Chalcopterix rutilans damselfly (Rambur) (Odonata, Polythoridae) are investigated with focused ion beam/scanning electron microscopy, transmission electron microscopy, and time-of-flight secondary ion mass spectrometry. The electron microscopy images reveal a natural photonic crystal as the source of the varying colors. The photonic crystal has a consistent number and thickness (∼195 nm) of the repeat units on the ventral side of the wing, which is consistent with the red color visible from the bottom side of the wing in all regions. The dorsal side of the wing shows strong color variations ranging from red to blue depending on the region. In the electron microscopy images, the dorsal side of the wing exhibits varied number and thicknesses of the repeat units. The repeat unit spacings for the red, yellow/green, and blue regions are approximately 195, 180, and 145 nm, respectively. Three-dimensional analysis of the natural photonic crystals by time-of-flight secondary ion mass spectrometry reveals that changes in the relative levels of Na, K, and eumelanin are responsible for the varying dielectric constant needed to generate the photonic crystal. The photonic crystal also appears to be assembled with a chemical tricomponent layer structure due to the enhancement of the CH 6 N 3 + species at every other interface between the high/low dielectric constant layers.

Characterization of (CA)n microsatellite repeats from large-insert clones.

PubMed

Litt, M; Browne, D

2001-05-01

The most laborious part of developing (CA)n microsatellite repeats as genetic markers is constructing DNA clones to permit determination of sequences flanking the microsatellites. When cosmids or large-insert phage clones are used as primary sources of (CA)n repeat markers, they have traditionally been subcloned into plasmid vectors such as pUC18 or M13 mp 18/19 cloning vectors to obtain fragments of suitable size for DNA sequencing. This unit presents an alternative approach whereby a set of degenerate sequencing primers that anneal directly to (CA)n microsatellites can be used to determine sequences that are inaccessible with vector-derived primers. Because the primers anneal to the repeat and not to the vector, they can be used with subclones containing inserts of several kilobases and should, in theory, always give sequence in the regions directly flanking the repeat. Degeneracy at the 3 end of each of these primers prevents elongation of primers that have annealed out-of-register. The most laborious part of developing (CA)n microsatellite repeats as genetic markers is constructing DNA clones to permit.

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

PubMed Central

Anwar, Tamanna; Khan, Asad U

2006-01-01

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. Availability 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 PMID:17597863

Design ATE systems for complex assemblies

NASA Astrophysics Data System (ADS)

Napier, R. S.; Flammer, G. H.; Moser, S. A.

1983-06-01

The use of ATE systems in radio specification testing can reduce the test time by approximately 90 to 95 percent. What is more, the test station does not require a highly trained operator. Since the system controller has full power over all the measurements, human errors are not introduced into the readings. The controller is immune to any need to increase output by allowing marginal units to pass through the system. In addition, the software compensates for predictable, repeatable system errors, for example, cabling losses, which are an inherent part of the test setup. With no variation in test procedures from unit to unit, there is a constant repeatability factor. Preparing the software, however, usually entails considerable expense. It is pointed out that many of the problems associated with ATE system software can be avoided with the use of a software-intensive, or computer-intensive, system organization. Its goal is to minimize the user's need for software development, thereby saving time and money.

Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases

PubMed Central

Feschenko, Vladimir V.; Rajman, Luis A.; Lovett, Susan T.

2003-01-01

Rearrangements between tandemly repeated DNA sequences are a common source of genetic instability. Such rearrangements underlie several human genetic diseases. In many organisms, the mismatch-repair (MMR) system functions to stabilize repeats when the repeat unit is short or when sequence imperfections are present between the repeats. We show here that the action of single-stranded DNA (ssDNA) exonucleases plays an additional, important role in stabilizing tandem repeats, independent of their role in MMR. For perfect repeats of ≈100 bp in Escherichia coli that are not susceptible to MMR, exonuclease (Exo)-I, ExoX, and RecJ exonuclease redundantly inhibit deletion. Our data suggest that >90% of potential deletion events are avoided by the combined action of these three exonucleases. Imperfect tandem repeats, less prone to rearrangements, are stabilized by both the MMR-pathway and ssDNA-specific exonucleases. For 100-bp repeats containing four mispairs, ExoI alone aborts most deletion events, even in the presence of a functional MMR system. By genetic analysis, we show that the inhibitory effect of ssDNA exonucleases on deletion formation is independent of the MutS and UvrD proteins. Exonuclease degradation of DNA displaced during the deletion process may abort slipped misalignment. Exonuclease action is therefore a significant force in genetic stabilization of many forms of repetitive DNA. PMID:12538867

Rational design of alpha-helical tandem repeat proteins with closed architectures

PubMed Central

Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L.; Bradley, Philip

2015-01-01

Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials1,2. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks3,4. The overall architecture of tandem repeat protein structures – which is dictated by the internal geometry and local packing of the repeat building blocks – is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners5–9, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis10. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid11 repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the N- and C-termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering12–20, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that – to our knowledge – is not yet present in the protein structure database21. PMID:26675735

Tandem-repeat protein domains across the tree of life.

PubMed

Jernigan, Kristin K; Bordenstein, Seth R

2015-01-01

Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20-40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species.

Different mechanisms are involved in the transcriptional activation by yeast heat shock transcription factor through two different types of heat shock elements.

PubMed

Hashikawa, Naoya; Yamamoto, Noritaka; Sakurai, Hiroshi

2007-04-06

The hydrophobic repeat is a conserved structural motif of eukaryotic heat shock transcription factor (HSF) that enables HSF to form a homotrimer. Homotrimeric HSF binds to heat shock elements (HSEs) consisting of three inverted repeats of the sequence nGAAn. Sequences consisting of four or more nGAAn units are bound cooperatively by two HSF trimers. We show that in Saccharomyces cerevisiae cells oligomerization-defective Hsf1 is not able to bind HSEs with three units and is not extensively phosphorylated in response to stress; it is therefore unable to activate genes containing this type of HSE. Several lines of evidence indicate that oligomerization is a prerequisite for stress-induced hyperphosphorylation of Hsf1. In contrast, oligomerization and hyperphosphorylation are not necessary for gene activation via HSEs with four units. Intragenic suppressor screening of oligomerization-defective hsf1 showed that an interface between adjacent DNA-binding domains is important for the binding of Hsf1 to the HSE. We suggest that Saccharomyces cerevisiae HSEs with different structures are regulated differently; HSEs with three units require Hsf1 to be both oligomerized and hyperphosphorylated, whereas HSEs with four or more units do not require either.

CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.

PubMed

Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine

2008-07-01

Clustered regularly interspaced short palindromic repeat (CRISPR) elements are a particular family of tandem repeats present in prokaryotic genomes, in almost all archaea and in about half of bacteria, and which participate in a mechanism of acquired resistance against phages. They consist in a succession of direct repeats (DR) of 24-47 bp separated by similar sized unique sequences (spacers). In the large majority of cases, the direct repeats are highly conserved, while the number and nature of the spacers are often quite diverse, even among strains of a same species. Furthermore, the acquisition of new units (DR + spacer) was shown to happen almost exclusively on one side of the locus. Therefore, the CRISPR presents an interesting genetic marker for comparative and evolutionary analysis of closely related bacterial strains. CRISPRcompar is a web service created to assist biologists in the CRISPR typing process. Two tools facilitates the in silico investigation: CRISPRcomparison and CRISPRtionary. This website is freely accessible at http://crispr.u-psud.fr/CRISPRcompar/.

Inter- and intraobserver repeatability of the Salford Gait Tool: an observation-based clinical gait assessment tool.

PubMed

Toro, Brigitte; Nester, Christopher J; Farren, Pauline C

2007-03-01

To evaluate the inter- and intraobserver repeatability of the Salford Gait Tool (SF-GT), a new observation-based gait assessment tool for evaluating sagittal plane cerebral palsy (CP) gait. Masked comparative evaluation. University in the United Kingdom. A convenience sample of 23 pediatric physical therapists with varying degrees of clinical experience recruited from the Greater Manchester area. Participants viewed videotapes of the sagittal plane gait of 13 children and used the SF-GT to analyze their 13 different gait styles on 2 occasions. Eleven children had hemiplegic, diplegic, or quadriplegic CP and 2 were neurologically intact. Inter- and intraobserver repeatability of hip, knee, and ankle joint positions at 6 different phases of the gait cycle. The SF-GT demonstrated good interobserver (77%) and intraobserver (75%) repeatability. We have established that the SF-GT is a repeatable clinical assessment tool with which to guide the diagnosis, treatment planning, and evaluation of interventions by pediatric physical therapists of sagittal plane gait deviations in CP.

Poly(phenylene)-based anion exchange membrane

DOEpatents

Hibbs, Michael [Albuquerque, NM; Cornelius, Christopher J [Albuquerque, NM; Fujimoto, Cy H [Albuquerque, NM

2011-02-15

A poly(phenylene) compound of copolymers that can be prepared with either random or multiblock structures where a first polymer has a repeat unit with a structure of four sequentially connected phenyl rings with a total of 2 pendant phenyl groups and 4 pendant tolyl groups and the second polymer has a repeat unit with a structure of four sequentially connected phenyl rings with a total of 6 pendant phenyl groups. The second polymer has chemical groups attached to some of the pendant phenyl groups selected from CH.sub.3, CH.sub.2Br, and CH.sub.2N(CH.sub.3).sub.3Br groups. When at least one group is CH.sub.2N(CH.sub.3).sub.3Br, the material functions as an anion exchange membrane.

Comparison of current meters used for stream gaging

USGS Publications Warehouse

Fulford, Janice M.; Thibodeaux, Kirk G.; Kaehrle, William R.

1994-01-01

The U.S. Geological Survey (USGS) is field and laboratory testing the performance of several current meters used throughout the world for stream gaging. Meters tested include horizontal-axis current meters from Germany, the United Kingdom, and the People's Republic of China, and vertical-axis and electromagnetic current meters from the United States. Summarized are laboratory test results for meter repeatability, linearity, and response to oblique flow angles and preliminary field testing results. All current meters tested were found to under- and over-register velocities; errors usually increased as the velocity and angle of the flow increased. Repeatability and linearity of all meters tested were good. In the field tests, horizontal-axis meters, except for the two meters from the People's Republic of China, registered higher velocity than did the vertical-axis meters.

Repeated unit cell (RUC) approach for pure bending analysis of coronary stents.

PubMed

Ju, Feng; Xia, Zihui; Zhou, Chuwei

2008-08-01

Flexibility is one of the key properties of coronary stents. The objective of this paper is to characterize the bending behaviour of stents through finite element analysis with repeated unit cell (RUC) models. General periodic boundary conditions for the RUC under the pure bending condition are formulated. It is found that the proposed RUC approach can provide accurate numerical results of bending behaviour of stents with much less computational costs. Bending stiffness, post-yield bending behaviour and the relationship between moment and bending curvature are investigated for Palmaz-Schatz stents and stents with the V- and S-shaped links. It is found that the effect of link geometry on the bending behaviour of stent is significant. The behaviour of stents subjected to cyclic bending is also investigated.

Studies on the primary structure of short polysaccharides using SEC MALDI mass spectroscopy.

PubMed

Garozzo, D; Spina, E; Cozzolino, R; Cescutti, P; Fett, W F

2000-01-12

The introduction of size-exclusion chromatography (SEC) analysis of polysaccharides prior to MALDI mass spectroscopy accounts for the determination of the molecular mass of the repeating unit when neutral homopolymers are investigated. In the case of natural polysaccharides characterised by more complicated structural features (presence of non-carbohydrate substituents, charged groups, etc.), this mass value usually is in agreement with more than one sugar composition. Therefore, it is not sufficient to give the correct monosaccharidic composition of the polysaccharide investigated. To solve this problem, MALDI spectra were recorded on the permethylated sample and post-source decay experiments were performed on precursor ions. In this way, the composition (in terms of Hex, HexNAc, etc.), size and sequence of the repeating unit were determined.

Distinct C9orf72-Associated Dipeptide Repeat Structures Correlate with Neuronal Toxicity

PubMed Central

Krans, Amy; Sawaya, Michael R.; Paulson, Henry L.; Todd, Peter K.; Barmada, Sami J.; Ivanova, Magdalena I.

2016-01-01

Hexanucleotide repeat expansions in C9orf72 are the most common inherited cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The expansions elicit toxicity in part through repeat-associated non-AUG (RAN) translation of the intronic (GGGGCC)n sequence into dipeptide repeat-containing proteins (DPRs). Little is known, however, about the structural characteristics and aggregation propensities of the dipeptide units comprising DPRs. To address this question, we synthesized dipeptide units corresponding to the three sense-strand RAN translation products, analyzed their structures by circular dichroism, electron microscopy and dye binding assays, and assessed their relative toxicity when applied to primary cortical neurons. Short, glycine-arginine (GR)3 dipeptides formed spherical aggregates and selectively reduced neuronal survival compared to glycine-alanine (GA)3 and glycine-proline (GP)3 dipeptides. Doubling peptide length had little effect on the structure of GR or GP peptides, but (GA)6 peptides formed β-sheet rich aggregates that bound thioflavin T and Congo red yet lacked the typical fibrillar morphology of amyloids. Aging of (GA)6 dipeptides increased their β-sheet content and enhanced their toxicity when applied to neurons. We also observed that the relative toxicity of each tested dipeptide was proportional to peptide internalization. Our results demonstrate that different C9orf72-related dipeptides exhibit distinct structural properties that correlate with their relative toxicity. PMID:27776165

Stability of Tandem Repeats in the Drosophila Melanogaster HSR-Omega Nuclear RNA

PubMed Central

Hogan, N. C.; Slot, F.; Traverse, K. L.; Garbe, J. C.; Bendena, W. G.; Pardue, M. L.

1995-01-01

The Drosophila melanogaster Hsr-omega locus produces a nuclear RNA containing >5 kb of tandem repeat sequences. These repeats are unique to Hsr-omega and show concerted evolution similar to that seen with classical satellite DNAs. In D. melanogaster the monomer is ~280 bp. Sequences of 191/2 monomers differ by 8 +/- 5% (mean +/- SD), when all pairwise comparisons are considered. Differences are single nucleotide substitutions and 1-3 nucleotide deletions/insertions. Changes appear to be randomly distributed over the repeat unit. Outer repeats do not show the decrease in monomer homogeneity that might be expected if homogeneity is maintained by recombination. However, just outside the last complete repeat at each end, there are a few fragments of sequence similar to the monomer. The sequences in these flanking regions are not those predicted for sequences decaying in the absence of recombination. Instead, the fragmentation of the sequence homology suggests that flanking regions have undergone more severe disruptions, possibly during an insertion or amplification event. Hsr-omega alleles differing in the number of repeats are detected and appear to be stable over a few thousand generations; however, both increases and decreases in repeat numbers have been observed. The new alleles appear to be as stable as their predecessors. No alleles of less than ~5 kb nor more than ~16 kb of repeats were seen in any stocks examined. The evidence that there is a limit on the minimum number of repeats is consistent with the suggestion that these repeats are important in the function of the unusual Hsr-omega nuclear RNA. PMID:7540581

Development of PCR-RFP and DNA barcoding plastic markers for yellow toadflax and Dalmatian toadflax

Treesearch

Andrew Boswell

2013-01-01

Yellow toadflax and Dalmatian toadflax are problematic invasive plant species in North America. Yellow toadflax was introduced multiple times to the United States from Europe, beginning in the late 1600s. Dalmatian toadflax has similarly been repeatedly introduced to the United States, starting in 1874. Both species are known to inhabit disturbed areas, competing for...

Variation: Use It or Misuse It--Replication and Its Variants

ERIC Educational Resources Information Center

Drummond, Gordon B.; Vowler, Sarah L.

2012-01-01

In this article, the authors talk about variation and how variation between measurements may be reduced if sampling is not random. They also talk about replication and its variants. A replicate is a repeated measurement from the same experimental unit. An experimental unit is the smallest part of an experiment or a study that can be subject to a…

Analytical relationships for prediction of the mechanical properties of additively manufactured porous biomaterials

PubMed Central

Hedayati, Reza

2016-01-01

Abstract Recent developments in additive manufacturing techniques have motivated an increasing number of researchers to study regular porous biomaterials that are based on repeating unit cells. The physical and mechanical properties of such porous biomaterials have therefore received increasing attention during recent years. One of the areas that have revived is analytical study of the mechanical behavior of regular porous biomaterials with the aim of deriving analytical relationships that could predict the relative density and mechanical properties of porous biomaterials, given the design and dimensions of their repeating unit cells. In this article, we review the analytical relationships that have been presented in the literature for predicting the relative density, elastic modulus, Poisson's ratio, yield stress, and buckling limit of regular porous structures based on various types of unit cells. The reviewed analytical relationships are used to compare the mechanical properties of porous biomaterials based on different types of unit cells. The major areas where the analytical relationships have improved during the recent years are discussed and suggestions are made for future research directions. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 3164–3174, 2016. PMID:27502358

You Are What You Eat

MedlinePlus

... contents. Back to Top Sugars In chemistry, a polymer is a substance that contains repeating units: Polyester and many plastics are examples of synthetic polymers. Proteins, nucleic acids and carbohydrates are natural "biopolymers" ...

Ventilation-Perfusion Relationships Following Experimental Pulmonary Contusion

DTIC Science & Technology

2007-06-14

696.7 6.1 to 565.0 24.3 Hounsfield units ), as did VOL (4.3 0.5 to 33.5 3.2%). Multivariate linear regression of MGSD, VOL, VD/VT, and QS vs. PaO2...parenchyma was separated into four regions based on the Hounsfield unit (HU) ranges reported by Gattinoni et al. (23) via a segmentation process executed...determined by repeated measures ANOVA. CT, computed tomography; MGSD, mean gray-scale density of the entire lung by CT scan; HU, Hounsfield units

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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-..cap alpha..-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 ofmore » the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz /sup 1/H and 125-MHz /sup 13/C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent ..beta..-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-..cap alpha..-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-..cap alpha..-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants.« less

Characterization of a tandemly repeated DNA sequence family originally derived by retroposition of tRNA(Glu) in the newt.

PubMed

Nagahashi, S; Endoh, H; Suzuki, Y; Okada, N

1991-11-20

A previous report from this laboratory showed that in vitro transcription of total genomic DNA of the newt Cynopus pyrrhogaster resulted in a discrete sized 8 S RNA, which represented highly repetitive and transcribable sequences with a glutamic acid tRNA-like structure in the newt genome. We isolated four independent clones from a newt genomic library and determined the complete sequences of three 2000 to 2400 base-pair PstI fragments spanning the 8 S RNA gene. The glutamic acid tRNA-related segment in the 8 S RNA gene contains the CCA sequence expected as the 3' terminus of a tRNA molecule. Further, the 11 nucleotides located 13 nucleotides upstream from one of the two transcription initiation sites of the 8 S RNA were found to be repeated in the region upstream from the termination site, suggesting that the original unit, which is shorter than the 8 S RNA, was retrotransposed via cDNA intermediates from the PolIII transcript. In the upstream region of the 8 S RNA gene, a 360 nucleotide unit containing the glutamic acid tRNA-related segment was found to be duplicated (clones NE1 and NE10) or triplicated (clone NE3). Except for the difference in the number of the 360 nucleotide unit, the three sequences of the 2000 to 2400 base-pair PstI fragment were essentially the same with only a few mutations and minor deletions. Inverse polymerase chain reaction and sequence determination of the products, together with a Southern hybridization experiment, demonstrated that the family consists of a tandemly repeated unit of 3300, 3700 or 4100 base-pairs. Thus during evolution, this family in the newt was created by retroposition via cDNA intermediates, followed by duplication or triplication of the 360 nucleotide unit and multiplication of the 3300 to 4100 base-pair region at the DNA level.

Lipase polystyrene giant amphiphiles.

PubMed

Velonia, Kelly; Rowan, Alan E; Nolte, Roeland J M

2002-04-24

A new type of giant amphiphilic molecule has been synthesized by covalently connecting a lipase enzyme headgroup to a maleimide-functionalized polystyrene tail (40 repeat units). The resulting biohybrid forms catalytic micellar rods in water.

United States Air Force Summer Faculty Research Program (1984). Program Management Report. Volume 3

DTIC Science & Technology

1984-12-01

Database Design 蕄 Raman Spectroscopy of Dr. Boake L. Plessy Glycosaminoglycans from -* Bovine Cornea 117 Study of Control Mixer Concept Dr. Kuldip S...simultaneously in polarized and non -polarized controls were repeated three times at 260-64, 368-70, 604-8-13, 735-7-40, 1277-80, 1760, 1775, and 1820 or four...times at S240-2-4, 1020 and 1874-8-90. Pooling replicates from the non -polarized components, six controls and two cAMP treatments, events repeating

De novo identification of highly diverged protein repeats by probabilistic consistency.

PubMed

Biegert, A; Söding, J

2008-03-15

An estimated 25% of all eukaryotic proteins contain repeats, which underlines the importance of duplication for evolving new protein functions. Internal repeats often correspond to structural or functional units in proteins. Methods capable of identifying diverged repeated segments or domains at the sequence level can therefore assist in predicting domain structures, inferring hypotheses about function and mechanism, and investigating the evolution of proteins from smaller fragments. We present HHrepID, a method for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess internal sequence symmetry, such as outer membrane beta-barrels. HHrepID uses HMM-HMM comparison to exploit evolutionary information in the form of multiple sequence alignments of homologs. In contrast to a previous method, the new method (1) generates a multiple alignment of repeats; (2) utilizes the transitive nature of homology through a novel merging procedure with fully probabilistic treatment of alignments; (3) improves alignment quality through an algorithm that maximizes the expected accuracy; (4) is able to identify different kinds of repeats within complex architectures by a probabilistic domain boundary detection method and (5) improves sensitivity through a new approach to assess statistical significance. Server: http://toolkit.tuebingen.mpg.de/hhrepid; Executables: ftp://ftp.tuebingen.mpg.de/pub/protevo/HHrepID

Divergence in centromere structure distinguishes related genomes in Coix lacryma-jobi and its wild relative.

PubMed

Han, Yonghua; Wang, Guixiang; Liu, Zhao; Liu, Jinhua; Yue, Wei; Song, Rentao; Zhang, Xueyong; Jin, Weiwei

2010-02-01

Knowledge about the composition and structure of centromeres is critical for understanding how centromeres perform their functional roles. Here, we report the sequences of one centromere-associated bacterial artificial chromosome clone from a Coix lacryma-jobi library. Two Ty3/gypsy-class retrotransposons, centromeric retrotransposon of C. lacryma-jobi (CRC) and peri-centromeric retrotransposon of C. lacryma-jobi, and a (peri)centromere-specific tandem repeat with a unit length of 153 bp were identified. The CRC is highly homologous to centromere-specific retrotransposons reported in grass species. An 80-bp DNA region in the 153-bp satellite repeat was found to be conserved to centromeric satellite repeats from maize, rice, and pearl millet. Fluorescence in situ hybridization showed that the three repetitive sequences were located in (peri-)centromeric regions of both C. lacryma-jobi and Coix aquatica. However, the 153-bp satellite repeat was only detected on 20 out of the 30 chromosomes in C. aquatica. Immunostaining with an antibody against rice CENH3 indicates that the 153-bp satellite repeat and CRC might be both the major components for functional centromeres, but not all the 153-bp satellite repeats or CRC sequences are associated with CENH3. The evolution of centromeric repeats of C. lacryma-jobi during the polyploidization was discussed.

Androgen receptor polyglutamine repeat length affects receptor activity and C2C12 cell development.

PubMed

Sheppard, Ryan L; Spangenburg, Espen E; Chin, Eva R; Roth, Stephen M

2011-10-20

Testosterone (T) has an anabolic effect on skeletal muscle and is believed to exert its local effects via the androgen receptor (AR). The AR harbors a polymorphic stretch of glutamine repeats demonstrated to inversely affect receptor transcriptional activity in prostate and kidney cells. The effects of AR glutamine repeat length on skeletal muscle are unknown. In this study we examined the effect of AR CAG repeat length on AR function in C2C12 cells. AR expression vectors harboring 14, 24, and 33 CAG repeats were used to assess AR transcriptional activity. C2C12 cell proliferation, differentiation, gene expression, myotube formation, and myonuclear fusion index were assessed. Transcriptional activity increased with increasing repeat length and in response to testosterone (AR14 = 3.91 ± 0.26, AR24 = 25.21 ± 1.72, AR33 = 36.08 ± 3.22 relative light units; P < 0.001). Ligand activation was increased for AR33 (2.10 ± 0.04) compared with AR14 (1.54 ± 0.09) and AR24 (1.57 ± 0.05, P < 0.001). AR mRNA expression was elevated in each stably transfected line. AR33 cell proliferation (20,512.3 ± 1,024.0) was decreased vs. AR14 (27,604.17 ± 1,425.3; P < 0.001) after 72 h. Decreased CK activity in AR14 cells (54.9 ± 2.9 units/μg protein) in comparison to AR33 (70.8 ± 8.1) (P < 0.05) was noted. The myonuclear fusion index was lower for AR14 (15.21 ± 3.24%) and AR33 (9.97 ± 3.14%) in comparison to WT (35.07 ± 5.60%, P < 0.001). AR14 and AR33 cells also displayed atypical myotube morphology. RT-PCR revealed genotype differences in myostatin and myogenin expression. We conclude that AR polyglutamine repeat length is directly associated with transcriptional activity and alters the growth and development of C2C12 cells. This polymorphism may contribute to the heritability of muscle mass in humans.

Tandem-repeat protein domains across the tree of life

PubMed Central

Jernigan, Kristin K.

2015-01-01

Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species. PMID:25653910

Fluorinated monomers useful for preparing fluorinated polyquinoline polymers

NASA Technical Reports Server (NTRS)

Hendricks, Neil H. (Inventor)

1994-01-01

A new class of polymers is provided, as well as the monomers used for their preparation. The polymers provided in accordance with practice of the present invention include repeating units comprising one or more quinoline groups, wherein at least a portion of the repeating units includes a hexafluoroisopropylidene (6F) group or a 1-aryl-2,2,2-trifluoroethylidene (3F) group, or both. The hexafluoroisopropylidene group is referred to herein as a 6F group and has the following structure: ##STR1## The 6F group includes a tetravalent carbon atom bound to two trifluoromethyl moieties, with its other two bonds forming linkages in the polymer chain. The 1-aryl-2,2,2-trifluoroethylidene group is referred to herein as a 3F group and has the following structure: ##STR2## wherein Ar' is an aryl group.

[Structural organization of 5S ribosomal DNA of Rosa rugosa].

PubMed

Tynkevych, Iu O; Volkov, R A

2014-01-01

In order to clarify molecular organization of the genomic region encoding 5S rRNA in diploid species Rosa rugosa several 5S rDNA repeated units were cloned and sequenced. Analysis of the obtained sequences revealed that only one length variant of 5S rDNA repeated units, which contains intact promoter elements in the intergenic spacer region (IGS) and appears to be transcriptionally active is present in the genome. Additionally, a limited number of 5S rDNA pseudogenes lacking a portion of coding sequence and the complete IGS was detected. A high level of sequence similarity (from 93.7 to 97.5%) between the IGS of major 5S rDNA variants of East Asian R. rugosa and North American R. nitida was found indicating comparatively recent divergence of these species.

Polymer Brushes Containing Sulfonated Sugar Repeat Units: Synthesis, Characterization and In Vitro Testing of Blood Coagulation Activation

PubMed Central

Ayres, N.; Holt, D. J.; Jones, C.F.; Corum, L. E.; Grainger, D. W.

2009-01-01

A new polymer brush chemistry containing sulfonated carbohydrate repeat units has been synthesized from silicon substrates using ATRP methods and characterized both in bulk and using surface analysis. The polymer brush was designed to act as a mimic for the naturally occurring sulfonated glycosaminoglycan, heparin, commonly used for modifying blood-contacting surfaces both in vitro and in vivo. Surface analysis showed conversion of brush saccharide precursor chemistry to the desired sulfonated polymer product. The sulfonated polymer brush surface was further analyzed using three conventional in vitro tests for blood compatibility -- plasma recalcification times, complement activation, and thrombin generation. The sulfonated polymer brush films on silicon oxide wafers exhibited better assay performance in these blood component assays than the unsulfonated sugar functionalized polymer brush in all tests performed. PMID:19859552

Molecular Structure Controlled Transitions between Free-Charge Generation and Trap Formation in a Conjugated Copolymer Series

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandit, Bill; Jackson, Nicholas E.; Zheng, Tianyue

2016-03-03

Charge transfer copolymers, where each repeating unit has at least one “donor” and one “acceptor” block, have played important roles in recent advances in organic photovoltaic (OPV) devices, however design criteria for these materials are still not completely clear. Here we show that the well-recognized LUMO-LUMO energy off-set design criterion for OPV materials using a fullerene acceptor is challenged in a series of copolymers, PTRn (n = 3, 5, 7 and 9), where n is the number of fused aromatic rings in the “donor” block and thienothiophene is the “acceptor” block in each repeating unit. Photoexcitation dynamics of PTRn copolymersmore » in solution and BHJ (bulk heterojunction) films demonstrated that local push-pull interactions between the “donor” block and the “acceptor” block weakens with increasing n, whereas the LUMO-LUMO off-set between the polymer and PC71BM (Phenyl-C71-butyric acid methyl ester) increases. Such a counter intuitive trend can be explained by local energetics of each repeating unit as a function of n. The energetic changes transform the copolymer with strong local charge transfer character for efficient hole-electron separation to localized hole-electron pairs with low mobility, despite the apparent increase of the polymer/PC71BM LUMO-LUMO off-set. This suggests the importance of local charge transfer character in these copolymers in the initial exciton splitting dynamics, which could ultimately be reflected in the device performance.« less

The influence of polymer architecture on the assembly of poly(ethylene oxide) grafted C60 fullerene clusters in aqueous solution: a molecular dynamics simulation study.

PubMed

Hooper, Justin B; Bedrov, Dmitry; Smith, Grant D

2009-03-28

The effect of polymer architecture on the aggregation behavior of C60 fullerenes tethered with a single chain of poly(ethylene oxide) (PEO) in aqueous solution has been investigated using coarse-grained, implicit solvent molecular dynamics simulations. The PEO-grafted fullerenes were comprised of a single tether of 60 repeat units represented as a linear polymer, a three-arm star (20 repeat units/arm) or a six-arm star (10 repeat units/arm). Additionally, the influence of arm length on self-assembly of the PEO-fullerene conjugates was investigated for the three-arm stars. Self-assembly is driven by favorable fullerene-fullerene and fullerene-PEO interactions. Our simulations reveal that it should be possible to control the size and geometry of the self-assembled fullerene aggregates in water through variation of PEO architecture and PEO molecular weight. We found that aggregate size and shape could be understood qualitatively in terms of the packing parameter concept that has been employed for diblock polymer and surfactant self-assembly. Higher molecular weight PEO (longer arms) and more compact PEO (more arms for the same molecular weight) resulted in greater steric repulsion between fullerenes, engendering greater aggregate surface curvature and hence the formation of smaller, more spherically shaped aggregates. Finally, weak attractive interactions between PEO and the fullerenes were found to play an important role in determining aggregate shape, size and the dynamics of self-assembly.

Vibrational spectroscopic study of cationic phosphorus dendrimers with aminoethylpiperidine terminal groups

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Tripathi, V.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2018-04-01

Two generations of phosphoric dendrimers with piperidine functional groups were synthesized for use in biology and medicine. Neutral samples are soluble in organic solvents but after protonation these dendrimers become water soluble and can be used for biological experiments. The FTIR and FT Raman spectra of two generations of dendrimers Gi constructed from the cyclotriphosphazene core, repeating units sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd P(S)< and aminoethylpiperidine end groups sbnd NHsbnd (CH2)2sbnd C5NH11 were recorded. The study of the IR spectra shows that the NH groups form hydrogen bonds. The calculation of the molecular structure and vibrational spectra of the first generation dendrimer was performed by the method of DFT. This molecule has flat, repeating units and a plane of symmetry passing through the core. The calculation of the distribution of potential energy made it possible to classify the bands in the experimental spectra of dendrimers. Amine groups are manifested in the form of a band of NH stretching vibrations at 3389 cm-1 in the IR spectrum of G1. NH+ stretching bands located at 2646 and 2540 cm-1 in the IR spectrum of G2. The stretching vibrations of NH+ groups are noticeably shifted to low frequencies due to the formation of a hydrogen bond with the chlorine atom. The line at 1575 cm-1 in the Raman spectrum of G1 is characteristic for repeating units.

Advanced Technical Data Study

DTIC Science & Technology

1975-01-29

will shut down automatically when condenser high pressure causes Pressure Limit Control high pressure switch to release. Press START switch (3...power cable (1) from facility pow- er. Troubleshoot cooling unit, for HI-LOW pressure switch repeated cutout. Refer to AGE ECU Cooling Unit...acti- vate when loss of air flow oc- curred, the pressure switch (3) failed to open circuit. Adjust or replace pressure switch . Refer to

Are We Facing a "Literacy Surplus" in the Workforces of the United States and Canada? Research Note.

ERIC Educational Resources Information Center

Sticht, Thomas G.

In the United States and Canada alike, expressions of concern over the fact that the demand for skilled workers far exceeds the current supply have been heard repeatedly. However, several studies would seem to indicate that, as familiar as these claims about the supply and demand for skilled workers may be, they are very contentious. If a Hudson…

Knowledge and Understanding of 21st Century Skills through Educator Externships: Programs in Southern New England

ERIC Educational Resources Information Center

Gibson-Cayouette, Lizann R.

2010-01-01

An acute shortage of a competent, highly-skilled workforce faces the United States workplace. Studies and reports from 1983 to present, repeatedly state that the education system in the United States must change to prepare the emergent workforce for success in the 21st century global challenges of both post-secondary education and the workplace.…

Comparative Characterization of Complete and Truncated Forms of Lactobacillus amylovorus α-Amylase and Role of the C-Terminal Direct Repeats in Raw-Starch Binding

PubMed Central

Rodriguez Sanoja, R.; Morlon-Guyot, J.; Jore, J.; Pintado, J.; Juge, N.; Guyot, J. P.

2000-01-01

Two constructs derived from the α-amylase gene (amyA) of Lactobacillus amylovorus were expressed in Lactobacillus plantarum, and their expression products were purified, characterized, and compared. These products correspond to the complete (AmyA) and truncated (AmyAΔ) forms of α-amylase; AmyAΔ lacks the 66-kDa carboxyl-terminal direct-repeating-unit region. AmyA and AmyAΔ exhibit similar amylase activities towards a range of soluble substrates (amylose, amylopectin and α-cyclodextrin, and soluble starch). The specific activities of the enzymes towards soluble starch are similar, but the KM and Vmax values of AmyAΔ were slightly higher than those of AmyA, whereas the thermal stability of AmyAΔ was lower than that of AmyA. In contrast to AmyA, AmyAΔ is unable to bind to β-cyclodextrin and is only weakly active towards glycogen. More striking is the fact that AmyAΔ cannot bind or hydrolyze raw starch, demonstrating that the carboxyl-terminal repeating-unit domain of AmyA is required for raw-starch binding activity. PMID:10919790

FAT1 Gene Alteration in Facioscapulohumeral Muscular Dystrophy Type 1.

PubMed

Park, Hyung Jun; Lee, Wookjae; Kim, Se Hoon; Lee, Jung Hwan; Shin, Ha Young; Kim, Seung Min; Park, Kee Duk; Lee, Ji Hyun; Choi, Young Chul

2018-03-01

Facioscapulohumeral muscular dystrophy type 1 (FSHD1) is caused by contraction of the D4Z4 repeat array. Recent studies revealed that the FAT1 expression is associated with disease activity of FSHD, and the FAT1 alterations result in myopathy with a FSHD-like phenotype. We describe a 59-year-old woman with both contracted D4Z4 repeat units and a FAT1 mutation. Shoulder girdle muscle weakness developed at the age of 56 years, and was followed by proximal leg weakness. When we examined her at 59 years of age, she displayed asymmetric and predominant weakness of facial and proximal muscles. Muscle biopsy showed increased variation in fiber size and multifocal degenerating fibers with lymphocytic infiltration. Southern blot analysis revealed 8 D4Z4 repeat units, and targeted sequencing of modifier genes demonstrated the c.10331 A>G variant in the FAT1 gene. This FAT1 variant has previously been reported as pathogenic variant in a patient with FSHD-like phenotype. Our study is the first report of a FAT1 mutation in a FSHD1 patient, and suggests that FAT1 alterations might work as a genetic modifier. © Copyright: Yonsei University College of Medicine 2018.

Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results.

PubMed

Just, Rebecca S; Irwin, Jodi A

2018-05-01

Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for enhanced genotyping and mixture deconvolution, the sequence variation among same-length products must be utilized in some form. Here, we propose use of the longest uninterrupted stretch (LUS) in allele designations as a simple method to represent sequence variation within the STR repeat regions and facilitate - in the nearterm - probabilistic interpretation of NGS-based typing results. An examination of published population data indicated that a reference LUS region is straightforward to define for most autosomal STR loci, and that using repeat unit plus LUS length as the allele designator can represent greater than 80% of the alleles detected by sequencing. A proof of concept study performed using a freely available probabilistic software demonstrated that the LUS length can be used in allele designations when a program does not require alleles to be integers, and that utilizing sequence information improves interpretation of both single-source and mixed contributor STR typing results as compared to using repeat unit information alone. The LUS concept for allele designation maintains the repeat-based allele nomenclature that will permit backward compatibility to extant STR databases, and the LUS lengths themselves will be concordant regardless of the NGS assay or analysis tools employed. Further, these biologically based, easy-to-derive designations uphold clear relationships between parent alleles and their stutter products, enabling analysis in fully continuous probabilistic programs that model stutter while avoiding the algorithmic complexities that come with string based searches. Though using repeat unit plus LUS length as the allele designator does not capture variation that occurs outside of the core repeat regions, this straightforward approach would permit the large majority of known STR sequence variation to be used for mixture deconvolution and, in turn, result in more informative mixture statistics in the near term. Ultimately, the method could bridge the gap from current length-based probabilistic systems to facilitate broader adoption of NGS by forensic DNA testing laboratories. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Improving patient handover between teams using a business improvement model: PDSA cycle.

PubMed

Luther, Vishal; Hammersley, Daniel; Chekairi, Ahmed

2014-01-01

Medical admission units are continuously under pressure to move patients off the unit to outlying medical wards and allow for new admissions. In a typical district general hospital, doctors working in these medical wards reported that, on average, three patients each week arrived from the medical admission unit before any handover was received, and a further two patients arrived without any handover at all. A quality improvement project was therefore conducted using a 'Plan, Do, Study, Act' cycle model for improvement to address this issue. P - Plan: as there was no framework to support doctors with handover, a series of standard handover procedures were designed. D - Do: the procedures were disseminated to all staff, and championed by key stakeholders, including the clinical director and matron of the medical admission unit. S - STUDY: Measurements were repeated 3 months later and showed no change in the primary end points. A - ACT: The post take ward round sheet was redesigned, creating a checkbox for a medical admission unit doctor to document that handover had occurred. Nursing staff were prohibited from moving the patient off the ward until this had been completed. This later evolved into a separate handover sheet. Six months later, a repeat study revealed that only one patient each week was arriving before or without a verbal handover. Using a 'Plan, Do, Study, Act' business improvement tool helped to improve patient care.

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

NASA Astrophysics Data System (ADS)

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.

Improving Photovoltaic Performance of a Fused-Ring Azepinedione Copolymer via a D-A-A Design.

PubMed

Zhang, Honghong; Li, Ting; Xiao, Zuo; Lei, Zhongli; Ding, Liming

2018-04-01

Two conjugated copolymer donors, PTTABDT and PBTTABDT, based on a fused-ring azepinedione acceptor unit, 5-(2-octyldodecyl)-4H-thieno[2',3':4,5]thieno[3,2-c]thieno[2',3':4,5]thieno[2,3-e]azepine-4,6(5H)-dione (TTA), are prepared. PTTABDT possesses a conventional donor-acceptor (D-A) structure with one TTA in the repeat unit, while PBTTABDT has a D-A-A structure with two TTAs in the repeat unit. Compared with PTTABDT, PBTTABDT shows a deeper highest occupied molecular orbital (HOMO) level, a narrower bandgap, and a higher hole mobility, and exhibits better performance in bulk heterojunction solar cells. Power conversion efficiencies of 6.18% and 7.81% are achieved from PTTABDT:PC 71 BM and PBTTABDT:PC 71 BM solar cells, respectively. The higher performance of PBTTABDT:PC 71 BM solar cells results from the enhanced open-circuit voltage (V oc ) and short-circuit current density (  J sc ). © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

40 CFR 62.14685 - May I conduct a repeat performance test to establish new operating limits?

Code of Federal Regulations, 2011 CFR

2011-07-01

... DESIGNATED FACILITIES AND POLLUTANTS Federal Plan Requirements for Commercial and Industrial Solid Waste Incineration Units That Commenced Construction On or Before November 30, 1999 Continuous Compliance...

40 CFR 62.14685 - May I conduct a repeat performance test to establish new operating limits?

Code of Federal Regulations, 2010 CFR

2010-07-01

... DESIGNATED FACILITIES AND POLLUTANTS Federal Plan Requirements for Commercial and Industrial Solid Waste Incineration Units That Commenced Construction On or Before November 30, 1999 Continuous Compliance...

Fates of live trees retained in forest cutting units, western Cascade Range, Oregon.

Treesearch

P.E. Busby; P. Adler; T.L. Warren; F.J. Swanson

2006-01-01

To assess the fate of live trees retained in dispersed patterns across cutting units in the western Cascade Range of Oregon, we conducted repeat surveys (1993 and 2001) of sites cut as early as 1983. Our objectives in this study are to (1) survey survival and mortality of trees retained at the time of harvest, (2) describe temporal patterns of windthrow and other...

Web-Based Army Repeatable Lesson in Operational Combat (WARLOC)

DTIC Science & Technology

2014-06-01

United States Army B.A., St. John’s University, 1996 Austin T. Starken Captain, United States Army B.S., Florida Institute of Technology, 2005 Submitted...Simulation Games. New York, NY: Continuum International Publishing Group, 2012. [25] J. Peterson , Playing at the World: A History of Simulating Wars, People...Serious Games and Virtual Worlds in Education, Professional Development, and Healthcare. Ed. Hershey , PA: IGI Global, 2013. [Online]. Available

Analytical relationships for prediction of the mechanical properties of additively manufactured porous biomaterials.

PubMed

Zadpoor, Amir Abbas; Hedayati, Reza

2016-12-01

Recent developments in additive manufacturing techniques have motivated an increasing number of researchers to study regular porous biomaterials that are based on repeating unit cells. The physical and mechanical properties of such porous biomaterials have therefore received increasing attention during recent years. One of the areas that have revived is analytical study of the mechanical behavior of regular porous biomaterials with the aim of deriving analytical relationships that could predict the relative density and mechanical properties of porous biomaterials, given the design and dimensions of their repeating unit cells. In this article, we review the analytical relationships that have been presented in the literature for predicting the relative density, elastic modulus, Poisson's ratio, yield stress, and buckling limit of regular porous structures based on various types of unit cells. The reviewed analytical relationships are used to compare the mechanical properties of porous biomaterials based on different types of unit cells. The major areas where the analytical relationships have improved during the recent years are discussed and suggestions are made for future research directions. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 3164-3174, 2016. © 2016 The Authors Journal of Biomedical Materials Research Part A Published by Wiley Periodicals, Inc.

Design issues concerning Iran`s Bushehr nuclear power plant VVER-1000 conversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carson, C.F.

On January 8, 1995, the Atomic Energy Organization of Iran (AEOI) signed a contract for $800 million with the Russian Federation Ministry for Atomic Energy (Minatom) to complete Bushehr nuclear power plant (BNPP) unit 1. The agreement called for a Russian VVER-1000/320 pressurized water reactor (PWR) to be successfully installed into the existing German-built BNPP facilities in 5 yr. System design differences, bomb damage, and environmental exposure are key issues with which Minatom must contend in order to fulfill the contract. The AEOI under the Shah of Iran envisioned Bushehr as the first of many nuclear power plants, with Iranmore » achieving 24 GW(electric) by 1993 and 34 GW(electric) by 2000. Kraftwerk Union AG (KWU) began construction of the two-unit plant near the Persian Gulf town of Halileh in 1975. Unit 1 was {approx}80% complete and unit 2 was {approx}50% complete when construction was interrupted by the 1979 Iranian Islamic revolution. Despite repeated AEOI attempts to lure KWU and other companies back to Iran to complete the plant, Western concerns about nuclear proliferation in Iran and repeated bombings of the plant during the 1980-1988 Iran-Iraq war dissuaded Germany from resuming construction.« less

When Your Baby's in the NICU (Neonatal Intensive Care Unit)

MedlinePlus

... place? With equipment designed for infants and medical staff specially trained in newborn care, the NICU is ... without having to repeatedly stick the baby. NICU staff try to make the infants' stay in the ...

DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes

NASA Technical Reports Server (NTRS)

Smith, G. K.; Jie, J.; Fox, G. E.; Gao, X.

1995-01-01

DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 < [(CTG)3]2 << (CAG)3.(CTG)3. The (CTG)3 duplex is stable and exhibits similar NMR spectra in solutions containing 0.1-4 M NaCl and at a pH range from 4.6 to 8.8. The (CTG)3 duplex, which contains multiple-T.T mismatches, displays many NMR spectral characteristics similar to those of B-form DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

Dithiopheneindenofluorene (TIF) Semiconducting Polymers with Very High Mobility in Field-Effect Transistors.

PubMed

Chen, Hu; Hurhangee, Michael; Nikolka, Mark; Zhang, Weimin; Kirkus, Mindaugas; Neophytou, Marios; Cryer, Samuel J; Harkin, David; Hayoz, Pascal; Abdi-Jalebi, Mojtaba; McNeill, Christopher R; Sirringhaus, Henning; McCulloch, Iain

2017-09-01

The charge-carrier mobility of organic semiconducting polymers is known to be enhanced when the energetic disorder of the polymer is minimized. Fused, planar aromatic ring structures contribute to reducing the polymer conformational disorder, as demonstrated by polymers containing the indacenodithiophene (IDT) repeat unit, which have both a low Urbach energy and a high mobility in thin-film-transistor (TFT) devices. Expanding on this design motif, copolymers containing the dithiopheneindenofluorene repeat unit are synthesized, which extends the fused aromatic structure with two additional phenyl rings, further rigidifying the polymer backbone. A range of copolymers are prepared and their electrical properties and thin-film morphology evaluated, with the co-benzothiadiazole polymer having a twofold increase in hole mobility when compared to the IDT analog, reaching values of almost 3 cm 2 V -1 s -1 in bottom-gate top-contact organic field-effect transistors. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harstad, E. N.; Harlow, Francis Harvey,; Schreyer, H. L.

Our goal is to develop constitutive relations for the behavior of a solid polymer during high-strain-rate deformations. In contrast to the classic thermodynamic techniques for deriving stress-strain response in static (equilibrium) circumstances, we employ a statistical-mechanics approach, in which we evolve a probability distribution function (PDF) for the velocity fluctuations of the repeating units of the chain. We use a Langevin description for the dynamics of a single repeating unit and a Lioville equation to describe the variations of the PDF. Moments of the PDF give the conservation equations for a single polymer chain embedded in other similar chains. Tomore » extract single-chain analytical constitutive relations these equations have been solved for representative loading paths. By this process we discover that a measure of nonuniform chain link displacement serves this purpose very well. We then derive an evolution equation for the descriptor function, with the result being a history-dependent constitutive relation.« less

Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins

PubMed Central

Ichikawa, Muneyoshi; Liu, Dinan; Kastritis, Panagiotis L.; Basu, Kaustuv; Hsu, Tzu Chin; Yang, Shunkai; Bui, Khanh Huy

2017-01-01

Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the axoneme that consists of nine doublet microtubules radially interlinked and longitudinally organized in multiple specific repeat units. Little is known, however, about how the axoneme allows cilia to be both actively bendable and sturdy or how it is assembled. To answer these questions, we used cryo-electron microscopy to structurally analyse several of the repeating units of the doublet at sub-nanometre resolution. This structural detail enables us to unambiguously assign α- and β-tubulins in the doublet microtubule lattice. Our study demonstrates the existence of an inner sheath composed of different kinds of microtubule inner proteins inside the doublet that likely stabilizes the structure and facilitates the specific building of the B-tubule. PMID:28462916

The structure of cell adhesion molecule uvomorulin. Insights into the molecular mechanism of Ca2+-dependent cell adhesion.

PubMed Central

Ringwald, M; Schuh, R; Vestweber, D; Eistetter, H; Lottspeich, F; Engel, J; Dölz, R; Jähnig, F; Epplen, J; Mayer, S

1987-01-01

We have determined the amino acid sequence of the Ca2+-dependent cell adhesion molecule uvomorulin as it appears on the cell surface. The extracellular part of the molecule exhibits three internally repeated domains of 112 residues which are most likely generated by gene duplication. Each of the repeated domains contains two highly conserved units which could represent putative Ca2+-binding sites. Secondary structure predictions suggest that the putative Ca2+-binding units are located in external loops at the surface of the protein. The protein sequence exhibits a single membrane-spanning region and a cytoplasmic domain. Sequence comparison reveals extensive homology to the chicken L-CAM. Both uvomorulin and L-CAM are identical in 65% of their entire amino acid sequence suggesting a common origin for both CAMs. Images Fig. 1. Fig. 4. Fig. 7. PMID:3501370

The effect of repeated bouts of backward walking on physiologic efficiency.

PubMed

Childs, John D; Gantt, Christy; Higgins, Dan; Papazis, Janet A; Franklin, Ronald; Metzler, Terri; Underwood, Frank B

2002-08-01

Previous studies have demonstrated an increased energy expenditure with novel tasks. With practice, the energy cost decreases as the body more efficiently recruits motor units. This study examined whether one becomes more efficient after repeated bouts of backward walking. The subjects were 7 healthy subjects between the ages of 23 and 49 years. A backward walking speed was calculated to elicit a VO(2) equal to 60% of the VO(2)max. There were 18 training sessions at the prescribed walking speed 3 d x wk(-1) for 20 min x d(-1). The backward walking speed required to elicit a fixed VO(2) increased between weeks 4 and 6 of the training period. This finding suggests that backward walking is indeed a novel task and that motor learning occurs as a result of practice, leading to a more efficient recruitment of motor units.

Investigation of Micro-Scale Architectural Effects on Damage of Composites

NASA Technical Reports Server (NTRS)

Stier, Bertram; Bednarcyk, Brett A.; Simon, Jaan W.; Reese, Stefanie

2015-01-01

This paper presents a three-dimensional, energy based, anisotropic, stiffness reduction, progressive damage model for composite materials and composite material constituents. The model has been implemented as a user-defined constitutive model within the Abaqus finite element software package and applied to simulate the nonlinear behavior of a damaging epoxy matrix within a unidirectional composite material. Three different composite microstructures were considered as finite element repeating unit cells, with appropriate periodicity conditions applied at the boundaries. Results representing predicted transverse tensile, longitudinal shear, and transverse shear stress-strain curves are presented, along with plots of the local fields indicating the damage progression within the microstructure. It is demonstrated that the damage model functions appropriately at the matrix scale, enabling localization of the damage to simulate failure of the composite material. The influence of the repeating unit cell geometry and the effect of the directionality of the applied loading are investigated and discussed.

Physical and chemical properties of some new perfluoropolyalkylether lubricants prepared by direct fluorination

NASA Technical Reports Server (NTRS)

Jones, W. R., Jr.; Bierschenk, T. R.; Juhlke, T. J.; Kawa, H.; Lagow, R. J.

1993-01-01

A series of perfluoropolyalkylether (PFPAE) fluids was synthesized by direct fluorination. Viscosity-temperature properties, oxidation stabilities, oxidation-corrosion properties, bulk modulus, lubricity, surface tension and density were measured. It was shown that as the carbon to oxygen ratio in the polymer repeating unit decreases, the viscometric properties improve, the fluids may become poorer boundary lubricants, the bulk modulus increases, the surface tension increases and the fluid density increases. The presence of difluoromethylene oxide units in the polymer does not significantly lower the oxidation and oxidation-corrosion stabilities as long as the difluoromethylene oxide units are separated by other units.

Catecholamines of the adrenal medula and their morphological changes during adaptation to repeated immobilization stress

NASA Technical Reports Server (NTRS)

Kvetnansky, R.; Mitro, A.; Mikulaj, L.; Hocman, G.

1980-01-01

Changes of the adrenal medulla of rats were studied in the course of adaptation to repeated immobilization stress. An increase in the number of cells in the adrenal medulla was found in the adapted animals; this increase was confirmed by weight indices of the medulla and by cell counts per surface unit. Simultaneous karyometric measurements of the nuclei of adrenal medulla cells and an analysis of the catecholamine contents in the adrenals explain the increased activity of the adrenal medulla in the course of adaptation.

Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8.

PubMed

Ba Abdullah, Mohammed M; Palermo, Richard D; Palser, Anne L; Grayson, Nicholas E; Kellam, Paul; Correia, Samantha; Szymula, Agnieszka; White, Robert E

2017-12-01

Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified through both coevolution with its host and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging because of the large number and lengths of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat 1 of EBV (IR1; also known as the BamW repeats) for more than 70 strains. The diversity of the latency protein EBV nuclear antigen leader protein (EBNA-LP) resides predominantly within the exons downstream of IR1. The integrity of the putative BWRF1 open reading frame (ORF) is retained in over 80% of strains, and deletions truncating IR1 always spare BWRF1. Conserved regions include the IR1 latency promoter (Wp) and one zone upstream of and two within BWRF1. IR1 is heterogeneous in 70% of strains, and this heterogeneity arises from sequence exchange between strains as well as from spontaneous mutation, with interstrain recombination being more common in tumor-derived viruses. This genetic exchange often incorporates regions of <1 kb, and allelic gene conversion changes the frequency of small regions within the repeat but not close to the flanks. These observations suggest that IR1-and, by extension, EBV-diversifies through both recombination and breakpoint repair, while concerted evolution of IR1 is driven by gene conversion of small regions. Finally, the prototype EBV strain B95-8 contains four nonconsensus variants within a single IR1 repeat unit, including a stop codon in the EBNA-LP gene. Repairing IR1 improves EBNA-LP levels and the quality of transformation by the B95-8 bacterial artificial chromosome (BAC). IMPORTANCE Epstein-Barr virus (EBV) infects the majority of the world population but causes illness in only a small minority of people. Nevertheless, over 1% of cancers worldwide are attributable to EBV. Recent sequencing projects investigating virus diversity to see if different strains have different disease impacts have excluded regions of repeating sequence, as they are more technically challenging. Here we analyze the sequence of the largest repeat in EBV (IR1). We first characterized the variations in protein sequences encoded across IR1. In studying variations within the repeat of each strain, we identified a mutation in the main laboratory strain of EBV that impairs virus function, and we suggest that tumor-associated viruses may be more likely to contain DNA mixed from two strains. The patterns of this mixing suggest that sequences can spread between strains (and also within the repeat) by copying sequence from another strain (or repeat unit) to repair DNA damage. Copyright © 2017 Ba abdullah et al.

The origin of the split B800 absorption peak in the LH2 complexes from Allochromatium vinosum.

PubMed

Löhner, Alexander; Carey, Anne-Marie; Hacking, Kirsty; Picken, Nichola; Kelly, Sharon; Cogdell, Richard; Köhler, Jürgen

2015-01-01

The absorption spectrum of the high-light peripheral light-harvesting (LH) complex from the photosynthetic purple bacterium Allochromatium vinosum features two strong absorptions around 800 and 850 nm. For the LH2 complexes from the species Rhodopseudomonas acidophila and Rhodospirillum molischianum, where high-resolution X-ray structures are available, similar bands have been observed and were assigned to two pigment pools of BChl a molecules that are arranged in two concentric rings (B800 and B850) with nine (acidophila) or eight (molischianum) repeat units, respectively. However, for the high-light peripheral LH complex from Alc. vinosum, the intruiging feature is that the B800 band is split into two components. We have studied this pigment-protein complex by ensemble CD spectroscopy and polarisation-resolved single-molecule spectroscopy. Assuming that the high-light peripheral LH complex in Alc. vinosum is constructed on the same modular principle as described for LH2 from Rps. acidophila and Rsp. molischianum, we used those repeat units as a starting point for simulating the spectra. We find the best agreement between simulation and experiment for a ring-like oligomer of 12 repeat units, where the mutual arrangement of the B800 and B850 rings resembles those from Rsp. molischianum. The splitting of the B800 band can be reproduced if both an excitonic coupling between dimers of B800 molecules and their interaction with the B850 manifold are taken into account. Such dimers predict an interesting apoprotein organisation as discussed below.

Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins

PubMed Central

Jung, Huihun; Pena-Francesch, Abdon; Saadat, Alham; Sebastian, Aswathy; Kim, Dong Hwan; Hamilton, Reginald F.; Albert, Istvan; Allen, Benjamin D.; Demirel, Melik C.

2016-01-01

Many globular and structural proteins have repetitions in their sequences or structures. However, a clear relationship between these repeats and their contribution to the mechanical properties remains elusive. We propose a new approach for the design and production of synthetic polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions. Our designed sequences are based on a structural protein produced in squid suction cups that has a segmented copolymer structure with amorphous and crystalline domains. We produced segmented polypeptides with varying repeat number, while keeping the lengths and compositions of the amorphous and crystalline regions fixed. We showed that mechanical properties of these synthetic proteins could be tuned by modulating their molecular weights. Specifically, the toughness and extensibility of synthetic polypeptides increase as a function of the number of tandem repeats. This result suggests that the repetitions in native squid proteins could have a genetic advantage for increased toughness and flexibility. PMID:27222581

Plasmid P1 replication: negative control by repeated DNA sequences.

PubMed Central

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, pieces of the incA fragment that each contain only three repeats destabilize P1 plasmids efficiently. This result makes it unlikely that incA specifies a regulatory product. Our in vivo results suggest that the repeating DNA sequence itself negatively controls replication by titrating a P1-determined protein, RepA, that is essential for replication. Consistent with this hypothesis is the observation that the RepA protein binds to the incA fragment in vitro. Images PMID:6387706

Brittle deformation during Alpine basal accretion and the origin of seismicity nests above the subduction interface

NASA Astrophysics Data System (ADS)

Menant, Armel; Angiboust, Samuel; Monié, Patrick; Oncken, Onno; Guigner, Jean-Michel

2018-04-01

Geophysical observations on active subduction zones have evidenced high seismicity clusters at 20-40 km depth in the fore-arc region whose origin remains controversial. We report here field observations of pervasive pseudotachylyte networks (interpreted as evidence for paleo-seismicity) in the now-exhumed Valpelline continental unit (Dent Blanche complex, NW. Alps, Italy), a tectonic sliver accreted to the upper plate at c. 30 km depth during the Paleocene Alpine subduction. Pre-alpine granulite-facies paragneiss from the core of the Valpelline unit are crosscut by widespread, mm to cm-thick pseudotachylyte veins. Co-seismic heating and subsequent cooling led to the formation of Ti-rich garnet rims, ilmenite needles, Ca-rich plagioclase, biotite microliths and hercynite micro-crystals. 39Ar-40Ar dating yields a 51-54 Ma age range for these veins, thus suggesting that frictional melting events occurred near peak burial conditions while the Valpelline unit was already inserted inside the duplex structure. In contrast, the base of the Valpelline unit underwent synchronous ductile and brittle, seismic deformation under water-bearing conditions followed by a re-equilibration at c. 40 Ma (39Ar-40Ar on retrograded pseudotachylyte veins) during exhumation-related deformation. Calculated rheological profiles suggest that pseudotachylyte veins from the dry core of the granulite unit record upper plate micro-seismicity (Mw 2-3) formed under very high differential stresses (>500 MPa) while the sheared base of the unit underwent repeated brittle-ductile deformation at much lower differential stresses (<40 MPa) in a fluid-saturated environment. These results demonstrate that some of the seismicity clusters nested along and above the plate interface may reflect the presence of stiff tectonic slivers rheologically analogous to the Valpelline unit acting as repeatedly breaking asperities in the basal accretion region of active subduction zones.

Polymer matrix electroluminescent materials and devices

DOEpatents

Marrocco, III, Matthew L.; Motamedi, Farshad J [Claremont, CA; Abdelrazzaq, Feras Bashir [Covina, CA; Abdelrazzaq, legal representative, Bashir Twfiq

2012-06-26

Photoluminescent and electroluminescent compositions are provided which comprise a matrix comprising aromatic repeat units covalently coordinated to a phosphorescent or luminescent metal ion or metal ion complexes. Methods for producing such compositions, and the electroluminescent devices formed therefrom, are also disclosed.

Best Practices Handbook: Traffic Engineering in Range Networks

DTIC Science & Technology

2016-03-01

units of measurement. Measurement Methodology - A repeatable measurement technique used to derive one or more metrics of interest . Network...Performance measures - Metrics that provide quantitative or qualitative measures of the performance of systems or subsystems of interest . Performance Metric

"The Same Tragic History of the Oppressed Must Not Be Repeated": Exploring the Unique Approach to Social Justice of Dr. Mitsunori Misawa

ERIC Educational Resources Information Center

Nakabayashi, Hayato

2016-01-01

Originally from Japan, Dr. Mitsunori Misawa is a professor of the Higher and Adult Education program in the Department of Leadership at the College of Education, Health and Human Sciences, at the University of Memphis in the United States. This paper introduces what led Dr. Misawa to study and work in the United States, how he came to pursue an…

Repeated Exposure to Neurotoxic Levels of Chlorpyriphos Alters Hippocampal Expression of Neurotrophins and Neuropeptides

DTIC Science & Technology

2016-01-13

Institute for Science and Engineering, Oak Ridge, TN 37831, United States bUnited States Army Center for Environmental Health Research (USACEHR...online 13 January 2016 Keywords: Chlorpyrifos Cholinesterase inhibition Gene expression Microarray miRNA Organophosphorus pesticide A B S T R A C T...Chlorpyrifos (CPF), an organophosphorus pesticide (OP), is one of the most widely used pesticides in the world. Subchronic exposures to CPF that do not

21 CFR 522.1680 - Oxytocin injection.

Code of Federal Regulations, 2012 CFR

2012-04-01

... as conditions require: mL U.S.P. units Cats 0.25 to 0.5 5 to 10. Dogs 0.25 to 1.5 5 to 30. Ewes, Sows... desirable. The following dosage is recommended and may be repeated as conditions require: mL U.S.P. units Cows 0.5 to 1.0 10 to 20. Sows 0.25 to 1.0 5 to 20. (2) Indications for use. Oxytocin may be used as a...

A tactile-output paging communication system for the deaf-blind

NASA Technical Reports Server (NTRS)

Baer, J. A.

1979-01-01

A radio frequency paging communication system that has coded vibrotactile outputs suitable for use by deaf-blind people was developed. In concept, the system consists of a base station transmitting and receiving unit and many on-body transmitting and receiving units. The completed system has seven operating modes: fire alarm; time signal; repeated single character Morse code; manual Morse code; emergency aid request; operational status test; and message acknowledge. The on-body units can be addressed in three ways: all units; a group of units; or an individual unit. All the functions developed were integrated into a single package that can be worn on the user's wrist. The control portion of the on-body unit is implemented by a microcomputer. The microcomputer is packaged in a custom-designed hybrid circuit to reduce its physical size.

Expert assessment of physical ergonomics at video-display unit workstations: repeatability, validity and responsiveness to changes.

PubMed

Ketola, Ritva; Toivonen, Risto; Luukkonen, Ritva; Takala, Esa-Pekka; Viikari-Juntura, Eira

2004-08-01

Inter-observer repeatability, validity and responsiveness to change were determined for an expert assessment method for video-display unit (VDU) workstation ergonomics. The aim was to determine to what extent the expert assessment of ergonomics is related to the technical measurements, tidiness and space, work chair ergonomics and responds to changes in these characteristics. Technical measurements and video-recordings before and 2 months after an ergonomic intervention were made for 109 VDU office workstations. Two experts in ergonomics analysed and rated the ergonomics of the workstations. A researcher analysed tidiness and available space. A physiotherapist classified the work chairs used according to their ergonomic properties. The intra-class correlation coefficient between the workstation ergonomic ratings of the two experts was 0.74 at the baseline and 0.81 at the follow-up. Workstation tidiness and space, and work chair ergonomics, had a strong effect on the assessments of both experts. For both experts a change in the locations of the mouse, the screen and the keyboard and values of tidiness and space and work chair ergonomics during the intervention showed a significant association with the ratings. The assessment method studied can be utilized by an expert in a repeatable manner both in cross-sectional and in longitudinal settings.

Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin.

PubMed

Marques, André; Ribeiro, Tiago; Neumann, Pavel; Macas, Jiří; Novák, Petr; Schubert, Veit; Pellino, Marco; Fuchs, Jörg; Ma, Wei; Kuhlmann, Markus; Brandt, Ronny; Vanzela, André L L; Beseda, Tomáš; Šimková, Hana; Pedrosa-Harand, Andrea; Houben, Andreas

2015-11-03

Holocentric chromosomes lack a primary constriction, in contrast to monocentrics. They form kinetochores distributed along almost the entire poleward surface of the chromatids, to which spindle fibers attach. No centromere-specific DNA sequence has been found for any holocentric organism studied so far. It was proposed that centromeric repeats, typical for many monocentric species, could not occur in holocentrics, most likely because of differences in the centromere organization. Here we show that the holokinetic centromeres of the Cyperaceae Rhynchospora pubera are highly enriched by a centromeric histone H3 variant-interacting centromere-specific satellite family designated "Tyba" and by centromeric retrotransposons (i.e., CRRh) occurring as genome-wide interspersed arrays. Centromeric arrays vary in length from 3 to 16 kb and are intermingled with gene-coding sequences and transposable elements. We show that holocentromeres of metaphase chromosomes are composed of multiple centromeric units rather than possessing a diffuse organization, thus favoring the polycentric model. A cell-cycle-dependent shuffling of multiple centromeric units results in the formation of functional (poly)centromeres during mitosis. The genome-wide distribution of centromeric repeat arrays interspersing the euchromatin provides a previously unidentified type of centromeric chromatin organization among eukaryotes. Thus, different types of holocentromeres exist in different species, namely with and without centromeric repetitive sequences.

Characterization of a chromosome-specific chimpanzee alpha satellite subset: Evolutionary relationship to subsets on human chromosomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warburton, P.E.; Gosden, J.; Lawson, D.

1996-04-15

Alpha satellite DNA is a tandemly repeated DNA family found at the centromeres of all primate chromosomes examined. The fundamental repeat units of alpha satellite DNA are diverged 169- to 172-bp monomers, often found to be organized in chromosome-specific higher-order repeat units. The chromosomes of human (Homo sapiens (HSA)), chimpanzee (Pan troglodytes (PTR) and Pan paniscus), and gorilla (Gorilla gorilla) share a remarkable similarity and synteny. It is of interest to ask if alpha satellite arrays at centromeres of homologous chromosomes between these species are closely related (evolving in an orthologous manner) or if the evolutionary processes that homogenize andmore » spread these arrays within and between chromosomes result in nonorthologous evolution of arrays. By using PCR primers specific for human chromosome 17-specific alpha satellite DNA, we have amplified, cloned, and characterized a chromosome-specific subset from the PTR chimpanzee genome. Hybridization both on Southern blots and in situ as well as sequence analysis show that this subset is most closely related, as expected, to sequences on HSA 17. However, in situ hybridization reveals that this subset is not found on the homologous chromosome in chimpanzee (PTR 19), but instead on PTR 12, which is homologous to HSA 2p. 40 refs., 3 figs.« less

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

PubMed Central

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. PMID:14627198

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

PubMed

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.

Incidence, patterns, and predictors of repeat pregnancies among HIV-infected women in the United Kingdom and Ireland, 1990-2009

PubMed Central

French, Clare E; Cortina-Borja, Mario; Thorne, Claire; Tookey, Pat A

2011-01-01

Objective To explore the pattern of repeat pregnancies among diagnosed HIV-infected women in the UK and Ireland, estimate the rate of these sequential pregnancies, and investigate the demographic and clinical characteristics of women experiencing them. Design Diagnosed HIV-infected pregnant women are reported through an active confidential reporting scheme to the National Study of HIV in Pregnancy and Childhood. Methods Pregnancies occurring during 1990-2009 were included. Multivariable analyses were conducted fitting Cox proportional hazards models. Results There were 14,096 pregnancies in 10,568 women; 2737 (25.9%) had two or more pregnancies reported. The rate of repeat pregnancies was 6.7 (95% CI: 6.5-7.0) per 100 woman-years. The proportion of pregnancies in women who already had at least one pregnancy reported increased from 20.3% (32/158) in 1997 to 38.6% (565/1465) in 2009 (p<0.001). In multivariable analysis the probability of repeat pregnancy significantly declined with increasing age at first pregnancy. Parity was also inversely associated with repeat pregnancy. Compared with women born in the UK or Ireland, those from Europe, Eastern Africa, and Southern Africa were less likely to have a repeat pregnancy, while women from Middle Africa and Western Africa were more likely to. Maternal health at first pregnancy was not associated with repeat pregnancy. Conclusions The number of diagnosed HIV-infected women in the UK and Ireland experiencing repeat pregnancies is increasing. Variations in the probability of repeat pregnancies, according to demographic and clinical characteristics, are an important consideration when planning reproductive health services and HIV care for people living with HIV. PMID:22227490

Solution structure of a repeated unit of the ABA-1 nematode polyprotein allergen of Ascaris reveals a novel fold and two discrete lipid-binding sites.

PubMed

Meenan, Nicola A G; Ball, Graeme; Bromek, Krystyna; Uhrín, Dušan; Cooper, Alan; Kennedy, Malcolm W; Smith, Brian O

2011-04-19

Nematode polyprotein allergens (NPAs) are an unusual class of lipid-binding proteins found only in nematodes. They are synthesized as large, tandemly repetitive polyproteins that are post-translationally cleaved into multiple copies of small lipid binding proteins with virtually identical fatty acid and retinol (Vitamin A)-binding characteristics. They are probably central to transport and distribution of small hydrophobic compounds between the tissues of nematodes, and may play key roles in nutrient scavenging, immunomodulation, and IgE antibody-based responses in infection. In some species the repeating units are diverse in amino acid sequence, but, in ascarid and filarial nematodes, many of the units are identical or near-identical. ABA-1A is the most common repeating unit of the NPA of Ascaris suum, and is closely similar to that of Ascaris lumbricoides, the large intestinal roundworm of humans. Immune responses to NPAs have been associated with naturally-acquired resistance to infection in humans, and the immune repertoire to them is under strict genetic control. The solution structure of ABA-1A was determined by protein nuclear magnetic resonance spectroscopy. The protein adopts a novel seven-helical fold comprising a long central helix that participates in two hollow four-helical bundles on either side. Discrete hydrophobic ligand-binding pockets are found in the N-terminal and C-terminal bundles, and the amino acid sidechains affected by ligand (fatty acid) binding were identified. Recombinant ABA-1A contains tightly-bound ligand(s) of bacterial culture origin in one of its binding sites. This is the first mature, post-translationally processed, unit of a naturally-occurring tandemly-repetitive polyprotein to be structurally characterized from any source, and it belongs to a new structural class. NPAs have no counterparts in vertebrates, so represent potential targets for drug or immunological intervention. The nature of the (as yet) unidentified bacterial ligand(s) may be pertinent to this, as will our characterization of the unusual binding sites.

Medium-sized tandem repeats represent an abundant component of the Drosophila virilis genome.

PubMed

Abdurashitov, Murat A; Gonchar, Danila A; Chernukhin, Valery A; Tomilov, Victor N; Tomilova, Julia E; Schostak, Natalia G; Zatsepina, Olga G; Zelentsova, Elena S; Evgen'ev, Michael B; Degtyarev, Sergey K H

2013-11-09

Previously, we developed a simple method for carrying out a restriction enzyme analysis of eukaryotic DNA in silico, based on the known DNA sequences of the genomes. This method allows the user to calculate lengths of all DNA fragments that are formed after a whole genome is digested at the theoretical recognition sites of a given restriction enzyme. A comparison of the observed peaks in distribution diagrams with the results from DNA cleavage using several restriction enzymes performed in vitro have shown good correspondence between the theoretical and experimental data in several cases. Here, we applied this approach to the annotated genome of Drosophila virilis which is extremely rich in various repeats. Here we explored the combined approach to perform the restriction analysis of D. virilis DNA. This approach enabled to reveal three abundant medium-sized tandem repeats within the D. virilis genome. While the 225 bp repeats were revealed previously in intergenic non-transcribed spacers between ribosomal genes of D. virilis, two other families comprised of 154 bp and 172 bp repeats were not described. Tandem Repeats Finder search demonstrated that 154 bp and 172 bp units are organized in multiple clusters in the genome of D. virilis. Characteristically, only 154 bp repeats derived from Helitron transposon are transcribed. Using in silico digestion in combination with conventional restriction analysis and sequencing of repeated DNA fragments enabled us to isolate and characterize three highly abundant families of medium-sized repeats present in the D. virilis genome. These repeats comprise a significant portion of the genome and may have important roles in genome function and structural integrity. Therefore, we demonstrated an approach which makes possible to investigate in detail the gross arrangement and expression of medium-sized repeats basing on sequencing data even in the case of incompletely assembled and/or annotated genomes.

Scales of magmatic replenishment and differentiation on an intermediate spreading mid-ocean ridge segment: Endeavour, Juan de Fuca Ridge

NASA Astrophysics Data System (ADS)

Dreyer, B. M.; Gill, J.; Clague, D. A.

2016-12-01

The aggregate chemistry of mid-ocean ridge (MOR) basalts cannot be produced by fractional crystallization alone. Recent modeling suggests that repeated magmatic replenishment is required (O'Neill and Jenner, 2012; Coogan and O'Hara, 2015; Shorttle, 2015). Does this inference hold when considering recent advancements in characterizing geological/volcanological context, geochemical variability, and temporal parameters on the scale of individual lava units (Rubin et al., 2009)? We evaluate the scales of magmatic replenishment through examination of compositionally diverse lavas from the Endeavour segment of the Juan de Fuca (JdF) MOR interpreted as comagmatic or coeruptive based on robust geological (Clague et al., 2014), geochemical (Gill et al., 2016), and geochronological (Jamieson et al., 2013; Clague et al., 2014) evidence. This approach is similar to that used for historical MOR eruptions (Rubin et al., 2001). We identified 15 "chemomagmatic" units that are spatially proximate and chemically relatable and separable that collectively represent eruptions since 11ka. Some units may be single lava flows. Other units appear to have erupted batches intermittently over hundreds to thousands of years during which chemically dissimilar lava also erupted. Melt evolution was modeled using MELTS for units with reasonably broad major element variations. Fractional crystallization models can adequately reproduce most of the major and incompatible trace element behavior observed within each unit. Consistent differences in trace element ratios between units argue against intermixing. Thus, magmatic batches typically lie within analytical resolution of fractional crystallizing systems, notwithstanding growing evidence that magmatic systems are repeatedly replenished at the segment scale. Melting and mixing of heterogeneous mantle sources are responsible for the overall compositional diversity at Endeavour. Chemomagmatic units, in contrast, reflect smaller scale processing of magma after exiting the melt column during ascent through the crust. Age and spatial relationships among the chemomagmatic units reflect fluctuations in productivity and composition during assembly of primitive mantle melts and the geometry of networked magma-hosting reservoirs.

Complex structure of knob DNA on maize chromosome 9. Retrotransposon invasion into heterochromatin.

PubMed Central

Ananiev, E V; Phillips, R L; Rines, H W

1998-01-01

The recovery of maize (Zea mays L.) chromosome addition lines of oat (Avena sativa L.) from oat x maize crosses enables us to analyze the structure and composition of specific regions, such as knobs, of individual maize chromosomes. A DNA hybridization blot panel of eight individual maize chromosome addition lines revealed that 180-bp repeats found in knobs are present in each of these maize chromosomes, but the copy number varies from approximately 100 to 25, 000. Cosmid clones with knob DNA segments were isolated from a genomic library of an oat-maize chromosome 9 addition line with the help of the 180-bp knob-associated repeated DNA sequence used as a probe. Cloned knob DNA segments revealed a complex organization in which blocks of tandemly arranged 180-bp repeating units are interrupted by insertions of other repeated DNA sequences, mostly represented by individual full size copies of retrotransposable elements. There is an obvious preference for the integration of retrotransposable elements into certain sites (hot spots) of the 180-bp repeat. Sequence microheterogeneity including point mutations and duplications was found in copies of 180-bp repeats. The 180-bp repeats within an array all had the same polarity. Restriction maps constructed for 23 cloned knob DNA fragments revealed the positions of polymorphic sites and sites of integration of insertion elements. Discovery of the interspersion of retrotransposable elements among blocks of tandem repeats in maize and some other organisms suggests that this pattern may be basic to heterochromatin organization for eukaryotes. PMID:9691055

Unique molecular architecture of silk fibroin in the waxmoth, Galleria mellonella.

PubMed

Zurovec, Michal; Sehnal, Frantisek

2002-06-21

Proteins of silk fibers are characterized by reiterations of amino acid repeats. Physical properties of the fiber are determined by the amino acid composition, the complexity of repetitive units, and arrangement of these units into higher order arrays. Except for very short motifs of 6-10 residues, the length of repetitive units and the number of these units concatenated in higher order assemblies vary in all spider and lepidopteran silks analyzed so far. This paper describes an exceptional silk protein represented by the 500-kDa heavy chain fibroin (H-fibroin) of the waxmoth, Galleria mellonella. Its non-repetitive N-terminal (175 residues) and C-terminal (60 residues) parts, the overall gene organization, and the nucleotide sequence around the TATA box show that it is homologous to the H-fibroins of other Lepidoptera. However, over 95% of the protein consists of highly ordered repetitive structures that are unmatched in other species. The repetitive region includes 11 assemblies AB(1)AB(1)AB(1)AB(2)(AB(2))AB(2) of remarkably conserved polypeptide repeats A (63 amino acid residues), B(1) (43 residues), and B(2) (18 residues). The repeats contain a high proportion of Gly (31.6%), Ala (23.8%), Ser (18.1%), and of residues with long hydrophobic side chains (16% for Leu, Ile, and Val combined). The presence of the GLGGLG and SSAASAA(AA) motifs suggests formation of pleated beta-sheets and their stacking into crystallites. Conspicuous conservation of the apolar sequence VIVI followed by DD or ED is interpreted as indicating the importance of hydrophobicity and electrostatic charge in H-fibroin cross-linking. The environment of G. mellonella larvae within bee cultures requires continuous production of silk that must be both strong and elastic. The spectacular arrangement of the repetitive H-fibroin region apparently evolved to meet these requirements.

Community-based pedestrian safety training in virtual reality : a pragmatic trial.

DOT National Transportation Integrated Search

2015-06-01

Child pedestrian injuries are a leading cause of mortality and morbidity across the United States : and the world. Repeated practice at the cognitive-perceptual task of crossing a street may lead to : safer pedestrian behavior. Virtual reality offers...

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

PubMed

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 amino acid tandem repeat proteins and also from known cell wall proteins with repeat sequences. Several putative roles in plant physiology can be inferred from the characteristics found.

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

PubMed Central

2012-01-01

Background 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. Results 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. Conclusions 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 amino acid tandem repeat proteins and also from known cell wall proteins with repeat sequences. Several putative roles in plant physiology can be inferred from the characteristics found. PMID:23134664

Quantifying the atomic-level mechanics of single long physisorbed molecular chains.

PubMed

Kawai, Shigeki; Koch, Matthias; Gnecco, Enrico; Sadeghi, Ali; Pawlak, Rémy; Glatzel, Thilo; Schwarz, Jutta; Goedecker, Stefan; Hecht, Stefan; Baratoff, Alexis; Grill, Leonhard; Meyer, Ernst

2014-03-18

Individual in situ polymerized fluorene chains 10-100 nm long linked by C-C bonds are pulled vertically from an Au(111) substrate by the tip of a low-temperature atomic force microscope. The conformation of the selected chains is imaged before and after manipulation using scanning tunneling microscopy. The measured force gradient shows strong and periodic variations that correspond to the step-by-step detachment of individual fluorene repeat units. These variations persist at constant intensity until the entire polymer is completely removed from the surface. Calculations based on an extended Frenkel-Kontorova model reproduce the periodicity and magnitude of these features and allow us to relate them to the detachment force and desorption energy of the repeat units. The adsorbed part of the polymer slides easily along the surface during the pulling process, leading to only small oscillations as a result of the high stiffness of the fluorenes and of their length mismatch with respect to the substrate surface structure. A significant lateral force also is caused by the sequential detachment of individual units. The gained insight into the molecule-surface interactions during sliding and pulling should aid the design of mechanoresponsive nanosystems and devices.

Consistent and reproducible positioning in longitudinal imaging for phenotyping genetically modified swine

NASA Astrophysics Data System (ADS)

Hammond, Emily; Dilger, Samantha K. N.; Stoyles, Nicholas; Judisch, Alexandra; Morgan, John; Sieren, Jessica C.

2015-03-01

Recent growth of genetic disease models in swine has presented the opportunity to advance translation of developed imaging protocols, while characterizing the genotype to phenotype relationship. Repeated imaging with multiple clinical modalities provides non-invasive detection, diagnosis, and monitoring of disease to accomplish these goals; however, longitudinal scanning requires repeatable and reproducible positioning of the animals. A modular positioning unit was designed to provide a fixed, stable base for the anesthetized animal through transit and imaging. Post ventilation and sedation, animals were placed supine in the unit and monitored for consistent vitals. Comprehensive imaging was performed with a computed tomography (CT) chest-abdomen-pelvis scan at each screening time point. Longitudinal images were rigidly registered, accounting for rotation, translation, and anisotropic scaling, and the skeleton was isolated using a basic thresholding algorithm. Assessment of alignment was quantified via eleven pairs of corresponding points on the skeleton with the first time point as the reference. Results were obtained with five animals over five screening time points. The developed unit aided in skeletal alignment within an average of 13.13 +/- 6.7 mm for all five subjects providing a strong foundation for developing qualitative and quantitative methods of disease tracking.

Accuracy, repeatability, and reproducibility of Artemis very high-frequency digital ultrasound arc-scan lateral dimension measurements

PubMed Central

Reinstein, Dan Z.; Archer, Timothy J.; Silverman, Ronald H.; Coleman, D. Jackson

2008-01-01

Purpose To determine the accuracy, repeatability, and reproducibility of measurement of lateral dimensions using the Artemis (Ultralink LLC) very high-frequency (VHF) digital ultrasound (US) arc scanner. Setting London Vision Clinic, London, United Kingdom. Methods A test object was measured first with a micrometer and then with the Artemis arc scanner. Five sets of 10 consecutive B-scans of the test object were performed with the scanner. The test object was removed from the system between each scan set. One expert observer and one newly trained observer separately measured the lateral dimension of the test object. Two-factor analysis of variance was performed. The accuracy was calculated as the average bias of the scan set averages. The repeatability and reproducibility coefficients were calculated. The coefficient of variation (CV) was calculated for repeatability and reproducibility. Results The test object was measured to be 10.80 mm wide. The mean lateral dimension bias was 0.00 mm. The repeatability coefficient was 0.114 mm. The reproducibility coefficient was 0.026 mm. The repeatability CV was 0.38%, and the reproducibility CV was 0.09%. There was no statistically significant variation between observers (P = .0965). There was a statistically significant variation between scan sets (P = .0036) attributed to minor vertical changes in the alignment of the test object between consecutive scan sets. Conclusion The Artemis VHF digital US arc scanner obtained accurate, repeatable, and reproducible measurements of lateral dimensions of the size commonly found in the anterior segment. PMID:17081860

Analysis of the mechanical behavior of a titanium scaffold with a repeating unit-cell substructure.

PubMed

Ryan, Garrett; McGarry, Patrick; Pandit, Abhay; Apatsidis, Dimitrios

2009-08-01

Titanium scaffolds with controlled microarchitecture have been developed for load bearing orthopedic applications. The controlled microarchitecture refers to a repeating array of unit-cells, composed of sintered titanium powder, which make up the scaffold structure. The objective of this current research was to characterize the mechanical performance of three scaffolds with increasing porosity, using finite element analysis (FEA) and to compare the results with experimental data. Scaffolds were scanned using microcomputed tomography and FEA models were generated from the resulting computer models. Macroscale and unit-cell models of the scaffolds were created. The material properties of the sintered titanium powders were first evaluated in mechanical tests and the data used in the FEA. The macroscale and unit-cell FEA models proved to be a good predictor of Young's modulus and yield strength. Although macroscale models showed similar failure patterns and an expected trend in UCS, strain at UCS did not compare well with experimental data. Since a rapid prototyping method was used to create the scaffolds, the original CAD geometries of the scaffold were also evaluated using FEA but they did not reflect the mechanical properties of the physical scaffolds. This indicates that at present, determining the actual geometry of the scaffold through computed tomography imaging is important. Finally, a fatigue analysis was performed on the scaffold to simulate the loading conditions it would experience as a spinal interbody fusion device.

Long-term consequences of pain in human neonates.

PubMed

Grunau, Ruth E; Holsti, Liisa; Peters, Jeroen W B

2006-08-01

The low tactile threshold in preterm infants when they are in the neonatal intensive care unit (NICU), while their physiological systems are unstable and immature, potentially renders them more vulnerable to the effects of repeated invasive procedures. There is a small but growing literature on pain and tactile responsivity following procedural pain in the NICU, or early surgery. Long-term effects of repeated pain in the neonatal period on neurodevelopment await further research. However, there are multiple sources of stress in the NICU, which contribute to inducing high overall 'allostatic load', therefore determining specific effects of neonatal pain in human infants is challenging.

Possible reduced penetrance of expansion of 44 to 47 CAG/CAA repeats in the TATA-binding protein gene in spinocerebellar ataxia type 17.

PubMed

Oda, Masaya; Maruyama, Hirofumi; Komure, Osamu; Morino, Hiroyuki; Terasawa, Hideo; Izumi, Yuishin; Imamura, Tohru; Yasuda, Minoru; Ichikawa, Keiji; Ogawa, Masafumi; Matsumoto, Masayasu; Kawakami, Hideshi

2004-02-01

Spinocerebellar ataxia type 17 (SCA17) is an autosomal dominant cerebellar ataxia caused by expansion of CAG/CAA trinucleotide repeats in the TATA-binding protein (TBP) gene. Because the number of triplets in patients with SCA17 in previous studies ranged from 43 to 63, the normal number of trinucleotide units has been considered to be 42 or less. However, some healthy subjects in SCA17 pedigrees carry alleles with the same number of expanded repeats as patients with SCA17. To investigate the minimum number of CAG/CAA repeats in the TBP gene that causes SCA17. We amplified the region of the TBP gene containing the CAG/CAA repeat by means of polymerase chain reaction and performed fragment and sequence analyses. The subjects included 734 patients with SCA (480 patients with sporadic SCA and 254 patients with familial SCA) without CAG repeat expansions at the SCA1, SCA2, Machado-Joseph disease, SCA6, SCA7, or dentatorubral-pallidolluysian atrophy loci, with 162 healthy subjects, 216 patients with Parkinson disease, and 195 with Alzheimer disease as control subjects. Eight patients with SCA possessed an allele with more than 43 CAG/CAA repeats. Among the non-SCA groups, alleles with 43 to 45 repeats were seen in 3 healthy subjects and 2 with Parkinson disease. In 1 SCA pedigree, a patient with possible SCA17 and her healthy sister had alleles with 45 repeats. A 34-year-old man carrying alleles with 47 and 44 repeats (47/44) had developed progressive cerebellar ataxia and myoclonus at 25 years of age, and he exhibited dementia and pyramidal signs. He was the only affected person in his pedigree, although his father and mother carried alleles with mildly expanded repeats (44/36 and 47/36, respectively). In another pedigree, 1 patient carried a 43-repeat allele, whereas another patient had 2 normal alleles, indicating that the 43-repeat allele may not be pathologic in this family. We estimate that 44 CAG/CAA repeats is the minimum number required to cause SCA17. However, the existence of unaffected subjects with mildly expanded triplets suggests that the TBP gene mutation may not penetrate fully. Homozygosity of alleles with mildly expanded triplet repeats in the TBP gene might contribute to the pathologic phenotype.

History Never Repeats Itself

ERIC Educational Resources Information Center

Burawoy, Michael

2009-01-01

In his presidential address Jess Gilbert examines two democratic experiments of the United States Department of Agriculture (USDA) during the New Deal: first, county planning that coordinated federal programs through citizen committees, and second, land redistribution to landless southern farmers, including a small number of black sharecroppers…

Variations in Missed Care Across Oncology Nursing Specialty Units.

PubMed

Villamin, Colleen; Anderson, Jacqueline; Fellman, Bryan; Urbauer, Diana; Brassil, Kelly

2018-04-19

An opportunity was identified to compare perceptions of the occurrence and types of missed care at a comprehensive cancer center. The purpose was to evaluate the difference in perceived occurrence and types of missed care between medical, surgical, and hematologic oncology units in the context of a newly implemented patient care delivery system, Primary Team Nursing (PTN). A descriptive, repeated-measures design was used. The MISSCARE survey was distributed electronically to 580 staff members across 6 inpatient units. Frequently perceived elements of missed nursing care were ambulation, turning every 2 hours, and care conference attendance. At the time of study implementation, surgical units reported 0.24 higher scores than medical units (P = .017); hematology units reported 0.26 lower scores than surgical units (P = .005). PTN status did not affect MISSCARE scores (P = .525). Study findings suggest that perceived missed care in a comprehensive cancer center is similar to that in other hospital settings.

Vital signs monitoring system

NASA Technical Reports Server (NTRS)

Steffen, Dale A. (Inventor); Sturm, Ronald E. (Inventor); Rinard, George A. (Inventor)

1981-01-01

A system is disclosed for monitoring vital physiological signs. Each of the system components utilizes a single hybrid circuit with each component having high accuracy without the necessity of repeated calibration. The system also has low power requirements, provides a digital display, and is of sufficiently small size to be incorporated into a hand-carried case for portable use. Components of the system may also provide independent outputs making the component useful, of itself, for monitoring one or more vital signs. The overall system preferably includes an ECG amplifier and cardiotachometer signal conditioner unit, an impedance pneumograph and respiration rate signal conditioner unit, a heart/breath rate processor unit, a temperature monitoring unit, a selector switch, a clock unit, and an LCD driver unit and associated LCDs, with the system being capable of being expanded as needed or desired, such as, for example, by addition of a systolic/diastolic blood pressure unit.

[Visual acuity and magnification requirement after ranibizumab in patients with wet age-related macular degeneration].

PubMed

Kloos, P; Bernasconi, P; Estermann, S; Bachmann, B; Rutishauser, Y; Thölen, A

2008-05-01

The purpose of this study was to examine the visual outcome by measuring visual acuity (VA) and magnification requirement (MR) in patients with wet AMD after repeated intravitreal injections of ranibizumab. A total of 195 eyes were treated with repeated intravitreal injections of ranibizumab "as needed". VA (Snellen chart) and MR (SZB reading chart) at baseline of 114 eyes with occult or minimally classic lesions, 42 eyes with predominantly classic lesions and 39 with retinal angiomatous proliferations (RAP) were compared at 3 and 6 months after beginning of treatment. The whole group of 195 patients with wet AMD (688 intravitreal injections within 6 months) demonstrated a mean improvement of VA of 0.72 lines after 3 months (p < 0.001) and 1.54 lines after 6 months (p < 0.001) and a mean improvement of MR of 0.59 log units after 3 months (p < 0.001) and 0.73 log units after 6 months (p < 0.001). Mean change in VA after 3 and 6 months demonstrated a significant improvement (p < 0.001 to p < 0.05) for eyes with occult CNV (+ 0.8 /+ 1.6 lines) and RAP (+ 1.2 /+ 1.9 lines) whereas mean improvement in VA for classic CNV (+ 0.02 /+ 0.87 lines) did not reach significance compared to baseline. Comparable results were obtained for the mean change of MR after 3 and 6 months for eyes with occult CNV (+ 0.75 log units/+ 0.92 log units). For eyes with RAP mean improvement of MR was + 0.74 log units after 3 months (p < 0.05) and it was not significant with + 0.8 log units after 6 months (p > 0.05). MR did not show a significant change during follow-up for classic CNV. Apart from eyes with classic CNV, in more than 90 % of the eyes both VA and MR remained stable or improved (loss < 3 lines in VA or deterioration of MR of < 3 log units). Although 45 % of the eyes with predominantly classic CNV had received photodynamic therapies with Verteporfin prior to the intravitreal injections with ranibizumab, MR remained stable in 80 % over 6 months. With repeated injections of ranibizumab "as needed", VA could be improved as well as MR could be lowered in a majority of patients with wet AMD and therefore reading ability could be optimized. Over 6 months the treatment frequency was lower compared to the monthly administration.

Antigenic determinants of Staphylococcus aureus type 5 and type 8 capsular polysaccharide vaccines.

PubMed

Fattom, A I; Sarwar, J; Basham, L; Ennifar, S; Naso, R

1998-10-01

Bacterial capsular polysaccharides (CP) are carbohydrate polymers comprised of repeating saccharide units. Several of these CP have side chains attached to their backbone structures. The side chains may include O-acetyl, phosphate, sialic acid, and other moieties. Those moieties represent the immunodominant epitopes and the most functional ones. The clinically significant Staphylococcus aureus type 5 CP (CP 5) and type 8 CP (CP 8) are comprised of a trisaccharide repeat unit with one O-acetyl group attached to each repeat unit. The immunogenicity of these CP and the functionality of antibodies to the backbone and the O-acetyl moieties were investigated. Immunization with the native CP conjugates (CP with 75% O-acetylation) elicited a high proportion of antibodies directed against the O-acetyl moiety. Nonetheless, all of the vaccinees produced antibodies to the backbone moieties as well. Conjugate vaccines made of de-O-acetylated CP elicited backbone antibodies only. Antibodies to both backbone and O-acetyl groups were found to be opsonic against S. aureus strains which varied in their O-acetyl content. Absorption studies with O-acetylated and de-O-acetylated CP showed that (i) native CP conjugates generated antibodies to both backbone and O-acetyl groups and (ii) O-acetylated isolates were opsonized by both populations of antibodies while the non-O-acetylated strains were predominantly opsonized by the backbone antibodies. These results suggest that S. aureus CP conjugate vaccines elicit multiple populations of antibodies with diverse specificities. Moreover, the antibodies of different specificities (backbone or O-acetyl) are all functional and efficient against the variations in bacterial CP that may occur among clinically significant S. aureus pathogenic isolates.

Size and sequence polymorphisms in the glutamate-rich protein gene of the human malaria parasite Plasmodium falciparum in Thailand.

PubMed

Pattaradilokrat, Sittiporn; Trakoolsoontorn, Chawinya; Simpalipan, Phumin; Warrit, Natapot; Kaewthamasorn, Morakot; Harnyuttanakorn, Pongchai

2018-01-22

The glutamate-rich protein (GLURP) of the malaria parasite Plasmodium falciparum is a key surface antigen that serves as a component of a clinical vaccine. Moreover, the GLURP gene is also employed routinely as a genetic marker for malarial genotyping in epidemiological studies. While extensive size polymorphisms in GLURP are well recorded, the extent of the sequence diversity of this gene is rarely investigated. The present study aimed to explore the genetic diversity of GLURP in natural populations of P. falciparum. The polymorphic C-terminal repetitive R2 region of GLURP sequences from 65 P. falciparum isolates in Thailand were generated and combined with the data from 103 worldwide isolates to generate a GLURP database. The collection was comprised of 168 alleles, encoding 105 unique GLURP subtypes, characterized by 18 types of amino acid repeat units (AAU). Of these, 28 GLURP subtypes, formed by 10 AAU types, were detected in P. falciparum in Thailand. Among them, 19 GLURP subtypes and 2 AAU types are described for the first time in the Thai parasite population. The AAU sequences were highly conserved, which is likely due to negative selection. Standard Fst analysis revealed the shared distributions of GLURP types among the P. falciparum populations, providing evidence of gene flow among the different demographic populations. Sequence diversity causing size variations in GLURP in Thai P. falciparum populations were detected, and caused by non-synonymous substitutions in repeat units and some insertion/deletion of aspartic acid or glutamic acid codons between repeat units. The P. falciparum population structure based on GLURP showed promising implications for the development of GLURP-based vaccines and for monitoring vaccine efficacy.

Sexuality and Intellectual Disability.

PubMed

Wenger, Jodi; Downes, Alison; Blum, Nathan; Augustyn, Marilyn

2015-10-01

Amad is a wonderful 16-year-old young man from Syria who has recently relocated to the United States from his war-torn native country. In his last few years in Syria, he was primarily at home with his mother, and they sought refuge with a maternal aunt in the United States seeking asylum and treatment of Amad's disability. At 8 years of age, he had intelligence testing in the United Arab Emirates, which showed a verbal intelligence score on the Wechsler intelligence scale for children (WISC) of 68 and a performance of 64. His working memory was 67 and his processing speed was 65. On arrival in the United States, his achievement was roughly at a third-grade level in Arabic. In the year and a half that he has been in the United States, he quickly improved his English skills, which he learned as a toddler. His father remains in Syria unable to safely immigrate and his mother is raising him alone in the United States with the help of her sister. They come to you for an urgent care visit because Amad recently was accused of sexual harassment by two girls at his high school. He is in a substantially separate program but is included for lunch and technology. While in the computer laboratory, he repeatedly approached the girls and asks them to "date" him, and on 1 occasion sat behind 1 girl and repeatedly reached out to stroke her long blonde hair. His mother is distraught because she recently found out that Amad also has a Facebook page and had been attempting to contact the same two girls on social media. The girls' parents recently threatened to file criminal harassment charges and Amad's mother comes to you asking for help with making Amad stop this activity. What would you do next?

Sexuality and Intellectual Disability.

PubMed

Wenger, Jodi; Downes, Alison; Blum, Nathan; Augustyn, Marilyn

Amad is a wonderful 16-year-old young man from Syria who has recently relocated to the United States from his war-torn native country. In his last few years in Syria, he was primarily at home with his mother, and they sought refuge with a maternal aunt in the United States seeking asylum and treatment of Amad's disability.At 8 years of age, he had intelligence testing in the United Arab Emirates, which showed a verbal intelligence score on the Wechsler intelligence scale for children (WISC) of 68 and a performance of 64. His working memory was 67 and his processing speed was 65. On arrival in the United States, his achievement was roughly at a third-grade level in Arabic. In the year and a half that he has been in the United States, he quickly improved his English skills, which he learned as a toddler. His father remains in Syria unable to safely immigrate and his mother is raising him alone in the United States with the help of her sister.They come to you for an urgent care visit because Amad recently was accused of sexual harassment by two girls at his high school. He is in a substantially separate program but is included for lunch and technology. While in the computer laboratory, he repeatedly approached the girls and asks them to "date" him, and on 1 occasion sat behind 1 girl and repeatedly reached out to stroke her long blonde hair.His mother is distraught because she recently found out that Amad also has a Facebook page and had been attempting to contact the same two girls on social media. The girls' parents recently threatened to file criminal harassment charges and Amad's mother comes to you asking for help with making Amad stop this activity. What would you do next?

A Self-Paced Physical Geology Laboratory.

ERIC Educational Resources Information Center

Watson, Donald W.

1983-01-01

Describes a self-paced geology course utilizing a diversity of instructional techniques, including maps, models, samples, audio-visual materials, and a locally developed laboratory manual. Mechanical features are laboratory exercises, followed by unit quizzes; quizzes are repeated until the desired level of competence is attained. (Author/JN)

Distribution of the FMR1 gene in females by race/ethnicity: women with diminished ovarian reserve versus women with normal fertility (SWAN study).

PubMed

Pastore, Lisa M; Young, Steven L; Manichaikul, Ani; Baker, Valerie L; Wang, Xin Q; Finkelstein, Joel S

2017-01-01

To study whether reported, but inconsistent, associations between the FMR1 CGG repeat lengths in the intermediate, high normal, or low normal range differentiate women diagnosed with diminished ovarian reserve (DOR) from population controls and whether associations vary by race/ethnic group. Case-control study. Academic and private fertility clinics. DOR cases (n = 129; 95 Whites, 22 Asian, 12 other) from five U.S. fertility clinics were clinically diagnosed, with regular menses and no fragile X syndrome family history. Normal fertility controls (n = 803; 386 Whites, 219 African-Americans, 102 Japanese, 96 Chinese) from the United States-based SWAN Study had one or more menstrual period in the 3 months pre-enrollment, one or more pregnancy, no history of infertility or hormone therapy, and menopause ≥46 years. Previously, the SWAN Chinese and Japanese groups had similar FMR1 CGG repeat lengths, thus they were combined. None. FMR1 CGG repeat lengths. Median CGG repeats were nearly identical by case/control group. DOR cases had fewer CGG repeats in the shorter FMR1 allele than controls among Whites, but this was not significant among Asians. White cases had fewer CGG repeats in the shorter allele than Asian cases. No significant differences were found in the high normal/intermediate range between cases and controls or by race/ethnic group within cases in the longer allele. This study refutes prior reports of an association between DOR and high normal/intermediate repeats and confirms an association between DOR and low normal repeats in Whites. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Declining trend in the use of repeat computed tomography for trauma patients admitted to a level I trauma center for traffic-related injuries.

PubMed

Psoter, Kevin J; Roudsari, Bahman S; Graves, Janessa M; Mack, Christopher; Jarvik, Jeffrey G

2013-06-01

To evaluate the trend in utilization of repeat (i.e. ≥2) computed tomography (CT) and to compare utilization patterns across body regions for trauma patients admitted to a level I trauma center for traffic-related injuries (TRI). We linked the Harborview Medical Center trauma registry (1996-2010) to the billing department data. We extracted the following variables: type and frequency of CTs performed, age, gender, race/ethnicity, insurance status, injury mechanism and severity, length of hospitalization, intensive care unit (ICU) admission and final disposition. TRIs were defined as motor vehicle collisions, motorcycle, bicycle and pedestrian-related injuries. Logistic regression was used to evaluate the association between utilization of different body region repeat (i.e. ≥2) CTs and year of admission, adjusting for patient and injury-related characteristics that could influence utilization patterns. A total of 28,431 patients were admitted for TRIs over the study period and 9499 (33%) received repeat CTs. From 1996 to 2010, the proportion of patients receiving repeat CTs decreased by 33%. Relative to 2000 and adjusting for other covariates, patients with TRIs admitted in 2010 had significantly lower odds of undergoing repeat head (OR=0.61; 95% CI: 0.49-0.76), pelvis (OR=0.37; 95% CI: 0.27-0.52), cervical spine (OR=0.23; 95% CI: 0.12-0.43), and maxillofacial CTs (OR=0.24; 95% CI: 0.10-0.57). However, they had higher odds of receiving repeat thoracic CTs (OR=1.86; 95% CI: 1.02-3.38). A significant decrease in the utilization of repeat CTs was observed in trauma patients presenting with traffic-related injuries over a 15-year period. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7.

PubMed

Vogler, Amy J; Keys, Christine; Nemoto, Yoshimi; Colman, Rebecca E; Jay, Zack; Keim, Paul

2006-06-01

Variable-number tandem repeat (VNTR) loci have shown a remarkable ability to discriminate among isolates of the recently emerged clonal pathogen Escherichia coli O157:H7, making them a very useful molecular epidemiological tool. However, little is known about the rates at which these sequences mutate, the factors that affect mutation rates, or the mechanisms by which mutations occur at these loci. Here, we measure mutation rates for 28 VNTR loci and investigate the effects of repeat copy number and mismatch repair on mutation rate using in vitro-generated populations for 10 E. coli O157:H7 strains. We find single-locus rates as high as 7.0 x 10(-4) mutations/generation and a combined 28-locus rate of 6.4 x 10(-4) mutations/generation. We observed single- and multirepeat mutations that were consistent with a slipped-strand mispairing mutation model, as well as a smaller number of large repeat copy number mutations that were consistent with recombination-mediated events. Repeat copy number within an array was strongly correlated with mutation rate both at the most mutable locus, O157-10 (r2= 0.565, P = 0.0196), and across all mutating loci. The combined locus model was significant whether locus O157-10 was included (r2= 0.833, P < 0.0001) or excluded (r2= 0.452, P < 0.0001) from the analysis. Deficient mismatch repair did not affect mutation rate at any of the 28 VNTRs with repeat unit sizes of >5 bp, although a poly(G) homomeric tract was destabilized in the mutS strain. Finally, we describe a general model for VNTR mutations that encompasses insertions and deletions, single- and multiple-repeat mutations, and their relative frequencies based upon our empirical mutation rate data.

Modelling of Fiber/Matrix Debonding of Composites Under Cyclic Loading

NASA Technical Reports Server (NTRS)

Naghipour, Paria; Pineda, Evan J.; Bednarcyk, Brett A.; Arnold, Steven M.

2013-01-01

The micromechanics theory, generalized method of cells (GMC), was employed to simulate the debonding of fiber/matrix interfaces, within a repeating unit cell subjected to global, cyclic loading, utilizing a cyclic crack growth law. Cycle dependent, interfacial debonding was implemented as a new module to the available GMC formulation. The degradation of interfacial stresses, with applied load cycles, was achieved via progressive evolution of the interfacial compliance. A periodic repeating unit cell, representing the fiber/matrix architecture of a composite, was subjected to combined normal and shear loadings, and degradation of the global transverse stress in successive cycles was monitored. The obtained results were compared to values from a corresponding finite element model. Reasonable agreement was achieved for combined normal and shear loading conditions, with minimal variation for pure loading cases. The local effects of interfacial debonding, and fatigue damage will later be combined as sub-models to predict the experimentally obtained fatigue life of Ti-15-3/Sic composites at the laminate level.

Framework for measuring adaptive knowledge-rich systems performance.

PubMed

Bushko, Renata G

2005-01-01

The universe is non repeatable in nature--most of events cannot be prestated and do not repeat themselves. The only way to create systems that are truly useful is to make them adaptive (able to reason by analogy and learn) and rich in knowledge (including common sense knowledge). Adaptive and knowledge-rich health management could get us closer to errorless health care where small incremental adjustments happen all the time preventing occurrence of an error. In the era of adaptive systems we need to have a way to evaluate their performance. Are they truly adaptive? How adaptive are they? Are they accurate enough? Are they fast enough? Are they cost effective? This chapter presents general framework for measuring adaptive knowledge-rich systems' performance and includes among others definitions of adaptiveness factor, britt (a unit of brittleness) and uso-quant (unit of usefulness of a piece of knowledge). Measuring adaptive knowledge-rich systems performance is one of the most important research areas that can have a big pay-off in healthcare now and in the future.

Porous Cross-Linked Polyimide-Urea Networks

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor); Nguyen, Baochau N. (Inventor)

2015-01-01

Porous cross-linked polyimide-urea networks are provided. The networks comprise a subunit comprising two anhydride end-capped polyamic acid oligomers in direct connection via a urea linkage. The oligomers (a) each comprise a repeating unit of a dianhydride and a diamine and a terminal anhydride group and (b) are formulated with 2 to 15 of the repeating units. The subunit was formed by reaction of the diamine and a diisocyanate to form a diamine-urea linkage-diamine group, followed by reaction of the diamine-urea linkage-diamine group with the dianhydride and the diamine to form the subunit. The subunit has been cross-linked via a cross-linking agent, comprising three or more amine groups, at a balanced stoichiometry of the amine groups to the terminal anhydride groups. The subunit has been chemically imidized to yield the porous cross-linked polyimide-urea network. Also provided are wet gels, aerogels, and thin films comprising the networks, and methods of making the networks.

Porous Cross-Linked Polyimide Networks

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor); Guo, Haiquan (Inventor)

2015-01-01

Porous cross-linked polyimide networks are provided. The networks comprise an anhydride end-capped polyamic acid oligomer. The oligomer (i) comprises a repeating unit of a dianhydride and a diamine and terminal anhydride groups, (ii) has an average degree of polymerization of 10 to 50, (iii) has been cross-linked via a cross-linking agent, comprising three or more amine groups, at a balanced stoichiometry of the amine groups to the terminal anhydride groups, and (iv) has been chemically imidized to yield the porous cross-linked polyimide network. Also provided are porous cross-linked polyimide aerogels comprising a cross-linked and imidized anhydride end-capped polyamic acid oligomer, wherein the oligomer comprises a repeating unit of a dianhydride and a diamine, and the aerogel has a density of 0.10 to 0.333 g/cm.sup.3 and a Young's modulus of 1.7 to 102 MPa. Also provided are thin films comprising aerogels, and methods of making porous cross-linked polyimide networks.

Carbon-bridged oligo(p-phenylenevinylene)s for photostable and broadly tunable, solution-processable thin film organic lasers

PubMed Central

Morales-Vidal, Marta; Boj, Pedro G.; Villalvilla, José M.; Quintana, José A.; Yan, Qifan; Lin, Nai-Ti; Zhu, Xiaozhang; Ruangsupapichat, Nopporn; Casado, Juan; Tsuji, Hayato; Nakamura, Eiichi; Díaz-García, María A.

2015-01-01

Thin film organic lasers represent a new generation of inexpensive, mechanically flexible devices for spectroscopy, optical communications and sensing. For this purpose, it is desired to develop highly efficient, stable, wavelength-tunable and solution-processable organic laser materials. Here we report that carbon-bridged oligo(p-phenylenevinylene)s serve as optimal materials combining all these properties simultaneously at the level required for applications by demonstrating amplified spontaneous emission and distributed feedback laser devices. A series of six compounds, with the repeating unit from 1 to 6, doped into polystyrene films undergo amplified spontaneous emission from 385 to 585 nm with remarkably low threshold and high net gain coefficients, as well as high photostability. The fabricated lasers show narrow linewidth (<0.13 nm) single mode emission at very low thresholds (0.7 kW cm−2), long operational lifetimes (>105 pump pulses for oligomers with three to six repeating units) and wavelength tunability across the visible spectrum (408–591 nm). PMID:26416643

Biosynthetic elongation of isolated teichuronic acid polymers via glucosyl- and N-acetylmannosaminuronosyltransferases from solubilized cytoplasmic membrane fragments of Micrococcus luteus.

PubMed Central

Hildebrandt, K M; Anderson, J S

1990-01-01

Cytoplasmic membrane fragments of Micrococcus luteus catalyze in vitro biosynthesis of teichuronic acid from uridine diphosphate D-glucose (UDP-glucose), uridine diphosphate N-acetyl-D-mannosaminuronic acid (UDP-ManNAcA), and uridine diphosphate N-acetyl-D-glucosamine. Membrane fragments solubilized with Thesit (dodecyl alcohol polyoxyethylene ether) can utilize UDP-glucose and UDP-ManNAcA to effect elongation of teichuronic acid isolated from native cell walls. When UDP-glucose is the only substrate supplied, the detergent-solubilized glucosyltransferase incorporates a single glucosyl residue onto each teichuronic acid acceptor. When both UDP-glucose and UDP-ManNAcA are supplied, the glucosyltransferase and the N-acetylmannosaminuronosyltransferase act cooperatively to elongate the teichuronic acid acceptor by multiple additions of the disaccharide repeat unit. As shown by polyacrylamide gel electrophoresis, low-molecular-weight fractions of teichuronic acid are converted to higher-molecular-weight polymers by the addition of as many as 17 disaccharide repeat units. Images PMID:2118507

A tensegrity model for hydrogen bond networks in proteins.

PubMed

Bywater, Robert P

2017-05-01

Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger - covalent bonds connecting the atoms in the molecular skeleton or weaker forces like the so-called hydrophobic interactions. It has been demonstrated that the latter operate independently from hydrogen bonds. Each category of interaction must, if the protein is to have a stable structure, balance out. The hypothesis here is that the entire hydrogen bond network is in balance without any compensating contributions from other types of interaction. For sidechain-sidechain, sidechain-backbone and backbone-backbone hydrogen bonds in proteins, tensegrity balance ("closure") is required over the entire length of the polypeptide chain that defines individually folding units in globular proteins ("domains") as well as within the repeating elements in fibrous proteins that consist of extended chain structures. There is no closure to be found in extended structures that do not have repeating elements. This suggests an explanation as to why globular domains, as well as the repeat units in fibrous proteins, have to have a defined number of residues. Apart from networks of sidechain-sidechain hydrogen bonds there are certain key points at which this closure is achieved in the sidechain-backbone hydrogen bonds and these are associated with demarcation points at the start or end of stretches of secondary structure. Together, these three categories of hydrogen bond achieve the closure that is necessary for the stability of globular protein domains as well as repeating elements in fibrous proteins.

Effect of chronic restraint stress on inhibitory gating in the auditory cortex of rats.

PubMed

Ma, Lanlan; Li, Wai; Li, Sibin; Wang, Xuejiao; Qin, Ling

2017-05-01

A fundamental adaptive mechanism of auditory function is inhibitory gating (IG), which refers to the attenuation of neural responses to repeated sound stimuli. IG is drastically impaired in individuals with emotional and cognitive impairments (i.e. posttraumatic stress disorder). The objective of this study was to test whether chronic stress impairs the IG of the auditory cortex (AC). We used the standard two-tone stimulus paradigm and examined the parametric qualities of IG in the AC of rats by recording the electrophysiological signals of a single-unit and local field potential (LFP) simultaneously. The main results of this study were that most of the AC neurons showed a weaker response to the second tone than to the first tone, reflecting an IG of the repeated input. A fast negative wave of LFP showed consistent IG across the sampled AC sites, whereas a slow positive wave of LFP had less IG effect. IG was diminished following chronic restraint stress at both, the single-unit and LFP level, due to the increase in response to the second tone. This study provided new evidence that chronic stress disrupts the physiological function of the AC. Lay Summary The effects of chronic stress on IG were investigated by recording both, single-unit spike and LFP activities, in the AC of rats. In normal rats, most of the single-unit and N25 LFP activities in the AC showed an IG effect. IG was diminished following chronic restraint stress at both, the single-unit and LFP level.

Crystal structure of alpha poly-p-xylylene.

NASA Technical Reports Server (NTRS)

Kubo, S.; Wunderlich, B.

1971-01-01

A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.

Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese

PubMed Central

Ebstein, Richard P.; Monakhov, Mikhail V.; Lu, Yunfeng; Jiang, Yushi; Lai, Poh San; Chew, Soo Hong

2015-01-01

Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal–conservative axis albeit contingent upon number of friends. In a large sample of 1771 Han Chinese university students in Singapore, we observed a significant main effect of association between the DRD4 exon III variable number of tandem repeats and political attitude. Subjects with two copies of the 4-repeat allele (4R/4R) were significantly more conservative. Our results provided evidence for a role of the DRD4 gene variants in contributing to individual differences in political attitude particularly in females and more generally suggested that associations between individual genes, and neurochemical pathways, contributing to traits relevant to the social sciences can be provisionally identified. PMID:26246555

Early-onset facioscapulohumeral muscular dystrophy type 1 with some atypical features.

PubMed

Dorobek, Małgorzata; van der Maarel, Silvère M; Lemmers, Richard J L F; Ryniewicz, Barbara; Kabzińska, Dagmara; Frants, Rune R; Gawel, Malgorzata; Walecki, Jerzy; Hausmanowa-Petrusewicz, Irena

2015-04-01

Facioscapulohumeral muscular dystrophy cases with facial weakness before the age of 5 and signs of shoulder weakness by the age of 10 are defined as early onset. Contraction of the D4Z4 repeat on chromosome 4q35 is causally related to facioscapulohumeral muscular dystrophy type 1, and the residual size of the D4Z4 repeat shows a roughly inverse correlation with the severity of the disease. Contraction of the D4Z4 repeat on chromosome 4q35 is believed to induce a local change in chromatin structure and consequent transcriptional deregulation of 4qter genes. We present early-onset cases in the Polish population that amounted to 21% of our total population with facioscapulohumeral muscular dystrophy. More than 27% of them presented with severe phenotypes (wheelchair dependency). The residual D4Z4 repeat sizes ranged from 1 to 4 units. In addition, even within early-onset facioscapulohumeral muscular dystrophy type 1 phenotypes, some cases had uncommon features (head drop, early disabling contractures, progressive ptosis, and respiratory insufficiency and cardiomyopathy). © The Author(s) 2014.

Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese.

PubMed

Ebstein, Richard P; Monakhov, Mikhail V; Lu, Yunfeng; Jiang, Yushi; Lai, Poh San; Chew, Soo Hong

2015-08-22

Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal-conservative axis albeit contingent upon number of friends. In a large sample of 1771 Han Chinese university students in Singapore, we observed a significant main effect of association between the DRD4 exon III variable number of tandem repeats and political attitude. Subjects with two copies of the 4-repeat allele (4R/4R) were significantly more conservative. Our results provided evidence for a role of the DRD4 gene variants in contributing to individual differences in political attitude particularly in females and more generally suggested that associations between individual genes, and neurochemical pathways, contributing to traits relevant to the social sciences can be provisionally identified. © 2015 The Author(s).

Prevalence of spinocerebellar ataxia 36 in a US population.

PubMed

Valera, Juliana M; Diaz, Tatyana; Petty, Lauren E; Quintáns, Beatriz; Yáñez, Zuleima; Boerwinkle, Eric; Muzny, Donna; Akhmedov, Dmitry; Berdeaux, Rebecca; Sobrido, Maria J; Gibbs, Richard; Lupski, James R; Geschwind, Daniel H; Perlman, Susan; Below, Jennifer E; Fogel, Brent L

2017-08-01

To assess the prevalence and clinical features of individuals affected by spinocerebellar ataxia 36 (SCA36) at a large tertiary referral center in the United States. A total of 577 patients with undiagnosed sporadic or familial cerebellar ataxia comprehensively evaluated at a tertiary referral ataxia center were molecularly evaluated for SCA36. Repeat primed PCR and fragment analysis were used to screen for the presence of a repeat expansion in the NOP56 gene. Fragment analysis of triplet repeat primed PCR products identified a GGCCTG hexanucleotide repeat expansion in intron 1 of NOP56 in 4 index cases. These 4 SCA36-positive families comprised 2 distinct ethnic groups: white (European) (2) and Asian (Japanese [1] and Vietnamese [1]). Individuals affected by SCA36 exhibited typical clinical features with gait ataxia and age at onset ranging between 35 and 50 years. Patients also suffered from ataxic or spastic limbs, altered reflexes, abnormal ocular movement, and cognitive impairment. In a US population, SCA36 was observed to be a rare disorder, accounting for 0.7% (4/577 index cases) of disease in a large undiagnosed ataxia cohort.

Survey and Analysis of Microsatellites in the Silkworm, Bombyx mori

PubMed Central

Prasad, M. Dharma; Muthulakshmi, M.; Madhu, M.; Archak, Sunil; Mita, K.; Nagaraju, J.

2005-01-01

We studied microsatellite frequency and distribution in 21.76-Mb random genomic sequences, 0.67-Mb BAC sequences from the Z chromosome, and 6.3-Mb EST sequences of Bombyx mori. We mined microsatellites of ≥15 bases of mononucleotide repeats and ≥5 repeat units of other classes of repeats. We estimated that microsatellites account for 0.31% of the genome of B. mori. Microsatellite tracts of A, AT, and ATT were the most abundant whereas their number drastically decreased as the length of the repeat motif increased. In general, tri- and hexanucleotide repeats were overrepresented in the transcribed sequences except TAA, GTA, and TGA, which were in excess in genomic sequences. The Z chromosome sequences contained shorter repeat types than the rest of the chromosomes in addition to a higher abundance of AT-rich repeats. Our results showed that base composition of the flanking sequence has an influence on the origin and evolution of microsatellites. Transitions/transversions were high in microsatellites of ESTs, whereas the genomic sequence had an equal number of substitutions and indels. The average heterozygosity value for 23 polymorphic microsatellite loci surveyed in 13 diverse silkmoth strains having 2–14 alleles was 0.54. Only 36 (18.2%) of 198 microsatellite loci were polymorphic between the two divergent silkworm populations and 10 (5%) loci revealed null alleles. The microsatellite map generated using these polymorphic markers resulted in 8 linkage groups. B. mori microsatellite loci were the most conserved in its immediate ancestor, B. mandarina, followed by the wild saturniid silkmoth, Antheraea assama. PMID:15371363

National prevalence rates of bully victimization among students with disabilities in the United States.

PubMed

Blake, Jamilia J; Lund, Emily M; Zhou, Qiong; Kwok, Oi-Man; Benz, Michael R

2012-12-01

This study examined the prevalence rates of bully victimization and risk for repeated victimization among students with disabilities using the Special Education Elementary Longitudinal Study and the National Longitudinal Transition Study-2 longitudinal datasets. Results revealed that a prevalence rate ranging from 24.5% in elementary school to 34.1% in middle school. This is one to one and a half times the national average for students without disabilities. The rate of bully victimization was highest for students with emotional disturbance across school levels. Findings from this study also indicated that students with disabilities who were bullied once were at high risk of being bullied repeatedly. Elementary and middle school students with autism and high school students with orthopedic impairments were at the greatest risk of experiencing repeated victimization. Implications of the findings are discussed. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Novel surface attachment mechanism of the Streptococcus pneumoniae protein PspA.

PubMed Central

Yother, J; White, J M

1994-01-01

Pneumococcal surface protein A (PspA) of Streptococcus pneumoniae has been found to utilize a novel mechanism for anchoring to the bacterial cell surface. In contrast to that of surface proteins from other gram-positive bacteria, PspA anchoring required choline-mediated interactions between the membrane-associated lipoteichoic acid and the C-terminal repeat region of PspA. Release of PspA from the cell surface could be effected by deletion of 5 of the 10 C-terminal repeat units, by high concentrations of choline, or by growth in choline-deficient medium. Other pneumococcal proteins, including autolysin, which has a similar C-terminal repeat region, were not released by these treatments. The attachment mechanism utilized by PspA thus appears to be uniquely adapted to exploit the unusual structure of the pneumococcal cell surface. Further, it has provided the means for rapid and simple isolation of immunogenic PspA from S. pneumoniae. Images PMID:7910604

Inter-laboratory comparison of multi-locus variable-number tandem repeat analysis (MLVA) for verocytotoxin-producing Escherichia coli O157 to facilitate data sharing.

PubMed

Holmes, A; Perry, N; Willshaw, G; Hanson, M; Allison, L

2015-01-01

Multi-locus variable number tandem repeat analysis (MLVA) is used in clinical and reference laboratories for subtyping verocytotoxin-producing Escherichia coli O157 (VTEC O157). However, as yet there is no common allelic or profile nomenclature to enable laboratories to easily compare data. In this study, we carried out an inter-laboratory comparison of an eight-loci MLVA scheme using a set of 67 isolates of VTEC O157. We found all but two isolates were identical in profile in the two laboratories, and repeat units were homogeneous in size but some were incomplete. A subset of the isolates (n = 17) were sequenced to determine the actual copy number of representative alleles, thereby enabling alleles to be named according to international consensus guidelines. This work has enabled us to realize the potential of MLVA as a portable, highly discriminatory and convenient subtyping method.

Mint Viruses: Beauty, Stealth and Disease

USDA-ARS?s Scientific Manuscript database

Mint has been cultivated for thousands of years for the unique fragrances produced by its volatile oils. The major areas of production include India, the United States, China, and Brazil. Mint is a vegetatively propagated crop and world-wide sharing of plant material along with repeated clonal propa...

40 CFR 60.2725 - May I conduct a repeat performance test to establish new operating limits?

Code of Federal Regulations, 2014 CFR

2014-07-01

... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) STANDARDS OF PERFORMANCE FOR NEW STATIONARY SOURCES Emissions Guidelines and Compliance Times for Commercial and Industrial Solid Waste Incineration Units Model... during any performance test used to demonstrate compliance. Model Rule—Monitoring ...

40 CFR 60.2725 - May I conduct a repeat performance test to establish new operating limits?

Code of Federal Regulations, 2013 CFR

2013-07-01

... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) STANDARDS OF PERFORMANCE FOR NEW STATIONARY SOURCES Emissions Guidelines and Compliance Times for Commercial and Industrial Solid Waste Incineration Units Model... during any performance test used to demonstrate compliance. Model Rule—Monitoring ...

Dedicated education unit: student perspectives.

PubMed

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.

Utilization of Exocellular Mannan from Rhodotorula glutinis as an Immunoreactive Antigen in Diagnosis of Leptospirosis

PubMed Central

Matsuo, Kouki; Isogai, Emiko; Araki, Yoshio

2000-01-01

Previously, Rhodotorula glutinis was reported to produce a large amount of exocellular mannan, having a repeating unit of →3)-d-Manp-(1→4)-d-Manp-(1→. Recently, we found that antigenic polysaccharides of Leptospira biflexa serovar patoc strain Patoc I have the same repeating unit and cross-react with antisera raised against extended strains of other leptospires (K. Matsuo, E. Isogai, and Y. Araki, Carbohydr. Res., in press). This structural identity and the difficulty of producing and isolating antigens led us to confirm the usefulness of Rhodotorula mannan as an immunoreactive antigen in a serological diagnosis of leptospirosis. In the present investigation, we confirmed the structural identity of an exocellular mannan isolated from R. glutinis AHU 3479 and tried to use it as an immunoreactive antigen in a serological diagnosis of leptospirosis. From its chemical analysis and 1H- and 13C-labeled nuclear magnetic resonance spectrometry, the Rhodotorula mannan was confirmed to consist of the same disaccharide units. Furthermore, such a preparation was shown to immunoreact to various sera from patients suffering with leptospirosis as well as to most rabbit antiserum preparations obtained from immunization with various strains of pathogenic leptospires. Therefore, the Rhodotorula mannan preparation is useful as an immunoreactive antigen in the serological diagnosis for leptospirosis. PMID:11015396

System Synchronizes Recordings from Separated Video Cameras

NASA Technical Reports Server (NTRS)

Nail, William; Nail, William L.; Nail, Jasper M.; Le, Doung T.

2009-01-01

A system of electronic hardware and software for synchronizing recordings from multiple, physically separated video cameras is being developed, primarily for use in multiple-look-angle video production. The system, the time code used in the system, and the underlying method of synchronization upon which the design of the system is based are denoted generally by the term "Geo-TimeCode(TradeMark)." The system is embodied mostly in compact, lightweight, portable units (see figure) denoted video time-code units (VTUs) - one VTU for each video camera. The system is scalable in that any number of camera recordings can be synchronized. The estimated retail price per unit would be about $350 (in 2006 dollars). The need for this or another synchronization system external to video cameras arises because most video cameras do not include internal means for maintaining synchronization with other video cameras. Unlike prior video-camera-synchronization systems, this system does not depend on continuous cable or radio links between cameras (however, it does depend on occasional cable links lasting a few seconds). Also, whereas the time codes used in prior video-camera-synchronization systems typically repeat after 24 hours, the time code used in this system does not repeat for slightly more than 136 years; hence, this system is much better suited for long-term deployment of multiple cameras.

Characterization of the COL2A1 VNTR polymorphism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berg, E.S.; Olaisen, B.

1993-05-01

The variable number of tandem repeat (VNTR) region 3{prime} to the collagen type II gene (COL2A1) was amplified in vitro by the polymerase chain reaction. Subsequent high-resolution gel electrophoresis showed that the five earlier reported alleles could be further subtyped. A total of 17 allelic variants with a heterozygosity of 73.0% were found in 202 unrelated Norwegians. DNA sequencing of 19 COL2A1 alleles has been performed. The internal organization of the VNTR was common for all alleles, as previously shown for a few alleles. Moreover, the polymorphism in the COL2A1 locus is mainly due to variation in the numbers ofmore » copies of two repeat units, containing 34 and 31 bp, respectively, and/or to small deletions in either of the two units. DNA sequencing of alleles with the same electrophoretic size revealed no heterogeneity such as an alternating order of the different units, a feature that might have been expected to be the result of unequal crossing-over events. The observed ordered structure of the VNTR and the possibility of single-stranded DNA from the cores in the VNTR forming hairpins and loops suggest that the COL2A1 polymorphism may have evolved mainly by replication slippage mechanisms. 23 refs., 2 figs., 3 tabs.« less

Natural Burkholderia mallei Infection in Dromedary, Bahrain

PubMed Central

Wernery, Ulrich; Wernery, Renate; Joseph, Marina; Al-Salloom, Fajer; Johnson, Bobby; Kinne, Joerg; Jose, Shanti; Jose, Sherry; Tappendorf, Britta; Hornstra, Heidie

2011-01-01

We confirm a natural infection of dromedaries with glanders. Multilocus variable number tandem repeat analysis of a Burkholderia mallei strain isolated from a diseased dromedary in Bahrain revealed close genetic proximity to strain Dubai 7, which caused an outbreak of glanders in horses in the United Arab Emirates in 2004. PMID:21762586

Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers

USDA-ARS?s Scientific Manuscript database

Genetic diversity of thirty five Psidium guajava accessions maintained at the USDA, National Plants Germplasm System, Hilo, HI, was characterized using 20 simple sequence repeat (SSR) markers. Diversity analysis detected a total of 178 alleles ranging from four to 16. The observed mean heterozygosit...

Research and Teaching: Think before (and after) You Speak: Practice and Self-Reflection Bolster Oral Communication Skills

ERIC Educational Resources Information Center

Sterling, Eleanor; Bravo, Adriana; Porzecanski, Ana Luz; Burks, Romi L.; Linder, Joshua; Langen, Tom; Fernandez, Denny; Ruby, Douglas; Bynum, Nora

2016-01-01

In this study, conservation biology faculty and practitioners from across the United States designed classroom exercises and teaching interventions intended to bolster oral communication skills. Through repeated oral presentation assignments integrated into course requirements, the authors examined individual student learning gains via…

Anti-Americanism: A Perfect Addition to a Russian Authoritarian’s Political Toolbox

DTIC Science & Technology

2013-12-01

Putin’s autobiographical interview book First Person. Primary source transcripts from the Russian government’s public online archives will be...80. 36 Ibid., 106. 20 could not directly affect the repeated snubbing that Yeltsin incurred from the West, the memories of how the United

A History of Adult Education in Germany (1800-1933).

ERIC Educational Resources Information Center

Pirtle, Wayne George

German adult education before 1933 stressed group experience in the family, clan, and culture rather than knowledge and the individual. Outside trends, expecially in England, Austria, Denmark, and the United States, repeatedly influenced the German movement. While lecture institutes, university extension, and other activities were important, the…

Interdisciplinary Practices in Ontario: Past, Present, and Future

ERIC Educational Resources Information Center

Clausen, Kurt W.; Drake, Susan M.

2010-01-01

In Canada, the province of Ontario has had a rather turbulent relationship with interdisciplinarity as it has tried to implement this practice into the public school system. Specifically, the provincial government has repeatedly attempted to introduce such reforms as integrated units, harmonized objectives, and open-concept, student-centered pods,…

PESTICIDE EXPOSURE AND POTENTIAL HEALTH EFFECTS IN YOUNG CHILDREN ALONG THE U.S.-MEXICO BORDER

EPA Science Inventory

The purpose of the Pesticides in Young Children - Border States Program is to assess the relationship of health outcomes in children living along the United States and Mexico border to repeated pesticide exposures via multiple sources and pathways. The present research program ...

78 FR 32356 - United States-Korea Free Trade Agreement

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-30

... possesses the required origin information; (2) the consistent application of the rules of origin to UKFTA... finding of either (a) repeated unlawful activity or (b) willful presentation of inaccurate origin... that a claim of origin for a textile or apparel good is accurate) or Article 4.3.5 (verification to...

Repeated holdout Cross-Validation of Model to Estimate Risk of Lyme Disease by Landscape Attributes

EPA Science Inventory

We previously modeled Lyme disease (LD) risk at the landscape scale; here we evaluate the model's overall goodness-of-fit using holdout validation. Landscapes were characterized within road-bounded analysis units (AU). Observed LD cases (obsLD) were ascertained per AU. Data were ...

Natural Burkholderia mallei infection in Dromedary, Bahrain.

PubMed

Wernery, Ulrich; Wernery, Renate; Joseph, Marina; Al-Salloom, Fajer; Johnson, Bobby; Kinne, Joerg; Jose, Shanti; Jose, Sherry; Tappendorf, Britta; Hornstra, Heidie; Scholz, Holger C

2011-07-01

We confirm a natural infection of dromedaries with glanders. Multilocus variable number tandem repeat analysis of a Burkholderia mallei strain isolated from a diseased dromedary in Bahrain revealed close genetic proximity to strain Dubai 7, which caused an outbreak of glanders in horses in the United Arab Emirates in 2004.

Is Education the Key to Global Economic Competitiveness?

ERIC Educational Resources Information Center

Mathis, William J.

2011-01-01

Contemporary test-based reforms are often grounded in the claim that test performance is the key to international economic competitiveness. However, this oft-repeated assertion lacks empirical support. According to the World Economic Forum, the United States' recent loss of economic competitiveness standing is due to macroeconomic instability…

PESTICIDE EXPOSURE AND POTENTIAL HEALTH EFFECTS IN YOUNG CHILDREN ALONG THE U.S. - MEXICO BORDER

EPA Science Inventory

The purpose of the Pesticides in Young Children - Border States Program is to assess the relationship between health status in children living along the United States and Mexico border and repeated pesticide exposures via multiple sources and pathways. Children's health has bee...

Response of invasive swallow-worts (Vincetoxicum spp.) to repeated artificial defoliation or clipping

USDA-ARS?s Scientific Manuscript database

The Eurasian vines pale swallow-wort (Vincetoxicum rossicum) (PSW) and black swallow-wort (V. nigrum) (BSW) are invasive perennials that have infested natural areas in the northeastern United States and southern Canada. A biological control program is being developed, though it is unclear how thes...

47 CFR 80.334 - False distress alerts.

Code of Federal Regulations, 2013 CFR

2013-10-01

....S. Coast Guard; (d) Was repeated; or (e) Was transmitted using a false identity. [68 FR 46968, Aug... § 80.334 False distress alerts. A distress alert is false if it was transmitted without any indication that a mobile unit or person was in distress and required immediate assistance. Transmitting a false...

47 CFR 80.334 - False distress alerts.

Code of Federal Regulations, 2014 CFR

2014-10-01

....S. Coast Guard; (d) Was repeated; or (e) Was transmitted using a false identity. [68 FR 46968, Aug... § 80.334 False distress alerts. A distress alert is false if it was transmitted without any indication that a mobile unit or person was in distress and required immediate assistance. Transmitting a false...

47 CFR 80.334 - False distress alerts.

Code of Federal Regulations, 2011 CFR

2011-10-01

....S. Coast Guard; (d) Was repeated; or (e) Was transmitted using a false identity. [68 FR 46968, Aug... § 80.334 False distress alerts. A distress alert is false if it was transmitted without any indication that a mobile unit or person was in distress and required immediate assistance. Transmitting a false...

47 CFR 80.334 - False distress alerts.

Code of Federal Regulations, 2010 CFR

2010-10-01

....S. Coast Guard; (d) Was repeated; or (e) Was transmitted using a false identity. [68 FR 46968, Aug... § 80.334 False distress alerts. A distress alert is false if it was transmitted without any indication that a mobile unit or person was in distress and required immediate assistance. Transmitting a false...

47 CFR 80.334 - False distress alerts.

Code of Federal Regulations, 2012 CFR

2012-10-01

....S. Coast Guard; (d) Was repeated; or (e) Was transmitted using a false identity. [68 FR 46968, Aug... § 80.334 False distress alerts. A distress alert is false if it was transmitted without any indication that a mobile unit or person was in distress and required immediate assistance. Transmitting a false...

Developmental Education Repeaters: Stories about Repetition

ERIC Educational Resources Information Center

O'Dell, Jade J.

2012-01-01

Developmental education students make up almost half of the community college population in the United States (Bettinger & Long, 2005). Approximately 42% of first-time freshmen at community colleges must enroll in at least one developmental education course in English, reading and/or math (NCES, 2010). Many developmental education students are…

Fused thiophene-based conjugated polymers and their use in optoelectronic devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Facchetti, Antonio; Marks, Tobin J.; Takai, Atsuro

The present teachings relate to polymeric compounds and their use as organic semiconductors in organic and hybrid optical, optoelectronic, and/or electronic devices such as photovoltaic cells, light emitting diodes, light emitting transistors, and field effect transistors. The disclosed compounds generally include as repeating units at least one annulated thienyl-vinylene-thienyl (TVT) unit and at least one other pi-conjugated unit. The annulated TVT unit can be represented by the formula: ##STR00001## where Cy.sup.1 and Cy.sup.2 can be a five- or six-membered carbocyclic ring. The annulated TVT unit can be optionally substituted at any available ring atom(s), and can be covalently linked tomore » the other pi-conjugated unit via either the thiophene rings or the carbocyclic rings Cy.sup.1 and Cy.sup.2. The other pi-conjugated unit can be a conjugated linear linker including one or more unsaturated bonds, or a conjugated cyclic linker including one or more carbocyclic and/or heterocyclic rings.« less

Remote water monitoring system

NASA Technical Reports Server (NTRS)

Grana, D. C.; Haynes, D. P. (Inventor)

1978-01-01

A remote water monitoring system is described that integrates the functions of sampling, sample preservation, sample analysis, data transmission and remote operation. The system employs a floating buoy carrying an antenna connected by lines to one or more sampling units containing several sample chambers. Receipt of a command signal actuates a solenoid to open an intake valve outward from the sampling unit and communicates the water sample to an identifiable sample chamber. Such response to each signal receipt is repeated until all sample chambers are filled in a sample unit. Each sample taken is analyzed by an electrochemical sensor for a specific property and the data obtained is transmitted to a remote sending and receiving station. Thereafter, the samples remain isolated in the sample chambers until the sampling unit is recovered and the samples removed for further laboratory analysis.

Genotyping of Brucella melitensis strains from dromedary camels (Camelus dromedarius) from the United Arab Emirates with multiple-locus variable-number tandem repeat analysis.

PubMed

Gyuranecz, Miklós; Wernery, Ulli; Kreizinger, Zsuzsa; Juhász, Judit; Felde, Orsolya; Nagy, Péter

2016-04-15

Camel brucellosis is a widespread zoonotic disease in camel-rearing countries caused by Brucella melitensis and Brucella abortus. The aim of this study was the first genetic analysis of B. melitensis strains isolated from dromedary camels (Camelus dromedarius) using multiple-locus variable-number tandem repeat analysis (MLVA). MLVA 16 and its MLVA 8 and MLVA11 subsets were used to determine the genotypes of 15 B. melitensis isolates from dromedary camels (11 strains) and other host species (4 strains) from the United Arab Emirates and the results were then compared to B. melitensis MLVA genotypes from other parts of the world. Five, including two novel genotypes were identified with MLVA 8. MLVA 16 further discriminated these five genotypes to ten variants. The eleven camel isolates clustered into four main genetic groups within the East-Mediterranean and African clades and this clustering correlated with the geographic origin of the hosts (United Arab Emirates, Kingdom of Saudi Arabia and Sudan) and the date of their isolation. The camel strains were also genetically related to strains isolated from wild and domestic ruminants from their close habitat or from other parts of the world. Although limited number of strains were analysed, based on our data imported animals from foreign countries, local small ruminants and wildlife species are hypothesized to be the main sources of camel brucellosis in the United Arab Emirates. MLVA was successfully applied to determine the epidemiological links between the different camel B. melitensis infections in the United Arab Emirates and it can be a beneficial tool in future disease control programs. Copyright © 2016 Elsevier B.V. All rights reserved.

Hospital costs associated with atrial fibrillation for ischemic stroke patients aged 18-64 years in the United States

PubMed Central

Wang, Guijing; Joo, Heesoo; Tong, Xin; George, Mary G.

2015-01-01

Background and purpose Hospital costs associated with atrial fibrillation (AFib) among stroke patients have not been well-studied, especially among people younger than 65 years. We estimated the AFib-associated hospital costs in U.S. patients aged 18-64 years. Methods We identified hospital admissions with a primary diagnosis of ischemic stroke from the 2010-2012 MarketScan Commercial Claims and Encounters inpatient datasets, excluding those with capitated health insurance plans, aged <18 or >64, missing geographic region, hospital costs below the 1st or above 99th percentile, and having carotid intervention (N=40,082). We searched the data for AFib and analyzed the costs for non-repeat and repeat stroke admissions separately. We estimated the AFib-associated costs using multivariate regression models controlling for age, sex, geographic region, and Charlson comorbidity index. Results Of the 33,500 non-repeat stroke admissions, 2,407 (7.2%) had AFib. Admissions with AFib cost $4,991 more than those without AFib ($23,770 vs. $18,779). For the 6,582 repeat stroke admissions, 397 (6.0%) had AFib. The costs were $3,260 more for those with AFib than those without ($24,119 vs. $20,929). After controlling for potential confounders, AFib-associated costs for non-repeat stroke admissions were $4,905, representing 20.6% of the total costs for the admissions. Both the hospital costs and the AFib-associated costs were associated with age, but not sex. AFib-associated costs for repeat stroke admissions were not significantly higher than for non-AFib patients, except for those aged 55-64 ($3,537). Conclusions AFib increased the hospital cost of ischemic stroke substantially. Further investigation on AFib-associated costs for repeat stroke admissions is needed. PMID:25851767

Vaginal birth after cesarean: new insights on maternal and neonatal outcomes.

PubMed

Guise, Jeanne-Marie; Denman, Mary Anna; Emeis, Cathy; Marshall, Nicole; Walker, Miranda; Fu, Rongwei; Janik, Rosalind; Nygren, Peggy; Eden, Karen B; McDonagh, Marian

2010-06-01

To systematically review the evidence about maternal and neonatal outcomes relating to vaginal birth after cesarean (VBAC). Relevant studies were identified from multiple searches of MEDLINE, DARE, and the Cochrane databases (1980 to September 2009) and from recent systematic reviews, reference lists, reviews, editorials, Web sites, and experts. Inclusion criteria limited studies to the English-language and human studies conducted in the United States and developed countries specifically evaluating birth after previous cesarean delivery. Studies focusing on high-risk maternal or neonatal conditions, including breech vaginal delivery, or fewer than 10 patients were excluded. Poor-quality studies were not included in analyses. We identified 3,134 citations and reviewed 963 articles for inclusion; 203 articles met the inclusion criteria and were quality rated. Overall rates of maternal harms were low for both trial of labor and elective repeat cesarean delivery. Although rare in both elective repeat cesarean delivery and trial of labor, maternal mortality was significantly increased for elective repeat cesarean delivery at 0.013% compared with 0.004% for trial of labor. The rates of maternal hysterectomy, hemorrhage, and transfusions did not differ significantly between trial of labor and elective repeat cesarean delivery. The rate of uterine rupture for all women with prior cesarean was 0.30%, and the risk was significantly increased for trial of labor (0.47% compared with 0.03% for elective repeat cesarean delivery). Perinatal mortality was also significantly increased for trial of labor (0.13% compared with 0.05% for elective repeat cesarean delivery). Overall the best evidence suggests that VBAC is a reasonable choice for the majority of women. Adverse outcomes were rare for both elective repeat cesarean delivery and trial of labor. Definitive studies are lacking to identify patients who are at greatest risk for adverse outcomes.

An analysis of on time evolution of landslide

NASA Astrophysics Data System (ADS)

Tsai, Chienwei; Lien, Huipang

2017-04-01

In recent years, the extreme hydrological phenomenon in Taiwan is obvious. Because the increase of heavy rainfall frequency has resulted in severe landslide disaster, the watershed management is very important and how to make the most effective governance within the limited funds is the key point. In recent years many scholars to develop empirical models said that virtually rainfall factors exist and as long as rainfall conditions are met the minimum requirements of the model, landslide will occur. However, rainfall is one of the elements to the landslide, but not the only one element. Rainfall, geology and earthquake all contributed to the landslide as well. Preliminary research found that many landslides occur at the same location constantly and after repeating landslide, the slope had the characteristic of landslide immunity over time, even if the rainfall exceeded the standard, the landslide could not be triggered in the near term. This study investigated the surface conditions of slope that occur repeated landslide. It is difficult to be the basis of subsequent anti-disaster if making rainfall is the only condition to contribute to the landslide. This study analyzes 50 landslides in 2004 2013. Repeated landslide is defined as existed landslide in satellite images of reference period which it's bare area is shrinking or disappearing gradually but the restoration occur landslide again in some period time. The statistical analysis of the study found that 96% of landslide has repeated landslide and on average repeated landslide occurs 3.4 years in 10 years by one year as the unit. The highest of repeated landslide happened in 2010. It would presume that Typhoon Morakot in 2010 brought torrential rain which suffered southern mountain areas severely so the areas occurred repeated landslide.

Human mismatch repair protein hMutLα is required to repair short slipped-DNAs of trinucleotide repeats.

PubMed

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.

Lower neurocognitive function in U-2 pilots

PubMed Central

Tate, David F.; Wood, Joe; Sladky, John H.; McDonald, Kent; Sherman, Paul M.; Kawano, Elaine S.; Rowland, Laura M.; Patel, Beenish; Wright, Susan N.; Hong, Elliot; Rasmussen, Jennifer; Willis, Adam M.; Kochunov, Peter V.

2014-01-01

Objective: Determine whether United States Air Force (USAF) U-2 pilots (U2Ps) with occupational exposure to repeated hypobaria had lower neurocognitive performance compared to pilots without repeated hypobaric exposure and whether U2P neurocognitive performance correlated with white matter hyperintensity (WMH) burden. Methods: We collected Multidimensional Aptitude Battery–II (MAB-II) and MicroCog: Assessment of Cognitive Functioning (MicroCog) neurocognitive data on USAF U2Ps with a history of repeated occupational exposure to hypobaria and compared these with control data collected from USAF pilots (AFPs) without repeated hypobaric exposure (U2Ps/AFPs MAB-II 87/83; MicroCog 93/80). Additional comparisons were performed between U2Ps with high vs low WMH burden. Results: U2Ps with repeated hypobaric exposure had significantly lower scores than control pilots on reasoning/calculation (U2Ps/AFPs 99.4/106.5), memory (105.5/110.9), information processing accuracy (102.1/105.8), and general cognitive functioning (103.5/108.5). In addition, U2Ps with high whole-brain WMH count showed significantly lower scores on reasoning/calculation (high/low 96.8/104.1), memory (102.9/110.2), general cognitive functioning (101.5/107.2), and general cognitive proficiency (103.6/108.8) than U2Ps with low WMH burden (high/low WMH mean volume 0.213/0.003 cm3 and mean count 14.2/0.4). Conclusion: In these otherwise healthy, highly functioning individuals, pilots with occupational exposure to repeated hypobaria demonstrated lower neurocognitive performance, albeit demonstrable on only some tests, than pilots without repeated exposure. Furthermore, within the U2P population, higher WMH burden was associated with lower neurocognitive test performance. Hypobaric exposure may be a risk factor for subtle changes in neurocognition. PMID:25008397

Fatigue in repeated-sprint exercise is related to muscle power factors and reduced neuromuscular activity.

PubMed

Mendez-Villanueva, Alberto; Hamer, Peter; Bishop, David

2008-07-01

The purpose of this study was (1) to determine the relationship between each individual's anaerobic power reserve (APR) [i.e., the difference between the maximum anaerobic (Pana) and aerobic power (Paer)] and fatigability during repeated-sprint exercise and (2) to examine the acute effects of repeated sprints on neuromuscular activity, as evidenced by changes in the surface electromyogram (EMG) signals. Eight healthy males carried out tests to determine Pana (defined as the highest power output attained during a 6-s cycling sprint), Paer (defined as the highest power output achieved during a progressive, discontinuous cycling test to failure) and a repeated cycling sprint test (10 x 6-s max sprints with 30 s rest). Peak power output (PPO) and mean power output (MPO) were calculated for each maximal 6-s cycling bout. Root mean square (RMS) was utilized to quantify EMG activity from the vastus lateralis (VL) muscle of the right leg. Over the ten sprints, PPO and MPO decreased by 24.6 and 28.3% from the maximal value (i.e., sprint 1), respectively. Fatigue index during repeated sprints was significantly correlated with APR (R = 0.87; P < 0.05). RMS values decreased over the ten sprints by 14.6% (+/-6.3%). There was a strong linear relationship (R2 = 0.97; P < 0.05) between the changes in MPO and EMG RMS from the vastus lateralis muscle during the ten sprints. The individual advantage in fatigue-resistance when performing a repeated sprint task was related with a lower anaerobic power reserve. Additionally, a suboptimal net motor unit activity might also impair the ability to repeatedly generate maximum power outputs.

Mi-STAR Unit Challenges serve as a model for integrating earth science and systems thinking in a Next Generation Science Standards (NGSS) aligned curriculum.

NASA Astrophysics Data System (ADS)

Gochis, E. E.; Tubman, S.; Matthys, T.; Bluth, G.; Oppliger, D.; Danhoff, B.; Huntoon, J. E.

2017-12-01

Michigan Science Teaching and Assessment Reform (Mi-STAR) is developing an NGSS-aligned middle school curriculum and associated teacher professional learning program in which science is taught and learned as an integrated body of knowledge that can be applied to address societal issues. With the generous support of the Herbert H. and Grace A. Dow Foundation, Mi-STAR has released several pilot-tested units through the Mi-STAR curriculum portal at mi-star.mtu.edu. Each of these units focuses on an ongoing `Unit Challenge' investigation that integrates STEM content across disciplinary boundaries, stimulates interest, and engages students in using scientific practices to address 21st century challenges. Each Mi-STAR unit is connected to a Unifying NGSS Crosscutting Concept (CCC) that allows students to recognize the concepts that are related to the phenomena or problems under investigation. In the 6th grade, students begin with an exploration of the CCC Systems and System Models. Through repeated applications across units, students refine their understanding of what a system is and how to model a complex Earth system. An example 6th grade unit entitled "Water on the Move: The Water Cycle," provides an example of how Mi-STAR approaches the use of Unifying CCCs and Unit Challenges to enhance middle school students' understanding of the interconnections of Earth system processes and human activities. Throughout the unit, students use a series of hands-on explorations and simulations to explore the hydrologic cycle and how human activity can alter Earth systems. Students develop new knowledge through repeated interactions with the Unit Challenge, which requires development of system models and construction of evidence-based arguments related to flooding problems in a local community. Students have the opportunity to make predictions about how proposed land-use management practices (e.g. development of a skate-park, rain garden, soccer field, etc.) can alter the earth-system processes. Students present their findings and recommendations in a public forum format. Student-learning outcomes are measured using a combination of formative and summative assessments that address students' proficiency with science and engineering content and practices in conjunction with the unit's Unifying CCC.

13C NMR spectroscopic analysis of poly(electrolyte) cement liquids.

PubMed

Watts, D C

1979-05-01

13C NMR spectroscopy has been applied to the analysis of carboxylic poly-acid cement liquids. Monomer incorporation, composition ratio, sequence statistics, and stereochemical configuration have been considered theoretically, and determined experimentally, from the spectra. Conventionally polymerized poly(acrylic acid) has an approximately random configuration, but other varieties may be synthesized. Two commercial glass-ionomer cement liquids both contain tartaric acid as a chelating additive but the composition of their poly-acids are different. Itaconic acid units, distributed randomly, constitute 21% of the repeating units in one of these polyelectrolytes.

Two different size classes of 5S rDNA units coexisting in the same tandem array in the razor clam Ensis macha: is this region suitable for phylogeographic studies?

PubMed

Fernández-Tajes, Juan; Méndez, Josefina

2009-12-01

For a study of 5S ribosomal genes (rDNA) in the razor clam Ensis macha, the 5S rDNA region was amplified and sequenced. Two variants, so-called type I or short repeat (approximately 430 bp) and type II or long repeat (approximately 735 bp), appeared to be the main components of the 5S rDNA of this species. Their spacers differed markedly, both in length and nucleotide composition. The organization of the two variants was investigated by amplifying the genomic DNA with primers based on the sequence of the type I and type II spacers. PCR amplification products with primers EMLbF and EMSbR showed that the long and short repeats are associated within the same tandem array, suggesting an intermixed arrangement of both spacers. Nevertheless, amplifications carried out with inverse primers EMSinvF/R and EMLinvF/R revealed that some short and long repeats are contiguous in the same tandem array. This is the first report of the coexistence of two variable spacers in the same tandem array in bivalve mollusks.

MitoSatPlant: mitochondrial microsatellites database of viridiplantae.

PubMed

Kumar, Manjeet; Kapil, Aditi; Shanker, Asheesh

2014-11-01

Microsatellites also known as simple sequence repeats (SSRs) consist of 1-6 nucleotide long repeating units. The importance of mitochondrial SSRs (mtSSRs) in fields like population genetics, plant phylogenetics and genome mapping motivated us to develop MitoSatPlant, a repository of plant mtSSRs. It contains information for perfect, imperfect and compound SSRs mined from 92 mitochondrial genomes of green plants, available at NCBI (as of 1 Feb 2014). A total of 72,798 SSRs were found, of which PCR primers were designed for 72,495 SSRs. Among all sequences, tetranucleotide repeats (26,802) were found to be most abundant whereas hexanucleotide repeats (2751) were detected with least frequency. MitoSatPlant was developed using SQL server 2008 and can be accessed through a front end designed in ASP.Net. It is an easy to use, user-friendly database and will prove to be a useful resource for plant scientists. To the best of our knowledge MitoSatPlant is the only database available for plant mtSSRs and can be freely accessed at http://compubio.in/mitosatplant/. Copyright © 2014 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Prevalence of spinocerebellar ataxia 36 in a US population

PubMed Central

Valera, Juliana M.; Diaz, Tatyana; Petty, Lauren E.; Quintáns, Beatriz; Yáñez, Zuleima; Boerwinkle, Eric; Muzny, Donna; Akhmedov, Dmitry; Berdeaux, Rebecca; Sobrido, Maria J.; Gibbs, Richard; Lupski, James R.; Geschwind, Daniel H.; Perlman, Susan; Below, Jennifer E.

2017-01-01

Objective: To assess the prevalence and clinical features of individuals affected by spinocerebellar ataxia 36 (SCA36) at a large tertiary referral center in the United States. Methods: A total of 577 patients with undiagnosed sporadic or familial cerebellar ataxia comprehensively evaluated at a tertiary referral ataxia center were molecularly evaluated for SCA36. Repeat primed PCR and fragment analysis were used to screen for the presence of a repeat expansion in the NOP56 gene. Results: Fragment analysis of triplet repeat primed PCR products identified a GGCCTG hexanucleotide repeat expansion in intron 1 of NOP56 in 4 index cases. These 4 SCA36-positive families comprised 2 distinct ethnic groups: white (European) (2) and Asian (Japanese [1] and Vietnamese [1]). Individuals affected by SCA36 exhibited typical clinical features with gait ataxia and age at onset ranging between 35 and 50 years. Patients also suffered from ataxic or spastic limbs, altered reflexes, abnormal ocular movement, and cognitive impairment. Conclusions: In a US population, SCA36 was observed to be a rare disorder, accounting for 0.7% (4/577 index cases) of disease in a large undiagnosed ataxia cohort. PMID:28761930

Opportunities to Foster Efficient Communication in Labor and Delivery Using Simulation.

PubMed

Daniels, Kay; Hamilton, Colleen; Crowe, Susan; Lipman, Steven S; Halamek, Louis P; Lee, Henry C

2017-01-01

Introduction  Communication errors are an important contributing factor in adverse outcomes in labor and delivery (L&D) units. The objective of this study was to identify common lapses in verbal communication using simulated obstetrical scenarios and propose alternative formats for communication. Methods  Health care professionals in L&D participated in three simulated clinical scenarios. Scenarios were recorded and reviewed to identify questions repeated within and across scenarios. Questions that were repeated more than once due to ineffective communication were identified. The frequency with which the questions were asked across simulations was identified. Results  Questions were commonly repeated both within and across 27 simulated scenarios. The median number of questions asked was 27 per simulated scenario. Commonly repeated questions focused on three general topics: (1) historical data/information (i.e., estimated gestational age), (2) maternal clinical status (i.e., estimated blood loss), and (3) personnel (i.e., "Has anesthesiologist been called?"). Conclusion  Inefficient verbal communication exists in the process of transferring information during obstetric emergencies. These findings can inform improved training and development of information displays to improve teamwork and communication. A visual display that can report static historical information and specific dynamic clinical data may facilitate optimal human performance.

The VNTR 2 repeat in MAOA and delinquent behavior in adolescence and young adulthood: associations and MAOA promoter activity

PubMed Central

Guo, Guang; Ou, Xiao-Ming; Roettger, Michael; Shih, Jean C

2010-01-01

Genetic studies of delinquent and criminal behavior are rare in spite of the wide recognition that individuals may differ in their propensity for delinquency and criminality. Using 2524 participants in Add Health in the United States, the present study demonstrates a link between the rare 2 repeat of the 30-bp VNTR in the MAOA gene and much higher levels of self-reported serious and violent delinquency. The evidence is based on a statistical association analysis and a functional analysis of MAOA promoter activity using two human brain-derived cell lines: neuroblastoma SH-SY5Y and human glioblastoma 1242-MG. The association analysis shows that men with a 2R report a level of serious delinquency and violent delinquency in adolescence and young adulthood that were about twice (CI: (0.21, 3.24), P = 0.025; and CI: (0.37, 2.5), P = 0.008 for serious and violent delinquency, respectively) as high as those for participants with the other variants. The results for women are similar, but weaker. In the functional analysis, the 2 repeat exhibits much lower levels of promoter activity than the 3 or 4 repeat. PMID:18212819

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

PubMed

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.

Diversity, Evolution, and Functionality of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Regions in the Fire Blight Pathogen Erwinia amylovora▿†

PubMed Central

Rezzonico, Fabio; Smits, Theo H. M.; Duffy, Brion

2011-01-01

The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system confers acquired heritable immunity against mobile nucleic acid elements in prokaryotes, limiting phage infection and horizontal gene transfer of plasmids. In CRISPR arrays, characteristic repeats are interspersed with similarly sized nonrepetitive spacers derived from transmissible genetic elements and acquired when the cell is challenged with foreign DNA. New spacers are added sequentially and the number and type of CRISPR units can differ among strains, providing a record of phage/plasmid exposure within a species and giving a valuable typing tool. The aim of this work was to investigate CRISPR diversity in the highly homogeneous species Erwinia amylovora, the causal agent of fire blight. A total of 18 CRISPR genotypes were defined within a collection of 37 cosmopolitan strains. Strains from Spiraeoideae plants clustered in three major groups: groups II and III were composed exclusively of bacteria originating from the United States, whereas group I generally contained strains of more recent dissemination obtained in Europe, New Zealand, and the Middle East. Strains from Rosoideae and Indian hawthorn (Rhaphiolepis indica) clustered separately and displayed a higher intrinsic diversity than that of isolates from Spiraeoideae plants. Reciprocal exclusion was generally observed between plasmid content and cognate spacer sequences, supporting the role of the CRISPR/Cas system in protecting against foreign DNA elements. However, in several group III strains, retention of plasmid pEU30 is inconsistent with a functional CRISPR/Cas system. PMID:21460108

Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora.

PubMed

Rezzonico, Fabio; Smits, Theo H M; Duffy, Brion

2011-06-01

The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system confers acquired heritable immunity against mobile nucleic acid elements in prokaryotes, limiting phage infection and horizontal gene transfer of plasmids. In CRISPR arrays, characteristic repeats are interspersed with similarly sized nonrepetitive spacers derived from transmissible genetic elements and acquired when the cell is challenged with foreign DNA. New spacers are added sequentially and the number and type of CRISPR units can differ among strains, providing a record of phage/plasmid exposure within a species and giving a valuable typing tool. The aim of this work was to investigate CRISPR diversity in the highly homogeneous species Erwinia amylovora, the causal agent of fire blight. A total of 18 CRISPR genotypes were defined within a collection of 37 cosmopolitan strains. Strains from Spiraeoideae plants clustered in three major groups: groups II and III were composed exclusively of bacteria originating from the United States, whereas group I generally contained strains of more recent dissemination obtained in Europe, New Zealand, and the Middle East. Strains from Rosoideae and Indian hawthorn (Rhaphiolepis indica) clustered separately and displayed a higher intrinsic diversity than that of isolates from Spiraeoideae plants. Reciprocal exclusion was generally observed between plasmid content and cognate spacer sequences, supporting the role of the CRISPR/Cas system in protecting against foreign DNA elements. However, in several group III strains, retention of plasmid pEU30 is inconsistent with a functional CRISPR/Cas system.

Critical care use during the course of serious illness.

PubMed

Iwashyna, Theodore J

2004-11-01

Despite its expense and importance, it is unknown how common critical care use is. We describe longitudinal patterns of critical care use among a nationally representative cohort of elderly patients monitored from the onset of common serious illnesses. A retrospective population-based cohort study of elderly patients in fee-for-service Medicare is used, with 1,108,060 Medicare beneficiaries at least 68 years of age and newly diagnosed with serious illnesses: 1 of 9 malignancies, stroke, congestive heart failure, hip fracture, or myocardial infarction. Medicare inpatient hospital claims from diagnosis until death (65.1%) or fixed-right censoring (more than 4 years) were reviewed. Distinct hospitalizations involving critical care use (intensive care unit or critical care unit) were counted and associated reimbursements were assessed; repeated use was defined as five or more such hospitalizations. Of the cohort, 54.9% used critical care at some time after diagnosis. Older patients were much less likely to ever use critical care (odds ratio, 0.31; comparing patients more than 90 years old with those 68-70 years old), even after adjustment. A total of 31,348 patients (2.8%) were repeated users of critical care; they accounted for 3.6 billion dollars in hospital charges and 1.4 billion dollars in Medicare reimbursement. We conclude that critical care use is common in serious chronic illness and is not associated solely with preterminal hospitalizations. Use is uneven, and a minority of patients who repeatedly use critical care account for disproportionate costs.

Early changes in Achilles tendon behaviour in vivo following downhill backwards walking.

PubMed

Joseph, C W; Bradshaw, E J; Furness, T P; Kemp, J; Clark, R A

2016-01-01

Downhill backwards walking causes repeated, cyclical loading of the muscle-tendon unit. The effect this type of repeated loading has on the mechanical behaviour of the Achilles tendon is presently unknown. This study aimed to investigate the biomechanical response of the Achilles tendon aponeurosis complex following a downhill backwards walking protocol. Twenty active males (age: 22.3 ± 3.0 years; mass: 74.7 ± 5.6 kg; height: 1.8 ± 0.7 m) performed 60 min of downhill (8.5°), backwards walking on a treadmill at -0.67 m · s(-1). Data were collected before, immediately post, and 24-, 48- and 168-h post-downhill backwards walking. Achilles tendon aponeurosis elongation, strain and stiffness were measured using ultrasonography. Muscle force decreased immediately post-downhill backward walking (P = 0.019). There were increases in Achilles tendon aponeurosis stiffness at 24-h post-downhill backward walking (307 ± 179.6 N · mm(-1), P = 0.004), and decreases in Achilles tendon aponeurosis strain during maximum voluntary contraction at 24 (3.8 ± 1.7%, P = 0.008) and 48 h (3.9 ± 1.8%, P = 0.002) post. Repeated cyclical loading of downhill backwards walking affects the behaviour of the muscle-tendon unit, most likely by altering muscle compliance, and these changes result in tendon stiffness increases.

Comparative Mitogenomics of the Assassin Bug Genus Peirates (Hemiptera: Reduviidae: Peiratinae) Reveal Conserved Mitochondrial Genome Organization of P. atromaculatus, P. fulvescens and P. turpis

PubMed Central

Zhao, Guangyu; Li, Hu; Zhao, Ping; Cai, Wanzhi

2015-01-01

In this study, we sequenced four new mitochondrial genomes and presented comparative mitogenomic analyses of five species in the genus Peirates (Hemiptera: Reduviidae). Mitochondrial genomes of these five assassin bugs had a typical set of 37 genes and retained the ancestral gene arrangement of insects. The A+T content, AT- and GC-skews were similar to the common base composition biases of insect mtDNA. Genomic size ranges from 15,702 bp to 16,314 bp and most of the size variation was due to length and copy number of the repeat unit in the putative control region. All of the control region sequences included large tandem repeats present in two or more copies. Our result revealed similarity in mitochondrial genomes of P. atromaculatus, P. fulvescens and P. turpis, as well as the highly conserved genomic-level characteristics of these three species, e.g., the same start and stop codons of protein-coding genes, conserved secondary structure of tRNAs, identical location and length of non-coding and overlapping regions, and conservation of structural elements and tandem repeat unit in control region. Phylogenetic analyses also supported a close relationship between P. atromaculatus, P. fulvescens and P. turpis, which might be recently diverged species. The present study indicates that mitochondrial genome has important implications on phylogenetics, population genetics and speciation in the genus Peirates. PMID:25689825

Repeated fault rupture recorded by paleoenvironmental changes in a wetland sedimentary sequence ponded against the Alpine Fault, New Zealand

NASA Astrophysics Data System (ADS)

Clark, K.; Berryman, K. R.; Cochran, U. A.; Bartholomew, T.; Turner, G. M.

2010-12-01

At Hokuri Creek, in south Westland, New Zealand, an 18 m thickness of Holocene sediments has accumulated against the upthrown side of the Alpine Fault. Recent fluvial incision has created numerous exposures of this sedimentary sequence. At a decimetre to metre scale there are two dominant types of sedimentary units: clastic-dominated, grey silt packages, and organic-dominated, light brown peaty-silt units. These units represent repeated alternations of the paleoenvironment due to fault rupture over the past 7000 years. We have located the event horizons within the sedimentary sequence, and identified evidence to support earthquake-driven paleoenvironmental change (rather than climatic variability), and developed a model of paleoenvironmental changes over a typical seismic cycle. To quantitatively characterise the sediments we use high resolution photography, x-ray imaging, magnetic-susceptibility and total carbon analysis. To understand the depositional environment we used diatom and pollen studies. The organic-rich units have very low magnetic susceptibility and density values, with high greyscale and high total carbon values. Diatoms indicate these units represent stable wetland environments with standing water and predominantly in-situ organic material deposition. The clastic-rich units are characterised by higher magnetic susceptibility and density values, with low greyscale and total carbon. The clastic-rich units represent environments of flowing water and deep pond settings that received predominantly catchment-derived silt and sand. The event horizon is located at the upper contact of the organic-rich horizons. The event horizon contact marks a drastic change in hydrologic regime as fault rupture changed the stream base level and there was a synchronous influx of clastic sediment as the catchment responded to earthquake shaking. During the interseismic period the flowing-water environment gradually stabilised and returned to an organic-rich wetland. Such cycles were repeated 18 times at Hokuri Creek. Evidence that fault rupture was responsible for the cyclical paleoenvironmental changes at Hokuri Creek include: the average time period for each organic- and clastic-rich couplet to be deposited approximately equals the long-term average Alpine Fault recurrence interval, and the most recent events recorded at Hokuri correlate to an earthquake dated in paleoseismic trenches 100 km along strike; fault rupture is the only mechanism that can create accommodation space for 18 m of sediment to accumulate, and the sedimentary units can be traced from the outcrop to the fault trace and show tectonic deformation. The record of 18 fault rupture events at Hokuri Creek is one of the longest records of surface ruptures on a major plate boundary fault. High-resolution dating and statistical treatment of the radiocarbon data (Biasi et al., this meeting) has resulted in major advances in understanding the long-term behaviour of the Alpine Fault (Berryman et al., this meeting).

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

ERIC Educational Resources Information Center

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…

Adhesive compositions and methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, Scott D.; Sendijarevic, Vahid; O'Connor, James

The present invention encompasses polyurethane adhesive compositions comprising aliphatic polycarbonate chains. In one aspect, the present invention encompasses polyurethane adhesives derived from aliphatic polycarbonate polyols and polyisocyanates wherein the polyol chains contain a primary repeating unit having a structure:. In another aspect, the invention provides articles comprising the inventive polyurethane compositions as well as methods of making such compositions.

Evaluating Communicative Language by Using Creative Dialogues

ERIC Educational Resources Information Center

de Souza Miranda, Mateus Emerson

2017-01-01

Students need opportunities to be creative and express themselves while learning a new language, during both classroom activities and tests at the end of a term or unit. The focus of the author's practice when assessing students' knowledge is to use creative dialogue techniques as a way to prevent students from simply repeating a given dialogue…

The Effects of Computerized Instruction and Systematic Presentation and Review of Math Fact Acquisition and Fluency

ERIC Educational Resources Information Center

Reynolds, Jennifer L.

2010-01-01

Cross country investigations have repeatedly demonstrated the disappointing math performance of students in the United States (Beatty, 1997; Ferrini-Mundy & Schmidt, 2005). The National Council of Teachers of Mathematics (2000) listed failure to rapidly recall basic facts as a common problem associated with disabilities in mathematics and…

16 CFR 1616.31 - Labeling, recordkeeping, retail display and guaranties.

Code of Federal Regulations, 2014 CFR

2014-01-01

... process of manufacture of each production unit of articles of children's sleepwear, or fabrics or related... content, and details of construction on all seams, fabrics, threads, stitches, and trims used in each... sufficient to repeat the prototype tests required by § 1616.4 of the Standard for all fabrics, seams, threads...

16 CFR § 1616.31 - Labeling, recordkeeping, retail display and guaranties.

Code of Federal Regulations, 2013 CFR

2013-01-01

... process of manufacture of each production unit of articles of children's sleepwear, or fabrics or related... content, and details of construction on all seams, fabrics, threads, stitches, and trims used in each... sufficient to repeat the prototype tests required by § 1616.4 of the Standard for all fabrics, seams, threads...

16 CFR 1616.31 - Labeling, recordkeeping, retail display and guaranties.

Code of Federal Regulations, 2011 CFR

2011-01-01

... process of manufacture of each production unit of articles of children's sleepwear, or fabrics or related... content, and details of construction on all seams, fabrics, threads, stitches, and trims used in each... sufficient to repeat the prototype tests required by § 1616.4 of the Standard for all fabrics, seams, threads...

16 CFR 1616.31 - Labeling, recordkeeping, retail display and guaranties.

Code of Federal Regulations, 2012 CFR

2012-01-01

... process of manufacture of each production unit of articles of children's sleepwear, or fabrics or related... content, and details of construction on all seams, fabrics, threads, stitches, and trims used in each... sufficient to repeat the prototype tests required by § 1616.4 of the Standard for all fabrics, seams, threads...

Problems of the Randomization Test for AB Designs

ERIC Educational Resources Information Center

Manolov, Rumen; Solanas, Antonio

2009-01-01

N = 1 designs imply repeated registrations of the behaviour of the same experimental unit and the measurements obtained are often few due to time limitations, while they are also likely to be sequentially dependent. The analytical techniques needed to enhance statistical and clinical decision making have to deal with these problems. Different…

National Prevalence Rates of Bully Victimization among Students with Disabilities in the United States

ERIC Educational Resources Information Center

Blake, Jamilia J.; Lund, Emily M.; Zhou, Qiong; Kwok, Oi-man; Benz, Michael R.

2012-01-01

This study examined the prevalence rates of bully victimization and risk for repeated victimization among students with disabilities using the Special Education Elementary Longitudinal Study and the National Longitudinal Transition Study-2 longitudinal datasets. Results revealed that a prevalence rate ranging from 24.5% in elementary school to…

Capitalization and Punctuation.

ERIC Educational Resources Information Center

Lewis, Teresa Marie

An elementary school unit on punctuation skills is divided into nine sections. Section 1 contains a pretest which is repeated in section 9 as a posttest. Section 2 consists of a series of punctuation mark caricatures to put on the classroom bulletin board. Sections 3 through 7 contain material on the following topics: end of sentence punctuation,…

Riparian Areas of the Southwest: Learning from Repeat Photographs

ERIC Educational Resources Information Center

Zaimes, George N.; Crimmins, Michael A.

2010-01-01

Spatial and temporal variability of riparian areas, as well as potential impacts from climate change, are concepts that land and water managers and stakeholders need to understand to effectively manage and protect riparian areas. Rapid population growth in the southwestern United States, and multiple-use designation of most riparian areas, makes…

The Central Hardwood Forest: its boundaries and physiographic provinces

Treesearch

James S. Fralish

2003-01-01

The Central Hardwood Forest (CHF) refers to the area where deciduous hardwood species overwhelmingly, but not exclusively, dominate the stands and cover types that occur as repeating units across the landscape. Transition zones where Central Hardwood species mix with species from adjacent regions identify boundaries of the region. These regions are the Northern...

The Central Hardwood Forest: Its Boundaries and Physiographic Provinces

Treesearch

James S. Fralish

2003-01-01

The Central Hardwood Forest (CHF) refers to the area where deciduous hardwood species overwhelmingly, but not exclusively, dominate the stands and cover types that occur as repeating units across the landscape. Transition zones where Central Hardwood species mix with species from adjacent regions identify boundaries of the region. These regions are the Northern...

Evaluation of predicted Medfly (Ceratitis capitata) quarantine length in the United States utilizing degree-day and agent-based models

USDA-ARS?s Scientific Manuscript database

Invasions by pest insects pose a significant threat to agriculture worldwide. In the case of Ceratitis capitata incursions on the US mainland, where it is not officially established, repeated detections are followed by quarantines to eliminate the invading population. However, it is notoriously diff...

Reputation Enhancement and School Delinquency: A Prospective Study Using the National Educational Longitudinal Survey [NELS:88

ERIC Educational Resources Information Center

Smith-Adcock, Sondra; Lee, Sang Min; Kerpelman, Jennifer; Majuta, Aaron; Young, Choi Bo

2013-01-01

High school delinquency, adolescent behaviors ranging from repeated school misconduct to being arrested, is a critical concern in the United States. Though widely believed that reputation is related to adolescent behavior, few studies have addressed the relationship between adolescent reputation and delinquency. Using the National Educational…

Language, Literacy, and the Older Refugee in America: Research Agenda for the 90s.

ERIC Educational Resources Information Center

Weinstein-Shr, Gail; Lewis, Nora E.

As the large immigrant/refugee population in the United States ages, mainstream institutions, such as schools, workplaces, and social services, are increasingly challenged to meet the needs of elders. Certain themes and difficulties in acculturation emerge repeatedly, including financial insecurities, health issues, loneliness and isolation,…

Ladder-Type Circuits Revisited

ERIC Educational Resources Information Center

Yoon, Sung Hyun

2007-01-01

Ladder-type circuits where a given unit is repeated infinitely many times are dealt with in many textbooks on electromagnetism as examples of filter circuits. Determining the impedance of such circuits seems to be regarded as simple, which may be due to the fact that the invariance of the infinite system under the operation of adding one more unit…

"Hiding in Plain Sight": An Interview with Cara Hoffman

ERIC Educational Resources Information Center

Hosey, Sara

2014-01-01

Cara Hoffman's work enacts George Orwell's imperative to "pay attention to the obvious" (an idea that several sympathetic characters repeat in her 2011 novel "So Much Pretty"), probing aspects of twenty-first century life in the United States that have become so accepted as to be unremarkable, such as epidemic levels of…

47 CFR 80.413 - On-board station equipment records.

Code of Federal Regulations, 2010 CFR

2010-10-01

... identification of the on-board station; (2) The number and type of repeater and mobile units used on-board the... 47 Telecommunication 5 2010-10-01 2010-10-01 false On-board station equipment records. 80.413... SERVICES STATIONS IN THE MARITIME SERVICES Station Documents § 80.413 On-board station equipment records...

47 CFR 80.413 - On-board station equipment records.

Code of Federal Regulations, 2012 CFR

2012-10-01

... identification of the on-board station; (2) The number and type of repeater and mobile units used on-board the... 47 Telecommunication 5 2012-10-01 2012-10-01 false On-board station equipment records. 80.413... SERVICES STATIONS IN THE MARITIME SERVICES Station Documents § 80.413 On-board station equipment records...

47 CFR 80.413 - On-board station equipment records.

Code of Federal Regulations, 2011 CFR

2011-10-01

... identification of the on-board station; (2) The number and type of repeater and mobile units used on-board the... 47 Telecommunication 5 2011-10-01 2011-10-01 false On-board station equipment records. 80.413... SERVICES STATIONS IN THE MARITIME SERVICES Station Documents § 80.413 On-board station equipment records...

47 CFR 80.413 - On-board station equipment records.

Code of Federal Regulations, 2014 CFR

2014-10-01

... identification of the on-board station; (2) The number and type of repeater and mobile units used on-board the... 47 Telecommunication 5 2014-10-01 2014-10-01 false On-board station equipment records. 80.413... SERVICES STATIONS IN THE MARITIME SERVICES Station Documents § 80.413 On-board station equipment records...

47 CFR 80.413 - On-board station equipment records.

Code of Federal Regulations, 2013 CFR

2013-10-01

... identification of the on-board station; (2) The number and type of repeater and mobile units used on-board the... 47 Telecommunication 5 2013-10-01 2013-10-01 false On-board station equipment records. 80.413... SERVICES STATIONS IN THE MARITIME SERVICES Station Documents § 80.413 On-board station equipment records...

A repeated-measures study of recreational water exposure, non-point source pollution, and risk of illness

EPA Science Inventory

Discharge of stormwater runoff onto beaches is a major cause of beach closings and advisories in the United States. Prospective studies of recreational water quality and health have often been limited to two time points (baseline and follow-up). Little is known about the risk of ...

Phylogeographic patterns of Armillaria ostoyae in the western United States

Treesearch

J. W. Hanna; N. B. Klopfenstein; M. -S. Kim; G. I. McDonald; J. A. Moore

2007-01-01

Nuclear ribosomal DNA regions (i.e. large subunit, internal transcribed spacer, 5.8S and intergenic spacer) were sequenced using a direct-polymerase chain reaction method from Armillaria ostoyae genets collected from the western USA. Many of the A. ostoyae genets contained heterogeneity among rDNA repeats, indicating intragenomic variation and likely intraspecific...

Estimating Summer Nutrient Concentrations in Northeastern Lakes from SPARROW Load Predictions and Modeled Lake Depth and Volume

EPA Science Inventory

Global nutrient cycles have been altered by use of fossil fuels and fertilizers resulting in increases in nutrient loads to aquatic systems. In the United States, excess nutrients have been repeatedly reported as the primary cause of lake water quality impairments. Setting nutr...

21 CFR 526.1696d - Penicillin G procaine-novobiocin for intramammary infusion.

Code of Federal Regulations, 2010 CFR

2010-04-01

... novobiocin as novobiocin sodium. For dry cows: 200,000 units of penicillin G procaine and 400 milligrams of... of use—(1) Lactating cows—(i) Amount. 10 milliliters in each infected quarter after milking. Repeat once after 24 hours. (ii) Indications for use. Treating lactating cows for mastitis caused by...

Modeling containment of large wildfires using generalized linear mixed-model analysis

Treesearch

Mark Finney; Isaac C. Grenfell; Charles W. McHugh

2009-01-01

Billions of dollars are spent annually in the United States to contain large wildland fires, but the factors contributing to suppression success remain poorly understood. We used a regression model (generalized linear mixed-model) to model containment probability of individual fires, assuming that containment was a repeated-measures problem (fixed effect) and...

Sources of Social Support among International College Students in the United States

ERIC Educational Resources Information Center

Bhochhibhoya, Amir; Dong, Yue; Branscum, Paul

2017-01-01

International students are challenged due to the abrupt change in social support. The purpose of this study was to operationalize different sources of social support and evaluate determinants of mental health among international students (n = 328). An instrument was developed to measure four distinct sources of social support. Repeated measures…

Binding Facilitates Attention Switching within Working Memory

ERIC Educational Resources Information Center

Bao, Min; Li, Zhi-Hao; Zhang, Da-Ren

2007-01-01

The authors investigated the units of selective attention within working memory. In Experiment 1, a group of participants kept 1 count and 1 location in working memory and updated them repeatedly in random order. Another group of participants were instructed to achieve the same goal by memorizing the verbal and spatial information in an…

Identification and characterization of six glycosyltransferases involved in the biosynthesis of a new bacterial exopolysaccharide in Paenibacillus elgii.

PubMed

Ou, Li; Ang, Li; Chujun, Zhang; Jingyu, Huang; Yongli, Meng; Shenjing, Yuan; Junhua, Huang; Xu, Gao; Yulong, Yao; Rui, Yin; Jinpan, Hu; Bin, Ding; Xiufang, Hu

2018-02-01

Paenibacillus elgii B69 produces a new xylose-containing exopolysaccharide (EPS) that effectively removes the pollutants from wastewater through flocculation. However, information about the biosynthesis of this EPS is limited. In this study, sequence analysis showed six putative glycosyltransferases (GTs) genes in polysaccharide gene clusters involved in glycosidic linkages of repeating units. Each gene was deleted and phenotypes were examined to understand the functions of these genes. Two of the genes were deleted successfully to encode a priming glucose GT and a side-chain xylose GT, but other genes were unsuccessfully deleted because of the accumulation of toxic intermediate products. The six genes were cloned and expressed in Escherichia coli, and the corresponding enzymes were purified. The activity of GTs was analyzed through mass spectrometry by using the purified membrane fraction as a lipid carrier receptor after a hexasaccharide repeated unit was reconstructed in vitro. The specificities of six different GTs and the building order of the hexasaccharide were characterized. This study provided a basis for future research on the biosynthetic pathway of EPS in Paenibacillus or other genera.

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

DOEpatents

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.

Structural study and conformational behavior of the two different lipopolysaccharide O-antigens produced by the cystic fibrosis pathogen Burkholderia multivorans.

PubMed

Ieranò, Teresa; Silipo, Alba; Cescutti, Paola; Leone, Maria Rosaria; Rizzo, Roberto; Lanzetta, Rosa; Parrilli, Michelangelo; Molinaro, Antonio

2009-07-20

Lipopolysaccharides (LPSs) are virulence factors expressed by gram-negative bacteria; they are among those mainly responsible for bacterial virulence. In this work we define the primary structure and the conformational features of the O-chain from the LPS produced by the highly virulent clinical isolate Burkholderia multivorans strain C1576, an opportunistic human pathogen isolated in a cystic fibrosis center and causative of an outbreak with lethal outcome. We demonstrate that the LPS from this clinical isolate consists of two O-polysaccharide chains present in different amounts and made up of repeating units, both containing deoxy sugar. Additionally, conformational studies have been performed to establish and compare the spatial arrangements of the two polysaccharides and differences in their shape have been highlighted. The comprehension of the structural and conformational features of the two repeating units may help to explain their biological significance, the molecular shape of the bacterial external surface, and the comprehension at the molecular level of the recognition mechanisms of the antibodies.

Coarse-Grained and Atomistic Modeling of Polyimides

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Hinkley, Jeffrey A.

2004-01-01

A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of BPDA (3,3,4,4' - biphenyltetracarboxylic dianhydride) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energy between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarsegrained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit.

Variable-number-of-tandem-repeats analysis of genetic diversity in Pasteuria ramosa.

PubMed

Mouton, L; Ebert, D

2008-05-01

Variable-number-of-tandem-repeats (VNTR) markers are increasingly being used in population genetic studies of bacteria. They were recently developed for Pasteuria ramosa, an endobacterium that infects Daphnia species. In the present study, we genotyped P. ramosa in 18 infected hosts from the United Kingdom, Belgium, and two lakes in the United States using seven VNTR markers. Two Daphnia species were collected: D. magna and D. dentifera. Six loci showed length polymorphism, with as many as five alleles identified for a single locus. Similarity coefficient calculations showed that the extent of genetic variation between pairs of isolates within populations differed according to the population, but it was always less than the genetic distances among populations. Analysis of the genetic distances performed using principal component analysis revealed strong clustering by location of origin, but not by host Daphnia species. Our study demonstrated that the VNTR markers available for P. ramosa are informative in revealing genetic differences within and among populations and may therefore become an important tool for providing detailed analysis of population genetics and epidemiology.

Fuel cell repeater unit including frame and separator plate

DOEpatents

Yamanis, Jean; Hawkes, Justin R; Chiapetta, Jr., Louis; Bird, Connie E; Sun, Ellen Y; Croteau, Paul F

2013-11-05

An example fuel cell repeater includes a separator plate and a frame establishing at least a portion of a flow path that is operative to communicate fuel to or from at least one fuel cell held by the frame relative to the separator plate. The flow path has a perimeter and any fuel within the perimeter flow across the at least one fuel cell in a first direction. The separator plate, the frame, or both establish at least one conduit positioned outside the flow path perimeter. The conduit is outside of the flow path perimeter and is configured to direct flow in a second, different direction. The conduit is fluidly coupled with the flow path.

Complete mitochondrial genome of the yellowtail clownfish Amphiprion clarkii (Pisces: Perciformes, Pomacentridae).

PubMed

Tao, Yong; Li, Jian-Long; Liu, Min; Hu, Xue-Yi

2016-01-01

In this study we determined the complete mitochondrial (mt) genome of the yellowtail clownfish Amphiprion clarkii using eight consensus primer pairs with a long PCR technique. The circular mtDNA molecule was 16,976 bp in size and the overall nucleotide composition of the H-strand was 29.15% A, 26.15% T, 15.67% G and 29.03% C, with an A + T bias. The complete mitogenome contained 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 1 control region (D-loop), and the gene order was typical of vertebrate mitogenomes. We determined five complete continuity tandem repeat units and one imperfect tandem repeat, all located downstream in the control region.

C9orf72 hexanucleotide repeat expansion and Guam amyotrophic lateral sclerosis-Parkinsonism-dementia complex.

PubMed

Dombroski, Beth A; Galasko, Douglas R; Mata, Ignacio F; Zabetian, Cyrus P; Craig, Ulla-Katrina; Garruto, Ralph M; Oyanagi, Kiyomitsu; Schellenberg, Gerard D

2013-06-01

High-prevalence foci of amyotrophic lateral sclerosis (ALS) and parkinsonism-dementia complex (PDC) exist in Japanese on the Kii Peninsula of Japan and in the Chamorros of Guam. Clinical and neuropathologic similarities suggest that the disease in these 2 populations may be related. Recent findings showed that some of the Kii Peninsula ALS cases had pathogenic C9orf72 repeat expansions, a genotype that causes ALS in Western populations. To perform genotyping among Guam residents to determine if the C9orf72 expanded repeat allele contributes to ALS-PDC in this population and to evaluate LRRK2 for mutations in the same population. Case-control series from neurodegenerative disease research programs on Guam that screened residents for ALS, PDC, and dementia. Study participants included 24 with ALS and 22 with PDC and 43 older control subjects with normal cognition ascertained between 1956 and 2006. All but one participant were Chamorro, the indigenous people of Guam. A single individual of white race/ethnicity with ALS was ascertained on Guam during the study. Participants were screened for C9orf72 hexanucleotide repeat length. Participants with repeat numbers in great excess of 30 were considered to have pathogenic repeat expansions. LRRK2 was screened for point mutations by DNA sequencing. We found a single individual with an expanded pathogenic hexanucleotide repeat. This individual of white race/ethnicity with ALS was living on Guam at the time of ascertainment but had been born in the United States. All Chamorro participants with ALS and PDC and control subjects had normal repeats, ranging from 2 to 17 copies. No pathogenic LRRK2 mutations were found. Unlike participants with ALS from the Kii Peninsula, C9orf72 expansions do not cause ALS-PDC in Chamorros. Likewise, LRRK2 mutations do not cause Guam ALS-PDC.

Effect of Repeat Copy Number on Variable-Number Tandem Repeat Mutations in Escherichia coli O157:H7

PubMed Central

Vogler, Amy J.; Keys, Christine; Nemoto, Yoshimi; Colman, Rebecca E.; Jay, Zack; Keim, Paul

2006-01-01

Variable-number tandem repeat (VNTR) loci have shown a remarkable ability to discriminate among isolates of the recently emerged clonal pathogen Escherichia coli O157:H7, making them a very useful molecular epidemiological tool. However, little is known about the rates at which these sequences mutate, the factors that affect mutation rates, or the mechanisms by which mutations occur at these loci. Here, we measure mutation rates for 28 VNTR loci and investigate the effects of repeat copy number and mismatch repair on mutation rate using in vitro-generated populations for 10 E. coli O157:H7 strains. We find single-locus rates as high as 7.0 × 10−4 mutations/generation and a combined 28-locus rate of 6.4 × 10−4 mutations/generation. We observed single- and multirepeat mutations that were consistent with a slipped-strand mispairing mutation model, as well as a smaller number of large repeat copy number mutations that were consistent with recombination-mediated events. Repeat copy number within an array was strongly correlated with mutation rate both at the most mutable locus, O157-10 (r2 = 0.565, P = 0.0196), and across all mutating loci. The combined locus model was significant whether locus O157-10 was included (r2 = 0.833, P < 0.0001) or excluded (r2 = 0.452, P < 0.0001) from the analysis. Deficient mismatch repair did not affect mutation rate at any of the 28 VNTRs with repeat unit sizes of >5 bp, although a poly(G) homomeric tract was destabilized in the mutS strain. Finally, we describe a general model for VNTR mutations that encompasses insertions and deletions, single- and multiple-repeat mutations, and their relative frequencies based upon our empirical mutation rate data. PMID:16740932

The repeat organizer, a specialized insulator element within the intergenic spacer of the Xenopus rRNA genes.

PubMed Central

Robinett, C C; O'Connor, A; Dunaway, M

1997-01-01

We have identified a novel activity for the region of the intergenic spacer of the Xenopus laevis rRNA genes that contains the 35- and 100-bp repeats. We devised a new assay for this region by constructing DNA plasmids containing a tandem repeat of rRNA reporter genes that were separated by the 35- and 100-bp repeat region and a rRNA gene enhancer. When the 35- and 100-bp repeat region is present in its normal position and orientation at the 3' end of the rRNA reporter genes, the enhancer activates the adjacent downstream promoter but not the upstream rRNA promoter on the same plasmid. Because this element can restrict the range of an enhancer's activity in the context of tandem genes, we have named it the repeat organizer (RO). The ability to restrict enhancer action is a feature of insulator elements, but unlike previously described insulator elements the RO does not block enhancer action in a simple enhancer-blocking assay. Instead, the activity of the RO requires that it be in its normal position and orientation with respect to the other sequence elements of the rRNA genes. The enhancer-binding transcription factor xUBF also binds to the repetitive sequences of the RO in vitro, but these sequences do not activate transcription in vivo. We propose that the RO is a specialized insulator element that organizes the tandem array of rRNA genes into single-gene expression units by promoting activation of a promoter by its proximal enhancers. PMID:9111359

Inheritance patterns of ATCCT repeat interruptions in spinocerebellar ataxia type 10 (SCA10) expansions.

PubMed

Landrian, Ivette; McFarland, Karen N; Liu, Jilin; Mulligan, Connie J; Rasmussen, Astrid; Ashizawa, Tetsuo

2017-01-01

Spinocerebellar ataxia type 10 (SCA10), an autosomal dominant cerebellar ataxia disorder, is caused by a non-coding ATTCT microsatellite repeat expansion in the ataxin 10 gene. In a subset of SCA10 families, the 5'-end of the repeat expansion contains a complex sequence of penta- and heptanucleotide interruption motifs which is followed by a pure tract of tandem ATCCT repeats of unknown length at its 3'-end. Intriguingly, expansions that carry these interruption motifs correlate with an epileptic seizure phenotype and are unstable despite the theory that interruptions are expected to stabilize expanded repeats. To examine the apparent contradiction of unstable, interruption-positive SCA10 expansion alleles and to determine whether the instability originates outside of the interrupted region, we sequenced approximately 1 kb of the 5'-end of SCA10 expansions using the ATCCT-PCR product in individuals across multiple generations from four SCA10 families. We found that the greatest instability within this region occurred in paternal transmissions of the allele in stretches of pure ATTCT motifs while the intervening interrupted sequences were stable. Overall, the ATCCT interruption changes by only one to three repeat units and therefore cannot account for the instability across the length of the disease allele. We conclude that the AT-rich interruptions locally stabilize the SCA10 expansion at the 5'-end but do not completely abolish instability across the entire span of the expansion. In addition, analysis of the interruption alleles across these families support a parsimonious single origin of the mutation with a shared distant ancestor.

Bioinformatic analyses implicate the collaborating meiotic crossover/chiasma proteins Zip2, Zip3, and Spo22/Zip4 in ubiquitin labeling

PubMed Central

Perry, Jason; Kleckner, Nancy; Börner, G. Valentin

2005-01-01

Zip2 and Zip3 are meiosis-specific proteins that, in collaboration with several partners, act at the sites of crossover-designated, axis-associated recombinational interactions to mediate crossover/chiasma formation. Here, Spo22 (also called Zip4) is identified as a probable functional collaborator of Zip2/3. The molecular roles of Zip2, Zip3, and Spo22/Zip4 are unknown. All three proteins are part of a small evolutionary cohort comprising similar homologs in four related yeasts. Zip3 is shown to contain a RING finger whose structural features most closely match those of known ubiquitin E3s. Further, Zip3 exhibits major domainal homologies to Rad18, a known DNA-binding ubiquitin E3. Also described is an approach to the identification and mapping of repeated protein sequence motifs, Alignment Based Repeat Annotation (ABRA), that we have developed. When ABRA is applied to Zip2 and Spo22/Zip4, they emerge as a 14-blade WD40-like repeat protein and a 22-unit tetratricopeptide repeat protein, respectively. WD40 repeats of Cdc20, Cdh1, and Cdc16 and tetratricopeptide repeats of Cdc16, Cdc23, and Cdc27, all components of the anaphase-promoting complex, are also analyzed. These and other findings suggest that Zip2, Zip3, and Zip4 act together to mediate a process that involves Zip3-mediated ubiquitin labeling, potentially as a unique type of ubiquitin-conjugating complex. PMID:16314568

The study design elements employed by researchers in preclinical animal experiments from two research domains and implications for automation of systematic reviews.

PubMed

O'Connor, Annette M; Totton, Sarah C; Cullen, Jonah N; Ramezani, Mahmood; Kalivarapu, Vijay; Yuan, Chaohui; Gilbert, Stephen B

2018-01-01

Systematic reviews are increasingly using data from preclinical animal experiments in evidence networks. Further, there are ever-increasing efforts to automate aspects of the systematic review process. When assessing systematic bias and unit-of-analysis errors in preclinical experiments, it is critical to understand the study design elements employed by investigators. Such information can also inform prioritization of automation efforts that allow the identification of the most common issues. The aim of this study was to identify the design elements used by investigators in preclinical research in order to inform unique aspects of assessment of bias and error in preclinical research. Using 100 preclinical experiments each related to brain trauma and toxicology, we assessed design elements described by the investigators. We evaluated Methods and Materials sections of reports for descriptions of the following design elements: 1) use of comparison group, 2) unit of allocation of the interventions to study units, 3) arrangement of factors, 4) method of factor allocation to study units, 5) concealment of the factors during allocation and outcome assessment, 6) independence of study units, and 7) nature of factors. Many investigators reported using design elements that suggested the potential for unit-of-analysis errors, i.e., descriptions of repeated measurements of the outcome (94/200) and descriptions of potential for pseudo-replication (99/200). Use of complex factor arrangements was common, with 112 experiments using some form of factorial design (complete, incomplete or split-plot-like). In the toxicology dataset, 20 of the 100 experiments appeared to use a split-plot-like design, although no investigators used this term. The common use of repeated measures and factorial designs means understanding bias and error in preclinical experimental design might require greater expertise than simple parallel designs. Similarly, use of complex factor arrangements creates novel challenges for accurate automation of data extraction and bias and error assessment in preclinical experiments.

Routine bacterial screening of apheresis platelets on Day 4 using a rapid test: a 4-year single-center experience.

PubMed

Dunbar, Nancy M; Kreuter, Justin D; Marx-Wood, Cynthia R; Dumont, Larry J; Szczepiorkowski, Zbigniew M

2013-10-01

The platelet (PLT) Pan Genera Detection test (PGD) is a rapid bacterial detection system used to screen PLTs for bacterial contamination. We report a single center 46-month experience with secondary screening of apheresis PLTs by PGD testing. Existing testing records of apheresis PLTs screened by PGD from July 2008 to April 2012 were reviewed. All PLT units were initially screened by routine postcollection culture methods. Secondary screening using PGD was performed for indated PLTs on PLT storage Day 4 and for outdated PLTs on Day 8. A total of 8535 apheresis PLTs were available in inventory during the study period. Of these, 5030 (58.9%) were dispensed and transfused before PGD testing and 3505 (41.1%) underwent PGD testing on Day 4. Twenty-five units tested on Day 4 were PGD initial reactive (0.71%). All were confirmed to be false positive by repeat PGD testing in triplicate (n=20) or by confirmatory culture (n=5). An additional 364 units that were PGD nonreactive on Day 4 were approved for transfusion on Day 6 or Day 7 due to urgent clinical need. A total of 371 outdated units underwent repeat PGD testing before discard on Day 8; all were nonreactive. Secondary PGD testing of culture-screened apheresis PLTs results in low yield in a medium-sized transfusion service. Use of PGD testing on Day 4 may allow for extension of the apheresis PLT shelf life to Day 7 for hospitals that face supply constraints. © 2013 American Association of Blood Banks.

Getting evidence-based pressure ulcer prevention into practice: a multi-faceted unit-tailored intervention in a hospital setting.

PubMed

Sving, Eva; Högman, Marieann; Mamhidir, Anna-Greta; Gunningberg, Lena

2016-10-01

The aim of the study was to evaluate whether a multi-faceted, unit-tailored intervention using evidenced-based pressure ulcer prevention affects (i) the performance of pressure ulcer prevention, (ii) the prevalence of pressure ulcers and (iii) knowledge and attitudes concerning pressure ulcer prevention among registered and assistant nurses. A quasi-experimental, clustered pre- and post-test design was used. Five units at a hospital setting were included. The intervention was based on the PARIHS framework and included a multi-professional team, training and repeated quality measurements. An established methodology was used to evaluate the prevalence and prevention of pressure ulcers. Nurses' knowledge and attitudes were evaluated using a validated questionnaire. A total of 506 patients were included, of whom 105 patients had a risk to develop pressure ulcer. More patients were provided pressure ulcer prevention care (P = 0·001) and more prevention care was given to each patient (P = 0·021) after the intervention. Corresponding results were shown in the group of patients assessed as being at risk for developing pressure ulcers. Nurses' knowledge about pressure ulcer prevention increased (P < 0·001). Positive attitudes towards pressure ulcer prevention remained high between pre- and post-test surveys. This multi-faceted unit-tailored intervention affected pressure ulcer prevention. Facilitation and repeated quality measurement together with constructed feedback of results seemed to be the most important factor for pressure ulcer prevention. © 2014 The Authors. International Wound Journal © 2014 Medicalhelplines.com Inc and John Wiley & Sons Ltd.

Effect of ionization, bedding, and feeding on air quality in a horse stable.

PubMed

Siegers, Esther Willemijn; Anthonisse, Milou; van Eerdenburg, Frank J C M; van den Broek, Jan; Wouters, Inge M; Westermann, Cornélie Martine

2018-05-01

Organic dust is associated with Equine asthma. Ionization should reduce airborne dust levels. To determine the effect of ionization of air, type of bedding, and feed on the levels of airborne dust, endotoxin, and fungal colonies in horse stables. 24 healthy University-owned horses occupied the stables. A randomized controlled cross-over study. Four units with 6 stables were equipped with an ionization installation (25 VA, 5000 Volt Direct Current). Horses were kept either on wood shavings and fed haylage (2 units), or on straw and fed dry hay (2 units). Measurements were performed with and without activated ionization, during daytime and nighttime, repeatedly over the course of a week and repeatedly during 4-6 weeks. Statistical analysis was performed using a mixed effect model with Akaike's Information Criterion for model reduction and 95% profile (log) likelihood confidence intervals (CI). Ionization did not alter concentrations of dust, endotoxin, or fungi, fewer. In the units with straw and hay, the concentration of dust, endotoxin, and fungi (difference in logarithmic mean 1.92 (95%CI 1.71-2.12); 2.86 (95%CI 2.59-3.14); 1.75 (95%CI 1.13-2.36)) were significantly higher compared to wood shavings and haylage. The installation of a negative air-ionizer in the horse stable did not reduce concentrations of dust, endotoxin, and viable fungal spores. The substantial effect of low dust bedding and feed is confirmed. Copyright © 2018 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

Acceleration Techniques for Recombination of Gases in Electrolysis Microactuators with Nafion®-Coated Electrocatalyst

PubMed Central

Sheybani, Roya; Meng, Ellis

2015-01-01

Recombination of electrolysis gases (oxidation of hydrogen and reduction of oxygen) is an important factor in operation efficiency of devices employing electrolysis such as actuators and also unitized regenerative fuel cells. Several methods of improving recombination speed and repeatability were developed for application to electrolysis microactuators with Nafion®-coated catalytic electrodes. Decreasing the electrolysis chamber volume increased the speed, consistency, and repeatability of the gas recombination rate. To further improve recombination performance, methods to increase the catalyst surface area, hydrophobicity, and availability were developed and evaluated. Of these, including in the electrolyte pyrolyzed-Nafion®-coated Pt segments contained in the actuator chamber accelerated recombination by increasing the catalyst surface area and decreasing the gas transport diffusion path. This approach also reduced variability in recombination encountered under varying actuator orientation (resulting in differing catalyst/gas bubble proximity) and increased the rate of recombination by 2.3 times across all actuator orientations. Repeatability of complete recombination for different generated gas volumes was studied through cycling. PMID:26251561

Airborne Radar Interferometric Repeat-Pass Processing

NASA Technical Reports Server (NTRS)

Hensley, Scott; Michel, Thierry R.; Jones, Cathleen E.; Muellerschoen, Ronald J.; Chapman, Bruce D.; Fore, Alexander; Simard, Marc; Zebker, Howard A.

2011-01-01

Earth science research often requires crustal deformation measurements at a variety of time scales, from seconds to decades. Although satellites have been used for repeat-track interferometric (RTI) synthetic-aperture-radar (SAR) mapping for close to 20 years, RTI is much more difficult to implement from an airborne platform owing to the irregular trajectory of the aircraft compared with microwave imaging radar wavelengths. Two basic requirements for robust airborne repeat-pass radar interferometry include the ability to fly the platform to a desired trajectory within a narrow tube and the ability to have the radar beam pointed in a desired direction to a fraction of a beam width. Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) is equipped with a precision auto pilot developed by NASA Dryden that allows the platform, a Gulfstream III, to nominally fly within a 5 m diameter tube and with an electronically scanned antenna to position the radar beam to a fraction of a beam width based on INU (inertial navigation unit) attitude angle measurements.

Fragmentary and incidental behaviour of columns, slabs and crystals

PubMed Central

Whiteley, Walter

2014-01-01

Between the study of small finite frameworks and infinite incidentally periodic frameworks, we find the real materials which are large, but finite, fragments that fit into the infinite periodic frameworks. To understand these materials, we seek insights from both (i) their analysis as large frameworks with associated geometric and combinatorial properties (including the geometric repetitions) and (ii) embedding them into appropriate infinite periodic structures with motions that may break the periodic structure. A review of real materials identifies a number of examples with a local appearance of ‘unit cells’ which repeat under isometries but perhaps in unusual forms. These examples also refocus attention on several new classes of infinite ‘periodic’ frameworks: (i) columns—three-dimensional structures generated with one repeating isometry and (ii) slabs—three-dimensional structures with two independent repeating translations. With this larger vision of structures to be studied, we find some patterns and partial results that suggest new conjectures as well as many additional open questions. These invite a search for new examples and additional theorems. PMID:24379423

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

PubMed

U'Ren, Jana M; Schupp, James M; Pearson, Talima; Hornstra, Heidie; Friedman, Christine L Clark; Smith, Kimothy L; Daugherty, Rebecca R Leadem; Rhoton, Shane D; Leadem, Ben; Georgia, Shalamar; Cardon, Michelle; Huynh, Lynn Y; DeShazer, David; Harvey, Steven P; Robison, Richard; Gal, Daniel; Mayo, Mark J; Wagner, David; Currie, Bart J; Keim, Paul

2007-03-30

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. 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. 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 identical using previous typing methods. Given the health threat to humans and livestock and the potential for B. pseudomallei to be released intentionally, MLVA could prove to be an important tool for fine-scale epidemiological or forensic tracking of this increasingly important environmental pathogen.

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

PubMed

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 prevalence of repeat teen birth has declined in recent years, nearly one in five teen births is a repeat birth. Large disparities exist in repeat teen births and use of the most effective contraceptive methods postpartum, which was reported by fewer than one out of four teen mothers. Evidence-based approaches are needed to reduce repeat teen childbearing. These include linking pregnant and parenting teens to home visiting and similar programs that address a broad range of needs, and offering postpartum contraception to teens, including long-acting methods of reversible contraception.

Molecular Electronic Shift Registers

NASA Technical Reports Server (NTRS)

Beratan, David N.; Onuchic, Jose N.

1990-01-01

Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.

Patterns and Trends in Grade Retention Rates in the United States, 1995-2010

ERIC Educational Resources Information Center

Warren, John Robert; Hoffman, Emily; Andrew, Megan

2014-01-01

Although grade retention may be consequential for a number of important educational and socioeconomic outcomes, we know surprisingly little about the actual rate at which students are made to repeat grades. We build on Hauser, Frederick, and Andrew's 2007 measure of grade retention using data from the 1995 through 2010 Current Population…

Restoring fire suppressed Texas pak woodlands to historic conditions using prescribed fire

Treesearch

Jeff C. Sparks; Michael C. Stambaugh; Eric L. Keith

2012-01-01

Comparable to many oak ecosystems across the eastern United States, oak woodlands in Texas display characteristics of changing composition and structure due to altered fire regimes. Information describing historic fire regimes suggests woodlands underwent relatively frequent and repeated burning prior to major Euro-American influence in the early 19th century. Oak...

Arnold's Advantages: How Governor Schwarzenegger Acquired English through De Facto Bilingual Education

ERIC Educational Resources Information Center

Ramos, Francisco; Krashen, Stephen

2013-01-01

Governor Arnold Schwarzenegger has repeatedly mentioned that immigrants to the United States should do what he did to acquire English: Avoid using their first languages and speak, listen to, and read a vast amount of materials in English--a combination he referred to as "immersion." Yet, Schwarzenegger's real path to successful English…

The effect of total organic carbon content and repeated irrigation on the persistence of E. coli O157:H7 on baby spinach

USDA-ARS?s Scientific Manuscript database

Introduction: Contaminated fresh-cut spinach and other leafy greens have caused foodborne illness in the United States. In response, growers are adopting recommendations stated in the California Leafy Greens Marketing Agreement (LGMA). The LGMA permits a maximum population of 126 Most Probable Nu...

Wood-plastic composites in the United States : the interfacing of two industries

Treesearch

Craig Clemons

2002-01-01

The term wood-plastic composites refers to any composites that contain wood (of any form) and thermosets or thermoplastics. Thermosets are plastics that, once cured, cannot be melted by reheating. These include resins such as epoxies and phenolics, plastics with which the forest products industry is most familiar. Thermoplastics are plastics that can be repeatedly...

Photochemical approaches to ordered polymers

NASA Technical Reports Server (NTRS)

Meador, Michael A.; Abdulaziz, Mahmoud; Meador, Mary Ann B.

1990-01-01

The photocyclization of o-benzyloxyphenyl ketone chromophores provides an efficient, high yield route to the synthesis of 2,3-diphenylbenzofurans. The synthesis and solution of photochemistry of a series of polymers containing this chromophore is described. The photocuring of these polymers is a potential new approach to the synthesis of highly conjugated polymers based upon a p-phenylene bisbenzofuran repeat unit.

77 FR 26704 - Fisheries of the Northeastern United States; Northeast Multispecies, Monkfish, Atlantic Sea...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-07

... fishing vessels to receive a credit of days-at-sea (DAS) under certain circumstances. A detailed explanation regarding the DAS credit provision is in the final rule and is not repeated here. The information collection requirements associated with the DAS credit provision were published at Sec. Sec. 648.53, 648.82...

Modeling Longitudinal Data with Generalized Additive Models: Applications to Single-Case Designs

ERIC Educational Resources Information Center

Sullivan, Kristynn J.; Shadish, William R.

2013-01-01

Single case designs (SCDs) are short time series that assess intervention effects by measuring units repeatedly over time both in the presence and absence of treatment. For a variety of reasons, interest in the statistical analysis and meta-analysis of these designs has been growing in recent years. This paper proposes modeling SCD data with…

Participatory Media for Teacher Professional Development: Toward a Self-Sustainable and Democratic Community of Practice

ERIC Educational Resources Information Center

Liu, Katrina; Miller, Richard; Jahng, Kyung Eun

2016-01-01

Financial and political pressures on the compulsory education teacher corps in the United States, as well as US higher education, demands a new approach to teacher professional development that shifts the focus away from repeated short-term university-based teacher professional development programmes and toward the nurturing of self-organized and…

"The Role of the Unit in Physics and Psychometrics": A Commentary

ERIC Educational Resources Information Center

Dunne, Timothy T.

2011-01-01

The challenge for a discussant of the Humphry article in this issue is that the profundity of the simple insights of the article, and the lucid arguments by which the insights are sustained, might be easily overlooked, undervalued, or misconstrued. At the risk of repeating major inferences already presented, one may note that the article…

Retrofit concept for small safety related stationary machines

NASA Astrophysics Data System (ADS)

Epple, S.; Jalba, C. K.; Muminovic, A.; Jung, R.

2017-05-01

More and more old machines have the problem that their control electronics’ lifecycle comes to its intended end of life, whilst the mechanics itself and process capability is still in very good condition. This article shows an example of a reactive ion etcher originally built in 1988, which was refitted with a new control concept. The original control unit was repaired several times based on manufacturer’s obsolescence management. At start of the retrofit project the integrated circuits were no longer available for further repair of the original control unit. Safety, repeatability and stability of the process were greatly improved.

MutSβ and histone deacetylase complexes promote expansions of trinucleotide repeats in human cells

PubMed Central

Gannon, Anne-Marie M.; Frizzell, Aisling; Healy, Evan; Lahue, Robert S.

2012-01-01

Trinucleotide repeat (TNR) expansions cause at least 17 heritable neurological diseases, including Huntington’s disease. Expansions are thought to arise from abnormal processing of TNR DNA by specific trans-acting proteins. For example, the DNA repair complex MutSβ (MSH2–MSH3 heterodimer) is required in mice for on-going expansions of long, disease-causing alleles. A distinctive feature of TNR expansions is a threshold effect, a narrow range of repeat units (∼30–40 in humans) at which mutation frequency rises dramatically and disease can initiate. The goal of this study was to identify factors that promote expansion of threshold-length CTG•CAG repeats in a human astrocytic cell line. siRNA knockdown of the MutSβ subunits MSH2 or MSH3 impeded expansions of threshold-length repeats, while knockdown of the MutSα subunit MSH6 had no effect. Chromatin immunoprecipitation experiments indicated that MutSβ, but not MutSα, was enriched at the TNR. These findings imply a direct role for MutSβ in promoting expansion of threshold-length CTG•CAG tracts. We identified the class II deacetylase HDAC5 as a novel promoting factor for expansions, joining the class I deacetylase HDAC3 that was previously identified. Double knockdowns were consistent with the possibility that MutSβ, HDAC3 and HDAC5 act through a common pathway to promote expansions of threshold-length TNRs. PMID:22941650

Repeated quick hot-and-chilling treatments for the inactivation of Escherichia coli O157:H7 in mung bean and radish seeds.

PubMed

Bari, Md Latiful; Sugiyama, Jun; Kawamoto, Shinnichi

2009-01-01

The majority of the seed sprout-related outbreaks have been associated with Escherichia coli O157:H7. Therefore, it is necessary to find an effective method to inactivate these organisms on the seeds prior to sprouting. This study was conducted to assess the effectiveness of repeated quick hot-and-chilling treatments with various chemicals to inactivate E. coli O157:H7 populations inoculated onto mung bean and radish seeds intended for sprout production and to determine the effect of these treatments on seed germination. The treatment time was 20 sec for quick hot and 20 sec for quick chilling in one repeat. Likewise up to five repeats were done throughout the experiments. The chemicals used for this study were electrolyzed acidic (EO) water, phytic acid (0.05%), oxalic acid (3%), surfcera(R), and alpha-torino water(R), and distilled water was used as control. The quick hot treatment was done with 75 degrees C, 70 degrees C, and 60 degrees C, and the chilling temperature was 0 degrees C. The treated seeds were then assessed for the efficacy of this treatment in reducing populations of the pathogens and the effects of repeated quick hot-and-chilling treatments on germination yield. It was found that repeating treatment at 75 degrees C for two or three repeats with phytic acid and oxalic acid could reduce 4.38-log colony-forming unit (CFU)/g of E. coli O157:H7 in mung bean seeds. EO water and distilled water were found equally effective at 75 degrees C for four or five repeats to inactivate E. coli O157:H7 in mung bean seeds. However, alpha-torino water(R) and surfcera(R) were not found effective in comparison to other sanitizers used in this experiment. Irrespective of sanitizer used, the germination yield of the mung bean seed was not affected significantly. On the other hand, distilled water, EO water, and alpha-torino water(R) at 75 degrees C for five repeats were found effective in reducing 5.80-log CFU/g of E. coli O157:H7 in radish seeds; however, the germination yield of the seed was affected significantly. Therefore, repeated quick hot-and-chilling treatments could be useful to decontaminate mung bean seeds intended for sprout production.

Management of severe VWD with cryoprecipitate collected by repeated apheresis of a single dedicated donor.

PubMed

Pomper, Gregory J; Rick, Margaret E; Epstein, Jay S; Read, Elizabeth J; Leitman, Susan F

2003-11-01

Rare and severe forms of VWD are associated with trace or absent VWF. The feasibility of supporting a child with severe VWD from birth through age 12 with cryoprecipitate derived from DDAVP-stimulated plasma exchange of a single dedicated donor is reported. An infant with excessive hemorrhage at circumcision was found to have Type 3 VWD. His father carried an allele with a mutation at the level of VWF mRNA expression but did not have a history of bleeding. Cryoprecipitate was prepared from serial DDAVP-stimulated plasma exchanges of the father. Repeated plasma-exchange donations were performed to provide all of the VWF needed for his son. An average of 14 cryoprecipitate units was prepared from each donation, and the units contained markedly elevated levels of FVIII:C. The cryoprecipitate was stored for up to 102 months. Components tested after more than 8 years of storage showed 48 to 130 percent of original FVIII:C activity. Ninety-seven percent of the bleeding episodes, such as epistaxis, tongue-biting accidents, and other minor lacerations, were successfully managed with a single 50- to 100-percent replacement dose of FVIII. The patient experienced normal growth and development and is free of any long-term sequelae attributable to his disease. Cryoprecipitate prepared by repeated plasma exchange of a VWD carrier provided excellent hemostatic function, even after storage intervals of more than a year. Plasma exchange of a committed donor was a cost-effective and safe option for long-term management of VWD.

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

PubMed

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.

Bacterial screening of apheresis platelets with a rapid test: a 113-month single center experience.

PubMed

Ruby, Kristen N; Thomasson, Reggie R; Szczepiorkowski, Zbigniew M; Dunbar, Nancy M

2018-04-17

The 2016 Food and Drug Administration draft guidance describes the use of a rapid test (RT) to enhance platelet transfusion safety and availability. This study reports a 113-month experience of screening of apheresis platelets (APs) by RT. From July 2008 to October 2015, all APs underwent an RT on Day 4. Day 6 and 7 units were transfused with transfusion medicine physician approval. Any units remaining on Day 8 had a second RT performed. From November 2015 to November 2017, APs underwent an RT on Day 5 with a repeat RT on Days 6 and 7. During both periods, positive RTs underwent confirmatory testing with culture when repeat testing was positive. A total of 9009 APs underwent an RT on Day 4 or 5. Of these, 45 (0.5%) were RT positive, with no true positives. A total of 754 underwent a second RT on Day 8, with no positives. Since November 2015, 1152 platelets have undergone a second RT on Day 6; 391 have undergone a third RT on Day 7. Of these, five (0.4%) were RT positive on Day 6, with no true positives. There were no septic transfusion reactions identified by passive surveillance at our institution during either study period. To date, we have not detected any true positives after performing 11,306 tests on 9009 APs. A total of 1906 underwent testing twice, and 391 underwent testing three times. We did not identify any conversions from negative to positive on repeat testing. © 2018 AABB.

The site-specific ribosomal DNA insertion element R1Bm belongs to a class of non-long-terminal-repeat retrotransposons.

PubMed Central

Xiong, Y; Eickbush, T H

1988-01-01

Two types of insertion elements, R1 and R2 (previously called type I and type II), are known to interrupt the 28S ribosomal genes of several insect species. In the silkmoth, Bombyx mori, each element occupies approximately 10% of the estimated 240 ribosomal DNA units, while at most only a few copies are located outside the ribosomal DNA units. We present here the complete nucleotide sequence of an R1 insertion from B. mori (R1Bm). This 5.1-kilobase element contains two overlapping open reading frames (ORFs) which together occupy 88% of its length. ORF1 is 461 amino acids in length and exhibits characteristics of retroviral gag genes. ORF2 is 1,051 amino acids in length and contains homology to reverse transcriptase-like enzymes. The analysis of 3' and 5' ends of independent isolates from the ribosomal locus supports the suggestion that R1 is still functioning as a transposable element. The precise location of the element within the genome implies that its transposition must occur with remarkable insertion sequence specificity. Comparison of the deduced amino acid sequences from six retrotransposons, R1 and R2 of B. mori, I factor and F element of Drosophila melanogaster, L1 of Mus domesticus, and Ingi of Trypanosoma brucei, reveals a relatively high level of sequence homology in the reverse transcriptase region. Like R1, these elements lack long terminal repeats. We have therefore named this class of related elements the non-long-terminal-repeat (non-LTR) retrotransposons. Images PMID:2447482

Evolution Analysis of Simple Sequence Repeats in Plant Genome.

PubMed

Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

2015-01-01

Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1-3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.

Heme oxygenase-1 gene promoter microsatellite polymorphism is associated with progressive atherosclerosis and incident cardiovascular disease.

PubMed

Pechlaner, Raimund; Willeit, Peter; Summerer, Monika; Santer, Peter; Egger, Georg; Kronenberg, Florian; Demetz, Egon; Weiss, Günter; Tsimikas, Sotirios; Witztum, Joseph L; Willeit, Karin; Iglseder, Bernhard; Paulweber, Bernhard; Kedenko, Lyudmyla; Haun, Margot; Meisinger, Christa; Gieger, Christian; Müller-Nurasyid, Martina; Peters, Annette; Willeit, Johann; Kiechl, Stefan

2015-01-01

The enzyme heme oxygenase-1 (HO-1) exerts cytoprotective effects in response to various cellular stressors. A variable number tandem repeat polymorphism in the HO-1 gene promoter region has previously been linked to cardiovascular disease. We examined this association prospectively in the general population. Incidence of stroke, myocardial infarction, or vascular death was registered between 1995 and 2010 in 812 participants of the Bruneck Study aged 45 to 84 years (49.4% males). Carotid atherosclerosis progression was quantified by high-resolution ultrasound. HO-1 variable number tandem repeat length was determined by polymerase chain reaction. Subjects with ≥32 tandem repeats on both HO-1 alleles compared with the rest of the population (recessive trait) featured substantially increased cardiovascular disease risk (hazard ratio [95% confidence interval], 5.45 [2.39, 12.42]; P<0.0001), enhanced atherosclerosis progression (median difference in atherosclerosis score [interquartile range], 2.1 [0.8, 5.6] versus 0.0 [0.0, 2.2] mm; P=0.0012), and a trend toward higher levels of oxidized phospholipids on apolipoprotein B-100 (median oxidized phospholipids/apolipoprotein B level [interquartile range], 11364 [4160, 18330] versus 4844 [3174, 12284] relative light units; P=0.0554). Increased cardiovascular disease risk in those homozygous for ≥32 repeats was also detected in a pooled analysis of 7848 participants of the Bruneck, SAPHIR, and KORA prospective studies (hazard ratio [95% confidence interval], 3.26 [1.50, 7.33]; P=0.0043). This study found a strong association between the HO-1 variable number tandem repeat polymorphism and cardiovascular disease risk confined to subjects with a high number of repeats on both HO-1 alleles and provides evidence for accelerated atherogenesis and decreased antioxidant defense in this vascular high-risk group. © 2014 American Heart Association, Inc.

Development of a Multiple-Locus Variable number of tandem repeat Analysis (MLVA) for Leptospira interrogans and its application to Leptospira interrogans serovar Australis isolates from Far North Queensland, Australia

PubMed Central

Slack, Andrew T; Dohnt, Michael F; Symonds, Meegan L; Smythe, Lee D

2005-01-01

Background Leptospirosis is a zoonotic disease caused by the genus, Leptospira. Leptospira interrogans is the most common genomospecies implicated in the disease. Epidemiological investigations are needed to distinguish outbreak situations or to trace reservoirs of the organisms. Current methodologies used for typing Leptospira have significant drawbacks. The development of an easy to perform yet high resolution method is needed for this organism. Methods In this study we have searched the available genomic sequence of L. interrogans serovar Copenhageni strain Fiocruz L1-130 for the presence of tandem repeats [1]. These repeats were evaluated against reference strains for diversity. Six loci were selected to create a Multiple Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) to explore the genetic diversity within L. interrogans serovar Australis clinical isolates from Far North Queensland. Results The 39 reference strains used for the development of the method displayed 39 distinct patterns. Diversity Indexes for the loci varied between 0.80 and 0.93 and the number of repeat units at each locus varied between less than one to 52 repeats. When the MLVA was applied to serovar Australis isolates three large clusters were distinguishable, each comprising various hosts including Rattus species, human and canines. Conclusion The MLVA described in this report, was easy to perform, analyse and was reproducible. The loci selected had high diversity allowing discrimination between serovars and also between strains within a serovar. This method provides a starting point on which improvements to the method and comparisons to other techniques can be made. PMID:15987533

Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension

PubMed Central

MacDonald, James T.; Kabasakal, Burak V.; Godding, David; Kraatz, Sebastian; Henderson, Louie; Barber, James; Freemont, Paul S.; Murray, James W.

2016-01-01

The ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemble. However, the generalized protein folding and design problem is unsolved. One approach to simplifying the problem is to use a repetitive protein as a scaffold. Repeat proteins are intrinsically modular, and their folding and structures are better understood than large globular domains. Here, we have developed a class of synthetic repeat proteins based on the pentapeptide repeat family of beta-solenoid proteins. We have constructed length variants of the basic scaffold and computationally designed de novo loops projecting from the scaffold core. The experimentally solved 3.56-Å resolution crystal structure of one designed loop matches closely the designed hairpin structure, showing the computational design of a backbone extension onto a synthetic protein core without the use of backbone fragments from known structures. Two other loop designs were not clearly resolved in the crystal structures, and one loop appeared to be in an incorrect conformation. We have also shown that the repeat unit can accommodate whole-domain insertions by inserting a domain into one of the designed loops. PMID:27573845

Geochemical surveys in the United States in relation to health.

USGS Publications Warehouse

Tourtelot, H.A.

1979-01-01

Geochemical surveys in relation to health may be classified as having one, two or three dimensions. One-dimensional surveys examine relations between concentrations of elements such as Pb in soils and other media and burdens of the same elements in humans, at a given time. The spatial distributions of element concentrations are not investigated. The primary objective of two-dimensional surveys is to map the distributions of element concentrations, commonly according to stratified random sampling designs based on either conceptual landscape units or artificial sampling strata, but systematic sampling intervals have also been used. Political units have defined sample areas that coincide with the units used to accumulate epidemiological data. Element concentrations affected by point sources have also been mapped. Background values, location of natural or technological anomalies and the geographic scale of variation for several elements often are determined. Three-dimensional surveys result when two-dimensional surveys are repeated to detect environmental changes. -Author

Studies of Phase Change Materials and a Latent Heat Storage Unit Used for a Natural Circulation Cooling/Latent Heat Storage System

NASA Astrophysics Data System (ADS)

Sakitani, Katsumi; Honda, Hiroshi

Experiments were performed to investigate feasibility of using organic materials as a PCM for a latent heat storage unit of a natural circulation cooling/latent heat storage system. This system was designed to cool a shelter accommodating telecommunication equipment located in subtropical deserts or similar regions without using a power source. Taking into account practical considerations and the results of various experiments regarding the thermodynamic properties, thermal degradation, and corrosiveness to metals, lauric acid and iron was selected for the PCM and the latent heat storage unit material, respectively. Cyclic heating and cooling of the latent heat storage unit undergoing solid-liquid phase change was repeated for more than 430 days. The results showed that the heating-cooling curve was almost unchanged between the early stage and the 1,870th cycle. It was concluded that the latent heat storage unit could be used safely for more than ten years as a component of the cooling system.

Tuberculosis Caused by Mycobacterium africanum, United States, 2004-2013.

PubMed

Sharma, Aditya; Bloss, Emily; Heilig, Charles M; Click, Eleanor S

2016-03-01

Mycobacterium africanum is endemic to West Africa and causes tuberculosis (TB). We reviewed reported cases of TB in the United States during 2004-2013 that had lineage assigned by genotype (spoligotype and mycobacterial interspersed repetitive unit variable number tandem repeats). M. africanum caused 315 (0.4%) of 73,290 TB cases with lineage assigned by genotype. TB caused by M. africanum was associated more with persons from West Africa (adjusted odds ratio [aOR] 253.8, 95% CI 59.9-1,076.1) and US-born black persons (aOR 5.7, 95% CI 1.2-25.9) than with US-born white persons. TB caused by M. africanum did not show differences in clinical characteristics when compared with TB caused by M. tuberculosis. Clustered cases defined as >2 cases in a county with identical 24-locus mycobacterial interspersed repetitive unit genotypes, were less likely for M. africanum (aOR 0.1, 95% CI 0.1-0.4), which suggests that M. africanum is not commonly transmitted in the United States.

Repeat prescribing of medications: A system‐centred risk management model for primary care organisations

PubMed Central

Price, Julie; Man, Shu Ling; Bartlett, Stephen; Taylor, Kate; Dinwoodie, Mark

2017-01-01

Abstract Rationale, aims and objectives Reducing preventable harm from repeat medication prescriptions is a patient safety priority worldwide. In the United Kingdom, repeat prescriptions items issued has doubled in the last 20 years from 5.8 to 13.3 items per patient per annum. This has significant resource implications and consequences for avoidable patient harms. Consequently, we aimed to test a risk management model to identify, measure, and reduce repeat prescribing system risks in primary care. Methods All 48 general medical practices in National Health Service (NHS) Lambeth Clinical Commissioning Group (an inner city area of south London in England) were recruited. Multiple interventions were implemented, including educational workshops, a web‐based risk monitoring system, and external reviews of repeat prescribing system risks by clinicians. Data were collected via documentation reviews and interviews and subject to basic thematic and descriptive statistical analyses. Results Across the 48 participating general practices, 62 unique repeat prescribing risks were identified on 505 occasions (eg, practices frequently experiencing difficulty interpreting medication changes on hospital discharge summaries), equating to a mean of 8.1 risks per practice (range: 1‐33; SD = 7.13). Seven hundred sixty‐seven system improvement actions were recommended across 96 categories (eg, alerting hospitals to illegible writing and delays with discharge summaries) with a mean of 15.6 actions per practice (range: 0‐34; SD = 8.0). Conclusions The risk management model tested uncovered important safety concerns and facilitated the development and communication of related improvement recommendations. System‐wide information on hazardous repeat prescribing and how this could be mitigated is very limited. The approach reported may have potential to close this gap and improve the reliability of general practice systems and patient safety, which should be of high interest to primary care organisations internationally. PMID:28370904

Activation of superficial dorsal horn neurons in the mouse by a PAR-2 agonist and 5-HT: potential role in itch.

PubMed

Akiyama, Tasuku; Merrill, Austin W; Carstens, Mirela Iodi; Carstens, E

2009-05-20

Itch, an unpleasant sensation associated with the desire to scratch, is symptomatic of dermatologic and systemic disorders that often resist antihistamine treatment. Histamine-independent itch mediators include serotonin (5-HT) and agonists of the protease-activated receptor-2 (PAR-2). We used behavior, Fos immunohistochemistry, and electrophysiology to investigate if these mediators activate spinal dorsal horn neurons in a manner consistent with itch. Intradermal (i.d.) injection of the PAR-2 agonist SLIGRL-NH(2) in the rostral back evoked bouts of directed hindlimb scratches over 20-30 min. Hindpaw injection of SLIGRL-NH(2) produced Fos staining in superficial dorsal horn which was then targeted for single-unit recording. Small id microinjections of SLIGRL-NH(2) or 5-HT identified responsive single units in the superficial dorsal horn of mice anesthetized with pentobarbital. Thirty-eight units characterized as wide dynamic range, nociceptive specific, or mechanically insensitive exhibited significantly increased firing after i.d. SLIGRL-NH(2) for 9 min, to partial (25%) tachyphylaxis with repeated injection. A majority additionally responded to 5-HT (70%), mustard oil (79%), and capsaicin (71%). Seven units isolated with the 5-HT search stimulus exhibited significant and prolonged responses to 5-HT with tachyphylaxis to repeated injections. The majority also responded to SLIGRL-NH(2), mustard oil, and capsaicin. The prolonged responses of superficial dorsal horn neurons to SLIGRL-NH(2) and 5-HT suggest a role in signaling itch. However, their responsiveness to algogens is inconsistent with itch specificity. Alternatively, such neurons may signal itch, whereas noxious stimulus levels recruit these and a larger population of pruritogen-insensitive cells to signal pain which masks or occludes the itch signal.

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

PubMed

Sarkar, Anita; Pérez, Serge

2012-11-14

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. 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. PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr.

The 2-MEV Model: Constancy of Adolescent Environmental Values within an 8-Year Time Frame

ERIC Educational Resources Information Center

Bogner, F. X.; Johnson, B.; Buxner, S.; Felix, L.

2015-01-01

The 2-MEV model is a widely used tool to monitor children's environmental perception by scoring individual values. Although the scale's validity has been confirmed repeatedly and independently as well as the scale is in usage within more than two dozen language units all over the world, longitudinal properties still need clarification. The purpose…

Molecular Typing of Pneumococci for Investigation of Linked Cases of Invasive Pneumococcal Disease ▿

PubMed Central

Pichon, Bruno; Moyce, Laura; Sheppard, Carmen; Slack, Mary; Turbitt, Deborah; Pebody, Richard; Spencer, David A.; Edwards, Justin; Krahé, Daniel; George, Robert

2010-01-01

In winter 2007-2008, an outbreak of pediatric pneumonia caused by serotype 5 pneumococci was identified in a northeast London suburb. Variable number of tandem repeat analyses clustered these pneumococci from the other serotype 5 pneumococci in the United Kingdom, highlighting the importance of this discriminative typing method in supporting epidemiological investigations. PMID:20164267

Growth and nutrition response of young sweetgum plantations to repeated nitrogen fertilization on two site types

Treesearch

D. Andrew Scott; James A. Burger; Donald J. Kaczmarek; Michael B. Kane

2004-01-01

Short-rotation intensive tree culture is being investigated in the southern United States as a method of producing hardwood fiber, but little is known about the early productivity and nutritional needs of these systems, especially on different site types. We studied the growth and foliar nutrition response of two sweetgum (Liquidambar styraciflua L...

Polymer compositions and methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, Scott D.; Willkomm, Wayne R.

The present invention encompasses polyurethane compositions comprising aliphatic polycarbonate chains. In one aspect, the present invention encompasses polyurethane foams, thermoplastics and elastomers derived from aliphatic polycarbonate polyols and polyisocyanates wherein the polyol chains contain a primary repeating unit having a structure: ##STR00001## In another aspect, the invention provides articles comprising the inventive foam and elastomer compositions as well as methods of making such compositions.

Using historical photography to monitor and assess threats over time

Treesearch

Don Evans

2010-01-01

Analysis of aerial photography is perhaps the best way to assess changes in landcover conditions. In the United States, most national forests have repeat photography on approximately a 10-year cycle. Analysis of this rich photo record can reveal changes in insect damage, fuels buildup, unmanaged off-highway vehicle use, loss of open space, and other land-cover...

What Works (and What Does Not) in Youth Violence Prevention: Rethinking the Questions and Finding New Answers

ERIC Educational Resources Information Center

Guerra, Nancy G.; Boxer, Paul; Cook, Clayton R.

2006-01-01

Dramatic rises in youth violence in the United States beginning in the 1980s coupled with high visibility acts such as school shootings have resulted in a corresponding proliferation of programs designed to prevent aggression and violence in children and youth. Parallel with this increasing programmatic expansion, there have been repeated calls…

Thinning, fire, and oak regeneration across a heterogeneous landscape in the eastern U.S.: 7-year results

Treesearch

Louis R. Iverson; Todd F. Hutchinson; Anantha M. Prasad; Matthew P. Peters

2008-01-01

We document an increase in oak and hickory advance regeneration, depending on landscape position, in the sixth year following mechanical thinning and repeated prescribed fires in southern Ohio, USA. Oak-dominated communities provide a multitude of human and natural resource values throughout the eastern United States, but their long-term sustainability is threatened...

Polyestercarbonates which exhibit improved processibility

DOEpatents

Krabbenhoft, Herman Otto

1999-01-01

The invention relates to a polyestercarbonate polymer which comprises repeating units of a mono-unsaturated aliphatic dicarboxylic acid having about 12 to about 20 carbon atoms. Preferred dicarboxylic acids for incorporation into the polymer are cis-octadec-9-enedioic acid or trans-octadec-9-enedioic acid. The use of these mono-unsaturated acids results in polymers with lower glass transition temperatures, and enhances processibility.

Advanced Neuroscience Interface Research

DTIC Science & Technology

2002-05-01

in vitro. Herein, we also report on the utilization of in vitro high -resolution MRS of a specimen of the same tumor with the ... The prior use of VEs to treat phobias has centered on the repeated presentation of the fear- inducing stimulus to the patient in such a manner that the ...inherent in pneumatic headphones (as sound propagates from the driver unit into the

An Investigation of the effectiveness of the Virginia Habitual Offender Act : a study conducted by the Virginia Transportation Research Council for the Advisory Committee to the Commission on VASAP : final report.

DOT National Transportation Integrated Search

1993-01-01

In 1968, Virginia passed the Habitual Offender Act (the Act), one of the first laws in the United States directed at motorists who repeatedly violate traffic laws. Persons adjudicated as habitual offenders are subject to long-term license revocation,...

Vertical distribution and persistence of soil organic carbon in fire-adapted longleaf pine forests

Treesearch

John R. Butnor; Lisa J. Samuelson; Kurt H. Johnsen; Peter H. Anderson; Carlos A. Gonzalez Benecke; Claudia M. Boot; M. Francesca Cotrufo; Katherine A. Heckman; Jason A. Jackson; Thomas A. Stokes; Stanley J. Zarnoch

2017-01-01

Longleaf pine (Pinus palustris Miller) forests in the southern United States are being restored and actively managed for a variety of goals including: forest products, biodiversity, C sequestration and forest resilience in the face of repeated isturbances from hurricanes and climate change. Managed southern pine forests can be sinks for atmospheric...

Eighty-eight years of change in a managed ponderosa pine forest

Treesearch

Helen Y. Smith; Stephen F. Arno

1999-01-01

This publication gives an overview of structural and other ecological changes associated with forest management and fire suppression since the early 1900's in a ponderosa pine forest, the most widespread forest type in the Western United States. Three sources of information are presented: (1) changes seen in a series of repeat photographs taken between 1909 and...

Post-fire surface fuel dynamics in California forests across three burn severity classes

Treesearch

Bianca N. I. Eskelson; Vicente J. Monleon

2018-01-01

Forest wildfires consume fuel and are followed by post-fire fuel accumulation. This study examines post-fire surface fuel dynamics over 9 years across a wide range of conditions characteristic of California fires in dry conifer and hardwood forests. We estimated post-fire surface fuel loadings (Mg ha _1) from 191 repeatedly measured United States...

Measuring the Effects of a Media Literacy Program on Conflict and Violence

ERIC Educational Resources Information Center

Scharrer, Erica

2009-01-01

A 5-session curricular unit on the topic of face-to-face conflict mediation and on-screen media violence was administered to 85 sixth graders. Repeated measures analyses were employed to study the 57 students for whom matched questionnaires were available. Results show students became more likely to choose a non-aggressive approach to two of three…

Crystallization of Stretched Polyimides: A Structure-Property Study

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A.; Dezern, James F.

2002-01-01

A simple rotational isomeric state model was used to detect the degree to which polyimide repeat units might align to give an extended crystal. It was found experimentally that the hallmarks of stretch-crystallization were more likely to occur in materials whose molecules could readily give extended, aligned conformations. A proposed screening criterion was 84% accurate in selecting crystallizing molecules.

Motivational Factors of Pay-for-Performance Plans in Educational Institutions: A Study of Select Private, Faith-Based Schools

ERIC Educational Resources Information Center

Wrobbel, Paul H.

2009-01-01

In the United States there is considerable focus on the need for continuous improvement in the quality of schools, including student achievement and teacher performance. Performance-based pay has been repeatedly suggested as a way to improve teaching in school systems. Therefore, a more thorough understanding of the differences in the perceptions…

Cofacial porphyrin-ferrocene dyads and a new class of conjugated porphyrin.

PubMed

Cammidge, Andrew N; Scaife, Peter J; Berber, Gûlen; Hughes, David L

2005-08-04

A porphyrin-ferrocene dyad has been synthesized in which there is close face-to-face contact between the two aromatic systems, providing a model for heterobimetallic polymers based on the same repeating unit. Attempts to synthesize the 2:1 adduct instead led to a remarkable intramolecular Heck-type cyclization which planarizes the system and extends the conjugation. [structure: see text

Response of upland oak and co-occurring competitor seedlings following single and repeated prescribed fires

Treesearch

Heather D. Alexander; Mary Arthur; David Loftis; Stephanie Green

2009-01-01

Studies within and outside the United States indicate recurring oak (Quercus spp.) regeneration problems. In deciduous forests of the eastern U.S., a prevailing explanation for this trend is that fire suppression leads to high competitor abundance and low understory light. In response, prescribed fire is increasingly used as a management tool to...

Polymer compositions and methods

DOEpatents

Allen, Scott D.; Willkomm, Wayne R.

2016-09-27

The present invention encompasses polyurethane compositions comprising aliphatic polycarbonate chains. In one aspect, the present invention encompasses polyurethane foams, thermoplastics and elastomers derived from aliphatic polycarbonate polyols and polyisocyanates wherein the polyol chains contain a primary repeating unit having a structure: ##STR00001## In another aspect, the invention provides articles comprising the inventive foam and elastomer compositions as well as methods of making such compositions.

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

NASA Astrophysics Data System (ADS)

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.

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nam, Ki Hyun; Haitjema, Charles; Liu, Xueqi

Clustered regularly interspaced short palindromic repeats (CRISPRs), together with an operon of CRISPR-associated (Cas) proteins, form an RNA-based prokaryotic immune system against exogenous genetic elements. Cas5 family proteins are found in several type I CRISPR-Cas systems. Here, we report the molecular function of subtype I-C/Dvulg Cas5d from Bacillus halodurans. We show that Cas5d cleaves pre-crRNA into unit length by recognizing both the hairpin structure and the 3 single stranded sequence in the CRISPR repeat region. Cas5d structure reveals a ferredoxin domain-based architecture and a catalytic triad formed by Y46, K116, and H117 residues. We further show that after pre-crRNA processing,more » Cas5d assembles with crRNA, Csd1, and Csd2 proteins to form a multi-sub-unit interference complex similar to Escherichia coli Cascade (CRISPR-associated complex for antiviral defense) in architecture. Our results suggest that formation of a crRNA-presenting Cascade-like complex is likely a common theme among type I CRISPR subtypes.« less

Conformational features of cepacian: the exopolysaccharide produced by clinical strains of Burkholderia cepacia.

PubMed

Nogueira, Carlos E Sampaio; Ruggiero, Jose R; Sist, Paola; Cescutti, Paola; Urbani, Ranieri; Rizzo, Roberto

2005-04-11

Conformational energy calculations and molecular dynamics investigations, both in water and in dimethyl sulfoxide, were carried out on the exopolysaccharide cepacian produced by the majority of the clinical strains of Burkholderia cepacia, an opportunistic pathogen causing serious lung infection in patients affected by cystic fibrosis, The investigation was aimed at defining the structural and conformational features, which might be relevant for clarification of the structure-function relationships of the polymer. The molecular dynamics calculations were carried out by Ramachandran-type energy plots of the disaccharides that constitute the polymer repeating unit. The dynamics of an oligomer composed of three repeating units were investigated in water and in Me2SO, a non-aggregating solvent. Analysis of the time persistence of hydrogen bonds showed the presence of a large number of favourable interactions in water, which were less evident in Me2SO. The calculations on the cepacian chain indicated that polymer conformational features in water were affected by the lateral chains, but were also largely dictated by the presence of solvent. Moreover, the large number of intra-chain hydrogen bonds in water disappeared in Me2SO solution, increasing the average dimension of the polymer chains.

Regions flanking ori sequences affect the replication efficiency of the mitochondrial genome of ori+ petite mutants from yeast.

PubMed

Rayko, E; Goursot, R; Cherif-Zahar, B; Melis, R; Bernardi, G

1988-03-31

The mitochondrial genomes of progenies from 26 crosses between 17 cytoplasmic, spontaneous, suppressive, ori+ petite mutants of Saccharomyces cerevisiae have been studied by electrophoresis of restriction fragments. Only parental genomes (or occasionally, genomes derived from them by secondary excisions) were found in the progenies of the almost 500 diploids investigated; no evidence for illegitimate, site-specific mitochondrial recombination was detected. One of the parental genomes was always found to be predominate over the other one, although to different extents in different crosses. This predominance appears to be due to a higher replication efficiency, which is correlated with a greater density of ori sequences on the mitochondrial genome (and with a shorter repeat unit size of the latter). Exceptions to the 'repeat-unit-size rule' were found, however, even when the parental mitochondrial genomes carried the same ori sequence. This indicates that noncoding, intergenic sequences outside ori sequences also play a role in modulating replication efficiency. Since in different petites such sequences differ in primary structure, size, and position relative to ori sequences, this modulation is likely to take place through an indirect effect on DNA and nucleoid structure.

Broad-spectrum non-toxic antiviral nanoparticles with a virucidal inhibition mechanism

NASA Astrophysics Data System (ADS)

Cagno, Valeria; Andreozzi, Patrizia; D'Alicarnasso, Marco; Jacob Silva, Paulo; Mueller, Marie; Galloux, Marie; Le Goffic, Ronan; Jones, Samuel T.; Vallino, Marta; Hodek, Jan; Weber, Jan; Sen, Soumyo; Janeček, Emma-Rose; Bekdemir, Ahmet; Sanavio, Barbara; Martinelli, Chiara; Donalisio, Manuela; Rameix Welti, Marie-Anne; Eleouet, Jean-Francois; Han, Yanxiao; Kaiser, Laurent; Vukovic, Lela; Tapparel, Caroline; Král, Petr; Krol, Silke; Lembo, David; Stellacci, Francesco

2018-02-01

Viral infections kill millions yearly. Available antiviral drugs are virus-specific and active against a limited panel of human pathogens. There are broad-spectrum substances that prevent the first step of virus-cell interaction by mimicking heparan sulfate proteoglycans (HSPG), the highly conserved target of viral attachment ligands (VALs). The reversible binding mechanism prevents their use as a drug, because, upon dilution, the inhibition is lost. Known VALs are made of closely packed repeating units, but the aforementioned substances are able to bind only a few of them. We designed antiviral nanoparticles with long and flexible linkers mimicking HSPG, allowing for effective viral association with a binding that we simulate to be strong and multivalent to the VAL repeating units, generating forces (~190 pN) that eventually lead to irreversible viral deformation. Virucidal assays, electron microscopy images, and molecular dynamics simulations support the proposed mechanism. These particles show no cytotoxicity, and in vitro nanomolar irreversible activity against herpes simplex virus (HSV), human papilloma virus, respiratory syncytial virus (RSV), dengue and lenti virus. They are active ex vivo in human cervicovaginal histocultures infected by HSV-2 and in vivo in mice infected with RSV.

Functional Genomics of the Aeromonas salmonicida Lipopolysaccharide O-Antigen and A-Layer from Typical and Atypical Strains

PubMed Central

Merino, Susana; de Mendoza, Elena; Canals, Rocío; Tomás, Juan M.

2015-01-01

The A. salmonicida A450 LPS O-antigen, encoded by the wbsalmo gene cluster, is exported through an ABC-2 transporter-dependent pathway. It represents the first example of an O-antigen LPS polysaccharide with three different monosaccharides in their repeating unit assembled by this pathway. Until now, only repeating units with one or two different monosaccharides have been described. Functional genomic analysis of this wbsalmo region is mostly in agreement with the LPS O-antigen structure of acetylated l-rhamnose (Rha), d-glucose (Glc), and 2-amino-2-deoxy-d-mannose (ManN). Between genes of the wbsalmo we found the genes responsible for the biosynthesis and assembly of the S-layer (named A-layer in these strains). Through comparative genomic analysis and in-frame deletions of some of the genes, we concluded that all the A. salmonicida typical and atypical strains, other than A. salmonicida subsp. pectinolytica strains, shared the same wbsalmo and presence of A-layer. A. salmonicida subsp. pectinolytica strains lack wbsalmo and A-layer, two major virulence factors, and this could be the reason they are the only ones not found as fish pathogens. PMID:26082990

Analysis of humpback whale sounds in shallow waters of the Southeastern Arabian Sea: An indication of breeding habitat.

PubMed

Mahanty, Madan M; Latha, G; Thirunavukkarasu, A

2015-06-01

The primary objective of this work was to present the acoustical identification of humpback whales, detected by using an autonomous ambient noise measurement system, deployed in the shallow waters of the Southeastern Arabian Sea (SEAS) during the period January to May 2011. Seven types of sounds were detected. These were characteristically upsweeps and downsweeps along with harmonics. Sounds produced repeatedly in a specific pattern were referred to as phrases (PQRS and ABC). Repeated phrases in a particular pattern were referred to as themes, and from the spectrographic analysis, two themes (I and II) were identified. The variation in the acoustic characteristics such as fundamental frequency, range, duration of the sound unit, and the structure of the phrases and themes are discussed. Sound units were recorded from mid-January to mid-March, with a peak in February, when the mean SST is approx. 28 degree C, and no presence was recorded after mid-March. The temporal and thematic structures strongly determine the functions of the humpback whale song form. Given the use of song in the SEAS, this area is possibly used as an active breeding habitat by humpback whales during the winter season.

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

PubMed

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.

Structural characterization of an all-aminosugar-containing capsular polysaccharide from Colwellia psychrerythraea 34H

PubMed Central

Casillo, Angela; Ståhle, Jonas; Parrilli, Ermenegilda; Sannino, Filomena; Mitchell, Daniel E.; Pieretti, Giuseppina; Gibson, Matthew I.; Marino, Gennaro; Lanzetta, Rosa; Parrilli, Michelangelo; Widmalm, Göran; Tutino, Maria L.; Corsaro, Maria M.

2017-01-01

Colwellia psychrerythraea strain 34H, a Gram-negative bacterium isolated from Arctic marine sediments, is considered a model to study the adaptation to cold environments. Recently, we demonstrated that C. psychrerythraea 34H produces two different extracellular polysaccharides, a capsular polysaccharide and a medium released polysaccharide, which confer cryoprotection to the bacterium. In this study, we report the structure of an additional capsular polysaccharide produced by Colwellia grown at a different temperature. The structure was determined using chemical methods, and one- and two-dimensional NMR spectroscopy. The results showed a trisaccharide repeating unit made up of only amino-sugar residues: N-acetyl-galactosamine, 2,4-diacetamido-2,4,6-trideoxy-glucose (bacillosamine), and 2-acetamido-2-deoxyglucuronic acid with the following structure: →4)-β-d-GlcpNAcA-(1→3)-β-d-QuipNAc4NAc-(1→3)-β-d-GalpNAc-(1→. The 3D model, generated in accordance with 1H,1H-NOE NMR correlations and consisting of ten repeating units, shows a helical structure. In contrast with the other extracellular polysaccharides produced from Colwellia at 4 °C, this molecule displays only a low ice recrystallization inhibition activity. PMID:28161737

Mollecarbamates, Molleureas, and Molledihydroisoquinolone, o-Carboxyphenethylamide Metabolites of the Ascidian Didemnum molle Collected in Madagascar.

PubMed

Issac, Michal; Aknin, Maurice; Gauvin-Bialecki, Anne; Pond, Christopher D; Barrows, Louis R; Kashman, Yoel; Carmeli, Shmuel

2017-06-23

The extract of a sample of the tunicate Didemnum molle (MAY13-117) collected in Mayotte afforded eight new metabolites, mollecarbamates A-D (1-4) and molleureas B-E (5-8), along with the two known natural products, N,N'-diphenylethyl urea (10) and molleurea A (11). Another sample of D. molle (MAD11-BA065) collected in Baie des Assassins, Madagascar, afforded molledihydroisoquinolone (9). Mollecarbamates 1-4 are a family of compounds that possess repeating o-carboxyphenethylamide units and a carbamate moiety, while the molleureas 5-8 contain tetra- and penta-repeating carboxyphenethylamide units and a urea bridge in different positions. Molledihydroisoquinolone (9) is a cyclic form of o-carboxyphenethylamide. We propose that these unique natural products are most probably produced by an unprecedented biosynthetic pathway that contains a yet unknown chorismate mutase variant. The structures of the compounds were elucidated by interpretation of the data from 1D and 2D NMR, HRESIMS, and MS/MS analyses of the positive ESIMS experiments. Compounds 1-8 were tested against pathogenic bacteria and in a cytoprotective HIV cell based assay but did not show any significant effects in these assays.

Lipophosphoglycan polymorphisms do not affect Leishmania amazonensis development in the permissive vectors Lutzomyia migonei and Lutzomyia longipalpis.

PubMed

Nogueira, Paula M; Guimarães, Agna C; Assis, Rafael R; Sadlova, Jovana; Myskova, Jitka; Pruzinova, Katerina; Hlavackova, Jana; Turco, Salvatore J; Torrecilhas, Ana C; Volf, Petr; Soares, Rodrigo P

2017-12-16

Lipophosphoglycan (LPG) is a dominant surface molecule of Leishmania promastigotes. Its species-specific polymorphisms are found mainly in the sugars that branch off the conserved Gal(β1,4)Man(α1)-PO 4 backbone of repeat units. Leishmania amazonensis is one of the most important species causing human cutaneous leishmaniasis in the New World. Here, we describe LPG intraspecific polymorphisms in two Le. amazonensis reference strains and their role during the development in three sand fly species. Strains isolated from Lutzomyia flaviscutellata (PH8) and from a human patient (Josefa) displayed structural polymorphism in the LPG repeat units, possessing side chains with 1 and 2 β-glucose or 1 to 3 β-galactose, respectively. Both strains successfully infected permissive vectors Lutzomyia longipalpis and Lutzomyia migonei and could colonize their stomodeal valve and differentiate into metacyclic forms. Despite bearing terminal galactose residues on LPG, Josefa could not sustain infection in the restrictive vector Phlebotomus papatasi. LPG polymorphisms did not affect the ability of Le. amazonensis to develop late-stage infections in permissive vectors. However, the non-establishment of infection in Ph. papatasi by Josefa strain suggested other LPG-independent factors in this restrictive vector.

Prevalence of human immunodeficiency virus type 1 p24 antigen in U.S. blood donors--an assessment of the efficacy of testing in donor screening. The HIV-Antigen Study Group.

PubMed

Alter, H J; Epstein, J S; Swenson, S G; VanRaden, M J; Ward, J W; Kaslow, R A; Menitove, J E; Klein, H G; Sandler, S G; Sayers, M H

1990-11-08

We performed a multicenter study in 1989 to determine whether screening whole-blood donors for human immunodeficiency virus type 1 (HIV-1) p24 antigen would improve transfusion safety by identifying carriers of the virus who are seronegative for HIV-1 antibody. More than 500,000 donations were tested at 13 U.S. blood centers with test kits from two manufacturers. Units found repeatedly reactive were retested in a central laboratory; if the results were positive, they were confirmed by a neutralization assay. A subgroup of units was also tested for HIV-1 by the polymerase chain reaction. Selected donors confirmed or not confirmed as having p24 antigen were contacted for follow-up interviews to identify risk factors and undergo retesting for HIV-1 markers. Positive tests for p24 antigen were confirmed by neutralization in five donors (0.001 percent of all donations tested), all of whom were also positive for HIV-1 antibody and HIV-1 by polymerase chain reaction. Three of the antigen-positive donors had other markers of infectious disease that would have resulted in the exclusion of their blood; two had risk factors for HIV-1 that should have led to self-exclusion. Of 220 blood units with repeatedly reactive p24 antigen whose presence could not be confirmed by neutralization (0.04 percent of the donations studied), none were positive for HIV-1 antibody, HIV-1 by polymerase chain reaction (120 units tested), or virus culture (76 units tested)--attesting to the specificity of confirmatory neutralization. The finding that no donation studied was positive for p24 antigen and negative for HIV-1 antibody suggests that screening donors for p24 antigen with tests of the current level of sensitivity would not add substantially to the safety of the U.S. blood supply.

Low D4Z4 copy number and gender difference in Korean patients with facioscapulohumeral muscular dystrophy type 1.

PubMed

Park, Hyung Jun; Hong, Ji-Man; Lee, Jung Hwan; Lee, Hyung Seok; Shin, Ha Young; Kim, Seung Min; Ki, Chang-Seok; Lee, Ji Hyun; Choi, Young-Chul

2015-11-01

The objective of this study was to investigate the clinical and genetic features of Korean patients with facioscapulohumeral muscular dystrophy type 1 (FSHD), and assessed the impact of molecular defects on phenotypic expression. We enrolled 104 FSHD patients from 87 unrelated Korean families with D4Z4 repeat array of less than 11 copies on 4q35. Sixty-one men and forty-three women were enrolled. Median D4Z4 copy number was 4 units and 99 (95%) Korean patients with FSHD carried 1-6 units. The median age at symptom onset was 13 [interquartile range: 8-17] years old. In 100 symptomatic patients, muscle weakness began in facial muscles in 58 patients, shoulder-girdle muscles in 37, and pelvic-girdle muscles in 5. Disease severity was significantly correlated with D4Z4 copy number. In addition, women were more severely affected than men even though there were no differences in age at examination or in D4Z4 copy number between the two genders. This gender difference among Korean patients was the opposite of analysis on individuals of European ancestry. In conclusion, the present study demonstrated the new diagnostic threshold for FSHD in Koreans based on the D4Z4 repeat array size distribution from 1 to 6 units and expanded the clinical spectrum. Copyright © 2015 Elsevier B.V. All rights reserved.

The Molecular Cytogenetic Characterization of Pistachio (Pistacia vera L.) Suggests the Arrest of Recombination in the Largest Heteropycnotic Pair HC1.

PubMed

Sola-Campoy, Pedro J; Robles, Francisca; Schwarzacher, Trude; Ruiz Rejón, Carmelo; de la Herrán, Roberto; Navajas-Pérez, Rafael

2015-01-01

This paper represents the first molecular cytogenetic characterization of the strictly dioecious pistachio tree (Pistacia vera L.). The karyotype was characterized by fluorescent in situ hybridization (FISH) with probes for 5S and 45S rDNAs, and the pistachio specific satellite DNAs PIVE-40, and PIVE-180, together with DAPI-staining. PIVE-180 has a monomeric unit of 176-178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree.

The Molecular Cytogenetic Characterization of Pistachio (Pistacia vera L.) Suggests the Arrest of Recombination in the Largest Heteropycnotic Pair HC1

PubMed Central

Sola-Campoy, Pedro J.; Robles, Francisca; Schwarzacher, Trude; Ruiz Rejón, Carmelo; de la Herrán, Roberto; Navajas-Pérez, Rafael

2015-01-01

This paper represents the first molecular cytogenetic characterization of the strictly dioecious pistachio tree (Pistacia vera L.). The karyotype was characterized by fluorescent in situ hybridization (FISH) with probes for 5S and 45S rDNAs, and the pistachio specific satellite DNAs PIVE-40, and PIVE-180, together with DAPI-staining. PIVE-180 has a monomeric unit of 176–178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree. PMID:26633808

Bioresorbable scaffolds for bone tissue engineering: optimal design, fabrication, mechanical testing and scale-size effects analysis.

PubMed

Coelho, Pedro G; Hollister, Scott J; Flanagan, Colleen L; Fernandes, Paulo R

2015-03-01

Bone scaffolds for tissue regeneration require an optimal trade-off between biological and mechanical criteria. Optimal designs may be obtained using topology optimization (homogenization approach) and prototypes produced using additive manufacturing techniques. However, the process from design to manufacture remains a research challenge and will be a requirement of FDA design controls to engineering scaffolds. This work investigates how the design to manufacture chain affects the reproducibility of complex optimized design characteristics in the manufactured product. The design and prototypes are analyzed taking into account the computational assumptions and the final mechanical properties determined through mechanical tests. The scaffold is an assembly of unit-cells, and thus scale size effects on the mechanical response considering finite periodicity are investigated and compared with the predictions from the homogenization method which assumes in the limit infinitely repeated unit cells. Results show that a limited number of unit-cells (3-5 repeated on a side) introduce some scale-effects but the discrepancies are below 10%. Higher discrepancies are found when comparing the experimental data to numerical simulations due to differences between the manufactured and designed scaffold feature shapes and sizes as well as micro-porosities introduced by the manufacturing process. However good regression correlations (R(2) > 0.85) were found between numerical and experimental values, with slopes close to 1 for 2 out of 3 designs. Copyright © 2015 IPEM. Published by Elsevier Ltd. All rights reserved.

Evidence That Intergenic Spacer Repeats of Drosophila Melanogaster Rrna Genes Function as X-Y Pairing Sites in Male Meiosis, and a General Model for Achiasmatic Pairing

PubMed Central

McKee, B. D.; Habera, L.; Vrana, J. A.

1992-01-01

In Drosophila melanogaster males, X-Y meiotic chromosome pairing is mediated by the nucleolus organizers (NOs) which are located in the X heterochromatin (Xh) and near the Y centromere. Deficiencies for Xh disrupt X-Y meiotic pairing and cause high frequencies of X-Y nondisjunction. Insertion of cloned rRNA genes on an Xh(-) chromosome partially restores normal X-Y pairing and disjunction. To map the sequences within an inserted, X-linked rRNA gene responsible for stimulating X-Y pairing, partial deletions were generated by P element-mediated destabilization of the insert. Complete deletions of the rRNA transcription unit did not interfere with the ability to stimulate X-Y pairing as long as most of the intergenic spacer (IGS) remained. Within groups of deletions that lacked the entire transcription unit and differed only in length of residual IGS material, pairing ability was proportional to the dose of 240-bp intergenic spacer repeats. Deletions of the complete rRNA transcription unit or of the 28S sequences alone blocked nucleolus formation, as determined by binding of an antinucleolar antibody, yet did not interfere with pairing ability, suggesting that X-Y pairing may not be mechanistically related to nucleolus formation. A model for achiasmatic pairing in Drosophila males based upon the combined action of topoisomerase I and a strand transferase is proposed. PMID:1330825

Drug-indiced aseptic meningitis: development of subacute sclerosing panencephalitis following repeated intraventricular infusion therapy with interferon alpha/beta.

PubMed

Imataka, George; Nakagawa, Eiji; Yamanouchi, Hideo; Arisaka, Osamu

2011-12-01

Interferon (IFN)-α was reported to be effective in longterm intrathecal treatment of subacute sclerosing panencephalitis (SSPE). However, the side effects related with longterm use of IFN-α/β are unclear. We evaluated the therapeutic effects of IFN-α/β in a 13-years-old patient with SSPE. The cerebrospinal fluid (CSF) measles antibody titer was 64 × NT/128×HI, IgG-index was 4.5, and the SSPE diagnosis was based on electroencephalography (Jabbour-stage II on admission). With Inosiplex (INP) given orally, IFN-α (3 × 10(6) units) was infused intraventricularly twice-a-week for 1-year. Resultantly, CSF cell count was elevated (2502/3), total protein and glucose levels were normal; however, DIAM occurred repeatedly. Consequently, reduced IFN-α (5 × 10(5) units) with hydrocorton was administered at 2-months interval for 19 months, during which, DIAM occurred four times. Therefore, IFN-β (3 × 10(6) units; twice-a-week) therapy was started and continued for 3 years. Although the symptoms were improved considerably, DIAM recurred after 15-months therapy and CSF cell counts were also elevated (2121/3). Since SSPE progressed to Jabbour-stage IV, indicated by irreversible consciousness disorder, IFN therapy was discontinued and INP monotherapy was followed for another 3 years. We, therefore, concluded that the longterm intraventricular IFN-α/β infusion therapy of SSPE involved the potential risk of DIAM with serious irreversible neurological sequelae and should be monitored carefully.

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

PubMed

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 observed. It was also observed that the primary neck response in these tests was flexion, not extension. This correlates well with recent findings from Japan and the United States showing a correlation between neck flexion and injury in accident replication simulations and postmortem human subjects (PMHS) studies, respectively. The present certification tests may not adequately control front cervical spine bumper characteristics, which are important for neck flexion response. The certification sled test also does not include the pelvis and so cannot be used to control pelvis response and does not substantially load the lumbar bumpers and so does not control these parts of the dummy. The stiffness of all spine bumpers and of the pelvis flesh should be much more tightly controlled. It is recommended that a method for certifying the front cervical bumpers should be developed. Recommendations are also made for tighter tolerance on the input parameters for the existing certification tests.

Magma-ice-sediment interactions and the origin of lava/hyaloclastite sequences in the Síða formation, South Iceland

USGS Publications Warehouse

Banik, Tenley J.; Wallace, Paul J.; Höskuldsson, Ármann; Miller, Calvin F.; Bacon, Charles R.; Furbish, David J.

2013-01-01

Products of subglacial volcanism can illuminate reconstructions of paleo-environmental conditions on both local and regional scales. Competing interpretations of Pleistocene conditions in south Iceland have been proposed based on an extensive sequence of repeating lava-and-hyaloclastite deposits in the Síða district. We propose here a new eruptive model and refine the glacial environment during eruption based on field research and analytical data for the Síða district lava/hyaloclastite units. Field observations from this and previous studies reveal a repeating sequence of cogenetic lava and hyaloclastite deposits extending many kilometers from their presumed eruptive source. Glasses from lava selvages and unaltered hyaloclastites have very low H2O, S, and CO2 concentrations, indicating significant degassing at or close to atmospheric pressure prior to quenching. We also present a scenario that demonstrates virtual co-emplacement of the two eruptive products. Our data and model results suggest repeated eruptions under thin ice or partially subaerial conditions, rather than eruption under a thick ice sheet or subglacial conditions as previously proposed.

5′CAG and 5′CTG Repeats Create Differential Impediment to the Progression of a Minimal Reconstituted T4 Replisome Depending on the Concentration of dNTPs

PubMed Central

Delagoutte, Emmanuelle; Baldacci, Giuseppe

2011-01-01

Instability of repetitive sequences originates from strand misalignment during repair or replicative DNA synthesis. To investigate the activity of reconstituted T4 replisomes across trinucleotide repeats (TNRs) during leading strand DNA synthesis, we developed a method to build replication miniforks containing a TNR unit of defined sequence and length. Each minifork consists of three strands, primer, leading strand template, and lagging strand template with a 5′ single-stranded (ss) tail. Each strand is prepared independently, and the minifork is assembled by hybridization of the three strands. Using these miniforks and a minimal reconstituted T4 replisome, we show that during leading strand DNA synthesis, the dNTP concentration dictates which strand of the structure-forming 5′CAG/5′CTG repeat creates the strongest impediment to the minimal replication complex. We discuss this result in the light of the known fluctuation of dNTP concentration during the cell cycle and cell growth and the known concentration balance among individual dNTPs. PMID:22096622

Everyone deserves a second chance: a decade of supports for teenage mothers.

PubMed

Hudgins, Rebekah; Erickson, Steve; Walker, Dion

2014-05-01

Georgia had the third highest 2010 repeat teenage birth rate in the United States and has had one of the worst rates for years. Since 2001, Georgia's Second Chance Home Network, administered by the Georgia Campaign for Adolescent Power and Potential, has provided housing and support to parenting teenagers--almost two-thirds of whom were in custody of and referred by Georgia's Department of Children and Family Services--to help them become nurturing and self-sufficient parents, to avoid repeat teenage pregnancies, and to promote healthy development of their children. Data were collected from each resident at intake, discharge, and three follow-up points at three, 12, and 24 months after discharge. Evaluation has consistently revealed improvements in several key outcomes, including education, housing, income, self-sufficiency, parenting, repeat pregnancy, and child outcomes. The 2012 evaluation revealed benefits in all these areas and found that those who stayed longer demonstrated better outcomes, especially related to the core outcomes of educational status, employment, and stable residence. Methods and findings about these outcomes are featured in this article.

Histone and ribosomal RNA repetitive gene clusters of the boll weevil are linked in a tandem array.

PubMed

Roehrdanz, R; Heilmann, L; Senechal, P; Sears, S; Evenson, P

2010-08-01

Histones are the major protein component of chromatin structure. The histone family is made up of a quintet of proteins, four core histones (H2A, H2B, H3 & H4) and the linker histones (H1). Spacers are found between the coding regions. Among insects this quintet of genes is usually clustered and the clusters are tandemly repeated. Ribosomal DNA contains a cluster of the rRNA sequences 18S, 5.8S and 28S. The rRNA genes are separated by the spacers ITS1, ITS2 and IGS. This cluster is also tandemly repeated. We found that the ribosomal RNA repeat unit of at least two species of Anthonomine weevils, Anthonomus grandis and Anthonomus texanus (Coleoptera: Curculionidae), is interspersed with a block containing the histone gene quintet. The histone genes are situated between the rRNA 18S and 28S genes in what is known as the intergenic spacer region (IGS). The complete reiterated Anthonomus grandis histone-ribosomal sequence is 16,248 bp.

Development of a prototype regenerable carbon dioxide absorber

NASA Technical Reports Server (NTRS)

Onischak, M.

1976-01-01

Design information was obtained for a new, regenerable carbon dioxide control system for extravehicular activity life support systems. Solid potassium carbonate was supported in a thin porous sheet form and fabricated into carbon dioxide absorber units. Carbon dioxide and water in the life support system atmosphere react with the potassium carbonate and form potassium bicarbonate. The bicarbonate easily reverts to the carbonate by heating to 150 deg C. The methods of effectively packing the sorbent material into EVA-sized units and the effects of inlet concentrations, flowrate, and temperature upon performance were investigated. The cycle life of the sorbent upon the repeated thermal regenerations was demonstrated through 90 cycles.

Molecular characterization of organic electronic films.

PubMed

DeLongchamp, Dean M; Kline, R Joseph; Fischer, Daniel A; Richter, Lee J; Toney, Michael F

2011-01-18

Organic electronics have emerged as a viable competitor to amorphous silicon for the active layer in low-cost electronics. The critical performance of organic electronic materials is closely related to their morphology and molecular packing. Unlike their inorganic counterparts, polymers combine complex repeat unit structure and crystalline disorder. This combination prevents any single technique from being able to uniquely solve the packing arrangement of the molecules. Here, a general methodology for combining multiple, complementary techniques that provide accurate unit cell dimensions and molecular orientation is described. The combination of measurements results in a nearly complete picture of the organic film morphology. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A case study in nonconformance and performance trend analysis

NASA Technical Reports Server (NTRS)

Maloy, Joseph E.; Newton, Coy P.

1990-01-01

As part of NASA's effort to develop an agency-wide approach to trend analysis, a pilot nonconformance and performance trending analysis study was conducted on the Space Shuttle auxiliary power unit (APU). The purpose of the study was to (1) demonstrate that nonconformance analysis can be used to identify repeating failures of a specific item (and the associated failure modes and causes) and (2) determine whether performance parameters could be analyzed and monitored to provide an indication of component or system degradation prior to failure. The nonconformance analysis of the APU did identify repeating component failures, which possibly could be reduced if key performance parameters were monitored and analyzed. The performance-trending analysis verified that the characteristics of hardware parameters can be effective in detecting degradation of hardware performance prior to failure.

Simultaneous Differentiation and Typing of Entamoeba histolytica and Entamoeba dispar

PubMed Central

Zaki, Mehreen; Meelu, Parool; Sun, Wei; Clark, C. Graham

2002-01-01

Sequences corresponding to some of the polymorphic loci previously reported from Entamoeba histolytica have been detected in Entamoeba dispar. Comparison of nucleotide sequences of two loci between E. dispar strain SAW760 and E. histolytica strain HM-1:IMSS revealed significant differences in both repeat and flanking regions. The tandem repeat units varied not only in sequence but also in number and arrangement between the two species at both the loci. Using the sequences obtained, primer pairs aimed at amplifying species-specific products were designed and tested on a variety of E. histolytica and E. dispar samples. Amplification results were in complete agreement with the original species classification in all cases, and the PCR products displayed discernible size and pattern variations among the isolates. PMID:11923344

[Customer satisfaction with a quality management system according to DIN EN ISO 9001:2000: Increase in the satisfaction of cooperating clinics].

PubMed

Beholz, Sven; Konertz, Wolfgang

2006-01-01

The evaluation of customers' satisfaction is elementary for any quality management system. In our university cardiac surgery unit that has been certified according to DIN EN ISO 9001:2000 the influence of repeated evaluation of the referring physicians' satisfaction conducted in the course of three consecutive years on structures and processes in the scope of the quality management system was examined. Customers' satisfaction with the possibility of access to the department could be increased by targeted interventions. Further interventions in the field of documentation led to a measurable increase in satisfaction with postoperative communication. Repeated annual evaluation of the satisfaction of referring physicians has proved to be a valuable tool in the process of continuous quality improvement.

Three novel polymorphic microsatellite markers for the glaucoma locus GLC1B by datamining tetranucleotide repeats on chromosome 2p12-q12

PubMed Central

2009-01-01

In order to identify new markers around the glaucoma locus GLC1B as a tool to refine its critical region at 2p11.2-2q11.2, we searched the critical region sequence obtained from the UCSC database for tetranucleotide (GATA)n and (GTCT)n repeats of at least 10 units in length. Three out of four potential microsatellite loci were found to be polymorphic, heterozygosity ranging from 64.56% to 79.59%. The identified markers are useful not only for GLC1B locus but also for the study of other disease loci at 2p11.2-2q11.2, a region with scarcity of microsatellite markers. PMID:21637444

Applying inoculation theory to the study of recidivism reduction in criminal prison inmates.

PubMed

Matusitz, Jonathan; Breen, Gerald-Mark

2013-10-01

The purpose of the authors through this study is to establish inoculation theory as a viable method in the prevention or reduction of recidivism in criminal prison inmate populations in the United States. The authors begin with a detailed literature review on inoculation. They also describe, in detail, recidivism in prisons. In doing so, they provide a series of interconnected topics, such as the total number of inmates in U.S. prisons, statistical displays of repeat offenders or subjects of recidivism, and the types of crimes often times repeated by convicted criminals. What comes afterwards is an explication of how inoculation theory can be applied in the context of reducing prisoner recidivism. The authors conclude this study with a discussion section that offers suggestions for future research.

Method for generating O.sub.2-rich gas from air using water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakano, Anna; Nakano, Jinichiro; Bennett, James P.

The present disclosure is directed to a method for enriching an inlet air stream utilizing a number of enrichment sub-units connected in series, where each enrichment sub-unit conducts both a dissolution and degasification cycle. Each enrichment sub-unit comprises a compressor, an aeration unit, a deaeration unit, and a pump for the recirculation of water between the aeration and deaeration units. The methodology provides a manner in which the relationship between the respective Henry's coefficients of the oxygen and nitrogen in water may be exploited to enrich the O.sub.2 volume percent and diminish the N.sub.2 volume percent over repeated dissolution andmore » degasification cycles. By utilizing a number of enrichment sub-units connected in series, the water contained in each enrichment sub-unit acts to progressively increase the O.sub.2 volume percent. Additional enrichment sub-units may be added and utilized until the O.sub.2 volume percent equals or exceeds a target O.sub.2 volume percent. In a particular embodiment, air having a general composition of about 78 vol. % N.sub.2 and 21 vol. % O.sub.2 is progressively enriched to provide a final mixture of about 92% vol. % O.sub.2 and 8% vol. % N.sub.2.« less

Huntington disease reduced penetrance alleles occur at high frequency in the general population

PubMed Central

Kay, Chris; Collins, Jennifer A.; Miedzybrodzka, Zosia; Madore, Steven J.; Gordon, Erynn S.; Gerry, Norman; Davidson, Mark; Slama, Ramy A.

2016-01-01

Objective: To directly estimate the frequency and penetrance of CAG repeat alleles associated with Huntington disease (HD) in the general population. Methods: CAG repeat length was evaluated in 7,315 individuals from 3 population-based cohorts from British Columbia, the United States, and Scotland. The frequency of ≥36 CAG alleles was assessed out of a total of 14,630 alleles. The general population frequency of reduced penetrance alleles (36–39 CAG) was compared to the prevalence of patients with HD with genetically confirmed 36–39 CAG from a multisource clinical ascertainment in British Columbia, Canada. The penetrance of 36–38 CAG repeat alleles for HD was estimated for individuals ≥65 years of age and compared against previously reported clinical penetrance estimates. Results: A total of 18 of 7,315 individuals had ≥36 CAG, revealing that approximately 1 in 400 individuals from the general population have an expanded CAG repeat associated with HD (0.246%). Individuals with CAG 36–37 genotypes are the most common (36, 0.096%; 37, 0.082%; 38, 0.027%; 39, 0.000%; ≥40, 0.041%). General population CAG 36–38 penetrance rates are lower than penetrance rates extrapolated from clinical cohorts. Conclusion: HD alleles with a CAG repeat length of 36–38 occur at high frequency in the general population. The infrequent diagnosis of HD at this CAG length is likely due to low penetrance. Another important contributing factor may be reduced ascertainment of HD in those of older age. PMID:27335115

Sunflower centromeres consist of a centromere-specific LINE and a chromosome-specific tandem repeat.

PubMed

Nagaki, Kiyotaka; Tanaka, Keisuke; Yamaji, Naoki; Kobayashi, Hisato; Murata, Minoru

2015-01-01

The kinetochore is a protein complex including kinetochore-specific proteins that plays a role in chromatid segregation during mitosis and meiosis. The complex associates with centromeric DNA sequences that are usually species-specific. In plant species, tandem repeats including satellite DNA sequences and retrotransposons have been reported as centromeric DNA sequences. In this study on sunflowers, a cDNA-encoding centromere-specific histone H3 (CENH3) was isolated from a cDNA pool from a seedling, and an antibody was raised against a peptide synthesized from the deduced cDNA. The antibody specifically recognized the sunflower CENH3 (HaCENH3) and showed centromeric signals by immunostaining and immunohistochemical staining analysis. The antibody was also applied in chromatin immunoprecipitation (ChIP)-Seq to isolate centromeric DNA sequences and two different types of repetitive DNA sequences were identified. One was a long interspersed nuclear element (LINE)-like sequence, which showed centromere-specific signals on almost all chromosomes in sunflowers. This is the first report of a centromeric LINE sequence, suggesting possible centromere targeting ability. Another type of identified repetitive DNA was a tandem repeat sequence with a 187-bp unit that was found only on a pair of chromosomes. The HaCENH3 content of the tandem repeats was estimated to be much higher than that of the LINE, which implies centromere evolution from LINE-based centromeres to more stable tandem-repeat-based centromeres. In addition, the epigenetic status of the sunflower centromeres was investigated by immunohistochemical staining and ChIP, and it was found that centromeres were heterochromatic.

Short-Sequence DNA Repeats in Prokaryotic Genomes

PubMed Central

van Belkum, Alex; Scherer, Stewart; van Alphen, Loek; Verbrugh, Henri

1998-01-01

Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10−4 per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant. PMID:9618442

Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family.

PubMed

Garcia, Sònia; Panero, José L; Siroky, Jiri; Kovarik, Ales

2010-08-16

In flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in approximately 200 species representing the family diversity and other closely related groups. Dominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes. Our results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units, their copy number and chromosomal organisation may occur within relatively short evolutionary time. We hypothesize that the 5S gene integration within the 35S unit might have repeatedly occurred during plant evolution, and probably once in Asteraceae.

Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

PubMed Central

2010-01-01

Background In flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in ~200 species representing the family diversity and other closely related groups. Results Dominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes. Conclusions Our results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units, their copy number and chromosomal organisation may occur within relatively short evolutionary time. We hypothesize that the 5S gene integration within the 35S unit might have repeatedly occurred during plant evolution, and probably once in Asteraceae. PMID:20712858

Description of chronostratigraphic units preserved as channel deposits and geomorphic processes following a basin-scale disturbance by a wildfire in Colorado

USGS Publications Warehouse

Moody, John A.; Martin, Deborah A.

2017-10-11

The consequence of a 1996 wildfire disturbance and a subsequent high-intensity summer convective rain storm (about 110 millimeters per hour) was the deposition of a sediment superslug in the Spring Creek basin (26.8 square kilometers) of the Front Range Mountains in Colorado. Spring Creek is a tributary to the South Platte River upstream from Strontia Springs Reservoir, which supplies domestic water for the cities of Denver and Aurora. Changes in a superslug were monitored over the course of 18 years (1996–2014) by repeat surveys at 18 channel cross sections spaced at nearly equal intervals along a 1,500-meter study reach and by a time series of photographs of each cross section. Surveys were not repeated at regular time intervals but after major changes caused by different geomorphic processes. The focus of this long-term study was to understand the evolution and internal alluvial architecture of chronostratigraphic units (defined as the volume of sediment deposited between two successive surveys), and the preservation or storage of these units in the superslug. The data are presented as a series of 18 narratives (one for each cross section) that summarize the changes, illustrate these changes with photographs, and provide a preservation plot showing the amount of each chronostratigraphic unit still remaining in June 2014.The most significant hydrologic change after the wildfire was an exponential decrease in peak discharge of flash floods caused by summer convective rain storms. In response to these hydrologic changes, all 18 locations went through an aggradation phase, an incision phase, and finally a stabilization phase. However, the architecture of the chronostratigraphic units differs from cross section to cross section, and units are characterized by either a laminar, fragmented, or hybrid alluvial architecture. In response to the decrease in peak-flood discharge and the increase in hillslope and riparian vegetation, Spring Creek abandoned many of the nearly horizontal erosional and depositional surfaces and left a landscape consisting of a series of cut-and-fill terraces as a legacy of this wildfire disturbance. 

Use of units of measurement error in anthropometric comparisons.

PubMed

Lucas, Teghan; Henneberg, Maciej

2017-09-01

Anthropometrists attempt to minimise measurement errors, however, errors cannot be eliminated entirely. Currently, measurement errors are simply reported. Measurement errors should be included into analyses of anthropometric data. This study proposes a method which incorporates measurement errors into reported values, replacing metric units with 'units of technical error of measurement (TEM)' by applying these to forensics, industrial anthropometry and biological variation. The USA armed forces anthropometric survey (ANSUR) contains 132 anthropometric dimensions of 3982 individuals. Concepts of duplication and Euclidean distance calculations were applied to the forensic-style identification of individuals in this survey. The National Size and Shape Survey of Australia contains 65 anthropometric measurements of 1265 women. This sample was used to show how a woman's body measurements expressed in TEM could be 'matched' to standard clothing sizes. Euclidean distances show that two sets of repeated anthropometric measurements of the same person cannot be matched (> 0) on measurements expressed in millimetres but can in units of TEM (= 0). Only 81 women can fit into any standard clothing size when matched using centimetres, with units of TEM, 1944 women fit. The proposed method can be applied to all fields that use anthropometry. Units of TEM are considered a more reliable unit of measurement for comparisons.

Acoustic Signaling by Singing Humpback Whales (Megaptera novaeangliae): What Role Does Reverberation Play?

PubMed

Mercado, Eduardo

2016-01-01

When humpback whales (Megaptera novaeangliae) sing in coastal waters, the units they produce can generate reverberation. Traditionally, such reverberant acoustic energy has been viewed as an incidental side-effect of high-amplitude, long-distance, sound transmission in the ocean. An alternative possibility, however, is that reverberation actually contributes to the structure and function of songs. In the current study, this possibility was assessed by analyzing reverberation generated by humpback whale song units, as well as the spectral structure of unit sequences, produced by singers from different regions. Acoustical analyses revealed that: (1) a subset of units within songs generated narrowband reverberant energy that in some cases persisted for periods longer than the interval between units; (2) these highly reverberant units were regularly repeated throughout the production of songs; and (3) units occurring before and after these units often contained spectral energy peaks at non-overlapping, adjacent frequencies that were systematically related to the bands of reverberant energy generated by the units. These findings strongly suggest that some singing humpback whales not only produce sounds conducive to long-duration reverberation, but also may sequentially structure songs to avoid spectral overlap between units and ongoing reverberation. Singer-generated reverberant energy that is received simultaneously with directly transmitted song units can potentially provide listening whales with spatial cues that may enable them to more accurately determine a singer's position.

Acoustic Signaling by Singing Humpback Whales (Megaptera novaeangliae): What Role Does Reverberation Play?

PubMed Central

Mercado, Eduardo

2016-01-01

When humpback whales (Megaptera novaeangliae) sing in coastal waters, the units they produce can generate reverberation. Traditionally, such reverberant acoustic energy has been viewed as an incidental side-effect of high-amplitude, long-distance, sound transmission in the ocean. An alternative possibility, however, is that reverberation actually contributes to the structure and function of songs. In the current study, this possibility was assessed by analyzing reverberation generated by humpback whale song units, as well as the spectral structure of unit sequences, produced by singers from different regions. Acoustical analyses revealed that: (1) a subset of units within songs generated narrowband reverberant energy that in some cases persisted for periods longer than the interval between units; (2) these highly reverberant units were regularly repeated throughout the production of songs; and (3) units occurring before and after these units often contained spectral energy peaks at non-overlapping, adjacent frequencies that were systematically related to the bands of reverberant energy generated by the units. These findings strongly suggest that some singing humpback whales not only produce sounds conducive to long-duration reverberation, but also may sequentially structure songs to avoid spectral overlap between units and ongoing reverberation. Singer-generated reverberant energy that is received simultaneously with directly transmitted song units can potentially provide listening whales with spatial cues that may enable them to more accurately determine a singer’s position. PMID:27907182

Process and pattern in the emergence of Phytophthora ramorum

Treesearch

Niklaus J. Grüwald; Matteo Garbelotto; Erica M. Goss; Kurt Heungens; Simone Prospero

2013-01-01

The invasive sudden oak death pathogen, Phytophthora ramorum, has emerged repeatedly since its first detection in the 1990s in the United States and Europe. This paper will explore recent research by several groups published in the review by Grünwald et al. (Grünwald, N.J.; Garbelotto, M.; Goss, E.M.; Heungens, K.; Prospero, S. 2012. Emergence of...

Useful Spanish for Medical and Hospital Personnel with a Bibliography on Hispanic Peoples in the United States.

ERIC Educational Resources Information Center

Cordasco, Francesco; Alvarez, Pablo Rivera

The manual gives vocabulary and sentence patterns which are considered basic or essential to medical personnel who work with Spanish-speaking patients. In most instances, only one way is given to express an idea or to ask a question. Sentence patterns and vocabulary that should be made active are repeated many times. The manual includes (1)…

A comparison of three erosion control mulches on decommissioned forest road corridors in the northern Rocky Mountains, United States

Treesearch

R. B. Foltz

2012-01-01

This study tested the erosion mitigation effectiveness of agricultural straw and two wood-based mulches for four years on decommissioned forest roads. Plots were installed on the loosely consolidated, bare soil to measure sediment production, mulch cover, and plant regrowth. The experimental design was a repeated measures, randomized block on two soil types common in...

Acquisition and amplification of a testis-expressed autosomal gene, SSL, by the Drosophila Y chromosome

PubMed Central

Kalmykova, Alla I.; Shevelyov, Yury Y.; Dobritsa, Anna A.; Gvozdev, Vladimir A.

1997-01-01

The acquisition of autosomal fertility genes has been proposed to be an important process in human Y chromosome evolution. For example, the Y-linked fertility factor DAZ (Deleted in Azoospermia) appears to have arisen after the transposition and tandem amplification of the autosomal DAZH gene. The Drosophila melanogaster Y chromosome contains tandemly repeated Su(Ste) units that are thought to affect male fertility as suppressors of the homologous X-linked Stellate repeats. Here we report the detection of a testis-expressed autosomal gene, SSL [Su(Ste)-like], that appears to be an ancestor of the Y-linked Su(Ste) units. SSL encodes a casein kinase 2 (CK2) β-subunit-like protein. Its putative ORF shares extensive (45%) homology with the genuine β-subunit of CK2 and retains the conserved C-terminal and Glu/Asp-rich domains that are essential for CK2 holoenzyme regulation. SSL maps within region 60D1–2 of D. melanogaster and D. simulans polytene chromosomes. We present evidence that SSL was derived from the genuine βCK2 gene by reverse transcription. This event resulted in the loss of the first three introns in the coding region of the SSL ancestor gene. Evolutionary analysis indicates that SSL has evolved under selective pressure at the translational level. Its sequence, especially in the 3′ region, is much closer to the Y-linked Su(Ste) tandem repeats than to the βCK2 gene. These results suggest that the acquisition of testis-specific autosomal genes may be important for the evolution of Drosophila as well as human Y chromosomes. PMID:9177211

Optimal Hydrophobicity in Ring-Opening Metathesis Polymerization-Based Protein Mimics Required for siRNA Internalization.

PubMed

deRonde, Brittany M; Posey, Nicholas D; Otter, Ronja; Caffrey, Leah M; Minter, Lisa M; Tew, Gregory N

2016-06-13

Exploring the role of polymer structure for the internalization of biologically relevant cargo, specifically siRNA, is of critical importance to the development of improved delivery reagents. Herein, we report guanidinium-rich protein transduction domain mimics (PTDMs) based on a ring-opening metathesis polymerization scaffold containing tunable hydrophobic moieties that promote siRNA internalization. Structure-activity relationships using Jurkat T cells and HeLa cells were explored to determine how the length of the hydrophobic block and the hydrophobic side chain compositions of these PTDMs impacted siRNA internalization. To explore the hydrophobic block length, two different series of diblock copolymers were synthesized: one series with symmetric block lengths and one with asymmetric block lengths. At similar cationic block lengths, asymmetric and symmetric PTDMs promoted siRNA internalization in the same percentages of the cell population regardless of the hydrophobic block length; however, with 20 repeat units of cationic charge, the asymmetric block length had greater siRNA internalization, highlighting the nontrivial relationships between hydrophobicity and overall cationic charge. To further probe how the hydrophobic side chains impacted siRNA internalization, an additional series of asymmetric PTDMs was synthesized that featured a fixed hydrophobic block length of five repeat units that contained either dimethyl (dMe), methyl phenyl (MePh), or diphenyl (dPh) side chains and varied cationic block lengths. This series was further expanded to incorporate hydrophobic blocks consisting of diethyl (dEt), diisobutyl (diBu), and dicyclohexyl (dCy) based repeat units to better define the hydrophobic window for which our PTDMs had optimal activity. High-performance liquid chromatography retention times quantified the relative hydrophobicities of the noncationic building blocks. PTDMs containing the MePh, diBu, and dPh hydrophobic blocks were shown to have superior siRNA internalization capabilities compared to their more and less hydrophobic counterparts, demonstrating a critical window of relative hydrophobicity for optimal internalization. This better understanding of how hydrophobicity impacts PTDM-induced internalization efficiencies will help guide the development of future delivery reagents.

Characteristic Fracture Spacing in Primary and Secondary Recovery from Naturally Fractured Reservoirs

NASA Astrophysics Data System (ADS)

Gong, J.; Rossen, W.

2015-12-01

We showed previously (Gong and Rossen, 2014a,b) that, if the fracture aperture distribution is broad enough in a naturally fractured reservoir, even one where the fracture network is well-connected, most fractures can be eliminated without significantly affecting the flow through the fracture network. During a waterflood or enhanced-oil-recovery (EOR) process, the production of oil depends on the supply of injected water or EOR agent. This suggests that the characteristic fracture spacing for the dual-porosity/dual-permeability simulation of waterflood or EOR in a naturally fractured reservoir should account not for all fractures but only the relatively small portion of the fracture network carrying almost all the injected water or EOR agent. In contrast, in primary production even a relatively small fracture represents an effective path for oil to flow to a production well. Thus in primary production the effective fracture spacing should include all the fractures. This distinction means that the "shape factor" in dual-porosity/dual-permeability reservoir simulators and the repeating unit in homogenization should depend on the process involved: specifically, it should be different for primary and secondary or tertiary recovery. We test this hypothesis in a simple representation of a fractured reservoir with a non-uniform distribution of fracture flow conductivities. We compare oil production, flow patterns in matrix, and the pattern of oil recovery around fractures with and without the "unimportant" fractures present. In primary production, all fractures which are much more permeable than matrix play a significant role in production. The shape factor or repeating-unit size should reflect the entire fracture distribution. In secondary or tertiary production, the role of fractures that carry relatively little flow depends on injection rate, the ratio of flow carried by the different fractures, and the permeability of matrix. In some cases, the appropriate shape factor or repeating-unit size for waterflood or EOR should reflect only those fractures that carry most of the flow. References:Gong, and Rossen, 14th ECMOR Conf., Catania, Sicily, 2014(a). Gong, and Rossen, Intl. Discrete Fracture Network Eng. Conf., Vancouver, Canada, 2014(b).

Contact and Length Dependent Effects in Single-Molecule Electronics

NASA Astrophysics Data System (ADS)

Hines, Thomas

Understanding charge transport in single molecules covalently bonded to electrodes is a fundamental goal in the field of molecular electronics. In the past decade, it has become possible to measure charge transport on the single-molecule level using the STM break junction method. Measurements on the single-molecule level shed light on charge transport phenomena which would otherwise be obfuscated by ensemble measurements of groups of molecules. This thesis will discuss three projects carried out using STM break junction. In the first project, the transition between two different charge transport mechanisms is reported in a set of molecular wires. The shortest wires show highly length dependent and temperature invariant conductance behavior, whereas the longer wires show weakly length dependent and temperature dependent behavior. This trend is consistent with a model whereby conduction occurs by coherent tunneling in the shortest wires and by incoherent hopping in the longer wires. Measurements are supported with calculations and the evolution of the molecular junction during the pulling process is investigated. The second project reports controlling the formation of single-molecule junctions by means of electrochemically reducing two axial-diazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in-situ between the molecule and gold electrodes. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond. Finally, the third project investigates the role that molecular conformation plays in the conductance of oligothiophene single-molecule junctions. Ethyl substituted oligothiophenes were measured and found to exhibit temperature dependent conductance and transition voltage for molecules with between two and six repeat units. While the molecule with only one repeat unit shows temperature invariant behavior. Density functional theory calculations show that at higher temperatures the oligomers with multiple repeat units assume a more planar conformation, which increases the conjugation length and decreases the effective energy barrier of the junction.

Structural analysis of the rDNA intergenic spacer of Brassica nigra: evolutionary divergence of the spacers of the three diploid Brassica species.

PubMed

Bhatia, S; Singh Negi, M; Lakshmikumaran, M

1996-11-01

EcoRI restriction of the B. nigra rDNA recombinants, isolated from a lambda genomic library, showed that the 3.9-kb fragment corresponded to the Intergenic Spacer (IGS), which was sequenced and found to be 3,928 bp in size. Sequence and dot-matrix analyses showed that the organization of the B. nigra rDNA IGS was typical of most rDNA spacers, consisting of a central repetitive region and flanking unique sequences on either side. The repetitive region was composed of two repeat families-RF 'A' and RF 'B.' The B. nigra RF 'A' consisted of a tandem array of three full-length copies of a 106-bp sequence element. RF 'B' was composed of 66 tandemly repeated elements. Each 'B' element was only 21-bp in size and this is the smallest repeat unit identified in plant rDNA to date. The putative transcription initiation site (TIS) was identified as nucleotide position 3,110. Based on the sequence analysis it was suggested that the present organization of the repeat families was generated by successive cycles of deletions and amplifications and was being maintained by homogenization processes such as gene conversion and crossing-over.A detailed comparison of the rDNA IGS sequences of the three diploid Brassica species-namely, B. nigra, B. campestris, and B. oleracea-was carried out. First, comparisons revealed that B. campestris and B. oleracea were close to each other as the repeat families in both showed high sequence homology between each other. Second, the repeat elements in both the species were organized in an interspersed manner. Third, a 52-bp sequence, present just downstream of the repeats in B. campestris, was found to be identical to the B. oleracea repeats, thereby suggesting a common progenitor. On the other hand, in B. nigra no interspersion pattern of organization of repeats was observed. Further, the B. nigra RF 'A' was identified as distinct from the repeat families of B. campestris and B. oleracea. Based on this analysis, it was suggested that during speciation B. campestris and B. oleracea evolved in one lineage whereas B. nigra diverged into a separate lineage. The comparative analysis of the IGS helped in identifying not only conserved ancestral sequence motifs of possible functional significance such as promoters and enhancers, but also sequences which showed variation between the three diploid species and were therefore identified as species-specific sequences.

Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements.

PubMed

Zhang, Quan; Ye, Yuzhen

2017-02-06

The CRISPR-Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR-Cas system consists of a CRISPR array of repeat and spacer units, and a locus of cas genes. The CRISPR and the cas locus are often located next to each other in the genomes. However, there is no quantitative estimate of the co-location. In addition, ad-hoc studies have shown that some non-CRISPR genomic elements contain repeat-spacer-like structures and are mistaken as CRISPRs. Using available genome sequences, we observed that a significant number of genomes have isolated cas loci and/or CRISPRs. We found that 11%, 22% and 28% of the type I, II and III cas loci are isolated (without CRISPRs in the same genomes at all or with CRISPRs distant in the genomes), respectively. We identified a large number of genomic elements that superficially reassemble CRISPRs but don't contain diverse spacers and have no companion cas genes. We called these elements false-CRISPRs and further classified them into groups, including tandem repeats and Staphylococcus aureus repeat (STAR)-like elements. This is the first systematic study to collect and characterize false-CRISPR elements. We demonstrated that false-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be useful for improving the annotation of CRISPR-Cas systems.

Spa Goers' Repeated Visits for Health and Wellness and the Influential Factors: An Exploratory Study of the UK Spa Goers.

PubMed

Choi, Myungsuk; Poade, Donna; Sohn, Minsung; Choi, Mankyu

2016-01-01

Dissemination of spa services across the globe and its market saturation drive demand for differentiated communication methods. This study aims to explore the influential factors on spa goers' repeated visits and their practical applications in the health and wellness spa industry. The identified factors were used as the measurement variables to examine the relation with spa goers' repeated visits. The proposed concept was tested by a mixed method combining a self-administered questionnaire and semistructured interview with 54 survey participants and 6 interviewees. It was meaningful to use a sample of the UK spa goers from the southwest region since global spa trends stem from the EU spas, and the United Kingdom is one of the market leaders. The data were analyzed using frequency, percentage, multiple logistic regression analysis, and coding process. The survey findings demonstrated that the most significant influential factor on the repeated spa visits is a memorable experience of which showed 13.7 times higher probability than the reference up-to-date facility. The details of memorable experiences were discovered throughout the interviews that include the rediscovery of self, feeling of connectedness, recharge for positive emotions, self-reward through escapism, and experience of noncommercialized local products and attractions. Therefore, using experiential marketing methods can be effective spa service marketing.

The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.

PubMed

Yi, Dong-Keun; Lee, Hae-Lim; Sun, Byung-Yun; Chung, Mi Yoon; Kim, Ki-Joong

2012-05-01

This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.

pH-responsive fluorescence chemical sensor constituted by conjugated polymers containing pyridine rings.

PubMed

Adachi, Naoya; Kaneko, Yuki; Sekiguchi, Kazuki; Sugiyama, Hiroki; Sugeno, Masafumi

2015-12-01

Poly(p-pyridinium phenylene ethynylene)s (PPyPE) functionalized with alternating donor-acceptor repeat units were synthesized by a Pd-catalyzed Sonogashira coupling reaction between diethynyl monomer and di-iodopyridine for use as a pH-responsive fluorescence chemical sensor. The synthesized PPyPE, containing pyridine units, was characterized by FT-IR, (1)H and (13)C NMR, UV-visible and fluorescence spectroscopies. We investigated the relationship between changes of optical properties and protonation/deprotonation of PPyPE containing pyridine units in solution. Addition of HCl decreased and red-shifted the fluorescence intensity of the conjugated polymers that contained pyridine rings; fluorescence intensity of the polymers increased upon addition of NaOH solution. The synthesized PPyPE was found to be an effective and reusable chemical sensor for pH sensing. Copyright © 2015 John Wiley & Sons, Ltd.

Shifts in the relationship between motor unit recruitment thresholds versus derecruitment thresholds during fatigue.

PubMed

Stock, Matt S; Mota, Jacob A

2017-12-01

Muscle fatigue is associated with diminished twitch force amplitude. We examined changes in the motor unit recruitment versus derecruitment threshold relationship during fatigue. Nine men (mean age = 26 years) performed repeated isometric contractions at 50% maximal voluntary contraction (MVC) knee extensor force until exhaustion. Surface electromyographic signals were detected from the vastus lateralis, and were decomposed into their constituent motor unit action potential trains. Motor unit recruitment and derecruitment thresholds and firing rates at recruitment and derecruitment were evaluated at the beginning, middle, and end of the protocol. On average, 15 motor units were studied per contraction. For the initial contraction, three subjects showed greater recruitment thresholds than derecruitment thresholds for all motor units. Five subjects showed greater recruitment thresholds than derecruitment thresholds for only low-threshold motor units at the beginning, with a mean cross-over of 31.6% MVC. As the muscle fatigued, many motor units were derecruited at progressively higher forces. In turn, decreased slopes and increased y-intercepts were observed. These shifts were complemented by increased firing rates at derecruitment relative to recruitment. As the vastus lateralis fatigued, the central nervous system's compensatory adjustments resulted in a shift of the regression line of the recruitment versus derecruitment threshold relationship. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

Comparison of the heat generation of light curing units.

PubMed

Bagis, Bora; Bagis, Yildirim; Ertas, Ertan; Ustaomer, Seda

2008-02-01

The aim of this study was to evaluate the heat generation of three different types of light curing units. Temperature increases were recorded from a distance of 1 mm from a thermocouple to the tip of three different types of light curing units including one quartz-tungsten halogen (QTH), one plasma arc (PAC), and one light emitting diode (LED) unit. An experimental model was designed to fix the 1 mm distance between the tip of the light curing units and the thermocouple wire. Temperature changes were recorded in 10 second intervals up to 40 seconds. (10, 20, 30, and 40 seconds). Temperature measurements were repeated three times for every light curing unit after a one hour standby period. Statistical analysis of the results was performed using the analysis of variance (ANOVA) and the Bonferroni Test. The highest temperature rises (54.4+/-1.65 degrees C) occurred during activation of a PAC light curing unit for every test period (p<.05). The least temperature increase (11.8+/-1.3 degrees C) occurred with a LED curing unit for each tested period except for the measurement of the temperature rise using the QTH curing unit at the tenth second interval (p<.05). These results indicate the choice of light activation unit and curing time is important when polymerizing light activated resin based restorations to avoid any thermal damage to the pulp.

Inferential control -- Part 1: Crude unit advanced controls pass accuracy and repeatability tests

DOE Office of Scientific and Technical Information (OSTI.GOV)

San, Y.P.; Landells, K.C.; Mackay, D.C.

1994-11-28

An inferential model is one that provides a quality for which an analyzer is not available. This type of model uses readily available physical measurements -- such as temperatures, pressures, and flow rates -- to infer a quality such as kerosine flash point. The No. 2 crude distillation unit (CDU-2) at Singapore Refining Co. Pte. Ltd.'s Pulau Merlimau refinery has a nominal 130,000 b/d capacity. It produces naphtha, kerosine, diesel, and residue products from a wide range of crude blends. Over the past 12 months, extensive advanced control applications have been implemented on the unit. This first of two articlesmore » will describe the control system and its implementation. The second will outline the project's achievements, including reduced quality giveaway and increased profits. The paper describes background of the company and unit, the process, project implementation, the Infer model, model tuning, closed-loop control, feed rate maximization, and economic monitoring.« less

Rules of parameter variation in homotype series of birdsong can indicate a 'sollwert' significance.

PubMed

Hultsch, H; Todt, D

1996-11-01

Various bird species produce songs which include homotype pattern series, i.e. segments composed of a number of repeated vocal units. We compared such units and analyzed the variation of their parameters, especially in the time and the frequency domain. In addition, we examined whether and how serial changes of both the range and the trend of variation were related to song constituents following the repetitions. Data evaluation showed that variation of specific serial parameters (e.g., unit pitch or unit duration) occurring in the whistle song-types of nightingales (Luscinia megarhynchos) were converging towards a distinct terminal value. Although song-types differed in this terminal value, it was found to play the role of a key cue ('sollwert'). The continuation of a song depended on a preceding attainment of its specific 'sollwert'. Our results suggest that the study of signal parameters and rules of their variations make a useful tool for the behavioral access to the properties of the control systems mediating serial signal performances.

Enclosed versus open nursing stations in adult acute care psychiatric settings: does the design affect the therapeutic milieu?

PubMed

Southard, Kelly; Jarrell, Ashley; Shattell, Mona M; McCoy, Thomas P; Bartlett, Robin; Judge, Christine A

2012-05-01

Specific efforts by hospital accreditation organizations encourage renovation of nursing stations, so nurses can better see, attend, and care for their patients. The purpose of this study was to examine the effect of nursing station design on the therapeutic milieu in an adult acute care psychiatric unit. A repeated cross-sectional, pretest-posttest design was used. Data were collected from a convenience sample of 81 patients and 25 nursing staff members who completed the Ward Atmosphere Scale. Pretest data were collected when the unit had an enclosed nursing station, and posttest data were collected after renovations to the unit created an open nursing station. No statistically significant differences were found in patient or staff perceptions of the therapeutic milieu. No increase in aggression toward staff was found, given patients' ease of access to the nursing station. More research is needed about the impact of unit design in acute care psychiatric settings. Copyright 2012, SLACK Incorporated.

From Concrete to Abstract in the Measurement of Length

NASA Astrophysics Data System (ADS)

Stephanou, Andreas; Fisher, William P., Jr.

2013-09-01

The concatenation of units of length is widely viewed as the paradigmatic expression of fundamental measurement. Survey, assessment, and test scores in educational and psychological measurement are often interpreted in ways that assume a concatenation of units to have been established, even though these assumptions are rarely stated or tested. A concatenation model for measurement is shown to be equivalent to a Rasch model: any two units of measurement placed end to end must together be of the same length as either one of them added to itself. This additive principle and a concatenation model of measurement together serve as a heuristic guide for organizing two experimental approaches to calibrating instruments for measuring length. The capacity to reproduce the unit of measurement from theory with no need for repeated empirical calibration experiments, as in the geometrical bisection of the line and the resultant halving of the length measure, is highlighted as essential to demonstrating a thorough understanding of the construct.

Structure-guided investigation of lipopolysaccharide O-antigen chain length regulators reveals regions critical for modal length control.

PubMed

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.

Contemporary patterns of spontaneous labor with normal neonatal outcomes.

PubMed

Zhang, Jun; Landy, Helain J; Branch, D Ware; Burkman, Ronald; Haberman, Shoshana; Gregory, Kimberly D; Hatjis, Christos G; Ramirez, Mildred M; Bailit, Jennifer L; Gonzalez-Quintero, Victor H; Hibbard, Judith U; Hoffman, Matthew K; Kominiarek, Michelle; Learman, Lee A; Van Veldhuisen, Paul; Troendle, James; Reddy, Uma M

2010-12-01

To use contemporary labor data to examine the labor patterns in a large, modern obstetric population in the United States. Data were from the Consortium on Safe Labor, a multicenter retrospective study that abstracted detailed labor and delivery information from electronic medical records in 19 hospitals across the United States. A total of 62,415 parturients were selected who had a singleton term gestation, spontaneous onset of labor, vertex presentation, vaginal delivery, and a normal perinatal outcome. A repeated-measures analysis was used to construct average labor curves by parity. An interval-censored regression was used to estimate duration of labor, stratified by cervical dilation at admission and centimeter by centimeter. Labor may take more than 6 hours to progress from 4 to 5 cm and more than 3 hours to progress from 5 to 6 cm of dilation. Nulliparous and multiparous women appeared to progress at a similar pace before 6 cm. However, after 6 cm, labor accelerated much faster in multiparous than in nulliparous women. The 95 percentiles of the second stage of labor in nulliparous women with and without epidural analgesia were 3.6 and 2.8 hours, respectively. A partogram for nulliparous women is proposed. In a large, contemporary population, the rate of cervical dilation accelerated after 6 cm, and progress from 4 cm to 6 cm was far slower than previously described. Allowing labor to continue for a longer period before 6 cm of cervical dilation may reduce the rate of intrapartum and subsequent repeat cesarean deliveries in the United States.

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

PubMed Central

Tong, Steven Y.C.; Holden, Matthew T.G.; Nickerson, Emma K.; Cooper, Ben S.; Köser, Claudio U.; Cori, Anne; Jombart, Thibaut; Cauchemez, Simon; Fraser, Christophe; Wuthiekanun, Vanaporn; Thaipadungpanit, Janjira; Hongsuwan, Maliwan; Day, Nicholas P.; Limmathurotsakul, Direk; Parkhill, Julian; Peacock, Sharon J.

2015-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infection. Whole-genome sequencing of MRSA has been used to define phylogeny and transmission in well-resourced healthcare settings, yet the greatest burden of nosocomial infection occurs in resource-restricted settings where barriers to transmission are lower. Here, we study the flux and genetic diversity of MRSA on ward and individual patient levels in a hospital where transmission was common. We repeatedly screened all patients on two intensive care units for MRSA carriage over a 3-mo period. All MRSA belonged to multilocus sequence type 239 (ST 239). We defined the population structure and charted the spread of MRSA by sequencing 79 isolates from 46 patients and five members of staff, including the first MRSA-positive screen isolates and up to two repeat isolates where available. Phylogenetic analysis identified a flux of distinct ST 239 clades over time in each intensive care unit. In total, five main clades were identified, which varied in the carriage of plasmids encoding antiseptic and antimicrobial resistance determinants. Sequence data confirmed intra- and interwards transmission events and identified individual patients who were colonized by more than one clade. One patient on each unit was the source of numerous transmission events, and deep sampling of one of these cases demonstrated colonization with a “cloud” of related MRSA variants. The application of whole-genome sequencing and analysis provides novel insights into the transmission of MRSA in under-resourced healthcare settings and has relevance to wider global health. PMID:25491771

Contemporary Patterns of Spontaneous Labor With Normal Neonatal Outcomes

PubMed Central

Zhang, Jun; Landy, Helain J.; Branch, D. Ware; Burkman, Ronald; Haberman, Shoshana; Gregory, Kimberly D.; Hatjis, Christos G.; Ramirez, Mildred M.; Bailit, Jennifer L.; Gonzalez-Quintero, Victor H.; Hibbard, Judith U.; Hoffman, Matthew K.; Kominiarek, Michelle; Learman, Lee A.; Van Veldhuisen, Paul; Troendle, James; Reddy, Uma M.

2013-01-01

Objective To use contemporary labor data to examine the labor patterns in a large, modern obstetric population in the United States. Methods Data were from the Consortium on Safe Labor, a multicenter retrospective study that abstracted detailed labor and delivery information from electronic medical records in 19 hospitals across the United States. A total of 62,415 parturients were selected who had a singleton term gestation, spontaneous onset of labor, vertex presentation, vaginal delivery, and a normal perinatal outcome. A repeated-measures analysis was used to construct average labor curves by parity. An interval-censored regression was used to estimate duration of labor stratified by cervical dilation at admission and centimeter by centimeter. Results Labor may take over 6 hours to progress from 4 to 5 cm and over 3 hours to progress from 5 to 6 cm of dilation. Nulliparas and multiparas appeared to progress at a similar pace before 6 cm. However, after 6 cm labor accelerated much faster in multiparas than in nulliparas. The 95th percentile of the 2nd stage of labor in nulliparas with and without epidural analgesia was 3.6 and 2.8 hours, respectively. A partogram for nulliparas is proposed. Conclusion In a large, contemporary population, the rate of cervical dilation accelerated after 6 cm and progress from 4 to 6 cm was far slower than previously described. Allowing labor to continue for a longer period before 6 cm of cervical dilation may reduce the rate of intrapartum and subsequent repeat cesarean deliveries in the United States. PMID:21099592

Automated quality checks on repeat prescribing.

PubMed Central

Rogers, Jeremy E; Wroe, Christopher J; Roberts, Angus; Swallow, Angela; Stables, David; Cantrill, Judith A; Rector, Alan L

2003-01-01

BACKGROUND: Good clinical practice in primary care includes periodic review of repeat prescriptions. Markers of prescriptions that may need review have been described, but manually checking all repeat prescriptions against the markers would be impractical. AIM: To investigate the feasibility of computerising the application of repeat prescribing quality checks to electronic patient records in United Kingdom (UK) primary care. DESIGN OF STUDY: Software performance test against benchmark manual analysis of cross-sectional convenience sample of prescribing documentation. SETTING: Three general practices in Greater Manchester, in the north west of England, during a 4-month period in 2001. METHOD: A machine-readable drug information resource, based on the British National Formulary (BNF) as the 'gold standard' for valid drug indications, was installed in three practices. Software raised alerts for each repeat prescribed item where the electronic patient record contained no valid indication for the medication. Alerts raised by the software in two practices were analysed manually. Clinical reaction to the software was assessed by semi-structured interviews in three practices. RESULTS: There was no valid indication in the electronic medical records for 14.8% of repeat prescribed items. Sixty-two per cent of all alerts generated were incorrect. Forty-three per cent of all incorrect alerts were as a result of errors in the drug information resource, 44% to locally idiosyncratic clinical coding, 8% to the use of the BNF without adaptation as a gold standard, and 5% to the inability of the system to infer diagnoses that, although unrecorded, would be 'obvious' to a clinical reading the record. The interviewed clinicians supported the goals of the software. CONCLUSION: Using electronic records for secondary decision support purposes will benefit from (and may require) both more consistent electronic clinical data collection across multiple sites, and reconciling clinicians' willingness to infer unstated but 'obvious' diagnoses with the machine's inability to do the same. PMID:14702902

A set of tetra-nucleotide core motif SSR markers for efficient identification of potato (Solanum tuberosum) cultivars.

PubMed

Kishine, Masahiro; Tsutsumi, Katsuji; Kitta, Kazumi

2017-12-01

Simple sequence repeat (SSR) is a popular tool for individual fingerprinting. The long-core motif (e.g. tetra-, penta-, and hexa-nucleotide) simple sequence repeats (SSRs) are preferred because they make it easier to separate and distinguish neighbor alleles. In the present study, a new set of 8 tetra-nucleotide SSRs in potato ( Solanum tuberosum ) is reported. By using these 8 markers, 72 out of 76 cultivars obtained from Japan and the United States were clearly discriminated, while two pairs, both of which arose from natural variation, showed identical profiles. The combined probability of identity between two random cultivars for the set of 8 SSR markers was estimated to be 1.10 × 10 -8 , confirming the usefulness of the proposed SSR markers for fingerprinting analyses of potato.

Trends in Repeat Births and Use of Postpartum Contraception Among Teens - United States, 2004-2015.

PubMed

Dee, Deborah L; Pazol, Karen; Cox, Shanna; Smith, Ruben A; Bower, Katherine; Kapaya, Martha; Fasula, Amy; Harrison, Ayanna; Kroelinger, Charlan D; D'Angelo, Denise; Harrison, Leslie; Koumans, Emilia H; Mayes, Nikki; Barfield, Wanda D; Warner, Lee

2017-04-28

Teen* childbearing (one or more live births before age 20 years) can have negative health, social, and economic consequences for mothers and their children (1). Repeat teen births (two or more live births before age 20 years) can constrain the mother's ability to take advantage of educational and workforce opportunities (2), and are more likely to be preterm or of low birthweight than first teen births (3). Despite the historic decline in the U.S. teen birth rate during 1991-2015, from 61.8 to 22.3 births per 1,000 females aged 15-19 years (4), many teens continue to have repeat births (3). The American College of Obstetricians and Gynecologists and the American Academy of Pediatrics both recommend that clinicians counsel women (including teens) during prenatal care about birth spacing and postpartum contraceptive use (5), including the safety and effectiveness of long-acting reversible methods that can be initiated immediately postpartum. To expand upon prior research assessing patterns and trends in repeat childbearing and postpartum contraceptive use among teens with a recent live birth (i.e., 2-6 months after delivery) (3), CDC analyzed data from the National Vital Statistics System natality files (2004 and 2015) and the Pregnancy Risk Assessment Monitoring System (PRAMS; 2004-2013). The number and proportion of teen births that were repeat births decreased from 2004 (82,997; 20.1%) to 2015 (38,324; 16.7%); in 2015, the percentage of teen births that were repeat births varied by state from 10.6% to 21.4%. Among sexually active teens with a recent live birth, postpartum use of the most effective contraceptive methods (intrauterine devices and contraceptive implants) increased from 5.3% in 2004 to 25.3% in 2013; however, in 2013, approximately one in three reported using either a least effective method (15.7%) or no method (17.2%). Strategies that comprehensively address the social and health care needs of teen parents can facilitate access to and use of effective methods of contraception and help prevent repeat teen births.

Polyimides Containing Silver Trifluoroacetylacetonate

NASA Technical Reports Server (NTRS)

Stoakley, Diane M.; St. Clair, Anne K.; Rancourt, James D.; Taylor, Larry T.; Caplan, Maggie L.

1994-01-01

Mechanically strong, flexible, thermally stable, electrically conductive films and coatings suitable for use in electronics industry made by incorporating silver trifluoroacetylacetonate into linear aromatic condensation polyimides. In experimental films, most successful combinations of flexibility and conductivity obtained by use of 1:1, 1:1.74, and 1:2 mole ratios of silver trifluoroacetylacetonate per polyimide repeat unit. Other concentrations of silver trifluoroacetylacetonate used with different heat-treatment schedules to obtain conductive silver-impregnated films.

The United States Army 1995 Modernization Plan. Force 21

DTIC Science & Technology

1995-04-06

being modified to support the requirements and new dangers of our changing times. It is often said that we study history so as not to repeat thu...intuitive sense of battle gained from study and expertise. Training remains the key to modem, combat-ready Light Forces. Effective modemization and...Devices, Simulators and Simulations (TADSS) Light Forces training is supported by the Combined Arms Training Strategy (CATS). CATS is a descriptive

Toxic Hazards Research Unit Annual Report: 1986

DTIC Science & Technology

1987-04-01

ileum-duodenum mandibular and mesenteric lymph nodes bone (sternum and both femurs) pancreas urinary bladder thyroid brain salivary glands lungs...Woodside, E.R. Kinkead, J.M. King, and L.J. Sullivan. 1971. Response of dogs to repeated intravenous injections of propylene glycol 4000 with notes on...Van Abbe. 1979. Safety evaluation of toothpaste containing chloroform. 1II. Long term studies in beagle dogs . J. Environ. Pathol. Toxicol. 2:835-851

Decontamination Efficacy Testing of COTS SteriFx Prodcuts for Mass Personnel and Casualty Decontamination

DTIC Science & Technology

2011-09-01

low‐cost, lightweight, single‐use individual product for field self ‐decontamination. Surface (skin) decontamination of Bacillus subtilis spores has...field spray decontamination unit was previously demonstrated in 2003 at Guantanamo Bay, Cuba (Dankert, 2003), and for wound healing with repeated...Technology on plastics, rubber and plastic tubing, and clothing. Demonstrate ability of CleanseFx to function as skin cleanser in military setting

Bioinspired Organic PV Cells Using Photosynthetic Pigment Complex for Energy Harvesting Materials

DTIC Science & Technology

2010-05-10

ultrafast laser spectroscopy. More recently the structures of the LH2 complexes has revealed the nonameric or octameric arrangement of repeating units...Scheme 1. Compartimentalization of light harvesting and charge separation. The antenna complexes( LH2 ,LH1-RC) efficiently realize various...photosynthetic functions using cofactors (BChl a and carotenoid) assembled into the apoproteins (LH1 and LH2 ). The light-harvesting mechanisms in these

Test Plans and Procedures for the Baseline SAF for BDS-D Sites (ModSAF). Volume 2

DTIC Science & Technology

1993-12-20

operations editor will no longer editor, appear in the EditorI Area. 64 I ADST/WDL/TR-93-W003271 VOLUME 2 of 2; Ver 1.0I 44200 Repeat steps 44120 thru...The unit operations 44200 to task the orange editor will no longer platoon to Move on the appear in the Editor route labeled "ort. Area. The vehicles

Biology and applications of human minisatellite loci.

PubMed

Armour, J A; Jeffreys, A J

1992-12-01

Highly repetitive minisatellites' include the most variable human loci described to date. They have proved invaluable in a wide variety of genetic analyses, and despite some controversies surrounding their practical implementation, have been extensively adopted in civil and forensic casework. Molecular analysis of internal allelic structure has provided detailed insights into the repeat-unit turnover mechanisms operating in germline mutations, which are ultimately responsible for the extreme variability seen at these loci.

Lincoln Laboratory Journal. Volume 22, Number 1, 2016

DTIC Science & Technology

2016-06-09

needs cyber ranges and other infrastructure to conduct scal- able, repeatable, scientific, realistic and inexpensive testing, training, and mission...support this mission, infrastructure is being upgraded to make it more efficient and secure. In “Secur- ing the U.S. Transportation Command,” Jeff...using the Electronic Key Management System (EKMS) or over a digital network by using the Key Manage- ment Infrastructure (KMI). The units must then

Analysis of genetic relationships between potato psyllid (Bactericera cockerelli) populations in the United States, Mexico and Guatemala using ITS2 and inter simple sequence repeat (ISSR) data

USDA-ARS?s Scientific Manuscript database

The potato psyllid, Bactericera cockerelli (Sulc), is an important factor in Zebra Complex (ZC), a disease that causes economic losses on potato crops. Although the exact cause of ZC is not yet known, it may be related to the toxicity of psyllid saliva, pathogens transmitted by this insect, or a com...

Romantic and Sexual Behavior in Young Adolescents: Repeated Surveys in a Population-Based Cohort

ERIC Educational Resources Information Center

Waylen, Andrea E.; Ness, Andrew; McGovern, Phil; Wolke, Dieter; Low, Nicola

2010-01-01

Adverse outcomes of teenage sexual activity are common in the United Kingdom. The authors used a computer-assisted interview to ask young adolescents aged 11 to 12 years (N = 6,856) and 12 to 13 years (N = 6,801) who were part of the Avon Longitudinal Study of Parents and Children about romantic and intimate behaviors. A total of 24% of 11- to…

Purification of preparative quantities of group B Streptococcus type III oligosaccharides.

PubMed

Paoletti, L C; Johnson, K D

1995-06-30

Many bacterial capsular polysaccharides are regularly repeating units of oligosaccharides. Bacterial oligosaccharides have been used in neoglycoconjugate vaccines and as reagents in the study of specific antibody binding. Unfortunately, separation methods have not been adequate for the purification of preparative quantities of bacterial oligosaccharides. Here we describe a size-exclusion procedure that resulted in the resolution of group B Streptococcus type III oligosaccharides composed of 4-25 sugars.

What is the Relationship Between Altitude and Weight in a Model Rocket?

NASA Technical Reports Server (NTRS)

Betz, Jonathan

1993-01-01

This experiment was designed to find a function of payload weight for altitude. The same rocket was launched a repeated number of times with the same engine and varying amounts of weight. After performing experimentation, it was calculated that the altitude in meters could be predicted with the equation A = (2.8(W exp 2)) - (70.6W + 310.3), with weight expressed in the unit ounces.

Workplace social capital and all-cause mortality: a prospective cohort study of 28,043 public-sector employees in Finland.

PubMed

Oksanen, Tuula; Kivimäki, Mika; Kawachi, Ichiro; Subramanian, S V; Takao, Soshi; Suzuki, Etsuji; Kouvonen, Anne; Pentti, Jaana; Salo, Paula; Virtanen, Marianna; Vahtera, Jussi

2011-09-01

We examined the association between workplace social capital and all-cause mortality in a large occupational cohort from Finland. We linked responses of 28 043 participants to surveys in 2000 to 2002 and in 2004 to national mortality registers through 2009. We used repeated measurements of self- and coworker-assessed social capital. We carried out Cox proportional hazard and fixed-effects logistic regressions. During the 5-year follow-up, 196 employees died. A 1-unit increase in the mean of repeat measurements of self-assessed workplace social capital (range 1-5) was associated with a 19% decrease in the risk of all-cause mortality (age- and gender-adjusted hazard ratio [HR] = 0.81; 95% confidence interval [CI] = 0.66, 0.99). The corresponding point estimate for the mean of coworker-assessed social capital was similar, although the association was less precisely estimated (age- and gender-adjusted HR = 0.77; 95% CI = 0.50, 1.20). In fixed-effects analysis, a 1-unit increase in self-assessed social capital across the 2 time points was associated with a lower mortality risk (odds ratio = 0.81; 95% CI = 0.55, 1.19). Workplace social capital appears to be associated with lowered mortality in the working-aged population.

Large-Scale Molecular Simulations on the Mechanical Response and Failure Behavior of a defective Graphene: Cases of 5-8-5 Defects

NASA Astrophysics Data System (ADS)

Wang, Shuaiwei; Yang, Baocheng; Yuan, Jinyun; Si, Yubing; Chen, Houyang

2015-10-01

Understanding the effect of defects on mechanical responses and failure behaviors of a graphene membrane is important for its applications. As examples, in this paper, a family of graphene with various 5-8-5 defects are designed and their mechanical responses are investigated by employing molecular dynamics simulations. The dependence of fracture strength and strain as well as Young’s moduli on the nearest neighbor distance and defect types is examined. By introducing the 5-8-5 defects into graphene, the fracture strength and strain become smaller. However, the Young’s moduli of DL (Linear arrangement of repeat unit 5-8-5 defect along zigzag-direction of graphene), DS (a Slope angle between repeat unit 5-8-5 defect and zigzag direction of graphene) and DZ (Zigzag-like 5-8-5 defects) defects in the zigzag direction become larger than those in the pristine graphene in the same direction. A maximum increase of 11.8% of Young’s modulus is obtained. Furthermore, the brittle cracking mechanism is proposed for the graphene with 5-8-5 defects. The present work may provide insights in controlling the mechanical properties by preparing defects in the graphene, and give a full picture for the applications of graphene with defects in flexible electronics and nanodevices.

Workplace Social Capital and All-Cause Mortality: A Prospective Cohort Study of 28 043 Public-Sector Employees in Finland

PubMed Central

Kivimäki, Mika; Kawachi, Ichiro; Subramanian, S. V.; Takao, Soshi; Suzuki, Etsuji; Kouvonen, Anne; Pentti, Jaana; Salo, Paula; Virtanen, Marianna; Vahtera, Jussi

2011-01-01

Objectives. We examined the association between workplace social capital and all-cause mortality in a large occupational cohort from Finland. Methods. We linked responses of 28 043 participants to surveys in 2000 to 2002 and in 2004 to national mortality registers through 2009. We used repeated measurements of self- and coworker-assessed social capital. We carried out Cox proportional hazard and fixed-effects logistic regressions. Results. During the 5-year follow-up, 196 employees died. A 1-unit increase in the mean of repeat measurements of self-assessed workplace social capital (range 1–5) was associated with a 19% decrease in the risk of all-cause mortality (age- and gender-adjusted hazard ratio [HR] = 0.81; 95% confidence interval [CI] = 0.66, 0.99). The corresponding point estimate for the mean of coworker-assessed social capital was similar, although the association was less precisely estimated (age- and gender-adjusted HR = 0.77; 95% CI = 0.50, 1.20). In fixed-effects analysis, a 1-unit increase in self-assessed social capital across the 2 time points was associated with a lower mortality risk (odds ratio = 0.81; 95% CI = 0.55, 1.19). Conclusions. Workplace social capital appears to be associated with lowered mortality in the working-aged population. PMID:21778502

Electronic Band Structure of Helical Polyisocyanides.

PubMed

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.

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

PubMed Central

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