A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).

PubMed

Churakov, Gennady; Smit, Arian F A; Brosius, Jürgen; Schmitz, Jürgen

2005-04-01

About half of the mammalian genome is composed of retroposons. Long interspersed elements (LINEs) and short interspersed elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages, except for the South American order Xenarthra, also termed Edentata (armadillos, anteaters, and sloths). Investigating this order, we discovered a novel high-copy-number family of tRNA derived SINEs in the nine-banded armadillo Dasypus novemcinctus, a species that successfully crossed the Central American land bridge to North America in the Pliocene. A specific computer algorithm was developed, and we detected and extracted 687 specific SINEs from databases. Termed DAS-SINEs, we further divided them into six distinct subfamilies. We extracted tRNA(Ala)-derived monomers, two types of dimers, and three subfamilies of chimeric fusion products of a tRNA(Ala) domain and an approximately 180-nt sequence of thus far unidentified origin. Comparisons of secondary structures of the DAS-SINEs' tRNA domains suggest selective pressure to maintain a tRNA-like D-arm structure in the respective founder RNAs, as shown by compensatory mutations. By analysis of subfamily-specific genetic variability, comparison of the proportion of direct repeats, and analysis of self-integrations as well as key events of dimerization and deletions or insertions, we were able to delineate the evolutionary history of the DAS-SINE subfamilies.

Differential growth of Mycobacterium leprae strains (SNP genotypes) in armadillos.

PubMed

Sharma, Rahul; Singh, Pushpendra; Pena, Maria; Subramanian, Ramesh; Chouljenko, Vladmir; Kim, Joohyun; Kim, Nayong; Caskey, John; Baudena, Marie A; Adams, Linda B; Truman, Richard W

2018-04-14

Leprosy (Hansen's Disease) has occurred throughout human history, and persists today at a low prevalence in most populations. Caused by Mycobacterium leprae, the infection primarily involves the skin, mucosa and peripheral nerves. The susceptible host range for Mycobacterium leprae is quite narrow. Besides humans, nine banded armadillos (Dasypus novemcinctus) and red squirrels (Sciurus vulgaris) are the only other natural hosts for M. leprae, but only armadillos recapitulate the disease as seen in humans. Armadillos across the Southern United States harbor a single predominant genotypic strain (SNP Type-3I) of M. leprae, which is also implicated in the zoonotic transmission of leprosy. We investigated, whether the zoonotic strain (3I) has any notable growth advantages in armadillos over another genetically distant strain-type (SNP Type-4P) of M. leprae, and if M. leprae strains manifest any notably different pathology among armadillos. We co-infected armadillos (n = 6) with 2 × 10 9 highly viable M. leprae of both strains and assessed the relative growth and dissemination of each strain in the animals. We also analyzed 12 additional armadillos, 6 each individually infected with the same quantity of either strain. The infections were allowed to fulminate and the clinical manifestations of the disease were noted. Animals were humanely sacrificed at the terminal stage of infection and the number of bacilli per gram of liver, spleen and lymph node tissue were enumerated by Q-PCR assay. The growth of M. leprae strain 4P was significantly higher (P < 0.05) than 3I when each strain was propagated individually in armadillos. Significantly (P < 0.0001) higher growth of the 4P strain also was confirmed among animals co-infected with both 3I and 4P strain types using whole genome sequencing. Interestingly, the zoonotic strain does not exhibit any growth advantage in these non-human hosts, but the varied proliferation of the two M. leprae strains within armadillos suggest there are notable pathological variations between M. leprae strain-types. Copyright © 2018. Published by Elsevier B.V.

Learning with "Armadillo Ray"

ERIC Educational Resources Information Center

Hubbard, Kathy; Terrell, Chelsea

2009-01-01

"Armadillo Ray," by John Beifuss, is the tale of a young, curious armadillo who wants to know what the moon is. He is joined in his quest by snakes, prairie dogs, sage grouse, and owls. The beauty of the book is its simplicity, illustrations and landscapes, and its potential links to reading, geography, science, and mathematics. In this…

Specific Armadillo Repeat Sequences Facilitate β-Catenin Nuclear Transport in Live Cells via Direct Binding to Nucleoporins Nup62, Nup153, and RanBP2/Nup358*

PubMed Central

Sharma, Manisha; Jamieson, Cara; Johnson, Michael; Molloy, Mark P.; Henderson, Beric R.

2012-01-01

β-Catenin transduces the Wnt signal from the membrane to nucleus, and certain gene mutations trigger its nuclear accumulation leading to cell transformation and cancer. β-Catenin shuttles between the nucleus and cytoplasm independent of classical Ran/transport receptor pathways, and this movement was previously hypothesized to involve the central Armadillo (Arm) domain. Fluorescence recovery after photobleaching (FRAP) assays were used to delineate functional transport regions of the Arm domain in living cells. The strongest nuclear import/export activity was mapped to Arm repeats R10–12 using both in vivo FRAP and in vitro export assays. By comparison, Arm repeats R3–8 of β-catenin were highly active for nuclear import but displayed a comparatively weak export activity. We show for the first time using purified components that specific Arm sequences of β-catenin interact directly in vitro with the FG repeats of the nuclear pore complex (NPC) components Nup62, Nup98, and Nup153, indicating an independent ability of β-catenin to traverse the NPC. Moreover, a proteomics screen identified RanBP2/Nup358 as a binding partner of Arm R10–12, and β-catenin was confirmed to interact with endogenous and ectopic forms of Nup358. We further demonstrate that knock-down of endogenous Nup358 and Nup62 impeded the rate of nuclear import/export of β-catenin to a greater extent than that of importin-β. The Arm R10–12 sequence facilitated transport even when β-catenin was bound to the Arm-binding partner LEF-1, and its activity was stimulated by phosphorylation at Tyr-654. These findings provide functional evidence that the Arm domain contributes to regulated β-catenin transport through direct interaction with the NPC. PMID:22110128

The zoogeomorphic characteristics of burrows and burrowing by nine-banded armadillos (Dasypus novemcinctus)

NASA Astrophysics Data System (ADS)

Sawyer, Carol F.; Brinkman, Donald C.; Walker, Vincent D.; Covington, Tyler D.; Stienstraw, Elizabeth A.

2012-07-01

Burrowing animals act like a geomorphic disturbance, changing the environment through soil excavation, landform creation and bioturbation. The potential zoogeomorphic effects of these actions include modification of surficial features, increased soil erosion, changes in the growth and distribution of vegetation, and modifications to soil fertility. The burrowing ninebanded armadillo (Dasypus novemcinctus) migrated to North America prior to the 1850s and has since continued to expand its habitat to the American Southeast and parts of the Midwest. Little data are available on the zoogeomorphic impact of the burrowing nature of this species, making it difficult to predict future implications of this animal as it continues to migrate into new regions. On the University of South Alabama campus, in Mobile, Alabama, armadillos are present on a 35-hectare unprotected forested preserve used by the university community for outdoor activities and research. To understand the potential zoogeomorphic impact of armadillo burrows on the local environment, morphometric measurements were recorded on 187 burrows located in the study area. Using dimensions of burrow entrances and minimum lengths of tunnels in calculations, armadillos excavated approximately 0.029 m3 to 0.04 m3 of soil from each burrow. The entrances to burrows averaged 33.5° in slope and tended to be located in a microhabitat of a fallen tree, exposed tree roots, or a sideslope. Persistent fall of forest litter and anthropogenic modifications makes positive identification of spoil mounds possible in approximately half of the burrow sites. Surface modification by armadillos is ongoing in the study area with over half of the burrows classified as active during the four-month project. We concluded that, for southern Alabama, armadillos prefer to excavate burrows into sideslopes, and that given the lack of ground cover, sandy soil, and humid climate, armadillos are an important zoogeomorphic agent in the region.

Patients affected by endemic pemphigus foliaceus in Colombia, South America exhibit autoantibodies to optic nerve sheath envelope cell junctions.

PubMed

Abreu-Velez, Ana Maria; Gao, Wendy; Howard, Michael S

2018-01-01

The majority of the patients affected by a new variant of endemic pemphigus foliaceus in El Bagre, Colombia (El Bagre EPF or pemphigus Abreu-Manu), have experienced vision problems; we have previously reported several ocular abnormalities. Here, we aimed to investigate reactivity to optic nerves in these patients. We utilized bovine, rat and mouse optic nerves, and performed immunofluorescence and confocal microscopy to test for optical nerve autoreactivity. We tested 45 patients affected by this disease and 45 controls from the endemic area matched by age, sex and work activity. Overall, 37 of the 45 patient sera reacted to the optic nerve envelope that is composed of leptomeninges; the reactivity was polyclonal and present mostly at the cell junctions (P < 0.001). The immune response was directed against optic nerve sheath cell junctions and the vessels inside it, as well as other molecules inside the nerve. No control cases were positive. Of interest, all the patient autoantibodies co-localized with commercial antibodies to desmoplakins I-II, myocardium-enriched zonula occludens-1- associated protein (MYZAP), armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF), and plakophilin-4 (p0071) from Progen Biotechnik (P < 0.001). We conclude that the majority of the patients affected by pemphigus Abreu-Manu have autoantibodies to optic nerve sheath envelope cell junctions. These antibodies also co-localize with armadillo repeat gene deleted in velo-cardio-facial syndrome, p0071 and desmoplakins I-II. The clinical significance of our findings remains unknown.

Ultrastructural characterisation of the olfactory mucosa of the armadillo Dasypus hybridus (Dasypodidae, Xenarthra)

PubMed Central

FERRARI, C. C.; CARMANCHAHI, P. D.; ALDANA MARCOS, H. J.; AFFANNI, J. M.

2000-01-01

The ultrastructure of the olfactory mucosa of the armadillo Dasypus hybridus was studied. A comparison with the olfactory mucosa of another armadillo (Chaetophractus villosus) was made. The olfactory mucosa of D. hybridus shows many features which are similar to those of other mammals. Interestingly, it differs from the olfactory mucosa of the armadillo C. villosus. A suggestion is made that these differences may be due to differences in the digging habits of these species. In Dasypus, the supporting cells (SCs) showed dense vacuoles, multivesicular bodies and lysosome-like bodies probably related with the endocytotic system. The SCs show a dense network of SER presumably associated with xenobiotic mechanisms. The olfactory receptor neurons exhibit lysosome-like bodies and multivesicular bodies in their perikarya. These organelles suggest the presence of an endocytotic system. Duct cells of Bowman's glands exhibit secretory activities. Bowman's glands are compound-branched tubulo-acinar mixed glands with merocrine secretory mechanisms. PMID:10739023

Behavioral responses of three armadillo species (Mammalia: Xenarthra) to an environmental enrichment program in Villavicencio, Colombia.

PubMed

Cortés Duarte, Alexandra; Trujillo, Fernando; Superina, Mariella

2016-07-01

Enrichment is a powerful tool to improve the welfare of animals under human care. Stress-related health and behavioral problems, as well as reproductive failure, are frequent in armadillos (Xenarthra, Cingulata, Dasypodidae) under human care, which hinders the development of successful ex situ conservation programs. Nevertheless, scientific studies on the effect of enrichment programs on armadillos are virtually non-existent. The objective of this study was to assess the impact of an enrichment program on the behavior of armadillos under human care. The behavior of 12 individuals of three species (Dasypus novemcinctus, D. sabanicola, and Cabassous unicinctus) maintained at Finca El Turpial, Villavicencio, Colombia, was recorded using scan sampling during three daily time blocks of 2 hr each before (4 weeks) and after (4 weeks) implementing an enrichment program. Enrichment did not stimulate the armadillos to change or extend their activity period. In general, activity levels were low during the entire study, and virtually no activity was recorded in the morning in any species, neither without nor with enrichment. The latter did, however, improve welfare by reducing abnormal and increasing natural foraging behaviors. All species were attracted by artificial termite mounds. Dasypus spp. showed special interest in cardboard boxes with food, while Cabassous was mainly attracted to hollow plastic balls filled with food. Our results suggest that separate enrichment programs need to be developed for different armadillo species, and that they should be applied during the time of day at which they are most active. Zoo Biol. 35:304-312, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Structural and biophysical properties of h-FANCI ARM repeat protein.

PubMed

Siddiqui, Mohd Quadir; Choudhary, Rajan Kumar; Thapa, Pankaj; Kulkarni, Neha; Rajpurohit, Yogendra S; Misra, Hari S; Gadewal, Nikhil; Kumar, Satish; Hasan, Syed K; Varma, Ashok K

2017-11-01

Fanconi anemia complementation groups - I (FANCI) protein facilitates DNA ICL (Inter-Cross-link) repair and plays a crucial role in genomic integrity. FANCI is a 1328 amino acids protein which contains armadillo (ARM) repeats and EDGE motif at the C-terminus. ARM repeats are functionally diverse and evolutionarily conserved domain that plays a pivotal role in protein-protein and protein-DNA interactions. Considering the importance of ARM repeats, we have explored comprehensive in silico and in vitro approach to examine folding pattern. Size exclusion chromatography, dynamic light scattering (DLS) and glutaraldehyde crosslinking studies suggest that FANCI ARM repeat exist as monomer as well as in oligomeric forms. Circular dichroism (CD) and fluorescence spectroscopy results demonstrate that protein has predominantly α- helices and well-folded tertiary structure. DNA binding was analysed using electrophoretic mobility shift assay by autoradiography. Temperature-dependent CD, Fluorescence spectroscopy and DLS studies concluded that protein unfolds and start forming oligomer from 30°C. The existence of stable portion within FANCI ARM repeat was examined using limited proteolysis and mass spectrometry. The normal mode analysis, molecular dynamics and principal component analysis demonstrated that helix-turn-helix (HTH) motif present in ARM repeat is highly dynamic and has anti-correlated motion. Furthermore, FANCI ARM repeat has HTH structural motif which binds to double-stranded DNA.

Taxonomic revision of the long-nosed armadillos, Genus Dasypus Linnaeus, 1758 (Mammalia, Cingulata)

PubMed Central

Patterson, Bruce D.; Cordeiro-Estrela, Pedro

2018-01-01

Dasypus is the most speciose genus of the order Cingulata, including approximately 40% of known living armadillos. Nine species are currently recognized, although comprehensive analyses of the entire genus have never been done. Our aim is to revise the taxonomy of the long-nosed armadillos and properly define the taxa. We examined 2126 specimens of Dasypus preserved in 39 different museum collections, including 17 type specimens. Three complementary methods were applied to explore morphological datasets both qualitatively and quantitatively. Qualitative morphological variation in discrete characters was assessed by direct observations of specimens. Linear morphometric variation was based on external data and cranial measurements of 887 adult skulls. The shape and size of the skull was abstracted through two-dimensional geometric morphometric analyses of dorsal, lateral and ventral views of respectively 421, 211, and 220 adult specimens. Our results converge on the recognition of eight living species (D. beniensis, D. kappleri, D. mazzai, D. novemcinctus, D. pastasae, D. pilosus, D. sabanicola, and D. septemcinctus), and three subspecies of D. septemcinctus (D. s. septemcinctus, D. s. hybridus, and a new subspecies from Cordoba described here). Information on type material, diagnosis, distribution, and taxonomic comments for each taxon are provided. We designate a lectotype for D. novemcinctus; and a neotype for Loricatus hybridus (= D. septemcinctus hybridus). PMID:29624590

Genomic evidence for rod monochromacy in sloths and armadillos suggests early subterranean history for Xenarthra

PubMed Central

Emerling, Christopher A.; Springer, Mark S.

2015-01-01

Rod monochromacy is a rare condition in vertebrates characterized by the absence of cone photoreceptor cells. The resulting phenotype is colourblindness and low acuity vision in dim-light and blindness in bright-light conditions. Early reports of xenarthrans (armadillos, sloths and anteaters) suggest that they are rod monochromats, but this has not been tested with genomic data. We searched the genomes of Dasypus novemcinctus (nine-banded armadillo), Choloepus hoffmanni (Hoffmann's two-toed sloth) and Mylodon darwinii (extinct ground sloth) for retinal photoreceptor genes and examined them for inactivating mutations. We performed PCR and Sanger sequencing on cone phototransduction genes of 10 additional xenarthrans to test for shared inactivating mutations and estimated the timing of inactivation for photoreceptor pseudogenes. We concluded that a stem xenarthran became an long-wavelength sensitive-cone monochromat following a missense mutation at a critical residue in SWS1, and a stem cingulate (armadillos, glyptodonts and pampatheres) and stem pilosan (sloths and anteaters) independently acquired rod monochromacy early in their evolutionary history following the inactivation of LWS and PDE6C, respectively. We hypothesize that rod monochromacy in armadillos and pilosans evolved as an adaptation to a subterranean habitat in the early history of Xenarthra. The presence of rod monochromacy has major implications for understanding xenarthran behavioural ecology and evolution. PMID:25540280

Cell junction protein armadillo repeat gene deleted in velo-cardio-facial syndrome is expressed in the skin and colocalizes with autoantibodies of patients affected by a new variant of endemic pemphigus foliaceus in Colombia.

PubMed

Abreu-Velez, Ana Maria; Yi, Hong; Howard, Michael S

2017-10-01

We previously described a new variant of endemic pemphigus foliaceus in El Bagre, Colombia, South America (El Bagre-EPF, or pemphigus Abreu-Manu). El Bagre-EPF differs from other types of EPF clinically, epidemiologically, immunologically and in its target antigens. We reported the presence of patient autoantibodies colocalizing with armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF), a catenin cell junction protein colocalizing with El Bagre-EPF autoantibodies in the heart and within pilosebaceous units along their neurovascular supply routes. Here we investigate the presence of ARVCF in skin and its possibility as a cutaneous El Bagre-EPF antigen. We used a case-control study, testing sera of 45 patients and 45 controls via direct and indirect immunofluorescence (DIF/IIF), confocal microscopy, immunoelectron microscopy and immunoblotting for the presence of ARVCF and its relationship with El Bagre-EPF autoantibodies in the skin. We also immunoadsorbed samples with desmoglein 1 (Dsg1) ectodomain (El Bagre-EPF antigen) by incubating with the positive ARVCF samples from DIF and IIF. ARVCF was expressed in all the samples from the cases and controls. Immunoadsorption with Dsg1 on positive ARVCF immunofluorescence DIF/IIF cases showed that the immune response was present against non-desmoglein 1 antigen(s). Overall, 40/45 patients showed colocalization of their autoantibodies with ARVCF in the epidermis; no controls from the endemic area displayed colocalization. We demonstrate that ARVCF is expressed in many areas of human skin, and colocalizes with the majority of El Bagre-EPF autoantibodies as a putative antigen.

Cell junction protein armadillo repeat gene deleted in velo-cardio-facial syndrome is expressed in the skin and colocalizes with autoantibodies of patients affected by a new variant of endemic pemphigus foliaceus in Colombia

PubMed Central

Abreu-Velez, Ana Maria; Yi, Hong; Howard, Michael S.

2017-01-01

Background We previously described a new variant of endemic pemphigus foliaceus in El Bagre, Colombia, South America (El Bagre-EPF, or pemphigus Abreu-Manu). El Bagre-EPF differs from other types of EPF clinically, epidemiologically, immunologically and in its target antigens. We reported the presence of patient autoantibodies colocalizing with armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF), a catenin cell junction protein colocalizing with El Bagre-EPF autoantibodies in the heart and within pilosebaceous units along their neurovascular supply routes. Here we investigate the presence of ARVCF in skin and its possibility as a cutaneous El Bagre-EPF antigen. Methods We used a case-control study, testing sera of 45 patients and 45 controls via direct and indirect immunofluorescence (DIF/IIF), confocal microscopy, immunoelectron microscopy and immunoblotting for the presence of ARVCF and its relationship with El Bagre-EPF autoantibodies in the skin. We also immunoadsorbed samples with desmoglein 1 (Dsg1) ectodomain (El Bagre-EPF antigen) by incubating with the positive ARVCF samples from DIF and IIF. Results ARVCF was expressed in all the samples from the cases and controls. Immunoadsorption with Dsg1 on positive ARVCF immunofluorescence DIF/IIF cases showed that the immune response was present against non-desmoglein 1 antigen(s). Overall, 40/45 patients showed colocalization of their autoantibodies with ARVCF in the epidermis; no controls from the endemic area displayed colocalization. Conclusions We demonstrate that ARVCF is expressed in many areas of human skin, and colocalizes with the majority of El Bagre-EPF autoantibodies as a putative antigen. PMID:29214101

PATTERNS OF MYCOBACTERIUM LEPRAE INFECTION IN WILD NINE-BANDED ARMADILLOS (DASYPUS NOVEMCINCTUS) IN MISSISSIPPI, USA.

PubMed

Perez-Heydrich, Carolina; Loughry, W J; Anderson, Corey Devin; Oli, Madan K

2016-07-01

The nine-banded armadillo ( Dasypus novemcinctus ) is the only known nonhuman reservoir of Mycobacterium leprae , the causative agent of Hansen's disease or leprosy. We conducted a 6-yr study on a wild population of armadillos in western Mississippi that was exposed to M. leprae to evaluate the importance of demographic and spatial risk factors on individual antibody status. We found that spatially derived covariates were not predictive of antibody status. Furthermore, analyses revealed no evidence of clustering by antibody-positive individuals. Lactating females and adult males had higher odds of being antibody positive than did nonlactating females. No juveniles or yearlings were antibody positive. Results of these analyses support the hypothesis that M. leprae infection patterns are spatially homogeneous within this armadillo population. Further research related to movement patterns, contact among individuals, antibody status, and environmental factors could help address hypotheses related to the role of environmental transmission on M. leprae infection and the mechanisms underlying the differential infection patterns among demographic groups.

A Large Complement of the Predicted Arabidopsis ARM Repeat Proteins Are Members of the U-Box E3 Ubiquitin Ligase Family1[w

PubMed Central

Mudgil, Yashwanti; Shiu, Shin-Han; Stone, Sophia L.; Salt, Jennifer N.; Goring, Daphne R.

2004-01-01

The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins. Using domain database predictions and models generated in this study, 108 Arabidopsis proteins were identified that contained a minimum of two ARM repeats with the majority of proteins containing four to eight ARM repeats. Clustering analysis showed that the 108 predicted Arabidopsis ARM repeat proteins could be divided into multiple groups with wide differences in their domain compositions and organizations. Interestingly, 41 of the 108 Arabidopsis ARM repeat proteins contained a U-box, a motif present in a family of E3 ligases, and these proteins represented the largest class of Arabidopsis ARM repeat proteins. In 14 of these U-box/ARM repeat proteins, there was also a novel conserved domain identified in the N-terminal region. Based on the phylogenetic tree, representative U-box/ARM repeat proteins were selected for further study. RNA-blot analyses revealed that these U-box/ARM proteins are expressed in a variety of tissues in Arabidopsis. In addition, the selected U-box/ARM proteins were found to be functional E3 ubiquitin ligases. Thus, these U-box/ARM proteins represent a new family of E3 ligases in Arabidopsis. PMID:14657406

A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family.

PubMed

Mudgil, Yashwanti; Shiu, Shin-Han; Stone, Sophia L; Salt, Jennifer N; Goring, Daphne R

2004-01-01

The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins. Using domain database predictions and models generated in this study, 108 Arabidopsis proteins were identified that contained a minimum of two ARM repeats with the majority of proteins containing four to eight ARM repeats. Clustering analysis showed that the 108 predicted Arabidopsis ARM repeat proteins could be divided into multiple groups with wide differences in their domain compositions and organizations. Interestingly, 41 of the 108 Arabidopsis ARM repeat proteins contained a U-box, a motif present in a family of E3 ligases, and these proteins represented the largest class of Arabidopsis ARM repeat proteins. In 14 of these U-box/ARM repeat proteins, there was also a novel conserved domain identified in the N-terminal region. Based on the phylogenetic tree, representative U-box/ARM repeat proteins were selected for further study. RNA-blot analyses revealed that these U-box/ARM proteins are expressed in a variety of tissues in Arabidopsis. In addition, the selected U-box/ARM proteins were found to be functional E3 ubiquitin ligases. Thus, these U-box/ARM proteins represent a new family of E3 ligases in Arabidopsis.

Apo and InsP[subscript 3]-bound crystal structures of the ligand-binding domain of an InsP[subscript 3] receptor

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

Lin, Chun-Chi; Baek, Kyuwon; Lu, Zhe

2012-05-08

We report the crystal structures of the ligand-binding domain (LBD) of a rat inositol 1,4,5-trisphosphate receptor (InsP{sub 3}R) in its apo and InsP{sub 3}-bound conformations. Comparison of these two conformations reveals that LBD's first {beta}-trefoil fold ({beta}-TF1) and armadillo repeat fold (ARF) move together as a unit relative to its second {beta}-trefoil fold ({beta}-TF2). Whereas apo LBD may spontaneously transition between gating conformations, InsP{sub 3} binding shifts this equilibrium toward the active state.

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.

Trypanosoma cruzi III from armadillos (Dasypus novemcinctus novemcinctus) from Northeastern Venezuela and its biological behavior in murine model. Risk of emergency of Chagas' disease.

PubMed

Morocoima, Antonio; Carrasco, Hernán J; Boadas, Johanna; Chique, José David; Herrera, Leidi; Urdaneta-Morales, Servio

2012-11-01

Trypanosoma cruzi, etiological agent of Chagas' disease, was isolated from armadillos (Dasypus novemcinctus novemcinctus) captured in rural communities Northeastern Venezuela from Nueva Esparta State (no endemic for Chagas' disease), Monagas and Anzoátegui States (endemics). The isolates, genetically typed by PCR-RFLP as belonging to the TcIII DTU, have demonstrated in murine model heterogenic parasitemia, mortality and histotropism with marked parasitism in cardiac, skeletal, and smooth myocytes that showed correlation with lymphobasophilic inflammatory infiltrates. Our finding of T. cruzi infected armadillos in Isla Margarita (Nueva Esparta State), together with reports of triatomine vectors in this region, the accentuated synanthropy of armadillos, intense economic activity, migration due to tourism and the lack of environmental education programs all of them represent risks that could cause the emergence of Chagas' disease in this area. This is the first report of the TcIII DTU in Northeastern Venezuela, thus widening the geographic distribution of this DTU. Copyright © 2012 Elsevier Inc. All rights reserved.

Anatomy of Shoulder Girdle Muscle Modifications and Walking Adaptation in the Scaly Chinese Pangolin (Manis Pentadactyla Pentadactyla: Pholidota) Compared with the Partially Osteoderm-Clad Armadillos (Dasypodidae).

PubMed

Kawashima, Tomokazu; Thorington, Richard W; Bohaska, Paula W; Chen, Yen-Jean; Sato, Fumi

2015-07-01

Because pangolins are unique mammals with a body and limbs almost entirely sheathed in hard keratinous overlapping scales and with digging and climbing abilities, the shoulder girdle muscles may differ significantly from those of other mammals including the partially osteoderm-clad armadillos. Therefore, we conducted a functional anatomical study of the shoulder girdle muscles in Chinese pangolins (Manis pentadactyla pentadactyla, Pholidota) and some armadillo species (Dasypodidae). Our CT scans revealed that the pangolin's overlapping scales are hard structures completely encasing the limbs. The armadillo's limbs, however, are covered with small relatively soft non-overlapping scales embedded in the skin, and articulate completely free of the hard osteodermal carapace. The attachments of some shoulder girdle muscles in the pangolin have moved from the surrounding edges of the scapula to the spine, and they, therefore, fully cover the scapula. In addition, some pangolin shoulder girdle muscles cross the shoulder joint to insert on the distal humerus, but this does not occur in armadillos. We cannot rule out the possibility that these muscle modifications represent adaptations for digging and/or climbing in pangolins. Our results and previous literature do not establish specific links between them and locomotive modes. However, we propose that the Chinese pangolin may use its derived muscular features when walking to move its armor-restricted forelimbs more effectively by swinging its head from side to side. © 2015 Wiley Periodicals, Inc.

Orientation selectivity in the visual cortex of the nine-banded armadillo

PubMed Central

Scholl, Benjamin; Rylee, Johnathan; Luci, Jeffrey J.; Priebe, Nicholas J.

2017-01-01

Orientation selectivity in primary visual cortex (V1) has been proposed to reflect a canonical computation performed by the neocortical circuitry. Although orientation selectivity has been reported in all mammals examined to date, the degree of selectivity and the functional organization of selectivity vary across mammalian clades. The differences in degree of orientation selectivity are large, from reports in marsupials that only a small subset of neurons are selective to studies in carnivores, in which it is rare to find a neuron lacking selectivity. Furthermore, the functional organization in cortex varies in that the primate and carnivore V1 is characterized by an organization in which nearby neurons share orientation preference while other mammals such as rodents and lagomorphs either lack or have only extremely weak clustering. To gain insight into the evolutionary emergence of orientation selectivity, we examined the nine-banded armadillo, a species within the early placental clade Xenarthra. Here we use a combination of neuroimaging, histological, and electrophysiological methods to identify the retinofugal pathways, locate V1, and for the first time examine the functional properties of V1 neurons in the armadillo (Dasypus novemcinctus) V1. Individual neurons were strongly sensitive to the orientation and often the direction of drifting gratings. We uncovered a wide range of orientation preferences but found a bias for horizontal gratings. The presence of strong orientation selectivity in armadillos suggests that the circuitry responsible for this computation is common to all placental mammals. NEW & NOTEWORTHY The current study shows that armadillo primary visual cortex (V1) neurons share the signature properties of V1 neurons of primates, carnivorans, and rodents. Furthermore, these neurons exhibit a degree of selectivity for stimulus orientation and motion direction similar to that found in primate V1. Our findings in armadillo visual cortex suggest that the functional properties of V1 neurons emerged early in the mammalian lineage, near the time of the divergence of marsupials. PMID:28053246

Commensal foraging by a fan-tailed warbler (Euthlypis lachrymosa) with a nine-banded armadillo (Dasypus nocemcinctus) in southwestern Mexico

Treesearch

Richard R. Schaefer; Jesse F. Fagan

2006-01-01

Many interspecific commensal foraging interactions involving birds have been documented. We describe an observation of commensal foraging by a fan-tailed warbler (Euthlypis lachrymosa) with a nine-banded armadillo (Dasypus novemcinctus) in Guerrero, southwestern Mexico. Our obsenation is similar to those reported from El Salvador...

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

Assessment of sperm survival and functional membrane integrity of the six-banded armadillo (Euphractus sexcinctus).

PubMed

Santos, E A A; Sousa, P C; Dias, C E V; Castelo, T S; Peixoto, G C X; Lima, G L; Ricarte, A R F; Simão, B R; Freitas, C I A; Silva, A R

2011-09-01

The objective was to evaluate sperm survival in the six-banded armadillo, using a thermoresistance test, and to compare sugar solutions with varying osmolarities to analyze the integrity of the functional sperm plasma membrane in this species. Twelve ejaculates were obtained from four mature males by electroejaculation and evaluated for sperm motility, vigor, live sperm, and morphology. Sperm survival was evaluated during a thermoresistance test at 34 °C (the body temperature of this species). The functional integrity of the plasma membrane was evaluated by means of the hypo-osmotic swelling test (HOST), using solutions of varying osmolarities (0, 50, 100, and 150 mOsm/L). During the thermoresistance test, at each evaluation, there was a reduction (P < 0.05) in mean values for sperm motility, sperm vigor, and percentage of live sperm (no movement was observed at 360 min). Sperm survival varied among individual armadillos (P < 0.05). In two individuals, sperm vigor was significantly enhanced when semen was diluted in Tris extender. The response of armadillo sperm to the HOST varied among individuals (P < 0.05). On average, maximal values (P < 0.05) of reactive sperm (59%) were detected with 50 mOsm/L solution; furthermore, this concentration had the largest significant positive correlation (r = 0.84) to live sperm percentage. In conclusion, six-banded armadillos had significant individual variation with regard to sperm survival in a thermoresistance test at 34 °C; in some individuals, sperm survived until 360 min. The use of a 50 mOsm/L fructose solution was recommended for conducting a HOST in this species. Copyright © 2011 Elsevier Inc. All rights reserved.

The sylvatic transmission cycle of Trypanosoma cruzi in a rural area in the humid Chaco of Argentina.

PubMed

Alvarado-Otegui, J A; Ceballos, L A; Orozco, M M; Enriquez, G F; Cardinal, M V; Cura, C; Schijman, A G; Kitron, U; Gürtler, R E

2012-10-01

Little is known about the sylvatic transmission cycle of Trypanosoma cruzi in the Gran Chaco ecoregion. We conducted surveys to identify the main sylvatic hosts of T. cruzi, parasite discrete typing units and vector species involved in Pampa del Indio, a rural area in the humid Argentinean Chaco. A total of 44 mammals from 14 species were captured and examined for infection by xenodiagnosis and polymerase chain reaction amplification of the hyper-variable region of kinetoplast DNA minicircles of T. cruzi (kDNA-PCR). Ten (22.7%) mammals were positive by xenodiagnosis or kDNA-PCR. Four of 11 (36%) Didelphis albiventris (white-eared opossums) and six of nine (67%) Dasypus novemcinctus (nine-banded armadillos) were positive by xenodiagnosis and or kDNA-PCR. Rodents, other armadillo species, felids, crab-eating raccoons, hares and rabbits were not infected. Positive animals were highly infectious to the bugs that fed upon them as determined by xenodiagnosis. All positive opossums were infected with T. cruzi I and all positive nine-banded armadillos with T. cruzi III. Extensive searches in sylvatic habitats using 718 Noireau trap-nights only yielded Triatoma sordida whereas no bug was collected in 26 light-trap nights. Four armadillos or opossums fitted with a spool-and-line device were successfully tracked to their refuges; only one Panstrongylus geniculatus was found in an armadillo burrow. No sylvatic triatomine was infected with T. cruzi by microscopical examination or kDNA-PCR. Our results indicate that two independent sylvatic transmission cycles of T. cruzi occur in the humid Chaco. The putative vectors of both cycles need to be identified conclusively. Copyright © 2012 Elsevier B.V. All rights reserved.

The sylvatic transmission cycle of Trypanosoma cruzi in a rural area in the humid Chaco of Argentina

PubMed Central

Alvarado-Otegui, J.A.; Ceballos, L.A.; Orozco, M.M.; Enriquez, G.F.; Cardinal, M.V.; Cura, C.; Schijman, A.G.; Kitron, U.; Gürtler, R.E.

2012-01-01

Little is known about the sylvatic transmission cycle of Trypanosoma cruzi in the Gran Chaco ecoregion. We conducted surveys to identify the main sylvatic hosts of T. cruzi, parasite discrete typing units and vector species involved in Pampa del Indio, a rural area in the humid Argentinean Chaco. A total of 44 mammals from 14 species was captured and examined for infection by xenodiagnosis and polymerase chain reaction amplification of the hyper-variable region of kinetoplast DNA minicircles of T. cruzi (kDNA-PCR). Ten (22.7%) mammals were positive by xenodiagnosis or kDNA-PCR. Four of 11 (36%) Didelphis albiventris (white-eared opossums) and six of nine (67%) Dasypus novemcinctus (nine-banded armadillos) were positive by xenodiagnosis and or kDNA-PCR. Rodents, other armadillo species, felids, crab-eating raccoons, hares and rabbits were not infected. Positive animals were highly infectious to the bugs that fed upon them as determined by xenodiagnosis. All positive opossums were infected with T. cruzi I and all positive nine-banded armadillos with T. cruzi III. Extensive searches in sylvatic habitats using 718 Noireau trap-nights only yielded Triatoma sordida whereas no bug was collected in 26 light-trap nights. Four armadillos or opossums fitted with a spool-and-line device were successfully tracked to their refuges; only one Panstrongylus geniculatus was found in an armadillo burrow. No sylvatic triatomine was infected with T. cruzi by microscopical examination or kDNA-PCR. Our results indicate that two independent sylvatic transmission cycles of T. cruzi occur in the humid Chaco. The putative vectors of both cycles need to be identified conclusively. PMID:22771688

LepVax, a defined subunit vaccine that provides effective pre-exposure and post-exposure prophylaxis of M. leprae infection.

PubMed

Duthie, Malcolm S; Pena, Maria T; Ebenezer, Gigi J; Gillis, Thomas P; Sharma, Rahul; Cunningham, Kelly; Polydefkis, Michael; Maeda, Yumi; Makino, Masahiko; Truman, Richard W; Reed, Steven G

2018-01-01

Sustained elimination of leprosy as a global health concern likely requires a vaccine. The current standard, BCG, confers only partial protection and precipitates paucibacillary (PB) disease in some instances. When injected into mice with the T helper 1 (Th1)-biasing adjuvant formulation Glucopyranosyl Lipid Adjuvant in stable emulsion (GLA-SE), a cocktail of three prioritized antigens (ML2055, ML2380 and ML2028) reduced M. leprae infection levels. Recognition and protective efficacy of a single chimeric fusion protein incorporating these antigens, LEP-F1, was confirmed in similar experiments. The impact of post-exposure immunization was then assessed in nine-banded armadillos that demonstrate a functional recapitulation of leprosy. Armadillos were infected with M. leprae 1 month before the initiation of post-exposure prophylaxis. While BCG precipitated motor nerve conduction abnormalities more rapidly and severely than observed for control infected armadillos, motor nerve injury in armadillos treated three times, at monthly intervals with LepVax was appreciably delayed. Biopsy of cutaneous nerves indicated that epidermal nerve fiber density was not significantly altered in M. leprae -infected animals although Remak Schwann cells of the cutaneous nerves in the distal leg were denser in the infected armadillos. Importantly, LepVax immunization did not exacerbate cutaneous nerve involvement due to M. leprae infection, indicating its safe use. There was no intraneural inflammation but a reduction of intra axonal edema suggested that LepVax treatment might restore some early sensory axonal function. These data indicate that post-exposure prophylaxis with LepVax not only appears safe but, unlike BCG, alleviates and delays the neurologic disruptions caused by M. leprae infection.

The recovery of ancient DNA from Dasypus bellus provides new possibilities for investigating late Pleistocene mammal response to climate change

NASA Astrophysics Data System (ADS)

Letts, Brandon; Shapiro, Beth

2010-05-01

Dasypus bellus, the 'beautiful armadillo,' is well known as a casualty of the Pleistocene megafaunal mass extinction event. Appearing in the fossil record about 2.5 Mya, D. bellus was widespread throughout the mid to southern United States and Mexico until it went extinct by about 10 kya. It was replaced by D. novemcinctus, the nine-banded armadillo, which is morphologically identical but smaller. The exact taxonomic status of D. bellus and its phylogenetic relationship with D. novemcinctus has been a subject of debate. In particular, it remains unresolved whether D. bellus was more closely related to North American than South American D. novemcinctus. To address this, we extracted and sequenced fragments of ancient mitochondrial DNA from surprisingly well-preserved remains of D. bellus recovered from Mefford Cave in Florida. Our results reveal a surprisingly close relationship between the extinct D. bellus and North American D. novemcinctus. Although southern climates have been considered inhospitable for the preservation of ancient DNA, thousands of bones per individual and the propensity of the armadillo to seek out shelter in caves makes preservation more likely than for other organisms. The armadillo may therefore make an excellent proxy organism for investigating the influence of climate change on animal populations south of the cold permafrost regions.

The Trinity River Greenway: A Prototype

DTIC Science & Technology

1972-06-01

study have gone into the formulation of a multipurpose plan of management designed to tame the raging waters of the Trinity, subdue its flooding crests...TABLE 6 MAMMALS OF THE STUDY AREA Shorttail Shrew (Blarina brevicauda) Beaver (Castor canadensis) Least Shrew (Crytotis parva) Armadillo (Dasypjs...property resulted. The Trinity became an J :enemy, a raging torrent to be tamed and eventually subdued. Meanwhile, thoughful men began to realize that

Reassessment of the hairy long-nosed armadillo "Dasypus" pilosus (Xenarthra, Dasypodidae) and revalidation of the genus Cryptophractus Fitzinger, 1856.

PubMed

Castro, Mariela C; Ciancio, Martín R; Pacheco, Víctor; Salas-Gismondi, Rodolfo M; Bostelmann, J Enrique; Carlini, Alfredo A

2015-04-14

The hairy long-nosed armadillo, currently referred as Dasypus (Cryptophractus) pilosus, is an enigmatic species endemic to montane cloud forests and subparamo of Peruvian Andes. Its strikingly different external features, which include the carapace concealed by abundant hair, the presence of more movable bands, and a slender skull, have raised questions regarding its taxonomic status as subgenus or as genus. This paper assesses this issue based on a cladistic study and provides a detailed comparative description of the species, including the first account on the distinctive ornamentation of its osteoderms. Based on several unique characters in the carapace, skull, mandible, and teeth, as well as on the external phylogenetic position relative to other Dasypus, we favor the assignment of the hairy long-nosed armadillo to other genus. As result, we revalidate the original generic epithet, so that the valid name of the species is Cryptophractus pilosus Fitzinger, 1856.

Functional and genomic analyses of alpha-solenoid proteins.

PubMed

Fournier, David; Palidwor, Gareth A; Shcherbinin, Sergey; Szengel, Angelika; Schaefer, Martin H; Perez-Iratxeta, Carol; Andrade-Navarro, Miguel A

2013-01-01

Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/.

The hidden anatomy of paranasal sinuses reveals biogeographically distinct morphotypes in the nine-banded armadillo (Dasypus novemcinctus).

PubMed

Billet, Guillaume; Hautier, Lionel; de Thoisy, Benoit; Delsuc, Frédéric

2017-01-01

With their Pan-American distribution, long-nosed armadillos (genus Dasypus ) constitute an understudied model for Neotropical biogeography. This genus currently comprises seven recognized species, the nine-banded armadillo ( D. novemcinctus ) having the widest distribution ranging from Northern Argentina to the South-Eastern US. With their broad diversity of habitats, nine-banded armadillos provide a useful model to explore the effects of climatic and biogeographic events on morphological diversity at a continental scale. Based on a sample of 136 skulls of Dasypus spp. belonging to six species, including 112 specimens identified as D. novemcinctus , we studied the diversity and pattern of variation of paranasal cavities, which were reconstructed virtually using µCT-scanning or observed through bone transparency. Our qualitative analyses of paranasal sinuses and recesses successfully retrieved a taxonomic differentiation between the traditional species D. kappleri , D. pilosus and D. novemcinctus but failed to recover diagnostic features between the disputed and morphologically similar D. septemcinctus and D. hybridus . Most interestingly, the high variation detected in our large sample of D. novemcinctus showed a clear geographical patterning, with the recognition of three well-separated morphotypes: one ranging from North and Central America and parts of northern South America west of the Andes, one distributed across the Amazonian Basin and central South America, and one restricted to the Guiana Shield. The question as to whether these paranasal morphotypes may represent previously unrecognized species is to be evaluated through a thorough revision of the Dasypus species complex integrating molecular and morphological data. Remarkably, our recognition of a distinct morphotype in the Guiana Shield area is congruent with the recent discovery of a divergent mitogenomic lineage in French Guiana. The inflation of the second medialmost pair of caudal frontal sinuses constitutes an unexpected morphological diagnostic feature for this potentially distinct species. Our results demonstrate the benefits of studying overlooked internal morphological structures in supposedly cryptic species revealed by molecular data. It also illustrates the under-exploited potential of the highly variable paranasal sinuses of armadillos for systematic studies.

The evolution of armadillos, anteaters and sloths depicted by nuclear and mitochondrial phylogenies: implications for the status of the enigmatic fossil Eurotamandua.

PubMed

Delsuc, F; Catzeflis, F M; Stanhope, M J; Douzery, E J

2001-08-07

The mammalian order Xenarthra (armadillos, anteaters and sloths) is one of the four major clades of placentals, but it remains poorly studied from the molecular phylogenetics perspective. We present here a study encompassing most of the order's diversity in order to establish xenarthrans' intra-ordinal relationships, discuss the evolution of their morphological characters, search for their extant sister group and specify the timing of their radiation with special emphasis on the status of the controversial fossil Eurotamandua. Sequences of three genes (nuclear exon 28 of the Von Willebrand factor and mitochondrial 12S and 16S rRNAs) are compared for eight of the 13 living genera. Phylogenetic analyses confirm the order's monophyly and that of its three major lineages: armadillos (Cingulata), anteaters (Vermilingua) and sloths ('Tardigrada', renamed in 'Folivora'), and our results strongly support the grouping of hairy xenarthrans (anteaters and sloths) into Pilosa. Within placentals, Afrotheria might be the first lineage to branch off, followed by Xenarthra. The morphological adaptative convergence between New World xenarthrans and Old World pangolins is confirmed. Molecular datings place the early emergence of armadillos around the Cretaceous/Tertiary boundary, followed by the divergence between anteaters and sloths in the Early Eocene era. These Tertiary dates contradict the concept of a very ancient origin of modern xenarthran lineages. They also question the placement of the purported fossil anteater (Eurotamandua) from the Middle Eocene period of Europe with the Vermilingua and instead suggest the independent and convergent evolution of this enigmatic taxon.

The evolution of armadillos, anteaters and sloths depicted by nuclear and mitochondrial phylogenies: implications for the status of the enigmatic fossil Eurotamandua.

PubMed Central

Delsuc, F.; Catzeflis, F. M.; Stanhope, M. J.; Douzery, E. J.

2001-01-01

The mammalian order Xenarthra (armadillos, anteaters and sloths) is one of the four major clades of placentals, but it remains poorly studied from the molecular phylogenetics perspective. We present here a study encompassing most of the order's diversity in order to establish xenarthrans' intra-ordinal relationships, discuss the evolution of their morphological characters, search for their extant sister group and specify the timing of their radiation with special emphasis on the status of the controversial fossil Eurotamandua. Sequences of three genes (nuclear exon 28 of the Von Willebrand factor and mitochondrial 12S and 16S rRNAs) are compared for eight of the 13 living genera. Phylogenetic analyses confirm the order's monophyly and that of its three major lineages: armadillos (Cingulata), anteaters (Vermilingua) and sloths ('Tardigrada', renamed in 'Folivora'), and our results strongly support the grouping of hairy xenarthrans (anteaters and sloths) into Pilosa. Within placentals, Afrotheria might be the first lineage to branch off, followed by Xenarthra. The morphological adaptative convergence between New World xenarthrans and Old World pangolins is confirmed. Molecular datings place the early emergence of armadillos around the Cretaceous/Tertiary boundary, followed by the divergence between anteaters and sloths in the Early Eocene era. These Tertiary dates contradict the concept of a very ancient origin of modern xenarthran lineages. They also question the placement of the purported fossil anteater (Eurotamandua) from the Middle Eocene period of Europe with the Vermilingua and instead suggest the independent and convergent evolution of this enigmatic taxon. PMID:11487408

Natural infection of gastrointestinal nematodes in long-nosed armadillos Dasypus novemcinctus Linnaeus, 1758 from Pantanal wetlands, Aquidauana sub-region, Mato Grosso do Sul State, with the description of Hadrostrongylus speciosum n. gen. et n. sp. (Molineidae: Anoplostrongylinae).

PubMed

Lux Hoppe, Estevam G; do Nascimento, Adjair Antonio

2007-03-15

This study evaluated the gastrointestinal helminth fauna of long-nosed armadillos, Dasypus novemcinctus, from the Pantanal wetlands, Aquidauana sub-region, Aquidauana County, Mato Grosso do Sul State, Brazil. Thirteen species of nematodes, comprising seven genera and four families, were recovered from their gastrointestinal tracts. The following descriptors of infection were determined: prevalence, variation of intensity, average intensity and abundance. Hadrostrongylus speciosum n. gen. et n. sp. is first described here.

Functional and Genomic Analyses of Alpha-Solenoid Proteins

PubMed Central

Fournier, David; Palidwor, Gareth A.; Shcherbinin, Sergey; Szengel, Angelika; Schaefer, Martin H.; Perez-Iratxeta, Carol; Andrade-Navarro, Miguel A.

2013-01-01

Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/. PMID:24278209

Dominant β-catenin mutations cause intellectual disability with recognizable syndromic features

PubMed Central

Tucci, Valter; Kleefstra, Tjitske; Hardy, Andrea; Heise, Ines; Maggi, Silvia; Willemsen, Marjolein H.; Hilton, Helen; Esapa, Chris; Simon, Michelle; Buenavista, Maria-Teresa; McGuffin, Liam J.; Vizor, Lucie; Dodero, Luca; Tsaftaris, Sotirios; Romero, Rosario; Nillesen, Willy N.; Vissers, Lisenka E.L.M.; Kempers, Marlies J.; Vulto-van Silfhout, Anneke T.; Iqbal, Zafar; Orlando, Marta; Maccione, Alessandro; Lassi, Glenda; Farisello, Pasqualina; Contestabile, Andrea; Tinarelli, Federico; Nieus, Thierry; Raimondi, Andrea; Greco, Barbara; Cantatore, Daniela; Gasparini, Laura; Berdondini, Luca; Bifone, Angelo; Gozzi, Alessandro; Wells, Sara; Nolan, Patrick M.

2014-01-01

The recent identification of multiple dominant mutations in the gene encoding β-catenin in both humans and mice has enabled exploration of the molecular and cellular basis of β-catenin function in cognitive impairment. In humans, β-catenin mutations that cause a spectrum of neurodevelopmental disorders have been identified. We identified de novo β-catenin mutations in patients with intellectual disability, carefully characterized their phenotypes, and were able to define a recognizable intellectual disability syndrome. In parallel, characterization of a chemically mutagenized mouse line that displays features similar to those of human patients with β-catenin mutations enabled us to investigate the consequences of β-catenin dysfunction through development and into adulthood. The mouse mutant, designated batface (Bfc), carries a Thr653Lys substitution in the C-terminal armadillo repeat of β-catenin and displayed a reduced affinity for membrane-associated cadherins. In association with this decreased cadherin interaction, we found that the mutation results in decreased intrahemispheric connections, with deficits in dendritic branching, long-term potentiation, and cognitive function. Our study provides in vivo evidence that dominant mutations in β-catenin underlie losses in its adhesion-related functions, which leads to severe consequences, including intellectual disability, childhood hypotonia, progressive spasticity of lower limbs, and abnormal craniofacial features in adults. PMID:24614104

Phylogeography of screaming hairy armadillo Chaetophractus vellerosus: Successive disjunctions and extinctions due to cyclical climatic changes in southern South America.

PubMed

Poljak, Sebastián; Ferreiro, Alejandro M; Chiappero, Marina B; Sánchez, Julieta; Gabrielli, Magalí; Lizarralde, Marta S

2018-01-01

Little is known about phylogeography of armadillo species native to southern South America. In this study we describe the phylogeography of the screaming hairy armadillo Chaetophractus vellerosus, discuss previous hypothesis about the origin of its disjunct distribution and propose an alternative one, based on novel information on genetic variability. Variation of partial sequences of mitochondrial DNA Control Region (CR) from 73 individuals from 23 localities were analyzed to carry out a phylogeographic analysis using neutrality tests, mismatch distribution, median-joining (MJ) network and paleontological records. We found 17 polymorphic sites resulting in 15 haplotypes. Two new geographic records that expand known distribution of the species are presented; one of them links the distributions of recently synonimized species C. nationi and C. vellerosus. Screaming hairy armadillo phylogeographic pattern can be addressed as category V of Avise: common widespread linages plus closely related lineages confined to one or a few nearby locales each. The older linages are distributed in the north-central area of the species distribution range in Argentina (i.e. ancestral area of distribution). C. vellerosus seems to be a low vagility species that expanded, and probably is expanding, its distribution range while presents signs of genetic structuring in central areas. To explain the disjunct distribution, a hypothesis of extinction of the species in intermediate areas due to quaternary climatic shift to more humid conditions was proposed. We offer an alternative explanation: long distance colonization, based on null genetic variability, paleontological record and evidence of alternance of cold/arid and temperate/humid climatic periods during the last million years in southern South America.

Phylogeography of screaming hairy armadillo Chaetophractus vellerosus: Successive disjunctions and extinctions due to cyclical climatic changes in southern South America

PubMed Central

Ferreiro, Alejandro M.; Chiappero, Marina B.; Sánchez, Julieta; Gabrielli, Magalí; Lizarralde, Marta S.

2018-01-01

Little is known about phylogeography of armadillo species native to southern South America. In this study we describe the phylogeography of the screaming hairy armadillo Chaetophractus vellerosus, discuss previous hypothesis about the origin of its disjunct distribution and propose an alternative one, based on novel information on genetic variability. Variation of partial sequences of mitochondrial DNA Control Region (CR) from 73 individuals from 23 localities were analyzed to carry out a phylogeographic analysis using neutrality tests, mismatch distribution, median-joining (MJ) network and paleontological records. We found 17 polymorphic sites resulting in 15 haplotypes. Two new geographic records that expand known distribution of the species are presented; one of them links the distributions of recently synonimized species C. nationi and C. vellerosus. Screaming hairy armadillo phylogeographic pattern can be addressed as category V of Avise: common widespread linages plus closely related lineages confined to one or a few nearby locales each. The older linages are distributed in the north-central area of the species distribution range in Argentina (i.e. ancestral area of distribution). C. vellerosus seems to be a low vagility species that expanded, and probably is expanding, its distribution range while presents signs of genetic structuring in central areas. To explain the disjunct distribution, a hypothesis of extinction of the species in intermediate areas due to quaternary climatic shift to more humid conditions was proposed. We offer an alternative explanation: long distance colonization, based on null genetic variability, paleontological record and evidence of alternance of cold/arid and temperate/humid climatic periods during the last million years in southern South America. PMID:29324793

Armc5 deletion causes developmental defects and compromises T-cell immune responses

PubMed Central

Hu, Yan; Lao, Linjiang; Mao, Jianning; Jin, Wei; Luo, Hongyu; Charpentier, Tania; Qi, Shijie; Peng, Junzheng; Hu, Bing; Marcinkiewicz, Mieczyslaw Martin; Lamarre, Alain; Wu, Jiangping

2017-01-01

Armadillo repeat containing 5 (ARMC5) is a cytosolic protein with no enzymatic activities. Little is known about its function and mechanisms of action, except that gene mutations are associated with risks of primary macronodular adrenal gland hyperplasia. Here we map Armc5 expression by in situ hybridization, and generate Armc5 knockout mice, which are small in body size. Armc5 knockout mice have compromised T-cell proliferation and differentiation into Th1 and Th17 cells, increased T-cell apoptosis, reduced severity of experimental autoimmune encephalitis, and defective immune responses to lymphocytic choriomeningitis virus infection. These mice also develop adrenal gland hyperplasia in old age. Yeast 2-hybrid assays identify 16 ARMC5-binding partners. Together these data indicate that ARMC5 is crucial in fetal development, T-cell function and adrenal gland growth homeostasis, and that the functions of ARMC5 probably depend on interaction with multiple signalling pathways. PMID:28169274

Genetic structuring in a relictual population of screaming hairy armadillo (Chaetophractus vellerosus) in Argentina revealed by a set of novel microsatellite loci.

PubMed

Nardelli, Maximiliano; Ibáñez, Ezequiel Alejandro; Dobler, Dara; Justy, Fabienne; Delsuc, Frédéric; Abba, Agustín Manuel; Cassini, Marcelo Hernán; Túnez, Juan Ignacio

2016-08-01

The screaming hairy armadillo (Chaetophractus vellerosus) is a mammal species containing disjunct and isolated populations. In order to assess the effect of habitat fragmentation and geographic isolation, we developed seven new microsatellite loci isolated from low-coverage genome shotgun sequencing data for this species. Among these loci, six microsatellites were found to be polymorphic with 8-26 alleles per locus detected across 69 samples analyzed from a relictual population of the species located in the northeast of the Buenos Aires Province (Argentina). Mean allelic richness and polymorphic information content were 15 and 0.75, with observed and expected heterozygosities ranging from 0.40 to 0.67 and 0.58 to 0.90, respectively. All loci showed departures from Hardy-Weinberg equilibrium. The analysis of population structure in this relictual population revealed three groups of individuals that are genetically differentiated. These newly developed microsatellites will constitute a very useful tool for the estimation of genetic diversity and structure, population dynamics, social structure, parentage and mating system in this little-studied armadillo species. Such genetic data will be particularly helpful for the development of conservation strategies for this isolated population and also for the endangered Bolivian populations previously recognized as a distinct species (Chaetophractus nationi).

Using non-invasive methods to characterize gonadal hormonal patterns of southern three-banded armadillos (Tolypeutes matacus) housed in North American zoos.

PubMed

Howell-Stephens, J; Bernier, D; Brown, J S; Mulkerin, D; Santymire, R M

2013-05-01

Understanding the basic reproductive biology and limitations to successful breeding of the southern three-banded armadillo (Tolypeutes matacus) is necessary to maintain viable zoo populations. Our objectives were to: 1) describe the reproductive biology using non-invasive, fecal hormone analysis; 2) assess influence of season on gonadal hormonal patterns in both the sexes; 3) characterize reproductive cyclicity and pregnancy in the female; and 4) characterize the onset of sexual maturity in males. Nineteen armadillos were monitored including: 13 (7 males, 6 females) from Lincoln Park Zoo and six (3 males, 3 females) from San Antonio Zoological Garden. Fecal samples (n=5220; 275/animal/yr) were collected 5 to 7 times a week for 1 year. Hormones were extracted from feces and analyzed for progestagen (females) and androgen (males) metabolite concentrations using enzyme immunoassays. Mean estrous cycle length (26.4±1.3 days) did not vary (P<0.05) among individuals (n=9). Mean gestation length (n=3) was 114.0±0.6 days long with mean fecal progestagen metabolites increasing 10-fold during pregnancy. Seasons did not influence (P<0.05) fecal androgen or progestagen metabolites. These data can assist with management decisions, which will directly affect the success of this species in zoos. Published by Elsevier B.V.

The structure of FMNL2-Cdc42 yields insights into the mechanism of lamellipodia and filopodia formation

NASA Astrophysics Data System (ADS)

Kühn, Sonja; Erdmann, Constanze; Kage, Frieda; Block, Jennifer; Schwenkmezger, Lisa; Steffen, Anika; Rottner, Klemens; Geyer, Matthias

2015-05-01

Formins are actin polymerization factors that elongate unbranched actin filaments at the barbed end. Rho family GTPases activate Diaphanous-related formins through the relief of an autoregulatory interaction. The crystal structures of the N-terminal domains of human FMNL1 and FMNL2 in complex with active Cdc42 show that Cdc42 mediates contacts with all five armadillo repeats of the formin with specific interactions formed by the Rho-GTPase insert helix. Mutation of three residues within Rac1 results in a gain-of-function mutation for FMNL2 binding and reconstitution of the Cdc42 phenotype in vivo. Dimerization of FMNL1 through a parallel coiled coil segment leads to formation of an umbrella-shaped structure that--together with Cdc42--spans more than 15 nm in diameter. The two interacting FMNL-Cdc42 heterodimers expose six membrane interaction motifs on a convex protein surface, the assembly of which may facilitate actin filament elongation at the leading edge of lamellipodia and filopodia.

Human APC sequesters beta-catenin even in the absence of GSK-3beta in a Drosophila model.

PubMed

Rao, P R; Makhijani, K; Shashidhara, L S

2008-04-10

There have been conflicting reports on the requirement of GSK-3beta-mediated phosphorylation of the tumor suppressor adenomatous polyposis coli (APC) vis-à-vis its ability to bind and degrade beta-catenin. Using a unique combination of loss of function for Shaggy/GSK-3beta and a gain of function for human APC in Drosophila, we show that misexpressed human APC (hAPC) can still sequester Armadillo/beta-catenin. In addition, human APC could suppress gain of Wnt/Wingless phenotypes associated with loss of Shaggy/GSK-3beta activity, suggesting that sequestered Armadillo/beta-catenin is non-functional. Based on these studies, we propose that binding per se of beta-catenin by APC does not require phosphorylation by GSK-3beta.

Priodontes maximus (Cingulata: Chlamyphoridae)

USGS Publications Warehouse

Carter, Tracy S.; Superina, Mariella; Leslie, David M.

2016-01-01

Priodontes maximus (Kerr, 1792), called the giant armadillo, is monotypic and by far the largest extant armadillo. Average adult weight is about 30kg (in captivity, as high as 80kg). Its carapace extends about halfway down its sides, making it impossible to curl up tightly. It is dark brown to black dorsally, with a broad light band around the lower part of its carapace. It primarily digs to escape, enhanced by its 20-cm, sickle-shaped nail on its 3rd forefingers. P. maximus is widely distributed in South America but nowhere abundant. It is affected by habitat loss and fragmentation, agriculture, hunting, collection for museum specimens, and illegal animal trafficking. P. maximus is listed as “Vulnerable” by the International Union for Conservation of Nature and Natural Resources.

Comparative anatomy and histology of xenarthran osteoderms.

PubMed

Hill, Robert V

2006-12-01

Reconstruction of soft tissues in fossil vertebrates is an enduring challenge for paleontologists. Because inferences must be based on evidence from hard tissues (typically bones or teeth), even the most complete fossils provide only limited information about certain organ systems. Osteoderms ("dermal armor") are integumentary bones with high fossilization potential that hold information about the anatomy of the skin in many extant and fossil amniotes. Their importance for functional morphology and phylogenetic research has recently been recognized, but studies have focused largely upon reptiles, in which osteoderms are most common. Among mammals, osteoderms occur only in members of the clade Xenarthra, which includes armadillos and their extinct relatives: glyptodonts, pampatheres, and, more distantly, ground sloths. Here, I present new information on the comparative morphology and histology of osteoderms and their associated soft tissues in 11 extant and fossil xenarthrans. Extinct mylodontid sloths possessed simple, isolated ossicles, the presence of which is likely plesiomorphic for Xenarthra. More highly derived osteoderms of glyptodonts, pampatheres, and armadillos feature complex articulations and surface ornamentation. Osteoderms of modern armadillos are physically associated with a variety of soft tissues, including nerve, muscle, gland, and connective tissue. In some cases, similar osteological features may be caused by two or more different tissue types, rendering soft-tissue inferences for fossil osteoderms equivocal. Certain osteological structures, however, are consistently associated with specific soft-tissue complexes and therefore represent a relatively robust foundation upon which to base soft-tissue reconstructions of extinct xenarthrans. Copyright 2006 Wiley-Liss, Inc.

Vertebral bending mechanics and xenarthrous morphology in the nine-banded armadillo (Dasypus novemcinctus).

PubMed

Oliver, Jillian D; Jones, Katrina E; Hautier, Lionel; Loughry, W J; Pierce, Stephanie E

2016-10-01

The vertebral column has evolved to accommodate the broad range of locomotor pressures found across vertebrate lineages. Xenarthran (armadillos, sloths and anteaters) vertebral columns are characterized by xenarthrous articulations, novel intervertebral articulations located in the posterior trunk that are hypothesized to stiffen the vertebral column to facilitate digging. To determine the degree to which xenarthrous articulations impact vertebral movement, we passively measured compliance and range of motion during ventroflexion, dorsiflexion and lateral bending across the thoracolumbar region of the nine-banded armadillo, Dasypus novemcinctus Patterns of bending were compared with changes in vertebral morphology along the column to determine which morphological features best predict intervertebral joint mechanics. We found that compliance was lower in post-diaphragmatic, xenarthrous vertebrae relative to pre-xenarthrous vertebrae in both sagittal and lateral planes of bending. However, we also found that range of motion was higher in this region. These changes in mechanics are correlated with the transition from pre-xenarthrous to xenarthrous vertebrae, as well as with the transition from thoracic to lumbar vertebrae. Our results thus substantiate the hypothesis that xenarthrous articulations stiffen the vertebral column. Additionally, our data suggest that xenarthrous articulations, and their associated enlarged metapophyses, also act to increase the range of motion of the post-diaphragmatic region. We propose that xenarthrous articulations perform the dual role of stiffening the vertebral column and increasing mobility, resulting in passively stable vertebrae that are capable of substantial bending under appropriate loads. © 2016. Published by The Company of Biologists Ltd.

Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans

PubMed Central

Gibb, Gillian C.; Condamine, Fabien L.; Kuch, Melanie; Enk, Jacob; Moraes-Barros, Nadia; Superina, Mariella; Poinar, Hendrik N.; Delsuc, Frédéric

2016-01-01

Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats. PMID:26556496

Leprosy (Hansen's Disease)

MedlinePlus

... See all Leprosy (Hansen's Disease) related NIAID Now posts Basic Research NIAID-funded investigators are developing the armadillo as a research animal model for human leprosy and developing improved skin test antigens to detect leprosy. Read more about leprosy ...

Lack of Sarcocystis neurona antibody response in Virginia opossums (Didelphis virginiana) fed Sarcocystis neurona-infected muscle tissue.

PubMed

Cheadle, M A; Lindsay, D S; Greiner, E C

2006-06-01

Serum was collected from laboratory-reared Virginia opossums (Didelphis virginiana) to determine whether experimentally infected opossums shedding Sarcocystis neurona sporocysts develop serum antibodies to S. neurona merozoite antigens. Three opossums were fed muscles from nine-banded armadillos (Dasypus novemcinctus), and 5 were fed muscles from striped skunks (Mephitis mephitis). Serum was also collected from 26 automobile-killed opossums to determine whether antibodies to S. neurona were present in these opossums. Serum was analyzed using the S. neurona direct agglutination test (SAT). The SAT was modified for use with a filter paper collection system. Antibodies to S. neurona were not detected in any of the serum samples from opossums, indicating that infection in the opossum is localized in the small intestine. Antibodies to S. neurona were detected in filter-paper-processed serum samples from 2 armadillos naturally infected with S. neurona.

Neuroglian and DE-cadherin activate independent cytoskeleton assembly pathways in Drosophila S2 cells.

PubMed

Dubreuil, R R; Grushko, T

1999-11-19

The cytoskeletal proteins spectrin and ankyrin colocalize with sites of E-cadherin-mediated cell-cell adhesion in mammalian cells. Here we examined the effects of Drosophila DE-cadherin expression on spectrin and ankyrin in Drosophila S2 tissue culture cells. DE-cadherin caused a dramatic change in the cytoplasmic concentration and distribution of armadillo, the Drosophila homolog of beta catenin. However, DE-cadherin expression had no detectable effect on the quantity or subcellular distribution of ankyrin or spectrin. In reciprocal experiments, recruitment of ankyrin and alphabeta spectrin to the plasma membrane by another cell adhesion molecule, neuroglian, had no effect on the quantity or distribution of armadillo. The results indicate that DE-cadherin-catenin complexes and neuroglian-spectrin/ankyrin complexes form by nonintersecting pathways. Recruitment of spectrin does not appear to be a conserved feature of DE-cadherin function. Copyright 1999 Academic Press.

Environmental enrichment for a mixed-species nocturnal mammal exhibit.

PubMed

Clark, Fay E; Melfi, Vicky A

2012-01-01

Environmental enrichment (EE) is an integral aspect of modern zoo animal management but, empirical evaluation of it is biased toward species housed in single-species groups. Nocturnal houses, where several nocturnal species are housed together, are particularly overlooked. This study investigated whether three species (nine-banded armadillos, Dasypus novemcinctus; Senegal bush babies, Galago senegalensis; two-toed sloths, Choloepus didactylus) in the nocturnal house at Paignton Zoo Environmental Park, UK could be enriched using food-based and sensory EE. Subjects were an adult male and female of each species. EE was deemed effective if it promoted target species-typical behaviors, behavioral diversity, and increased use of enriched exhibit zones. Results from generalized linear mixed models demonstrated that food-based EE elicited the most positive behavioral effects across species. One set of food-based EEs (Kong®, termite mound and hanging food) presented together was associated with a significant increase in species-typical behaviors, increased behavioral diversity, and increased use of enriched exhibit zones in armadillos and bush babies. Although one type of sensory EE (scented pine cones) increased overall exhibit use in all species, the other (rainforest sounds) was linked to a significant decrease in species-typical behavior in bush babies and sloths. There were no intra or interspecies conflicts over EE, and commensalism occurred between armadillos and bush babies. Our data demonstrate that simple food-based and sensory EE can promote positive behavioral changes in a mixed-species nocturnal mammal exhibit. We suggest that both food and sensory EE presented concurrently will maximize opportunities for naturalistic activity in all species. © 2011 Wiley Periodicals, Inc.

Sea-Level Flight Demonstration and Altitude Characterization of a LO2/LCH4 Based Accent Propulsion Lander

NASA Technical Reports Server (NTRS)

Collins, Jacob; Hurlbert, Eric; Romig, Kris; Melcher, John; Hobson, Aaron; Eaton, Phil

2009-01-01

A 1,500 lbf thrust-class liquid oxygen (LO2)/Liquid Methane (LCH4) rocket engine was developed and tested at both sea-level and simulated altitude conditions. The engine was fabricated by Armadillo Aerospace (AA) in collaboration with NASA Johnson Space Center. Sea level testing was conducted at Armadillo Aerospace facilities at Caddo Mills, TX. Sea-level tests were conducted using both a static horizontal test bed and a vertical take-off and landing (VTOL) test bed capable of lift-off and hover-flight in low atmosphere conditions. The vertical test bed configuration is capable of throttling the engine valves to enable liftoff and hover-flight. Simulated altitude vacuum testing was conducted at NASA Johnson Space Center White Sands Test Facility (WSTF), which is capable of providing altitude simulation greater than 120,000 ft equivalent. The engine tests demonstrated ignition using two different methods, a gas-torch and a pyrotechnic igniter. Both gas torch and pyrotechnic ignition were demonstrated at both sea-level and vacuum conditions. The rocket engine was designed to be configured with three different nozzle configurations, including a dual-bell nozzle geometry. Dual-bell nozzle tests were conducted at WSTF and engine performance data was achieved at both ambient pressure and simulated altitude conditions. Dual-bell nozzle performance data was achieved over a range of altitude conditions from 90,000 ft to 50,000 ft altitude. Thrust and propellant mass flow rates were measured in the tests for specific impulse (Isp) and C* calculations.

Armadillos, Boatbills & Crocodiles.

ERIC Educational Resources Information Center

Berkovits, Annette; Greenblatt, Esther

1980-01-01

Recounts the unique partnership in science instruction developed between Nassau and Suffolk County (New York) schools and the Bronx Zoo to provide educational experiences for handicapped and mentally retarded students. Discussion focuses on a five-phase program developed for 200 elementary secondary students from Rosemary Kennedy Center through…

The alterations in the extracellular matrix composition guide the repair of damaged liver tissue

PubMed Central

Klaas, Mariliis; Kangur, Triin; Viil, Janeli; Mäemets-Allas, Kristina; Minajeva, Ave; Vadi, Krista; Antsov, Mikk; Lapidus, Natalia; Järvekülg, Martin; Jaks, Viljar

2016-01-01

While the cellular mechanisms of liver regeneration have been thoroughly studied, the role of extracellular matrix (ECM) in liver regeneration is still poorly understood. We utilized a proteomics-based approach to identify the shifts in ECM composition after CCl4 or DDC treatment and studied their effect on the proliferation of liver cells by combining biophysical and cell culture methods. We identified notable alterations in the ECM structural components (eg collagens I, IV, V, fibronectin, elastin) as well as in non-structural proteins (eg olfactomedin-4, thrombospondin-4, armadillo repeat-containing x-linked protein 2 (Armcx2)). Comparable alterations in ECM composition were seen in damaged human livers. The increase in collagen content and decrease in elastic fibers resulted in rearrangement and increased stiffness of damaged liver ECM. Interestingly, the alterations in ECM components were nonhomogenous and differed between periportal and pericentral areas and thus our experiments demonstrated the differential ability of selected ECM components to regulate the proliferation of hepatocytes and biliary cells. We define for the first time the alterations in the ECM composition of livers recovering from damage and present functional evidence for a coordinated ECM remodelling that ensures an efficient restoration of liver tissue. PMID:27264108

Mechanical Properties of β-Catenin Revealed by Single-Molecule Experiments

PubMed Central

Valbuena, Alejandro; Vera, Andrés Manuel; Oroz, Javier; Menéndez, Margarita; Carrión-Vázquez, Mariano

2012-01-01

β-catenin is a central component of the adaptor complex that links cadherins to the actin cytoskeleton in adherens junctions and thus, it is a good candidate to sense and transmit mechanical forces to trigger specific changes inside the cell. To fully understand its molecular physiology, we must first investigate its mechanical role in mechanotransduction within the cadherin system. We have studied the mechanical response of β-catenin to stretching using single-molecule force spectroscopy and molecular dynamics. Unlike most proteins analyzed to date, which have a fixed mechanical unfolding pathway, the β-catenin armadillo repeat region (ARM) displays low mechanostability and multiple alternative unfolding pathways that seem to be modulated by its unstructured termini. These results are supported by steered molecular dynamics simulations, which also predict its mechanical stabilization and unfolding pathway restrictions when the contiguous α-helix of the C-terminal unstructured region is included. Furthermore, simulations of the ARM/E-cadherin cytosolic tail complex emulating the most probable stress geometry occurring in vivo show a mechanical stabilization of the interaction whose magnitude correlates with the length of the stretch of the cadherin cytosolic tail that is in contact with the ARM region. PMID:23083718

A comparative study of bio-inspired protective scales using 3D printing and mechanical testing.

PubMed

Martini, Roberto; Balit, Yanis; Barthelat, Francois

2017-06-01

Flexible natural armors from fish, alligators or armadillo are attracting an increasing amount of attention for their unique combinations of hardness, flexibility and light weight. The extreme contrast of stiffness between hard scales and surrounding soft tissues gives rise to unusual and attractive mechanisms, which now serve as models for the design of bio-inspired armors. Despite this growing interest, there is little guideline for the choice of materials, optimum thickness, size, shape and arrangement for the protective scales. In this work, we explore how the geometry and arrangement of hard scales can be tailored to promote scale-scale interactions. We use 3D printing to fabricate arrays of scales with increasingly complex geometries and arrangements, from simple squares with no overlap to complex ganoid-scales with overlaps and interlocking features. We performed puncture tests and flexural tests on each of the 3D printed materials, and we report the puncture resistance - compliance characteristics of each design on an Ashby chart. The interactions between the scales can significantly increase the resistance to puncture, and these interactions can be maximized by tuning the geometry and arrangement of the scales. Interestingly, the designs that offer the best combinations of puncture resistance and flexural compliance are similar to the geometry and arrangement of natural teleost and ganoid scales, which suggests that natural evolution has shaped these systems to maximize flexible protection. This study yields new insights into the mechanisms of natural dermal armor, and also suggests new designs for personal protective systems. Flexible natural armors from fishes, alligators or armadillos are attracting an increasing amount of attention for their unique and attractive combinations of hardness, flexibility and low weight. Despite a growing interest in bio-inspired flexible protection, there is still little guideline for the choice of materials, optimum thickness, size, shape and arrangement of the protective scales. In this work, we explore how the geometry and arrangement of hard scales affect puncture resistance and flexural compliance, using 3D printing and mechanical testing. Our main finding is that the performance of the scaled skin in terms of puncture resistance can be significantly improved by slight changes in their geometry and arrangement. Our results also suggest that natural evolution has shaped scaled skins to maximize flexible protection. This study yields new insights into the mechanics of natural dermal armors, and also suggests new designs for personal protective systems. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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

Sharma, Manisha; Jamieson, Cara; Lui, Christina

β-catenin is a key mediator of Wnt signaling and its deregulated nuclear accumulation can drive cancer progression. While the central armadillo (Arm) repeats of β-catenin stimulate nuclear entry, the N- and C-terminal “tail” sequences are thought to regulate turnover and transactivation. We show here that the N- and C-tails are also potent transport sequences. The unstructured tails of β-catenin, when individually fused to a GFP-reporter, could enter and exit the nucleus rapidly in live cells. Proximity ligation assays and pull-down assays identified a weak interaction between the tail sequences and the FG-repeats of nucleoporins, consistent with a possible direct translocationmore » of β-catenin through the nuclear pore complex. Extensive alanine mutagenesis of the tail sequences revealed that nuclear translocation of β-catenin was dependent on specific uniformly distributed patches of hydrophobic residues, whereas the mutagenesis of acidic amino acids had no effect. Moreover, the mutation of hydrophobic patches within the N-tail and C-tail of full length β-catenin reduced nuclear transport rate and diminished its ability to activate transcription. We propose that the tail sequences can contribute to β-catenin transport and suggest a possible similar role for hydrophobic unstructured regions in other proteins. - Highlights: • We show that the N- and C-tails of beta-catenin possess nuclear transport activity. • Nuclear transport of the N- or C-tails requires specific hydrophobic amino acids. • Mutagenesis of the N-terminus diminished nuclear entry of full-length beta-catenin. • We propose the N-tail contributes to beta-catenin nuclear entry and transactivation.« less

KCTD1 Suppresses Canonical Wnt Signaling Pathway by Enhancing β-catenin Degradation

PubMed Central

Wang, Fangmei; Huang, Wenhuan; Liang, Zhongheng; Xiao, Yuzhong; Wei, Ke; Wan, Zhenxing; Hu, Xiang; Xiang, Shuanglin; Ding, Xiaofeng; Zhang, Jian

2014-01-01

The canonical Wnt signaling pathway controls normal embryonic development, cellular proliferation and growth, and its aberrant activity results in human carcinogenesis. The core component in regulation of this pathway is β-catenin, but molecular regulation mechanisms of β-catenin stability are not completely known. Here, our recent studies have shown that KCTD1 strongly inhibits TCF/LEF reporter activity. Moreover, KCTD1 interacted with β-catenin both in vivo by co-immunoprecipitation as well as in vitro through GST pull-down assays. We further mapped the interaction regions to the 1-9 armadillo repeats of β-catenin and the BTB domain of KCTD1, especially Position Ala-30 and His-33. Immunofluorescence analysis indicated that KCTD1 promotes the cytoplasmic accumulation of β-catenin. Furthermore, protein stability assays revealed that KCTD1 enhances the ubiquitination/degradation of β-catenin in a concentration-dependent manner in HeLa cells. And the degradation of β-catenin mediated by KCTD1 was alleviated by the proteasome inhibitor, MG132. In addition, KCTD1-mediated β-catenin degradation was dependent on casein kinase 1 (CK1)- and glycogen synthase kinase-3β (GSK-3β)-mediated phosphorylation and enhanced by the E3 ubiquitin ligase β-transducin repeat-containing protein (β-TrCP). Moreover, KCTD1 suppressed the expression of endogenous Wnt downstream genes and transcription factor AP-2α. Finally, we found that Wnt pathway member APC and tumor suppressor p53 influence KCTD1-mediated downregulation of β-catenin. These results suggest that KCTD1 functions as a novel inhibitor of Wnt signaling pathway. PMID:24736394

Resource selection and its implications for wide-ranging mammals of the brazilian cerrado.

PubMed

Vynne, Carly; Keim, Jonah L; Machado, Ricardo B; Marinho-Filho, Jader; Silveira, Leandro; Groom, Martha J; Wasser, Samuel K

2011-01-01

Conserving animals beyond protected areas is critical because even the largest reserves may be too small to maintain viable populations for many wide-ranging species. Identification of landscape features that will promote persistence of a diverse array of species is a high priority, particularly, for protected areas that reside in regions of otherwise extensive habitat loss. This is the case for Emas National Park, a small but important protected area located in the Brazilian Cerrado, the world's most biologically diverse savanna. Emas Park is a large-mammal global conservation priority area but is too small to protect wide-ranging mammals for the long-term and conserving these populations will depend on the landscape surrounding the park. We employed novel, noninvasive methods to determine the relative importance of resources found within the park, as well as identify landscape features that promote persistence of wide-ranging mammals outside reserve borders. We used scat detection dogs to survey for five large mammals of conservation concern: giant armadillo (Priodontes maximus), giant anteater (Myrmecophaga tridactyla), maned wolf (Chrysocyon brachyurus), jaguar (Panthera onca), and puma (Puma concolor). We estimated resource selection probability functions for each species from 1,572 scat locations and 434 giant armadillo burrow locations. Results indicate that giant armadillos and jaguars are highly selective of natural habitats, which makes both species sensitive to landscape change from agricultural development. Due to the high amount of such development outside of the Emas Park boundary, the park provides rare resource conditions that are particularly important for these two species. We also reveal that both woodland and forest vegetation remnants enable use of the agricultural landscape as a whole for maned wolves, pumas, and giant anteaters. We identify those features and their landscape compositions that should be prioritized for conservation, arguing that a multi-faceted approach is required to protect these species.

Characterisation of glycoconjugate sugar residues in the vomeronasal organ of the armadillo Chaetophractus villosus (Mammalia, xenarthra)

PubMed Central

CARMANCHAHI, P. D.; FERRARI, C. C.; ALDANA MARCOS, H. J.; AFFANNI, J. M.; SONEZ, C. A.; PAZ, D. A.

2000-01-01

Conventional carbohydrate histochemistry and the binding patterns of 21 lectins were analysed to characterise the glycoconjugate content in the components of the vomeronasal organ of the armadillo Chaetophractus villosus. The mucomicrovillous complex of the sensory epithelium bound most of the lectins studied. No reaction was observed with Con A, PSA, S-Con A and SBA, and the sustentacular cells were stained with UEA-I, DSL, LEL, STL and Con A. The vomeronasal receptor neurons were labelled with S-WGA, WGA, PNA, UEA-I, STL, Con A, S-Con A, ECL and RCA120. The basal cell layer reacted with S-WGA, WGA, LCA, UEA-I, DSL, LEL, STL, Con A, JAC and VVA. The nonsensory epithelium exhibited a differential staining in relation to the different components. The mucociliary complex stained with ECL, DBA, JAC, RCA120, STL, LCA, PHA-E, PHA-L, LEL, BSL-I and VVA. However, SJA and UEA-I stained the mucus complex lining a subpopulation of columnar cells. The cytoplasm and cell membranes of columnar cells was labelled with DBA, DSL and LCA. The apical region of these cells exhibited moderate reactivity with LEL and SJA. None of the lectins bound specifically to secretory granules of the nonsecretory cells. Basal cells of the nonsensory epithelium were labelled with DSL, LEL, LCA, BSL-I and STL. The vomeronasal glands showed a positive reaction with WGA, DSL, LEL, LCA, DBA, PNA, RCA120 and SBA. Subpopulations of acinar cells were observed with ECL, S-WGA, Con A, S-Con A and DBA. PNA and RCA120 stained the cells lining the glandular ducts. In comparison with previous results obtained in the olfactory mucosa of the same group of armadillos, the carbohydrate composition of the vomeronasal organ sensory epithelium differed from the olfactory sensory epithelium. This is probably related to the different nature of molecules involved in the perireceptor processes. PMID:10853958

Resource Selection and Its Implications for Wide-Ranging Mammals of the Brazilian Cerrado

PubMed Central

Vynne, Carly; Keim, Jonah L.; Machado, Ricardo B.; Marinho-Filho, Jader; Silveira, Leandro; Groom, Martha J.; Wasser, Samuel K.

2011-01-01

Conserving animals beyond protected areas is critical because even the largest reserves may be too small to maintain viable populations for many wide-ranging species. Identification of landscape features that will promote persistence of a diverse array of species is a high priority, particularly, for protected areas that reside in regions of otherwise extensive habitat loss. This is the case for Emas National Park, a small but important protected area located in the Brazilian Cerrado, the world's most biologically diverse savanna. Emas Park is a large-mammal global conservation priority area but is too small to protect wide-ranging mammals for the long-term and conserving these populations will depend on the landscape surrounding the park. We employed novel, noninvasive methods to determine the relative importance of resources found within the park, as well as identify landscape features that promote persistence of wide-ranging mammals outside reserve borders. We used scat detection dogs to survey for five large mammals of conservation concern: giant armadillo (Priodontes maximus), giant anteater (Myrmecophaga tridactyla), maned wolf (Chrysocyon brachyurus), jaguar (Panthera onca), and puma (Puma concolor). We estimated resource selection probability functions for each species from 1,572 scat locations and 434 giant armadillo burrow locations. Results indicate that giant armadillos and jaguars are highly selective of natural habitats, which makes both species sensitive to landscape change from agricultural development. Due to the high amount of such development outside of the Emas Park boundary, the park provides rare resource conditions that are particularly important for these two species. We also reveal that both woodland and forest vegetation remnants enable use of the agricultural landscape as a whole for maned wolves, pumas, and giant anteaters. We identify those features and their landscape compositions that should be prioritized for conservation, arguing that a multi-faceted approach is required to protect these species. PMID:22205984

Gnathostomiasis in a Wild-Caught Nine-Banded Armadillo (Dasypus Novemcinctus)

DTIC Science & Technology

1993-12-01

were below nal host. In addition, many paratenic hosts aid in transmis- normal limits. Peripheral circulation was poor. When the sion through predation ...debris. H&E stain. caused by the aberrant mi-,ttk,, or q l~rv.a form of this 120x. 631 \\ol 41:, No ki Laltmatoryv Aimal Sci,,ac 1),v,111 er 1 992

I Feel Like an Armadillo: A Look at College Seniors and Recent Graduates Using Erik Erikson's Model of "Identity Versus Role-Diffusion."

ERIC Educational Resources Information Center

Jaurigue, Rebecca

Developmental psychologist Erik Erikson observed that achieving a sense of self, an identity, was the important psychosocial task facing adolescents. The conflict lies in discovering and defining that identity despite parental and societal demands, changing values and opportunities, the influence of friends, and lovers, education, and finances.…

Regulation of the protein kinase activity of Shaggy(Zeste-white3) by components of the wingless pathway in Drosophila cells and embryos.

PubMed

Ruel, L; Stambolic, V; Ali, A; Manoukian, A S; Woodgett, J R

1999-07-30

The protein-serine kinase Shaggy(Zeste-white3) (Sgg(Zw3)) is the Drosophila homolog of mammalian glycogen synthase kinase-3 and has been genetically implicated in signal transduction pathways necessary for the establishment of patterning. Sgg(Zw3) is a putative component of the Wingless (Wg) pathway, and epistasis analyses suggest that Sgg(Zw3) function is repressed by Wg signaling. Here, we have investigated the biochemical consequences of Wg signaling with respect to the Sgg(Zw3) protein kinase in two types of Drosophila cell lines and in embryos. Our results demonstrate that Sgg(Zw3) activity is inhibited following exposure of cells to Wg protein and by expression of downstream components of Wg signaling, Drosophila frizzled 2 and dishevelled. Wg-dependent inactivation of Sgg(Zw3) is accompanied by serine phosphorylation. We also show that the level of Sgg(Zw3) activity regulates the stability of Armadillo protein and modulates the level of phosphorylation of D-Axin and Armadillo. Together, these results provide direct biochemical evidence in support of the genetic model of Wg signaling and provide a model for dissecting the molecular interactions between the signaling proteins.

KSC-07pd0148

NASA Image and Video Library

2007-01-19

KENNEDY SPACE CENTER, FLA. -- Seen at NASA's Kennedy Space Center, this nine-banded armadillo may be looking for food. Introduced to Florida in the early 1900's, this species is found statewide in areas with dense ground cover and sandy soil. Nine bands of plates cover the body from shoulder to hip and 12 bands cover the long tail. It has a small, tapered head and snout and a long tongue. Its ears are long and hairless. It has sparse white hairs on its belly. Its diet is composed of insects, especially beetles, and other invertebrates plus some plant foods such as cedars and beautyberries. It is primarily nocturnal, sedentary, solitary and a burrower. It digs a series of dens. The multiple entrances are usually protected by stumps, palmettos, or trees. Many other animals also use armadillo dens. KSC shares a boundary with the Merritt Island Wildlife Nature Refuge. The refuge is a habitat for more than 310 species of birds, 25 mammals, 117 fishes and 65 amphibians and reptiles. In addition, the Refuge supports 19 endangered or threatened wildlife species on Federal or State lists, more than any other single refuge in the U.S. Photo credit: NASA/Ken Thornsley

KSC-07pd0146

NASA Image and Video Library

2007-01-19

KENNEDY SPACE CENTER, FLA. -- Seen at NASA's Kennedy Space Center, this nine-banded armadillo may be looking for food. Introduced to Florida in the early 1900's, this species is found statewide in areas with dense ground cover and sandy soil. Nine bands of plates cover the body from shoulder to hip and 12 bands cover the long tail. It has a small, tapered head and snout and a long tongue. Its ears are long and hairless. It has sparse white hairs on its belly. Its diet is composed of insects, especially beetles, and other invertebrates plus some plant foods such as cedars and beautyberries. It is primarily nocturnal, sedentary, solitary and a burrower. It digs a series of dens. The multiple entrances are usually protected by stumps, palmettos, or trees. Many other animals also use armadillo dens. KSC shares a boundary with the Merritt Island Wildlife Nature Refuge. The refuge is a habitat for more than 310 species of birds, 25 mammals, 117 fishes and 65 amphibians and reptiles. In addition, the Refuge supports 19 endangered or threatened wildlife species on Federal or State lists, more than any other single refuge in the U.S. Photo credit: NASA/Ken Thornsley

KSC-07pd0147

NASA Image and Video Library

2007-01-19

KENNEDY SPACE CENTER, FLA. -- Seen at NASA's Kennedy Space Center, this nine-banded armadillo may be looking for food. Introduced to Florida in the early 1900's, this species is found statewide in areas with dense ground cover and sandy soil. Nine bands of plates cover the body from shoulder to hip and 12 bands cover the long tail. It has a small, tapered head and snout and a long tongue. Its ears are long and hairless. It has sparse white hairs on its belly. Its diet is composed of insects, especially beetles, and other invertebrates plus some plant foods such as cedars and beautyberries. It is primarily nocturnal, sedentary, solitary and a burrower. It digs a series of dens. The multiple entrances are usually protected by stumps, palmettos, or trees. Many other animals also use armadillo dens. KSC shares a boundary with the Merritt Island Wildlife Nature Refuge. The refuge is a habitat for more than 310 species of birds, 25 mammals, 117 fishes and 65 amphibians and reptiles. In addition, the Refuge supports 19 endangered or threatened wildlife species on Federal or State lists, more than any other single refuge in the U.S. Photo credit: NASA/Ken Thornsley

Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution

PubMed Central

Wu, Jianping; Li, Zhangqiang; Xie, Tian; Peng, Wei; Yin, Changcheng; Li, Xueming; Scheres, Sjors H.W.; Shi, Yigong; Yan, Nieng

2014-01-01

The ryanodine receptors (RyRs) are high-conductance intracellular Ca2+ channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organization and approximately 5000 residues in each protomer. Here we report the structure of the rabbit RyR1 in complex with its modulator FKBP12 at an overall resolution of 3.8 Å, determined by single-particle electron cryo-microscopy. Three previously uncharacterized domains, named Central, Handle, and Helical domains, display the armadillo repeat fold. These domains, together with the amino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of conformational changes. The channel domain exhibits the voltage-gated ion channel superfamily fold with distinct features. A negative charge-enriched hairpin loop connecting S5 and the pore helix is positioned above the entrance to the selectivity filter vestibule. The four elongated S6 segments form a right-handed helical bundle that closes the pore at the cytoplasmic border of the membrane. Allosteric regulation of the pore by the cytoplasmic domains is mediated through extensive interactions between the Central domains and the channel domain. These structural features explain high ion conductance by RyRs and the long-range allosteric regulation of channel activities. PMID:25517095

β-Catenin recognizes a specific RNA motif in the cyclooxygenase-2 mRNA 3′-UTR and interacts with HuR in colon cancer cells

PubMed Central

Kim, Inae; Kwak, Hoyun; Lee, Hee Kyu; Hyun, Soonsil; Jeong, Sunjoo

2012-01-01

RNA-binding proteins regulate multiple steps of RNA metabolism through both dynamic and combined binding. In addition to its crucial roles in cell adhesion and Wnt-activated transcription in cancer cells, β-catenin regulates RNA alternative splicing and stability possibly by binding to target RNA in cells. An RNA aptamer was selected for specific binding to β-catenin to address RNA recognition by β-catenin more specifically. Here, we characterized the structural properties of the RNA aptamer as a model and identified a β-catenin RNA motif. Similar RNA motif was found in cellular RNA, Cyclooxygenase-2 (COX-2) mRNA 3′-untranslated region (3′-UTR). More significantly, the C-terminal domain of β-catenin interacted with HuR and the Armadillo repeat domain associated with RNA to form the RNA–β-catenin–HuR complex in vitro and in cells. Furthermore, the tertiary RNA–protein complex was predominantly found in the cytoplasm of colon cancer cells; thus, it might be related to COX-2 protein level and cancer progression. Taken together, the β-catenin RNA aptamer was valuable for deducing the cellular RNA aptamer and identifying novel and oncogenic RNA–protein networks in colon cancer cells. PMID:22544606

Structural basis for the recognition of Asef by adenomatous polyposis coli

PubMed Central

Zhang, Zhenyi; Chen, Leyi; Gao, Lei; Lin, Kui; Zhu, Liang; Lu, Yang; Shi, Xiaoshan; Gao, Yuan; Zhou, Jing; Xu, Ping; Zhang, Jian; Wu, Geng

2012-01-01

Adenomatous polyposis coli (APC) regulates cell-cell adhesion and cell migration through activating the APC-stimulated guanine nucleotide-exchange factor (GEF; Asef), which is usually autoinhibited through the binding between its Src homology 3 (SH3) and Dbl homology (DH) domains. The APC-activated Asef stimulates the small GTPase Cdc42, which leads to decreased cell-cell adherence and enhanced cell migration. In colorectal cancers, truncated APC constitutively activates Asef and promotes cancer cell migration and angiogenesis. Here, we report crystal structures of the human APC/Asef complex. We find that the armadillo repeat domain of APC uses a highly conserved surface groove to recognize the APC-binding region (ABR) of Asef, conformation of which changes dramatically upon binding to APC. Key residues on APC and Asef for the complex formation were mutated and their importance was demonstrated by binding and activity assays. Structural superimposition of the APC/Asef complex with autoinhibited Asef suggests that the binding between APC and Asef might create a steric clash between Asef-DH domain and APC, which possibly leads to a conformational change in Asef that stimulates its GEF activity. Our structures thus elucidate the molecular mechanism of Asef recognition by APC, as well as provide a potential target for pharmaceutical intervention against cancers. PMID:21788986

Optimization conditions of samples saponification for tocopherol analysis.

PubMed

Souza, Aloisio Henrique Pereira; Gohara, Aline Kirie; Rodrigues, Ângela Claudia; Ströher, Gisely Luzia; Silva, Danielle Cristina; Visentainer, Jesuí Vergílio; Souza, Nilson Evelázio; Matsushita, Makoto

2014-09-01

A full factorial design 2(2) (two factors at two levels) with duplicates was performed to investigate the influence of the factors agitation time (2 and 4 h) and the percentage of KOH (60% and 80% w/v) in the saponification of samples for the determination of α, β and γ+δ-tocopherols. The study used samples of peanuts (cultivar armadillo), produced and marketed in Maringá, PR. The factors % KOH and agitation time were significant, and an increase in their values contributed negatively to the responses. The interaction effect was not significant for the response δ-tocopherol, and the contribution of this effect to the other responses was positive, but less than 10%. The ANOVA and response surfaces analysis showed that the most efficient saponification procedure was obtained using a 60% (w/v) solution of KOH and with an agitation time of 2 h. Copyright © 2014 Elsevier Ltd. All rights reserved.

US Army Medical Research and Development Technical Report

DTIC Science & Technology

1975-07-01

very similar in extent and appearance to naturally occurring human infections and the armadillo appears to be the best experimental model for...guinea pig skin produced by intradermal injection of toxin fractions resemble the early changes in naturally occurring human infections. In both there... naturally occurring human infections. In both there is extensive necrosis, undermining of the margins of the lesions and a spreading contiguous necrosis

Arthropods: Vectors of Disease Agents

DTIC Science & Technology

1994-07-01

vector or glands in the tick legs. Filarid in some tick species, individuals of be passively regurgitated during worms (eg, dog heartworm) devel- which...Australia and an arthropod serves as the vector passively regurgitated during blood- Antarctica. An estimated 50 million transferring the etiologic agent...opossums, Biological ɝ More common in racoons, armadillos dogs than people Garbage, sewage, etc Mechanical NA I akwoator% %ledionc %.j. 2i, \\.I

Effectiveness of scat-detection dogs in determining species presence in a tropical savanna landscape.

PubMed

Vynne, Carly; Skalski, John R; Machado, Ricardo B; Groom, Martha J; Jácomo, Anah T A; Marinho-Filho, Jader; Ramos Neto, Mario B; Pomilla, Cristina; Silveira, Leandro; Smith, Heath; Wasser, Samuel K

2011-02-01

Most protected areas are too small to sustain populations of wide-ranging mammals; thus, identification and conservation of high-quality habitat for those animals outside parks is often a high priority, particularly for regions where extensive land conversion is occurring. This is the case in the vicinity of Emas National Park, a small protected area in the Brazilian Cerrado. Over the last 40 years the native vegetation surrounding the park has been converted to agriculture, but the region still supports virtually all of the animals native to the area. We determined the effectiveness of scat-detection dogs in detecting presence of five species of mammals threatened with extinction by habitat loss: maned wolf (Chrysocyon brachyurus), puma (Puma concolor), jaguar (Panthera onca), giant anteater (Myrmecophaga tridactyla), and giant armadillo (Priodontes maximus). The probability of scat detection varied among the five species and among survey quadrats of different size, but was consistent across team, season, and year. The probability of occurrence, determined from the presence of scat, in a randomly selected site within the study area ranged from 0.14 for jaguars, which occur primarily in the forested areas of the park, to 0.91 for maned wolves, the most widely distributed species in our study area. Most occurrences of giant armadillos in the park were in open grasslands, but in the agricultural matrix they tended to occur in riparian woodlands. At least one target species occurred in every survey quadrat, and giant armadillos, jaguars, and maned wolves were more likely to be present in quadrats located inside than outside the park. The effort required for detection of scats was highest for the two felids. We were able to detect the presence for each of five wide-ranging species inside and outside the park and to assign occurrence probabilities to specific survey sites. Thus, scat dogs provide an effective survey tool for rare species even when accurate detection likelihoods are required. We believe the way we used scat-detection dogs to determine the presence of species can be applied to the detection of other mammalian species in other ecosystems. ©2010 Society for Conservation Biology.

Trabecular architecture in the forelimb epiphyses of extant xenarthrans (Mammalia).

PubMed

Amson, Eli; Arnold, Patrick; van Heteren, Anneke H; Canoville, Aurore; Nyakatura, John A

2017-01-01

Bone structure has a crucial role in the functional adaptations that allow vertebrates to conduct their diverse lifestyles. Much has been documented regarding the diaphyseal structure of long bones of tetrapods. However, the architecture of trabecular bone, which is for instance found within the epiphyses of long bones, and which has been shown experimentally to be extremely plastic, has received little attention in the context of lifestyle adaptations (virtually only in primates). We therefore investigated the forelimb epiphyses of extant xenarthrans, the placental mammals including the sloths, anteaters, and armadillos. They are characterised by several lifestyles and degrees of fossoriality involving distinct uses of their forelimb. We used micro computed tomography data to acquire 3D trabecular parameters at regions of interest (ROIs) for all extant genera of xenarthrans (with replicates). Traditional, spherical, and phylogenetically informed statistics (including the consideration of size effects) were used to characterise the functional signal of these parameters. Several trabecular parameters yielded functional distinctions. The main direction of the trabeculae distinguished lifestyle categories for one ROI (the radial trochlea). Among the other trabecular parameters, it is the degree of anisotropy (i.e., a preferential alignment of the trabeculae) that yielded the clearest functional signal. For all ROIs, the armadillos, which represent the fully terrestrial and fossorial category, were found as characterised by a greater degree of anisotropy (i.e., more aligned trabeculae). Furthermore, the trabeculae of the humeral head of the most fossorial armadillos were also found to be more anisotropic than in the less fossorial species. Most parameters were marked by an important intraspecific variability and by a size effect, which could, at least partly, be masking the functional signal. But for some parameters, the degree of anisotropy in particular, a clear functional distinction was recovered. Along with data on primates, our findings suggest that a trabecular architecture characterised by a greater degree of anisotropy is to be expected in species in which the relevant epiphyses withstand a restricted range of load directions. Trabecular architecture therefore is a promising research avenue for the reconstruction of lifestyles in extinct or cryptic species.

Leishmaniasis in Texas: Isolation of Leishmania mexicana from Neotoma Micropus

DTIC Science & Technology

1990-01-01

leishmaniasis cases in Texas, 2) Lutzomyia anthophora, a sand fly which has transmitted Leishmania mexicana under laboratory conditions (Endris et al., 1984...Addis, 1945). Other vertebrates such as opossums, hispid cotton rats, and armadillos and other sand flies such as Lutzomyia diabolica and Lutzomyia texana...Leishmania mexicana by a North American sand fly, Lutzomyia anthophora (Diptera: Psychodidae). Journal of Medical Entomology 24: 243- 247. GRIMALDI, G. Jr

Female reproductive tract of the lesser anteater (Tamandua tetradactyla, myrmecophagidae, Xenarthra). Anatomy and histology.

PubMed

Rossi, L F; Luaces, J P; Marcos, H J Aldana; Cetica, P D; Gachen, G; Jimeno, G Pérez; Merani, M S

2011-11-01

The morphological and histological features of the unusual reproductive tract of the female lesser anteater, Tamandua tetradactyla (Myrmecophagidae, Xenarthra), are described for the first time. The present study aimed to establish the main similarities and differences between this species and other xenarthrans. The populations of this species are declining rapidly for a number of reasons and our study is relevant to diverse programs related to its conservation. Studies were carried out on five female genital tracts of adult specimens. Ovaries were ovoid, presenting a medulla completely surrounded by the cortex, differently from that described in other xenarthans. Like in Dasypus but different from all other armadillos studied, single oocyte follicles were observed and a simple the uterus. The uterovaginal canal connects the uterus with the urogenital sinus. The simple columnar epithelium of the uterovaginal canal ends abruptly at a septum which resembles a hymen, where the transitional epithelium of the urogenital sinus appears. This ancestral feature is shared with that of other armadillos, except Tolypeutes matacus, which has a true vagina. Characteristics of the reproductive tract and sperm morphology of other Xenarthra are comparatively discussed. These observations suggest that important reproductive features are shared between the family Myrmecophagidae and the genus Dasypus, a basal group in the phylogeny of Xenarthra. Copyright © 2011 Wiley-Liss, Inc.

Methods for extracting climate indicator data from social media.

NASA Astrophysics Data System (ADS)

Fuka, M. Z.; Fuka, D. R.

2011-12-01

This paper shows how we've used the R software suite to extract climate indicator data from Twitter. In the course of this research we've collected extensive data sets of unsolicited observations ("tweets") for hundreds of climate-related phenological, biological, epidemiological and meteorological effects. R has proved itself in our work as a useful tool for manipulating those large data sets. Our experience from this effort has yielded a variety of insights on using R to extract geophysics-specific information from publicly accessible social media sources. We illustrate our methodology by mapping tweeted US armadillo sightings to explore the impact of climate variability on the extent of the animal's range. This example usefully demonstrates R's technical capabilities in collecting, time-stamping, geolocating, analyzing, visualizing and otherwise processing climate-related data derived from unsolicited social media postings. We also "mash-up" the data sets with those acquired by more traditional means, for example, temperature and precipitation data across the armadillo's US range. Our data-handling practice is extendable to social sharing services other than Twitter, providing the environmental modeling community an opportunity to access largely untapped resources of non-traditional climate indicator data to better understand the effects of climate change at local, regional and global scales.

The intervals method: a new approach to analyse finite element outputs using multivariate statistics

PubMed Central

De Esteban-Trivigno, Soledad; Püschel, Thomas A.; Fortuny, Josep

2017-01-01

Background In this paper, we propose a new method, named the intervals’ method, to analyse data from finite element models in a comparative multivariate framework. As a case study, several armadillo mandibles are analysed, showing that the proposed method is useful to distinguish and characterise biomechanical differences related to diet/ecomorphology. Methods The intervals’ method consists of generating a set of variables, each one defined by an interval of stress values. Each variable is expressed as a percentage of the area of the mandible occupied by those stress values. Afterwards these newly generated variables can be analysed using multivariate methods. Results Applying this novel method to the biological case study of whether armadillo mandibles differ according to dietary groups, we show that the intervals’ method is a powerful tool to characterize biomechanical performance and how this relates to different diets. This allows us to positively discriminate between specialist and generalist species. Discussion We show that the proposed approach is a useful methodology not affected by the characteristics of the finite element mesh. Additionally, the positive discriminating results obtained when analysing a difficult case study suggest that the proposed method could be a very useful tool for comparative studies in finite element analysis using multivariate statistical approaches. PMID:29043107

Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants.

PubMed

Wistow, Graeme; Bernstein, Steven L; Wyatt, M Keith; Behal, Amita; Touchman, Jeffrey W; Bouffard, Gerald; Smith, Don; Peterson, Katherine

2002-06-15

To explore the expression profile of the human lens and to provide a resource for microarray studies, expressed sequence tag (EST) analysis has been performed on cDNA libraries from adult lenses. A cDNA library was constructed from two adult (40 year old) human lenses. Over two thousand clones were sequenced from the unamplified, un-normalized library. The library was then normalized and a further 2200 sequences were obtained. All the data were analyzed using GRIST (GRouping and Identification of Sequence Tags), a procedure for gene identification and clustering. The lens library (by) contains a low percentage of non-mRNA contaminants and a high fraction (over 75%) of apparently full length cDNA clones. Approximately 2000 reads from the unamplified library yields 810 clusters, potentially representing individual genes expressed in the lens. After normalization, the content of crystallins and other abundant cDNAs is markedly reduced and a similar number of reads from this library (fs) yields 1455 unique groups of which only two thirds correspond to named genes in GenBank. Among the most abundant cDNAs is one for a novel gene related to glutamine synthetase, which was designated "lengsin" (LGS). Analyses of ESTs also reveal examples of alternative transcripts, including a major alternative splice form for the lens specific membrane protein MP19. Variant forms for other transcripts, including those encoding the apoptosis inhibitor Livin and the armadillo repeat protein ARVCF, are also described. The lens cDNA libraries are a resource for gene discovery, full length cDNAs for functional studies and microarrays. The discovery of an abundant, novel transcript, lengsin, and a major novel splice form of MP19 reflect the utility of unamplified libraries constructed from dissected tissue. Many novel transcripts and splice forms are represented, some of which may be candidates for genetic diseases.

β catenin in health: A review

PubMed Central

Prakash, Sharada; Swaminathan, Uma

2015-01-01

β catenin belongs to the armadillo family of proteins. It plays a crucial role in developmental and homeostatic processes. Wnts are a family of 19 secreted glycoproteins that transduce multiple signaling cascades, including the canonical Wnt/β catenin pathway, Wnt/Ca2+ pathway and the Wnt/polarity pathway. This is a review on β catenin, Wnt proteins and their secretion, the signaling pathway, the associated factors and the crucial role of β catenin in odontogenesis. PMID:26604501

Utilizing Xenarthra (Tree Sloth, Anteater, Armadillo, Ground Sloth, Glyptodont, and Pampathere) Cranial Material to Evaluate Students' Understanding of This Thing Called Science

ERIC Educational Resources Information Center

Shaw, Barbara J.; Ruedas, Luis A.

2012-01-01

Two-thirds of U.S. citizens do not understand the scientific process. There is a clear misunderstanding about what science is--and is not--both in our society and in the classroom. Furthermore, students below basic proficiency are locked into an achievement gap. In response, the No Child Left Behind Act was passed in 2001. Since then, there has…

PCR-based approach to SINE isolation: simple and complex SINEs.

PubMed

Borodulina, Olga R; Kramerov, Dmitri A

2005-04-11

Highly repeated copies of short interspersed elements (SINEs) occur in eukaryotic genomes. The distribution of each SINE family is usually restricted to some genera, families, or orders. SINEs have an RNA polymerase III internal promoter, which is composed of boxes A and B. Here we propose a method for isolation of novel SINE families based on genomic DNA PCR with oligonucleotide identical to box A as a primer. Cloning of the size-heterogeneous PCR-products and sequencing of their terminal regions allow determination of SINE structure. Using this approach, two novel SINE families, Rhin-1 and Das-1, from the genomes of great horseshoe bat (Rhinolophus ferrumequinum) and nine-banded armadillo (Dasypus novemcinctus), respectively, were isolated and studied. The distribution of Rhin-1 is restricted to two of six bat families tested. Copies of this SINE are characterized by frequent internal insertions and significant length (200-270 bp). Das-1 being only 90 bp in length is one of the shortest SINEs known. Most of Das-1 nucleotide sequences demonstrate significant similarity to alanine tRNA which appears to be an evolutionary progenitor of this SINE. Together with three other known SINEs (ID, Vic-1, and CYN), Das-1 constitutes a group of simple SINEs. Interestingly, three SINE families of this group are alanine tRNA-derived. Most probably, this tRNA gave rise to short and simple but successful SINEs several times during mammalian evolution.

The requirement of sterol glucoside for pexophagy in yeast is dependent on the species and nature of peroxisome inducers.

PubMed

Nazarko, Taras Y; Polupanov, Andriy S; Manjithaya, Ravi R; Subramani, Suresh; Sibirny, Andriy A

2007-01-01

Sterol glucosyltransferase, Ugt51/Atg26, is essential for both micropexophagy and macropexophagy of methanol-induced peroxisomes in Pichia pastoris. However, the role of this protein in pexophagy in other yeast remained unclear. We show that oleate- and amine-induced peroxisomes in Yarrowia lipolytica are degraded by Atg26-independent macropexophagy. Surprisingly, Atg26 was also not essential for macropexophagy of oleate- and amine-induced peroxisomes in P. pastoris, suggesting that the function of sterol glucoside (SG) in pexophagy is both species and peroxisome inducer specific. However, the rates of degradation of oleate- and amine-induced peroxisomes in P. pastoris were reduced in the absence of SG, indicating that P. pastoris specifically uses sterol conversion by Atg26 to enhance selective degradation of peroxisomes. However, methanol-induced peroxisomes apparently have lost the redundant ability to be degraded without SG. We also show that the P. pastoris Vac8 armadillo repeat protein is not essential for macropexophagy of methanol-, oleate-, or amine-induced peroxisomes, which makes PpVac8 the first known protein required for the micropexophagy, but not for the macropexophagy, machinery. The uniqueness of Atg26 and Vac8 functions under different pexophagy conditions demonstrates that not only pexophagy inducers, such as glucose or ethanol, but also the inducers of peroxisomes, such as methanol, oleate, or primary amines, determine the requirements for subsequent pexophagy in yeast.

Radiation hybrid mapping of genes in the lithium-sensitive wnt signaling pathway.

PubMed

Rhoads, A R; Karkera, J D; Detera-Wadleigh, S D

1999-09-01

Lithium, an effective drug in the treatment of bipolar disorder, has been proposed to disrupt the Wnt signaling pathway. To facilitate analysis of the possible involvement of elements of the Wnt pathway in human bipolar disorder, a high resolution radiation hybrid mapping (RHM) of these genes was performed. A fine physical location has been obtained for Wnt 7A, frizzled 3, 4 and 5, dishevelled 1, 2 and 3, GSK3beta, axin, alpha-catenin, the Armadillo repeat-containing genes (delta-catenin and ARVCF), and a frizzled-like protein (frpHE) using the Stanford Human Genome Center (SHGC) G3 panel. Most of these genes were previously mapped by fluorescence in situ hybridization (FISH). Frizzled 4, axin and frpHE did not have a previous chromosomal assignment and were linked by RHM to chromosome markers, SHGC-35131 at 11q22.1, NIB1488 at 16p13.3 and D7S2919 at 7p15.2, respectively. Interestingly, some of these genes were found to map within potential regions underlying susceptibility to bipolar disorder and schizophrenia as well as disorders of neurodevelopmental origin. This alternative approach of establishing the precise location of selected genetic components of a candidate pathway and determining if they map within previously defined susceptibility loci should help to identify plausible candidate genes that warrant further analysis through association and mutational scanning.

A proposed role for selective autophagy in regulating auxin-dependent lateral root development under phosphate starvation in Arabidopsis.

PubMed

Sankaranarayanan, Subramanian; Samuel, Marcus A

2015-01-01

Plants respond to limited soil nutrient availability by inducing more lateral roots (LR) to increase the root surface area. At the cellular level, nutrient starvation triggers the process of autophagy through which bulk degradation of cellular materials is achieved to facilitate nutrient mobilization. Whether there is any link between the cellular autophagy and induction of LR had remained unknown. We recently showed that the S-Domain receptor Kinase (ARK2) and U Box/Armadillo Repeat-Containing E3 ligase (PUB9) module is required for lateral root formation under phosphate starvation in Arabidopsis thaliana.(1) We also showed that PUB9 localized to autophagic bodies following either activation by ARK2 or under phosphate starvation and ark2-1/pub9-1 plants displayed lateral root defects with inability to accumulate auxin in the root tips under phosphate starvation.(1) Supplementing exogenous auxin was sufficient to rescue the LR defects in ark2-1/pub9-1 mutant. Blocking of autophagic responses in wild-type Arabidopsis also resulted in inhibition of both lateral roots and auxin accumulation in the root tips indicating the importance of autophagy in mediating auxin accumulation under phosphate starved conditions.(1) Here, we propose a model for ARK2/AtPUB9 module in regulation of lateral root development via selective autophagy.

Morphology of the tongue of Vermilingua (Xenarthra: Pilosa) and evolutionary considerations.

PubMed

Casali, Daniel M; Martins-Santos, Elisângela; Santos, André L Q; Miranda, Flávia R; Mahecha, Germán A B; Perini, Fernando A

2017-10-01

The tongue of anteaters (Xenarthra, Pilosa, Vermilingua) is a highly specialized for myrmecophagy. Here, we describe the topography and histology of the tongue, and compare it to that of other xenarthrans and other myrmecophagous eutherian mammals. The tongue of Vermilingua is long and slender, with an apical protuberance, which differs between Myrmecophagidae and Cyclopes didactylus. In the former, the rostral region is conical, and in the latter, it is dorsoventrally compressed, as observed in sloths. The tongue of Vermilingua has filiform and circumvallate papillae on the surface; foliate and fungiform papillae are absent. The filiform papillae of Myrmecophaga tridactyla are simple all over the tongue, differing from Tamandua tetradactyla and Cyclopes didactylus, which present composed filiform papillae in the rostral and middle regions. Histologically, the tongue has a peculiar organization of muscular and neurovascular tissues, differing from the usual mammalian pattern. However, the tongue structure is less divergent in Cyclopes. The presence of two circumvallate papillae is common to the three major clades of Xenarthra (Cingulata, Folivora and Vermilingua). In each group, the tongue may reflect functional features related to myrmecophagous (anteaters and some armadillos), omnivorous (remaining armadillos) and folivorous (sloths) feeding habits. The similarities between the tongues of Vermiligua and other non-xenarthran eutherian myrmecophagous mammals are somewhat general and, under close inspection, superficial, being an example of different lineages achieving the same morphofunctional adaptations through distinct evolutionary pathways. © 2017 Wiley Periodicals, Inc.

ATLANTIC-CAMTRAPS: a dataset of medium and large terrestrial mammal communities in the Atlantic Forest of South America.

PubMed

Lima, Fernando; Beca, Gabrielle; Muylaert, Renata L; Jenkins, Clinton N; Perilli, Miriam L L; Paschoal, Ana Maria O; Massara, Rodrigo L; Paglia, Adriano P; Chiarello, Adriano G; Graipel, Maurício E; Cherem, Jorge J; Regolin, André L; Oliveira Santos, Luiz Gustavo R; Brocardo, Carlos R; Paviolo, Agustín; Di Bitetti, Mario S; Scoss, Leandro M; Rocha, Fabiana L; Fusco-Costa, Roberto; Rosa, Clarissa A; Da Silva, Marina X; Hufnagell, Ludmila; Santos, Paloma M; Duarte, Gabriela T; Guimarães, Luiza N; Bailey, Larissa L; Rodrigues, Flávio Henrique G; Cunha, Heitor M; Fantacini, Felipe M; Batista, Graziele O; Bogoni, Juliano A; Tortato, Marco A; Luiz, Micheli R; Peroni, Nivaldo; De Castilho, Pedro V; Maccarini, Thiago B; Filho, Vilmar Picinatto; Angelo, Carlos De; Cruz, Paula; Quiroga, Verónica; Iezzi, María E; Varela, Diego; Cavalcanti, Sandra M C; Martensen, Alexandre C; Maggiorini, Erica V; Keesen, Fabíola F; Nunes, André V; Lessa, Gisele M; Cordeiro-Estrela, Pedro; Beltrão, Mayara G; De Albuquerque, Anna Carolina F; Ingberman, Bianca; Cassano, Camila R; Junior, Laury Cullen; Ribeiro, Milton C; Galetti, Mauro

2017-11-01

Our understanding of mammal ecology has always been hindered by the difficulties of observing species in closed tropical forests. Camera trapping has become a major advance for monitoring terrestrial mammals in biodiversity rich ecosystems. Here we compiled one of the largest datasets of inventories of terrestrial mammal communities for the Neotropical region based on camera trapping studies. The dataset comprises 170 surveys of medium to large terrestrial mammals using camera traps conducted in 144 areas by 74 studies, covering six vegetation types of tropical and subtropical Atlantic Forest of South America (Brazil and Argentina), and present data on species composition and richness. The complete dataset comprises 53,438 independent records of 83 species of mammals, includes 10 species of marsupials, 15 rodents, 20 carnivores, eight ungulates and six armadillos. Species richness averaged 13 species (±6.07 SD) per site. Only six species occurred in more than 50% of the sites: the domestic dog Canis familiaris, crab-eating fox Cerdocyon thous, tayra Eira barbara, south American coati Nasua nasua, crab-eating raccoon Procyon cancrivorus and the nine-banded armadillo Dasypus novemcinctus. The information contained in this dataset can be used to understand macroecological patterns of biodiversity, community, and population structure, but also to evaluate the ecological consequences of fragmentation, defaunation, and trophic interactions. © 2017 by the Ecological Society of America.

Finite Element Analysis of the Cingulata Jaw: An Ecomorphological Approach to Armadillo’s Diets

PubMed Central

Serrano-Fochs, Sílvia; De Esteban-Trivigno, Soledad; Marcé-Nogué, Jordi; Fortuny, Josep; Fariña, Richard A.

2015-01-01

Finite element analyses (FEA) were applied to assess the lower jaw biomechanics of cingulate xenarthrans: 14 species of armadillos as well as one Pleistocene pampathere (11 extant taxa and the extinct forms Vassallia, Eutatus and Macroeuphractus). The principal goal of this work is to comparatively assess the biomechanical capabilities of the mandible based on FEA and to relate the obtained stress patterns with diet preferences and variability, in extant and extinct species through an ecomorphology approach. The results of FEA showed that omnivorous species have stronger mandibles than insectivorous species. Moreover, this latter group of species showed high variability, including some similar biomechanical features of the insectivorous Tolypeutes matacus and Chlamyphorus truncatus to those of omnivorous species, in agreement with reported diets that include items other than insects. It remains unclear the reasons behind the stronger than expected lower jaw of Dasypus kappleri. On the other hand, the very strong mandible of the fossil taxon Vassallia maxima agrees well with the proposed herbivorous diet. Moreover, Eutatus seguini yielded a stress pattern similar to Vassalia in the posterior part of the lower jaw, but resembling that of the stoutly built Macroeuphractus outesi in the anterior part. The results highlight the need for more detailed studies on the natural history of extant armadillos. FEA proved a powerful tool for biomechanical studies in a comparative framework. PMID:25919313

Recruitment of β-Catenin to N-Cadherin Is Necessary for Smooth Muscle Contraction*

PubMed Central

Wang, Tao; Wang, Ruping; Cleary, Rachel A.; Gannon, Olivia J.; Tang, Dale D.

2015-01-01

β-Catenin is a key component that connects transmembrane cadherin with the actin cytoskeleton at the cell-cell interface. However, the role of the β-catenin/cadherin interaction in smooth muscle has not been well characterized. Here stimulation with acetylcholine promoted the recruitment of β-catenin to N-cadherin in smooth muscle cells/tissues. Knockdown of β-catenin by lentivirus-mediated shRNA attenuated smooth muscle contraction. Nevertheless, myosin light chain phosphorylation at Ser-19 and actin polymerization in response to contractile activation were not reduced by β-catenin knockdown. In addition, the expression of the β-catenin armadillo domain disrupted the recruitment of β-catenin to N-cadherin. Force development, but not myosin light chain phosphorylation and actin polymerization, was reduced by the expression of the β-catenin armadillo domain. Furthermore, actin polymerization and microtubules have been implicated in intracellular trafficking. In this study, the treatment with the inhibitor latrunculin A diminished the interaction of β-catenin with N-cadherin in smooth muscle. In contrast, the exposure of smooth muscle to the microtubule depolymerizer nocodazole did not affect the protein-protein interaction. Together, these findings suggest that smooth muscle contraction is mediated by the recruitment of β-catenin to N-cadherin, which may facilitate intercellular mechanotransduction. The association of β-catenin with N-cadherin is regulated by actin polymerization during contractile activation. PMID:25713069

Analyzing nature's protective design: The glyptodont body armor.

PubMed

du Plessis, Anton; Broeckhoven, Chris; Yadroitsev, Igor; Yadroitsava, Ina; le Roux, Stephan Gerhard

2018-06-01

Many animal species evolved some form of body armor, such as scales of fish and bony plates or osteoderms of reptiles. Although a protective function is often taken for granted, recent studies show that body armor might comprise multiple functionalities and is shaped by trade-offs among these functionalities. Hence, despite the fact that natural body armor might serve as bio-inspiration for the development of artificial protective materials, focussing on model systems in which body armor serves a solely protective function might be pivotal. In this study, we investigate the osteoderms of Glyptotherium arizonae, an extinct armadillo-like mammal in which body armor evolved as protection against predators and/or tail club blows of conspecifics. By using a combination of micro-computed tomography, reverse-engineering, stress simulations and mechanical testing of 3D printed models, we show that the combination of dense compact layers and porous lattice core might provide an optimized combination of strength and high energy absorption. Copyright © 2018 Elsevier Ltd. All rights reserved.

Autosomal recessive mutations in nuclear transport factor KPNA7 are associated with infantile spasms and cerebellar malformation.

PubMed

Paciorkowski, Alex R; Weisenberg, Judy; Kelley, Joshua B; Spencer, Adam; Tuttle, Emily; Ghoneim, Dalia; Thio, Liu Lin; Christian, Susan L; Dobyns, William B; Paschal, Bryce M

2014-05-01

Nuclear import receptors of the KPNA family recognize the nuclear localization signal in proteins and together with importin-β mediate translocation into the nucleus. Accordingly, KPNA family members have a highly conserved architecture with domains that contact the nuclear localization signal and bind to importin-β. Here, we describe autosomal recessive mutations in KPNA7 found by whole exome sequencing in a sibling pair with severe developmental disability, infantile spasms, subsequent intractable epilepsy consistent with Lennox-Gastaut syndrome, partial agenesis of the corpus callosum, and cerebellar vermis hypoplasia. The mutations mapped to exon 7 in KPNA7 result in two amino-acid substitutions, Pro339Ala and Glu344Gln. On the basis of the crystal structure of the paralog KPNA2 bound to a bipartite nuclear localization signal from the retinoblastoma protein, the amino-acid substitutions in the affected subjects were predicted to occur within the seventh armadillo repeat that forms one of the two nuclear localization signal-binding sites in KPNA family members. Glu344 is conserved in all seven KPNA proteins, and we found that the Glu354Gln mutation in KPNA2 is sufficient to reduce binding to the retinoblastoma nuclear localization signal to approximately one-half that of wild-type protein. Our data show that compound heterozygous mutations in KPNA7 are associated with a human neurodevelopmental disease, and provide the first example of a human disease associated with mutation of a nuclear transport receptor.

Autosomal recessive mutations in nuclear transport factor KPNA7 are associated with infantile spasms and cerebellar malformation

PubMed Central

Paciorkowski, Alex R; Weisenberg, Judy; Kelley, Joshua B; Spencer, Adam; Tuttle, Emily; Ghoneim, Dalia; Thio, Liu Lin; Christian, Susan L; Dobyns, William B; Paschal, Bryce M

2014-01-01

Nuclear import receptors of the KPNA family recognize the nuclear localization signal in proteins and together with importin-β mediate translocation into the nucleus. Accordingly, KPNA family members have a highly conserved architecture with domains that contact the nuclear localization signal and bind to importin-β. Here, we describe autosomal recessive mutations in KPNA7 found by whole exome sequencing in a sibling pair with severe developmental disability, infantile spasms, subsequent intractable epilepsy consistent with Lennox–Gastaut syndrome, partial agenesis of the corpus callosum, and cerebellar vermis hypoplasia. The mutations mapped to exon 7 in KPNA7 result in two amino-acid substitutions, Pro339Ala and Glu344Gln. On the basis of the crystal structure of the paralog KPNA2 bound to a bipartite nuclear localization signal from the retinoblastoma protein, the amino-acid substitutions in the affected subjects were predicted to occur within the seventh armadillo repeat that forms one of the two nuclear localization signal-binding sites in KPNA family members. Glu344 is conserved in all seven KPNA proteins, and we found that the Glu354Gln mutation in KPNA2 is sufficient to reduce binding to the retinoblastoma nuclear localization signal to approximately one-half that of wild-type protein. Our data show that compound heterozygous mutations in KPNA7 are associated with a human neurodevelopmental disease, and provide the first example of a human disease associated with mutation of a nuclear transport receptor. PMID:24045845

Molecular and clinical evidence for an ARMC5 tumor syndrome: concurrent inactivating germline and somatic mutations are associated with both primary macronodular adrenal hyperplasia and meningioma.

PubMed

Elbelt, Ulf; Trovato, Alessia; Kloth, Michael; Gentz, Enno; Finke, Reinhard; Spranger, Joachim; Galas, David; Weber, Susanne; Wolf, Cristina; König, Katharina; Arlt, Wiebke; Büttner, Reinhard; May, Patrick; Allolio, Bruno; Schneider, Jochen G

2015-01-01

Primary macronodular adrenal hyperplasia (PMAH) is a rare cause of Cushing's syndrome, which may present in the context of different familial multitumor syndromes. Heterozygous inactivating germline mutations of armadillo repeat containing 5 (ARMC5) have very recently been described as cause for sporadic PMAH. Whether this genetic condition also causes familial PMAH in association with other neoplasias is unclear. The aim of the present study was to delineate the molecular cause in a large family with PMAH and other neoplasias. Whole-genome sequencing and comprehensive clinical and biochemical phenotyping was performed in members of a PMAH affected family. Nodules derived from adrenal surgery and pancreatic and meningeal tumor tissue were analyzed for accompanying somatic mutations in the identified target genes. PMAH presenting either as overt or subclinical Cushing's syndrome was accompanied by a heterozygous germline mutation in ARMC5 (p.A110fs*9) located on chromosome 16. Analysis of tumor tissue showed different somatic ARMC5 mutations in adrenal nodules supporting a second hit hypothesis with inactivation of a tumor suppressor gene. A damaging somatic ARMC5 mutation was also found in a concomitant meningioma (p.R502fs) but not in a pancreatic tumor, suggesting biallelic inactivation of ARMC5 as causal also for the intracranial meningioma. Our analysis further confirms inherited inactivating ARMC5 mutations as a cause of familial PMAH and suggests an additional role for the development of concomitant intracranial meningiomas.

Structures of the APC–ARM domain in complexes with discrete Amer1/WTX fragments reveal that it uses a consensus mode to recognize its binding partners

PubMed Central

Zhang, Zhenyi; Akyildiz, Senem; Xiao, Yafei; Gai, Zhongchao; An, Ying; Behrens, Jürgen; Wu, Geng

2015-01-01

The tumor suppressor APC employs its conserved armadillo repeat (ARM) domain to recognize many of its binding partners, including Amer1/WTX, which is mutated in Wilms' tumor and bone overgrowth syndrome. The APC–Amer1 complex has important roles in regulating Wnt signaling and cell adhesion. Three sites A1, A2, and A3 of Amer1 have been reported to mediate its interaction with APC-ARM. In this study, crystal structures of APC–ARM in complexes with Amer1-A1, -A2, and -A4, which is newly identified in this work, were determined. Combined with our GST pull-down, yeast two-hybrid, and isothermal titration calorimetry (ITC) assay results using mutants of APC and Amer1 interface residues, our structures demonstrate that Amer1-A1, -A2, and -A4, as well as other APC-binding proteins such as Asef and Sam68, all employ a common recognition pattern to associate with APC–ARM. In contrast, Amer1-A3 binds to the C-terminal side of APC–ARM through a bipartite interaction mode. Composite mutations on either APC or Amer1 disrupting all four interfaces abrogated their association in cultured cells and impaired the membrane recruitment of APC by Amer1. Our study thus comprehensively elucidated the recognition mechanism between APC and Amer1, and revealed a consensus recognition sequence employed by various APC–ARM binding partners. PMID:27462415

Structures of the APC-ARM domain in complexes with discrete Amer1/WTX fragments reveal that it uses a consensus mode to recognize its binding partners.

PubMed

Zhang, Zhenyi; Akyildiz, Senem; Xiao, Yafei; Gai, Zhongchao; An, Ying; Behrens, Jürgen; Wu, Geng

2015-01-01

The tumor suppressor APC employs its conserved armadillo repeat (ARM) domain to recognize many of its binding partners, including Amer1/WTX, which is mutated in Wilms' tumor and bone overgrowth syndrome. The APC-Amer1 complex has important roles in regulating Wnt signaling and cell adhesion. Three sites A1, A2, and A3 of Amer1 have been reported to mediate its interaction with APC-ARM. In this study, crystal structures of APC-ARM in complexes with Amer1-A1, -A2, and -A4, which is newly identified in this work, were determined. Combined with our GST pull-down, yeast two-hybrid, and isothermal titration calorimetry (ITC) assay results using mutants of APC and Amer1 interface residues, our structures demonstrate that Amer1-A1, -A2, and -A4, as well as other APC-binding proteins such as Asef and Sam68, all employ a common recognition pattern to associate with APC-ARM. In contrast, Amer1-A3 binds to the C-terminal side of APC-ARM through a bipartite interaction mode. Composite mutations on either APC or Amer1 disrupting all four interfaces abrogated their association in cultured cells and impaired the membrane recruitment of APC by Amer1. Our study thus comprehensively elucidated the recognition mechanism between APC and Amer1, and revealed a consensus recognition sequence employed by various APC-ARM binding partners.

Plakophilin-1, a Novel Wnt Signaling Regulator, Is Critical for Tooth Development and Ameloblast Differentiation

PubMed Central

Arai, Chieko; Yamada, Aya; Saito, Kan; Ishikawa, Masaki; Xue, Han; Funada, Keita; Haruyama, Naoto; Yamada, Yoshihiko; Fukumoto, Satoshi; Takahashi, Ichiro

2016-01-01

Tooth morphogenesis is initiated by reciprocal interactions between the ectoderm and neural crest-derived mesenchyme, and the Wnt signaling pathway is involved in this process. We found that Plakophilin (PKP)1, which is associated with diseases such as ectodermal dysplasia/skin fragility syndrome, was highly expressed in teeth and skin, and was upregulated during tooth development. We hypothesized that PKP1 regulates Wnt signaling via its armadillo repeat domain in a manner similar to β-catenin. To determine its role in tooth development, we performed Pkp1 knockdown experiments using ex vivo organ cultures and cell cultures. Loss of Pkp1 reduced the size of tooth germs and inhibited dental epithelial cell proliferation, which was stimulated by Wnt3a. Furthermore, transfected PKP1-emerald green fluorescent protein was translocated from the plasma membrane to the nucleus upon stimulation with Wnt3a and LiCl, which required the PKP1 N terminus (amino acids 161 to 270). Localization of PKP1, which is known as an adhesion-related desmosome component, shifted to the plasma membrane during ameloblast differentiation. In addition, Pkp1 knockdown disrupted the localization of Zona occludens 1 in tight junctions and inhibited ameloblast differentiation; the two proteins were shown to directly interact by immunoprecipitation. These results implicate the participation of PKP1 in early tooth morphogenesis as an effector of canonical Wnt signaling that controls ameloblast differentiation via regulation of the cell adhesion complex. PMID:27015268

Evolutionary patterns of bone histology and bone compactness in xenarthran mammal long bones.

PubMed

Straehl, Fiona R; Scheyer, Torsten M; Forasiepi, Analía M; MacPhee, Ross D; Sánchez-Villagra, Marcelo R

2013-01-01

Bone microstructure reflects physiological characteristics and has been shown to contain phylogenetic and ecological signals. Although mammalian long bone histology is receiving increasing attention, systematic examination of the main clades has not yet been performed. Here we describe the long bone microstructure of Xenarthra based on thin sections representing twenty-two species. Additionally, patterns in bone compactness of humeri and femora are investigated. The primary bone tissue of xenarthran long bones is composed of a mixture of woven, parallel-fibered and lamellar bone. The vascular canals have a longitudinal, reticular or radial orientation and are mostly arranged in an irregular manner. Concentric rows of vascular canals and laminar organization of the tissue are only found in anteater bones. The long bones of adult specimens are marked by dense Haversian bone, a feature that has been noted for most groups of mammals. In the long bones of armadillos, secondary osteons have an oblique orientation within the three-dimensional bone tissue, thus resulting in their irregular shape when the bones are sectioned transversely. Secondary remodeling is generally more extensive in large taxa than in small taxa, and this could be caused by increased loading. Lines of arrested growth are assumed to be present in all specimens, but they are restricted to the outermost layer in bones of armadillos and are often masked by secondary remodeling in large taxa. Parameters of bone compactness show a pattern in the femur that separates Cingulata and Pilosa (Folivora and Vermilingua), with cingulates having a lower compactness than pilosans. In addition, cingulates show an allometric relationship between humeral and femoral bone compactness.

Validation of Armadillo officinalis Dumèril, 1816 (Crustacea, Isopoda, Oniscidea) as a bioindicator: in vivo study of air benzene exposure.

PubMed

Agodi, A; Oliveri Conti, G; Barchitta, M; Quattrocchi, A; Lombardo, B M; Montesanto, G; Messina, G; Fiore, M; Ferrante, M

2015-04-01

This study tests the potential for using Armadillo officinalis as a bioindicator of exposure to and activation of benzene metabolic pathways using an in vivo model. A. officinalis specimens collected in a natural reserve were divided into a control and three test groups exposed to 2.00, 5.32 or 9.09 µg/m(3) benzene for 24h. Three independent tests were performed to assess model reproducibility. Animals were dissected to obtain three pooled tissue samples per group: hepatopancreas (HEP), other organs and tissues (OOT), and exoskeleton (EXO). Muconic acid (MA), S-phenylmercapturic acid (S-PMA), two human metabolites of benzene, and changes in mtDNA copy number, a human biomarker of benzene exposure, were determined in each sample; benzene was determined only in EXO. MA was measured by high-performance liquid chromatography (HPLC) with ultraviolet (UV) detection, S-PMA by triple quadrupole mass spectrometer liquid chromatography with electro spray ionization (LC-MS-ESI-TQD), mtDNA by real-time quantitative PCR and end-point PCR, and benzene by quadrupole mass spectrometer head-space gas chromatography (HSGC-MS). MA and S-PMA levels rose both in HEP and OOT; EXO exhibited increasing benzene concentrations; and mtDNA copy number rose in HEP but not in OOT samples. Overall, our findings demonstrate that A. officinalis is a sensitive bioindicator of air benzene exposure and show for the first time its ability to reproduce human metabolic dynamics. Copyright © 2015 Elsevier Inc. All rights reserved.

Brain tumor specifies intermediate progenitor cell identity by attenuating β-catenin/Armadillo activity

PubMed Central

Komori, Hideyuki; Xiao, Qi; McCartney, Brooke M.; Lee, Cheng-Yu

2014-01-01

During asymmetric stem cell division, both the daughter stem cell and the presumptive intermediate progenitor cell inherit cytoplasm from their parental stem cell. Thus, proper specification of intermediate progenitor cell identity requires an efficient mechanism to rapidly extinguish the activity of self-renewal factors, but the mechanisms remain unknown in most stem cell lineages. During asymmetric division of a type II neural stem cell (neuroblast) in the Drosophila larval brain, the Brain tumor (Brat) protein segregates unequally into the immature intermediate neural progenitor (INP), where it specifies INP identity by attenuating the function of the self-renewal factor Klumpfuss (Klu), but the mechanisms are not understood. Here, we report that Brat specifies INP identity through its N-terminal B-boxes via a novel mechanism that is independent of asymmetric protein segregation. Brat-mediated specification of INP identity is critically dependent on the function of the Wnt destruction complex, which attenuates the activity of β-catenin/Armadillo (Arm) in immature INPs. Aberrantly increasing Arm activity in immature INPs further exacerbates the defects in the specification of INP identity and enhances the supernumerary neuroblast mutant phenotype in brat mutant brains. By contrast, reducing Arm activity in immature INPs suppresses supernumerary neuroblast formation in brat mutant brains. Finally, reducing Arm activity also strongly suppresses supernumerary neuroblasts induced by overexpression of klu. Thus, the Brat-dependent mechanism extinguishes the function of the self-renewal factor Klu in the presumptive intermediate progenitor cell by attenuating Arm activity, balancing stem cell maintenance and progenitor cell specification. PMID:24257623

StaRProtein, A Web Server for Prediction of the Stability of Repeat Proteins

PubMed Central

Xu, Yongtao; Zhou, Xu; Huang, Meilan

2015-01-01

Repeat proteins have become increasingly important due to their capability to bind to almost any proteins and the potential as alternative therapy to monoclonal antibodies. In the past decade repeat proteins have been designed to mediate specific protein-protein interactions. The tetratricopeptide and ankyrin repeat proteins are two classes of helical repeat proteins that form different binding pockets to accommodate various partners. It is important to understand the factors that define folding and stability of repeat proteins in order to prioritize the most stable designed repeat proteins to further explore their potential binding affinities. Here we developed distance-dependant statistical potentials using two classes of alpha-helical repeat proteins, tetratricopeptide and ankyrin repeat proteins respectively, and evaluated their efficiency in predicting the stability of repeat proteins. We demonstrated that the repeat-specific statistical potentials based on these two classes of repeat proteins showed paramount accuracy compared with non-specific statistical potentials in: 1) discriminate correct vs. incorrect models 2) rank the stability of designed repeat proteins. In particular, the statistical scores correlate closely with the equilibrium unfolding free energies of repeat proteins and therefore would serve as a novel tool in quickly prioritizing the designed repeat proteins with high stability. StaRProtein web server was developed for predicting the stability of repeat proteins. PMID:25807112

Stability of hard plates on soft substrates and application to the design of bioinspired segmented armor

NASA Astrophysics Data System (ADS)

Martini, R.; Barthelat, F.

2016-07-01

Flexible natural armors from fish, alligators or armadillo are attracting an increasing amount of attention from their unique and attractive combinations of hardness, flexibility and light weight. In particular, the extreme contrast of stiffness between hard plates and surrounding soft tissues give rise to unusual and attractive mechanisms, which now serve as model for the design of bio-inspired armors. Despite a growing interest in bio-inspired flexible protection, there is little guidelines as to the choice of materials, optimum thickness, size, shape and arrangement for the protective plates. In this work, we focus on a failure mode we recently observed on natural and bio-inspired scaled armors: the unstable tilting of individual scales subjected to off-centered point forces. We first present a series of experiments on this system, followed by a model based on contact mechanics and friction. We condense the result into a single stability diagram which capture the key parameters that govern the onset of plate tilting from a localized force. We found that the stability of individual plates is governed by the location of the point force on the plate, by the friction at the surface of the plate, by the size of the plate and by the stiffness of the substrate. We finally discuss how some of these parameters can be optimized at the design stage to produce bio-inspired protective systems with desired combination of surface hardness, stability and flexural compliance.

Androgen-induced alterations in endometrial proteins crucial in recurrent miscarriages.

PubMed

Rahman, Tanzil Ur; Ullah, Kamran; Guo, Meng-Xi; Pan, Hai-Tao; Liu, Juan; Ren, Jun; Jin, Lu-Yang; Zhou, Yu-Zhong; Cheng, Yi; Sheng, Jian-Zhong; Huang, He-Feng

2018-05-15

High androgen level impairs endometrial receptivity in women experiences the recurrent miscarriage. The mechanism of androgen actions on endometrium is still uncertain. We hypothesized that androgen has a direct effect on the endometrium in women with recurrent miscarriage. In the present study, we assess the impact of androgen (A 2 ) at high concentration (10 -7 M) on Ishikawa cells compared with the physiological concentration of androgen (10 -9 M). To go into deeper analysis, we use global stable isotopes labeled profiling tactic using iTRAQ reagents, followed by 2D LC-MS/MS. We determine 175 non-redundant proteins, and 18 of these were quantified. The analysis of differentially expressed proteins (DEPs) identified 8 up-regulated proteins and 10 down-regulated in the high androgen group. These DEPs were examined by ingenuity pathway (IPA) analysis and established that these proteins might play vital roles in recurrent miscarriage and endometrium receptivity. In addition, proteins cyclin-dependent kinase inhibitor 2a (CDKN2a), endothelial protein C receptor (EPCR), armadillo repeat for velocardiofacial (ARVCF) were independently confirmed using western blot. Knockdown of CDKN2a significantly decreased the expression level of CDKN2a protein in ishikawa cells, and decreased migration ( p < 0.01), invasion ( p < 0.05), proliferation ( p < 0.05), and the rate of Jar spheroid attachment ( p < 0.05) to Ishikawa cell monolayer. The present results suggest that androgen at high concentration could alter the expression levels of proteins related to endometrium development and embryo implantation, which might be a cause of the impaired endometrial receptivity and miscarriage.

Clinicopathological correlates of adrenal Cushing's syndrome.

PubMed

Duan, Kai; Hernandez, Karen Gomez; Mete, Ozgur

2015-06-01

Endogenous Cushing's syndrome is a rare endocrine disorder that incurs significant cardiovascular morbidity and mortality, due to glucocorticoid excess. It comprises adrenal (20%) and non-adrenal (80%) aetiologies. While the majority of cases are attributed to pituitary or ectopic corticotropin (ACTH) overproduction, primary cortisol-producing adrenal cortical lesions are increasingly recognised in the pathophysiology of Cushing's syndrome. Our understanding of this disease has progressed substantially over the past decade. Recently, important mechanisms underlying the pathogenesis of adrenal hypercortisolism have been elucidated with the discovery of mutations in cyclic AMP signalling (PRKACA, PRKAR1A, GNAS, PDE11A, PDE8B), armadillo repeat containing 5 gene (ARMC5) a putative tumour suppressor gene, aberrant G-protein-coupled receptors, and intra-adrenal secretion of ACTH. Accurate subtyping of Cushing's syndrome is crucial for treatment decision-making and requires a complete integration of clinical, biochemical, imaging and pathology findings. Pathological correlates in the adrenal glands include hyperplasia, adenoma and carcinoma. While the most common presentation is diffuse adrenocortical hyperplasia secondary to excess ACTH production, this entity is usually treated with pituitary or ectopic tumour resection. Therefore, when confronted with adrenalectomy specimens in the setting of Cushing's syndrome, surgical pathologists are most commonly exposed to adrenocortical adenomas, carcinomas and primary macronodular or micronodular hyperplasia. This review provides an update on the rapidly evolving knowledge of adrenal Cushing's syndrome and discusses the clinicopathological correlations of this important disease. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Clinicopathological correlates of adrenal Cushing's syndrome.

PubMed

Duan, Kai; Gomez Hernandez, Karen; Mete, Ozgur

2015-03-01

Endogenous Cushing's syndrome is a rare endocrine disorder that incurs significant cardiovascular morbidity and mortality, due to glucocorticoid excess. It comprises adrenal (20%) and non-adrenal (80%) aetiologies. While the majority of cases are attributed to pituitary or ectopic corticotropin (ACTH) overproduction, primary cortisol-producing adrenal cortical lesions are increasingly recognised in the pathophysiology of Cushing's syndrome. Our understanding of this disease has progressed substantially over the past decade. Recently, important mechanisms underlying the pathogenesis of adrenal hypercortisolism have been elucidated with the discovery of mutations in cyclic AMP signalling (PRKACA, PRKAR1A, GNAS, PDE11A, PDE8B), armadillo repeat containing 5 gene (ARMC5) a putative tumour suppressor gene, aberrant G-protein-coupled receptors, and intra-adrenal secretion of ACTH. Accurate subtyping of Cushing's syndrome is crucial for treatment decision-making and requires a complete integration of clinical, biochemical, imaging and pathology findings. Pathological correlates in the adrenal glands include hyperplasia, adenoma and carcinoma. While the most common presentation is diffuse adrenocortical hyperplasia secondary to excess ACTH production, this entity is usually treated with pituitary or ectopic tumour resection. Therefore, when confronted with adrenalectomy specimens in the setting of Cushing's syndrome, surgical pathologists are most commonly exposed to adrenocortical adenomas, carcinomas and primary macronodular or micronodular hyperplasia. This review provides an update on the rapidly evolving knowledge of adrenal Cushing's syndrome and discusses the clinicopathological correlations of this important disease. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

A recessive mutation in the DSP gene linked to cardiomyopathy, skin fragility and hair defects impairs the binding of desmoplakin to epidermal keratins and the muscle-specific intermediate filament desmin.

PubMed

Favre, B; Begré, N; Borradori, L

2018-06-07

Desmoplakin (DSP) is a cytolinker of the plakin family. It mediates the connection of intermediate filaments (IFs) to desmosomes, intercellular adhesion junctions. The carboxyl (C)-terminal tail of DSP binds to IFs, while its amino-terminal part interacts with the armadillo proteins plakophilins and plakoglobin that in turn associate with the desmosomal cadherin desmogleins and desmocollins 1 . This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Plakins: a family of versatile cytolinker proteins.

PubMed

Leung, Conrad L; Green, Kathleen J; Liem, Ronald K H

2002-01-01

By connecting cytoskeletal elements to each other and to junctional complexes, the plakin family of cytolinkers plays a crucial role in orchestrating cellular development and maintaining tissue integrity. Plakins are built from combinations of interacting domains that bind to microfilaments, microtubules, intermediate filaments, cell-adhesion molecules and members of the armadillo family. Plakins are involved in both inherited and autoimmune diseases that affect the skin, neuronal tissue, and cardiac and skeletal muscle. Here, we describe the members of the plakin family and their interaction partners, and give examples of the cellular defects that result from their dysfunction.

NASA and X PRIZE Announce Winners of Lunar Lander Challenge

NASA Image and Video Library

2009-11-05

NASA and the X PRIZE Foundation announced the winners of the Northrop Grumman Lunar Lander Challenge at an awards ceremony at the Rayburn House Office Building, Thursday, Nov. 5, 2009 in Washington, DC. From left to right, George Nield, Associate Administrator of Commercial Space Transportation, FAA; Charles Bolden, NASA Administrator; Doug Comstock, Director, Innovative Partnerships Program, NASA; David Masten, CEO, Masten Space Systems; Phil Eaton, VP, Operations, Armadillo Aerospace; U.S. Rep. Ralph Hall (R-TX); Peter Diamandis, Chairman and CEO, X PRIZE Foundation and Mitch Waldman, VP, Advanced Programs & Technology, Northrop Grumman. Photo Credit: (NASA/Carla Cioffi)

Cilia- and Flagella-Associated Protein 69 Regulates Olfactory Transduction Kinetics in Mice

PubMed Central

Dong, Frederick N.

2017-01-01

Animals detect odorous chemicals through specialized olfactory sensory neurons (OSNs) that transduce odorants into neural electrical signals. We identified a novel and evolutionarily conserved protein, cilia- and flagella-associated protein 69 (CFAP69), in mice that regulates olfactory transduction kinetics. In the olfactory epithelium, CFAP69 is enriched in OSN cilia, where olfactory transduction occurs. Bioinformatic analysis suggests that a large portion of CFAP69 can form Armadillo-type α-helical repeats, which may mediate protein–protein interactions. OSNs lacking CFAP69, remarkably, displayed faster kinetics in both the on and off phases of electrophysiological responses at both the neuronal ensemble level as observed by electroolfactogram and the single-cell level as observed by single-cell suction pipette recordings. In single-cell analysis, OSNs lacking CFAP69 showed faster response integration and were able to fire APs more faithfully to repeated odor stimuli. Furthermore, both male and female mutant mice that specifically lack CFAP69 in OSNs exhibited attenuated performance in a buried food pellet test when a background of the same odor to the food pellet was present even though they should have better temporal resolution of coding olfactory stimulation at the peripheral. Therefore, the role of CFAP69 in the olfactory system seems to be to allow the olfactory transduction machinery to work at a precisely regulated range of response kinetics for robust olfactory behavior. SIGNIFICANCE STATEMENT Sensory receptor cells are generally thought to evolve to respond to sensory cues as fast as they can. This idea is consistent with mutational analyses in various sensory systems, where mutations of sensory receptor cells often resulted in reduced response size and slowed response kinetics. Contrary to this idea, we have found that there is a kinetic “damper” present in the olfactory transduction cascade of the mouse that slows down the response kinetics and, by doing so, it reduces the peripheral temporal resolution in coding odor stimuli and allows for robust olfactory behavior. This study should trigger a rethinking of the significance of the intrinsic speed of sensory transduction and the pattern of the peripheral coding of sensory stimuli. PMID:28495971

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

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

Pauci- and Multibacillary Leprosy: Two Distinct, Genetically Neglected Diseases

PubMed Central

Gaschignard, Jean; Grant, Audrey Virginia; Thuc, Nguyen Van; Orlova, Marianna; Cobat, Aurélie; Huong, Nguyen Thu; Ba, Nguyen Ngoc; Thai, Vu Hong; Abel, Laurent; Schurr, Erwin; Alcaïs, Alexandre

2016-01-01

After sustained exposure to Mycobacterium leprae, only a subset of exposed individuals develops clinical leprosy. Moreover, leprosy patients show a wide spectrum of clinical manifestations that extend from the paucibacillary (PB) to the multibacillary (MB) form of the disease. This “polarization” of leprosy has long been a major focus of investigation for immunologists because of the different immune response in these two forms. But while leprosy per se has been shown to be under tight human genetic control, few epidemiological or genetic studies have focused on leprosy subtypes. Using PubMed, we collected available data in English on the epidemiology of leprosy polarization and the possible role of human genetics in its pathophysiology until September 2015. At the genetic level, we assembled a list of 28 genes from the literature that are associated with leprosy subtypes or implicated in the polarization process. Our bibliographical search revealed that improved study designs are needed to identify genes associated with leprosy polarization. Future investigations should not be restricted to a subanalysis of leprosy per se studies but should instead contrast MB to PB individuals. We show the latter approach to be the most powerful design for the identification of genetic polarization determinants. Finally, we bring to light the important resource represented by the nine-banded armadillo model, a unique animal model for leprosy. PMID:27219008

Evolutionary Patterns of Bone Histology and Bone Compactness in Xenarthran Mammal Long Bones

PubMed Central

Straehl, Fiona R.; Scheyer, Torsten M.; Forasiepi, Analía M.; MacPhee, Ross D.; Sánchez-Villagra, Marcelo R.

2013-01-01

Bone microstructure reflects physiological characteristics and has been shown to contain phylogenetic and ecological signals. Although mammalian long bone histology is receiving increasing attention, systematic examination of the main clades has not yet been performed. Here we describe the long bone microstructure of Xenarthra based on thin sections representing twenty-two species. Additionally, patterns in bone compactness of humeri and femora are investigated. The primary bone tissue of xenarthran long bones is composed of a mixture of woven, parallel-fibered and lamellar bone. The vascular canals have a longitudinal, reticular or radial orientation and are mostly arranged in an irregular manner. Concentric rows of vascular canals and laminar organization of the tissue are only found in anteater bones. The long bones of adult specimens are marked by dense Haversian bone, a feature that has been noted for most groups of mammals. In the long bones of armadillos, secondary osteons have an oblique orientation within the three-dimensional bone tissue, thus resulting in their irregular shape when the bones are sectioned transversely. Secondary remodeling is generally more extensive in large taxa than in small taxa, and this could be caused by increased loading. Lines of arrested growth are assumed to be present in all specimens, but they are restricted to the outermost layer in bones of armadillos and are often masked by secondary remodeling in large taxa. Parameters of bone compactness show a pattern in the femur that separates Cingulata and Pilosa (Folivora and Vermilingua), with cingulates having a lower compactness than pilosans. In addition, cingulates show an allometric relationship between humeral and femoral bone compactness. PMID:23874932

Radiocarbon dating of extinct fauna in the Americas recovered from tar pits

NASA Astrophysics Data System (ADS)

Jull, A. J. T.; Iturralde-Vinent, M.; O'Malley, J. M.; MacPhee, R. D. E.; McDonald, H. G.; Martin, P. S.; Moody, J.; Rincón, A.

2004-08-01

We have obtained radiocarbon dates by accelerator mass spectrometry on bones of extinct large mammals from tar pits. Results on some samples of Glyptodon and Holmesina (extinct large mammals similar to armadillos) yielded ages of >25 and >21 ka, respectively. We also studied the radiocarbon ages of three different samples of bones from the extinct Cuban ground sloth, Parocnus bownii, which yielded dates ranging from 4960 ± 280 to 11 880 ± 420 yr BP. In order to remove the tar component pretreat the samples sufficiently to obtain reliable dates, we cleaned the samples by Soxhlet extraction in benzene. Resulting samples of collagenous material were often small.

Study of repeater technology for advanced multifunctional communications satellites

NASA Technical Reports Server (NTRS)

1972-01-01

Investigations are presented concerning design concepts and implementation approaches for the satellite communication repeater subsystems of advanced multifunctional satellites. In such systems the important concepts are the use of multiple antenna beams, repeater switching (routing), and efficient spectrum utilization through frequency reuse. An information base on these techniques was developed and tradeoff analyses were made of repeater design concepts, with the work design taken in a broad sense to include modulation beam coverage patterns. There were five major areas of study: requirements analysis and processing; study of interbeam interference in multibeam systems; characterization of multiple-beam switching repeaters; estimation of repeater weight and power for a number of alternatives; and tradeoff analyses based on these weight and power data.

Isolation and characterization of a J domain protein that interacts with ARC1 from ornamental kale (Brassica oleracea var. acephala).

PubMed

Lan, Xingguo; Yang, Jia; Cao, Mingming; Wang, Yanhong; Kawabata, Saneyuki; Li, Yuhua

2015-05-01

A novel J domain protein, JDP1, was isolated from ornamental kale. The C-terminus of JDP1 specifically interacted with ARC1, which has a conserved role in self-incompatibility signaling. Armadillo (ARM)-repeat containing 1 (ARC1) plays a conserved role in self-incompatibility signaling across the Brassicaceae and functions downstream of the S-locus receptor kinase. Here, we identified a J domain protein 1 (JDP1) that interacts with ARC1 using a yeast two-hybrid screen against a stigma cDNA library from ornamental kale (Brassica oleracea var. acephala). JDP1, a 38.4-kDa protein with 344 amino acids, is a member of the Hsp40 family. Fragment JDP1(57-344), originally isolated from a yeast two-hybrid cDNA library, interacted specifically with ARC1 in yeast two-hybrid assays. The N-terminus of JDP1 (JDP1(1-68)) contains a J domain, and the C-terminus of JDP1 (JDP1(69-344)) contains an X domain of unknown function. However, JDP1(69-344) was required and sufficient for interaction with ARC1 in yeast two-hybrid assays and in vitro binding assays. Moreover, JDP1(69-344) regulated the trafficking of ARC1 from the cytoplasm to the plasma membrane by interacting with ARC1 in Arabidopsis mesophyll protoplasts. Finally, Tyr(8) in the JDP1 N-terminal region was identified to be the specific site for regulating the interaction between JDP1 and BoARC1 in yeast two-hybrid assays. Possible roles of JDP1 as an interactor with ARC1 in Brassica are discussed.

Isolation of Mycobacterium avium subsp. paratuberculosis from Free-Ranging Birds and Mammals on Livestock Premises

PubMed Central

Corn, Joseph L.; Manning, Elizabeth J. B.; Sreevatsan, Srinand; Fischer, John R.

2005-01-01

Surveys for Mycobacterium avium subsp. paratuberculosis infection in free-ranging mammals and birds were conducted on nine dairy and beef cattle farms in Wisconsin and Georgia. Specimens were collected from 774 animals representing 25 mammalian and 22 avian species. Specimens of ileum, liver, intestinal lymph nodes, and feces were harvested from the larger mammals; a liver specimen and the gastrointestinal tract were harvested from birds and small mammals. Cultures were performed by using radiometric culture and acid-fast isolates were identified by 16S/IS900/IS1311 PCR and mycobactin dependency characteristics. M. avium subsp. paratuberculosis was cultured from tissues and feces from 39 samples from 30 animals representing nine mammalian and three avian species. The prevalence of infected wild animals by premises ranged from 2.7 to 8.3% in Wisconsin and from 0 to 6.0% in Georgia. Shedding was documented in seven (0.9%) animals: three raccoons, two armadillos, one opossum, and one feral cat. The use of two highly polymorphic short sequence repeat loci for analysis of 29 of the 39 strains identified 10 alleles. One allelic pattern broadly shared in domestic ruminants (“7,5”) appeared in approximately one-third of the wildlife M. avium subsp. paratuberculosis isolates studied. Given the few cases of shedding by free-ranging animals compared to the volume of contaminated manure produced by infected domestic ruminant livestock, contamination of the farm environment by infected wildlife was negligible. Wildlife may, however, have epidemiological significance for farms where M. avium subsp. paratuberculosis recently has been eliminated or on farms free of M. avium subsp. paratuberculosis but located in the geographic vicinity of farms with infected livestock. PMID:16269731

Structural basis for the regulation of nuclear import of Epstein-Barr virus nuclear antigen 1 (EBNA1) by phosphorylation of the nuclear localization signal

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

Nakada, Ryohei; Hirano, Hidemi; Structural Biology Research Center, Graduate School of Science, Nagoya University

Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is expressed in every EBV-positive tumor and is essential for the maintenance, replication, and transcription of the EBV genome in the nucleus of host cells. EBNA1 is a serine phosphoprotein, and it has been shown that phosphorylation of S385 in the nuclear localization signal (NLS) of EBNA1 increases the binding affinity to the nuclear import adaptor importin-α1 as well as importin-α5, and stimulates nuclear import of EBNA1. To gain insights into how phosphorylation of the EBNA1 NLS regulates nuclear import, we have determined the crystal structures of two peptide complexes of importin-α1: onemore » with S385-phosphorylated EBNA1 NLS peptide, determined at 2.0 Å resolution, and one with non-phosphorylated EBNA1 NLS peptide, determined at 2.2 Å resolution. The structures show that EBNA1 NLS binds to the major and minor NLS-binding sites of importin-α1, and indicate that the binding affinity of the EBNA1 NLS to the minor NLS-binding site could be enhanced by phosphorylation of S385 through electrostatic interaction between the phosphate group of phospho-S385 and K392 of importin-α1 (corresponding to R395 of importin-α5) on armadillo repeat 8. - Highlights: • Nuclear import of EBNA1 can be regulated by phosphorylation of NLS. • Crystal structures of importin-α1 bound to the NLS peptides of EBNA1 are solved. • Structures provide insights into how phosphorylation can regulate nuclear import.« less

Neural System Antigens Are Recognized by Autoantibodies from Patients Affected by a New Variant of Endemic Pemphigus Foliaceus in Colombia

PubMed Central

Howard, Michael S.; Yi, Hong; Gao, Weiqing; Hashimoto, Takashi; Grossniklaus, Hans E.

2015-01-01

Background Endemic pemphigus foliaceus (EPF), is also known as “fogo selvagem” or “wild fire,” reflecting the intense burning sensation of the skin reported by patients with this disease. Based on this finding, we tested for neural autoreactivity in patients affected by a new variant of EPF (El Bagre-EPF). Methods We tested 20 El Bagre-EPF patients, 20 normal controls from the endemic area, and 20 age- and sex-matched normal controls from outside the endemic area. We tested for autoreactivity to several immunoglobulins and complement. Both human skin and bovine tail were used as antigens. Results We detected autoreactivity to neural structures, mechanoreceptors, nerves, perineural cell layers of the arachnoid envelope around the optic nerve, brain structures, and to neuromuscular spindles; these structures colocalized with several neural markers. The patient antibodies also colocalized with desmoplakins 1 and 2, with the armadillo repeat protein deleted in velo-cardio-facial syndrome and with p0071 antibodies. Autoreactivity was also found associated with neurovascular bundles innervating the skin, and immunoelectron microscopy using protein A gold against patient antibodies was positive against the nerve axons. Paucicellularity of the intraepidermal nerve endings and defragmentation of the neural plexus were seen in 70% of the cases and not in the controls from the endemic area (p<0.005). Neuropsychological and/or behavioral symptoms were detected in individuals from the endemic area, including sensorimotor axonal neuropathy. Conclusions Our findings may explain for the first time the “pose of pemphigus,” representing a dorsiflexural posture seen in EPF patients vis-a-vis the weakness of the extensor nerves, and furthermore, the autoreactivity to nerves in EPF could explain the “burning sensation” encountered in EPF disease. PMID:21210298

Neural system antigens are recognized by autoantibodies from patients affected by a new variant of endemic pemphigus foliaceus in Colombia.

PubMed

Abreu-Velez, Ana Maria; Howard, Michael S; Yi, Hong; Gao, Weiqing; Hashimoto, Takashi; Grossniklaus, Hans E

2011-06-01

Endemic pemphigus foliaceus (EPF), is also known as "fogo selvagem" or "wild fire," reflecting the intense burning sensation of the skin reported by patients with this disease. Based on this finding, we tested for neural autoreactivity in patients affected by a new variant of EPF (El Bagre-EPF). We tested 20 El Bagre-EPF patients, 20 normal controls from the endemic area, and 20 age- and sex-matched normal controls from outside the endemic area. We tested for autoreactivity to several immunoglobulins and complement. Both human skin and bovine tail were used as antigens. We detected autoreactivity to neural structures, mechanoreceptors, nerves, perineural cell layers of the arachnoid envelope around the optic nerve, brain structures, and to neuromuscular spindles; these structures colocalized with several neural markers. The patient antibodies also colocalized with desmoplakins 1 and 2, with the armadillo repeat protein deleted in velo-cardio-facial syndrome and with p0071 antibodies. Autoreactivity was also found associated with neurovascular bundles innervating the skin, and immunoelectron microscopy using protein A gold against patient antibodies was positive against the nerve axons. Paucicellularity of the intraepidermal nerve endings and defragmentation of the neural plexus were seen in 70% of the cases and not in the controls from the endemic area (p<0.005). Neuropsychological and/or behavioral symptoms were detected in individuals from the endemic area, including sensorimotor axonal neuropathy. Our findings may explain for the first time the "pose of pemphigus," representing a dorsiflexural posture seen in EPF patients vis-a-vis the weakness of the extensor nerves, and furthermore, the autoreactivity to nerves in EPF could explain the "burning sensation" encountered in EPF disease.

Cardiac rhythm and pacemaking abnormalities in patients affected by endemic pemphigus in Colombia may be the result of deposition of autoantibodies, complement, fibrinogen, and other molecules.

PubMed

Abreu Velez, Ana Maria; Howard, Michael S; Velazquez-Velez, Jorge Enrique

2018-05-01

We previously showed that one-third of patients affected by endemic pemphigus foliaceus in El Bagre, Colombia (El Bagre-EPF), display autoreactivity to the heart. The purpose of this study was to investigate rhythm disturbances with the presence of autoantibodies and correlate them with ECG changes in these patients. We performed a study comparing 30 patients and 30 controls from the endemic area, matched by demographics, including age, sex, weight, work activities, and comorbidities. ECG as well as direct and indirect immunofluorescence, immunohistochemistry, and confocal microscopic studies focusing on cardiac node abnormalities were performed. Autopsies of 7 patients also were reviewed. The main ECG abnormalities seen in the El Bagre-EPF patients were sinus bradycardia (in one-half), followed by left bundle branch block, left posterior fascicular block, and left anterior fascicular block compared with the controls. One-third of the patients displayed polyclonal autoantibodies against the sinoatrial and/or AV nodes and the His bundle correlating with rhythm anomalies and delays in the cardiac conduction system (P <.01). The patient antibodies colocalized with commercial antibodies to desmoplakins I and II, p0071, armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF), and myocardium-enriched zonula occludens-1-associated protein (MYZAP; Progen Biotechnik) (P <.01). One-third of the patients affected by El Bagre-EPF have rhythm abnormalities that slow the conduction of impulses in cardiac nodes and the cardiac conduction system. These abnormalities likely occur as a result of deposition of autoantibodies, complement, and other inflammatory molecules. We show for the first time that MYZAP is present in cardiac nodes. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

A class I ADP-ribosylation factor GTPase-activating protein is critical for maintaining directional root hair growth in Arabidopsis.

PubMed

Yoo, Cheol-Min; Wen, Jiangqi; Motes, Christy M; Sparks, J Alan; Blancaflor, Elison B

2008-08-01

Membrane trafficking and cytoskeletal dynamics are important cellular processes that drive tip growth in root hairs. These processes interact with a multitude of signaling pathways that allow for the efficient transfer of information to specify the direction in which tip growth occurs. Here, we show that AGD1, a class I ADP ribosylation factor GTPase-activating protein, is important for maintaining straight growth in Arabidopsis (Arabidopsis thaliana) root hairs, since mutations in the AGD1 gene resulted in wavy root hair growth. Live cell imaging of growing agd1 root hairs revealed bundles of endoplasmic microtubules and actin filaments extending into the extreme tip. The wavy phenotype and pattern of cytoskeletal distribution in root hairs of agd1 partially resembled that of mutants in an armadillo repeat-containing kinesin (ARK1). Root hairs of double agd1 ark1 mutants were more severely deformed compared with single mutants. Organelle trafficking as revealed by a fluorescent Golgi marker was slightly inhibited, and Golgi stacks frequently protruded into the extreme root hair apex of agd1 mutants. Transient expression of green fluorescent protein-AGD1 in tobacco (Nicotiana tabacum) epidermal cells labeled punctate bodies that partially colocalized with the endocytic marker FM4-64, while ARK1-yellow fluorescent protein associated with microtubules. Brefeldin A rescued the phenotype of agd1, indicating that the altered activity of an AGD1-dependent ADP ribosylation factor contributes to the defective growth, organelle trafficking, and cytoskeletal organization of agd1 root hairs. We propose that AGD1, a regulator of membrane trafficking, and ARK1, a microtubule motor, are components of converging signaling pathways that affect cytoskeletal organization to specify growth orientation in Arabidopsis root hairs.

A Class I ADP-Ribosylation Factor GTPase-Activating Protein Is Critical for Maintaining Directional Root Hair Growth in Arabidopsis1[W][OA

PubMed Central

Yoo, Cheol-Min; Wen, Jiangqi; Motes, Christy M.; Sparks, J. Alan; Blancaflor, Elison B.

2008-01-01

Membrane trafficking and cytoskeletal dynamics are important cellular processes that drive tip growth in root hairs. These processes interact with a multitude of signaling pathways that allow for the efficient transfer of information to specify the direction in which tip growth occurs. Here, we show that AGD1, a class I ADP ribosylation factor GTPase-activating protein, is important for maintaining straight growth in Arabidopsis (Arabidopsis thaliana) root hairs, since mutations in the AGD1 gene resulted in wavy root hair growth. Live cell imaging of growing agd1 root hairs revealed bundles of endoplasmic microtubules and actin filaments extending into the extreme tip. The wavy phenotype and pattern of cytoskeletal distribution in root hairs of agd1 partially resembled that of mutants in an armadillo repeat-containing kinesin (ARK1). Root hairs of double agd1 ark1 mutants were more severely deformed compared with single mutants. Organelle trafficking as revealed by a fluorescent Golgi marker was slightly inhibited, and Golgi stacks frequently protruded into the extreme root hair apex of agd1 mutants. Transient expression of green fluorescent protein-AGD1 in tobacco (Nicotiana tabacum) epidermal cells labeled punctate bodies that partially colocalized with the endocytic marker FM4-64, while ARK1-yellow fluorescent protein associated with microtubules. Brefeldin A rescued the phenotype of agd1, indicating that the altered activity of an AGD1-dependent ADP ribosylation factor contributes to the defective growth, organelle trafficking, and cytoskeletal organization of agd1 root hairs. We propose that AGD1, a regulator of membrane trafficking, and ARK1, a microtubule motor, are components of converging signaling pathways that affect cytoskeletal organization to specify growth orientation in Arabidopsis root hairs. PMID:18539780

Ligand binding by repeat proteins: natural and designed

PubMed Central

Grove, Tijana Z; Cortajarena, Aitziber L; Regan, Lynne

2012-01-01

Repeat proteins contain tandem arrays of small structural motifs. As a consequence of this architecture, they adopt non-globular, extended structures that present large, highly specific surfaces for ligand binding. Here we discuss recent advances toward understanding the functional role of this unique modular architecture. We showcase specific examples of natural repeat proteins interacting with diverse ligands and also present examples of designed repeat protein–ligand interactions. PMID:18602006

Dasypodidae Borner, 1919 (Insecta, Hymenoptera): Proposed emendation of spelling to Dasypodaidae, so removing the homonymy with Dasypodidae Gray, 1821 (Mammalia, Xenarthra)

USGS Publications Warehouse

Alexander, B.A.; Michener, C.D.; Gardner, A.L.

1998-01-01

The family-group name DASYPODIDAE Borner, 1919 (Insecta, Hymenoptera) is a junior homonym Of DASYPODIDAE Gray, 1821 (Mammalia, Xenarthra). It is proposed that the homonymy between the two names, which relate to short-tongued bees and armadillos respectively, should be removed by emending the stem of the generic name Dasypoda Latreille, 1802, on which the insect familygroup name is based, to give DASYPODAIDAE, while leaving the mammalian name (based on Dasypus Linnaeus, 1758) unchanged. Dasypus novemcinctus Linnaeus, 1758, the type species of Dasypus, has a wide distribution in the southern United States, Central and South America. The genus Dasypoda ranges throughout most of the Palearctic region.

Mechanisms of pulmonary cyst pathogenesis in Birt-Hogg-Dube syndrome: The stretch hypothesis.

PubMed

Kennedy, John C; Khabibullin, Damir; Henske, Elizabeth P

2016-04-01

Loss-of-function mutations in the folliculin gene (FLCN) on chromosome 17p cause Birt-Hogg-Dube syndrome (BHD), which is associated with cystic lung disease. The risk of lung collapse (pneumothorax) in BHD patients is 50-fold higher than in the general population. The cystic lung disease in BHD is distinctive because the cysts tend to be basilar, subpleural and lentiform, differentiating BHD from most other cystic lung diseases. Recently, major advances in elucidating the primary functions of the folliculin protein have been made, including roles in mTOR and AMPK signaling via the interaction of FLCN with FNIP1/2, and cell-cell adhesion via the physical interaction of FLCN with plakophilin 4 (PKP4), an armadillo-repeat containing protein that interacts with E-cadherin and is a component of the adherens junctions. In addition, in just the last three years, the pulmonary impact of FLCN deficiency has been examined for the first time. In mouse models, evidence has emerged that AMPK signaling and cell-cell adhesion are involved in alveolar enlargement. In addition, the pathologic features of human BHD cysts have been recently comprehensively characterized. The "stretch hypothesis" proposes that cysts in BHD arise because of fundamental defects in cell-cell adhesion, leading to repeated respiration-induced physical stretch-induced stress and, over time, expansion of alveolar spaces particularly in regions of the lung with larger changes in alveolar volume and at weaker "anchor points" to the pleura. This hypothesis ties together many of the new data from cellular and mouse models of BHD and from the human pathologic studies. Critical questions remain. These include whether the consequences of stretch-induced cyst formation arise through a destructive/inflammatory program or a proliferative program (or both), whether cyst initiation involves a "second hit" genetic event inactivating the remaining wild-type copy of FLCN (as is known to occur in BHD-associated renal cell carcinomas), and whether cyst initiation involves exclusively the epithelial compartment versus an interaction between the epithelium and mesenchyme. Ultimately, understanding the mechanisms of cystic lung disease in BHD may help to elucidate the pathogenesis of primary spontaneous pneumothorax, with more than 20,000 cases reported annually in the United States alone. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dicotyledon Weed Quantification Algorithm for Selective Herbicide Application in Maize Crops.

PubMed

Laursen, Morten Stigaard; Jørgensen, Rasmus Nyholm; Midtiby, Henrik Skov; Jensen, Kjeld; Christiansen, Martin Peter; Giselsson, Thomas Mosgaard; Mortensen, Anders Krogh; Jensen, Peter Kryger

2016-11-04

The stricter legislation within the European Union for the regulation of herbicides that are prone to leaching causes a greater economic burden on the agricultural industry through taxation. Owing to the increased economic burden, research in reducing herbicide usage has been prompted. High-resolution images from digital cameras support the studying of plant characteristics. These images can also be utilized to analyze shape and texture characteristics for weed identification. Instead of detecting weed patches, weed density can be estimated at a sub-patch level, through which even the identification of a single plant is possible. The aim of this study is to adapt the monocot and dicot coverage ratio vision (MoDiCoVi) algorithm to estimate dicotyledon leaf cover, perform grid spraying in real time, and present initial results in terms of potential herbicide savings in maize. The authors designed and executed an automated, large-scale field trial supported by the Armadillo autonomous tool carrier robot. The field trial consisted of 299 maize plots. Half of the plots (parcels) were planned with additional seeded weeds; the other half were planned with naturally occurring weeds. The in-situ evaluation showed that, compared to conventional broadcast spraying, the proposed method can reduce herbicide usage by 65% without measurable loss in biological effect.

Modeling, construction and experimental validation of actuated rolling dynamics of the cylindrical Transforming Roving-Rolling Explorer (TRREx)

NASA Astrophysics Data System (ADS)

Edwin, L.; Mazzoleni, A.; Gemmer, T.; Ferguson, S.

2017-03-01

Planetary surface exploration technology over the past few years has seen significant advancements on multiple fronts. Robotic exploration platforms are becoming more sophisticated and capable of embarking on more challenging missions. More unconventional designs, particularly transforming architectures that have multiple modes of locomotion, are being studied. This work explores the capabilities of one such novel transforming rover called the Transforming Roving-Rolling Explorer (TRREx). Biologically inspired by the armadillo and the golden-wheel spider, the TRREx has two modes of locomotion: it can traverse on six wheels like a conventional rover on benign terrain, but can transform into a sphere when necessary to negotiate steep rugged slopes. The ability to self-propel in the spherical configuration, even in the absence of a negative gradient, increases the TRREx's versatility and its concept value. This paper describes construction and testing of a prototype cylindrical TRREx that demonstrates that "actuated rolling" can be achieved, and also presents a dynamic model of this prototype version of the TRREx that can be used to investigate the feasibility and value of such self-propelled locomotion. Finally, we present results that validate our dynamic model by comparing results from computer simulations made using the dynamic model to experimental results acquired from test runs using the prototype.

Dicotyledon Weed Quantification Algorithm for Selective Herbicide Application in Maize Crops

PubMed Central

Laursen, Morten Stigaard; Jørgensen, Rasmus Nyholm; Midtiby, Henrik Skov; Jensen, Kjeld; Christiansen, Martin Peter; Giselsson, Thomas Mosgaard; Mortensen, Anders Krogh; Jensen, Peter Kryger

2016-01-01

The stricter legislation within the European Union for the regulation of herbicides that are prone to leaching causes a greater economic burden on the agricultural industry through taxation. Owing to the increased economic burden, research in reducing herbicide usage has been prompted. High-resolution images from digital cameras support the studying of plant characteristics. These images can also be utilized to analyze shape and texture characteristics for weed identification. Instead of detecting weed patches, weed density can be estimated at a sub-patch level, through which even the identification of a single plant is possible. The aim of this study is to adapt the monocot and dicot coverage ratio vision (MoDiCoVi) algorithm to estimate dicotyledon leaf cover, perform grid spraying in real time, and present initial results in terms of potential herbicide savings in maize. The authors designed and executed an automated, large-scale field trial supported by the Armadillo autonomous tool carrier robot. The field trial consisted of 299 maize plots. Half of the plots (parcels) were planned with additional seeded weeds; the other half were planned with naturally occurring weeds. The in-situ evaluation showed that, compared to conventional broadcast spraying, the proposed method can reduce herbicide usage by 65% without measurable loss in biological effect. PMID:27827908

Mammalian genome projects reveal new growth hormone (GH) sequences. Characterization of the GH-encoding genes of armadillo (Dasypus novemcinctus), hedgehog (Erinaceus europaeus), bat (Myotis lucifugus), hyrax (Procavia capensis), shrew (Sorex araneus), ground squirrel (Spermophilus tridecemlineatus), elephant (Loxodonta africana), cat (Felis catus) and opossum (Monodelphis domestica).

PubMed

Wallis, Michael

2008-01-15

Mammalian growth hormone (GH) sequences have been shown previously to display episodic evolution: the sequence is generally strongly conserved but on at least two occasions during mammalian evolution (on lineages leading to higher primates and ruminants) bursts of rapid evolution occurred. However, the number of mammalian orders studied previously has been relatively limited, and the availability of sequence data via mammalian genome projects provides the potential for extending the range of GH gene sequences examined. Complete or nearly complete GH gene sequences for six mammalian species for which no data were previously available have been extracted from the genome databases-Dasypus novemcinctus (nine-banded armadillo), Erinaceus europaeus (western European hedgehog), Myotis lucifugus (little brown bat), Procavia capensis (cape rock hyrax), Sorex araneus (European shrew), Spermophilus tridecemlineatus (13-lined ground squirrel). In addition incomplete data for several other species have been extended. Examination of the data in detail and comparison with previously available sequences has allowed assessment of the reliability of deduced sequences. Several of the new sequences differ substantially from the consensus sequence previously determined for eutherian GHs, indicating greater variability than previously recognised, and confirming the episodic pattern of evolution. The episodic pattern is not seen for signal sequences, 5' upstream sequence or synonymous substitutions-it is specific to the mature protein sequence, suggesting that it relates to the hormonal function. The substitutions accumulated during the course of GH evolution have occurred mainly on the side of the hormone facing away from the receptor, in a non-random fashion, and it is suggested that this may reflect interaction of the receptor-bound hormone with other proteins or small ligands.

Trypanosoma cruzi IIc: Phylogenetic and Phylogeographic Insights from Sequence and Microsatellite Analysis and Potential Impact on Emergent Chagas Disease

PubMed Central

Llewellyn, Martin S.; Lewis, Michael D.; Acosta, Nidia; Yeo, Matthew; Carrasco, Hernan J.; Segovia, Maikell; Vargas, Jorge; Torrico, Faustino; Miles, Michael A.; Gaunt, Michael W.

2009-01-01

Trypanosoma cruzi, the etiological agent of Chagas disease, is highly genetically diverse. Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI, TcIIa, TcIIb, TcIIc, TcIId, and TcIIe. Molecular dating suggests that T. cruzi is likely to have been an endemic infection of neotropical mammalian fauna for many millions of years. Here we have applied a panel of 49 polymorphic microsatellite markers developed from the online T. cruzi genome to document genetic diversity among 53 isolates belonging to TcIIc, a lineage so far recorded almost exclusively in silvatic transmission cycles but increasingly a potential source of human infection. These data are complemented by parallel analysis of sequence variation in a fragment of the glucose-6-phosphate isomerase gene. New isolates confirm that TcIIc is associated with terrestrial transmission cycles and armadillo reservoir hosts, and demonstrate that TcIIc is far more widespread than previously thought, with a distribution at least from Western Venezuela to the Argentine Chaco. We show that TcIIc is truly a discrete T. cruzi lineage, that it could have an ancient origin and that diversity occurs within the terrestrial niche independently of the host species. We also show that spatial structure among TcIIc isolates from its principal host, the armadillo Dasypus novemcinctus, is greater than that among TcI from Didelphis spp. opossums and link this observation to differences in ecology of their respective niches. Homozygosity in TcIIc populations and some linkage indices indicate the possibility of recombination but cannot yet be effectively discriminated from a high genome-wide frequency of gene conversion. Finally, we suggest that the derived TcIIc population genetic data have a vital role in determining the origin of the epidemiologically important hybrid lineages TcIId and TcIIe. PMID:19721699

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

Comparing Dynamic Treatment Regimes Using Repeated-Measures Outcomes: Modeling Considerations in SMART Studies

PubMed Central

Lu, Xi; Nahum-Shani, Inbal; Kasari, Connie; Lynch, Kevin G.; Oslin, David W.; Pelham, William E.; Fabiano, Gregory; Almirall, Daniel

2016-01-01

A dynamic treatment regime (DTR) is a sequence of decision rules, each of which recommends a treatment based on a patient’s past and current health status. Sequential, multiple assignment, randomized trials (SMARTs) are multi-stage trial designs that yield data specifically for building effective DTRs. Modeling the marginal mean trajectories of a repeated-measures outcome arising from a SMART presents challenges, because traditional longitudinal models used for randomized clinical trials do not take into account the unique design features of SMART. We discuss modeling considerations for various forms of SMART designs, emphasizing the importance of considering the timing of repeated measures in relation to the treatment stages in a SMART. For illustration, we use data from three SMART case studies with increasing level of complexity, in autism, child attention deficit hyperactivity disorder (ADHD), and adult alcoholism. In all three SMARTs we illustrate how to accommodate the design features along with the timing of the repeated measures when comparing DTRs based on mean trajectories of the repeated-measures outcome. PMID:26638988

Comparing dynamic treatment regimes using repeated-measures outcomes: modeling considerations in SMART studies.

PubMed

Lu, Xi; Nahum-Shani, Inbal; Kasari, Connie; Lynch, Kevin G; Oslin, David W; Pelham, William E; Fabiano, Gregory; Almirall, Daniel

2016-05-10

A dynamic treatment regime (DTR) is a sequence of decision rules, each of which recommends a treatment based on a patient's past and current health status. Sequential, multiple assignment, randomized trials (SMARTs) are multi-stage trial designs that yield data specifically for building effective DTRs. Modeling the marginal mean trajectories of a repeated-measures outcome arising from a SMART presents challenges, because traditional longitudinal models used for randomized clinical trials do not take into account the unique design features of SMART. We discuss modeling considerations for various forms of SMART designs, emphasizing the importance of considering the timing of repeated measures in relation to the treatment stages in a SMART. For illustration, we use data from three SMART case studies with increasing level of complexity, in autism, child attention deficit hyperactivity disorder, and adult alcoholism. In all three SMARTs, we illustrate how to accommodate the design features along with the timing of the repeated measures when comparing DTRs based on mean trajectories of the repeated-measures outcome. Copyright © 2015 John Wiley & Sons, Ltd.

Omnibus Tests for Interactions in Repeated Measures Designs with Dichotomous Dependent Variables.

ERIC Educational Resources Information Center

Serlin, Ronald C.; Marascuilo, Leonard A.

When examining a repeated measures design with independent groups for a significant group by trial interaction, classical analysis of variance or multivariate procedures can be used if the assumptions underlying the tests are met. Neither procedure may be justified for designs with small sample sizes and dichotomous dependent variables. An omnibus…

Mission design concepts for repeat groundtrack orbits and application to the ICESat mission

NASA Astrophysics Data System (ADS)

Pie, Nadege

The primary objective of the NASA sponsored ICESat mission is to study the short and long term changes in the ice mass in the Greenland and Antarctica regions. The satellite was therefore placed into a frozen near-polar near-circular repeat groundtrack to ensure an adequate coverage of the polar regions while keeping the groundtrack periodic and reducing the variations in the orbital elements, and more specifically the semi-major axis of the ICESat orbit. After launch, a contingency plan had to be devised to compensate for a laser that dangerously compromised the lifetime of the ICESat mission. This new plan makes an intensive use of the ICESat subcycles, a characteristic of the repeat groundtrack orbits often over-looked. The subcycle of a repeat groundtrack orbit provide global coverage within a time shorter than the groundtrack repetition period. For a satellite with an off-nadir pointing capacity, the subcycles provide near-repeat tracks which represents added opportunity for altimetry measurement over a specific track. The ICESat subcycles were also used in a very innovative fashion to reposition the satellite within its repeat cycle via orbital maneuvers called phasing maneuver. The necessary theoretical framework is provided for the subcycle analysis and the implementation of phasing maneuvers for any future repeat orbit mission. In the perspective of performing cross-validation of missions like CryoSat using the ICESat off-nadir capacity, a study was conducted to determine the geolocations of crossovers between two different repeat groundtrack Keplerian orbits. The general analytical solution was applied to ICESat vs. several other repeat groundtrack orbit mission, including the future ICESat-II mission. ICESat's repeat groundtrack orbit was designed using a disturbing force model that includes only the Earth geopotential. Though the third body effect from the Sun and the Moon was neglected in the orbit design, it does in fact disrupt the repeatability condition of the groundtrack and consequently implies orbit correction maneuvers. The perturbations on ICESat orbit due to the third body effect are studied as a preliminary work towards including these forces in the design of the future ICESat-II repeat groundtrack orbit.

Improved variance estimation of classification performance via reduction of bias caused by small sample size.

PubMed

Wickenberg-Bolin, Ulrika; Göransson, Hanna; Fryknäs, Mårten; Gustafsson, Mats G; Isaksson, Anders

2006-03-13

Supervised learning for classification of cancer employs a set of design examples to learn how to discriminate between tumors. In practice it is crucial to confirm that the classifier is robust with good generalization performance to new examples, or at least that it performs better than random guessing. A suggested alternative is to obtain a confidence interval of the error rate using repeated design and test sets selected from available examples. However, it is known that even in the ideal situation of repeated designs and tests with completely novel samples in each cycle, a small test set size leads to a large bias in the estimate of the true variance between design sets. Therefore different methods for small sample performance estimation such as a recently proposed procedure called Repeated Random Sampling (RSS) is also expected to result in heavily biased estimates, which in turn translates into biased confidence intervals. Here we explore such biases and develop a refined algorithm called Repeated Independent Design and Test (RIDT). Our simulations reveal that repeated designs and tests based on resampling in a fixed bag of samples yield a biased variance estimate. We also demonstrate that it is possible to obtain an improved variance estimate by means of a procedure that explicitly models how this bias depends on the number of samples used for testing. For the special case of repeated designs and tests using new samples for each design and test, we present an exact analytical expression for how the expected value of the bias decreases with the size of the test set. We show that via modeling and subsequent reduction of the small sample bias, it is possible to obtain an improved estimate of the variance of classifier performance between design sets. However, the uncertainty of the variance estimate is large in the simulations performed indicating that the method in its present form cannot be directly applied to small data sets.

Status of a UAV SAR Designed for Repeat Pass Interferometry for Deformation Measurements

NASA Technical Reports Server (NTRS)

Hensley, Scott; Wheeler, Kevin; Hoffman, Jim; Miller, Tim; Lou, Yunling; Muellerschoen, Ron; Zebker, Howard; Madsen, Soren; Rosen, Paul

2004-01-01

Under the NASA ESTO sponsored Instrument Incubator Program we have designed a lightweight, reconfigurable polarimetric L-band SAR designed for repeat pass deformation measurements of rapidly deforming surfaces of geophysical interest such as volcanoes or earthquakes. This radar will be installed on an unmanned airborne vehicle (UAV) or a lightweight, high-altitude, and long endurance platform such as the Proteus. After a study of suitable available platforms we selected the Proteus for initial development and testing of the system. We want to control the repeat track capability of the aircraft to be within a 10 m tube to support the repeat deformation capability. We conducted tests with the Proteus using real-time GPS with sub-meter accuracy to see if pilots could fly the aircraft within the desired tube. Our results show that pilots are unable to fly the aircraft with the desired accuracy and therefore an augmented autopilot will be required to meet these objectives. Based on the Proteus flying altitude of 13.7 km (45,000 ft), we are designing a fully polarimetric L-band radar with 80 MHz bandwidth and 16 km range swath. This radar will have an active electronic beam steering antenna to achieve Doppler centroid stability that is necessary for repeat-pass interferometry (RPI). This paper will present are design criteria, current design and expected science applications.

Detection of Rickettsia bellii and Rickettsia amblyommii in Amblyomma longirostre (Acari: Ixodidae) from Bahia state, Northeast Brazil.

PubMed

McIntosh, Douglas; Bezerra, Rodrigo Alves; Luz, Hermes Ribeiro; Faccini, João Luiz Horacio; Gaiotto, Fernanda Amato; Giné, Gastón Andrés Fernandez; Albuquerque, George Rego

2015-01-01

Studies investigating rickettsial infections in ticks parasitizing wild animals in the Northeast region of Brazil have been confined to the detection of Rickettsia amblyommii in immature stages of Amblyomma longirostre collected from birds in the state of Bahia, and in immatures and females of Amblyomma auricularium collected from the striped hog-nosed skunk (Conepatus semistriatus) and armadillos (Euphractus sexcinctus) in the state of Pernambuco. The current study extends the distribution of R. amblyommii (strain Aranha), which was detected in A. longirostre collected from the thin-spined porcupine Chaetomys subspinosus and the hairy dwarf porcupine Coendou insidiosus. In addition, we report the first detection of Rickettsia bellii in adults of A. longirostre collected from C. insidiosus in the state of Bahia.

Genetic characterization of Toxoplasma gondii from Brazilian wildlife revealed abundant new genotypes.

PubMed

Vitaliano, S N; Soares, H S; Minervino, A H H; Santos, A L Q; Werther, K; Marvulo, M F V; Siqueira, D B; Pena, H F J; Soares, R M; Su, C; Gennari, S M

2014-12-01

This study aimed to isolate and genotype T. gondii from Brazilian wildlife. For this purpose, 226 samples were submitted to mice bioassay and screened by PCR based on 18S rRNA sequences. A total of 15 T. gondii isolates were obtained, including samples from four armadillos (three Dasypus novemcinctus, one Euphractus sexcinctus), three collared anteaters (Tamandua tetradactyla), three whited-lipped peccaries (Tayassu pecari), one spotted paca (Cuniculus paca), one oncilla (Leopardus tigrinus), one hoary fox (Pseudalopex vetulus), one lineated woodpecker (Dryocopus lineatus) and one maned wolf (Chrysocyon brachyurus). DNA from the isolates, originated from mice bioassay, and from the tissues of the wild animal, designated as "primary samples", were genotyped by PCR-restriction fragment length polymorphism (PCR/RFLP), using 12 genetic markers (SAG1, SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L258, PK1, CS3 and Apico). A total of 17 genotypes were identified, with 13 identified for the first time and four already reported in published literature. Results herein obtained corroborate previous studies in Brazil, confirming high diversity and revealing unique genotypes in this region. Given most of genotypes here identified are different from previous studies in domestic animals, future studies on T. gondii from wildlife is of interest to understand population genetics and structure of this parasite.

Genetic characterization of Toxoplasma gondii from Brazilian wildlife revealed abundant new genotypes

PubMed Central

Vitaliano, S.N.; Soares, H.S.; Minervino, A.H.H.; Santos, A.L.Q.; Werther, K.; Marvulo, M.F.V.; Siqueira, D.B.; Pena, H.F.J.; Soares, R.M.; Su, C.; Gennari, S.M.

2014-01-01

This study aimed to isolate and genotype T. gondii from Brazilian wildlife. For this purpose, 226 samples were submitted to mice bioassay and screened by PCR based on 18S rRNA sequences. A total of 15 T. gondii isolates were obtained, including samples from four armadillos (three Dasypus novemcinctus, one Euphractus sexcinctus), three collared anteaters (Tamandua tetradactyla), three whited-lipped peccaries (Tayassu pecari), one spotted paca (Cuniculus paca), one oncilla (Leopardus tigrinus), one hoary fox (Pseudalopex vetulus), one lineated woodpecker (Dryocopus lineatus) and one maned wolf (Chrysocyon brachyurus). DNA from the isolates, originated from mice bioassay, and from the tissues of the wild animal, designated as “primary samples”, were genotyped by PCR–restriction fragment length polymorphism (PCR/RFLP), using 12 genetic markers (SAG1, SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L258, PK1, CS3 and Apico). A total of 17 genotypes were identified, with 13 identified for the first time and four already reported in published literature. Results herein obtained corroborate previous studies in Brazil, confirming high diversity and revealing unique genotypes in this region. Given most of genotypes here identified are different from previous studies in domestic animals, future studies on T. gondii from wildlife is of interest to understand population genetics and structure of this parasite. PMID:25426424

Population Fisher information matrix and optimal design of discrete data responses in population pharmacodynamic experiments.

PubMed

Ogungbenro, Kayode; Aarons, Leon

2011-08-01

In the recent years, interest in the application of experimental design theory to population pharmacokinetic (PK) and pharmacodynamic (PD) experiments has increased. The aim is to improve the efficiency and the precision with which parameters are estimated during data analysis and sometimes to increase the power and reduce the sample size required for hypothesis testing. The population Fisher information matrix (PFIM) has been described for uniresponse and multiresponse population PK experiments for design evaluation and optimisation. Despite these developments and availability of tools for optimal design of population PK and PD experiments much of the effort has been focused on repeated continuous variable measurements with less work being done on repeated discrete type measurements. Discrete data arise mainly in PDs e.g. ordinal, nominal, dichotomous or count measurements. This paper implements expressions for the PFIM for repeated ordinal, dichotomous and count measurements based on analysis by a mixed-effects modelling technique. Three simulation studies were used to investigate the performance of the expressions. Example 1 is based on repeated dichotomous measurements, Example 2 is based on repeated count measurements and Example 3 is based on repeated ordinal measurements. Data simulated in MATLAB were analysed using NONMEM (Laplace method) and the glmmML package in R (Laplace and adaptive Gauss-Hermite quadrature methods). The results obtained for Examples 1 and 2 showed good agreement between the relative standard errors obtained using the PFIM and simulations. The results obtained for Example 3 showed the importance of sampling at the most informative time points. Implementation of these expressions will provide the opportunity for efficient design of population PD experiments that involve discrete type data through design evaluation and optimisation.

Patients with a new variant of endemic pemphigus foliaceus have autoantibodies against arrector pili muscle, colocalizing with MYZAP, p0071, desmoplakins 1 and 2 and ARVCF.

PubMed

Abreu-Velez, A M; Valencia-Yepes, C A; Upegui-Zapata, Y A; Upegui-Quiceno, E; Mesa-Herrera, N R; Velazquez-Velez, J E; Howard, M S

2017-12-01

We identified a new variant of endemic pemphigus foliaceus in El Bagre, Colombia, South America, which we term El Bagre-EPF, and observed reactivity to arrector pili muscle (APM), thus we tested for autoimmunity to APM. We took skin biopsies from 30 patients with El Bagre-EPF and 30 healthy controls (HCs) matched by age, sex and occupation, who were all from the endemic area, and tested these using direct immunofluorescence (DIF), confocal microscopy, immunohistochemistry and immunoblotting (IB). Of the 30 patients with El Bagre-EPF, 27 had autoantibodies to APM that colocalized with commercial antibodies to myocardium-enriched zonula occludens-1-associated protein (MYZAP), desmoplakin (DP)1 and DP2, plakophilin 4, and Armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF) (P < 0.001, Fisher exact test). The positive staining also colocalized with Junctional Adhesion Molecule 1 (JAM-A), a control antibody for gap cell junctions. No HC samples were positive. In 27 of the 30 patients, serum that was APM-positive also displayed IB colocalization of their autoantibody molecular weights with the Progen antibodies (P < 0.001, Fisher exact test). Patients affected by El Bagre-EPF have autoantibodies to APM, colocalizing with the antibodies MYZAP, ARVCF, p0071, DP1 and DP2, suggesting that these molecules are El Bagre-EPF antigens. Further, all of these antigens represent components of cell junctions, indicating that the immune response is directed, at least partially, against cell junctions. The immune response in patients affected by El Bagre-EPF is polyclonal, and it includes B and T lymphocytes, mast cells, IgG, IgA, IgM, IgD, IgE, fibrinogen, albumin, complement/C1q, C3c and C4. © 2017 British Association of Dermatologists.

Patients affected by a new variant of endemic pemphigus foliaceus have autoantibodies colocalizing with MYZAP, p0071, desmoplakins 1-2 and ARVCF, causing renal damage.

PubMed

Abreu-Velez, A M; Howard, M S; Yi, H; Florez-Vargas, A A

2018-05-16

We have previously reported that about 30% of patients affected by a new variant of endemic pemphigus foliaceus (EPF) in El Bagre, Colombia (termed El Bagre-EPF or pemphigus Abreu-Manu) have systemic compromise. In the current study, we focused on studying autoreactivity to the kidney and its pathological correlations. To investigate patients with El Bagre-EPF for renal compromise. We performed a case-control study, enrolling 57 patients with El Bagre-EPF and 57 controls from the endemic area, matched by age, sex, race, work activity, demographics and comorbidities. We took skin and renal biopsies; performed direct and indirect immunofluorescence, immunohistochemistry (IHC), confocal microscopy, immunoblotting, direct and indirect immune electron microscopy; and tested kidney function in all living patients. We also used IHC to study seven kidney autopsy samples. Of the 57 patients, 19 had autoantibodies to kidney, with polyclonal reactivity (P < 0.01). Most cases were positive along the basement membrane of the proximal tubules, but in some cases there was also positivity against the glomeruli and/or mixed patterns. Fifteen patients had increases in serum urea and creatinine compared with controls (P < 0.01). The autoantibodies colocalized with commercial antibodies to desmoplakins I and II, p0071, armadillo repeat gene deleted in velo-cardio-facial syndrome (ARCVF) and myocardium-enriched zonula occludens-1-associated protein (MYZAP) (P < 0.01). All of the kidney disease autopsies showed alterations, mostly in the vessels. We demonstrate for the first time that one-third of patients with El Bagre-EPF have polyclonal autoantibodies to kidney. The kidneys showed a mixed histological pattern resembling lupus nephritis, with a diffuse proliferative Class IV (G) global diffuse pattern in active lesions, and additional interposition of membranoproliferative glomerulonephritis. © 2018 British Association of Dermatologists.

Crystal structure of importin-α3 bound to the nuclear localization signal of Ran-binding protein 3.

PubMed

Koyama, Masako; Matsuura, Yoshiyuki

2017-09-23

Ran-binding protein 3 (RanBP3) is a primarily nuclear Ran-binding protein that functions as an accessory factor in the Ran GTPase system. RanBP3 associates with Ran-specific nucleotide exchange factor RCC1 and enhances its catalytic activity towards Ran. RanBP3 also promotes CRM1-mediated nuclear export as well as CRM1-independent nuclear export of β-catenin, Smad2, and Smad3. Nuclear import of RanBP3 is dependent on the nuclear import adaptor protein importin-α and, RanBP3 is imported more efficiently by importin-α3 than by other members of the importin-α family. Protein kinase signaling pathways control nucleocytoplasmic transport through phosphorylation of RanBP3 at Ser58, immediately C-terminal to the nuclear localization signal (NLS) in the N-terminal region of RanBP3. Here we report the crystal structure of human importin-α3 bound to an N-terminal fragment of human RanBP3 containing the NLS sequence that is necessary and sufficient for nuclear import. The structure reveals that RanBP3 binds to importin-α3 residues that are strictly conserved in all seven isoforms of human importin-α at the major NLS-binding site, indicating that the region of importin-α outside the NLS-binding site, possibly the autoinhibotory importin-β1-binding domain, may be the key determinant for the preferential binding of RanBP3 to importin-α3. Computational docking simulation indicates that phosphorylation of RanBP3 at Ser58 could potentially stabilize the association of RanBP3 with importin-α through interactions between the phosphate moiety of phospho-Ser58 of RanBP3 and a cluster of basic residues (Arg96 and Lys97 in importin-α3) on armadillo repeat 1 of importin-α. Copyright © 2017 Elsevier Inc. All rights reserved.

Design Science Research toward Designing/Prototyping a Repeatable Model for Testing Location Management (LM) Algorithms for Wireless Networking

ERIC Educational Resources Information Center

Peacock, Christopher

2012-01-01

The purpose of this research effort was to develop a model that provides repeatable Location Management (LM) testing using a network simulation tool, QualNet version 5.1 (2011). The model will provide current and future protocol developers a framework to simulate stable protocol environments for development. This study used the Design Science…

Power analysis for multivariate and repeated measures designs: a flexible approach using the SPSS MANOVA procedure.

PubMed

D'Amico, E J; Neilands, T B; Zambarano, R

2001-11-01

Although power analysis is an important component in the planning and implementation of research designs, it is often ignored. Computer programs for performing power analysis are available, but most have limitations, particularly for complex multivariate designs. An SPSS procedure is presented that can be used for calculating power for univariate, multivariate, and repeated measures models with and without time-varying and time-constant covariates. Three examples provide a framework for calculating power via this method: an ANCOVA, a MANOVA, and a repeated measures ANOVA with two or more groups. The benefits and limitations of this procedure are discussed.

35. ALTERNATE DESIGN USING THROUGH ARCH SPANS, WITH ARCH REPEATED ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

35. ALTERNATE DESIGN USING THROUGH ARCH SPANS, WITH ARCH REPEATED BETWEEN TOWER LEGS, AND ASHLAR MASONRY WALLS AND PYLONS Pen-and-ink drawing by project architect Alfred Eichler, 1934. - Sacramento River Bridge, Spanning Sacramento River at California State Highway 275, Sacramento, Sacramento County, CA

Diversity, Seasonality, and Context of Mammalian Roadkills in the Southern Great Plains

NASA Astrophysics Data System (ADS)

Smith-Patten, Brenda D.; Patten, Michael A.

2008-06-01

Thousands of mammals are killed annually from vehicle collisions, making the issue an important one for conservation biologists and environmental managers. We recorded all readily identifiable kills on or immediately adjacent to roads in the southern Great Plains from March 2004-March 2007. We also recorded distance traveled, whether a road was paved or divided, the number of lanes, and prevailing habitat. Surveys were opportunistic and were conducted by car during conditions of good visibility. Over our 239 surveys and >16,500 km traveled, we recorded 1412 roadkills from 18 different mammal species (size ranged from Sciurus squirrels to the white-tailed deer, Odocolieus virginianus). The overall kill rate was 8.50 / 100 km. Four species were prone to collisions: the Virginia opossum ( Didelphis virginiana), nine-banded armadillo ( Dasypus novemcinctus), striped skunk ( Mephitis mephitis), and northern raccoon ( Procyon lotor). Together they accounted for approximately 85% (1198) of all roadkills. Mortality rate differed significantly between 2- and 4-lane roads (8.39 versus 7.79 / 100 km). Kill rates were significantly higher on paved versus unpaved roads (8.60 versus 3.65 / 100 km), but did not depend on whether a road was divided. Roadkills were higher in spring than in fall (1.5×), winter (1.4×), or summer (1.3×). The spring peak (in kills / 100 km) was driven chiefly by the armadillo (2.76 in spring/summer versus 0.73 in autumn/winter) and opossum (2.65 versus 1.47). By contrast, seasonality was dampened by a late winter/early spring peak in skunk mortalities, for which 41% occurred in the 6-week period of mid-February through March. The raccoon did not exhibit a strong seasonal pattern. Our data are consistent with dispersal patterns of these species. Our results underscore the high rate of highway mortality in the southern plains, as well as differences in seasonality and road type that contribute to mortality. Conservation and management efforts should focus on creating underpasses or using other means to reduce roadkill rates.

Dynamic modeling and mobility analysis of the transforming roving-rolling explorer (TRREx) as it Traverses Rugged Martian Terrain

NASA Astrophysics Data System (ADS)

Edwin, Lionel E.; Mazzoleni, Andre P.

2016-03-01

All planetary surface exploration missions thus far have employed traditional rovers with a rocker-bogie suspension. These rovers can navigate moderately rough and flat terrain, but are not designed to traverse rugged terrain with steep slopes. The fact is, however, that the most scientifically interesting missions require exploration platforms with capabilities for navigating such types of rugged terrain. This issue motivates the development of new kinds of rovers that take advantage of the latest advances in robotic technologies to traverse rugged terrain efficiently. This work analyzes one such rover concept called the Transforming Roving-Rolling Explorer (TRREx) that is principally aimed at addressing the above issue. Biologically inspired by the way the armadillo curls up into a ball when threatened, and the way the golden wheel spider uses the dynamic advantages of a sphere to roll down hills when escaping danger, the TRREx rover can traverse like a traditional 6-wheeled rover over conventional terrain, but can also transform itself into a sphere, when necessary, to travel down steep inclines, or navigate rough terrain. This paper investigates the mobility of the TRREx when it is in its rolling mode, i.e. when it is a sphere and can steer itself through actuations that shift its center of mass to achieve the desired direction of roll. A mathematical model describing the dynamics of the rover in this spherical configuration is presented, and actuated rolling is demonstrated through computer simulation. Parametric analyzes that investigate the rover's mobility as a function of its design parameters are also presented. This work highlights the contribution of the spherical rolling mode to the enhanced mobility of the TRREx rover and how it could enable challenging surface exploration missions in the future.

Testing Multiple Outcomes in Repeated Measures Designs

ERIC Educational Resources Information Center

Lix, Lisa M.; Sajobi, Tolulope

2010-01-01

This study investigates procedures for controlling the familywise error rate (FWR) when testing hypotheses about multiple, correlated outcome variables in repeated measures (RM) designs. A content analysis of RM research articles published in 4 psychology journals revealed that 3 quarters of studies tested hypotheses about 2 or more outcome…

Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats.

PubMed

Urvoas, Agathe; Guellouz, Asma; Valerio-Lepiniec, Marie; Graille, Marc; Durand, Dominique; Desravines, Danielle C; van Tilbeurgh, Herman; Desmadril, Michel; Minard, Philippe

2010-11-26

Repeat proteins have a modular organization and a regular architecture that make them attractive models for design and directed evolution experiments. HEAT repeat proteins, although very common, have not been used as a scaffold for artificial proteins, probably because they are made of long and irregular repeats. Here, we present and validate a consensus sequence for artificial HEAT repeat proteins. The sequence was defined from the structure-based sequence analysis of a thermostable HEAT-like repeat protein. Appropriate sequences were identified for the N- and C-caps. A library of genes coding for artificial proteins based on this sequence design, named αRep, was assembled using new and versatile methodology based on circular amplification. Proteins picked randomly from this library are expressed as soluble proteins. The biophysical properties of proteins with different numbers of repeats and different combinations of side chains in hypervariable positions were characterized. Circular dichroism and differential scanning calorimetry experiments showed that all these proteins are folded cooperatively and are very stable (T(m) >70 °C). Stability of these proteins increases with the number of repeats. Detailed gel filtration and small-angle X-ray scattering studies showed that the purified proteins form either monomers or dimers. The X-ray structure of a stable dimeric variant structure was solved. The protein is folded with a highly regular topology and the repeat structure is organized, as expected, as pairs of alpha helices. In this protein variant, the dimerization interface results directly from the variable surface enriched in aromatic residues located in the randomized positions of the repeats. The dimer was crystallized both in an apo and in a PEG-bound form, revealing a very well defined binding crevice and some structure flexibility at the interface. This fortuitous binding site could later prove to be a useful binding site for other low molecular mass partners. Copyright © 2010 Elsevier Ltd. All rights reserved.

A designed repeat protein as an affinity capture reagent

PubMed Central

Speltz, Elizabeth B.; Brown, Rebecca S.H.; Hajare, Holly S.; Schlieker, Christian; Regan, Lynne

2017-01-01

Repeat proteins are an attractive target for protein engineering and design. We have focused our attention on the design and engineering of one particular class - tetratricopeptide repeat (TPR) proteins. In previous work we have shown that the structure and stability of TPR proteins can be manipulated in a rational fashion [Cortajarena 2011; Main 2003]. Building on those studies, we have designed and characterized a number of different peptide-binding TPR modules and we have also assembled these modules into supramolecular arrays [Cortajarena 2009; Cortajarena 2008; Jackrel 2009; Kajander 2007]. Here we focus on the development of one such TPR-peptide interaction for a practical application – affinity purification. We illustrate the general utility of our designed protein interaction. Furthermore, this example highlights how basic research on protein-peptide interactions can lead to the development of novel reagents with important practical applications. PMID:26517897

A Characterization of BIB Designs Based on v Treatments in Blocks of Size k Whose Number of Blocks is at Least vCk.

DTIC Science & Technology

1981-01-01

Discrete Math . 6, 189-200. Foody, W. and A. Hedayat, (1977). On theory and applications of BIB designs with repeated blocks. Ann. Statist. 5, i •, 932...945. Corrections: Ann. Statist. 7 (1979). 925. van Lint, J.I1. and H.J. Ryser (1972). Block designs with repeated blocks. Discrete Math ., 3, 381-396

On the repeated measures designs and sample sizes for randomized controlled trials.

PubMed

Tango, Toshiro

2016-04-01

For the analysis of longitudinal or repeated measures data, generalized linear mixed-effects models provide a flexible and powerful tool to deal with heterogeneity among subject response profiles. However, the typical statistical design adopted in usual randomized controlled trials is an analysis of covariance type analysis using a pre-defined pair of "pre-post" data, in which pre-(baseline) data are used as a covariate for adjustment together with other covariates. Then, the major design issue is to calculate the sample size or the number of subjects allocated to each treatment group. In this paper, we propose a new repeated measures design and sample size calculations combined with generalized linear mixed-effects models that depend not only on the number of subjects but on the number of repeated measures before and after randomization per subject used for the analysis. The main advantages of the proposed design combined with the generalized linear mixed-effects models are (1) it can easily handle missing data by applying the likelihood-based ignorable analyses under the missing at random assumption and (2) it may lead to a reduction in sample size, compared with the simple pre-post design. The proposed designs and the sample size calculations are illustrated with real data arising from randomized controlled trials. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Power of Models in Longitudinal Study: Findings from a Full-Crossed Simulation Design

ERIC Educational Resources Information Center

Fang, Hua; Brooks, Gordon P.; Rizzo, Maria L.; Espy, Kimberly Andrews; Barcikowski, Robert S.

2009-01-01

Because the power properties of traditional repeated measures and hierarchical multivariate linear models have not been clearly determined in the balanced design for longitudinal studies in the literature, the authors present a power comparison study of traditional repeated measures and hierarchical multivariate linear models under 3…

Workforce Diversity: Monitoring Employment Trends in Public Organizations.

ERIC Educational Resources Information Center

Guajardo, Salomon A.

1999-01-01

Presents the use of research designs that can be used by human resource specialists to evaluate and monitor work force diversity and minority employment. Compares results of Repeated Measure Analyses of Variance with One Within-subjects Factor design with Repeated Measure Analyses of Variance with One Within-subjects Factor by job category. (JOW)

Analyzing Multivariate Repeated Measures Designs: A Comparison of Two Approximate Degrees of Freedom Procedures

ERIC Educational Resources Information Center

Lix, Lisa M.; Algina, James; Keselman, H. J.

2003-01-01

The approximate degrees of freedom Welch-James (WJ) and Brown-Forsythe (BF) procedures for testing within-subjects effects in multivariate groups by trials repeated measures designs were investigated under departures from covariance homogeneity and normality. Empirical Type I error and power rates were obtained for least-squares estimators and…

Counterbalancing and Other Uses of Repeated-Measures Latin-Square Designs: Analyses and Interpretations.

ERIC Educational Resources Information Center

Reese, Hayne W.

1997-01-01

Recommends that when repeated-measures Latin-square designs are used to counterbalance treatments across a procedural variable or to reduce the number of treatment combinations given to each participant, effects be analyzed statistically, and that in all uses, researchers consider alternative interpretations of the variance associated with the…

Localization of the human {beta}-catenin gene (CTNNB1) to 3p21: A region implicated in tumor development

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

Kraus, C.; Liehr, T.; Ballhausen, G.

1994-09-01

The human {beta}-catenin locus (CTNNB1) was mapped by in situ fluorescence analysis to band p21 on the short arm of chromosome 3, a region frequently affected by somatic alterations in a variety of tumors. PCR primers for the genomic amplification of {beta}-catenin sequences were selected on the basis of homology to exon 4 of the Drosophila armadillo gene. Analysis of a panel of somatic cell hybrids confirmed the localization of {beta}-catenin on human chromosome 3. Furthermore, exclusion mapping of three hybrids carrying defined fragments of the short arm of human chromosome 3 allowed us to determine the position of themore » CTNNB1 locus close to the marker D3S2 in 3p21. 22 refs., 3 figs.« less

Evolution-Inspired Computational Design of Symmetric Proteins.

PubMed

Voet, Arnout R D; Simoncini, David; Tame, Jeremy R H; Zhang, Kam Y J

2017-01-01

Monomeric proteins with a number of identical repeats creating symmetrical structures are potentially very valuable building blocks with a variety of bionanotechnological applications. As such proteins do not occur naturally, the emerging field of computational protein design serves as an excellent tool to create them from nonsymmetrical templates. Existing pseudo-symmetrical proteins are believed to have evolved from oligomeric precursors by duplication and fusion of identical repeats. Here we describe a computational workflow to reverse-engineer this evolutionary process in order to create stable proteins consisting of identical sequence repeats.

Orexins Mediate Sex Differences in the Stress Response and in Cognitive Flexibility.

PubMed

Grafe, Laura A; Cornfeld, Amanda; Luz, Sandra; Valentino, Rita; Bhatnagar, Seema

2017-04-15

Women are twice as likely as men to experience stress-related psychiatric disorders. The biological basis of these sex differences is poorly understood. Orexins are altered in anxious and depressed patients. Using a rat model of repeated stress, we examined whether orexins contribute to sex differences in outcomes relevant to stress-related psychiatric diseases. Behavioral, neural, and endocrine habituation to repeated restraint stress and subsequent cognitive flexibility was examined in adult male and female rats. In parallel, orexin expression and activation were determined in both sexes, and chromatin immunoprecipitation was used to determine transcription factors acting at the orexin promoter. Designer receptors exclusively activated by designer drugs were used to inhibit orexin activation throughout repeated restraint to determine if the stress-related impairments in female rats could be reduced. Female rats exhibited impaired habituation to repeated restraint with subsequent deficits in cognitive flexibility compared with male rats. Increased orexin expression and activation were observed in female rats compared with male rats. The higher expression of orexin messenger RNA in female rats was due to actions of glucocorticoid receptors on the orexin promoter, as determined by chromatin immunoprecipitation. Inhibition of orexins using designer receptors exclusively activated by designer drugs in female rats throughout repeated restraint abolished their heightened hypothalamic-pituitary-adrenal responsivity and reduced stress-induced cognitive impairments. Orexins mediate the impairments in adaptations to repeated stress and in subsequent cognitive flexibility exhibited by female rats and provide evidence for a broader role for orexins in mediating functions relevant to stress-related psychiatric diseases. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Effects of Covariance Heterogeneity on Three Procedures for Analyzing Multivariate Repeated Measures Designs.

ERIC Educational Resources Information Center

Vallejo, Guillermo; Fidalgo, Angel; Fernandez, Paula

2001-01-01

Estimated empirical Type I error rate and power rate for three procedures for analyzing multivariate repeated measures designs: (1) the doubly multivariate model; (2) the Welch-James multivariate solution (H. Keselman, M. Carriere, a nd L. Lix, 1993); and (3) the multivariate version of the modified Brown-Forsythe procedure (M. Brown and A.…

Criminal Behavior and Repeat Violent Trauma: A Case-Control Study.

PubMed

Nanney, John T; Conrad, Erich J; McCloskey, Michael; Constans, Joseph I

2015-09-01

Repeat violent injury is common among young urban men and is increasingly a focus of trauma center-based injury prevention efforts. Though understanding risk factors for repeat violent injury may be critical in designing such interventions, this knowledge is limited. This study aims to determine which criminal behaviors, both before and after the initial trauma, predict repeat violent trauma. Gun, violent, and drug crimes are expected to increase risk of subsequent violent injury among victims of violence. A case-control design examined trauma registry and publicly available criminal data for all male patients aged <40 years presenting for violent trauma between April 2006 and December 2011 (N=1,142) to the sole Level 1 trauma center in a city with high rates of violence. Logistic regression was used to determine criminal behaviors predictive of repeat violent injury. Data were obtained and analyzed between January 2013 and June 2014. Regarding crimes committed before the first injury, only drug crime (OR=5.32) predicted repeat violent trauma. With respect to crimes committed after the initial injury, illegal gun possession (OR=2.70) predicted repeat victimization. Initiating gun (OR=3.53) or drug crime (OR=5.12) was associated with increased risk. Prior drug involvement may identify young male victims of violence as at high risk of repeat violent injury. Gun carrying and initiating drug involvement after the initial injury may increase risk of repeat injury and may be important targets for interventions aimed at preventing repeat violent trauma. Published by Elsevier Inc.

High-speed and low-power repeater for VLSI interconnects

NASA Astrophysics Data System (ADS)

Karthikeyan, A.; Mallick, P. S.

2017-10-01

This paper proposes a repeater for boosting the speed of interconnects with low power dissipation. We have designed and implemented at 45 and 32 nm technology nodes. Delay and power dissipation performances are analyzed for various voltage levels at these technology nodes using Spice simulations. A significant reduction in delay and power dissipation are observed compared to a conventional repeater. The results show that the proposed high-speed low-power repeater has a reduced delay for higher load capacitance. The proposed repeater is also compared with LPTG CMOS repeater, and the results shows that the proposed repeater has reduced delay. The proposed repeater can be suitable for high-speed global interconnects and has the capacity to drive large loads.

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.

Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts.

PubMed

Disney, Matthew D

2013-12-01

RNA is an important yet vastly underexploited target for small molecule chemical probes or lead therapeutics. Small molecules have been used successfully to modulate the function of the bacterial ribosome, viral RNAs and riboswitches. These RNAs are either highly expressed or can be targeted using substrate mimicry, a mainstay in the design of enzyme inhibitors. However, most cellular RNAs are neither highly expressed nor have a lead small molecule inhibitor, a significant challenge for drug discovery efforts. Herein, I describe the design of small molecules targeting expanded repeating transcripts that cause myotonic muscular dystrophy (DM). These test cases illustrate the challenges of designing small molecules that target RNA and the advantages of targeting repeating transcripts. Lastly, I discuss how small molecules might be more advantageous than oligonucleotides for targeting RNA. Copyright © 2013 Elsevier Ltd. All rights reserved.

Repeated Reading, Turn Taking, and Augmentative and Alternative Communication (AAC)

ERIC Educational Resources Information Center

Edmister, Evette; Wegner, Jane

2015-01-01

This single participant multiple baseline research design measured the effects of repeatedly reading narrative books to children who used voice output augmentative communication devices to communicate. The study sought to determine if there was a difference observed in the number of turns taken when reading stories repeatedly. Three girls ranging…

Wnt Signaling Cross-Talks with JH Signaling by Suppressing Met and gce Expression

PubMed Central

Abdou, Mohamed; Peng, Cheng; Huang, Jianhua; Zyaan, Ola; Wang, Sheng; Li, Sheng; Wang, Jian

2011-01-01

Juvenile hormone (JH) plays key roles in controlling insect growth and metamorphosis. However, relatively little is known about the JH signaling pathways. Until recent years, increasing evidence has suggested that JH modulates the action of 20-hydroxyecdysone (20E) by regulating expression of broad (br), a 20E early response gene, through Met/Gce and Kr-h1. To identify other genes involved in JH signaling, we designed a novel Drosophila genetic screen to isolate mutations that derepress JH-mediated br suppression at early larval stages. We found that mutations in three Wnt signaling negative regulators in Drosophila, Axin (Axn), supernumerary limbs (slmb), and naked cuticle (nkd), caused precocious br expression, which could not be blocked by exogenous JHA. A similar phenotype was observed when armadillo (arm), the mediator of Wnt signaling, was overexpressed. qRT-PCR revealed that Met, gce and Kr-h1expression was suppressed in the Axn, slmb and nkd mutants as well as in arm gain-of-function larvae. Furthermore, ectopic expression of gce restored Kr-h1 expression but not Met expression in the arm gain-of-function larvae. Taken together, we conclude that Wnt signaling cross-talks with JH signaling by suppressing transcription of Met and gce, genes that encode for putative JH receptors. The reduced JH activity further induces down-regulation of Kr-h1expression and eventually derepresses br expression in the Drosophila early larval stages. PMID:22087234

A Correction for the Epsilon Approximate Test in Repeated Measures Designs with Two or More Independent Groups.

ERIC Educational Resources Information Center

Lecoutre, Bruno

1991-01-01

The routine epsilon approximate test in repeated measures designs when the condition of circularity is unfulfilled uses an erroneous formula in the case of two or more groups. Because this may lead to underestimation of the deviation from circularity when the subject number is small, a correction is proposed. (Author/SLD)

A Comparison of the Bootstrap-F, Improved General Approximation, and Brown-Forsythe Multivariate Approaches in a Mixed Repeated Measures Design

ERIC Educational Resources Information Center

Seco, Guillermo Vallejo; Izquierdo, Marcelino Cuesta; Garcia, M. Paula Fernandez; Diez, F. Javier Herrero

2006-01-01

The authors compare the operating characteristics of the bootstrap-F approach, a direct extension of the work of Berkovits, Hancock, and Nevitt, with Huynh's improved general approximation (IGA) and the Brown-Forsythe (BF) multivariate approach in a mixed repeated measures design when normality and multisample sphericity assumptions do not hold.…

Advances in the Application of Designed Ankyrin Repeat Proteins (DARPins) as Research Tools and Protein Therapeutics.

PubMed

Boersma, Ykelien L

2018-01-01

Nonimmunoglobulin scaffolds have been developed to overcome the limitations of monoclonal antibodies with regard to stability and size. Of these scaffolds, the class of designed ankyrin repeat proteins (DARPins) has advanced the most in biochemical and biomedical applications. This review focuses on the recent progress in DARPin technology, highlighting the scaffold's potential and possibilities.

KSC-2012-4343

NASA Image and Video Library

2012-08-09

CAPE CANAVERAL, Fla. – At the Shuttle Landing Facility at NASA’s Kennedy Space Center in Florida, the Morpheus prototype lander begins to lift off of the ground during a free-flight test. Testing of the prototype lander had been ongoing at NASA’s Johnson Space Center in Houston in preparation for its first free-flight test at Kennedy Space Center. Morpheus was manufactured and assembled at JSC and Armadillo Aerospace. Morpheus is large enough to carry 1,100 pounds of cargo to the moon – for example, a humanoid robot, a small rover, or a small laboratory to convert moon dust into oxygen. The primary focus of the test is to demonstrate an integrated propulsion and guidance, navigation and control system that can fly a lunar descent profile to exercise the Autonomous Landing and Hazard Avoidance Technology, or ALHAT, safe landing sensors and closed-loop flight control. For more information on Project Morpheus, visit http://morpheuslander.jsc.nasa.gov/. Photo credit: NASA

Generation of genome-modified Drosophila cell lines using SwAP.

PubMed

Franz, Alexandra; Brunner, Erich; Basler, Konrad

2017-10-02

The ease of generating genetically modified animals and cell lines has been markedly increased by the recent development of the versatile CRISPR/Cas9 tool. However, while the isolation of isogenic cell populations is usually straightforward for mammalian cell lines, the generation of clonal Drosophila cell lines has remained a longstanding challenge, hampered by the difficulty of getting Drosophila cells to grow at low densities. Here, we describe a highly efficient workflow to generate clonal Cas9-engineered Drosophila cell lines using a combination of cell pools, limiting dilution in conditioned medium and PCR with allele-specific primers, enabling the efficient selection of a clonal cell line with a suitable mutation profile. We validate the protocol by documenting the isolation, selection and verification of eight independently Cas9-edited armadillo mutant Drosophila cell lines. Our method provides a powerful and simple workflow that improves the utility of Drosophila cells for genetic studies with CRISPR/Cas9.

In vitro susceptibility of Mycobacterium leprae to oxygen-mediated damage.

PubMed

Dhople, A M

1996-01-01

In order to evaluate factors responsible for the failure of Mycobacterium leprae to multiply in cell-free cultures in vitro studies were undertaken to determine the possible poisoning of the organism by hydroxide and superoxide radicals produced in the growth medium. The superoxide dismutase activity was very low, 10% of the levels found in armadillo cells, while measured activity of catalase and glutathione peroxidase was negligible. Susceptibility of M. leprae to hydrogen peroxide was enhanced by potassium iodide but not by lactoperoxidase. The addition of high amounts of catalase completely prevented hydrogen peroxide-mediated killing of M. leprae. Superoxide generated by the action of xanthine oxidase on xanthine was lethal to M. leprae, but superoxide dismutase added to the reaction mixture gave significant protection. Thus superoxide radicals may be a major cause for the sudden termination of growth of M. leprae in primary cultures and also for failure of subcultures.

Endoparasites of fat-tailed mouse opossums (Thylamys: Didelphidae) from northwestern Argentina and southern Bolivia, with the description of a new species of tapeworm.

PubMed

Jiménez, F Agustín; Braun, Janet K; Campbell, Mariel L; Gardner, Scott L

2008-10-01

The parasite fauna of 2 species of fat-tailed mouse opossums from northwestern Argentina is herein presented. Five species of helminths were found, i.e., Pterygodermatites kozeki, Hoineffia simplispicula, Oligacanthorhynchus sp., and a new species of tapeworm, Mathevotaenia sanmartini n. sp. (Cyclophyllidea: Anoplocephalidae). The new species is characterized by a calyciform scolex, relatively few testes (32), and a long cirrus sac; it occurs in fat-tailed mouse opossums at localities above 4,000 m. Those characters make it different from 6 species known to occur in marsupials from the New World, and from other species occurring in armadillos and bats. Didelphoxyuris thylamisis, H. simplicispicula, and Oligacanthorhynchus sp. appear to occur in marmosas from the Yungas region. In contrast, both P. kozeki and M. sanmartini n. sp. appear to occur exclusively in the Puna.

Mammals of South America, Volume 1, Marsupials, Xenarthrans, Shrews, and Bats

USGS Publications Warehouse

Gardner, A.L.

2007-01-01

The vast terrain between Panama and Tierra del Fuego contains some of the world?s richest mammalian fauna, but until now it has lacked a comprehensive systematic reference to the identification, distribution, and taxonomy of its mammals. The first such book of its kind and the inaugural volume in a three-part series, Mammals of South America both summarizes existing information and encourages further research of the mammals indigenous to the region. Containing identification keys and brief descriptions of each order, family, and genus, the first volume of Mammals of South America covers marsupials, shrews, armadillos, sloths, anteaters, and bats. Species accounts include taxonomic descriptions, synonymies, keys to identification, distributions with maps and a gazetteer of marginal localities, lists of recognized subspecies, brief summaries of natural history information, and discussions of issues related to taxonomic interpretations. Highly anticipated and much needed, this book will be a landmark contribution to mammalogy, zoology, tropical biology, and conservation biology.

Reduced Expression of SARM in Mouse Spleen during Polymicrobial Sepsis.

PubMed

Gong, Yu; Zou, Lin; Cen, Dongzhi; Chao, Wei; Chen, Dunjin

2016-12-01

Objective Immune dysfunction, including prominent apoptosis of immune cells and decreased functioning of the remaining immune cells, plays a central role in the pathogenesis of sepsis. Sterile α and HEAT/armadillo motif-containing protein (SARM) is implicated in the regulation of immune cell apoptosis. This study aimed to elucidate SARM contributes to sepsis-induced immune cell death and immunosuppression. Methods A mouse model of polymicrobial sepsis was generated by cecum ligation and puncture (CLP). SARM gene and protein expression, caspase 3 cleavage and intracellular ATP production were measured in the mouse spleens. Results CLP-induced polymicrobial sepsis specifically attenuated both the gene and protein expression of SARM in the spleens. Moreover, the attenuation of SARM expression synchronized with splenocyte apoptosis, as evidenced by increased caspase 3 cleavage and ATP depletion. Conclusions These findings suggest that SARM is a potential regulator of sepsis-induced splenocyte apoptosis.

Effects of repeated Valsalva maneuver straining on cardiac and vasoconstrictive baroreflex responses

NASA Technical Reports Server (NTRS)

Convertino, Victor A.; Ratliff, Duane A.; Doerr, Donald F.; Ludwig, David A.; Muniz, Gary W.; Benedetti, Erik; Chavarria, Jose; Koreen, Susan; Nguyen, Claude; Wang, Jeff

2003-01-01

INTRODUCTION: We hypothesized that repeated respiratory straining maneuvers (repeated SM) designed to elevate arterial BPs (arterial baroreceptor loading) would acutely increase baroreflex responses. METHODS: We tested this hypothesis by measuring cardiac baroreflex responses to carotid baroreceptor stimulation (neck pressures), and changes in heart rate and diastolic BP after reductions in BP induced by a 15-s Valsalva maneuver in 10 female and 10 male subjects at 1, 3, 6, and 24 h after performing repeated SM. Baroreflex responses were also measured in each subject at 1, 3, 6, and 24 h at the same time on a separate day without repeated SM (control) in a randomized, counter-balanced cross-over experimental design. RESULTS: There was no statistical difference in carotid-cardiac and peripheral vascular baroreflex responses measured across time following repeated SM compared with the control condition. Integrated cardiac baroreflex response (deltaHR/ deltaSBP) measured during performance of a Valsalva maneuver was increased by approximately 50% to 1.1 +/- 0.2 bpm x mm Hg(-1) at 1 h and 1.0 +/- 0.1 bpm x mm Hg(-1) at 3 h following repeated SM compared with the control condition (0.7 +/- 0.1 bpm x mm Hg(-1) at both 1 and 3 h, respectively). However, integrated cardiac baroreflex response after repeated SM returned to control levels at 6 and 24 h after training. These responses did not differ between men and women. CONCLUSIONS: Our results are consistent with the notion that arterial baroreceptor loading induced by repeated SM increased aortic, but not carotid, cardiac baroreflex responses for as long as 3 h after repeated SM. We conclude that repeated SM increases cardiac baroreflex responsiveness which may provide patients, astronauts, and high-performance aircraft pilots with protection from development of orthostatic hypotension.

Fluid-Structure Interaction in a Fluid-Filled Composite Structure Subjected to Low Velocity Impact

DTIC Science & Technology

2016-06-01

for creating an E-glass composite cubic structure and a pendulum was designed and built to provide a repeatable low velocity impact. The behavior of...structure and a pendulum was designed and built to provide a repeatable low velocity impact. The behavior of the composite structure was studied at various...SET-UP .......................................................31  1.  Impact Pendulum

Splashing Our Way to Playfulness! An Aquatic Playgroup for Young Children with Autism, A Repeated Measures Design

ERIC Educational Resources Information Center

Fabrizi, Sarah E.

2015-01-01

This study investigated the effectiveness of an aquatic playgroup on the playfulness of children, ages 2 to 3 with autism spectrum disorder. Using a repeated measures design, we followed 10 children and their caregivers who participated in a 6-week aquatic playgroup in southwest Florida. Four dyads completed the entire 12-week study period. The…

Robustness of crossover trials against subject drop-out - Examples of perpetually connected designs.

PubMed

Godolphin, P J; Godolphin, E J

2017-01-01

When performing a repeated measures experiment, such as a clinical trial, there is a risk of subject drop-out during the experiment. If one or more subjects leave the study prematurely, a situation could arise where the eventual design is disconnected, implying that very few treatment contrasts for both direct effects and carryover effects are estimable. This paper aims to identify experimental conditions where this problem with the eventual design can be avoided. It is shown that in the class of uniformly balanced repeated measurement designs consisting of two or more Latin squares, there are planned designs with the following useful property. Provided that all subjects have completed the first two periods of study, such a design will not be replaced by a disconnected eventual design due to drop-out, irrespective of the type of drop-out behaviour that may occur. Designs with this property are referred to as perpetually connected. These experimental conditions are identified and examined in the paper and an example of at least one perpetually connected uniformly balanced repeated measurement design is given in each case. The results improve upon previous contributions in the literature that have been confined largely to cases in which drop-out occurs only in the final periods of study.

A novel magnet based 3D printed marker wand as basis for repeated in-shoe multi segment foot analysis: a proof of concept.

PubMed

Eerdekens, Maarten; Staes, Filip; Pilkington, Thomas; Deschamps, Kevin

2017-01-01

Application of in-shoe multi-segment foot kinematic analyses currently faces a number of challenges, including: (i) the difficulty to apply regular markers onto the skin, (ii) the necessity for an adequate shoe which fits various foot morphologies and (iii) the need for adequate repeatability throughout a repeated measure condition. The aim of this study therefore was to design novel magnet based 3D printed markers for repeated in-shoe measurements while using accordingly adapted modified shoes for a specific multi-segment foot model. Multi-segment foot kinematics of ten participants were recorded and kinematics of hindfoot, midfoot and forefoot were calculated. Dynamic trials were conducted to check for intra and inter-session repeatability when combining novel markers and modified shoes in a repeated measures design. Intraclass correlation coefficients were calculated to determine reliability. Both repeatability and reliability were proven to be good to excellent with maximum joint angle deviations of 1.11° for intra-session variability and 1.29° for same-day inter-session variability respectively and ICC values of >0.91. The novel markers can be reliably used in future research settings using in-shoe multi-segment foot kinematic analyses with multiple shod conditions.

Efficient production of artificially designed gelatins with a Bacillus brevis system.

PubMed

Kajino, T; Takahashi, H; Hirai, M; Yamada, Y

2000-01-01

Artificially designed gelatins comprising tandemly repeated 30-amino-acid peptide units derived from human alphaI collagen were successfully produced with a Bacillus brevis system. The DNA encoding the peptide unit was synthesized by taking into consideration the codon usage of the host cells, but no clones having a tandemly repeated gene were obtained through the above-mentioned strategy. Minirepeat genes could be selected in vivo from a mixture of every possible sequence encoding an artificial gelatin by randomly ligating the mixed sequence unit and transforming it into Escherichia coli. Larger repeat genes constructed by connecting minirepeat genes obtained by in vivo selection were also stable in the expression host cells. Gelatins derived from the eight-unit and six-unit repeat genes were extracellularly produced at the level of 0.5 g/liter and easily purified by ammonium sulfate fractionation and anion-exchange chromatography. The purified artificial gelatins had the predicted N-terminal sequences and amino acid compositions and a solgel property similar to that of the native gelatin. These results suggest that the selection of a repeat unit sequence stable in an expression host is a shortcut for the efficient production of repetitive proteins and that it can conveniently be achieved by the in vivo selection method. This study revealed the possible industrial application of artificially designed repetitive proteins.

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.

Power analysis for multivariate and repeated measurements designs via SPSS: correction and extension of D'Amico, Neilands, and Zambarano (2001).

PubMed

Osborne, Jason W

2006-05-01

D'Amico, Neilands, and Zambarano (2001) published SPSS syntax to perform power analyses for three complex procedures: ANCOVA, MANOVA, and repeated measures ANOVA. Unfortunately, the published SPSS syntax for performing the repeated measures analysis needed some minor revision in order to perform the analysis correctly. This article presents the corrected syntax that will successfully perform the repeated measures analysis and provides some guidance on modifying the syntax to customize the analysis.

Case study: videogame distraction reduces behavioral distress in a preschool-aged child undergoing repeated burn dressing changes: a single-subject design.

PubMed

Sil, Soumitri; Dahlquist, Lynnda M; Burns, Andrew J

2013-04-01

This single-subject design study evaluated the feasibility and efficacy of passive and interactive videogame distraction on behavioral distress for a preschool-aged child receiving repeated burn dressing changes. A 4-year-old girl underwent 3 baseline and 10 videogame distraction sessions (5 passive and 5 interactive) using a restricted alternating treatments design. Observed behavioral distress was coded, and parents and nurses rated the child's distress and cooperative behavior. Relative to baseline, behavioral distress decreased and cooperative behavior increased immediately after the onset of videogame distraction. Single Case Randomization Tests revealed significantly lower behavioral distress and greater cooperation during interactive videogame distraction relative to passive videogame distraction. Interactive videogame distraction appears to be a feasible and effective pain management strategy for a preschool-aged child undergoing repeated painful medical procedures.

Lithography hotspot discovery at 70nm DRAM 300mm fab: process window qualification using design base binning

NASA Astrophysics Data System (ADS)

Chen, Daniel; Chen, Damian; Yen, Ray; Cheng, Mingjen; Lan, Andy; Ghaskadvi, Rajesh

2008-11-01

Identifying hotspots--structures that limit the lithography process window--become increasingly important as the industry relies heavily on RET to print sub-wavelength designs. KLA-Tencor's patented Process Window Qualification (PWQ) methodology has been used for this purpose in various fabs. PWQ methodology has three key advantages (a) PWQ Layout--to obtain the best sensitivity (b) Design Based Binning--for pattern repeater analysis (c) Intelligent sampling--for the best DOI sampling rate. This paper evaluates two different analysis strategies for SEM review sampling successfully deployed at Inotera Memories, Inc. We propose a new approach combining the location repeater and pattern repeaters. Based on a recent case study the new sampling flow reduces the data analysis and sampling time from 6 hours to 1.5 hour maintaining maximum DOI sample rate.

Does Repeated Reading Improve Reading Fluency and Comprehension for Struggling Adolescent Readers?

ERIC Educational Resources Information Center

Still, Kristine Lynn; Flynt, Christine A.

2012-01-01

This was a 12-week study that explored the effects of repeated peer readings on struggling adolescent readers. It was a quasi-experimental design with one treatment group and one control group. There were two small group English classes that were consistently using the repeated reading strategy (the treatment group) and students in the co-teach…

Comparison of Repeated and Non-Repeated Readings on the Reading Performances of Students with Emotional and Behavioral Disorders

ERIC Educational Resources Information Center

Escarpio, Raul; Barbetta, Patricia M.

2016-01-01

This study used an alternating treatments design to compare the effects of three conditions on the reading fluency, errors, and comprehension of four, sixth-grade students with emotional and behavioral disorders (EBD) who were struggling readers. The conditions were (a) repeated readings in which participants read three times a passage of 100 or…

Abscisic Acid Is a Major Regulator of Grape Berry Ripening Onset: New Insights into ABA Signaling Network

PubMed Central

Pilati, Stefania; Bagagli, Giorgia; Sonego, Paolo; Moretto, Marco; Brazzale, Daniele; Castorina, Giulia; Simoni, Laura; Tonelli, Chiara; Guella, Graziano; Engelen, Kristof; Galbiati, Massimo; Moser, Claudio

2017-01-01

Grapevine is a world-wide cultivated economically relevant crop. The process of berry ripening is non-climacteric and does not rely on the sole ethylene signal. Abscisic acid (ABA) is recognized as an important hormone of ripening inception and color development in ripening berries. In order to elucidate the effect of this signal at the molecular level, pre-véraison berries were treated ex vivo for 20 h with 0.2 mM ABA and berry skin transcriptional modulation was studied by RNA-seq after the treatment and 24 h later, in the absence of exogenous ABA. This study highlighted that a small amount of ABA triggered its own biosynthesis and had a transcriptome-wide effect (1893 modulated genes) characterized by the amplification of the transcriptional response over time. By comparing this dataset with the many studies on ripening collected within the grapevine transcriptomic compendium Vespucci, an extended overlap between ABA- and ripening modulated gene sets was observed (71% of the genes), underpinning the role of this hormone in the regulation of berry ripening. The signaling network of ABA, encompassing ABA metabolism, transport and signaling cascade, has been analyzed in detail and expanded based on knowledge from other species in order to provide an integrated molecular description of this pathway at berry ripening onset. Expression data analysis was combined with in silico promoter analysis to identify candidate target genes of ABA responsive element binding protein 2 (VvABF2), a key upstream transcription factor of the ABA signaling cascade which is up-regulated at véraison and also by ABA treatments. Two transcription factors, VvMYB143 and VvNAC17, and two genes involved in protein degradation, Armadillo-like and Xerico-like genes, were selected for in vivo validation by VvABF2-mediated promoter trans-activation in tobacco. VvNAC17 and Armadillo-like promoters were induced by ABA via VvABF2, while VvMYB143 responded to ABA in a VvABF2-independent manner. This knowledge of the ABA cascade in berry skin contributes not only to the understanding of berry ripening regulation but might be useful to other areas of viticultural interest, such as bud dormancy regulation and drought stress tolerance. PMID:28680438

Tick fauna from two locations in the Brazilian savannah.

PubMed

Szabó, Matias Pablo Juan; Olegário, Maria Marlene Martins; Santos, André Luiz Quagliatto

2007-01-01

The Cerrado is Brazil's tropical savannah, which is arguably under greater threat than the Amazon rainforest. The Cerrado Biome of tropical South America covers about 2 million km(2) and is considered a biodiversity hot spot which means that it is especially rich in endemic species and particularly threatened by human activities. The Cerrado is increasingly exposed to agricultural activities which enhance the likelihood of mixing parasites from rural, urban and wildlife areas. Information about ticks from the Cerrado biome is scarce. In this report tick species free-living, on domestic animals and on a few wild animals in two farms in the Cerrado biome (Nova Crixás and Araguapaz municipalities, Goiás State, Brazil) are described. Amblyomma cajennense was the first and Amblyomma parvum the second host-seeking tick species found. Only two other tick species were found free-living: one Amblyomma nodosum and three Amblyomma naponense nymphs. Cattle were infested with Boophilus microplus and A. cajennense. Buffalos were infested with B. microplus and A. parvum. Dogs were infested with A. cajennense, Amblyomma ovale, A. parvum and Rhipicephalus sanguineus ticks. Anocentor nitens, B. microplus, A. cajennense, and A. parvum were found on horses. Amblyomma auricularium were found attached to nine-banded armadillos and Amblyomma rotundatum to red-footed tortoise, cururu toads and a rattlesnake. The latter was also infested with an adult A. cajennense. No tick was found on a goat, a tropical rat snake and a yellow armadillo. Among the observations the infestation of several domestic animals with A. parvum seems be the main feature. It suggests that this species might become a pest. However, the life cycle of A. parvum in nature, as well as its disease vectoring capacity, are largely unknown. It would be important to determine if it is a species expanding its geographic range by adaptation to new hosts or if it has been maintained in high numbers at definite locations by specific and still undetermined conditions. A higher prevalence of A. cajennense in most Brazilian biomes, with the exception of rainforests, was already shown before. Thus this species is favored by deforestation and is an important research target as it is the most common vector associated with the Brazilian spotted fever.

Social Stories: Mechanisms of Effectiveness in Increasing Game Play Skills in Children Diagnosed with Autism Spectrum Disorder Using a Pretest Posttest Repeated Measures Randomized Control Group Design

ERIC Educational Resources Information Center

Quirmbach, Linda M.; Lincoln, Alan J.; Feinberg-Gizzo, Monica J.; Ingersoll, Brooke R.; Andrews, Siri M.

2009-01-01

An increasing body of literature has indicated that social stories are an effective way to teach individuals diagnosed with autism appropriate social behavior. This study compared two formats of a social story targeting the improvement of social skills during game play using a pretest posttest repeated measures randomized control group design. A…

Virtual surgical planning and 3D printing in repeat calvarial vault reconstruction for craniosynostosis: technical note.

PubMed

LoPresti, Melissa; Daniels, Bradley; Buchanan, Edward P; Monson, Laura; Lam, Sandi

2017-04-01

Repeat surgery for restenosis after initial nonsyndromic craniosynostosis intervention is sometimes needed. Calvarial vault reconstruction through a healed surgical bed adds a level of intraoperative complexity and may benefit from preoperative and intraoperative definitions of biometric and aesthetic norms. Computer-assisted design and manufacturing using 3D imaging allows the precise formulation of operative plans in anticipation of surgical intervention. 3D printing turns virtual plans into anatomical replicas, templates, or customized implants by using a variety of materials. The authors present a technical note illustrating the use of this technology: a repeat calvarial vault reconstruction that was planned and executed using computer-assisted design and 3D printed intraoperative guides.

Sequence repeats and protein structure

NASA Astrophysics Data System (ADS)

Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

2012-11-01

Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

Case Study: Videogame Distraction Reduces Behavioral Distress in a Preschool-Aged Child Undergoing Repeated Burn Dressing Changes: A Single-Subject Design

PubMed Central

Sil, Soumitri; Burns, Andrew J.

2013-01-01

Objective This single-subject design study evaluated the feasibility and efficacy of passive and interactive videogame distraction on behavioral distress for a preschool-aged child receiving repeated burn dressing changes. Method A 4-year-old girl underwent 3 baseline and 10 videogame distraction sessions (5 passive and 5 interactive) using a restricted alternating treatments design. Observed behavioral distress was coded, and parents and nurses rated the child’s distress and cooperative behavior. Results Relative to baseline, behavioral distress decreased and cooperative behavior increased immediately after the onset of videogame distraction. Single Case Randomization Tests revealed significantly lower behavioral distress and greater cooperation during interactive videogame distraction relative to passive videogame distraction. Conclusions Interactive videogame distraction appears to be a feasible and effective pain management strategy for a preschool-aged child undergoing repeated painful medical procedures. PMID:23248343

Association of heme oxygenase-1 GT-repeat polymorphism with blood pressure phenotypes and its relevance to future cardiovascular mortality risk: an observation based on arsenic-exposed individuals.

PubMed

Wu, Meei-Maan; Chiou, Hung-Yi; Chen, Chi-Ling; Hsu, Ling-I; Lien, Li-Ming; Wang, Chih-Hao; Hsieh, Yi-Chen; Wang, Yuan-Hung; Hsueh, Yu-Mei; Lee, Te-Chang; Cheng, Wen-Fang; Chen, Chien-Jen

2011-12-01

Heme oxygenase (HO)-1 is up-regulated as a cellular defense responding to stressful stimuli in experimental studies. A GT-repeat length polymorphism in the HO-1 gene promoter was inversely correlated to HO-1 induction. Here, we reported the association of GT-repeat polymorphism with blood pressure (BP) phenotypes, and their interaction on cardiovascular (CV) mortality risk in arsenic-exposed cohorts. Associations of GT-repeat polymorphism with BP phenotypes were investigated at baseline in a cross-sectional design. Effect of GT-repeat polymorphism on CV mortality was investigated in a longitudinal design stratified by hypertension. GT-repeat variants were grouped by S (<27 repeats) or L (≥ 27 repeats) alleles. Multivariate analyses were used to estimate the effect size after accounting for CV covariates. Totally, 894 participants were recruited and analyzed. At baseline, carriers with HO-1 S alleles had lower diastolic BP (L/S genotypes, P = 0.014) and a lower possibility of being hypertensive (L/S genotypes, P = 0.048). After follow-up, HO-1 S allele was significantly associated with a reduced CV risk in hypertensive participants [relative mortality ratio (RMR) 0.27 (CI 0.11, 0.69), P = 0.007] but not in normotensive. Hypertensive participants without carrying the S allele had a 5.23-fold increased risk [RMR 5.23 (CI 1.99, 13.69), P = 0.0008] of CV mortality compared with normotensive carrying the S alleles. HO-1 short GT-repeat polymorphism may play a protective role in BP regulation and CV mortality risk in hypertensive individuals against environmental stressors. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

PubMed Central

Tong, Helin; Chen, You; Wang, Jingyi; Chen, Yeyuan; Sun, Guangming; He, Junhu; Wu, Yaoting

2013-01-01

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region. PMID:24024187

The Role of Feedback and Differences between Good and Poor Decoders in a Repeated Word Reading Paradigm in First Grade

ERIC Educational Resources Information Center

van Gorp, Karly; Segers, Eliane; Verhoeven, Ludo

2017-01-01

The direct, retention, and transfer effects of repeated word and pseudoword reading were studied in a pretest, training, posttest, retention design. First graders (48 good readers, 47 poor readers) read 25 CVC words and 25 CVC pseudowords in ten repeated word reading sessions, preceded and followed by a transfer task with a different set of items.…

Repeater For A Digital-Communication Bus

NASA Technical Reports Server (NTRS)

Torres-Guzman, Esteban; Olson, Stephen; Heaps, Tim

1993-01-01

Digital repeater circuit designed to extend range of communication on MIL-STD-1553 bus beyond original maximum allowable length of 300 ft. Circuit provides two-way communication, one way at time, and conforms to specifications of MIL-STD-1553. Crosstalk and instability eliminated.

[Review of research design and statistical methods in Chinese Journal of Cardiology].

PubMed

Zhang, Li-jun; Yu, Jin-ming

2009-07-01

To evaluate the research design and the use of statistical methods in Chinese Journal of Cardiology. Peer through the research design and statistical methods in all of the original papers in Chinese Journal of Cardiology from December 2007 to November 2008. The most frequently used research designs are cross-sectional design (34%), prospective design (21%) and experimental design (25%). In all of the articles, 49 (25%) use wrong statistical methods, 29 (15%) lack some sort of statistic analysis, 23 (12%) have inconsistencies in description of methods. There are significant differences between different statistical methods (P < 0.001). The correction rates of multifactor analysis were low and repeated measurement datas were not used repeated measurement analysis. Many problems exist in Chinese Journal of Cardiology. Better research design and correct use of statistical methods are still needed. More strict review by statistician and epidemiologist is also required to improve the literature qualities.

The effect of emotional design and online customer review on customer repeat purchase intention in online stores

NASA Astrophysics Data System (ADS)

Dewi, D. S.; Sudiarno, A.; Saputra, H.; Dewi, R. S.

2018-04-01

The internet users in Indonesia has increased rapidly over the last decade. A survey conducted by Association of Internet Service Providers Indonesia shows that the internet users has reached 34.9% of total population in Indonesia. The increase of internet users has led to a shift in trading practice from conventional trade to online trade. It is predicted in the next years the number of online consumers in Indonesia will continue to increase, provide many opportunity for online business. The huge number of internet users is not necesarily followed by the high number of e-purchase. It is therefore become the interest of many researchers to investigate factors that influence the decision on online purchasing.This research proposes a model that assess the effect of emotional design and customer review to customer intention on e-repeat purchase. Online questionnaire is designed and is distributed randomly through google forms. There are 187 respondent filled the questionnaire from which only 162 respondents actually have experience in online purchase. These data are then processed by using statistical analysis. A model is developed by applying structural equation modeling (SEM) approach. This study revealed that customer reviews especially objective reviews has a significant effect toward repeat purchase. Whereas emotional design particularly visual attractiveness also shows a significant effect toward e-repeat purchase.

Arm-Gal4 inheritance influences development and lifespan in Drosophila melanogaster.

PubMed

Slade, F A; Staveley, B E

2015-10-19

The UAS-Gal4 ectopic expression system is a widely used and highly valued tool that allows specific gene expression in Drosophila melanogaster. Yeast transcription factor Gal4 can be directed using D. melanogaster transcriptional control elements, and is often assumed to have little effect on the organism. By evaluation of the consequences of maternal and paternal inheritance of a Gal4 transgene under the transcriptional regulation of armadillo control elements (arm-Gal4), we demonstrated that Gal4 expression could be detrimental to development and longevity. Male progeny expressing arm-Gal4 in the presence of UAS-lacZ transgene had reduced numbers and size of ommatidia, compared to flies expressing UAS-lacZ transgene under the control of other Gal4 transgenes. Aged at 25°C, the median life span of male flies with maternally inherited elav-Gal4 was 70 days, without a responding transgene or with UAS-lacZ. The median life span of maternally inherited arm-Gal4 male flies without a responding transgene was 48 days, and 40 days with the UAS-lacZ transgene. A partial rescue of this phenotype was observed with the expression of UAS-lacZ under paternal arm-Gal4 control, having an average median lifespan of 60 days. This data suggests that arm-Gal4 has detrimental effects on Drosophila development and lifespan that are directly dependent upon parental inheritance, and that the benign responder and reporter gene UAS-lacZ may influence D. melanogaster development. These findings should be taken into consideration during the design and execution of UAS-Gal4 expression experiments.

Suitability of open-field autorefractors as pupillometers and instrument design effects.

PubMed

Otero, Carles; Aldaba, Mikel; Ferrer, Oriol; Gascón, Andrea; Ondategui-Parra, Juan C; Pujol, Jaume

2017-01-01

To determine the agreement and repeatability of the pupil measurement obtained with VIP-200 (Neuroptics), PowerRef II (Plusoptix), WAM-5500 (Grand Seiko) and study the effects of instrument design on pupillometry. Forty patients were measured twice in low, mid and high mesopic. Repeatability was analyzed with the within-subject standard deviation (Sw) and paired t -tests. Agreement was studied with Bland-Altman plots and repeated measures ANOVA. Instrument design analysis consisted on measuring pupil size with PowerRef II simulating monocular and binocular conditions as well as with proximity cues and without proximity cues. The mean difference (±standard deviation) between test-retest for low, mid and high mesopic conditions were, respectively: -0.09 (±0.16), -0.05 (±0.18) and -0.08 (±0.23) mm for Neuroptics, -0.05 (±0.17), -0.12 (±0.23) and -0.17 (±0.34) mm for WAM-5500, -0.04 (±0.27), -0.13 (±0.37) and -0.11 (±0.28) mm for PowerRef II. Regarding agreement with Neuroptics, the mean difference for low, mid and high mesopic conditions were, respectively: -0.48 (±0.35), -0.83 (±0.52) and -0.38 (±0.56) mm for WAM-5500, -0.28 (±0.56), -0.70 (±0.55) and -0.61 (±0.54) mm for PowerRef II. The mean difference of binocular minus monocular pupil measurements was: -0.83 (±0.87) mm; and with proximity cues minus without proximity cues was: -0.30 (±0.77) mm. All the instruments show similar repeat-ability. In all illumination conditions, agreement of Neuroptics with WAM-5500 and PowerRef II is not good enough, which can be partially induced due to their open field design.

Improved PCR-Based Detection of Soil Transmitted Helminth Infections Using a Next-Generation Sequencing Approach to Assay Design.

PubMed

Pilotte, Nils; Papaiakovou, Marina; Grant, Jessica R; Bierwert, Lou Ann; Llewellyn, Stacey; McCarthy, James S; Williams, Steven A

2016-03-01

The soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world's most economically depressed locations. With growing emphasis on disease mapping and eradication, the availability of accurate and cost-effective diagnostic measures is of paramount importance to global control and elimination efforts. While real-time PCR-based molecular detection assays have shown great promise, to date, these assays have utilized sub-optimal targets. By performing next-generation sequencing-based repeat analyses, we have identified high copy-number, non-coding DNA sequences from a series of soil transmitted pathogens. We have used these repetitive DNA elements as targets in the development of novel, multi-parallel, PCR-based diagnostic assays. Utilizing next-generation sequencing and the Galaxy-based RepeatExplorer web server, we performed repeat DNA analysis on five species of soil transmitted helminths (Necator americanus, Ancylostoma duodenale, Trichuris trichiura, Ascaris lumbricoides, and Strongyloides stercoralis). Employing high copy-number, non-coding repeat DNA sequences as targets, novel real-time PCR assays were designed, and assays were tested against established molecular detection methods. Each assay provided consistent detection of genomic DNA at quantities of 2 fg or less, demonstrated species-specificity, and showed an improved limit of detection over the existing, proven PCR-based assay. The utilization of next-generation sequencing-based repeat DNA analysis methodologies for the identification of molecular diagnostic targets has the ability to improve assay species-specificity and limits of detection. By exploiting such high copy-number repeat sequences, the assays described here will facilitate soil transmitted helminth diagnostic efforts. We recommend similar analyses when designing PCR-based diagnostic tests for the detection of other eukaryotic pathogens.

The last half-repeat of transcription activator-like effector (TALE) is dispensable and thereby TALE-based technology can be simplified.

PubMed

Zheng, Chong-Ke; Wang, Chun-Lian; Zhang, Xiao-Ping; Wang, Fu-Jun; Qin, Teng-Fei; Zhao, Kai-Jun

2014-09-01

To activate the expression of host genes that contribute to pathogen growth, pathogenic Xanthomonas bacteria inject their transcription activator-like effectors (TALEs) into plant cells and the TALEs bind to target gene promoters by the central repeat region consisting of near-perfect 34-amino-acid repeats (34-aa repeats). Based on the recognition codes between the 34-aa repeats and the targeted nucleotides, TALE-based technologies, such as designer TALEs (dTALEs) and TALE nucleases (TALENs), have been developed. Amazingly, every natural TALE invariantly has a truncated last half-repeat (LHR) at the end of the 34-aa repeats. Consequently, all the reported dTALEs and TALENs also harbour their LHRs. Here, we show that the LHRs in dTALEs are dispensable for the function of gene activation by both transient expression assays in Nicotiana benthamiana and gene-specific targeting in the rice genome, indicating that TALEs might originate from a single progenitor. In the light of this finding, we demonstrate that dTALEs can be constructed through two simple steps. Moreover, the activation strengths of dTALEs lacking the LHR are comparable with those of dTALEs harbouring the LHR. Our results provide new insights into the origin of natural TALEs, and will facilitate the simplification of the design and assembly of TALE-based tools, such as dTALEs and TALENs, in the near future. © 2014 BSPP AND JOHN WILEY & SONS LTD.

Subgrade characterization for highway pavement design.

DOT National Transportation Integrated Search

2000-12-01

Subgrade soil characterization expressed in terms of Resilient Modulus (MR) has become crucial for pavement design. For a new design, MR : values are generally obtained by conducting repeated triaxial tests on reconstituted/undisturbed cylindrical sp...

Mystery shopping and coaching as a form of audit and feedback to improve community pharmacy management of non-prescription medicine requests: an intervention study

PubMed Central

Schneider, Carl Richard; Naughtin, Clare Louise; Wilson, Frances; de Almeida Neto, Abilio Cesar; Moles, Rebekah Jane

2017-01-01

Objectives To determine whether repeated mystery shopping visits with feedback improve pharmacy performance over nine visits and to determine what factors predict an appropriate outcome. Design Prospective, parallel, repeated intervention, repeated measures mystery shopping (pseudopatient) design. Setting Thirty-six community pharmacies in metropolitan Sydney, Australia in March–October 2015. Participants Sixty-one University of Sydney pharmacy undergraduates acted as mystery shoppers. Students enrolled in their third year of Bachelor of Pharmacy in 2015 were eligible to participate. Any community pharmacy in the Sydney metropolitan region was eligible to take part and was selected through convenience sampling. Intervention Repeated mystery shopping with immediate feedback and coaching. Outcome measures Outcome for each given scenario (appropriate or not) and questioning scores for each interaction. Results Five hundred and twenty-one visits were analysed, of which 54% resulted in an appropriate outcome. Questioning scores and the proportion of interactions resulting in an appropriate outcome significantly improved over time (P<0.001). Involvement of pharmacists, visit number, increased questioning score and the prescribed scenario were predictors of an appropriate outcome (P=0.008, P=0.022, P<0.001 and P<0.001, respectively). Interactions involving a pharmacist had greater scores than those without (P<0.001). Conclusions Repeated mystery shopping visits with feedback were associated with improved pharmacy performance over time. Future work should focus on the role of non-pharmacist staff and design interventions accordingly. PMID:29247115

Structure-Based Rational Design of a Toll-like Receptor 4 (TLR4) Decoy Receptor with High Binding Affinity for a Target Protein

PubMed Central

Lee, Sang-Chul; Hong, Seungpyo; Park, Keunwan; Jeon, Young Ho; Kim, Dongsup; Cheong, Hae-Kap; Kim, Hak-Sung

2012-01-01

Repeat proteins are increasingly attracting much attention as alternative scaffolds to immunoglobulin antibodies due to their unique structural features. Nonetheless, engineering interaction interface and understanding molecular basis for affinity maturation of repeat proteins still remain a challenge. Here, we present a structure-based rational design of a repeat protein with high binding affinity for a target protein. As a model repeat protein, a Toll-like receptor4 (TLR4) decoy receptor composed of leucine-rich repeat (LRR) modules was used, and its interaction interface was rationally engineered to increase the binding affinity for myeloid differentiation protein 2 (MD2). Based on the complex crystal structure of the decoy receptor with MD2, we first designed single amino acid substitutions in the decoy receptor, and obtained three variants showing a binding affinity (KD) one-order of magnitude higher than the wild-type decoy receptor. The interacting modes and contributions of individual residues were elucidated by analyzing the crystal structures of the single variants. To further increase the binding affinity, single positive mutations were combined, and two double mutants were shown to have about 3000- and 565-fold higher binding affinities than the wild-type decoy receptor. Molecular dynamics simulations and energetic analysis indicate that an additive effect by two mutations occurring at nearby modules was the major contributor to the remarkable increase in the binding affinities. PMID:22363519

More Lessons from a Master Teacher! Frank Wachowiak.

ERIC Educational Resources Information Center

Morris, Jimmy

1989-01-01

Presents two printmaking lessons for children inspired by master art teacher, Frank Wachowiak. "Repeated Motifs and Designs" uses vegetables and found objects to make prints emphasizing repeat patterns. "Fish Under the Sea" uses white liquid glue to make line prints with strong linear compositions. (LS)

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

The Critical Importance of Retrieval--and Spacing--for Learning.

PubMed

Soderstrom, Nicholas C; Kerr, Tyson K; Bjork, Robert A

2016-02-01

We examined the impact of repeated testing and repeated studying on long-term learning. In Experiment 1, we replicated Karpicke and Roediger's (2008) influential results showing that once information can be recalled, repeated testing on that information enhances learning, whereas restudying that information does not. We then examined whether the apparent ineffectiveness of restudying might be attributable to the spacing differences between items that were inherent in the between-subjects design employed by Karpicke and Roediger. When we controlled for these spacing differences by manipulating the various learning conditions within subjects in Experiment 2, we found that both repeated testing and restudying improved learning, and that learners' awareness of the relative mnemonic benefits of these strategies was enhanced. These findings contribute to understanding how two important factors in learning-test-induced retrieval processes and spacing-can interact, and they illustrate that such interactions can play out differently in between-subjects and within-subjects experimental designs. © The Author(s) 2015.

Indexing system for optical beam steering

NASA Technical Reports Server (NTRS)

Sullivan, Mark T.; Cannon, David M.; Debra, Daniel B.; Young, Jeffrey A.; Mansfield, Joseph A.; Carmichael, Roger E.; Lissol, Peter S.; Pryor, G. M.; Miklosy, Les G.; Lee, Jeffrey H.

1990-01-01

This paper describes the design and testing of an indexing system for optical-beam steering. The cryogenic beam-steering mechanism is a 360-degree rotation device capable of discrete, high-precision alignment positions. It uses low-precision components for its rough alignment and kinematic design to meet its stringent repeatability and stability requirements (of about 5 arcsec). The principal advantages of this design include a decoupling of the low-precision, large angular motion from the high-precision alignment, and a power-off alignment position that potentially extends the life or hold time of cryogenic systems. An alternate design, which takes advantage of these attributes while reducing overall motion, is also presented. Preliminary test results show the kinematic mount capable of sub-arc second repeatability.

Repeat sample intraocular pressure variance in induced and naturally ocular hypertensive monkeys.

PubMed

Dawson, William W; Dawson, Judyth C; Hope, George M; Brooks, Dennis E; Percicot, Christine L

2005-12-01

To compare repeat-sample means variance of laser induced ocular hypertension (OH) in rhesus monkeys with the repeat-sample mean variance of natural OH in age-range matched monkeys of similar and dissimilar pedigrees. Multiple monocular, retrospective, intraocular pressure (IOP) measures were recorded repeatedly during a short sampling interval (SSI, 1-5 months) and a long sampling interval (LSI, 6-36 months). There were 5-13 eyes in each SSI and LSI subgroup. Each interval contained subgroups from the Florida with natural hypertension (NHT), induced hypertension (IHT1) Florida monkeys, unrelated (Strasbourg, France) induced hypertensives (IHT2), and Florida age-range matched controls (C). Repeat-sample individual variance means and related IOPs were analyzed by a parametric analysis of variance (ANOV) and results compared to non-parametric Kruskal-Wallis ANOV. As designed, all group intraocular pressure distributions were significantly different (P < or = 0.009) except for the two (Florida/Strasbourg) induced OH groups. A parametric 2 x 4 design ANOV for mean variance showed large significant effects due to treatment group and sampling interval. Similar results were produced by the nonparametric ANOV. Induced OH sample variance (LSI) was 43x the natural OH sample variance-mean. The same relationship for the SSI was 12x. Laser induced ocular hypertension in rhesus monkeys produces large IOP repeat-sample variance mean results compared to controls and natural OH.

ECCM Scheme against Interrupted Sampling Repeater Jammer Based on Parameter-Adjusted Waveform Design

PubMed Central

Wei, Zhenhua; Peng, Bo; Shen, Rui

2018-01-01

Interrupted sampling repeater jamming (ISRJ) is an effective way of deceiving coherent radar sensors, especially for linear frequency modulated (LFM) radar. In this paper, for a simplified scenario with a single jammer, we propose a dynamic electronic counter-counter measure (ECCM) scheme based on jammer parameter estimation and transmitted signal design. Firstly, the LFM waveform is transmitted to estimate the main jamming parameters by investigating the discontinuousness of the ISRJ’s time-frequency (TF) characteristics. Then, a parameter-adjusted intra-pulse frequency coded signal, whose ISRJ signal after matched filtering only forms a single false target, is designed adaptively according to the estimated parameters, i.e., sampling interval, sampling duration and repeater times. Ultimately, for typical jamming scenes with different jamming signal ratio (JSR) and duty cycle, we propose two particular ISRJ suppression approaches. Simulation results validate the effective performance of the proposed scheme for countering the ISRJ, and the trade-off relationship between the two approaches is demonstrated. PMID:29642508

Simple sequence repeat marker loci discovery using SSR primer.

PubMed

Robinson, Andrew J; Love, Christopher G; Batley, Jacqueline; Barker, Gary; Edwards, David

2004-06-12

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. With the increase in the availability of DNA sequence information, an automated process to identify and design PCR primers for amplification of SSR loci would be a useful tool in plant breeding programs. We report an application that integrates SPUTNIK, an SSR repeat finder, with Primer3, a PCR primer design program, into one pipeline tool, SSR Primer. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. The results are parsed to Primer3 for locus-specific primer design. The script makes use of a Web-based interface, enabling remote use. This program has been written in PERL and is freely available for non-commercial users by request from the authors. The Web-based version may be accessed at http://hornbill.cspp.latrobe.edu.au/

[Imported mycosis: a review of paracoccidioidomycosis].

PubMed

Bousquet, A; Dussart, C; Drouillard, I; Charbel, E C; Boiron, P

2007-12-01

Population migration is increasing the number of systemic mycosis cases, a condition little or not present in Metropolitan France, thus often weakly documented for medical teams. Paracoccidioidomycosis is a systemic mycosis geographically confined to Latin America. The causative agent is Paracoccidioides brasiliensis, a dimorphic fungus present at ground level. Discovering that the armadillo was a new host allowed documenting the ideal conditions for this fungus development. The mortality rate is currently 1.45 for one million people and the disease affects mainly farmers. The mode of infection is respiratory and all organs and mucous membranes can be affected by lymphatic dissemination. The chronic form with pulmonary, cutaneous and oral lesions is the most important. The diagnosis can be carried out by direct examination of samples revealing the presence of budding yeasts, as well as culture at 25 and 37 degrees C. Antifungals like the sulfamethoxazole-trimethoprime combination, amphotericin B, but especially azole derivatives are use in the therapeutic management of patients. Detection and gp 43 antigen assay is useful for the patient's follow-up.

An Apicomplexan Actin-Binding Protein Serves as a Connector and Lipid Sensor to Coordinate Motility and Invasion.

PubMed

Jacot, Damien; Tosetti, Nicolò; Pires, Isa; Stock, Jessica; Graindorge, Arnault; Hung, Yu-Fu; Han, Huijong; Tewari, Rita; Kursula, Inari; Soldati-Favre, Dominique

2016-12-14

Apicomplexa exhibit a unique form of substrate-dependent gliding motility central for host cell invasion and parasite dissemination. Gliding is powered by rearward translocation of apically secreted transmembrane adhesins via their interaction with the parasite actomyosin system. We report a conserved armadillo and pleckstrin homology (PH) domain-containing protein, termed glideosome-associated connector (GAC), that mediates apicomplexan gliding motility, invasion, and egress by connecting the micronemal adhesins with the actomyosin system. TgGAC binds to and stabilizes filamentous actin and specifically associates with the transmembrane adhesin TgMIC2. GAC localizes to the apical pole in invasive stages of Toxoplasma gondii and Plasmodium berghei, and apical positioning of TgGAC depends on an apical lysine methyltransferase, TgAKMT. GAC PH domain also binds to phosphatidic acid, a lipid mediator associated with microneme exocytosis. Collectively, these findings indicate a central role for GAC in spatially and temporally coordinating gliding motility and invasion. Copyright © 2016 Elsevier Inc. All rights reserved.

Mammal madness: is the mammal tree of life not yet resolved?

PubMed Central

Foley, Nicole M.; Springer, Mark S.

2016-01-01

Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90–110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position and divergence time of the root of placental mammals, and certain ‘hard nodes’ such as the Laurasiatheria polytomy and Paenungulata that seem impossible to resolve. Here, we explore recent consensus and conflict among mammalian phylogenetic studies and explore the reasons for the remaining conflicts. The question of whether the mammal tree of life is or can be ever resolved is also addressed. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325836

Validation of qPCR Methods for the Detection of Mycobacterium in New World Animal Reservoirs.

PubMed

Housman, Genevieve; Malukiewicz, Joanna; Boere, Vanner; Grativol, Adriana D; Pereira, Luiz Cezar M; Silva, Ita de Oliveira; Ruiz-Miranda, Carlos R; Truman, Richard; Stone, Anne C

2015-11-01

Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tuberculosis complex, MTBC) continue to impact modern human populations. Therefore, methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats. Here we tested for mycobacterial-specific single- and multi-copy loci using qPCR. In a trial study in which armadillos were artificially infected with M. leprae, these techniques were specific and sensitive to pathogen detection, while more traditional ELISAs were only specific. These assays were then employed in a case study to detect M. leprae as well as MTBC in wild marmosets. All marmosets were negative for M. leprae DNA, but 14 were positive for the mycobacterial rpoB gene assay. Targeted capture and sequencing of rpoB and other MTBC genes validated the presence of mycobacterial DNA in these samples and revealed that qPCR is useful for identifying mycobacterial-infected animal hosts.

Molecular identification of Coccidioides spp. in soil samples from Brazil

PubMed Central

2011-01-01

Background Since 1991 several outbreaks of acute coccidioidomycosis (CM) were diagnosed in the semi-arid Northeast of Brazil, mainly related to disturbance of armadillo burrows caused by hunters while digging them for the capture of these animals. This activity causes dust contaminated with arthroconidia of Coccidioides posadasii, which, once inhaled, cause the mycosis. We report on the identification of C. posadasii in soil samples related to outbreaks of CM. Results Twenty four soil samples had their DNA extracted and subsequently submitted to a semi-nested PCR technique using specific primers. While only 6 (25%) soil samples were positive for C. posadasii by mice inoculation, all (100%) were positive by the molecular tool. Conclusion This methodology represents a simple, sensitive and specific molecular technique to determine the environmental distribution of Coccidioides spp. in endemic areas, but cannot distinguish the species. Moreover, it may be useful to identify culture isolates. Key-words: 1. Coccidioidomycosis. 2. Coccidioides spp. 3. C. posadasii. 4. Semi-arid. 5. Semi-nested PCR PMID:21575248

Changes in the cutting efficiency of different types of dental diamond rotary instrument with repeated cuts and disinfection.

PubMed

Bae, Jin-Hyuk; Yi, Jaeyoung; Kim, Sungtae; Shim, June-Sung; Lee, Keun-Woo

2014-01-01

Cutting efficiency is one of the most important factors to consider when a specific dental diamond rotary instrument is selected. However, the selection of a dental diamond rotary instrument is based on clinical experience rather than any scientific evidence. The purpose of this study was to identify how the cutting efficiency of different types of dental diamond rotary instrument changed with repeated cuts and disinfection. Four types of diamond rotary instrument from 2 dental manufacturers (Shofu, Jin Dental) were investigated with a high-speed air-turbine handpiece. The groups were as follows: S cham group (n=10): chamfer design from Shofu; J cham group (n=10): chamfer design from Jin Dental; S thin group (n=10): thin tapered design from Shofu; J thin group (n=10): thin tapered design from Jin Dental. Changes in the cutting efficiency of diamond rotary instruments on glass ceramic blocks were measured after repeated cuts. Changes in cutting efficiency also were measured for 30 diamond rotary instruments, the same type as those used in group J cham after disinfection with ethylene oxide gas, immersion in solution, or autoclaving. One-way ANOVA, 2-way ANOVA, and repeated-measures ANOVA were used to identify differences in cutting efficiency, in total cutting efficiency, and change trend in cutting efficiency (α=.05). The Tukey honestly significant difference method was used for the post hoc tests. The principal metal components of the diamond rotary instruments were detected with x-ray spectrometry. The mean (standard deviation [SD]) total cutting efficiency after 10 cuts in the 4 groups was in the following order: J cham group (0.210 ± 0.064 g/min) > S cham group (0.170 ± 0.064 g/min) > J thin group (0.130 ± 0.042 g/min) > S thin group (0.010 ± 0.040 g/min) (P<.05).The decrease in the cutting efficiency was greatest after the first cut. The cutting efficiency was not influenced by repeated disinfection. The cutting efficiencies of diamond rotary instruments with different designs and particle sizes showed a decreasing trend after repeated cuts but did not show any change after various disinfecting procedures. Copyright © 2014 Editorial Council for the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

Comparative Robustness of Recent Methods for Analyzing Multivariate Repeated Measures Designs

ERIC Educational Resources Information Center

Seco, Guillermo Vallejo; Gras, Jaime Arnau; Garcia, Manuel Ato

2007-01-01

This study evaluated the robustness of two recent methods for analyzing multivariate repeated measures when the assumptions of covariance homogeneity and multivariate normality are violated. Specifically, the authors' work compares the performance of the modified Brown-Forsythe (MBF) procedure and the mixed-model procedure adjusted by the…

Repeating Input-Based Tasks with Young Beginner Learners

ERIC Educational Resources Information Center

Shintani, Natsuko

2012-01-01

The study reported in this article investigated task-repetition with young Japanese children. Fifteen children with no prior knowledge of English completed a communicative listening task that was designed to introduce new vocabulary. The same task was repeated nine times over five weeks. In line with Allwright's (1984) claim that "interaction…

Progress Report and Topical Survey, 1980-1981.

DTIC Science & Technology

1981-03-01

Introduction. .. ........................... 1 TOPICAL SURVEY: GAMES WITH INCOMPLETE INFORMATION .. ........ 2 1. Extensive Games .. ..................... 3...2. Finitely Repeated Games .. ................. 9 3. Infinitely Repeated Games .. ................ 12 4. Nonrandomized Strategies...been focused on the application of results from game theory. Although this is only one of the several approaches to organizational design in the

Variance Estimation Using Replication Methods in Structural Equation Modeling with Complex Sample Data

ERIC Educational Resources Information Center

Stapleton, Laura M.

2008-01-01

This article discusses replication sampling variance estimation techniques that are often applied in analyses using data from complex sampling designs: jackknife repeated replication, balanced repeated replication, and bootstrapping. These techniques are used with traditional analyses such as regression, but are currently not used with structural…

ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants

PubMed Central

Kapil, Aditi; Rai, Piyush Kant; Shanker, Asheesh

2014-01-01

Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1–6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants. Database URL: www.compubio.in/chlorossrdb/ PMID:25380781

ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants.

PubMed

Kapil, Aditi; Rai, Piyush Kant; Shanker, Asheesh

2014-01-01

Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1-6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants. Database URL: www.compubio.in/chlorossrdb/ © The Author(s) 2014. Published by Oxford University Press.

A smart way to identify and extract repeated patterns of a layout

NASA Astrophysics Data System (ADS)

Wei, Fang; Gu, Tingting; Chu, Zhihao; Zhang, Chenming; Chen, Han; Zhu, Jun; Hu, Xinyi; Du, Chunshan; Wan, Qijian; Liu, Zhengfang

2018-03-01

As integrated circuits (IC) technology moves forward, manufacturing process is facing more and more challenges. Optical proximity correction (OPC) has been playing an important role in the whole manufacturing process. In the deep sub-micron technology, OPC engineers not only need to guarantee the layout designs to be manufacturable but also take a more precise control of the critical patterns to ensure a high performance circuit. One of the tasks that would like to be performed is the consistency checking as the identical patterns under identical context should have identical OPC results in theory, like SRAM regions. Consistency checking is essentially a technique of repeated patterns identification, extraction and derived patterns (i.e. OPC results) comparison. The layout passing to the OPC team may not have enough design hierarchical information either because the original designs may have undergone several layout processing steps or some other unknown reasons. This paper presents a generic way to identify and extract repeated layout structures in SRAM regions purely based on layout pattern analysis through Calibre Pattern Matching and Calibre equation-based DRC (eqDRC). Without Pattern Matching and eqDRC, it will take lots of effort to manually get it done by trial and error, it is almost impossible to automate the pattern analysis process. Combining Pattern Matching and eqDRC opens a new way to implement this flow. The repeated patterns must have some fundamental features for measurement of pitches in the horizontal and vertical direction separately by Calibre eqDRC and meanwhile can be a helper to generate some anchor points which will be the starting points for Pattern Matching to capture patterns. The informative statistical report from the pattern search tells the match counts individually for each patterns captured. Experiment shows that this is a smart way of identifying and extracting repeated structures effectively. The OPC results are the derived layers on these repeated structures, by running pattern search using design layers as pattern layers and OPC results as marker layers, it is an easy job to compare the consistency.

Precision and repeatability of the Optotrak 3020 motion measurement system.

PubMed

States, R A; Pappas, E

2006-01-01

Several motion analysis systems are used by researchers to quantify human motion and to perform accurate surgical procedures. The Optotrak 3020 is one of these systems and despite its widespread use there is not any published information on its precision and repeatability. We used a repeated measures design study to evaluate the precision and repeatability of the Optotrak 3020 by measuring distance and angle in three sessions, four distances and three conditions (motion, static vertical, and static tilted). Precision and repeatability were found to be excellent for both angle and distance although they decreased with increasing distance from the sensors and with tilt from the plane of the sensors. Motion did not have a significant effect on the precision of the measurements. In conclusion, the measurement error of the Optotrak is minimal. Further studies are needed to evaluate its precision and repeatability under human motion conditions.

Mission design for NISAR repeat-pass Interferometric SAR

NASA Astrophysics Data System (ADS)

Alvarez-Salazar, Oscar; Hatch, Sara; Rocca, Jennifer; Rosen, Paul; Shaffer, Scott; Shen, Yuhsyen; Sweetser, Theodore; Xaypraseuth, Peter

2014-10-01

The proposed spaceborne NASA-ISRO SAR (NISAR) mission would use the repeat-pass interferometric Synthetic Aperture Radar (InSAR) technique to measure the changing shape of Earth's surface at the centimeter scale in support of investigations in solid Earth and cryospheric sciences. Repeat-pass InSAR relies on multiple SAR observations acquired from nearly identical positions of the spacecraft as seen from the ground. Consequently, there are tight constraints on the repeatability of the orbit, and given the narrow field of view of the radar antenna beam, on the repeatability of the beam pointing. The quality and accuracy of the InSAR data depend on highly precise control of both orbital position and observatory pointing throughout the science observation life of the mission. This paper describes preliminary NISAR requirements and rationale for orbit repeatability and attitude control in order to meet science requirements. A preliminary error budget allocation and an implementation approach to meet these allocations are also discussed.

Retinoic acid-induced differentiation of retrovirus-infected HL-60 cells is associated with enhanced transcription from the viral long terminal repeat

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

Collins, S.J.

1988-11-01

The author infected different human leukemic cell lines with an amphotropic retrovirus vector (designated PA317/N2) which confers G418 resistance and contains the Moloney murine leukemia virus long terminal repeat. In retrovirus-infected G418-resistant HL-60 cells, induction of granulocyte differentiation by retinoic acid was invariably accompanied by a marked increase (5- to 10-fold) in the transcriptional activity of the integrated retroviral long terminal repeat.

Valerian

MedlinePlus

... the likelihood of bias inherent in the study design [ 12 ]. Although all nine trials had flaws, three ... withdrawal . The first study used a repeated-measures design; 128 volunteers were given 400 mg of an ...

Estimating open population site occupancy from presence-absence data lacking the robust design.

PubMed

Dail, D; Madsen, L

2013-03-01

Many animal monitoring studies seek to estimate the proportion of a study area occupied by a target population. The study area is divided into spatially distinct sites where the detected presence or absence of the population is recorded, and this is repeated in time for multiple seasons. However, when occupied sites are detected with probability p < 1, the lack of a detection does not imply lack of occupancy. MacKenzie et al. (2003, Ecology 84, 2200-2207) developed a multiseason model for estimating seasonal site occupancy (ψt ) while accounting for unknown p. Their model performs well when observations are collected according to the robust design, where multiple sampling occasions occur during each season; the repeated sampling aids in the estimation p. However, their model does not perform as well when the robust design is lacking. In this paper, we propose an alternative likelihood model that yields improved seasonal estimates of p and Ψt in the absence of the robust design. We construct the marginal likelihood of the observed data by conditioning on, and summing out, the latent number of occupied sites during each season. A simulation study shows that in cases without the robust design, the proposed model estimates p with less bias than the MacKenzie et al. model and hence improves the estimates of Ψt . We apply both models to a data set consisting of repeated presence-absence observations of American robins (Turdus migratorius) with yearly survey periods. The two models are compared to a third estimator available when the repeated counts (from the same study) are considered, with the proposed model yielding estimates of Ψt closest to estimates from the point count model. Copyright © 2013, The International Biometric Society.

Approximate analysis for repeated eigenvalue problems with applications to controls-structure integrated design

NASA Technical Reports Server (NTRS)

Kenny, Sean P.; Hou, Gene J. W.

1994-01-01

A method for eigenvalue and eigenvector approximate analysis for the case of repeated eigenvalues with distinct first derivatives is presented. The approximate analysis method developed involves a reparameterization of the multivariable structural eigenvalue problem in terms of a single positive-valued parameter. The resulting equations yield first-order approximations to changes in the eigenvalues and the eigenvectors associated with the repeated eigenvalue problem. This work also presents a numerical technique that facilitates the definition of an eigenvector derivative for the case of repeated eigenvalues with repeated eigenvalue derivatives (of all orders). Examples are given which demonstrate the application of such equations for sensitivity and approximate analysis. Emphasis is placed on the application of sensitivity analysis to large-scale structural and controls-structures optimization problems.

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.

[Analysis of variance of repeated data measured by water maze with SPSS].

PubMed

Qiu, Hong; Jin, Guo-qin; Jin, Ru-feng; Zhao, Wei-kang

2007-01-01

To introduce the method of analyzing repeated data measured by water maze with SPSS 11.0, and offer a reference statistical method to clinical and basic medicine researchers who take the design of repeated measures. Using repeated measures and multivariate analysis of variance (ANOVA) process of the general linear model in SPSS and giving comparison among different groups and different measure time pairwise. Firstly, Mauchly's test of sphericity should be used to judge whether there were relations among the repeatedly measured data. If any (P

Quantitative analysis of TALE-DNA interactions suggests polarity effects.

PubMed

Meckler, Joshua F; Bhakta, Mital S; Kim, Moon-Soo; Ovadia, Robert; Habrian, Chris H; Zykovich, Artem; Yu, Abigail; Lockwood, Sarah H; Morbitzer, Robert; Elsäesser, Janett; Lahaye, Thomas; Segal, David J; Baldwin, Enoch P

2013-04-01

Transcription activator-like effectors (TALEs) have revolutionized the field of genome engineering. We present here a systematic assessment of TALE DNA recognition, using quantitative electrophoretic mobility shift assays and reporter gene activation assays. Within TALE proteins, tandem 34-amino acid repeats recognize one base pair each and direct sequence-specific DNA binding through repeat variable di-residues (RVDs). We found that RVD choice can affect affinity by four orders of magnitude, with the relative RVD contribution in the order NG > HD ≈ NN > NI > NK. The NN repeat preferred the base G over A, whereas the NK repeat bound G with 10(3)-fold lower affinity. We compared AvrBs3, a naturally occurring TALE that recognizes its target using some atypical RVD-base combinations, with a designed TALE that precisely matches 'standard' RVDs with the target bases. This comparison revealed unexpected differences in sensitivity to substitutions of the invariant 5'-T. Another surprising observation was that base mismatches at the 5' end of the target site had more disruptive effects on affinity than those at the 3' end, particularly in designed TALEs. These results provide evidence that TALE-DNA recognition exhibits a hitherto un-described polarity effect, in which the N-terminal repeats contribute more to affinity than C-terminal ones.

Increasing Positive Perceptions of Counseling: The Importance of Repeated Exposures

ERIC Educational Resources Information Center

Kaplan, Scott A.; Vogel, David L.; Gentile, Douglas A.; Wade, Nathaniel G.

2012-01-01

This study assesses the effectiveness of repeated exposures to a video intervention based on the Elaboration Likelihood Model. The video was designed to increase help-seeking attitudes and perceptions of peer norms and to decrease the stigma associated with seeking counseling. Participants were 290 undergraduates who were randomly assigned to a…

Near-Peer Teaching in Paramedic Education: A Repeated Measures Design

ERIC Educational Resources Information Center

Williams, Brett; Nguyen, David

2017-01-01

The transition of the Australian paramedic discipline from vocation education and training to the higher education sector has seen a sharp rise in interest in near-peer teaching (NPT). The objective of this study was to examine satisfaction levels of NPT over one academic semester among undergraduate paramedic students. A repeated measured design…

Evaluating the Performance of Repeated Measures Approaches in Replicating Experimental Benchmark Results

ERIC Educational Resources Information Center

McConeghy, Kevin; Wing, Coady; Wong, Vivian C.

2015-01-01

Randomized experiments have long been established as the gold standard for addressing causal questions. However, experiments are not always feasible or desired, so observational methods are also needed. When multiple observations on the same variable are available, a repeated measures design may be used to assess whether a treatment administered…

Using Repeated Reading to Improve Reading Speed and Comprehension in Students with Visual Impairments

ERIC Educational Resources Information Center

Savaiano, Mackenzie E.; Hatton, Deborah D.

2013-01-01

Introduction: This study evaluated whether children with visual impairments who receive repeated reading instruction exhibit an increase in their oral reading rate and comprehension and a decrease in oral reading error rates. Methods: A single-subject, changing-criterion design replicated across three participants was used to demonstrate the…

Improvements in Anatomy Knowledge When Utilizing a Novel Cyclical "Observe-Reflect-Draw-Edit-Repeat" Learning Process

ERIC Educational Resources Information Center

Backhouse, Mark; Fitzpatrick, Michael; Hutchinson, Joseph; Thandi, Charankumal S.; Keenan, Iain D.

2017-01-01

Innovative educational strategies can provide variety and enhance student learning while addressing complex logistical and financial issues facing modern anatomy education. "Observe-Reflect-Draw-Edit-Repeat" (ORDER), a novel cyclical artistic process, has been designed based on cognitivist and constructivist learning theories, and on…

Familiarity with Content and Syllogistic Reasoning.

ERIC Educational Resources Information Center

Mast, Terrill A.; And Others

Forty-four education and 44 dental students were administered a 30-item syllogism test containing five syllogic forms six times repeated in three different content forms--technical dental terms, common dental terms, and content-free (letters). Data were analyzed using a two-factor with repeated measures on one factor design. It was found that…

Improving cellulase productivity of Penicillium oxalicum RE-10 by repeated fed-batch fermentation strategy.

PubMed

Han, Xiaolong; Song, Wenxia; Liu, Guodong; Li, Zhonghai; Yang, Piao; Qu, Yinbo

2017-03-01

Medium optimization and repeated fed-batch fermentation were performed to improve the cellulase productivity by P. oxalicum RE-10 in submerged fermentation. First, Plackett-Burman design (PBD) and central composite design (CCD) were used to optimize the medium for cellulase production. PBD demonstrated wheat bran and NaNO 3 had significant influences on cellulase production. The CCD results showed the maximum filter paper activity (FPA) production of 8.61U/mL could be achieved in Erlenmeyer flasks. The maximal FPA reached 12.69U/mL by submerged batch fermentation in a 7.5-L stirred tank, 1.76-fold higher than that on the original medium. Then, the repeated fed-batch fermentation strategy was performed successfully for increasing the cellulase productivity from 105.75U/L/h in batch fermentation to 158.38U/L/h. The cellulase activity and the glucan conversion of delignined corn cob residue hydrolysis had no significant difference between the enzymes sampled from different cycles of the repeated fed-batch fermentation and that from batch culture. Copyright © 2016 Elsevier Ltd. All rights reserved.

7 CFR 801.11 - Related design requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Related design requirements. 801.11 Section 801.11... FOR GRAIN INSPECTION EQUIPMENT § 801.11 Related design requirements. (a) Suitability. The design... tolerances prescribed in §§ 801.3 through 801.10, be capable of repeating its results when the equipment is...

The Value of Interrupted Time-Series Experiments for Community Intervention Research

PubMed Central

Biglan, Anthony; Ary, Dennis; Wagenaar, Alexander C.

2015-01-01

Greater use of interrupted time-series experiments is advocated for community intervention research. Time-series designs enable the development of knowledge about the effects of community interventions and policies in circumstances in which randomized controlled trials are too expensive, premature, or simply impractical. The multiple baseline time-series design typically involves two or more communities that are repeatedly assessed, with the intervention introduced into one community at a time. It is particularly well suited to initial evaluations of community interventions and the refinement of those interventions. This paper describes the main features of multiple baseline designs and related repeated-measures time-series experiments, discusses the threats to internal validity in multiple baseline designs, and outlines techniques for statistical analyses of time-series data. Examples are given of the use of multiple baseline designs in evaluating community interventions and policy changes. PMID:11507793

Optimising experimental design for MEG resting state functional connectivity measurement.

PubMed

Liuzzi, Lucrezia; Gascoyne, Lauren E; Tewarie, Prejaas K; Barratt, Eleanor L; Boto, Elena; Brookes, Matthew J

2017-07-15

The study of functional connectivity using magnetoencephalography (MEG) is an expanding area of neuroimaging, and adds an extra dimension to the more common assessments made using fMRI. The importance of such metrics is growing, with recent demonstrations of their utility in clinical research, however previous reports suggest that whilst group level resting state connectivity is robust, single session recordings lack repeatability. Such robustness is critical if MEG measures in individual subjects are to prove clinically valuable. In the present paper, we test how practical aspects of experimental design affect the intra-subject repeatability of MEG findings; specifically we assess the effect of co-registration method and data recording duration. We show that the use of a foam head-cast, which is known to improve co-registration accuracy, increased significantly the between session repeatability of both beamformer reconstruction and connectivity estimation. We also show that recording duration is a critical parameter, with large improvements in repeatability apparent when using ten minute, compared to five minute recordings. Further analyses suggest that the origin of this latter effect is not underpinned by technical aspects of source reconstruction, but rather by a genuine effect of brain state; short recordings are simply inefficient at capturing the canonical MEG network in a single subject. Our results provide important insights on experimental design and will prove valuable for future MEG connectivity studies. Copyright © 2016. Published by Elsevier Inc.

WebDASC: a web-based dietary assessment software for 8-11-year-old Danish children.

PubMed

Biltoft-Jensen, A; Trolle, E; Christensen, T; Islam, N; Andersen, L F; Egenfeldt-Nielsen, S; Tetens, I

2014-01-01

  The present study describes the development and formative evaluation of the Web-based Dietary Assessment Software for Children (WebDASC). WebDASC is part of the OPUS project ('Optimal well-being, development and health for Danish children through a healthy New Nordic Diet') and was intended to measure dietary change resulting from a school-based intervention.   WebDASC was developed as a self-administered tool that could be used by 8-11-year-old children with or without parent's aid. The development of WebDASC followed a prototyping approach: focus groups, informal interviews, literature review, and usability tests preceded its release. Special consideration was given to age-appropriate design issues.   In WebDASC an animated armadillo guides respondents through six daily eating occasions and helps them report foods and beverages previously consumed. A database of 1300 food items is available either through category browse or free text search, aided by a spell check application. A type-in format is available for foods not otherwise found through category browse or text search. Amount consumed is estimated by selecting the closest portion size among four different digital images. WebDASC includes internal checks for frequently forgotten foods, and the following features to create motivation: a food-meter displaying cumulative weight of foods reported, a most popular food ranking, and a computer game with a high score list.   WebDASC was developed as an intuitive, cost-effective, and engaging method to collect detailed dietary data from 8- to 11-year-old children. Preliminary testing demonstrated that it was well accepted among children. © 2012 The Authors. Journal of Human Nutrition and Dietetics © 2012 The British Dietetic Association Ltd.

Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights

PubMed Central

Kumar, Amitha Sampath; Sowpati, Divya Tej; Mishra, Rakesh K.

2016-01-01

Microsatellites or simple sequence repeats (SSR) are abundant, highly diverse stretches of short DNA repeats present in all genomes. Tandem mono/tri/hexanucleotide repeats in the coding regions contribute to single amino acids repeats (SAARs) in the proteome. While SSRs in the coding region always result in amino acid repeats, a majority of SAARs arise due to a combination of various codons representing the same amino acid and not as a consequence of SSR events. Certain amino acids are abundant in repeat regions indicating a positive selection pressure behind the accumulation of SAARs. By analysing 22 proteomes including the human proteome, we explored the functional and structural relationship of amino acid repeats in an evolutionary context. Only ~15% of repeats are present in any known functional domain, while ~74% of repeats are present in the disordered regions, suggesting that SAARs add to the functionality of proteins by providing flexibility, stability and act as linker elements between domains. Comparison of SAAR containing proteins across species reveals that while shorter repeats are conserved among orthologs, proteins with longer repeats, >15 amino acids, are unique to the respective organism. Lysine repeats are well conserved among orthologs with respect to their length and number of occurrences in a protein. Other amino acids such as glutamic acid, proline, serine and alanine repeats are generally conserved among the orthologs with varying repeat lengths. These findings suggest that SAARs have accumulated in the proteome under positive selection pressure and that they provide flexibility for optimal folding of functional/structural domains of proteins. The insights gained from our observations can help in effective designing and engineering of proteins with novel features. PMID:27893794

An Attempt To Develop An "Intelligent" Lens Design Program

NASA Astrophysics Data System (ADS)

Viswanathan, V. K.; Bohachevsky, I. O.; Cotter, T. P.

1986-02-01

We are developing a lens design program intended to operate without user intervention, and to improve its performance with repeated usage. The methodology and current status will be discussed in this paper.

Unmixing the Mixing Cost: Contributions from Dimensional Relevance and Stimulus-Response Suppression

ERIC Educational Resources Information Center

Mari-Beffa, Paloma; Cooper, Stephen; Houghton, George

2012-01-01

When participants repeat the same task in a context in which the task may also switch (a mixed block), performance deteriorates compared to when there is only one task repeating (a pure block). Three experiments were designed to assess how perceptual and motor transitions influenced this mixing cost. Experiment 1 provided three pure block…

Spanish Vocabulary-Bridging Technology-Enhanced Instruction for Young English Language Learners' Word Learning

ERIC Educational Resources Information Center

Leacox, Lindsey; Jackson, Carla Wood

2014-01-01

This study examined preschool and kindergarten English language learners (ELLs) attending a migrant summer programme and their vocabulary word learning during both adult-read and technology-enhanced repeated readings. In a within-subject design, 24 ELLs (four to six years old) engaged in repeated readings in a control and a treatment condition. In…

Effect Sizes and their Intervals: The Two-Level Repeated Measures Case

ERIC Educational Resources Information Center

Algina, James; Keselman, H. J.; Penfield, Randall D.

2005-01-01

Probability coverage for eight different confidence intervals (CIs) of measures of effect size (ES) in a two-level repeated measures design was investigated. The CIs and measures of ES differed with regard to whether they used least squares or robust estimates of central tendency and variability, whether the end critical points of the interval…

Repeated Interviews with Children Who Are the Alleged Victims of Sexual Abuse

ERIC Educational Resources Information Center

Katz, Carmit; Hershkowitz, Irit

2013-01-01

Objective: The present study was designed to test the effects of repeated retrievals in the course of forensic investigations with children who are the alleged victims of sexual abuse. Method: Using the National Institute of Child Health and Human Development protocol, 56 children participated in a first free-recall interview that was followed by…

Pairwise Multiple Comparisons in Single Group Repeated Measures Analysis.

ERIC Educational Resources Information Center

Barcikowski, Robert S.; Elliott, Ronald S.

Research was conducted to provide educational researchers with a choice of pairwise multiple comparison procedures (P-MCPs) to use with single group repeated measures designs. The following were studied through two Monte Carlo (MC) simulations: (1) The T procedure of J. W. Tukey (1953); (2) a modification of Tukey's T (G. Keppel, 1973); (3) the…

The Effects of Repeated Readings on the Reading Performances of Hispanic English Language Learners with Specific Learning Disabilities

ERIC Educational Resources Information Center

Landa, Katrina G.; Barbetta, Patricia M.

2017-01-01

A multiple probe across participants design was used to explore the effects of repeated readings on the reading fluency, errors, and comprehension of 4, third-to-fifth grade English language learners (ELLs) with specific learning disabilities (SLD). Also, generalization measures to untaught passages and maintenance data were collected. In…

Delayed Auditory Feedback in the Treatment of Stuttering: Clients as Consumers

ERIC Educational Resources Information Center

Van Borsel, John; Reunes, Gert; Van den Bergh, Nathalie

2003-01-01

Purpose: To investigate the effect of repeated exposure to delayed auditory feedback (DAF) during a 3-month period outside a clinical environment and with only minimal clinical guidance on speech fluency in people who stutter. Method: A pretest-post-test design was used with repeated exposure to DAF during 3 months as the independent variable.…

The potential benefits of repeated measure experiments for fish disease-challenge host-pathogen investigations.

PubMed

Hall, L Malcolm; Collins, Catherine; Collet, Bertrand

2018-02-02

The utility of molecular response data arising from in-vivo single and repeated measure fish disease-challenge experiments is compared. An in-silico 'experiment' involving the generation of two imaginary immune-molecule quantity response profiles over time for individual animals was carried out. Daily 'observed' molecule quantities were drawn from the 'known' individual response profiles to mimic the results of single and repeated measurement. The results indicate that repeated measure experiments are required to infer individual level response profiles, and that these experiments also provide more accurate summary statistics and data more suited to inferring the dependent ordering of the molecular response. Additionally repeated measure experiments utilise fewer animals than single measure experiments. These results are described alongside a discussion of experimental methodological issues pertinent to the adoption of aquatic animal repeated measure experimental designs. We conclude that investigators need to take particular care when making inferences from single measure experiments and that serious consideration should be given to using repeated measure experiments for in-vivo fish disease-challenge investigations. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

PubMed Central

Quiroz, Felipe García; Chilkoti, Ashutosh

2015-01-01

Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-assembly in nature and in man-made material systems. Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level. PMID:26390327

Design of a blood-freezing system for leukemia research

NASA Technical Reports Server (NTRS)

Williams, T. E.; Cygnarowicz, T. A.

1978-01-01

Leukemia research involves the use of cryogenic freezing and storage equipment. In a program being carried out at the National Cancer Institute (NCI), bone marrow (white blood cells) was frozen using a standard cryogenic biological freezer. With this system, it is difficult to maintain the desired rate of freezing and repeatability from sample to sample. A freezing system was developed that satisfies the requirements for a repeatable, constant freezing rate. The system was delivered to NIC and is now operational. This report describes the design of the major subsystems, the analyses, the operating procedure, and final system test results.

Design-Comparable Effect Sizes in Multiple Baseline Designs: A General Modeling Framework

ERIC Educational Resources Information Center

Pustejovsky, James E.; Hedges, Larry V.; Shadish, William R.

2014-01-01

In single-case research, the multiple baseline design is a widely used approach for evaluating the effects of interventions on individuals. Multiple baseline designs involve repeated measurement of outcomes over time and the controlled introduction of a treatment at different times for different individuals. This article outlines a general…

Prediction of resilient modulus from soil index properties.

DOT National Transportation Integrated Search

2004-11-01

Subgrade soil characterization in terms of Resilient Modulus (MR) has become crucial for pavement design. For a new : design, MR values are generally obtained by conducting repeated load triaxial tests on reconstituted/undisturbed cylindrical : speci...

Prediction of resilient modulus from soil index properties

DOT National Transportation Integrated Search

2004-11-01

Subgrade soil characterization in terms of Resilient Modulus (MR) has become crucial for pavement design. For a new design, MR values are generally obtained by conducting repeated load triaxial tests on reconstituted/undisturbed cylindrical specimens...

Falling weight deflectometer for estimating subgrade resilient moduli.

DOT National Transportation Integrated Search

2003-12-01

Subgrade soil characterization expressed in terms of resilient modulus, MR, has become crucial for pavement design. For : new pavement design, MR values are generally obtained by conducting repeated load triaxial tests on reconstituted/undisturbed : ...

Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification.

PubMed

Li, Lixin; Piatek, Marek J; Atef, Ahmed; Piatek, Agnieszka; Wibowo, Anjar; Fang, Xiaoyun; Sabir, J S M; Zhu, Jian-Kang; Mahfouz, Magdy M

2012-03-01

Transcription activator-like effectors (TALEs) can be used as DNA-targeting modules by engineering their repeat domains to dictate user-selected sequence specificity. TALEs have been shown to function as site-specific transcriptional activators in a variety of cell types and organisms. TALE nucleases (TALENs), generated by fusing the FokI cleavage domain to TALE, have been used to create genomic double-strand breaks. The identity of the TALE repeat variable di-residues, their number, and their order dictate the DNA sequence specificity. Because TALE repeats are nearly identical, their assembly by cloning or even by synthesis is challenging and time consuming. Here, we report the development and use of a rapid and straightforward approach for the construction of designer TALE (dTALE) activators and nucleases with user-selected DNA target specificity. Using our plasmid set of 100 repeat modules, researchers can assemble repeat domains for any 14-nucleotide target sequence in one sequential restriction-ligation cloning step and in only 24 h. We generated several custom dTALEs and dTALENs with new target sequence specificities and validated their function by transient expression in tobacco leaves and in vitro DNA cleavage assays, respectively. Moreover, we developed a web tool, called idTALE, to facilitate the design of dTALENs and the identification of their genomic targets and potential off-targets in the genomes of several model species. Our dTALE repeat assembly approach along with the web tool idTALE will expedite genome-engineering applications in a variety of cell types and organisms including plants.

Mechanical unfolding of an ankyrin repeat protein.

PubMed

Serquera, David; Lee, Whasil; Settanni, Giovanni; Marszalek, Piotr E; Paci, Emanuele; Itzhaki, Laura S

2010-04-07

Ankryin repeat proteins comprise tandem arrays of a 33-residue, predominantly alpha-helical motif that stacks roughly linearly to produce elongated and superhelical structures. They function as scaffolds mediating a diverse range of protein-protein interactions, and some have been proposed to play a role in mechanical signal transduction processes in the cell. Here we use atomic force microscopy and molecular-dynamics simulations to investigate the natural 7-ankyrin repeat protein gankyrin. We find that gankyrin unfolds under force via multiple distinct pathways. The reactions do not proceed in a cooperative manner, nor do they always involve fully stepwise unfolding of one repeat at a time. The peeling away of half an ankyrin repeat, or one or more ankyrin repeats, occurs at low forces; however, intermediate species are formed that are resistant to high forces, and the simulations indicate that in some instances they are stabilized by nonnative interactions. The unfolding of individual ankyrin repeats generates a refolding force, a feature that may be more easily detected in these proteins than in globular proteins because the refolding of a repeat involves a short contraction distance and incurs a low entropic cost. We discuss the origins of the differences between the force- and chemical-induced unfolding pathways of ankyrin repeat proteins, as well as the differences between the mechanics of natural occurring ankyrin repeat proteins and those of designed consensus ankyin repeat and globular proteins. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Maintaining confidentiality in prospective studies: anonymous repeated measurements via email (ARME) procedure.

PubMed

Carli, Vladimir; Hadlaczky, Gergö; Wasserman, Camilla; Stingelin-Giles, Nicola; Reiter-Theil, Stella; Wasserman, Danuta

2012-02-01

Respecting and protecting the confidentiality of data and the privacy of individuals regarding the information that they have given as participants in a research project is a cornerstone of complying with accepted research standards. However, in longitudinal studies, establishing and maintaining privacy is often challenging because of the necessity of repeated contact with participants. A novel internet-based solution is introduced here, which maintains privacy while at the same time ensures linkage of data to individual participants in a repeated measures design. With the use of the anonymous repeated measurements via email (ARME) procedure, two separate one-way communication systems are established through ad hoc email accounts and a secure study website. Strengths and limitations of the approach are discussed.

Time code dissemination experiment via the SIRIO-1 VHF transponder

NASA Technical Reports Server (NTRS)

Detoma, E.; Gobbo, G.; Leschiutta, S.; Pettiti, V.

1982-01-01

An experiment to evaluate the possibility of disseminating a time code via the SIRIO-1 satellite, by using the onboard VHF repeater is described. The precision in the synchronization of remote clocks was expected to be of the order of 0.1 to 1 ms. The RF carrier was in the VHF band, so that low cost receivers could be used and then a broader class of users could be served. An already existing repeater, even if not designed specifically for communications could be utilized; the operation of this repeater was not intended to affect any other function of the spacecraft (both the SHF repeater and the VHF telemetry link were active during the time code dissemination via the VHF transponder).

A Method for WD40 Repeat Detection and Secondary Structure Prediction

PubMed Central

Wang, Yang; Jiang, Fan; Zhuo, Zhu; Wu, Xian-Hui; Wu, Yun-Dong

2013-01-01

WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction. PMID:23776530

Heralded quantum repeater based on the scattering of photons off single emitters using parametric down-conversion source.

PubMed

Song, Guo-Zhu; Wu, Fang-Zhou; Zhang, Mei; Yang, Guo-Jian

2016-06-28

Quantum repeater is the key element in quantum communication and quantum information processing. Here, we investigate the possibility of achieving a heralded quantum repeater based on the scattering of photons off single emitters in one-dimensional waveguides. We design the compact quantum circuits for nonlocal entanglement generation, entanglement swapping, and entanglement purification, and discuss the feasibility of our protocols with current experimental technology. In our scheme, we use a parametric down-conversion source instead of ideal single-photon sources to realize the heralded quantum repeater. Moreover, our protocols can turn faulty events into the detection of photon polarization, and the fidelity can reach 100% in principle. Our scheme is attractive and scalable, since it can be realized with artificial solid-state quantum systems. With developed experimental technique on controlling emitter-waveguide systems, the repeater may be very useful in long-distance quantum communication.

Heralded quantum repeater based on the scattering of photons off single emitters using parametric down-conversion source

PubMed Central

Song, Guo-Zhu; Wu, Fang-Zhou; Zhang, Mei; Yang, Guo-Jian

2016-01-01

Quantum repeater is the key element in quantum communication and quantum information processing. Here, we investigate the possibility of achieving a heralded quantum repeater based on the scattering of photons off single emitters in one-dimensional waveguides. We design the compact quantum circuits for nonlocal entanglement generation, entanglement swapping, and entanglement purification, and discuss the feasibility of our protocols with current experimental technology. In our scheme, we use a parametric down-conversion source instead of ideal single-photon sources to realize the heralded quantum repeater. Moreover, our protocols can turn faulty events into the detection of photon polarization, and the fidelity can reach 100% in principle. Our scheme is attractive and scalable, since it can be realized with artificial solid-state quantum systems. With developed experimental technique on controlling emitter-waveguide systems, the repeater may be very useful in long-distance quantum communication. PMID:27350159

Effect of repeated earthquake on inelastic moment resisting concrete frame

NASA Astrophysics Data System (ADS)

Tahara, R. M. K.; Majid, T. A.; Zaini, S. S.; Faisal, A.

2017-10-01

This paper investigates the response of inelastic moment resisting concrete building under repeated earthquakes. 2D models consist of 3-storey, 6-storey and 9-storey representing low to medium rise building frame were designed using seismic load and ductility class medium (DCM) according to the requirements set by Euro Code 8. Behaviour factor and stiffness degradation were also taken into consideration. Seven sets of real repeated earthquakes as opposed to artificial earthquakes data were used. The response of the frame was measured in terms of the inter-storey drift and maximum displacement. By adopting repeated earthquake, the recorded mean IDR increased in the range of 3% - 21%. Similarly, in the case of maximum displacement, the values also increased from 20 mm to 40 mm. The findings concluded that the effect of using repeated earthquake in seismic analysis considerably influenced the inter-storey drift and the maximum displacement.

Genome-wide characterization and selection of expressed sequence tag simple sequence repeat primers for optimized marker distribution and reliability in peach

USDA-ARS?s Scientific Manuscript database

Expressed sequence tag (EST) simple sequence repeats (SSRs) in Prunus were mined, and flanking primers designed and used for genome-wide characterization and selection of primers to optimize marker distribution and reliability. A total of 12,618 contigs were assembled from 84,727 ESTs, along with 34...

A Primer on Longitudinal Data Analysis in Education. Technical Report #1320

ERIC Educational Resources Information Center

Nese, Joseph F. T.; Lai, Cheng-Fei; Anderson, Daniel

2013-01-01

Longitudinal data analysis in education is the study growth over time. A longitudinal study is one in which repeated observations of the same variables are recorded for the same individuals over a period of time. This type of research is known by many names (e.g., time series analysis or repeated measures design), each of which can imply subtle…

Children's False Memory and True Disclosure in the Face of Repeated Questions

ERIC Educational Resources Information Center

Schaaf, Jennifer M.; Alexander, Kristen Weede; Goodman, Gail S.

2008-01-01

The current study was designed to investigate children's memory and suggestibility for events differing in valence (positive or negative) and veracity (true or false). A total of 82 3- and 5-year-olds were asked repeated questions about true and false events, either in a grouped order (i.e., all questions about a certain event asked consecutively)…

Increasing Fluency in Disabled Middle School Readers: Repeated Reading Utilizing above Grade Level Reading Passages

ERIC Educational Resources Information Center

Paige, David D.

2006-01-01

This study examined the effects of repeated reading using above grade level narrative passages on: (a) reading rate as measured in words per minute (wpm) and (b) reading miscues. A single group, pretest-posttest design was used to measure the treatment effects. The study group consisted of 11, sixth grade African-American students with learning…

Comparing the Efficiency of Repeated Reading and Listening-While-Reading to Improve Fluency and Comprehension

ERIC Educational Resources Information Center

Hawkins, Renee O.; Marsicano, Richard; Schmitt, Ara J.; McCallum, Elizabeth; Musti-Rao, Shobana

2015-01-01

An alternating treatments design was used to compare the effects of two reading fluency interventions on the oral reading fluency and maze accuracy of four fourth-grade students. Also, by taking into account time spent in intervention, the efficiency of the two interventions was compared. In the adult-mediated repeated reading (RR) condition,…

Effects of Repeated Social Disruption on the Serotonergic and Dopaminergic Systems in two Genetic Lines of White Leghorn Layers

USDA-ARS?s Scientific Manuscript database

The study was designed to examine whether there are genetic differences in response to repeated social disruption (RSD). Two genetic strains of White Leghorn hens were used in the study; i.e., HGPS (the line selected for high group production and survivability), and DXL (DeKalb XL commercial line). ...

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.

Microsatellite analysis in the genome of Acanthaceae: An in silico approach.

PubMed

Kaliswamy, Priyadharsini; Vellingiri, Srividhya; Nathan, Bharathi; Selvaraj, Saravanakumar

2015-01-01

Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future.

47 CFR 25.144 - Licensing provisions for the 2.3 GHz satellite digital audio radio service.

Code of Federal Regulations, 2012 CFR

2012-10-01

... (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25... frequencies and emission designators of such communications, and the frequencies and emission designators used... repeaters will communicate, the frequencies and emission designators of such communications, and the...

47 CFR 25.144 - Licensing provisions for the 2.3 GHz satellite digital audio radio service.

Code of Federal Regulations, 2010 CFR

2010-10-01

... (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25... frequencies and emission designators of such communications, and the frequencies and emission designators used... repeaters will communicate, the frequencies and emission designators of such communications, and the...

47 CFR 25.144 - Licensing provisions for the 2.3 GHz satellite digital audio radio service.

Code of Federal Regulations, 2011 CFR

2011-10-01

... (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25... frequencies and emission designators of such communications, and the frequencies and emission designators used... repeaters will communicate, the frequencies and emission designators of such communications, and the...

47 CFR 25.144 - Licensing provisions for the 2.3 GHz satellite digital audio radio service.

Code of Federal Regulations, 2013 CFR

2013-10-01

... (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25... frequencies and emission designators of such communications, and the frequencies and emission designators used... repeaters will communicate, the frequencies and emission designators of such communications, and the...

Project Management in Instructional Design: ADDIE Is Not Enough

ERIC Educational Resources Information Center

Van Rooij, Shahron Williams

2010-01-01

In the digital age, instructional designers must possess both a sound instructional design knowledge base and solid project management skills that will enable them to complete courseware projects on time, on budget and in conformance with client expectations. Project management skills include the ability to apply repeatable processes, along with…

Portable FWD (Prima 100) for in-situ subgrade evaluation.

DOT National Transportation Integrated Search

2006-06-01

Subgrade soil characterization measured in terms of resilient modulus, MR, has been a prerequisite for pavement design. For new pavement design, MR is obtained by conducting repeated load triaxial tests on reconstituted/undisturbed cylindrical specim...

Improved specificity of TALE-based genome editing using an expanded RVD repertoire.

PubMed

Miller, Jeffrey C; Zhang, Lei; Xia, Danny F; Campo, John J; Ankoudinova, Irina V; Guschin, Dmitry Y; Babiarz, Joshua E; Meng, Xiangdong; Hinkley, Sarah J; Lam, Stephen C; Paschon, David E; Vincent, Anna I; Dulay, Gladys P; Barlow, Kyle A; Shivak, David A; Leung, Elo; Kim, Jinwon D; Amora, Rainier; Urnov, Fyodor D; Gregory, Philip D; Rebar, Edward J

2015-05-01

Transcription activator-like effector (TALE) proteins have gained broad appeal as a platform for targeted DNA recognition, largely owing to their simple rules for design. These rules relate the base specified by a single TALE repeat to the identity of two key residues (the repeat variable diresidue, or RVD) and enable design for new sequence targets via modular shuffling of these units. A key limitation of these rules is that their simplicity precludes options for improving designs that are insufficiently active or specific. Here we address this limitation by developing an expanded set of RVDs and applying them to improve the performance of previously described TALEs. As an extreme example, total conversion of a TALE nuclease to new RVDs substantially reduced off-target cleavage in cellular studies. By providing new RVDs and design strategies, these studies establish options for developing improved TALEs for broader application across medicine and biotechnology.

Isolation and characterization of novel microsatellite markers from the sika deer (Cervus nippon) genome.

PubMed

Li, Y M; Bai, C Y; Niu, W P; Yu, H; Yang, R J; Yan, S Q; Zhang, J Y; Zhang, M J; Zhao, Z H

2015-09-28

Microsatellite markers are widely and evenly distributed, and are highly polymorphic. Rapid and convenient detection through automated analysis means that microsatellite markers are widely used in the construction of plant and animal genetic maps, in quantitative trait loci localization, marker-assisted selection, identification of genetic relationships, and genetic diversity and phylogenetic tree construction. However, few microsatellite markers remain to be isolated. We used streptavidin magnetic beads to affinity-capture and construct a (CA)n microsatellite DNA-enriched library from sika deer. We selected sequences containing more than six repeats to design primers. Clear bands were selected, which were amplified using non-specific primers following PCR amplification to screen polymorphisms in a group of 65 unrelated sika deer. The positive clone rate reached 82.9% by constructing the enriched library, and we then selected positive clones for sequencing. There were 395 sequences with CA repeats, and the CA repeat number was 4-105. We selected sequences containing more than six repeats to design primers, of which 297 pairs were designed. We next selected clear bands and used non-specific primers to amplify following PCR amplification. In total, 245 pairs of primers were screened. We then selected 50 pairs of primers to randomly screen for polymorphisms. We detected 47 polymorphic and 3 monomorphic loci in 65 unrelated sika deer. These newly isolated and characterized microsatellite loci can be used to construct genetic maps and for lineage testing in deer. In addition, they can be used for comparative genomics between Cervidae species.

Modulation of the multistate folding of designed TPR proteins through intrinsic and extrinsic factors

PubMed Central

Phillips, J J; Javadi, Y; Millership, C; Main, E R G

2012-01-01

Tetratricopeptide repeats (TPRs) are a class of all alpha-helical repeat proteins that are comprised of 34-aa helix-turn-helix motifs. These stack together to form nonglobular structures that are stabilized by short-range interactions from residues close in primary sequence. Unlike globular proteins, they have few, if any, long-range nonlocal stabilizing interactions. Several studies on designed TPR proteins have shown that this modular structure is reflected in their folding, that is, modular multistate folding is observed as opposed to two-state folding. Here we show that TPR multistate folding can be suppressed to approximate two-state folding through modulation of intrinsic stability or extrinsic environmental variables. This modulation was investigated by comparing the thermodynamic unfolding under differing buffer regimes of two distinct series of consensus-designed TPR proteins, which possess different intrinsic stabilities. A total of nine proteins of differing sizes and differing consensus TPR motifs were each thermally and chemically denatured and their unfolding monitored using differential scanning calorimetry (DSC) and CD/fluorescence, respectively. Analyses of both the DSC and chemical denaturation data show that reducing the total stability of each protein and repeat units leads to observable two-state unfolding. These data highlight the intimate link between global and intrinsic repeat stability that governs whether folding proceeds by an observably two-state mechanism, or whether partial unfolding yields stable intermediate structures which retain sufficient stability to be populated at equilibrium. PMID:22170589

Armc8 expression was elevated during atypia-to-carcinoma progression and associated with cancer development of breast carcinoma.

PubMed

Fan, Chuifeng; Zhao, Yang; Mao, Xiaoyun; Miao, Yuan; Lin, Xuyong; Jiang, Guiyang; Zhang, Xiupeng; Han, Qiang; Luan, Lan; Wang, Enhua

2014-11-01

Armadillo repeat-containing protein 8 (Armc8) is a key factor to regulate cell membrane adhesion complex through promoting α-catenin degradation. However, its expression and function in human malignant tumors are largely unknown. Here, we present our study investigating Armc8 expression in tumor and non-tumor breast tissues including 45 normal epithelia, 53 lesions of hyperplasia with or without dysplasia, 22 benign tumors, and 92 carcinomas including 28 carcinomas in situ and 64 infiltrating carcinomas using immunohistochemistry (IHC) and Western blotting study. Armc8 expression was detected mainly in the cytoplasm with occasional membrane immunostaining. The positive rate of Armc8 expression in normal breast epithelia (8.9%, four out of 45) was very low. No significant difference was found between Armc8 expression in usual ductal hyperplasia (UDH) (11.1%, two out of 18), benign breast tumors including intraductal papilloma (10.0%, one out of 10) and fibroadenoma (8.3%, one out of 12), and normal breast epithelia (p>0.05). Elevated expression of Armc8 was found in breast epithelia with dysplasia (24.0%, six out of 25) compared to that in normal breast epithelia, UDH, and benign breast tumors (p<0.05). Armc8 expression in breast carcinoma including breast carcinoma in situ (10/28, 35.7%), infiltrating ductal carcinoma (60.7%, 34/56), and infiltrating lobular carcinoma (50.0%, 4/8) was higher than that in normal breast epithelia, UDH, benign breast tumors, and breast epithelia with dysplasia (p<0.05). The highest expression of Armc8 was found in infiltrating breast carcinoma (59.4%, 38/64) compared to all the other breast tissues. Higher Armc8 expression was found to be linked to lymph node metastasis and advanced tumor-node-metastasis (TNM) stages (III+IV) in infiltrating breast carcinoma (p<0.05). We further confirmed Armc8 expression in breast epithelial cell line MCF10A and breast carcinoma cell lines including MCF-7, MDA-MB-231, and ZR751 using Western blotting and immunofluorescent study. These results indicate that the elevated expression of Armc8 may be involved in carcinogenesis including atypia-to-carcinoma progression and cancer development of breast carcinoma.

Evidence to support horses as natural intermediate hosts for Sarcocystis neurona.

PubMed

Mullaney, Thomas; Murphy, Alice J; Kiupel, Matti; Bell, Julia A; Rossano, Mary G; Mansfield, Linda S

2005-10-10

Opossums (Didelphis spp.) are the definitive host for the protozoan parasite Sarcocystis neurona, the causative agent of equine protozoal myeloencephalitis (EPM). Opossums shed sporocysts in feces that can be ingested by true intermediate hosts (cats, raccoons, skunks, armadillos and sea otters). Horses acquire the parasite by ingestion of feed or water contaminated by opossum feces. However, horses have been classified as aberrant intermediate hosts because the terminal asexual sarcocyst stage that is required for transmission to the definitive host has not been found in their tissues despite extensive efforts to search for them [Dubey, J.P., Lindsay, D.S., Saville, W.J., Reed, S.M., Granstrom, D.E., Speer, C.A., 2001b. A review of Sarcocystis neurona and equine protozoal myeloencephalitis (EPM). Vet. Parasitol. 95, 89-131]. In a 4-month-old filly with neurological disease consistent with EPM, we demonstrate schizonts in the brain and spinal cord and mature sarcocysts in the tongue and skeletal muscle, both with genetic and morphological characteristics of S. neurona. The histological and electron microscopic morphology of the schizonts and sarcocysts were identical to published features of S. neurona [Stanek, J.F., Dubey, J.P., Oglesbee, M.J., Reed, S.M., Lindsay, D.S., Capitini, L.A., Njoku, C.J., Vittitow, K.L., Saville, W.J., 2002. Life cycle of Sarcocystis neurona in its natural intermediate host, the raccoon, Procyon lotor. J. Parasitol. 88, 1151-1158]. DNA from schizonts and sarcocysts from this horse produced Sarcocystis specific 334bp PCR products [Tanhauser, S.M., Yowell, C.A., Cutler, T.J., Greiner, E.C., MacKay, R.J., Dame, J.B., 1999. Multiple DNA markers differentiate Sarcocystis neurona and Sarcocystis falcatula. J. Parasitol. 85, 221-228]. Restriction fragment length polymorphism (RFLP) analysis of these PCR products showed banding patterns characteristic of S. neurona. Sequencing, alignment and comparison of both schizont and sarcocyst DNA amplicons showed 100% identity. Although Koch's postulates have not been demonstrated in this case study, the finding of mature, intact S. neurona schizonts and sarcocysts in the tissues of this single horse strongly suggests that horses have the potential to act as intermediate hosts. Further studies are needed to demonstrate Koch's postulates with repeated transfer of S. neurona between opossums and horses.

Layered Architectures for Quantum Computers and Quantum Repeaters

NASA Astrophysics Data System (ADS)

Jones, Nathan C.

This chapter examines how to organize quantum computers and repeaters using a systematic framework known as layered architecture, where machine control is organized in layers associated with specialized tasks. The framework is flexible and could be used for analysis and comparison of quantum information systems. To demonstrate the design principles in practice, we develop architectures for quantum computers and quantum repeaters based on optically controlled quantum dots, showing how a myriad of technologies must operate synchronously to achieve fault-tolerance. Optical control makes information processing in this system very fast, scalable to large problem sizes, and extendable to quantum communication.

A high-precision velocity measuring system design for projectiles based on S-shaped laser screen

NASA Astrophysics Data System (ADS)

Liu, Huayi; Qian, Zheng; Yu, Hao; Li, Yutao

2018-03-01

The high-precision measurement of the velocity of high-speed flying projectile is of great significance for the evaluation and development of modern weapons. The velocity of the high-speed flying projectile is usually measured by laser screen velocity measuring system. But this method cannot achieve the repeated measurements, so we cannot make an indepth evaluation of the uncertainty about the measuring system. This paper presents a design based on S-shaped laser screen velocity measuring system. This design can achieve repeated measurements. Therefore, it can effectively reduce the uncertainty of the velocity measuring system. In addition, we made a detailed analysis of the uncertainty of the measuring system. The measurement uncertainty is 0.2% when the velocity of the projectile is about 200m/s.

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

PubMed

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

2018-02-01

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

Computer-Aided Design Of Turbine Blades And Vanes

NASA Technical Reports Server (NTRS)

Hsu, Wayne Q.

1988-01-01

Quasi-three-dimensional method for determining aerothermodynamic configuration of turbine uses computer-interactive analysis and design and computer-interactive graphics. Design procedure executed rapidly so designer easily repeats it to arrive at best performance, size, structural integrity, and engine life. Sequence of events in aerothermodynamic analysis and design starts with engine-balance equations and ends with boundary-layer analysis and viscous-flow calculations. Analysis-and-design procedure interactive and iterative throughout.

Risks of repeated miscarriage.

PubMed

George, Lena; Granath, Fredrik; Johansson, Anna L V; Olander, Bodil; Cnattingius, Sven

2006-03-01

There is a lack of well-designed epidemiological studies of possible risk factors for repeated miscarriage. In this Swedish population-based case-control study, we investigated the association between sociodemographic and anthropometric factors, obstetric history and life-style factors, with respect to the risks of first-trimester repeated miscarriage. Information on maternal characteristics was collected through in-person interviews. Plasma blood samples were analysed for cotinine and folate concentrations. Adjusted odds ratios (OR) with 95% confidence interval [CI] were used to estimate the relative risk of repeated miscarriage. The risks of repeated miscarriage were increased for women aged > or = 35 years (adjusted OR 2.9 [95% CI 1.4, 5.8]), as well as for women aged < or = 24 years (OR 2.8 [95% CI 1.1, 6.8]). Women with a history of at least one preceding miscarriage prior to the two index pregnancies, women reporting prolonged time to conceive, and women with a history of myoma, faced a more than fourfold increased risk of repeated miscarriage. Smokers were at an increased risk of repeated miscarriage (OR 2.1 [95% CI 1.1, 4.1]). Among non-smoking women with high caffeine intake, there was an increased risk of repeated miscarriage, whereas there was no such association among smokers. Low plasma folate levels were not associated with increased risks.

Cryogenic probe station for on-wafer characterization of electrical devices

NASA Astrophysics Data System (ADS)

Russell, Damon; Cleary, Kieran; Reeves, Rodrigo

2012-04-01

A probe station, suitable for the electrical characterization of integrated circuits at cryogenic temperatures is presented. The unique design incorporates all moving components inside the cryostat at room temperature, greatly simplifying the design and allowing automated step and repeat testing. The system can characterize wafers up to 100 mm in diameter, at temperatures <20 K. It is capable of highly repeatable measurements at millimeter-wave frequencies, even though it utilizes a Gifford McMahon cryocooler which typically imposes limits due to vibration. Its capabilities are illustrated by noise temperature and S-parameter measurements on low noise amplifiers for radio astronomy, operating at 75-116 GHz.

Production of xylooligosaccharide from wheat bran by microwave assisted enzymatic hydrolysis.

PubMed

Wang, Tseng-Hsing; Lu, Shin

2013-06-01

The effective production of xylooligosaccharides (XOS) from wheat bran was investigated. Wheat bran contains rich hemicellulose which can be hydrolyzed by enzyme; the XOS were obtained by microwave assisted enzymatic hydrolysis. To improve the productivity of XOS, repeated microwave assisted enzymatic hydrolysis and activated carbon adsorption method was chosen to eliminate macromolecules in the XOS. On the basis of experimental data, an industrial XOS production process consisting of pretreatment, repeated microwave assisted enzymatic treatment and purification was designed. Using the designed process, 3.2g dry of purified XOS was produced from 50 g dry wheat bran powder. Copyright © 2012 Elsevier Ltd. All rights reserved.

Repeated hematopoietic stem and progenitor cell mobilization without depletion of the bone marrow stem and progenitor cell pool in mice after repeated administration of recombinant murine G-CSF.

PubMed

de Kruijf, Evert-Jan F M; van Pel, Melissa; Hagoort, Henny; Kruysdijk, Donnée; Molineux, Graham; Willemze, Roel; Fibbe, Willem E

2007-05-01

Administration of recombinant-human G-CSF (rhG-CSF) is highly efficient in mobilizing hematopoietic stem and progenitor cells (HSC/HPC) from the bone marrow (BM) toward the peripheral blood. This study was designed to investigate whether repeated G-CSF-induced HSC/HPC mobilization in mice could lead to a depletion of the bone marrow HSC/HPC pool with subsequent loss of mobilizing capacity. To test this hypothesis Balb/c mice were treated with a maximum of 12 repeated 5-day cycles of either 10 microg rhG-CSF/day or 0.25 microg rmG-CSF/day. Repeated administration of rhG-CSF lead to strong inhibition of HSC/HPC mobilization toward the peripheral blood and spleen after >4 cycles because of the induction of anti-rhG-CSF antibodies. In contrast, after repeated administration of rmG-CSF, HSC/HPC mobilizing capacity remained intact for up to 12 cycles. The number of CFU-GM per femur did not significantly change for up to 12 cycles. We conclude that repeated administration of G-CSF does not lead to depletion of the bone marrow HSC/HPC pool.

KSC-07pd2276

NASA Image and Video Library

2007-08-07

KENNEDY SPACE CENTER, FLA. -- A baby nine-banded armadillo makes its way along the roadside near Launch Pad 39A where Space Shuttle Endeavour waits for launch on mission STS-118. Introduced to Florida in the early 1900s, this species is found statewide in areas with dense ground cover and sandy soil. Nine bands of plates cover the body from shoulder to hip and 12 bands cover the long tail. It has a small, tapered head and snout and a long tongue. Its ears are long and hairless. and it has sparse white hairs on its belly. Its diet is composed of insects, especially beetles, and other invertebrates plus some plant foods such as cedars and beautyberries. It is primarily nocturnal, sedentary, solitary and a burrower. It digs a series of dens with multiple entrances usually protected by stumps, palmettos or trees. KSC shares a boundary with the Merritt Island Wildlife Nature Refuge. The refuge is a habitat for more than 310 species of birds, 25 mammals, 117 fishes and 65 amphibians and reptiles. Photo credit: NASA/Ken Thornsley

Serologic survey for Toxoplasma gondii in wild animals in Florida.

PubMed

Burridge, M J; Bigler, W J; Forrester, D J; Hennemann, J M

1979-11-01

Blood samples were collected for serum separation from 114 species of wild animals (25 species of mammals, 82 species of birds, and 7 species of reptiles) in Florida. Each of the 3,471 samples was tested for antibodies to Toxoplasma gondii, using the indirect hemagglutination test. The highest prevalences of T gondii antibodies were 19% in armadillos (Dasypus novemcinctus), 18% in raccoons (Procyon lotor), 13% in black rats (Rattus rattus), and 11% in opossums (Didelphis marsupialis). Antibody prevalences were significantly higher in male than in female raccoons (P less than 0.05) and in adult than in nonadult raccoons and opossums (P less than 0.005). A high proportion of seropositive animals was found in three other mammalian species: 4 of 4 black bears (Ursus americanus), 2 of 3 bobcats (Lynx rufus), and 2 of 8 Norway rats (Rattus norvegicus) tested. Antibodies were found in 8 of the 1,279 avian serums; they were not found in any of the 13 reptilian serums tested. There were no significant geographic variations in antibody prevalence in any species.

naked cuticle targets dishevelled to antagonize Wnt signal transduction

PubMed Central

Rousset, Raphaël; Mack, Judith A.; Wharton, Keith A.; Axelrod, Jeffrey D.; Cadigan, Ken M.; Fish, Matthew P.; Nusse, Roel; Scott, Matthew P.

2001-01-01

In Drosophila embryos the protein Naked cuticle (Nkd) limits the effects of the Wnt signal Wingless (Wg) during early segmentation. nkd loss of function results in segment polarity defects and embryonic death, but how nkd affects Wnt signaling is unknown. Using ectopic expression, we find that Nkd affects, in a cell-autonomous manner, a transduction step between the Wnt signaling components Dishevelled (Dsh) and Zeste-white 3 kinase (Zw3). Zw3 is essential for repressing Wg target-gene transcription in the absence of a Wg signal, and the role of Wg is to relieve this inhibition. Our double-mutant analysis shows that, in contrast to Zw3, Nkd acts when the Wg pathway is active to restrain signal transduction. Yeast two hybrid and in vitro experiments indicate that Nkd directly binds to the basic-PDZ region of Dsh. Specially timed Nkd overexpression is capable of abolishing Dsh function in a distinct signaling pathway that controls planar-cell polarity. Our results suggest that Nkd acts directly through Dsh to limit Wg activity and thus determines how efficiently Wnt signals stabilize Armadillo (Arm)/β-catenin and activate downstream genes. PMID:11274052

Performance analysis of wideband data and television channels. [space shuttle communications

NASA Technical Reports Server (NTRS)

Geist, J. M.

1975-01-01

Several aspects are discussed of space shuttle communications, including the return link (shuttle-to-ground) relayed through a satellite repeater (TDRS). The repeater exhibits nonlinear amplification and an amplitude-dependent phase shift. Models were developed for various link configurations, and computer simulation programs based on these models are described. Certain analytical results on system performance were also obtained. For the system parameters assumed, the results indicate approximately 1 db degradation relative to a link employing a linear repeater. While this degradation is dependent upon the repeater, filter bandwidths, and modulation parameters used, the programs can accommodate changes to any of these quantities. Thus the programs can be applied to determine the performance with any given set of parameters, or used as an aid in link design.

The Case for Use of Simple Difference Scores to Test the Significance of Differences in Mean Rates of Change in Controlled Repeated Measurements Designs

ERIC Educational Resources Information Center

Overall, John E.; Tonidandel, Scott

2010-01-01

A previous Monte Carlo study examined the relative powers of several simple and more complex procedures for testing the significance of difference in mean rates of change in a controlled, longitudinal, treatment evaluation study. Results revealed that the relative powers depended on the correlation structure of the simulated repeated measurements.…

Obstetric and psychological characteristics of women seeking multiple abortions in the region of Monastir (Tunisia): results of a cross-sectional design.

PubMed

El Mhamdi, Sana; Ben Salah, Arwa; Bouanene, Ines; Hlaiem, Imen; Hadhri, Saloua; Maatouk, Wahiba; Soltani, Mohamed

2015-05-10

Repeat abortion is a public health concern favored by many obstetric and social factors. The purpose of our study was to identify associated factors to repeated abortion in the region of Monastir (Tunisia). Common mental disorders (CMD) such as anxiety and depression were also evaluated in women seeking voluntary repeated abortion. We carried out a cross sectional study between January and April 2013 in the Reproductive Health Center (RHC) of the region of Monastir in Tunisia (This study is part of a prospective design on mental disorders and intimate partner violence among women seeking abortions in the RHC). Among women referred to the RHC we selected those seeking voluntary abortion (medical or surgical method). Data on women's demographic characters, knowledge and practices about contraceptive methods and abortion were collected the abortion day via a structured questionnaire. Data about anxiety and depression status were evaluated during the post-abortal control visit at 3-4 weeks following pregnancy termination. Of the 500 interviewed women, 211 (42.2 %; CI95% [37.88 - 46.52]) were seeking repeated abortions. Multivariate analysis showed that increased age, lower level of women school education, single status, poor knowledge about birth control methods and history of conflict/abuse by a male partner, were uniquely associated with undergoing repeat compared with initial abortion. CMD were significantly higher in women undergoing second or subsequent abortion (51.1 %) single and lower educated women. Women relating a history of conflicts/abuse report more CMD than others (30.6 % vs 20.8 %). Health facilities providing abortion services need to pay more attention to women seeking repeat abortion. Further studies are needed to well establish the relation between the number of abortion and the occurrence and the severity of CMD.

An Automated Inpatient Split-dose Bowel Preparation System Improves Colonoscopy Quality and Reduces Repeat Procedures.

PubMed

Yadlapati, Rena; Johnston, Elyse R; Gluskin, Adam B; Gregory, Dyanna L; Cyrus, Rachel; Werth, Lindsay; Ciolino, Jody D; Grande, David P; Keswani, Rajesh N

2017-07-19

Inpatient colonoscopy preparations are often inadequate, compromising patient safety and procedure quality, while resulting in greater hospital costs. The aims of this study were to: (1) design and implement an electronic inpatient split-dose bowel preparation order set; (2) assess the intervention's impact upon preparation adequacy, repeated colonoscopies, hospital days, and costs. We conducted a single center prospective pragmatic quasiexperimental study of hospitalized adults undergoing colonoscopy. The experimental intervention was designed using DMAIC (define, measure, analyze, improve, and control) methodology. Prospective data collected over 12 months were compared with data from a historical preintervention cohort. The primary outcome was bowel preparation quality and secondary outcomes included number of repeated procedures, hospital days, and costs. On the basis of a Delphi method and DMAIC process, we created an electronic inpatient bowel preparation order set inclusive of a split-dose bowel preparation algorithm, automated orders for rescue medications, and nursing bowel preparation checks. The analysis data set included 969 patients, 445 (46%) in the postintervention group. The adequacy of bowel preparation significantly increased following intervention (86% vs. 43%; P<0.01) and proportion of repeated procedures decreased (2.0% vs. 4.6%; P=0.03). Mean hospital days from bowel preparation initiation to discharge decreased from 8.0 to 6.9 days (P=0.02). The intervention resulted in an estimated 1-year cost-savings of $46,076 based on a reduction in excess hospital days associated with repeated and delayed procedures. Our interdisciplinary initiative targeting inpatient colonoscopy preparations significantly improved quality and reduced repeat procedures, and hospital days. Other institutions should consider utilizing this framework to improve inpatient colonoscopy value.

Establishment of design criteria for acceptable failure modes and fail safe considerations for the space shuttle structural system

NASA Technical Reports Server (NTRS)

Westrup, R. W.

1971-01-01

The application of general design approaches for preventing failures due to repeated load cycles is briefly discussed. Program objective, mission requirements, and structural design criteria are summarized. Discrete structural elements and associated sections were selected for detailed strength, fatigue, and fracture mechanics investigations.

Chapter 3. Planning and design for habitat monitoring

Treesearch

Christina D. Vojta; Lyman L. McDonald; C. Kenneth Brewer; Kevin S. McKelvey; Mary M Rowland; Michael I. Goldstein

2013-01-01

This chapter provides guidance for designing a habitat monitoring program so that it will meet the monitoring objective, will be repeatable, and will adequately represent habitat within the spatial extent of interest. Although a number of excellent resources are available for planning and designing a monitoring program for wildlife populations (e.g., Busch and Trexler...

A Standardized Mean Difference Effect Size for Multiple Baseline Designs across Individuals

ERIC Educational Resources Information Center

Hedges, Larry V.; Pustejovsky, James E.; Shadish, William R.

2013-01-01

Single-case designs are a class of research methods for evaluating treatment effects by measuring outcomes repeatedly over time while systematically introducing different condition (e.g., treatment and control) to the same individual. The designs are used across fields such as behavior analysis, clinical psychology, special education, and…

37 CFR 202.20 - Deposit of copies and phonorecords for copyright registration.

Code of Federal Regulations, 2010 CFR

2010-07-01

... motion pictures made from pre-existing black and white motion pictures, in addition to the deposit of one... work consists of a repeated pictorial or graphic design, the complete design and at least part of one.... (xviii) Architectural works. (A) For designs of unconstructed buildings, the deposit must consist of one...

Prevalence and Determinants of Repeat Mammography Among Women from a Developing Country.

PubMed

Salinas-Martínez, Ana María; Gaspar-Rivera, Jimena Estefanía; Juárez-Pérez, Oscar; Montañez-Sauceda, José Roberto; Núñez-Rocha, Georgina Mayela; Guzmán-de-la-Garza, Francisco Javier; Mathiew-Quirós, Álvaro

2017-04-01

Failures in repeat mammography decrease the potential benefits of screening; however, it is notable that the recent use of mammography is more frequently studied than repeat use. We estimated the prevalence and analyzed determinants for repeat mammography among women from Mexico, a developing country of Latin America. It was a two-stage study with an initial cross-sectional design (n = 1045) and a final case-control design that involved women of at least 45 years of age with no history of breast, ovarian, or uterine cancer. Case subjects were those with three or more mammograms in the last 5 years, with the last one carried out within the last two years (n = 444); control subjects included those who underwent ≥3 mammograms throughout their life with the most recent carried out >2 years ago (n = 444). Through interviews, we evaluated context-dependency, fulfillment of expected outcomes, self-efficacy, and risk perception, among other factors. We estimated the prevalence with 95 % confidence intervals (CI), and odds ratios (OR) using multivariate binary logistic regression. The prevalence of repeat mammography was 40.4 % (95 % CI 37.4-43.4). Self-efficacy demonstrated the highest effect on repeat use (OR 7.7, 95 % CI 4.7-12.6), followed by awareness context-dependency (OR 4.9, 95 % CI 3.3-7.2), the use of Papanicolaou testing (OR 3.5, 95 % CI 2.3-5.2), the fulfillment of expected waiting time outcome (OR 2.4, 95 % CI 1.2-4.7), and context-dependency related to self-referral/health provider referral (OR 2.4, 95 % CI 1.7-3.4), independent of risk perception, age, education, and positive emotional state of mind. The study showed a need for increasing the prevalence of promoting awareness of the determining factors of repeat mammography, which is a necessary component in the early detection of breast cancer.

Extraction and utilization of the repeating patterns for CP writing in mask making

NASA Astrophysics Data System (ADS)

Shoji, Masahiro; Inoue, Tadao; Yamabe, Masaki

2010-05-01

In May 2006, the Mask Design, Drawing, and Inspection Technology Research Department (Mask D2I) at the Association of Super-Advanced Electronics Technologies (ASET) launched a 4-year program for reducing mask manufacturing cost and TAT by concurrent optimization of Mask Data Preparation (MDP), mask writing, and mask inspection [1]. Figure 1 shows an outline of the project at Mask D2I at ASET. As one of the tasks being pursued at the Mask Design Data Technology Research Laboratory we have evaluated the effect of reducing the writing shot counts by utilizing the repeating patterns, and that showed positive impact on mask making by using CP writing. During the past four years, we have developed a software to extract repeating patterns from fractured OPCed mask data and have evaluated the efficiency of reducing the writing shot counts using the repeating patterns with this software. In this evaluation, we have used many actual device production data obtained from the member companies of Mask D2I. To the extraction software, we added new functions for extracting common repeating patterns from a set of multiple masks, and studied how this step affects the ratio of reducing the shot counts in comparison to the case of utilization of the repeating patterns for single mask. We have also developed a software that uses the result of extracting repeating patterns and prepares writing-data for the MCC/CP writing system which has been developed at the Mask Writing Equipment Technology Research Laboratory. With this software, we have examined how EB proximity effect on CP writing affects in reducing the shot count where CP shots with large CD errors have to be divided into VSB shots. In this paper we will report on making common CP mask from a set of multiple actual device data by using these software, and will also report on the results of CP writing and calculation of writing-TAT by MCC/CP writing system.

Factors affecting consumer usage and acceptance of child restraints

DOT National Transportation Integrated Search

1983-09-01

This study was designed to focus on two factors with potential relevance to the child restraint device (CRD) usage problem: CRD design and directions for use; problems of initial users and repeated users were targeted for consideration. Ultimate obje...

Test-retest reliability of pulse amplitude tonometry measures of vascular endothelial function: implications for clinical trial design.

PubMed

McCrea, Cindy E; Skulas-Ray, Ann C; Chow, Mosuk; West, Sheila G

2012-02-01

Endothelial dysfunction is an important outcome for assessing vascular health in intervention studies. However, reliability of the standard non-invasive method (flow-mediated dilation) is a significant challenge for clinical applications and multicenter trials. We evaluated the repeatability of pulse amplitude tonometry (PAT) to measure change in pulse wave amplitude during reactive hyperemia (Itamar Medical Ltd, Caesarea, Israel). Twenty healthy adults completed two PAT tests (mean interval = 19.5 days) under standardized conditions. PAT-derived measures of endothelial function (reactive hyperemia index, RHI) and arterial stiffness (augmentation index, AI) showed strong repeatability (intra-class correlations = 0.74 and 0.83, respectively). To guide future research, we also analyzed sample size requirements for a range of effect sizes. A crossover design powered at 0.90 requires 28 participants to detect a 15% change in RHI. Our study is the first to show that PAT measurements are repeatable in adults over an interval greater than 1 week.

Effect of Occupational Therapy-Led Playgroups in Early Intervention on Child Playfulness and Caregiver Responsiveness: A Repeated-Measures Design.

PubMed

Fabrizi, Sarah E; Ito, Max A; Winston, Kristin

2016-01-01

This study's objective was to investigate the effects of a community playgroup on the playfulness of children with special needs ages 15 mo to 3 yr and the responsiveness of their caregivers. Using a pretest-posttest, repeated-measures design, we evaluated 8 child-caregiver dyads participating in an 8-wk occupational therapist-led community playgroup recruited from a purposive sample enrolled in early intervention. Video recordings from four time points over 4 mo were used to determine playfulness (Test of Playfulness) of the child and the responsiveness of the caregiver. Blinded raters assessed playfulness and responsiveness outcomes. A repeated-measures analysis of variance demonstrated that participation in the playgroup significantly increased child playfulness (ηp² = .89, p < .01). Analysis did not detect a change in caregiver responsiveness. The results of this study have implications for the use of playgroups in comprehensive occupational therapy practice in early intervention. Copyright © 2016 by the American Occupational Therapy Association, Inc.

Placebo non-response measure in sequential parallel comparison design studies.

PubMed

Rybin, Denis; Doros, Gheorghe; Pencina, Michael J; Fava, Maurizio

2015-07-10

The Sequential Parallel Comparison Design (SPCD) is one of the novel approaches addressing placebo response. The analysis of SPCD data typically classifies subjects as 'placebo responders' or 'placebo non-responders'. Most current methods employed for analysis of SPCD data utilize only a part of the data collected during the trial. A repeated measures model was proposed for analysis of continuous outcomes that permitted the inclusion of information from all subjects into the treatment effect estimation. We describe here a new approach using a weighted repeated measures model that further improves the utilization of data collected during the trial, allowing the incorporation of information that is relevant to the placebo response, and dealing with the problem of possible misclassification of subjects. Our simulations show that when compared to the unweighted repeated measures model method, our approach performs as well or, under certain conditions, better, in preserving the type I error, achieving adequate power and minimizing the mean squared error. Copyright © 2015 John Wiley & Sons, Ltd.

Transforming Roving-Rolling Explorer (TRREx) for Planetary Exploration

NASA Astrophysics Data System (ADS)

Edwin, Lionel Ernest

All planetary surface exploration missions thus far have employed traditional rovers with a rocker-bogie suspension. These rovers can navigate moderately rough and flat terrain, but are not designed to traverse rugged terrain with steep slopes. The fact is, however, that many scientifically interesting missions require exploration platforms with capabilities for navigating such types of chaotic terrain. This issue motivates the development of new kinds of rovers that take advantage of the latest advances in robotic technologies to traverse rugged terrain efficiently. This dissertation proposes and analyses one such rover concept called the Transforming Roving-Rolling Explorer (TRREx) that is principally aimed at addressing the above issue. Biologically inspired by the way the armadillo curls up into a ball when threatened, and the way the golden wheel spider uses the dynamic advantages of a sphere to roll down hills when escaping danger, the novel TRREx rover can traverse like a traditional 6-wheeled rover over conventional terrain, but can also transform itself into a sphere, when necessary, to travel down steep inclines, or navigate rough terrain. This work presents the proposed design architecture and capabilities followed by the development of mathematical models and experiments that facilitate the mobility analysis of the TRREx in the rolling mode. The ability of the rover to self-propel in the rolling mode in the absence of a negative gradient increases its versatility and concept value. Therefore, a dynamic model of a planar version of the problem is first used to investigate the feasibility and value of such self-propelled locomotion - 'actuated rolling'. Construction and testing of a prototype Planar/Cylindrical TRREx that is capable of demonstrating actuated rolling is presented, and the results from the planar dynamic model are experimentally validated. This planar model is then built upon to develop a mathematical model of the spherical TRREx in the rolling mode, i.e. when the rover is a sphere and can steer itself through actuations that shift its center of mass to achieve the desired direction of roll. Case studies that demonstrate the capabilities of the rover in rolling mode and parametric analyses that investigate the dependence of the rover's mobility on its design are presented. This work highlights the contribution of the spherical rolling mode to the enhanced mobility of the TRREx rover and how it could enable challenging surface exploration missions in the future. It represents an important step toward developing a rover capable of traversing a variety of terrains that are impassible by the current fleet of rover designs, and thus has the potential to revolutionize planetary surface exploration.

Anesthetic efficacy of a repeated intraosseous injection following a primary intraosseous injection.

PubMed

Jensen, Joanne; Nusstein, John; Drum, Melissa; Reader, Al; Beck, Mike

2008-02-01

The purpose of this prospective, randomized, single-blinded study was to determine the anesthetic efficacy of a repeated intraosseous injection given 30 minutes after a primary intraosseous injection. Using a crossover design, 55 subjects randomly received a primary X-tip intraosseous injection (Dentsply Inc, York, PA) of 1.4 mL of 2% lidocaine with epinephrine (using the Wand; Milestone Scientific, Deerfield, IL) and a repeated intraosseous or mock injection at 30 minutes in two appointments. The first molar and adjacent teeth were pulp tested every 2 minutes for a total of 120 minutes. Success was defined as obtaining two consecutive 80 readings with the electric pulp tester. Success of the initial intraosseous injection was 100% for the first molar. The repeated intraosseous injection mimicked the initial intraosseous injection in terms of pulpal anesthesia and statistically provided another 15 minutes of pulpal anesthesia. In conclusion, using the methodology presented, repeating the intraosseous injection 30 minutes after an initial intraosseous injection will provide an additional 15 minutes of pulpal anesthesia.

Two-Hierarchy Entanglement Swapping for a Linear Optical Quantum Repeater

NASA Astrophysics Data System (ADS)

Xu, Ping; Yong, Hai-Lin; Chen, Luo-Kan; Liu, Chang; Xiang, Tong; Yao, Xing-Can; Lu, He; Li, Zheng-Da; Liu, Nai-Le; Li, Li; Yang, Tao; Peng, Cheng-Zhi; Zhao, Bo; Chen, Yu-Ao; Pan, Jian-Wei

2017-10-01

Quantum repeaters play a significant role in achieving long-distance quantum communication. In the past decades, tremendous effort has been devoted towards constructing a quantum repeater. As one of the crucial elements, entanglement has been created in different memory systems via entanglement swapping. The realization of j -hierarchy entanglement swapping, i.e., connecting quantum memory and further extending the communication distance, is important for implementing a practical quantum repeater. Here, we report the first demonstration of a fault-tolerant two-hierarchy entanglement swapping with linear optics using parametric down-conversion sources. In the experiment, the dominant or most probable noise terms in the one-hierarchy entanglement swapping, which is on the same order of magnitude as the desired state and prevents further entanglement connections, are automatically washed out by a proper design of the detection setting, and the communication distance can be extended. Given suitable quantum memory, our techniques can be directly applied to implementing an atomic ensemble based quantum repeater, and are of significant importance in the scalable quantum information processing.

Two-Hierarchy Entanglement Swapping for a Linear Optical Quantum Repeater.

PubMed

Xu, Ping; Yong, Hai-Lin; Chen, Luo-Kan; Liu, Chang; Xiang, Tong; Yao, Xing-Can; Lu, He; Li, Zheng-Da; Liu, Nai-Le; Li, Li; Yang, Tao; Peng, Cheng-Zhi; Zhao, Bo; Chen, Yu-Ao; Pan, Jian-Wei

2017-10-27

Quantum repeaters play a significant role in achieving long-distance quantum communication. In the past decades, tremendous effort has been devoted towards constructing a quantum repeater. As one of the crucial elements, entanglement has been created in different memory systems via entanglement swapping. The realization of j-hierarchy entanglement swapping, i.e., connecting quantum memory and further extending the communication distance, is important for implementing a practical quantum repeater. Here, we report the first demonstration of a fault-tolerant two-hierarchy entanglement swapping with linear optics using parametric down-conversion sources. In the experiment, the dominant or most probable noise terms in the one-hierarchy entanglement swapping, which is on the same order of magnitude as the desired state and prevents further entanglement connections, are automatically washed out by a proper design of the detection setting, and the communication distance can be extended. Given suitable quantum memory, our techniques can be directly applied to implementing an atomic ensemble based quantum repeater, and are of significant importance in the scalable quantum information processing.

Structural studies of CNG repeats

PubMed Central

Kiliszek, Agnieszka; Rypniewski, Wojciech

2014-01-01

CNG repeats (where N denotes one of the four natural nucleotides) are abundant in the human genome. Their tendency to undergo expansion can lead to hereditary diseases known as TREDs (trinucleotide repeat expansion disorders). The toxic factor can be protein, if the abnormal gene is expressed, or the gene transcript, or both. The gene transcripts have attracted much attention in the biomedical community, but their molecular structures have only recently been investigated. Model RNA molecules comprising CNG repeats fold into long hairpins whose stems generally conform to an A-type helix, in which the non-canonical N-N pairs are flanked by C-G and G-C pairs. Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands. The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design. Here is a brief survey of the CNG structures published to date. PMID:24939898

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…

Microsatellite analysis in the genome of Acanthaceae: An in silico approach

PubMed Central

Kaliswamy, Priyadharsini; Vellingiri, Srividhya; Nathan, Bharathi; Selvaraj, Saravanakumar

2015-01-01

Background: Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. Objective: The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. Materials and Methods: The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. Results: Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. Conclusion: The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future. PMID:25709226

Engineering DNA Backbone Interactions Results in TALE Scaffolds with Enhanced 5-Methylcytosine Selectivity.

PubMed

Rathi, Preeti; Witte, Anna; Summerer, Daniel

2017-11-08

Transcription activator-like effectors (TALEs) are DNA major-groove binding proteins widely used for genome targeting. TALEs contain an N-terminal region (NTR) and a central repeat domain (CRD). Repeats of the CRD selectively recognize each one DNA nucleobase, offering programmability. Moreover, repeats with selectivity for 5-methylcytosine (5mC) and its oxidized derivatives can be designed for analytical applications. However, both TALE domains also nonspecifically interact with DNA phosphates via basic amino acids. To enhance the 5mC selectivity of TALEs, we aimed to decrease the nonselective binding energy of TALEs. We substituted basic amino acids with alanine in the NTR and identified TALE mutants with increased selectivity. We then analysed conserved, DNA phosphate-binding KQ diresidues in CRD repeats and identified further improved mutants. Combination of mutations in the NTR and CRD was highly synergetic and resulted in TALE scaffolds with up to 4.3-fold increased selectivity in genomic 5mC analysis via affinity enrichment. Moreover, transcriptional activation in HEK293T cells by a TALE-VP64 construct based on this scaffold design exhibited a 3.5-fold increased 5mC selectivity. This provides perspectives for improved 5mC analysis and for the 5mC-conditional control of TALE-based editing constructs in vivo.

Variable-Number Tandem Repeats That Are Useful in Genotyping Isolates of Salmonella enterica subsp. enterica Serovars Typhimurium and Newport▿

PubMed Central

Witonski, D. ; Stefanova, R.; Ranganathan, A.; Schutze, G. E.; Eisenach, K. D.; Cave, M. D.

2006-01-01

The genome of Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 was analyzed for direct repeats, and 54 sequences containing variable-number tandem repeat loci were identified. Ten primer pairs that anneal upstream and downstream of each selected locus were designed and used to amplify PCR targets in isolates of S. enterica serovars Typhimurium and Newport. Four of the 10 loci did not show polymorphism in the length of products. Six loci were selected for analysis. Isolates of S. enterica serovars Typhimurium and Newport that were related to specific outbreaks and showed identical pulsed-field gel electrophoresis patterns were indistinguishable by the length of the six variable-number tandem repeats. Isolates that differed in their pulsed-field gel electrophoresis patterns showed polymorphism in variable-number tandem repeat profiles. Length of the products was confirmed by DNA sequence analysis. Only 2 of the 10 loci contained exact integers of the direct repeat. Eight loci contained partial copies. The partial copies were maintained at the ends of the variable-number tandem repeat loci in all isolates. In spite of having partial copies that were maintained in all isolates, the number of direct repeats at a locus was polymorphic. Six variable-number tandem repeat loci were useful in distinguishing isolates of S. enterica serovars Typhimurium and Newport that had different pulsed-field gel electrophoresis patterns and in identifying outbreak-associated cases that shared a common pulsed-field gel pattern. PMID:16943354

Spectroscopic insights into quadruplexes of five-repeat telomere DNA sequences upon G-block damage.

PubMed

Dvořáková, Zuzana; Vorlíčková, Michaela; Renčiuk, Daniel

2017-11-01

The DNA lesions, resulting from oxidative damage, were shown to destabilize human telomere four-repeat quadruplex and to alter its structure. Long telomere DNA, as a repetitive sequence, offers, however, other mechanisms of dealing with the lesion: extrusion of the damaged repeat into loop or shifting the quadruplex position by one repeat. Using circular dichroism and UV absorption spectroscopy and polyacrylamide electrophoresis, we studied consequences of lesions at different positions of the model five-repeat human telomere DNA sequences on the structure and stability of their quadruplexes in sodium and in potassium. The repeats affected by lesion are preferentially positioned as terminal overhangs of the core quadruplex structurally similar to the four-repeat one. Forced affecting of the inner repeats leads to presence of variety of more parallel folds in potassium. In sodium the designed models form mixture of two dominant antiparallel quadruplexes whose population varies with the position of the affected repeat. The shapes of quadruplex CD spectra, namely the height of dominant peaks, significantly correlate with melting temperatures. Lesion in one guanine tract of a more than four repeats long human telomere DNA sequence may cause re-positioning of its quadruplex arrangement associated with a shift of the structure to less common quadruplex conformations. The type of the quadruplex depends on the loop position and external conditions. The telomere DNA quadruplexes are quite resistant to the effect of point mutations due to the telomere DNA repetitive nature, although their structure and, consequently, function might be altered. Copyright © 2017. Published by Elsevier B.V.

The Missing Treatment Design Element: Continuity of Treatment When Multiple Postobservations Are Used in Time-Series and Repeated Measures Study Designs

ERIC Educational Resources Information Center

Barnette, J. Jackson; Wallis, Anne Baber

2005-01-01

We rely a great deal on the schematic descriptions that represent experimental and quasi-experimental design arrangements, as well as the discussions of threats to validity associated with these, provided by Campbell and his associates: Stanley, Cook, and Shadish. Some of these designs include descriptions of treatments removed, removed and then…

Muscle deoxygenation and neural drive to the muscle during repeated sprint cycling.

PubMed

Racinais, Sébastien; Bishop, David; Denis, Romain; Lattier, Grégory; Mendez-Villaneuva, Alberto; Perrey, Stéphane

2007-02-01

To investigate muscle deoxygenation and neural drive-related changes during repeated cycling sprints in a fatiguing context. Nine healthy male subjects performed a repeated-sprint test (consisting of 10 x 6-s maximal sprints interspaced by 30 s of recovery). Oxygen uptake was measured breath-by-breath; muscle deoxygenation of the vastus lateralis was assessed continuously using the near-infrared spectroscopy technique. Surface electromyograms (RMS) of both vastus lateralis and biceps femoris were also recorded. Furthermore, before and after the repeated-sprint test, the percentage of muscle activation by voluntary drive (twitch-interpolated method) was measured during a maximal voluntary contraction. Consistent with previous research, our data showed a significant power decrement during repeated-sprint exercise. There was also a progressive muscle deoxygenation, but our data showed that the ability of the subjects to use available O2 throughout the entire repeated-sprint test was well preserved. Our data displayed a significant decrement in the RMS activity during the acceleration phase of each sprint across the repeated-sprint exercise. Moreover, decrement in motor drive was confirmed after exercise by a significant decrease in both percentage of voluntary activation and RMS/M-wave ratio during a maximal voluntary contraction. In this experimental design, our findings suggest that the ability to repeat short-duration (6 s) sprints was associated with the occurrence of both peripheral and central fatigue.

Revisiting the TALE repeat.

PubMed

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

2014-04-01

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

A protocol for better design, application, and communication of population viability analyses.

PubMed

Pe'er, Guy; Matsinos, Yiannis G; Johst, Karin; Franz, Kamila W; Turlure, Camille; Radchuk, Viktoriia; Malinowska, Agnieszka H; Curtis, Janelle M R; Naujokaitis-Lewis, Ilona; Wintle, Brendan A; Henle, Klaus

2013-08-01

Population viability analyses (PVAs) contribute to conservation theory, policy, and management. Most PVAs focus on single species within a given landscape and address a specific problem. This specificity often is reflected in the organization of published PVA descriptions. Many lack structure, making them difficult to understand, assess, repeat, or use for drawing generalizations across PVA studies. In an assessment comparing published PVAs and existing guidelines, we found that model selection was rarely justified; important parameters remained neglected or their implementation was described vaguely; limited details were given on parameter ranges, sensitivity analysis, and scenarios; and results were often reported too inconsistently to enable repeatability and comparability. Although many guidelines exist on how to design and implement reliable PVAs and standards exist for documenting and communicating ecological models in general, there is a lack of organized guidelines for designing, applying, and communicating PVAs that account for their diversity of structures and contents. To fill this gap, we integrated published guidelines and recommendations for PVA design and application, protocols for documenting ecological models in general and individual-based models in particular, and our collective experience in developing, applying, and reviewing PVAs. We devised a comprehensive protocol for the design, application, and communication of PVAs (DAC-PVA), which has 3 primary elements. The first defines what a useful PVA is; the second element provides a workflow for the design and application of a useful PVA and highlights important aspects that need to be considered during these processes; and the third element focuses on communication of PVAs to ensure clarity, comprehensiveness, repeatability, and comparability. Thereby, DAC-PVA should strengthen the credibility and relevance of PVAs for policy and management, and improve the capacity to generalize PVA findings across studies. © 2013 Society for Conservation Biology.

A repulsive magnetic force driven translation micromirror

NASA Astrophysics Data System (ADS)

Xue, Yuan; Zuo, Hui; He, Siyuan

2017-10-01

This paper presents a repulsive magnetic force driven micromirror with large displacement and high surface quality which well solves the limitation of the previous design, i.e. large variation in translation starting position and low repeatability, caused by the touching points between the moving film and substrate before and in operation. The new design utilizes a driving mechanism, i.e. permanent magnet ring above and electromagnet underneath the moving film, to lift the moving film from touching the substrate and generate a repulsive magnetic force (instead of attractive force in the previous design) to push the moving film up and away from the substrate for translation. Due to the touching, the previous design has to pre-oscillate for 20-30 min at 1 Hz before usage (after resting for a few hours) to reduce the starting position variation from ~15 µm to 3-4 µm. Even after the pre-oscillation, the repeatability is still low, which is 14.2% because of the touching in operation. In the design presented in this paper, the touching between the moving film and the substrate is completely eliminated before and in operation. As a result, the starting position of the translating mirror is constant each time and the repeatability is  <1%. In addition, this design does not need the residual stress gradient to curve up the moving film. The maximum displacement of 144 µm can be achieved when 140 mA current is applied on the electromagnet. As an application, the micromirror is used as the movable mirror in a Michelson interferometer to measure the wavelength of a laser beam. The result shows a measurement accuracy of 2.19% for a 532 nm laser beam.

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…

Reduced biceps femoris myoelectrical activity influences eccentric knee flexor weakness after repeat sprint running.

PubMed

Timmins, R G; Opar, D A; Williams, M D; Schache, A G; Dear, N M; Shield, A J

2014-08-01

The aim of this study was to determine whether declines in knee flexor strength following overground repeat sprints were related to changes in hamstrings myoelectrical activity. Seventeen recreationally active men completed maximal isokinetic concentric and eccentric knee flexor strength assessments at 180°/s before and after repeat sprint running. Myoelectrical activity of the biceps femoris (BF) and medial hamstrings (MHs) was measured during all isokinetic contractions. Repeated measures mixed model [fixed factors = time (pre- and post-repeat sprint) and leg (dominant and nondominant), random factor = participants] design was fitted with the restricted maximal likelihood method. Repeat sprint running resulted in significant declines in eccentric, and concentric, knee flexor strength (eccentric = 26 ± 4 Nm, 15% P < 0.001; concentric 11 ± 2 Nm, 10% P < 0.001). Eccentric BF myoelectrical activity was significantly reduced (10%; P = 0.035). Concentric BF and all MH myoelectrical activity were not altered. The declines in maximal eccentric torque were associated with the change in eccentric BF myoelectrical activity (P = 0.013). Following repeat sprint running, there were preferential declines in the myoelectrical activity of the BF, which explained declines in eccentric knee flexor strength. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

PubMed Central

Jewell, Erica; Robinson, Andrew; Savage, David; Erwin, Tim; Love, Christopher G.; Lim, Geraldine A. C.; Li, Xi; Batley, Jacqueline; Spangenberg, German C.; Edwards, David

2006-01-01

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at . PMID:16845092

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery.

PubMed

Jewell, Erica; Robinson, Andrew; Savage, David; Erwin, Tim; Love, Christopher G; Lim, Geraldine A C; Li, Xi; Batley, Jacqueline; Spangenberg, German C; Edwards, David

2006-07-01

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html.

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.

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids

PubMed Central

Sales, Mark; Plecs, Joseph J.; Holton, James M.; Alber, Tom

2007-01-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Å resolution using a designed metal binding site to coordinate a single Yb2+ ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Å. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures. PMID:17766380

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.

PubMed

Sales, Mark; Plecs, Joseph J; Holton, James M; Alber, Tom

2007-10-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Angstrom resolution using a designed metal binding site to coordinate a single Yb(2+) ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Angstrom. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures.

Empirical Tryout of a New Statistic for Detecting Temporally Inconsistent Responders.

PubMed

Kerry, Matthew J

2018-01-01

Statistical screening of self-report data is often advised to support the quality of analyzed responses - For example, reduction of insufficient effort responding (IER). One recently introduced index based on Mahalanobis's D for detecting outliers in cross-sectional designs replaces centered scores with difference scores between repeated-measure items: Termed person temporal consistency ( D 2 ptc ). Although the adapted D 2 ptc index demonstrated usefulness in simulation datasets, it has not been applied to empirical data. The current study addresses D 2 ptc 's low uptake by critically appraising its performance across three empirical applications. Independent samples were selected to represent a range of scenarios commonly encountered by organizational researchers. First, in Sample 1, a repeat-measure of future time perspective (FTP) inexperienced working adults (age >40-years; n = 620) indicated that temporal inconsistency was significantly related to respondent age and item reverse-scoring. Second, in repeat-measure of team efficacy aggregations, D 2 ptc successfully detected team-level inconsistency across repeat-performance cycles. Thirdly, the usefulness of the D 2 ptc was examined in an experimental study dataset of subjective life expectancy indicated significantly more stable responding in experimental conditions compared to controls. The empirical findings support D 2 ptc 's flexible and useful application to distinct study designs. Discussion centers on current limitations and further extensions that may be of value to psychologists screening self-report data for strengthening response quality and meaningfulness of inferences from repeated-measures self-reports. Taken together, the findings support the usefulness of the newly devised statistic for detecting IER and other extreme response patterns.

Repeated Impact Method and Devices to Simulate the Impact Fatigue Property of Drillstring

NASA Astrophysics Data System (ADS)

Lin, Y. H.; Li, B.; Pan, J.; Li, Q.; Liu, W. Y.; Pan, Y.

2017-05-01

It is well known that drillstring failures are a pendent problem in drilling engineering, because of the fatigue accumulation caused by the low amplitude-repeated impact. In order to reveal the effect of low amplitude-repeated impact on the failure mechanism of the drillstring, a repeated impact method and instrument have been developed based on the Charpy impact method, by which a series of tests have been performed in the condition of non-corrosive medium and with H2S environment respective. Test results of non-corrosive medium environment indicates that, with the increase of single impact energy, the low amplitude-repeated impact resistance of drillstring decreases significantly; For H2S corrosion environment, the low amplitude-repeated impact resistances with H2S is much lower than that without H2S corrosion, and high strength material such as V-150 drillstring is more sensitive to H2S corrosion media. Furthermore, based on the experiment data, the accumulation fatigue model to predict the service life of the drillstring is developed, which could be used to predict the fatigue life. Research fruits are very vital to select a suitable rotational speed for drilling job and drillstring design.

The effects of test-enhanced learning on long-term retention in AAN annual meeting courses.

PubMed

Larsen, Douglas P; Butler, Andrew C; Aung, Wint Y; Corboy, John R; Friedman, Deborah I; Sperling, Michael R

2015-02-17

We measured the long-term retention of knowledge gained through selected American Academy of Neurology annual meeting courses and compared the effects of repeated quizzing (known as test-enhanced learning) and repeated studying on that retention. Participants were recruited from 4 annual meeting courses. All participants took a pretest. This randomized, controlled trial utilized a within-subjects design in which each participant experienced 3 different postcourse activities with each activity performed on different material. Each key information point from the course was randomized in a counterbalanced fashion among participants to one of the 3 activities: repeated short-answer quizzing, repeated studying, and no further exposure to the materials. A final test covering all information points from the course was taken 5.5 months after the course. Thirty-five participants across the 4 courses completed the study. Average score on the pretest was 36%. Performance on the final test showed that repeated quizzing led to significantly greater long-term retention relative to both repeated studying (55% vs 46%; t[34] = 3.28, SEM = 0.03, p = 0.01, d = 0.49) and no further exposure (55% vs 44%; t[34] = 3.16, SEM = 0.03, p = 0.01, d = 0.58). Relative to the pretest baseline, repeated quizzing helped participants to retain almost twice as much of the knowledge acquired from the course compared to repeated studying or no further exposure. Whereas annual meeting continuing medical education (CME) courses lead to long-term gains in knowledge, when repeated quizzing is added, retention is significantly increased. CME planners may consider adding repeated quizzing to increase the impact of their courses. © 2015 American Academy of Neurology.

How do repeat suicide attempters differ from first timers? An exploratory record based analysis

PubMed Central

Menon, Vikas; Kattimani, Shivanand; Sarkar, Siddharth; Mathan, Kaliaperumal

2016-01-01

Background: Evidence indicates that repeat suicide attempters, as a group, may differ from 1st time attempters. The identification of repeat attempters is a powerful but underutilized clinical variable. Aims: In this research, we aimed to compare individuals with lifetime histories of multiple attempts with 1st time attempters to identify factors predictive of repeat attempts. Setting and Design: This was a retrospective record based study carried out at a teaching cum Tertiary Care Hospital in South India. Methods: Relevant data was extracted from the clinical records of 1st time attempters (n = 362) and repeat attempters (n = 61) presenting to a single Tertiary Care Center over a 4½ year period. They were compared on various sociodemographic and clinical parameters. The clinical measures included Presumptive Stressful Life Events Scale, Beck Hopelessness Scale, Coping Strategies Inventory – Short Form, and the Global Assessment of Functioning Scale. Statistical Analysis Used: First time attempters and repeaters were compared using appropriate inferential statistics. Logistic regression was used to identify independent predictors of repeat attempts. Results: The two groups did not significantly differ on sociodemographic characteristics. Repeat attempters were more likely to have given prior hints about their act (χ2 = 4.500, P = 0.034). In the final regression model, beck hopelessness score emerged as a significant predictor of repeat suicide attempts (odds ratio = 1.064, P = 0.020). Conclusion: Among suicide attempters presenting to the hospital, the presence of hopelessness is a predictor of repeat suicide attempts, independent of clinical depression. This highlights the importance of considering hopelessness in the assessment of suicidality with a view to minimize the risk of future attempts. PMID:26933353

The effects of test-enhanced learning on long-term retention in AAN annual meeting courses

PubMed Central

Butler, Andrew C.; Aung, Wint Y.; Corboy, John R.; Friedman, Deborah I.; Sperling, Michael R.

2015-01-01

Objective: We measured the long-term retention of knowledge gained through selected American Academy of Neurology annual meeting courses and compared the effects of repeated quizzing (known as test-enhanced learning) and repeated studying on that retention. Methods: Participants were recruited from 4 annual meeting courses. All participants took a pretest. This randomized, controlled trial utilized a within-subjects design in which each participant experienced 3 different postcourse activities with each activity performed on different material. Each key information point from the course was randomized in a counterbalanced fashion among participants to one of the 3 activities: repeated short-answer quizzing, repeated studying, and no further exposure to the materials. A final test covering all information points from the course was taken 5.5 months after the course. Results: Thirty-five participants across the 4 courses completed the study. Average score on the pretest was 36%. Performance on the final test showed that repeated quizzing led to significantly greater long-term retention relative to both repeated studying (55% vs 46%; t[34] = 3.28, SEM = 0.03, p = 0.01, d = 0.49) and no further exposure (55% vs 44%; t[34] = 3.16, SEM = 0.03, p = 0.01, d = 0.58). Relative to the pretest baseline, repeated quizzing helped participants to retain almost twice as much of the knowledge acquired from the course compared to repeated studying or no further exposure. Conclusions: Whereas annual meeting continuing medical education (CME) courses lead to long-term gains in knowledge, when repeated quizzing is added, retention is significantly increased. CME planners may consider adding repeated quizzing to increase the impact of their courses. PMID:25609761

Accumulate-Repeat-Accumulate-Accumulate Codes

NASA Technical Reports Server (NTRS)

Divsalar, Dariush; Dolinar, Samuel; Thorpe, Jeremy

2007-01-01

Accumulate-repeat-accumulate-accumulate (ARAA) codes have been proposed, inspired by the recently proposed accumulate-repeat-accumulate (ARA) codes. These are error-correcting codes suitable for use in a variety of wireless data-communication systems that include noisy channels. ARAA codes can be regarded as serial turbolike codes or as a subclass of low-density parity-check (LDPC) codes, and, like ARA codes they have projected graph or protograph representations; these characteristics make it possible to design high-speed iterative decoders that utilize belief-propagation algorithms. The objective in proposing ARAA codes as a subclass of ARA codes was to enhance the error-floor performance of ARA codes while maintaining simple encoding structures and low maximum variable node degree.

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.

High-speed quantum networking by ship

NASA Astrophysics Data System (ADS)

Devitt, Simon J.; Greentree, Andrew D.; Stephens, Ashley M.; van Meter, Rodney

2016-11-01

Networked entanglement is an essential component for a plethora of quantum computation and communication protocols. Direct transmission of quantum signals over long distances is prevented by fibre attenuation and the no-cloning theorem, motivating the development of quantum repeaters, designed to purify entanglement, extending its range. Quantum repeaters have been demonstrated over short distances, but error-corrected, global repeater networks with high bandwidth require new technology. Here we show that error corrected quantum memories installed in cargo containers and carried by ship can provide a exible connection between local networks, enabling low-latency, high-fidelity quantum communication across global distances at higher bandwidths than previously proposed. With demonstrations of technology with sufficient fidelity to enable topological error-correction, implementation of the quantum memories is within reach, and bandwidth increases with improvements in fabrication. Our approach to quantum networking avoids technological restrictions of repeater deployment, providing an alternate path to a worldwide Quantum Internet.

High-speed quantum networking by ship

PubMed Central

Devitt, Simon J.; Greentree, Andrew D.; Stephens, Ashley M.; Van Meter, Rodney

2016-01-01

Networked entanglement is an essential component for a plethora of quantum computation and communication protocols. Direct transmission of quantum signals over long distances is prevented by fibre attenuation and the no-cloning theorem, motivating the development of quantum repeaters, designed to purify entanglement, extending its range. Quantum repeaters have been demonstrated over short distances, but error-corrected, global repeater networks with high bandwidth require new technology. Here we show that error corrected quantum memories installed in cargo containers and carried by ship can provide a exible connection between local networks, enabling low-latency, high-fidelity quantum communication across global distances at higher bandwidths than previously proposed. With demonstrations of technology with sufficient fidelity to enable topological error-correction, implementation of the quantum memories is within reach, and bandwidth increases with improvements in fabrication. Our approach to quantum networking avoids technological restrictions of repeater deployment, providing an alternate path to a worldwide Quantum Internet. PMID:27805001

High-speed quantum networking by ship.

PubMed

Devitt, Simon J; Greentree, Andrew D; Stephens, Ashley M; Van Meter, Rodney

2016-11-02

Networked entanglement is an essential component for a plethora of quantum computation and communication protocols. Direct transmission of quantum signals over long distances is prevented by fibre attenuation and the no-cloning theorem, motivating the development of quantum repeaters, designed to purify entanglement, extending its range. Quantum repeaters have been demonstrated over short distances, but error-corrected, global repeater networks with high bandwidth require new technology. Here we show that error corrected quantum memories installed in cargo containers and carried by ship can provide a exible connection between local networks, enabling low-latency, high-fidelity quantum communication across global distances at higher bandwidths than previously proposed. With demonstrations of technology with sufficient fidelity to enable topological error-correction, implementation of the quantum memories is within reach, and bandwidth increases with improvements in fabrication. Our approach to quantum networking avoids technological restrictions of repeater deployment, providing an alternate path to a worldwide Quantum Internet.

[Analysis on genetic polymorphism of 5 STR loci selected from X chromosome].

PubMed

Liu, Qi-ji; Gong, Yao-qin; Zhang, Xi-yu; Gao, Gui-min; Li, Jiang-xia; Guo, Yi-shou

2005-02-01

To select short tandem repeats(STR) from X chromosome. STR is a universal genetic marker that has changeable polymorphism and stable heredity in human genome. It is a specific DNA segment composed of 2-6 base pairs as its core sequence. It is an ideal DNA marker used in linkage analysis and gene mapping. In this study, 8 short tandem repeats were selected from two genomic clones on X chromosome by using BCM Search Launcher. Primers amplifying the STR loci were designed by using Primer 3.0 according to the unique sequence flanking the STRs. Polymorphisms of the short tandem repeats in Chinese population were evaluated by PCR amplification and PAGE. Five of these STRs were polymorphic. Chi-square test indicated that the distribution of genotypes agreed with Hardy-Weinberg equilibrium (P>0.05). Five polymorphic short tandem repeats have been identified on chromosome X and will be useful for linkage analysis and gene mapping.

Dynamic 3D shape of the plantar surface of the foot using coded structured light: a technical report

PubMed Central

2014-01-01

Background The foot provides a crucial contribution to the balance and stability of the musculoskeletal system, and accurate foot measurements are important in applications such as designing custom insoles/footwear. With better understanding of the dynamic behavior of the foot, dynamic foot reconstruction techniques are surfacing as useful ways to properly measure the shape of the foot. This paper presents a novel design and implementation of a structured-light prototype system providing dense three dimensional (3D) measurements of the foot in motion. The input to the system is a video sequence of a foot during a single step; the output is a 3D reconstruction of the plantar surface of the foot for each frame of the input. Methods Engineering and clinical tests were carried out to test the accuracy and repeatability of the system. Accuracy experiments involved imaging a planar surface from different orientations and elevations and measuring the fitting errors of the data to a plane. Repeatability experiments were done using reconstructions from 27 different subjects, where for each one both right and left feet were reconstructed in static and dynamic conditions over two different days. Results The static accuracy of the system was found to be 0.3 mm with planar test objects. In tests with real feet, the system proved repeatable, with reconstruction differences between trials one week apart averaging 2.4 mm (static case) and 2.8 mm (dynamic case). Conclusion The results obtained in the experiments show positive accuracy and repeatability results when compared to current literature. The design also shows to be superior to the systems available in the literature in several factors. Further studies need to be done to quantify the reliability of the system in clinical environments. PMID:24456711

Dynamic 3D shape of the plantar surface of the foot using coded structured light: a technical report.

PubMed

Thabet, Ali K; Trucco, Emanuele; Salvi, Joaquim; Wang, Weijie; Abboud, Rami J

2014-01-23

The foot provides a crucial contribution to the balance and stability of the musculoskeletal system, and accurate foot measurements are important in applications such as designing custom insoles/footwear. With better understanding of the dynamic behavior of the foot, dynamic foot reconstruction techniques are surfacing as useful ways to properly measure the shape of the foot. This paper presents a novel design and implementation of a structured-light prototype system providing dense three dimensional (3D) measurements of the foot in motion. The input to the system is a video sequence of a foot during a single step; the output is a 3D reconstruction of the plantar surface of the foot for each frame of the input. Engineering and clinical tests were carried out to test the accuracy and repeatability of the system. Accuracy experiments involved imaging a planar surface from different orientations and elevations and measuring the fitting errors of the data to a plane. Repeatability experiments were done using reconstructions from 27 different subjects, where for each one both right and left feet were reconstructed in static and dynamic conditions over two different days. The static accuracy of the system was found to be 0.3 mm with planar test objects. In tests with real feet, the system proved repeatable, with reconstruction differences between trials one week apart averaging 2.4 mm (static case) and 2.8 mm (dynamic case). The results obtained in the experiments show positive accuracy and repeatability results when compared to current literature. The design also shows to be superior to the systems available in the literature in several factors. Further studies need to be done to quantify the reliability of the system in clinical environments.

Everyday eating experiences of chocolate and non-chocolate snacks impact postprandial anxiety, energy and emotional states.

PubMed

Martin, François-Pierre J; Antille, Nicolas; Rezzi, Serge; Kochhar, Sunil

2012-06-01

Social and psychological stressors are both a part of daily life and are increasingly recognized as contributors to individual susceptibility to develop diseases and metabolic disorders. The present study investigated how snacks differing in sensory properties and presentation can influence ratings of affect in consumers with different levels of dispositional anxiety. This study examines the relationships between a pre-disposition to anxiety and food using a repeated exposures design with three interspersed test days over a period of two weeks. The study was conducted on ninety free-living male (n = 28) and female (n = 62) Dutch participants aged between 18 and 35 years old, with a BMI between 18 and 25 kg/m(2) and different anxiety trait levels assessed using State-Trait Anxiety Inventory tests. The study was randomized by age, gender, anxiety trait score, and followed a parallel open design. Three test products: dark chocolate, a milk chocolate snack and crackers with cheese spread (control), which differed in composition, sensory properties and presentation, were evaluated. Changes in self-reported anxiety, emotion, and energetic states were assessed as a function of eating the snacks just after consumption and up to one hour. The repeated exposure design over a period of two weeks enabled the investigations of potential cumulative effects of regular consumption of the food products. The milk chocolate snack resulted in the decrease of anxiety in high anxiety trait subjects, whereas dark chocolate and cheese and crackers respectively improved the anxiety level and the energetic state of low anxiety trait participants. The mood effects were not altered with repeated exposure, and the magnitude of changes was similar on each test day, which illustrates the repeatability of the effects of the food on subjective measures of postprandial wellness.

Everyday Eating Experiences of Chocolate and Non-Chocolate Snacks Impact Postprandial Anxiety, Energy and Emotional States

PubMed Central

Martin, François-Pierre J.; Antille, Nicolas; Rezzi, Serge; Kochhar, Sunil

2012-01-01

Social and psychological stressors are both a part of daily life and are increasingly recognized as contributors to individual susceptibility to develop diseases and metabolic disorders. The present study investigated how snacks differing in sensory properties and presentation can influence ratings of affect in consumers with different levels of dispositional anxiety. This study examines the relationships between a pre-disposition to anxiety and food using a repeated exposures design with three interspersed test days over a period of two weeks. The study was conducted on ninety free-living male (n = 28) and female (n = 62) Dutch participants aged between 18 and 35 years old, with a BMI between 18 and 25 kg/m2 and different anxiety trait levels assessed using State-Trait Anxiety Inventory tests. The study was randomized by age, gender, anxiety trait score, and followed a parallel open design. Three test products: dark chocolate, a milk chocolate snack and crackers with cheese spread (control), which differed in composition, sensory properties and presentation, were evaluated. Changes in self-reported anxiety, emotion, and energetic states were assessed as a function of eating the snacks just after consumption and up to one hour. The repeated exposure design over a period of two weeks enabled the investigations of potential cumulative effects of regular consumption of the food products. The milk chocolate snack resulted in the decrease of anxiety in high anxiety trait subjects, whereas dark chocolate and cheese and crackers respectively improved the anxiety level and the energetic state of low anxiety trait participants. The mood effects were not altered with repeated exposure, and the magnitude of changes was similar on each test day, which illustrates the repeatability of the effects of the food on subjective measures of postprandial wellness. PMID:22822453

Research on a new fiber-optic axial pressure sensor of transformer winding based on fiber Bragg grating

NASA Astrophysics Data System (ADS)

Liu, Yuan; Li, Lianqing; Zhao, Lin; Wang, Jiqiang; Liu, Tongyu

2017-12-01

Based on the principle of the fiber Bragg grating, a new type of fiber-optic pressure sensor for axial force measurement of transformer winding is designed, which is designed with the structure of bending plate beam, the optimization of the packaging process, and material of the sensor. Through the calibration experiment to calibrate the sensor, the field test results of the Taikai transformer factory show that the sensitivity of the sensor is 0.133 pm/kPa and the repeatability error is 2.7% FS. The data of the fiber-optic pressure sensor in different positions maintain consistent and repeatable, which can meet the requirement of the real-time monitoring of the axial force of transformer winding.

Design and characterization of a wearable macrobending fiber optic sensor for human joint angle determination

NASA Astrophysics Data System (ADS)

Silva, Ana S.; Catarino, André; Correia, Miguel V.; Frazão, Orlando

2013-12-01

The work presented here describes the development and characterization of intensity fiber optic sensor integrated in a specifically designed piece of garment to measure elbow flexion. The sensing head is based on macrobending incorporated in the garment, and the increase of curvature number was studied in order to investigate which scheme provided a good result in terms of sensitivity and repeatability. Results showed the configuration that assured a higher sensitivity (0.644 dBm/deg) and better repeatability was the one with four loops. Ultimately, this sensor can be used for rehabilitation purposes to monitor human joint angles, namely, elbow flexion on stroke survivors while performing the reach functional task, which is the most common upper-limb human gesture.

47 CFR 25.144 - Licensing provisions for the 2.3 GHz satellite digital audio radio service.

Code of Federal Regulations, 2014 CFR

2014-10-01

... (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25... of such communications, and the frequencies and emission designators used by the repeaters to re..., the frequencies and emission designators of such communications, and the frequencies and emission...

Increasing Nutrition Literacy: Testing the Effectiveness of Print, Web Site, and Game Modalities

ERIC Educational Resources Information Center

Silk, Kami J.; Sherry, John; Winn, Brian; Keesecker, Nicole; Horodynski, Mildred A.; Sayir, Aylin

2008-01-01

Objective: To examine the effectiveness of three modalities for delivery of nutrition education. Design: Between-subjects, repeated-measures design. Setting: Data were collected at community agencies or during home visits. Participants: Low-income, European American and African American mothers (N = 155). Intervention: Participants were exposed to…

Investigation of the use of resilient modulus for Louisiana soils in the design of pavements: final report.

DOT National Transportation Integrated Search

1994-06-01

The 1986 AASHTO Guide for the Design of Pavement Structures has adopted the use of resilient modulus (M,) as a fundamental proponent to characterize flexible pavement materials. The resilient modulus is defmed as the ratio of the repeated axial devia...

Justification for the Carzo-Yanouzas Experiment on Flat and Tall Structures

ERIC Educational Resources Information Center

Carzo, Rocco, Jr.; Yanouzas, John N.

1970-01-01

Replies to Hummon's criticism (EA 500 730) of experiment, justifying use of split-plot repeated measures design, and tests for homogeneity support the use of this design. Variables considered to be not under control are explained as attributes of structure or as variables having inconsequential effects. (Author/KJ)

Masked Repetition Priming Treatment for Anomia

ERIC Educational Resources Information Center

Silkes, JoAnn P.

2018-01-01

Purpose: Masked priming has been suggested as a way to directly target implicit lexical retrieval processes in aphasia. This study was designed to investigate repeated use of masked repetition priming to improve picture naming in individuals with anomia due to aphasia. Method: A single-subject, multiple-baseline design was used across 6 people…

The effect of four user interface concepts on visual scan pattern similarity and information foraging in a complex decision making task.

PubMed

Starke, Sandra D; Baber, Chris

2018-07-01

User interface (UI) design can affect the quality of decision making, where decisions based on digitally presented content are commonly informed by visually sampling information through eye movements. Analysis of the resulting scan patterns - the order in which people visually attend to different regions of interest (ROIs) - gives an insight into information foraging strategies. In this study, we quantified scan pattern characteristics for participants engaging with conceptually different user interface designs. Four interfaces were modified along two dimensions relating to effort in accessing information: data presentation (either alpha-numerical data or colour blocks), and information access time (all information sources readily available or sequential revealing of information required). The aim of the study was to investigate whether a) people develop repeatable scan patterns and b) different UI concepts affect information foraging and task performance. Thirty-two participants (eight for each UI concept) were given the task to correctly classify 100 credit card transactions as normal or fraudulent based on nine transaction attributes. Attributes varied in their usefulness of predicting the correct outcome. Conventional and more recent (network analysis- and bioinformatics-based) eye tracking metrics were used to quantify visual search. Empirical findings were evaluated in context of random data and possible accuracy for theoretical decision making strategies. Results showed short repeating sequence fragments within longer scan patterns across participants and conditions, comprising a systematic and a random search component. The UI design concept showing alpha-numerical data in full view resulted in most complete data foraging, while the design concept showing colour blocks in full view resulted in the fastest task completion time. Decision accuracy was not significantly affected by UI design. Theoretical calculations showed that the difference in achievable accuracy between very complex and simple decision making strategies was small. We conclude that goal-directed search of familiar information results in repeatable scan pattern fragments (often corresponding to information sources considered particularly important), but no repeatable complete scan pattern. The underlying concept of the UI affects how visual search is performed, and a decision making strategy develops. This should be taken in consideration when designing for applied domains. Copyright © 2018 Elsevier Ltd. All rights reserved.

[SSR loci information analysis in transcriptome of Andrographis paniculata].

PubMed

Li, Jun-Ren; Chen, Xiu-Zhen; Tang, Xiao-Ting; He, Rui; Zhan, Ruo-Ting

2018-06-01

To study the SSR loci information and develop molecular markers, a total of 43 683 Unigenes in transcriptome of Andrographis paniculata were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MicroSAtellite software, SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 14 135 SSR loci were found in the transcriptome of A. paniculata, which distributed in 9 973 Unigenes with a distribution frequency of 32.36%. Di-nucleotide and Tri-nucleotide repeat were the main types, accounted for 75.54% of all SSRs. The repeat motifs of AT/AT and CCG/CGG were the predominant repeat types of Di-nucleotide and Tri-nucleotide, respectively. A total of 4 740 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. Ten pairs of primers in 20 pairs of randomly picked primers produced fragments with expected molecular size. The gene function of Unigenes containing SSR were mostly related to the basic metabolism function of A. paniculata. The SSR markers in transcriptome of A. paniculata show rich type, strong specificity and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. Copyright© by the Chinese Pharmaceutical Association.

Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity.

PubMed

Childs-Disney, Jessica L; Yildirim, Ilyas; Park, HaJeung; Lohman, Jeremy R; Guan, Lirui; Tran, Tuan; Sarkar, Partha; Schatz, George C; Disney, Matthew D

2014-02-21

Myotonic dystrophy type 2 (DM2) is an incurable neuromuscular disorder caused by a r(CCUG) expansion (r(CCUG)(exp)) that folds into an extended hairpin with periodically repeating 2×2 nucleotide internal loops (5'CCUG/3'GUCC). We designed multivalent compounds that improve DM2-associated defects using information about RNA-small molecule interactions. We also report the first crystal structure of r(CCUG) repeats refined to 2.35 Å. Structural analysis of the three 5'CCUG/3'GUCC repeat internal loops (L) reveals that the CU pairs in L1 are each stabilized by one hydrogen bond and a water-mediated hydrogen bond, while CU pairs in L2 and L3 are stabilized by two hydrogen bonds. Molecular dynamics (MD) simulations reveal that the CU pairs are dynamic and stabilized by Na(+) and water molecules. MD simulations of the binding of the small molecule to r(CCUG) repeats reveal that the lowest free energy binding mode occurs via the major groove, in which one C residue is unstacked and the cross-strand nucleotides are displaced. Moreover, we modeled the binding of our dimeric compound to two 5'CCUG/3'GUCC motifs, which shows that the scaffold on which the RNA-binding modules are displayed provides an optimal distance to span two adjacent loops.

Evidence-based severity assessment: Impact of repeated versus single open-field testing on welfare in C57BL/6J mice.

PubMed

Bodden, Carina; Siestrup, Sophie; Palme, Rupert; Kaiser, Sylvia; Sachser, Norbert; Richter, S Helene

2018-01-15

According to current guidelines on animal experiments, a prospective assessment of the severity of each procedure is mandatory. However, so far, the classification of procedures into different severity categories mainly relies on theoretic considerations, since it is not entirely clear which of the various procedures compromise the welfare of animals, or, to what extent. Against this background, a systematic empirical investigation of the impact of each procedure, including behavioral testing, seems essential. Therefore, the present study was designed to elucidate the effects of repeated versus single testing on mouse welfare, using one of the most commonly used paradigms for behavioral phenotyping in behavioral neuroscience, the open-field test. In an independent groups design, laboratory mice (Mus musculus f. domestica) experienced either repeated, single, or no open-field testing - procedures that are assigned to different severity categories. Interestingly, testing experiences did not affect fecal corticosterone metabolites, body weights, elevated plus-maze or home cage behavior differentially. Thus, with respect to the assessed endocrinological, physical, and behavioral outcome measures, no signs of compromised welfare could be detected in mice that were tested in the open-field repeatedly, once, or, not at all. These findings challenge current classification guidelines and may, furthermore, stimulate systematic research on the severity of single procedures involving living animals. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of a biaxial compression device for biological samples: preliminary experimental results for a closed cell foam.

PubMed

Little, J P; Tevelen, G; Adam, C J; Evans, J H; Pearcy, M J

2009-07-01

Biological tissues are subjected to complex loading states in vivo and in order to define constitutive equations that effectively simulate their mechanical behaviour under these loads, it is necessary to obtain data on the tissue's response to multiaxial loading. Single axis and shear testing of biological tissues is often carried out, but biaxial testing is less common. We sought to design and commission a biaxial compression testing device, capable of obtaining repeatable data for biological samples. The apparatus comprised a sealed stainless steel pressure vessel specifically designed such that a state of hydrostatic compression could be created on the test specimen while simultaneously unloading the sample along one axis with an equilibrating tensile pressure. Thus a state of equibiaxial compression was created perpendicular to the long axis of a rectangular sample. For the purpose of calibration and commissioning of the vessel, rectangular samples of closed cell ethylene vinyl acetate (EVA) foam were tested. Each sample was subjected to repeated loading, and nine separate biaxial experiments were carried out to a maximum pressure of 204 kPa (30 psi), with a relaxation time of two hours between them. Calibration testing demonstrated the force applied to the samples had a maximum error of 0.026 N (0.423% of maximum applied force). Under repeated loading, the foam sample demonstrated lower stiffness during the first load cycle. Following this cycle, an increased stiffness, repeatable response was observed with successive loading. While the experimental protocol was developed for EVA foam, preliminary results on this material suggest that this device may be capable of providing test data for biological tissue samples. The load response of the foam was characteristic of closed cell foams, with consolidation during the early loading cycles, then a repeatable load-displacement response upon repeated loading. The repeatability of the test results demonstrated the ability of the test device to provide reproducible test data and the low experimental error in the force demonstrated the reliability of the test data.

Novel CO2 laser robotic controller outperforms experienced laser operators in tasks of accuracy and performance repeatability.

PubMed

Wong, Yu-Tung; Finley, Charles C; Giallo, Joseph F; Buckmire, Robert A

2011-08-01

To introduce a novel method of combining robotics and the CO(2) laser micromanipulator to provide excellent precision and performance repeatability designed for surgical applications. Pilot feasibility study. We developed a portable robotic controller that appends to a standard CO(2) laser micromanipulator. The robotic accuracy and laser beam path repeatability were compared to six experienced users of the industry standard micromanipulator performing the same simulated surgical tasks. Helium-neon laser beam video tracking techniques were employed. The robotic controller demonstrated superiority over experienced human manual micromanipulator control in accuracy (laser path within 1 mm of idealized centerline), 97.42% (standard deviation [SD] 2.65%), versus 85.11% (SD 14.51%), P = .018; and laser beam path repeatability (area of laser path divergence on successive trials), 21.42 mm(2) (SD 4.35 mm(2) ) versus 65.84 mm(2) (SD 11.93 mm(2) ), P = .006. Robotic micromanipulator control enhances accuracy and repeatability for specific laser tasks. Computerized control opens opportunity for alternative user interfaces and additional safety features. Copyright © 2011 The American Laryngological, Rhinological, and Otological Society, Inc.

Structural studies of CNG repeats.

PubMed

Kiliszek, Agnieszka; Rypniewski, Wojciech

2014-07-01

CNG repeats (where N denotes one of the four natural nucleotides) are abundant in the human genome. Their tendency to undergo expansion can lead to hereditary diseases known as TREDs (trinucleotide repeat expansion disorders). The toxic factor can be protein, if the abnormal gene is expressed, or the gene transcript, or both. The gene transcripts have attracted much attention in the biomedical community, but their molecular structures have only recently been investigated. Model RNA molecules comprising CNG repeats fold into long hairpins whose stems generally conform to an A-type helix, in which the non-canonical N-N pairs are flanked by C-G and G-C pairs. Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands. The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design. Here is a brief survey of the CNG structures published to date. © Published by Oxford University Press on behalf of Nucleic Acids Research.

Typing Clostridium difficile strains based on tandem repeat sequences

PubMed Central

2009-01-01

Background Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies. Results This report presents results from a systematic screen for variation in repetitive DNA in the genome of C. difficile. We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. Based on an investigation of 154 C. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. Conclusion We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile. Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. PMID:19133124

Stress responses to repeated exposure to a combined physical and social evaluative laboratory stressor in young healthy males.

PubMed

Boyle, N B; Lawton, C; Arkbåge, K; West, S G; Thorell, L; Hofman, D; Weeks, A; Myrissa, K; Croden, F; Dye, L

2016-01-01

Repeated exposure to homotypic laboratory psychosocial stressors typically instigates rapid habituation in hypothalamic-pituitary-adrenal (HPA) axis-mediated stress responses in humans. However, emerging evidence suggests the combination of physical stress and social evaluative threat may be sufficient to attenuate this response habituation. Neuroendocrine, cardiovascular and subjective stress responses following repeated exposure to a combined physical and social evaluative stress protocol were assessed to examine the habituation response dynamic in this context. The speech task of the Trier social stress test (TSST; Kirschbaum et al., 1993) and the socially evaluated cold pressor task (SECPT; Schwabe et al., 2008) were administered in a combined stressor protocol. Salivary cortisol, cardiovascular and subjective stress responses to a non-stress control and repeat stressor exposure separated by six weeks were examined in males (N=24) in a crossover manner. Stressor exposure resulted in significant elevations in all stress parameters. In contrast to the commonly reported habituation in cortisol response, a comparable post-stress response was demonstrated. Cortisol, heart rate and subjective stress responses were also characterised by a heightened response in anticipation to repeated stress exposure. Blood pressure responses were comparatively uniform across repeated exposures. Findings suggest a combined physical and social evaluative stressor is a potentially useful method for study designs that require repeated presentation of a homotypic stressor. Copyright © 2015 Elsevier Ltd. All rights reserved.

Is testing a more effective learning strategy than note-taking?

PubMed

Rummer, Ralf; Schweppe, Judith; Gerst, Kathleen; Wagner, Simon

2017-09-01

The testing effect is both robust and generalizable. However, most of the underlying studies compare testing to a rather ineffective control condition: massed repeated reading. This article therefore compares testing with note-taking, which has been shown to be more effective than repeated reading. Experiment 1 is based on a 3 × 3 between-participants design with the factors learning condition (repeated reading vs. repeated testing vs. repeated note-taking) and final test delay (5 min vs. 1 week vs. 2 weeks). It shows that in the immediate condition, learning performance is best after note-taking. After 1 week, both the note-taking and the testing groups outperform the rereading group, and after 2 weeks, testing is superior to both note-taking and rereading. Since repeated notetaking may not be the most effective (and common) operationalization of note-taking, Experiment 2 contrasts repeated testing with 2 other note-taking conditions: note-taking plus note-reading and note-taking plus testing (with only a 2-week final test delay). Both conditions that include a testing phase result in better long-term learning than note-taking plus note-reading. In summary, our findings indicate that-in the long run-testing is a powerful learning tool both in isolation and in combination with note-taking. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Improving power to detect changes in blood miRNA expression by accounting for sources of variability in experimental designs.

PubMed

Daniels, Sarah I; Sillé, Fenna C M; Goldbaum, Audrey; Yee, Brenda; Key, Ellen F; Zhang, Luoping; Smith, Martyn T; Thomas, Reuben

2014-12-01

Blood miRNAs are a new promising area of disease research, but variability in miRNA measurements may limit detection of true-positive findings. Here, we measured sources of miRNA variability and determine whether repeated measures can improve power to detect fold-change differences between comparison groups. Blood from healthy volunteers (N = 12) was collected at three time points. The miRNAs were extracted by a method predetermined to give the highest miRNA yield. Nine different miRNAs were quantified using different qPCR assays and analyzed using mixed models to identify sources of variability. A larger number of miRNAs from a publicly available blood miRNA microarray dataset with repeated measures were used for a bootstrapping procedure to investigate effects of repeated measures on power to detect fold changes in miRNA expression for a theoretical case-control study. Technical variability in qPCR replicates was identified as a significant source of variability (P < 0.05) for all nine miRNAs tested. Variability was larger in the TaqMan qPCR assays (SD = 0.15-0.61) versus the qScript qPCR assays (SD = 0.08-0.14). Inter- and intraindividual and extraction variability also contributed significantly for two miRNAs. The bootstrapping procedure demonstrated that repeated measures (20%-50% of N) increased detection of a 2-fold change for approximately 10% to 45% more miRNAs. Statistical power to detect small fold changes in blood miRNAs can be improved by accounting for sources of variability using repeated measures and choosing appropriate methods to minimize variability in miRNA quantification. This study demonstrates the importance of including repeated measures in experimental designs for blood miRNA research. See all the articles in this CEBP Focus section, "Biomarkers, Biospecimens, and New Technologies in Molecular Epidemiology." ©2014 American Association for Cancer Research.

Measurements of Repeated Tightening and Loosening Torque of Seven Different Implant/Abutment Connection Designs and Their Modifications: An In Vitro Study.

PubMed

Butkevica, Alena; Nathanson, Dan; Pober, Richard; Strating, Herman

2018-02-01

Repeated tightening and loosening of the abutment screw may alter its mechanical and physical properties affecting the optimal torque and ultimate reliability of an implant/abutment connection. The purpose of this study was to evaluate the effect of repeated tightening and loosening of implant/abutment screws on the loosening torque of implant/abutment connections of commercially available implant systems. Seven different implant/abutment connections and their modifications were tested. The screws of each system were tightened according to the manufacturer's specifications. After 20 minutes the screws were loosened. This procedure was repeated ten times, and the differences between the 1st and 10th cycle were expressed as a percentage change RTq(%) and correlated with initial torque, the number of threads, the length of shank, and thread surface area employing Spearman's analysis. All systems showed significant differences in residual torque (RTq) value (p < 0.05) between the 1st and 10th cycle except groups 6 and 11 (p > 0.05). All connections but group 3 (p = 1.000) showed a significant change from the initial torque (ITq) to the RTq values. The first successive RTq values increased in two connection groups 1 and 2. The remaining connections showed reduced RTq values ranging from -1.2 % (group 5) to -23.5% (group 6). The RTq values declined gradually with every repeated tightening in groups 1, 2, 3, 8, 9, 11, 12. In group 2, after the tenth tightening the RTq was still above the ITq value. Only length of shank demonstrated a correlation with the RTq(%) change over the successive tightening loosening cycles (p < 0.05). Repeated tightening and loosening of implant/abutment screws caused varying torque level changes among the different systems. These observations can probably be attributed to connection design. Limiting the number of tightening/loosening cycles in clinical and laboratory procedures is advisable for most of the implant systems tested. © 2016 by the American College of Prosthodontists.

Application of Regression-Discontinuity Analysis in Pharmaceutical Health Services Research

PubMed Central

Zuckerman, Ilene H; Lee, Euni; Wutoh, Anthony K; Xue, Zhenyi; Stuart, Bruce

2006-01-01

Objective To demonstrate how a relatively underused design, regression-discontinuity (RD), can provide robust estimates of intervention effects when stronger designs are impossible to implement. Data Sources/Study Setting Administrative claims from a Mid-Atlantic state Medicaid program were used to evaluate the effectiveness of an educational drug utilization review intervention. Study Design Quasi-experimental design. Data Collection/Extraction Methods A drug utilization review study was conducted to evaluate a letter intervention to physicians treating Medicaid children with potentially excessive use of short-acting β2-agonist inhalers (SAB). The outcome measure is change in seasonally-adjusted SAB use 5 months pre- and postintervention. To determine if the intervention reduced monthly SAB utilization, results from an RD analysis are compared to findings from a pretest–posttest design using repeated-measure ANOVA. Principal Findings Both analyses indicated that the intervention significantly reduced SAB use among the high users. Average monthly SAB use declined by 0.9 canisters per month (p<.001) according to the repeated-measure ANOVA and by 0.2 canisters per month (p<.001) from RD analysis. Conclusions Regression-discontinuity design is a useful quasi-experimental methodology that has significant advantages in internal validity compared to other pre–post designs when assessing interventions in which subjects' assignment is based on cutoff scores for a critical variable. PMID:16584464

Designs that Fly: What the History of Aeronautics Tells Us about the Future of Design-Based Research in Education

ERIC Educational Resources Information Center

O'Neill, D. Kevin

2012-01-01

For almost two decades, there has been growing interest in what design-based research (DBR) can contribute to both educational practice and theory. Since its introduction into the literature, this orientation to educational research has repeatedly been likened to aeronautical engineering as a way to clarify its nature and argue its potential. This…

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

The importance of position and path repeatability on force at the knee during six-DOF joint motion.

PubMed

Darcy, Shon P; Gil, Jorge E; Woo, Savio L-Y; Debski, Richard E

2009-06-01

Mechanical devices, such as robotic manipulators have been designed to measure joint and ligament function because of their ability to position a diarthrodial joint in six degrees-of-freedom with fidelity. However, the precision and performance of these testing devices vary. Therefore, the objective of this study was to determine the effect of systematic errors in position and path repeatability of two high-payload robotic manipulators (Manipulators 1 and 2) on the resultant forces at the knee. Using a porcine knee, the position and path repeatability of these manipulators were determined during passive flexion-extension with a coordinate measuring machine. The position repeatability of Manipulator 1 was 0.3 mm in position and 0.2 degrees in orientation while Manipulator 2 had a better position repeatability of 0.1 mm in position and 0.1 degrees in orientation throughout the range of positions examined. The corresponding variability in the resultant force at the knee for these assigned positions was 32+/-33 N for Manipulator 1 and 4+/-1 N for Manipulator 2. Furthermore, the repeatability of the trajectory of each manipulator while moving between assigned positions (path repeatability) was 0.8 mm for Manipulator 1 while the path repeatability for Manipulator 2 was improved (0.1 mm). These path discrepancies produced variability in the resultant force at the knee of 44+/-24 and 21+/-8 N, respectively, for Manipulators 1 and 2 primarily due to contact between the articular surfaces of the tibia and femur. Therefore, improved position and path repeatability yields lower variability in the resultant forces at the knee. Although position repeatability has been the most common criteria for evaluating biomechanical testing devices, the current study has clearly demonstrated that path repeatability can have an even larger effect on the variability in resultant force at the knee. Consequently, the repeatability of the path followed by the joint throughout its prescribed trajectory is as important as the repeatability of the joint at reaching positions making up its trajectory, particularly when joint contact occurs.

A retrospective descriptive study of the characteristics of deliberate self-poisoning patients with single or repeat presentations to an Australian emergency medicine network in a one year period.

PubMed

Martin, Catherine A; Chapman, Rose; Rahman, Asheq; Graudins, Andis

2014-08-23

A proportion of deliberate self-poisoning (DSP) patients present repeatedly to the emergency department (ED). Understanding the characteristics of frequent DSP patients and their presentation is a first step to implementing interventions that are designed to prevent repeated self-poisoning. All DSP presentations to three networked Australian ED's were retrospectively identified from the ED electronic medical record and hospital scanned medical records for 2011. Demographics, types of drugs ingested, emergency department length of stay and disposition for the repeat DSP presenters were extracted and compared to those who presented once with DSP in a one year period. Logistic regression was used to analyse repeat versus single DSP data. The study determined 755 single presenters and 93 repeat DSP presenters. The repeat presenters contributed to 321 DSP presentations. They were more likely to be unemployed (61.0% versus 39.9%, p = 0.008) and have a psychiatric illness compared to single presenters (36.6% versus 15.5%, p < 0.001). Repeat presenters were less likely to receive a toxicology consultation (11.5% versus 27.3%, p < 0.001) and were more likely to abscond from the ED (7.5% versus 3.4%, p = 0.004). Repeat presenters were more likely to ingest paracetamol and antipsychotics than single presenters. The defined daily dose for the most common antipsychotic ingested, quetiapine, was less in the repeat presenter group (median 1.9 [IQR: 1.3-3.5]) compared with the single presenter group (4 [1.4-9.5]), (OR 0.85, 95% CI 0.74-0.99). Patients who present repeatedly to the ED with DSP have pre-existing disadvantages, with increased likelihood of being unemployed and having a mental illness. These patients are also more likely to have health service inequities given the greater likelihood to abscond from the ED and lower likelihood of receiving toxicology consultation for their DSP. Early recognition of repeat DSP patients in the ED may facilitate the development of individualised care plans with the aim to reduce repeat episodes of self-poisoning and subsequent risk of successful suicide.

Immunization with Bacillus Spores Expressing Toxin A Peptide Repeats Protects against Infection with Clostridium difficile Strains Producing Toxins A and B ▿ †

PubMed Central

Permpoonpattana, Patima; Hong, Huynh A.; Phetcharaburanin, Jutarop; Huang, Jen-Min; Cook, Jenny; Fairweather, Neil F.; Cutting, Simon M.

2011-01-01

Clostridium difficile is a leading cause of nosocomial infection in the developed world. Two toxins, A and B, produced by most strains of C. difficile are implicated as virulence factors, yet only recently has the requirement of these for infection been investigated by genetic manipulation. Current vaccine strategies are focused mostly on parenteral delivery of toxoids. In this work, we have used bacterial spores (Bacillus subtilis) as a delivery vehicle to evaluate the carboxy-terminal repeat domains of toxins A and B as protective antigens. Our findings are important and show that oral immunization of the repeat domain of toxin A is sufficient to confer protection in a hamster model of infection designed to closely mimic the human course of infection. Importantly, neutralizing antibodies to the toxin A repeat domain were shown to be cross-reactive with the analogous domain of toxin B and, being of high avidity, provided protection against challenge with a C. difficile strain producing toxins A and B (A+B+). Thus, although many strains produce both toxins, antibodies to only toxin A can mediate protection. Animals vaccinated with recombinant spores were fully able to survive reinfection, a property that is particularly important for a disease with which patients are prone to relapse. We show that mucosal immunization, not parenteral delivery, is required to generate secretory IgA and that production of these neutralizing polymeric antibodies correlates with protection. This work demonstrates that an effective vaccine against C. difficile can be designed around two attributes, mucosal delivery and the repeat domain of toxin A. PMID:21482682

Repeated rat-forced swim test: reducing the number of animals to evaluate gradual effects of antidepressants.

PubMed

Mezadri, T J; Batista, G M; Portes, A C; Marino-Neto, J; Lino-de-Oliveira, C

2011-02-15

The forced swim test (FST) is a pre-clinical test to short and long term treatment with antidepressant drugs (ADT), which requires between-subject designs. Herein a modified protocol of the FST using within-subject design (repeated rat-FST) was evaluated. Male Wistar rats were submitted to 15 min of swimming (Day 1: pretest) followed by three subsequent 5 min-swimming tests one week apart (Day 2: test, Day 7: retest 1, Day 14: retest 2). To determine the temporal and factorial characteristics of the variables scored in the repeated rat-FST, the protocol was carried out in untreated animals (E1). To validate the method, daily injections of Fluoxetine (FLX, 2.5mg/kg, i.p.) or saline were given over a 2-week period (E2). Tests and retests have been videotaped for further register of the latency, frequency and duration of behaviors. Over retesting the latency to immobility decreased whereas duration of immobility tended to increase. Factorial analysis revealed that the test, the retest 1 as well as the retest 2 have variables suitable to detection of antidepressant-like effects of ADT. Compared to saline, FLX chronically administrated reduced duration of immobility whereas increased duration of swimming in retest 2. The data suggest that repeated rat-FST detected the gradual increase in the efficacy of low doses of FLX over time. Therefore, repeated rat-FST seemed suitable to detect short and long term effects of selective serotonin reuptake inhibitors, or other ADT, thus reducing the number of animals used in the screenings of this type of compounds. © 2010 Elsevier B.V. All rights reserved.

The Enigma of Rapid Repeat Pregnancy: A Qualitative Study of Teen Mothers.

PubMed

Conroy, K N; Engelhart, T G; Martins, Y; Huntington, N L; Snyder, A F; Coletti, K D; Cox, J E

2016-06-01

Rapid repeat pregnancy accounts for 18% of teen pregnancies and leads to adverse health, economic, and developmental outcomes for teen mothers and their children. Few interventions have been successful in reducing rapid repeat pregnancy. In this qualitative study we examined adolescent mothers' perceptions of their decision-making and behaviors that helped prevent or promote a rapid repeat pregnancy. DESIGN, SETTING, PARTICIPANTS, INTERVENTIONS, AND MAIN OUTCOME MEASURES: Semistructured interviews were conducted with 31 adolescent mothers, aged 16-21 years; 15 of these subjects experienced a repeat pregnancy within a year of their first child's birth and 16 had not. Two researchers used a grounded, inductive technique to identify emergent themes; interviews were subsequently coded accordingly. Counts were tabulated of the number of times themes were endorsed among those with or without a repeat pregnancy. Four overarching themes emerged from the interviews: intentionality regarding pregnancy planning, patients' degree of independence in making contraceptive choices, sense of control over life experience, and barriers to follow-through on contraceptive planning. Teens who had not experienced a rapid repeat pregnancy more often endorsed themes of intentionality in preventing or promoting a pregnancy, independence in decision-making, and feelings of control over their experience. Ambivalence and lack of decision-making about seeking another pregnancy were frequently endorsed by mothers who had experienced a second pregnancy. Decision-making regarding seeking or preventing a rapid repeat pregnancy is complex for teen mothers; techniques to help support decision-making or to delay pregnancy until decision-repeat making is complete might be important in reducing rapid pregnancy. Copyright © 2015 North American Society for Pediatric and Adolescent Gynecology. Published by Elsevier Inc. All rights reserved.

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

New Trends in Paracoccidioidomycosis Epidemiology

PubMed Central

Martinez, Roberto

2017-01-01

Paracoccidioidomycosis is a systemic fungal disease occurring in Latin America and more prevalent in South America. The disease is caused by the dimorphic fungus Paracoccidioides spp. whose major hosts are humans and armadillos. The fungus grows in soil and its infection is associated with exposure to the rural environment and to agricultural activities, with a higher risk in coffee and tobacco plantations. Population studies assessing the reactivity to Paracoccidioides spp. antigens by intradermal reaction or serological tests have detected previous subclinical infections in a significant proportion of healthy individuals living in various endemic countries. Paracoccidioidomycosis-disease is manifested by a small minority of infected individuals. The risk of developing the disease and its type of clinical form are related to the personal and life style characteristics of infected individuals, including genetic background, age, sex, ethnicity, smoking habit, alcohol drinking, and eventual cellular immunosuppression. Brazil, Colombia, Venezuela, Argentina, and Ecuador have endemic areas that had already been defined in the 20th century. The incidence of paracoccidioidomycosis can be altered by climate phenomena and mainly by human migration and occupation of poorly explored territories. In Brazil, the endemy tends to expand towards the North and Center-West around the Amazon Region. PMID:29371520

Self-association of the APC tumor suppressor is required for the assembly, stability, and activity of the Wnt signaling destruction complex

PubMed Central

Kunttas-Tatli, Ezgi; Roberts, David M.; McCartney, Brooke M.

2014-01-01

The tumor suppressor adenomatous polyposis coli (APC) is an essential negative regulator of Wnt signaling through its activity in the destruction complex with Axin, GSK3β, and CK1 that targets β-catenin/Armadillo (β-cat/Arm) for proteosomal degradation. The destruction complex forms macromolecular particles we termed the destructosome. Whereas APC functions in the complex through its ability to bind both β-cat and Axin, we hypothesize that APC proteins play an additional role in destructosome assembly through self-association. Here we show that a novel N-terminal coil, the APC self-association domain (ASAD), found in vertebrate and invertebrate APCs, directly mediates self-association of Drosophila APC2 and plays an essential role in the assembly and stability of the destructosome that regulates β-cat degradation in Drosophila and human cells. Consistent with this, removal of the ASAD from the Drosophila embryo results in β-cat/Arm accumulation and aberrant Wnt pathway activation. These results suggest that APC proteins are required not only for the activity of the destructosome, but also for the assembly and stability of this macromolecular machine. PMID:25208568

Morphology and identification of the mature larvae of several species of the genus Otiorhynchus (Coleoptera, Curculionidae, Entiminae) from Central Europe with an update of the life history traits.

PubMed

Gosik, Rafał; Sprick, Peter; Skuhrovec, Jiří; Deruś, Magdalena; Hommes, Martin

2016-05-05

The mature larvae of 14 Otiorhynchus taxa are described: O. (Otiorhynchus) armadillo (Rossi, 1792), O. (Nehrodistus) armatus Boheman, 1846, O. (Otiorhynchus) aurifer Boheman, 1843, O. (Pocodalemes) crataegi Germar, 1824, Otiorhynchus (Arammichnus) indefinitus Reitter, 1912 (syn. O. dieckmanni Magnano, 1979), O. (Choilisanus) raucus (Fa-bricius, 1777) and 3 taxa of the O. (Otiorhynchus) tenebricosus complex (Herbst, 1784), O. (Otiorhynchus) clavipes (Bonsdorff, 1785), O. (Otiorhynchus) fuscipes (Olivier, 1807) and O. (Otiorhynchus) lugdunensis Boheman, 1843, are described and illustrated for the first time. The larvae of (Otiorhynchus) meridionalis Gyllenhal, 1834, O. (Pendragon) ovatus (Linnaeus, 1758), O. (Zustalestus) rugosostriatus (Goeze, 1777), O. (Metopiorrhynchus) singularis (Linnaeus, 1767), and O. (Dorymerus) sulcatus (Fabricius, 1775) are redescribed and illustrated, and new characters are added. Important characters of the mature larvae (e.g. chaetotaxy, shape of head and body) are explained in detail and illustrated. A key to the identification of the mature larvae of 19 Otiorhynchus taxa is provided. Breeding and collecting data of the larvae are given, and the study is completed by a current overview on the life histories of all treated species.

Discrete typing units of Trypanosoma cruzi identified in rural dogs and cats in the humid Argentinean Chaco

PubMed Central

ENRIQUEZ, G.F.; CARDINAL, M.V.; OROZCO, M.M.; LANATI, L.; SCHIJMAN, A.G.; GÜRTLER, R.E.

2013-01-01

SUMMARY The discrete typing units (DTUs) of Trypanosoma cruzi that infect domestic dogs and cats have rarely been studied. With this purpose we conducted a cross-sectional xenodiagnostic survey of dog and cat populations residing in two infested rural villages in Pampa del Indio, in the humid Argentine Chaco. Parasites were isolated by culture from 44 dogs and 12 cats with a positive xenodiagnosis. DTUs were identified from parasite culture samples using a strategy based on multiple polymerase-chain reactions. TcVI was identified in 37 of 44 dogs and in 10 of 12 cats, whereas TcV was identified in five dogs and in two cats –a new finding for cats. No mixed infections were detected. The occurrence of two dogs infected with TcIII –classically found in armadillos– suggests a probable link with the local sylvatic transmission cycle involving Dasypus novemcinctus armadillos and a potential risk of human infection with TcIII. Our study reinforces the importance of dogs and cats as domestic reservoir hosts and sources of various DTUs infecting humans, and suggests a link between dogs and the sylvatic transmission cycle of TcIII. PMID:23058180

δ-Catenin Increases the Stability of EGFR by Decreasing c-Cbl Interaction and Enhances EGFR/Erk1/2 Signaling in Prostate Cancer.

PubMed

Shrestha, Nensi; Shrestha, Hridaya; Ryu, Taeyong; Kim, Hangun; Simkhada, Shishli; Cho, Young-Chang; Park, So-Yeon; Cho, Sayeon; Lee, Kwang-Youl; Lee, Jae-Hyuk; Kim, Kwonseop

2018-04-30

δ-Catenin, a member of the p120-catenin subfamily of armadillo proteins, reportedly increases during the late stage of prostate cancer. Our previous study demonstrates that δ-catenin increases the stability of EGFR in prostate cancer cell lines. However, the molecular mechanism behind δ-catenin-mediated enhanced stability of EGFR was not explored. In this study, we hypothesized that δ-catenin enhances the protein stability of EGFR by inhibiting its lysosomal degradation that is mediated by c-casitas b-lineage lymphoma (c-Cbl), a RING domain E3 ligase. c-Cbl monoubiquitinates EGFR and thus facilitates its internalization, followed by lysosomal degradation. We observed that δ-catenin plays a key role in EGFR stability and downstream signaling. δ-Catenin competes with c-Cbl for EGFR binding, which results in a reduction of binding between c-Cbl and EGFR and thus decreases the ubiquitination of EGFR. This in turn increases the expression of membrane bound EGFR and enhances EGFR/Erk1/2 signaling. Our findings add a new perspective on the role of δ-catenin in enhancing EGFR/Erk1/2 signaling-mediated prostate cancer.

Cranial osteology of the pampathere Holmesina floridanus (Xenarthra: Cingulata; Blancan NALMA), including a description of an isolated petrosal bone

PubMed Central

Lyon, Lauren M.

2017-01-01

The present study entails descriptions of several well-preserved skulls from the pampathere species Holmesina floridanus, recovered from Pliocene localities in central Florida and housed in the collections of the Florida Museum of Natural History. Bone by bone descriptions have allowed detailed reconstructions of cranial morphology. Cranial foramina are described and illustrated in detail, and their contents inferred. The first ever description of an isolated pampathere petrosal is also included. Cranial osteology of Holmesina floridanus is compared to that of Pleistocene species of Holmesina from both North and South America (Holmesina septentrionalis, Holmesina occidentalis), as well as to the other well-known pampathere genera, to closely related taxa among glyptodonts (Propalaehoplophorus), and to extinct and extant armadillos (Proeutatus, Euphractus). This study identifies a suite of apomorphic cranial features that serve to diagnose a putative, progressive series of more inclusive monophyletic groups, including the species Holmesina floridanus, the genus Holmesina, pampatheres, pampatheres plus glyptodonts, and a clade formed by pampatheres, glyptodonts, and Proeutatus. The study highlights the need for further anatomical investigations of pampathere cranial anatomy, especially those using modern scanning technology, and for analyses of pampathere phylogenetic relationships. PMID:29250462

Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals

PubMed Central

Meredith, Robert W.; Gatesy, John; Murphy, William J.; Ryder, Oliver A.; Springer, Mark S.

2009-01-01

Vestigial structures occur at both the anatomical and molecular levels, but studies documenting the co-occurrence of morphological degeneration in the fossil record and molecular decay in the genome are rare. Here, we use morphology, the fossil record, and phylogenetics to predict the occurrence of “molecular fossils” of the enamelin (ENAM) gene in four different orders of placental mammals (Tubulidentata, Pholidota, Cetacea, Xenarthra) with toothless and/or enamelless taxa. Our results support the “molecular fossil” hypothesis and demonstrate the occurrence of frameshift mutations and/or stop codons in all toothless and enamelless taxa. We then use a novel method based on selection intensity estimates for codons (ω) to calculate the timing of iterated enamel loss in the fossil record of aardvarks and pangolins, and further show that the molecular evolutionary history of ENAM predicts the occurrence of enamel in basal representatives of Xenarthra (sloths, anteaters, armadillos) even though frameshift mutations are ubiquitous in ENAM sequences of living xenarthrans. The molecular decay of ENAM parallels the morphological degeneration of enamel in the fossil record of placental mammals and provides manifest evidence for the predictive power of Darwin's theory. PMID:19730686

Molecular view of ligands specificity for CAG repeats in anti-Huntington therapy.

PubMed

Bochicchio, Anna; Rossetti, Giulia; Tabarrini, Oriana; Krauβ, Sybille; Carloni, Paolo

2015-10-13

Huntington's disease is a fatal and devastating neurodegenerative genetic disorder for which there is currently no cure. It is characterized by Huntingtin protein's mRNA transcripts with 36 or more CAG repeats. Inhibiting the formation of pathological complexes between these expanded transcripts and target proteins may be a valuable strategy against the disease. Yet, the rational design of molecules specifically targeting the expanded CAG repeats is limited by the lack of structural information. Here, we use well-tempered metadynamics-based free energy calculations to investigate pose and affinity of two ligands targeting CAG repeats for which affinities have been previously measured. The first consists of two 4-guanidinophenyl rings linked by an ester group. It is the most potent ligand identified so far, with Kd = 60(30) nM. The second consists of a 4-phenyl dihydroimidazole and 4-1H-indole dihydroimidazole connected by a C-C bond (Kd = 700(80) nM). Our calculations reproduce the experimental affinities and uncover the recognition pattern between ligands' and their RNA target. They also provide a molecular basis for the markedly different affinity of the two ligands for CAG repeats as observed experimentally. These findings may pave the way for a structure-based hit-to-lead optimization to further improve ligand selectivity toward CAG repeat-containing mRNAs.

Recent social conditions affect boldness repeatability in individual sticklebacks.

PubMed

Jolles, Jolle Wolter; Aaron Taylor, Benjamin; Manica, Andrea

2016-02-01

Animal personalities are ubiquitous across the animal kingdom and have been shown both to influence individual behaviour in the social context and to be affected by it. However, little attention has been paid to possible carryover effects of social conditions on personality expression, especially when individuals are alone. Here we investigated how the recent social context affected the boldness and repeatability of three-spined sticklebacks, Gasterosteus aculeatus , during individual assays. We housed fish either solitarily, solitarily part of the time or socially in groups of four, and subjected them twice to a risk-taking task. The social conditions had a large effect on boldness repeatability, with fish housed solitarily before the trials showing much higher behavioural repeatability than fish housed socially, for which repeatability was not significant. Social conditions also had a temporal effect on the boldness of the fish, with only fish housed solitarily taking more risks during the first than the second trial. These results show that recent social conditions can thus affect the short-term repeatability of behaviour and obfuscate the expression of personality even in later contexts when individuals are alone. This finding highlights the need to consider social housing conditions when designing personality studies and emphasizes the important link between animal personality and the social context by showing the potential role of social carryover effects.

Recent social conditions affect boldness repeatability in individual sticklebacks

PubMed Central

Jolles, Jolle Wolter; Aaron Taylor, Benjamin; Manica, Andrea

2016-01-01

Animal personalities are ubiquitous across the animal kingdom and have been shown both to influence individual behaviour in the social context and to be affected by it. However, little attention has been paid to possible carryover effects of social conditions on personality expression, especially when individuals are alone. Here we investigated how the recent social context affected the boldness and repeatability of three-spined sticklebacks, Gasterosteus aculeatus, during individual assays. We housed fish either solitarily, solitarily part of the time or socially in groups of four, and subjected them twice to a risk-taking task. The social conditions had a large effect on boldness repeatability, with fish housed solitarily before the trials showing much higher behavioural repeatability than fish housed socially, for which repeatability was not significant. Social conditions also had a temporal effect on the boldness of the fish, with only fish housed solitarily taking more risks during the first than the second trial. These results show that recent social conditions can thus affect the short-term repeatability of behaviour and obfuscate the expression of personality even in later contexts when individuals are alone. This finding highlights the need to consider social housing conditions when designing personality studies and emphasizes the important link between animal personality and the social context by showing the potential role of social carryover effects. PMID:26949265

New paradigm in ankyrin repeats: Beyond protein-protein interaction module.

PubMed

Islam, Zeyaul; Nagampalli, Raghavendra Sashi Krishna; Fatima, Munazza Tamkeen; Ashraf, Ghulam Md

2018-04-01

Classically, ankyrin repeat (ANK) proteins are built from tandems of two or more repeats and form curved solenoid structures that are associated with protein-protein interactions. These are short, widespread structural motif of around 33 amino acids repeats in tandem, having a canonical helix-loop-helix fold, found individually or in combination with other domains. The multiplicity of structural pattern enables it to form assemblies of diverse sizes, required for their abilities to confer multiple binding and structural roles of proteins. Three-dimensional structures of these repeats determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. Recent work on the ANK has proposed novel structural information, especially protein-lipid, protein-sugar and protein-protein interaction. Self-assembly of these repeats was also shown to prevent the associated protein in forming filaments. In this review, we summarize the latest findings and how the new structural information has increased our understanding of the structural determinants of ANK proteins. We discussed latest findings on how these proteins participate in various interactions to diversify the ANK roles in numerous biological processes, and explored the emerging and evolving field of designer ankyrins and its framework for protein engineering emphasizing on biotechnological applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluating Simulation Methodologies to Determine Best Strategies to Maximize Student Learning.

PubMed

Scherer, Yvonne K; Foltz-Ramos, Kelly; Fabry, Donna; Chao, Ying-Yu

2016-01-01

Limited evidence exists as to the most effective ways to provide simulation experiences to maximize student learning. This quasi-experimental study investigated 2 different strategies repeated versus 1 exposure and participation versus observation on student outcomes following exposure to a high-fidelity acute asthma exacerbation of asthma scenario. Immediate repeated exposure resulted in significantly higher scores on knowledge, student satisfaction and self-confidence, and clinical performance measures than a single exposure. Significant intergroup differences were found on participants' satisfaction and self-confidence as compared with observers. Implications for nurse educators include expanding the observer role when designing repeated exposure to simulations and integrating technical, cognitive, and behavioral outcomes as a way for faculty to evaluate students' clinical performance. Published by Elsevier Inc.

Universal test fixture for monolithic mm-wave integrated circuits calibrated with an augmented TRD algorithm

NASA Technical Reports Server (NTRS)

Romanofsky, Robert R.; Shalkhauser, Kurt A.

1989-01-01

The design and evaluation of a novel fixturing technique for characterizing millimeter wave solid state devices is presented. The technique utilizes a cosine-tapered ridge guide fixture and a one-tier de-embedding procedure to produce accurate and repeatable device level data. Advanced features of this technique include nondestructive testing, full waveguide bandwidth operation, universality of application, and rapid, yet repeatable, chip-level characterization. In addition, only one set of calibration standards is required regardless of the device geometry.

Dynamic Accuracy of Inertial Magnetic Sensor Modules

DTIC Science & Technology

2016-12-01

and the cost of the YEI 3-space data-logging sensor was justified. C. PREVIOUS WORK In [7], Jeremy Cookson built a low-cost pendulum with an optical...encoder to test the dynamic accuracy of MARG sensor modules. The pendulum was designed in order to execute dynamic, repeatable tests in a single...3DM-GX1 and 3DM-GX3-25 sensors. In [8], Leslie Landry developed similar repeatable tests and utilized the pendulum to test the dynamic accuracy of

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

A Marine Aerosol Reference Tank system as a breaking wave analogue

NASA Astrophysics Data System (ADS)

Stokes, M. D.; Deane, G. B.; Prather, K.; Bertram, T. H.; Ruppel, M. J.; Ryder, O. S.; Brady, J. M.; Zhao, D.

2012-12-01

In order to better understand the processes governing the production of marine aerosols a repeatable, controlled method for their generation is required. The Marine Aerosol Reference Tank (MART) has been designed to closely approximate oceanic conditions by producing an evolving bubble plume and surface foam patch. The tank utilizes an intermittently plunging sheet of water and large volume tank reservoir to simulate turbulence, plume and foam formation, and is monitored volumetrically and acoustically to ensure the repeatability of conditions.

A Military-Relevant Model of Closed Concussive Head Injury: Longitudinal Studies Characterizing and Validating Single and Repetitive mTBI

DTIC Science & Technology

2014-10-01

Research Program (CCCRP). Provided in this Year 2 Annual Report are the results of our Phase I studies focused on characterizing the neuropathologic...effects of a single concussive impact to repeated concussive impacts using the PCI model. Phase I studies have been completed and these results set...the foundation for Phase II studies designed to evaluate the effects of repeated concussions that occur prior to and after the resolution of the

Design and analysis of an automatic method of measuring silicon-controlled-rectifier holding current

NASA Technical Reports Server (NTRS)

Maslowski, E. A.

1971-01-01

The design of an automated SCR holding-current measurement system is described. The circuits used in the measurement system were designed to meet the major requirements of automatic data acquisition, reliability, and repeatability. Performance data are presented and compared with calibration data. The data verified the accuracy of the measurement system. Data taken over a 48-hr period showed that the measurement system operated satisfactorily and met all the design requirements.

The Integration of Green Chemistry Experiments with Sustainable Development Concepts in Pre-Service Teachers' Curriculum: Experiences from Malaysia

ERIC Educational Resources Information Center

Karpudewan, Mageswary; Ismail, Zurida Hg; Mohamed, Norita

2009-01-01

Purpose: The purpose of this paper is to introduce green chemistry experiments as laboratory-based pedagogy and to evaluate effectiveness of green chemistry experiments in delivering sustainable development concepts (SDCs) and traditional environmental concepts (TECs). Design/methodology/approach: Repeated measure design was employed to evaluate…

Modified Brown-Forsythe Procedure for Testing Interaction Effects in Split-Plot Designs

ERIC Educational Resources Information Center

Vallejo, Guillermo; Ato, Manuel

2006-01-01

The standard univariate and multivariate methods are conventionally used to analyze continuous data from groups by trials repeated measures designs, in spite of being extremely sensitive to departures from the multisample sphericity assumption when group sizes are unequal. However, in the last 10 years several authors have offered alternative…

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…

Evidence-Centered Design for Simulation-Based Assessment. CRESST Report 800

ERIC Educational Resources Information Center

Mislevy, Robert J.

2011-01-01

Simulations provide opportunities for individuals to learn and develop skills for situations that may be expensive, time-consuming, or dangerous. Careful design can support a person's learning by tailoring the features of situations to his or her skill level(s), allowing repeated attempts, and by providing timely feedback. Furthermore, simulations…

The Effect of School Uniform on Incidental Physical Activity among 10-Year-Old Children

ERIC Educational Resources Information Center

Norrish, Hannah; Farringdon, Fiona; Bulsara, Max; Hands, Beth

2012-01-01

The school setting provides a unique opportunity to promote physical activity in children by ensuring adequate time, appropriate facilities and education guidance is offered. However school uniform design could also limit physical activity. A repeated measures crossover design was used to compare school recess and lunchtime physical activity over…

Effects of Thinking Style on Design Strategies: Using Bridge Construction Simulation Programs

ERIC Educational Resources Information Center

Sun, Chuen-Tsai; Wang, Dai-Yi; Chang, Yu-Yeh

2013-01-01

Computer simulation users can freely control operational factors and simulation results, repeat processes, make changes, and learn from simulation environment feedback. The focus of this paper is on simulation-based design tools and their effects on student learning processes in a group of 101 Taiwanese senior high school students. Participants…

Ireland's Generic Repeat Design Schools Programme

ERIC Educational Resources Information Center

Sheppard, Tony

2011-01-01

The Irish Department of Education and Skills (DoE) is strongly committed to energy efficiency and to reducing CO[subscript 2] by developing and implementing energy level ceilings in relation to school design that aim to remain below half of the accepted good practice in the field. This approach works within normal departmental budgetary limits to…

KWICgrouper--Designing a Tool for Corpus-Driven Concordance Analysis

ERIC Educational Resources Information Center

O'Donnell, Matthew Brook

2008-01-01

The corpus-driven analysis of concordance data often results in the identification of groups of lines in which repeated patterns around the node item establish membership in a particular function meaning group (Mahlberg, 2005). This paper explains the KWICgrouper, a concept designed to support this kind of concordance analysis. Groups are defined…

Learning Opportunities for Nurses Working within Home Care

ERIC Educational Resources Information Center

Lundgren, Solveig

2011-01-01

Purpose: The purpose of this study is to explore home care nurses' experience of learning in a multicultural environment. Design/methodology/approach: The study was based on qualitative research design. Data were collected through repeated interviews with registered home care nurses working in a multicultural area. The data were analyzed through a…

Design of tryptophan-containing mutants of the symmetrical Pizza protein for biophysical studies.

PubMed

Noguchi, Hiroki; Mylemans, Bram; De Zitter, Elke; Van Meervelt, Luc; Tame, Jeremy R H; Voet, Arnout

2018-03-18

β-propeller proteins are highly symmetrical, being composed of a repeated motif with four anti-parallel β-sheets arranged around a central axis. Recently we designed the first completely symmetrical β-propeller protein, Pizza6, consisting of six identical tandem repeats. Pizza6 is expected to prove a useful building block for bionanotechnology, and also a tool to investigate the folding and evolution of β-propeller proteins. Folding studies are made difficult by the high stability and the lack of buried Trp residues to act as monitor fluorophores, so we have designed and characterized several Trp-containing Pizza6 derivatives. In total four proteins were designed, of which three could be purified and characterized. Crystal structures confirm these mutant proteins maintain the expected structure, and a clear redshift of Trp fluorescence emission could be observed upon denaturation. Among the derivative proteins, Pizza6-AYW appears to be the most suitable model protein for future folding/unfolding kinetics studies as it has a comparable stability as natural β-propeller proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

Tool and Fixture Design

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

Graham, Mark W.

2015-07-28

In a manufacturing process, a need is identified and a product is created to fill this need. While design and engineering of the final product is important, the tools and fixtures that aid in the creation of the final product are just as important, if not more so. Power supplies assembled at the TA-55 PF-5 have been designed by an excellent engineering team. The task in PF-5 now is to ensure that all steps of the assembly and manufacturing process can be completed safely, reliably, and in a quality repeatable manner. One of these process steps involves soldering fine wiresmore » to an electrical connector. During the process development phase, the method of soldering included placing the power supply in a vice in order to manipulate it into a position conducive to soldering. This method is unacceptable from a reliability, repeatability, and ergonomic standpoint. To combat these issues, a fixture was designed to replace the current method. To do so, a twelve step engineering design process was used to create the fixture that would provide a solution to a multitude of problems, and increase the safety and efficiency of production.« less

Tuboimpedance: A New Test of Eustachian Tube Function.

PubMed

Smith, Matthew E; Zou, Charlie C; Blythe, Andrew J C; Tysome, James R

2017-04-01

Objective Eustachian tube (ET) dysfunction is most frequently caused by a failure of the ET to adequately open; however, there is currently no reliable method of assessing this. Tubomanometry has recently shown good interindividual repeatability as a measure of ET function by measuring middle ear pressure after the application of regulated nasopharyngeal pressures during swallowing. We present the first reports of a novel test: middle ear impedance measurements during standard nasopharyngeal pressure application (tuboimpedance). We assess repeatability in healthy ears and any advantages over tubomanometry. Study Design Exploratory cohort diagnosis study. Setting Tertiary referral center. Subjects Twenty screened, healthy ears (10 volunteers). Methods Tubomanometry and tuboimpedance tests were performed while individuals swallowed with applied nasopharyngeal pressures of 20, 30, 40, and 50 mbar. Eustachian tube opening detection rate and test repeatability (measured by intraclass correlation coefficient [ICC]) for immediate and delayed repeats at each pressure were compared. Results ET opening was detected more frequently using tuboimpedance, with a 100% detection rate using a nasopharyngeal pressure of 30 mbar or more, compared to 88% to 96% with tubomanometry. Detection of ET opening at 20 mbar was possible with tuboimpedance. Repeatability of both tests was mostly strong (ICC >0.7) for both immediate and delayed repeats. Repeatability for the tubomanometry R value was only fair to moderate. Conclusion Tuboimpedance may provide a repeatable measure of ET opening that is easier to perform due to lower nasopharyngeal pressures required and fewer issues with poor ear-probe sealing. Further assessment in patients with different forms of ET dysfunction is required.

The development and reliability of a repeated anaerobic cycling test in female ice hockey players.

PubMed

Wilson, Kier; Snydmiller, Gary; Game, Alex; Quinney, Art; Bell, Gordon

2010-02-01

The purpose of this study was to develop and assess the reliability of a repeated anaerobic power cycling test designed to mimic the repeated sprinting nature of the sport of ice hockey. Nineteen female varsity ice hockey players (mean X +/- SD age, height and body mass = 21 +/- 2 yr, 166.6 +/- 6.3 cm and 62.3 +/- 7.3) completed 3 trials of a repeated anaerobic power test on a Monark cycle ergometer on different days. The test consisted of "all-out" cycling for 5 seconds separated by 10 seconds of low-intensity cycling, repeated 4 times. The relative load factor used for the resistance setting was equal to 0.095 kg per kilogram body mass. There was no significant difference between the peak 5-second power output (PO), mean PO, or the fatigue index (%) among the 3 different trials. The peak 5-second PO was 702.6 +/- 114.8 w and 11.3 +/- 1.1 w x kg, whereas the mean PO across the 4 repeats was 647.1 +/- 96.3 w and 10.4 +/- 1.0 w x kg averaged for the 3 different tests. The fatigue index averaged 17.8 +/- 6.5%. The intraclass correlation coefficient for peak 5-second, mean PO, and fatigue index was 0.82, 0.86, and 0.82, respectively. This study reports the methodology of a repeated anaerobic power cycling test that was reliable for the measurement of PO and calculated fatigue index in varsity women ice hockey players and can be used as a laboratory-based assessment of repeated anaerobic fitness.

Endocarditis due to Micrococcus sedentarius incertae sedis.

PubMed Central

Old, D C; McNeill, G P

1979-01-01

The clinical and bacteriological features of a case of endocarditis are described in which a Gram-positive coccus, presently designated Micrococcus sedentarius incertae sedis, was repeatedly isolated. PMID:512056

Genetic Fingerprinting Using Microsatellite Markers in a Multiplex PCR Reaction: A Compilation of Methodological Approaches from Primer Design to Detection Systems.

PubMed

Krüger, Jacqueline; Schleinitz, Dorit

2017-01-01

Microsatellites are polymorphic DNA loci comprising repeated sequence motifs of two to five base pairs which are dispersed throughout the genome. Genotyping of microsatellites is a widely accepted tool for diagnostic and research purposes such as forensic investigations and parentage testing, but also in clinics (e.g. monitoring of bone marrow transplantation), as well as for the agriculture and food industries. The co-amplification of several short tandem repeat (STR) systems in a multiplex reaction with simultaneous detection helps to obtain more information from a DNA sample where its availability may be limited. Here, we introduce and describe this commonly used genotyping technique, providing an overview on available resources on STRs, multiplex design, and analysis.

A fault-tolerant small world topology control model in ad hoc networks for search and rescue

NASA Astrophysics Data System (ADS)

Tan, Mian; Fang, Ling; Wu, Yue; Zhang, Bo; Chang, Bowen; Holme, Petter; Zhao, Jing

2018-02-01

Due to their self-organized, multi-hop and distributed characteristics, ad hoc networks are useful in search and rescue. Topology control models need to be designed for energy-efficient, robust and fast communication in ad hoc networks. This paper proposes a topology control model which specializes for search and rescue-Compensation Small World-Repeated Game (CSWRG)-which integrates mobility models, constructing small world networks and a game-theoretic approach to the allocation of resources. Simulation results show that our mobility models can enhance the communication performance of the constructed small-world networks. Our strategy, based on repeated game, can suppress selfish behavior and compensate agents that encounter selfish or faulty neighbors. This model could be useful for the design of ad hoc communication networks.

A Mobile Text Message Intervention to Reduce Repeat Suicidal Episodes: Design and Development of Reconnecting After a Suicide Attempt (RAFT)

PubMed Central

Shand, Fiona; Morley, Kirsten; Batterham, Philip J; Petrie, Katherine; Reda, Bill; Berrouiguet, Sofian; Haber, Paul S; Carter, Gregory; Christensen, Helen

2017-01-01

Background Suicide is a leading cause of death, particularly among young people. Continuity of care following discharge from hospital is critical, yet this is a time when individuals often lose contact with health care services. Offline brief contact interventions following a suicide attempt can reduce the number of repeat attempts, and text message (short message service, SMS) interventions are currently being evaluated. Objective The aim of this study was to extend postattempt caring contacts by designing a brief Web-based intervention targeting proximal risk factors and the needs of this population during the postattempt period. This paper details the development process and describes the realized system. Methods To inform the design of the intervention, a lived experience design group was established. Participants were asked about their experiences of support following their suicide attempt, their needs during this time, and how these could be addressed in a brief contact eHealth intervention. The intervention design was also informed by consultation with lived experience panels external to the project and a clinical design group. Results Prompt outreach following discharge, initial distraction activities with low cognitive demands, and ongoing support over an extended period were identified as structural requirements of the intervention. Key content areas identified included coping with distressing feelings, safety planning, emotional regulation and acceptance, coping with suicidal thoughts, connecting with others and interpersonal relationships, and managing alcohol consumption. Conclusions The RAFT (Reconnecting AFTer a suicide attempt) text message brief contact intervention combines SMS contacts with additional Web-based brief therapeutic content targeting key risk factors. It has the potential to reduce the number of repeat suicidal episodes and to provide accessible, acceptable, and cost-effective support for individuals who may not otherwise seek face-to-face treatment. A pilot study to test the feasibility and acceptability of the RAFT intervention is underway. PMID:29237584

Systematic review finds major deficiencies in sample size methodology and reporting for stepped-wedge cluster randomised trials

PubMed Central

Martin, James; Taljaard, Monica; Girling, Alan; Hemming, Karla

2016-01-01

Background Stepped-wedge cluster randomised trials (SW-CRT) are increasingly being used in health policy and services research, but unless they are conducted and reported to the highest methodological standards, they are unlikely to be useful to decision-makers. Sample size calculations for these designs require allowance for clustering, time effects and repeated measures. Methods We carried out a methodological review of SW-CRTs up to October 2014. We assessed adherence to reporting each of the 9 sample size calculation items recommended in the 2012 extension of the CONSORT statement to cluster trials. Results We identified 32 completed trials and 28 independent protocols published between 1987 and 2014. Of these, 45 (75%) reported a sample size calculation, with a median of 5.0 (IQR 2.5–6.0) of the 9 CONSORT items reported. Of those that reported a sample size calculation, the majority, 33 (73%), allowed for clustering, but just 15 (33%) allowed for time effects. There was a small increase in the proportions reporting a sample size calculation (from 64% before to 84% after publication of the CONSORT extension, p=0.07). The type of design (cohort or cross-sectional) was not reported clearly in the majority of studies, but cohort designs seemed to be most prevalent. Sample size calculations in cohort designs were particularly poor with only 3 out of 24 (13%) of these studies allowing for repeated measures. Discussion The quality of reporting of sample size items in stepped-wedge trials is suboptimal. There is an urgent need for dissemination of the appropriate guidelines for reporting and methodological development to match the proliferation of the use of this design in practice. Time effects and repeated measures should be considered in all SW-CRT power calculations, and there should be clarity in reporting trials as cohort or cross-sectional designs. PMID:26846897

Automated computation of femoral angles in dogs from three-dimensional computed tomography reconstructions: Comparison with manual techniques.

PubMed

Longo, F; Nicetto, T; Banzato, T; Savio, G; Drigo, M; Meneghello, R; Concheri, G; Isola, M

2018-02-01

The aim of this ex vivo study was to test a novel three-dimensional (3D) automated computer-aided design (CAD) method (aCAD) for the computation of femoral angles in dogs from 3D reconstructions of computed tomography (CT) images. The repeatability and reproducibility of three manual radiography, manual CT reconstructions and the aCAD method for the measurement of three femoral angles were evaluated: (1) anatomical lateral distal femoral angle (aLDFA); (2) femoral neck angle (FNA); and (3) femoral torsion angle (FTA). Femoral angles of 22 femurs obtained from 16 cadavers were measured by three blinded observers. Measurements were repeated three times by each observer for each diagnostic technique. Femoral angle measurements were analysed using a mixed effects linear model for repeated measures to determine the levels of intra-observer agreement (repeatability) and inter-observer agreement (reproducibility). Repeatability and reproducibility of measurements using the aCAD method were excellent (intra-class coefficients, ICCs≥0.98) for all three angles assessed. Manual radiography and CT exhibited excellent agreement for the aLDFA measurement (ICCs≥0.90). However, FNA repeatability and reproducibility were poor (ICCs<0.8), whereas FTA measurement showed slightly higher ICCs values, except for the radiographic reproducibility, which was poor (ICCs<0.8). The computation of the 3D aCAD method provided the highest repeatability and reproducibility among the tested methodologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Timeseries Toolbox - A Web Application to Enable Accessible, Reproducible Time Series Analysis

NASA Astrophysics Data System (ADS)

Veatch, W.; Friedman, D.; Baker, B.; Mueller, C.

2017-12-01

The vast majority of data analyzed by climate researchers are repeated observations of physical process or time series data. This data lends itself of a common set of statistical techniques and models designed to determine trends and variability (e.g., seasonality) of these repeated observations. Often, these same techniques and models can be applied to a wide variety of different time series data. The Timeseries Toolbox is a web application designed to standardize and streamline these common approaches to time series analysis and modeling with particular attention to hydrologic time series used in climate preparedness and resilience planning and design by the U. S. Army Corps of Engineers. The application performs much of the pre-processing of time series data necessary for more complex techniques (e.g. interpolation, aggregation). With this tool, users can upload any dataset that conforms to a standard template and immediately begin applying these techniques to analyze their time series data.

Investigation of C9orf72 in 4 Neurodegenerative Disorders

PubMed Central

Xi, Zhengrui; Zinman, Lorne; Grinberg, Yakov; Moreno, Danielle; Sato, Christine; Bilbao, Juan M.; Ghani, Mahdi; Hernández, Isabel; Ruiz, Agustín; Boada, Mercè; Morón, Francisco J.; Lang, Anthony E.; Marras, Connie; Bruni, Amalia; Colao, Rosanna; Maletta, Raffaele G.; Puccio, Gianfranco; Rainero, Innocenzo; Pinessi, Lorenzo; Galimberti, Daniela; Morrison, Karen E.; Moorby, Catriona; Stockton, Joanne D.; Masellis, Mario; Black, Sandra E.; Hazrati, Lili-Naz; Liang, Yan; van Haersma de With, Jan; Fornazzari, Luis; Villagra, Roque; Rojas-Garcia, Ricardo; Clarimón, Jordi; Mayeux, Richard; Robertson, Janice; St George-Hyslop, Peter; Rogaeva, Ekaterina

2014-01-01

Objective To estimate the allele frequency of C9orf72 (G4C2) repeats in amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), Alzheimer disease (AD), and Parkinson disease (PD). Design The number of repeats was estimated by a 2-step genotyping strategy. For expansion carriers, we sequenced the repeat flanking regions and obtained APOE genotypes and MAPT H1/H2 haplotypes. Setting Hospitals specializing in neurodegenerative disorders. Subjects We analyzed 520 patients with FTLD, 389 patients with ALS, 424 patients with AD, 289 patients with PD, 602 controls, 18 families, and 29 patients with PD with the LRRK2 G2019S mutation. Main Outcome Measure The expansion frequency. Results Based on a prior cutoff (>30 repeats), the expansion was detected in 9.3% of patients with ALS, 5.2% of patients with FTLD, and 0.7% of patients with PD but not in controls or patients with AD. It was significantly associated with family history of ALS or FTLD and age at onset of FTLD. Phenotype variation (ALS vs FTLD) was not associated with MAPT, APOE, or variability in the repeat flanking regions. Two patients with PD were carriers of 39 and 32 repeats with questionable pathological significance, since the 39-repeat allele does not segregate with PD. No expansion or intermediate alleles (20–29 repeats) were found among the G2019S carriers and AD cases with TAR DNA-binding protein 43–positive inclusions. Surprisingly, the frequency of the 10-repeat allele was marginally increased in all 4 neurodegenerative diseases compared with controls, indicating the presence of an unknown risk variation in the C9orf72 locus. Conclusions The C9orf72 expansion is a common cause of ALS and FTLD, but not of AD or PD. Our study raises concern about a reliable cutoff for the pathological repeat number, which is important in the utility of genetic screening. PMID:22964832

Variability in objective and subjective measures affects baseline values in studies of patients with COPD

PubMed Central

Ha, Jae Wook; Couper, David J.; O’Neal, Wanda K.; Barr, R. Graham; Bleecker, Eugene R.; Carretta, Elizabeth E.; Cooper, Christopher B.; Doerschuk, Claire M.; Drummond, M Bradley; Han, MeiLan K.; Hansel, Nadia N.; Kim, Victor; Kleerup, Eric C.; Martinez, Fernando J.; Rennard, Stephen I.; Tashkin, Donald; Woodruff, Prescott G.; Paine, Robert; Curtis, Jeffrey L.; Kanner, Richard E.

2017-01-01

Rationale Understanding the reliability and repeatability of clinical measurements used in the diagnosis, treatment and monitoring of disease progression is of critical importance across all disciplines of clinical practice and in clinical trials to assess therapeutic efficacy and safety. Objectives Our goal is to understand normal variability for assessing true changes in health status and to more accurately utilize this data to differentiate disease characteristics and outcomes. Methods Our study is the first study designed entirely to establish the repeatability of a large number of instruments utilized for the clinical assessment of COPD in the same subjects over the same period. We utilized SPIROMICS participants (n = 98) that returned to their clinical center within 6 weeks of their baseline visit to repeat complete baseline assessments. Demographics, spirometry, questionnaires, complete blood cell counts (CBC), medical history, and emphysema status by computerized tomography (CT) imaging were obtained. Results Pulmonary function tests (PFTs) were highly repeatable (ICC’s >0.9) but the 6 minute walk (6MW) was less so (ICC = 0.79). Among questionnaires, the Saint George’s Respiratory Questionnaire (SGRQ) was most repeatable. Self-reported clinical features, such as exacerbation history, and features of chronic bronchitis, often produced kappa values <0.6. Reported age at starting smoking and average number of cigarettes smoked were modestly repeatable (kappa = 0.76 and 0.79). Complete blood counts (CBC) variables produced intraclass correlation coefficients (ICC) values between 0.6 and 0.8. Conclusions PFTs were highly repeatable, while subjective measures and subject recall were more variable. Analyses using features with poor repeatability could lead to misclassification and outcome errors. Hence, care should be taken when interpreting change in clinical features based on measures with low repeatability. Efforts to improve repeatability of key clinical features such as exacerbation history and chronic bronchitis are warranted. PMID:28934249

Fine-tuning gene networks using simple sequence repeats

PubMed Central

Egbert, Robert G.; Klavins, Eric

2012-01-01

The parameters in a complex synthetic gene network must be extensively tuned before the network functions as designed. Here, we introduce a simple and general approach to rapidly tune gene networks in Escherichia coli using hypermutable simple sequence repeats embedded in the spacer region of the ribosome binding site. By varying repeat length, we generated expression libraries that incrementally and predictably sample gene expression levels over a 1,000-fold range. We demonstrate the utility of the approach by creating a bistable switch library that programmatically samples the expression space to balance the two states of the switch, and we illustrate the need for tuning by showing that the switch’s behavior is sensitive to host context. Further, we show that mutation rates of the repeats are controllable in vivo for stability or for targeted mutagenesis—suggesting a new approach to optimizing gene networks via directed evolution. This tuning methodology should accelerate the process of engineering functionally complex gene networks. PMID:22927382

Modified method of recording and reproducing natural head position with a multicamera system and a laser level.

PubMed

Liu, Xiao-jing; Li, Qian-qian; Pang, Yuan-jie; Tian, Kai-yue; Xie, Zheng; Li, Zi-li

2015-06-01

As computer-assisted surgical design becomes increasingly popular in maxillofacial surgery, recording patients' natural head position (NHP) and reproducing it in the virtual environment are vital for preoperative design and postoperative evaluation. Our objective was to test the repeatability and accuracy of recording NHP using a multicamera system and a laser level. A laser level was used to project a horizontal reference line on a physical model, and a 3-dimensional image was obtained using a multicamera system. In surgical simulation software, the recorded NHP was reproduced in the virtual head position by registering the coordinate axes with the horizontal reference on both the frontal and lateral views. The repeatability and accuracy of the method were assessed using a gyroscopic procedure as the gold standard. The interclass correlation coefficients for pitch and roll were 0.982 (0.966, 0.991) and 0.995 (0.992, 0.998), respectively, indicating a high degree of repeatability. Regarding accuracy, the lack of agreement in orientation between the new method and the gold standard was within the ranges for pitch (-0.69°, 1.71°) and for roll (-0.92°, 1.20°); these have no clinical significance. This method of recording and reproducing NHP with a multicamera system and a laser level is repeatable, accurate, and clinically feasible. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

The effects of repeated exposure to graphic fear appeals on cigarette packages: A field experiment.

PubMed

Dijkstra, Arie; Bos, Colin

2015-03-01

Experimental studies on the effects of graphic fear appeals on cigarette packages typically expose smokers in a single session to a fear appeal, although in practice the exposure is always repeated. The present study applied an improved study design with repeated exposure to fear appeals on cigarette packages. In this field-experiment, 118 smokers were assigned to 1 of 2 conditions with either graphic fear appeals or textual warnings on their cigarette packages. During 3 weeks, fear and disgust were assessed 6 times. The intention to quit smoking after 3 weeks and quitting activity during the 3 weeks were the dependent measures. The effects of 3 pretest individual difference moderators were tested: disengagement beliefs, number of cigarettes smoked a day, and readiness to quit. Three weeks of exposure to the graphic fear appeals led to a stronger intention to quit, but only when smokers scored low on disengagement beliefs, or were heavier smokers. In addition, smokers low in disengagement more often reported to have cut down on smoking in the graphic condition. There were no indications of habituation of fear and disgust over the 3 weeks. The effects of graphic fear appeals depended on smokers' characteristics: The moderators may explain the mixed findings in the literature. The lack of habituation may be caused by the renewal of the graphics every few days. The used field-experimental design with natural repeated exposure to graphics is promising. (c) 2015 APA, all rights reserved).

Repeat rates in digital chest radiography and strategies for improvement.

PubMed

Fintelmann, Florian; Pulli, Benjamin; Abedi-Tari, Faezeh; Trombley, Maureen; Shore, Mary-Theresa; Shepard, Jo-Anne; Rosenthal, Daniel I

2012-05-01

To determine the repeat rate (RR) of chest radiographs acquired with portable computed radiography (CR) and installed direct radiography (DR) and to develop and assess strategies designed to decrease the RR. The RR and reasons for repeated digital chest radiographs were documented over the course of 16 months while a task force of thoracic radiologists, technologist supervisors, technologists, and information technology specialists continued to examine the workflow for underlying causes. Interventions decreasing the RR were designed and implemented. The initial RR of digital chest radiographs was 3.6% (138/3818) for portable CR and 13.3% (476/3575) for installed DR systems. By combining RR measurement with workflow analysis, targets for technical and teaching interventions were identified. The interventions decreased the RR to 1.8% (81/4476) for portable CR and to 8.2% (306/3748) for installed DR. We found the RR of direct digital chest radiography to be significantly higher than that of computed chest radiography. We believe this is due to the ease with which repeat images can be obtained and discarded, and it suggests the need for ongoing surveillance of RR. We were able to demonstrate that strategies to lower the RR, which had been developed in the era of film-based imaging, can be adapted to the digital environment. On the basis of our findings, we encourage radiologists to assess their own departmental RRs for direct digital chest radiography and to consider similar interventions if necessary to achieve acceptable RRs for this modality.

Pilot and Repeat Trials as Development Tools Associated with Demonstration of Bioequivalence.

PubMed

Fuglsang, Anders

2015-05-01

The purpose of this work is to use simulated trials to study how pilot trials can be implemented in relation to bioequivalence testing, and how the use of the information obtained at the pilot stage can influence the overall chance of showing bioequivalence (power) or the chance of approving a truly bioinequivalent product (type I error). The work also covers the use of repeat pivotal trials since the difference between a pilot trial followed by a pivotal trial and a pivotal trial followed by a repeat trial is mainly a question of whether a conclusion of bioequivalence can be allowed after the first trial. Repeating a pivotal trial after a failed trial involves dual or serial testing of the bioequivalence null hypothesis, and the paper illustrates how this may inflate the type I error up to almost 10%. Hence, it is questioned if such practice is in the interest of patients. Tables for power, type I error, and sample sizes are provided for a total of six different decision trees which allow the developer to use either the observed geometric mean ratio (GMR) from the first or trial or to assume that the GMR is 0.95. In cases when the true GMR can be controlled so as not to deviate more from unity than 0.95, sequential design methods ad modum Potvin may be superior to pilot trials. The tables provide a quantitative basis for choosing between sequential designs and pivotal trials preceded by pilot trials.

Proceedings of the Symposium on Psychology in the Department of Defense (8th) Held in Colorado Springs, Colorado on 21-23 April 1982

DTIC Science & Technology

1982-12-01

readily visible but still represent low level flight. 33 Experimental Design and Pc,cedures. The experimental design used in this study was a 3 X 2...October 1979. Winer, B.J. Statistical principles in experimental design . New York: McGraw-Hill, 1971. 47 NONTRADITIONAL ADMISSIONS FACTORS: THE SPECIAL...Quasi- Experimental Designs for Research. Chicago: Rand McNally, 1963. R.C. Carter and H. Sbisa. Human Performance tests for repeated measurements

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.

Recent high-speed ballistics experiments at ORNL

NASA Astrophysics Data System (ADS)

Combs, S. K.; Gouge, M. J.; Baylor, L. R.; Fisher, P. W.; Foster, C. A.; Foust, C. R.; Milora, S. L.; Qualls, A. L.

Oak Ridge National Laboratory (ORNL) has been developing pellet injectors for plasma fueling experiments on magnetic confinement devices for almost 20 years. With these devices, pellets (1 to 8 mm in diameter) composed of hydrogen isotopes are formed (at temperatures less than 20 K) and typically accelerated to speeds of (approximately) 1.0 to 2.0 km/s for injection into plasmas of experimental fusion devices. A variety of pellet injector designs have been developed at ORNL, including repeating pneumatic injectors (single- and multiple-barrel light gas guns) that can inject up to hundreds of pellets for long-pulse plasma operation. The repeating pneumatic injectors are of particular importance because long-pulse fueling is required for present large experimental fusion devices, with steady-state operation the objective for future fusion reactors. In this paper, recent advancements in the development of repeating pneumatic injectors are described, including (1) a small-bore (1.8-mm), high-firing-rate (10-Hz) version of a single-stage light gas gun; (2) a repeating single-stage light gas gun for 8-mm-diam tritium pellets; (3) a repeating two-stage light gas gun for operation at higher pellet velocities; and (4) a steady-state hydrogen extruder feed system.

Recent high-speed ballistics experiments at ORNL

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

Combs, S.K.; Gouge, M.J.; Baylor, L.R.

1994-12-31

Oak Ridge National Laboratory (ORNL) has been developing pellet injectors for plasma fueling experiments on magnetic confinement devices for almost 20 years. With these devices, pellets (1 to 8 mm in diameter) composed of hydrogen isotopes are formed (at temperatures <20 K) and typically accelerated to speeds of {approximately} 1.0 to 2.0 km/s for injection into plasmas of experimental fusion devices. A variety of pellet injector designs have been developed at ORNL, including repeating pneumatic injectors (single- and multiple-barrel light gas guns) that can inject up to hundreds of pellets for long-pulse plasma operation. The repeating pneumatic injectors are ofmore » particular importance because long-pulse fueling is required for present large experimental fusion devices, with steady-state operation the objective for future fusion reactors. In this paper, recent advancements in the development of repeating pneumatic injectors are described, including (1) a small-bore (1.8-mm), high-firing-rate (10-Hz) version of a single-stage light gas gun; (2) a repeating single-stage light gas gun for 8-mm-diam tritium pellets; (3) a repeating two-stage light gas gun for operation at higher pellet velocities; and (4) a steady-state hydrogen extruder feed system.« less

Programmable DNA-binding proteins from Burkholderia provide a fresh perspective on the TALE-like repeat domain

PubMed Central

de Lange, Orlando; Wolf, Christina; Dietze, Jörn; Elsaesser, Janett; Morbitzer, Robert; Lahaye, Thomas

2014-01-01

The tandem repeats of transcription activator like effectors (TALEs) mediate sequence-specific DNA binding using a simple code. Naturally, TALEs are injected by Xanthomonas bacteria into plant cells to manipulate the host transcriptome. In the laboratory TALE DNA binding domains are reprogrammed and used to target a fused functional domain to a genomic locus of choice. Research into the natural diversity of TALE-like proteins may provide resources for the further improvement of current TALE technology. Here we describe TALE-like proteins from the endosymbiotic bacterium Burkholderia rhizoxinica, termed Bat proteins. Bat repeat domains mediate sequence-specific DNA binding with the same code as TALEs, despite less than 40% sequence identity. We show that Bat proteins can be adapted for use as transcription factors and nucleases and that sequence preferences can be reprogrammed. Unlike TALEs, the core repeats of each Bat protein are highly polymorphic. This feature allowed us to explore alternative strategies for the design of custom Bat repeat arrays, providing novel insights into the functional relevance of non-RVD residues. The Bat proteins offer fertile grounds for research into the creation of improved programmable DNA-binding proteins and comparative insights into TALE-like evolution. PMID:24792163

Smart repeater system for communications interoperability during multiagency law enforcement operations

NASA Astrophysics Data System (ADS)

Crutcher, Richard I.; Jones, R. W.; Moore, Michael R.; Smith, S. F.; Tolley, Alan L.; Rochelle, Robert W.

1997-02-01

A prototype 'smart' repeater that provides interoperability capabilities for radio communication systems in multi-agency and multi-user scenarios is being developed by the Oak Ridge National Laboratory. The smart repeater functions as a deployable communications platform that can be dynamically reconfigured to cross-link the radios of participating federal, state, and local government agencies. This interconnection capability improves the coordination and execution of multi-agency operations, including coordinated law enforcement activities and general emergency or disaster response scenarios. The repeater provides multiple channels of operation in the 30-50, 118-136, 138-174, and 403-512 MHz land mobile communications and aircraft bands while providing the ability to cross-connect among multiple frequencies, bands, modulation types, and encryption formats. Additionally, two telephone interconnects provide links to the fixed and cellular telephone networks. The 800- and 900-MHz bands are not supported by the prototype, but the modular design of the system accommodates future retrofits to extend frequency capabilities with minimal impact to the system. Configuration of the repeater is through a portable personal computer with a Windows-based graphical interface control screen that provides dynamic reconfiguration of network interconnections and formats.

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

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

Torella, JP; Boehm, CR; Lienert, F

2013-12-28

In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminatormore » parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.« less

Flexible Magnets Are Not Effective in Decreasing Pain Perception and Recovery Time After Muscle Microinjury

PubMed Central

Borsa, Paul A.; Liggett, Charles L.

1998-01-01

Objective: To assess the therapeutic effects of flexible magnets on pain perception, intramuscular swelling, range of motion, and muscular strength in individuals with a muscle microinjury. Design and Setting: This experiment was a single-blind, placebo study using a repeated-measures design. Subjects performed an intense exercise protocol to induce a muscle microinjury. After pretreatment measurements were recorded, subjects were randomly assigned to an experimental (magnet), placebo (imitation magnet), or control (no magnet) group. Posttreatment measurements were repeated at 24, 48, and 72 hours. Subjects: Forty-five healthy subjects participated in the study. Measurements: Subjects were measured repeatedly for pain perception, upper arm girth, range of motion, and static force production. Four separate univariate analyses of variances were used to reveal statistically significant mean (±SD) differences between variables over time. Interaction effects were analyzed using Scheffe post hoc analysis. Results: Analysis of variance revealed no statistically significant (P > .05) mean differences between conditions for any dependent pretreatment and posttreatment measurements. No significant interaction effects were demonstrated between conditions and times. Conclusions: No significant therapeutic effects on pain control and muscular dysfunction were observed in subjects wearing flexible magnets. ImagesFig 2.Fig 3. PMID:16558503

Assisted Vacations for Men with Dementia and Their Caregiving Spouses: Evaluation of Health-Related Effects

ERIC Educational Resources Information Center

Wilz, Gabriele; Fink-Heitz, Margit

2008-01-01

Purpose: In this study, we conducted the first evaluation of assisted vacations for persons with dementia and their caregivers in the field of caregiving research. Design and Methods: We used a quasi-experimental, two-group, repeated measures design with two measuring times (preintervention, 3-month follow-up) to examine whether assisted vacations…

The Design and Validation of a Parent-Report Questionnaire for Assessing the Characteristics and Quality of Early Intervention over Time

ERIC Educational Resources Information Center

Young, Alys; Gascon-Ramos, Maria; Campbell, Malcolm; Bamford, John

2009-01-01

This article concerns a parent-report repeat questionnaire to evaluate the quality of multiprofessional early intervention following early identification of deafness. It discusses the rationale for the design of the instrument, its theoretical underpinnings, its psychometric properties, and its usability. Results for the validity and reliability…

Measuring Multidimensional Latent Growth. Research Report. ETS RR-10-24

ERIC Educational Resources Information Center

Rijmen, Frank

2010-01-01

As is the case for any statistical model, a multidimensional latent growth model comes with certain requirements with respect to the data collection design. In order to measure growth, repeated measurements of the same set of individuals are required. Furthermore, the data collection design should be specified such that no individual is given the…

76 FR 11844 - Aviation Rulemaking Advisory Committee; Transport Airplane and Engine Issue Area-Phase 2 of Low...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-03

... new designs, the working group should state the rationale and not repeat the information previously... design changes, or would an operational rule be sufficient? In responding, the working group should... the public that the ARAC working group has completed activity for Phase 1 of the task and will begin...

Theory-Driven Intervention Improves Calcium Intake, Osteoporosis Knowledge, and Self-Efficacy in Community-Dwelling Older Black Adults

ERIC Educational Resources Information Center

Babatunde, Oyinlola T.; Himburg, Susan P.; Newman, Frederick L.; Campa, Adriana; Dixon, Zisca

2011-01-01

Objective: To assess the effectiveness of an osteoporosis education program to improve calcium intake, knowledge, and self-efficacy in community-dwelling older Black adults. Design: Randomized repeated measures experimental design. Setting: Churches and community-based organizations. Participants: Men and women (n = 110) 50 years old and older…

37 CFR 202.20 - Deposit of copies and phonorecords for copyright registration.

Code of Federal Regulations, 2014 CFR

2014-07-01

... motion pictures made from pre-existing black and white motion pictures, in addition to the deposit of one... work consists of a repeated pictorial or graphic design, the complete design and at least part of one... one complete copy of the best edition of each issue included in the group registration, or a digital...

Experimental designs for a Benign Paroxysmal Positional Vertigo model

PubMed Central

2013-01-01

Background The pathology of the Benign Paroxysmal Positional Vertigo (BPPV) is detected by a clinician through maneuvers consisting of a series of consecutive head turns that trigger the symptoms of vertigo in patient. A statistical model based on a new maneuver has been developed in order to calculate the volume of endolymph displaced after the maneuver. Methods A simplification of the Navier‐Stokes problem from the fluids theory has been used to construct the model. In addition, the same cubic splines that are commonly used in kinematic control of robots were used to obtain an appropriate description of the different maneuvers. Then experimental designs were computed to obtain an optimal estimate of the model. Results D‐optimal and c‐optimal designs of experiments have been calculated. These experiments consist of a series of specific head turns of duration Δt and angle α that should be performed by the clinician on the patient. The experimental designs obtained indicate the duration and angle of the maneuver to be performed as well as the corresponding proportion of replicates. Thus, in the D‐optimal design for 100 experiments, the maneuver consisting of a positive 30° pitch from the upright position, followed by a positive 30° roll, both with a duration of one and a half seconds is repeated 47 times. Then the maneuver with 60° /6° pitch/roll during half a second is repeated 16 times and the maneuver 90° /90° pitch/roll during half a second is repeated 37 times. Other designs with significant differences are computed and compared. Conclusions A biomechanical model was derived to provide a quantitative basis for the detection of BPPV. The robustness study for the D‐optimal design, with respect to the choice of the nominal values of the parameters, shows high efficiencies for small variations and provides a guide to the researcher. Furthermore, c‐optimal designs give valuable assistance to check how efficient the D‐optimal design is for the estimation of each of the parameters. The experimental designs provided in this paper allow the physician to validate the model. The authors of the paper have held consultations with an ENT consultant in order to align the outline more closely to practical scenarios. PMID:23509996

Interventions for Preventing Unintended, Rapid Repeat Pregnancy Among Adolescents: A Review of the Evidence and Lessons From High-Quality Evaluations

PubMed Central

Norton, Maureen; Chandra-Mouli, Venkatraman; Lane, Cate

2017-01-01

Background: In 2017, of the 22.5 million parenting adolescents (ages 15–19) in 60 countries, approximately 4.1 million gave birth to a second or higher-order child. Adolescent pregnancy in general, and rapid repeat pregnancies specifically, expose young mothers and their children to multiple health and socioeconomic risks. The purpose of this article is to review the impact of interventions designed to prevent unintended, rapid repeat pregnancies among adolescents, including those aimed at changing norms to postpone “intended” closely spaced pregnancies to promote healthy spacing. Methods: We searched PubMed and other databases for evaluations of interventions published in English from 1990 through 2016. We included evaluations that assessed a programmatic intervention specifically designed to prevent rapid repeat pregnancy (occurring less than 24 months after the index birth) or birth (occurring less than 33 months after the index birth), or that reported on contraceptive continuation for at least 2 years. We first assessed the quality of the evaluations, then ranked the interventions based on the quality of the evaluation and the level of impact on repeat pregnancy or birth (statistically significant impact, positive trends but not statistically significant, or no impact) to identify the most effective interventions. Finally, we extracted program design and implementation lessons from the interventions included in the high-quality evaluations. Results: Our search identified 2,187 articles, of which 40 evaluations met the inclusion criteria (24=high quality, 14=moderate quality, 2=less rigorous). We found 14 high-quality evaluations in which the intervention achieved a statistically significant impact on repeat pregnancy or birth. These interventions fell into 5 broad categories: (1) contraceptive services and information, with proactive monitoring of contraceptive use and outreach to families; (2) postpartum contraceptive counseling and services provided soon after delivery; (3) activities that help adolescents improve planning skills, including preparing contraceptive plans; (4) social and behavioral change activities that help adolescents understand the role contraception can play in determining positive life outcomes, and the implications of their reproductive health decisions for their future; and (5) activities that provide mentoring, goal setting, and motivation. Conclusion: Effective interventions that prevent rapid adolescent childbearing link clinical contraceptive services with non-clinical activities that build planning skills, enhance understanding of the role that contraceptives can play in determining positive life outcomes, and provide mentoring and goal setting. Recognizing potentially synergistic effects, we recommend testing various combinations of these interventions, with access to contraception as the foundational activity. PMID:29284694

A retrospective descriptive study of the characteristics of deliberate self-poisoning patients with single or repeat presentations to an Australian emergency medicine network in a one year period

PubMed Central

2014-01-01

Background A proportion of deliberate self-poisoning (DSP) patients present repeatedly to the emergency department (ED). Understanding the characteristics of frequent DSP patients and their presentation is a first step to implementing interventions that are designed to prevent repeated self-poisoning. Methods All DSP presentations to three networked Australian ED’s were retrospectively identified from the ED electronic medical record and hospital scanned medical records for 2011. Demographics, types of drugs ingested, emergency department length of stay and disposition for the repeat DSP presenters were extracted and compared to those who presented once with DSP in a one year period. Logistic regression was used to analyse repeat versus single DSP data. Results The study determined 755 single presenters and 93 repeat DSP presenters. The repeat presenters contributed to 321 DSP presentations. They were more likely to be unemployed (61.0% versus 39.9%, p = 0.008) and have a psychiatric illness compared to single presenters (36.6% versus 15.5%, p < 0.001). Repeat presenters were less likely to receive a toxicology consultation (11.5% versus 27.3%, p < 0.001) and were more likely to abscond from the ED (7.5% versus 3.4%, p = 0.004). Repeat presenters were more likely to ingest paracetamol and antipsychotics than single presenters. The defined daily dose for the most common antipsychotic ingested, quetiapine, was less in the repeat presenter group (median 1.9 [IQR: 1.3-3.5]) compared with the single presenter group (4 [1.4-9.5]), (OR 0.85, 95% CI 0.74-0.99). Conclusion Patients who present repeatedly to the ED with DSP have pre-existing disadvantages, with increased likelihood of being unemployed and having a mental illness. These patients are also more likely to have health service inequities given the greater likelihood to abscond from the ED and lower likelihood of receiving toxicology consultation for their DSP. Early recognition of repeat DSP patients in the ED may facilitate the development of individualised care plans with the aim to reduce repeat episodes of self-poisoning and subsequent risk of successful suicide. PMID:25148692

Repeatability of the Oxford Foot Model in children with foot deformity.

PubMed

McCahill, Jennifer; Stebbins, Julie; Koning, Bart; Harlaar, Jaap; Theologis, Tim

2018-03-01

The Oxford Foot Model (OFM) is a multi-segment, kinematic model developed to assess foot motion. It has previously been assessed for repeatability in healthy populations. To determine the OFM's reliability for detecting foot deformity, it is important to know repeatability in pathological conditions. The aim of the study was to assess the repeatability of the OFM in children with foot deformity. Intra-tester repeatability was assessed for 45 children (15 typically developing, 15 hemiplegic, 15 clubfoot). Inter-tester repeatability was assessed in the clubfoot population. The mean absolute differences between testers (clubfoot) and sessions (clubfoot and hemiplegic) were calculated for each of 15 clinically relevant, kinematic variables and compared to typically developing children. Children with clubfoot showed a mean difference between visits of 2.9° and a mean difference between raters of 3.6° Mean absolute differences were within one degree for the intra and inter-rater reliability in 12/15 variables. Hindfoot rotation, forefoot/tibia abduction and forefoot supination were the most variable between testers. Overall the clubfoot data were less variable than the typically developing population. Children with hemiplegia demonstrated slightly higher differences between sessions (mean 4.1°), with the most reliable data in the sagittal plane, and largest differences in the transverse plane. The OFM was designed to measure different types of foot deformity. The results of this study show that it provides repeatable results in children with foot deformity. To be distinguished from measurement artifact, changes in foot kinematics as a result of intervention or natural progression over time must be greater than the repeatability reported here. Copyright © 2018 Elsevier B.V. All rights reserved.

Anesthetic efficacy of a repeated intraosseous injection given 30 min following an inferior alveolar nerve block/intraosseous injection.

PubMed

Reitz, J; Reader, A; Nist, R; Beck, M; Meyers, W J

1998-01-01

To determine whether a repeated intraosseous (IO) injection would increase or prolong pulpal anesthesia, we measured the degree of anesthesia obtained by a repeated IO injection given 30 min following a combination inferior alveolar nerve block/intraosseous injection (IAN/IO) in mandibular second premolars and in first and second molars. Using a repeated-measures design, we randomly assigned 38 subjects to receive two combinations of injections at two separate appointments. The combinations were an IAN/IO injection followed approximately 30 min later by another IO injection of 0.9 ml of 2% lidocaine with 1:100,000 epinephrine and a combination IAN/IO injection followed approximately 30 min later by a mock IO injection. The second premolar, first molar, and second molar were blindly tested with an Analytic Technology pulp tester at 2-min cycles for 120 min postinjection. Anesthesia was considered successful when two consecutive readings of 80 were obtained. One hundred percent of the subjects had lip numbness with IAN/IO and with IAN/IO plus repeated IO techniques. Rates of anesthetic success for the IAN/IO and for the IAN/IO plus repeated IO injection, respectively, were 100% and 97% for the second premolar, 95% and 95% for the first molar, and 87% and 87% for the second molar. The repeated IO injection increased pulpal anesthesia for approximately 14 min in the second premolar and for 6 min in the first molar, but no statistically significant differences (P > 0.05) were shown. In conclusion, the repeated IO injection of 0.9 ml of 2% lidocaine with 1:100,000 epinephrine given 30 min following a combination IAN/IO injection did not significantly increase pulpal anesthesia in mandibular second premolars or in first and second molars.

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.

Test Methodologies for Personal Protective Equipment Against Anti-Personnel Mine Blast (Methodologies d’essais pour le materiel de protection prsonnel contre le souffle produit par les mines antipersonnel)

DTIC Science & Technology

2004-03-01

probabilistic by design. Finally, as the fragments disperse, fragment density decreases, and the probability of a fragment strike drops rapidly. Given the...Any PPE subjected to such testing needs to be exposed repeatedly to several mines in order to obtain a sufficient number of strikes . This will allow...velocity of each fragment, and the location of fragment strikes cannot be controlled precisely. This means that the same test must be repeated a

A Marine Aerosol Reference Tank system as a breaking wave analogue for the production of foam and sea-spray aerosols

NASA Astrophysics Data System (ADS)

Stokes, M. D.; Deane, G. B.; Prather, K.; Bertram, T. H.; Ruppel, M. J.; Ryder, O. S.; Brady, J. M.; Zhao, D.

2013-04-01

In order to better understand the processes governing the production of marine aerosols a repeatable, controlled method for their generation is required. The Marine Aerosol Reference Tank (MART) has been designed to closely approximate oceanic conditions by producing an evolving bubble plume and surface foam patch. The tank utilizes an intermittently plunging sheet of water and large volume tank reservoir to simulate turbulence, plume and foam formation, and the water flow is monitored volumetrically and acoustically to ensure the repeatability of conditions.

Social stories: mechanisms of effectiveness in increasing game play skills in children diagnosed with autism spectrum disorder using a pretest posttest repeated measures randomized control group design.

PubMed

Quirmbach, Linda M; Lincoln, Alan J; Feinberg-Gizzo, Monica J; Ingersoll, Brooke R; Andrews, Siri M

2009-02-01

An increasing body of literature has indicated that social stories are an effective way to teach individuals diagnosed with autism appropriate social behavior. This study compared two formats of a social story targeting the improvement of social skills during game play using a pretest posttest repeated measures randomized control group design. A total of 45 children diagnosed with Autism Spectrum Disorder (ASD) ages 7-14 were randomly assigned to standard, directive, or control story conditions. Results demonstrated that the standard and directive story formats were equally as effective in eliciting, generalizing and maintaining the targeted social skills in participants who had prior game play experience and Verbal Comprehension Index (VCI) scores from the WISC-IV intelligence test in the borderline range or above.

Measurement properties of continuous text reading performance tests.

PubMed

Brussee, Tamara; van Nispen, Ruth M A; van Rens, Ger H M B

2014-11-01

Measurement properties of tests to assess reading acuity or reading performance have not been extensively evaluated. This study aims to provide an overview of the literature on available continuous text reading tests and their measurement properties. A literature search was performed in PubMed, Embase and PsycInfo. Subsequently, information on design and content of reading tests, study design and measurement properties were extracted using consensus-based standards for selection of health measurement instruments. Quality of studies, reading tests and measurement properties were systematically assessed using pre-specified criteria. From 2334 identified articles, 20 relevant articles were found on measurement properties of three reading tests in various languages: IReST, MNread Reading Test and Radner Reading Charts. All three reading tests scored high on content validity. Reproducibility studies (repeated measurements between different testing sessions) of the IReST and MNread of commercially available reading tests in different languages were missing. The IReST scored best on inter-language comparison, the MNread scored well in repeatability studies (repeated measurements under the same conditions) and the Radner showed good reproducibility in studies. Although in daily practice there are other continuous text reading tests available meeting the criteria of this review, measurement properties were described in scientific studies for only three of them. Of the few available studies, the quality and content of study design and methodology used varied. For testing existing reading tests and the development of new ones, for example in other languages, we make several recommendations, including careful description of patient characteristics, use of objective and subjective lighting levels, good control of working distance, documentation of the number of raters and their training, careful documentation of scoring rules and the use of Bland-Altman analyses or similar for reproducibility and repeatability studies. © 2014 The Authors Ophthalmic & Physiological Optics © 2014 The College of Optometrists.

Duration of in vivo endotoxin tolerance in horses.

PubMed

Holcombe, Susan J; Jacobs, Carrie C; Cook, Vanessa L; Gandy, Jeffery C; Hauptman, Joseph G; Sordillo, Lorraine M

2016-05-01

Endotoxemia models are used to study mechanisms and treatments of early sepsis. Repeated endotoxin exposures induce periods of endotoxin tolerance, characterized by diminished proinflammatory responses to lipopolysaccharide (LPS) and modulated production of proinflammatory cytokines. Repeated measure designs using equine endotoxemia models are rarely performed, despite the advantages associated with reduced variability, because the altered responsiveness would confound study results and because the duration of equine endotoxin tolerance is unknown. We determined the interval of endotoxin tolerance, in vivo, in horses based on physical, clinicopathologic, and proinflammatory gene expression responses to repeated endotoxin exposures. Six horses received 30 ng/kg LPS in saline infused over 30 min. Behavior pain scores, physical examination parameters, and blood for complete blood count and proinflammatory gene expression were obtained at predetermined intervals for 24h. Horses received a total of 3 endotoxin exposures. The first exposure was LPS 1, followed 7 days later by LPS 7 or 14-21 days later by LPS 14-21. Lipopolysaccharide exposures were allocated in a randomized, crossover design. Lipopolysaccharide produced clinical and clinicopathologic signs of endotoxemia and increased expression of tumor necrosis factor alpha (TNFα), interleukin (IL)-6 and IL-8, P<0.001. Horses exhibited evidence of endotoxin tolerance following LPS 7 but not following LPS 14-21. Horses had significantly lower pain scores, heart rates, respiratory rates and duration of fever, after LPS 7 compared to LPS 1 and LPS 14-21, P<0.001, and expression of TNFα was lower in the whole blood of horses after LPS 7, P=0.05. Clinical parameters and TNFα gene expression were similar or slightly increased in horses following LPS 14-21 compared to measurements made in horses following LPS 1, suggesting that endotoxin tolerance had subsided. A minimum of 3 weeks between experiments is warranted if repeated measures designs are used to assess in vivo response to endotoxin in horses. Copyright © 2016 Elsevier B.V. All rights reserved.

Anterior segment biometry during accommodation imaged with ultra-long scan depth optical coherence tomography

PubMed Central

Du, Chixin; Shen, Meixiao; Li, Ming; Zhu, Dexi; Wang, Michael R.; Wang, Jianhua

2012-01-01

Purpose To measure by ultra-long scan depth optical coherence tomography (UL-OCT) dimensional changes in the anterior segment of human eyes during accommodation. Design Evaluation of diagnostic test or technology. Participants Forty-one right eyes of healthy subjects with a mean age of 34 years (range, 22–41 years) and a mean refraction of −2.5±2.6 diopters (D) were imaged in two repeated measurements at minimal and maximal accommodation. Methods A specially adapted designed UL-OCT instrument was used to image from the front surface of the cornea to the back surface of the crystalline lens. Custom software corrected the optical distortion of the images and yielded the biometric measurements. The coefficient of repeatability (COR) and the intraclass correlation coefficient (ICC) were calculated to evaluate the repeatability and reliability. Main Outcome Measures Anterior segment parameters and associated repeatability and reliability upon accommodation. The dimensional results included central corneal thickness (CCT), anterior chamber depth and width (ACD, ACW), pupil diameter (PD), lens thickness (LT), anterior segment length (ASL=ACD+LT), lens central position (LCP=ACD+1/2LT) and horizontal radii of the lens anterior and posterior surface curvatures (LAC, LPC). Results Repeated measurements of each variable within each accommodative state did not differ significantly (P>0.05). The CORs and ICCs for CCT, ACW, ACD, LT, LCP, and ASL were excellent (1.2% to 3.59% and 0.998 to 0.877, respectively). They were higher for PD (18.90% to 21.63% and 0.880 to 0.874, respectively), and moderate for LAC and LPC (34.86% to 42.72% and 0.669 to 0.251, respectively) in the two accommodative states. Compared to minimal accommodation, PD, ACD, LAC, LPC, and LCP decreased and LT and ASL increased significantly at maximal accommodation (P<0.05), while CCT and ACW did not change (P>0.05). Conclusions UL-OCT measured changes in anterior segment dimensions during accommodation with good repeatability and reliability. During accommodation, the back surface of the lens became steeper as the lens moved forward. PMID:22902211

Effect of gender on fatigue and recovery following maximal intensity repeated sprint performance.

PubMed

Laurent, C M; Green, J M; Bishop, P A; Sjökvist, J; Schumacker, R E; Richardson, M T; Curtner-Smith, M

2010-09-01

This study investigated the effects of gender on repeated, maximal-intensity intermittent sprint exercise following variable day-to-day recovery periods. Sixteen volunteers (8 men, 8 women) performed four trials of high-intensity intermittent sprint exercise consisting of three bouts of eight 30 m sprints (total of 24 sprints). Following completion of the baseline trial, in repeated-measures design, participants were assigned, in counter-balanced order, variable recovery periods of 24, 48, and 72 h whereupon they repeated an identical exercise trial. Results from a series of 4 (trial) x 3 (bout) repeated measures ANOVAs revealed men produced significantly (P < 0.01) faster times throughout all bouts and trials of repeated sprint exercise. Additionally, women exhibited significantly lower (P < 0.05) blood lactate concentration and significantly lower (P < 0.05) decrement in performance, indicating increased resistance to fatigue during repeated exercise sessions. There were no significant differences (P > 0.05) between genders for heart rate or rating of perceived exertion during or following trials. There were no significant differences for overall sprint performance within either gender among trials. These results indicate men, while able to produce higher absolute power outputs (i.e., lower sprint time), demonstrate higher decrement scores within a trial compared to women, thus suggesting women may recover faster and fatigue less. Also, gender differences affecting recovery within in a trial were observed to be diminished between trials (i.e., day-to-day recovery) of maximal intermittent sprint work evidenced by the observed stability of performance between trials following various recovery durations.

One-Year Outcomes from the CASAWORKS for Families Intervention for Substance-Abusing Women on Welfare

ERIC Educational Resources Information Center

Mclellan, A. Thomas; Gutman, Marjorie; Lynch, Kevin; Mckay, James R.; Ketterlinus, Robert; Morgenstern, Jon; Woolis, Diana

2003-01-01

Aim: To evaluate the effectiveness of a multiservice intervention designed to move substance-abusing women on welfare to sobriety and self-sufficiency by addressing their substance abuse, domestic violence, employment, and basic needs. Design: A field evaluation with repeated measures at 6 and 12 months on an intent-to-treat sample of 529 women…

Mitigation of Cognitive Bias with a Serious Game: Two Experiments Testing Feedback Timing and Source

ERIC Educational Resources Information Center

Dunbar, Norah E.; Jensen, Matthew L.; Miller, Claude H.; Bessarabova, Elena; Lee, Yu-Hao; Wilson, Scott N.; Elizondo, Javier; Adame, Bradley J.; Valacich, Joseph; Straub, Sara; Burgoon, Judee K.; Lane, Brianna; Piercy, Cameron W.; Wilson, David; King, Shawn; Vincent, Cindy; Schuetzler, Ryan M.

2017-01-01

One of the benefits of using digital games for education is that games can provide feedback for learners to assess their situation and correct their mistakes. We conducted two studies to examine the effectiveness of different feedback design (timing, duration, repeats, and feedback source) in a serious game designed to teach learners about…

47 CFR 54.202 - Additional requirements for Commission designation of eligible telecommunications carriers.

Code of Federal Regulations, 2011 CFR

2011-10-01

...-mounted antenna or other equipment; (3) Adjusting the nearest cell tower; (4) Adjusting network or...) Employing, leasing or constructing an additional cell site, cell extender, repeater, or other similar...

47 CFR 54.202 - Additional requirements for Commission designation of eligible telecommunications carriers.

Code of Federal Regulations, 2010 CFR

2010-10-01

...-mounted antenna or other equipment; (3) Adjusting the nearest cell tower; (4) Adjusting network or...) Employing, leasing or constructing an additional cell site, cell extender, repeater, or other similar...

Quality assurance of road roughness measurement.

DOT National Transportation Integrated Search

2000-01-01

This report describes a study designed to establish the accuracy and repeatability of high-speed, road-profiling equipment. This effort focused on a series of roughness validation sites. The study addresses selecting the appropriate sites, determinin...

A Guide to Sentencing DUI Offenders

DOT National Transportation Integrated Search

1996-03-01

This sentencing guide is designed to assist judges and prosecutors in reducing recidivism among people convicted of drinking and driving offenses. Today's driving under the influence (DUI) arrestee is often a repeat offender and resistant to deterren...

Control of Echolalic Speech in Psychotic Children

ERIC Educational Resources Information Center

Carr, Edward G.; And Others

1975-01-01

Immediate echolalia (repeating what someone has just said) was studied in a series of replicated single-subject designs across six schizophrenic and five normal children (all ranging in age from 2 to 15 years). (Author/SBH)

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...

Genomic tools for behavioural ecologists to understand repeatable individual differences in behaviour.

PubMed

Bengston, Sarah E; Dahan, Romain A; Donaldson, Zoe; Phelps, Steven M; van Oers, Kees; Sih, Andrew; Bell, Alison M

2018-06-01

Behaviour is a key interface between an animal's genome and its environment. Repeatable individual differences in behaviour have been extensively documented in animals, but the molecular underpinnings of behavioural variation among individuals within natural populations remain largely unknown. Here, we offer a critical review of when molecular techniques may yield new insights, and we provide specific guidance on how and whether the latest tools available are appropriate given different resources, system and organismal constraints, and experimental designs. Integrating molecular genetic techniques with other strategies to study the proximal causes of behaviour provides opportunities to expand rapidly into new avenues of exploration. Such endeavours will enable us to better understand how repeatable individual differences in behaviour have evolved, how they are expressed and how they can be maintained within natural populations of animals.

Analysis of longitudinal "time series" data in toxicology.

PubMed

Cox, C; Cory-Slechta, D A

1987-02-01

Studies focusing on chronic toxicity or on the time course of toxicant effect often involve repeated measurements or longitudinal observations of endpoints of interest. Experimental design considerations frequently necessitate between-group comparisons of the resulting trends. Typically, procedures such as the repeated-measures analysis of variance have been used for statistical analysis, even though the required assumptions may not be satisfied in some circumstances. This paper describes an alternative analytical approach which summarizes curvilinear trends by fitting cubic orthogonal polynomials to individual profiles of effect. The resulting regression coefficients serve as quantitative descriptors which can be subjected to group significance testing. Randomization tests based on medians are proposed to provide a comparison of treatment and control groups. Examples from the behavioral toxicology literature are considered, and the results are compared to more traditional approaches, such as repeated-measures analysis of variance.

Taking the Lag out of Jet Lag through Model-Based Schedule Design

PubMed Central

Dean, Dennis A.; Forger, Daniel B.; Klerman, Elizabeth B.

2009-01-01

Travel across multiple time zones results in desynchronization of environmental time cues and the sleep–wake schedule from their normal phase relationships with the endogenous circadian system. Circadian misalignment can result in poor neurobehavioral performance, decreased sleep efficiency, and inappropriately timed physiological signals including gastrointestinal activity and hormone release. Frequent and repeated transmeridian travel is associated with long-term cognitive deficits, and rodents experimentally exposed to repeated schedule shifts have increased death rates. One approach to reduce the short-term circadian, sleep–wake, and performance problems is to use mathematical models of the circadian pacemaker to design countermeasures that rapidly shift the circadian pacemaker to align with the new schedule. In this paper, the use of mathematical models to design sleep–wake and countermeasure schedules for improved performance is demonstrated. We present an approach to designing interventions that combines an algorithm for optimal placement of countermeasures with a novel mode of schedule representation. With these methods, rapid circadian resynchrony and the resulting improvement in neurobehavioral performance can be quickly achieved even after moderate to large shifts in the sleep–wake schedule. The key schedule design inputs are endogenous circadian period length, desired sleep–wake schedule, length of intervention, background light level, and countermeasure strength. The new schedule representation facilitates schedule design, simulation studies, and experiment design and significantly decreases the amount of time to design an appropriate intervention. The method presented in this paper has direct implications for designing jet lag, shift-work, and non-24-hour schedules, including scheduling for extreme environments, such as in space, undersea, or in polar regions. PMID:19543382

An "Intelligent" Optical Design Program

NASA Astrophysics Data System (ADS)

Bohachevsky, I. O.; Viswanathan, V. K.; Woodfin, G.

1984-06-01

Described is a general approach to the development of computer programs capable of designing image-forming optical systems without human intervention and of improving their performance with repeated attempts. The approach utilizes two ideas: 1) interpretation of technical design as a mapping in the configuration space of technical characteristics and 2) development of an "intelligent" routine that recognizes global optima. Examples of lens systems designed and used in the development of the general approach are presented, current status of the project is summarized, and plans for the future efforts are indicated.

Conceptual design and issues of the laser inertial fusion test (LIFT) reactor—targets and chamber systems

NASA Astrophysics Data System (ADS)

Norimatsu, T.; Kozaki, Y.; Shiraga, H.; Fujita, H.; Okano, K.; Members of LIFT Design Team

2017-11-01

We present the conceptual design of an experimental laser fusion plant known as the laser inertial fusion test (LIFT) reactor. The conceptual design aims at technically connecting a single-shot experiment and a commercial power plant. The LIFT reactor is designed on a three-phase scheme, where each phase has specific goals and the dedicated chambers of each phase are driven by the same laser. Technical issues related to the chamber technology including radiation safety to repeat burst mode operation are discussed in this paper.

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species

PubMed Central

Diekmann, Kerstin; Hodkinson, Trevor R.; Barth, Susanne

2012-01-01

Background and Aims Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne ‘Cashel’. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Methods Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. Key Results All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A8 mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. Conclusions The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species. PMID:22419761

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species.

PubMed

Diekmann, Kerstin; Hodkinson, Trevor R; Barth, Susanne

2012-11-01

Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne 'Cashel'. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A(8) mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species.

Relationship Between Skating Economy and Performance During a Repeated-Shift Test in Elite and Subelite Ice Hockey Players.

PubMed

Lamoureux, Nicholas R; Tomkinson, Grant R; Peterson, Benjamin J; Fitzgerald, John S

2018-04-01

Lamoureux, NR, Tomkinson, GR, Peterson, BJ, and Fitzgerald, JS. Relationship between skating economy and performance during a repeated-shift test in elite and subelite ice hockey players. J Strength Cond Res 32(4): 1109-1113, 2018-The purpose of this study was to determine the importance of skating economy to fatigue during repeated high-intensity efforts of a simulated ice hockey shift. Forty-five collegiate and Junior A male ice hockey players (aged 18-24 years) performed a continuous graded exercise test using a skate treadmill. Breath-by-breath data for oxygen consumption (V[Combining Dot Above]O2) and respiratory exchange ratio were collected and used to derive energy expenditure (EE) averaged over the final 10 seconds of each stage. Economy was determined as the slope of the regression line relating V[Combining Dot Above]O2 and EE against skating speed separately. Participants also completed 8 bouts of maximal ice skating through a course designed to simulate typical shift, with timing gates determining first half, second half, and total fatigue decrement, calculated by a percent decrement score. Partial correlation was used to determine the association between economy measures and decrement during the repeated-shift test. Twenty-six participants met inclusion criteria and were included in data analysis. Skating economy measures (both relative V[Combining Dot Above]O2 and EE) were very likely moderate positive correlates of total fatigue decrement (r [95% confidence interval]: V[Combining Dot Above]O2, 0.46 [0.09, 0.72] and EE, 0.44, [0.06, 0.71]) but not with first or second gate decrement. Our results indicate that skating economy plays an important role in fatigue resistance over repeated on-ice sprints designed to simulate a typical shift. This supports the use of technical skating coaching and training techniques to enhance skating economy as a means of improving ice hockey performance.

Validation of a Hartmann-Moiré wavefront sensor with large dynamic range.

PubMed

Wei, Xin; Van Heugten, Tony; Thibos, Larry

2009-08-03

Our goal was to validate the accuracy, repeatability, sensitivity, and dynamic range of a Hartmann-Moiré (HM) wavefront sensor (PixelOptics, Inc.) designed for ophthalmic applications. Testing apparatus injected a 4 mm diameter monochromatic (532 nm) beam of light into the wavefront sensor for measurement. Controlled amounts of defocus and astigmatism were introduced into the beam with calibrated spherical (-20D to + 18D) and cylindrical (-8D to + 8D) lenses. Repeatability was assessed with three repeated measurements within a 2-minute period. Correlation coefficients between mean wavefront measurements (n = 3) and expected wavefront vergence for both sphere and cylinder lenses were >0.999. For spherical lenses, the sensor was accurate to within 0.1D over the range from -20D to + 18D. For cylindrical lenses, the sensor was accurate to within 0.1D over the range from -8D to + 8D. The primary limitation to demonstrating an even larger dynamic range was the increasingly critical requirements for optical alignment. Sensitivity to small changes of vergence was constant over the instrument's full dynamic range. Repeatability of measurements for fixed condition was within 0.01D. The Hartmann-Moiré wavefront sensor measures defocus and astigmatism accurately and repeatedly with good sensitivity over a large dynamic range required for ophthalmic applications.

Beverage Intake Assessment Questionnaire: Relative Validity and Repeatability in a Spanish Population with Metabolic Syndrome from the PREDIMED-PLUS Study.

PubMed

Ferreira-Pêgo, Cíntia; Nissensohn, Mariela; Kavouras, Stavros A; Babio, Nancy; Serra-Majem, Lluís; Martín Águila, Adys; Mauromoustakos, Andy; Álvarez Pérez, Jacqueline; Salas-Salvadó, Jordi

2016-07-30

We assess the repeatability and relative validity of a Spanish beverage intake questionnaire for assessing water intake from beverages. The present analysis was performed within the framework of the PREDIMED-PLUS trial. The study participants were adults (aged 55-75) with a BMI ≥27 and <40 kg/m², and at least three components of Metabolic Syndrome (MetS). A trained dietitian completed the questionnaire. Participants provided 24-h urine samples, and the volume and urine osmolality were recorded. The repeatability of the baseline measurement at 6 and 1 year was examined by paired Student's t-test comparisons. A total of 160 participants were included in the analysis. The Bland-Altman analysis showed relatively good agreement between total daily fluid intake assessed using the fluid-specific questionnaire, and urine osmolality and 24-h volume with parameter estimates of -0.65 and 0.22, respectively (R² = 0.20; p < 0.001). In the repeatability test, no significant differences were found between neither type of beverage nor total daily fluid intake at 6 months and 1-year assessment, compared to baseline. The proposed fluid-specific assessment questionnaire designed to assess the consumption of water and other beverages in Spanish adult individuals was found to be relatively valid with good repeatability.

Programmable DNA-binding proteins from Burkholderia provide a fresh perspective on the TALE-like repeat domain.

PubMed

de Lange, Orlando; Wolf, Christina; Dietze, Jörn; Elsaesser, Janett; Morbitzer, Robert; Lahaye, Thomas

2014-06-01

The tandem repeats of transcription activator like effectors (TALEs) mediate sequence-specific DNA binding using a simple code. Naturally, TALEs are injected by Xanthomonas bacteria into plant cells to manipulate the host transcriptome. In the laboratory TALE DNA binding domains are reprogrammed and used to target a fused functional domain to a genomic locus of choice. Research into the natural diversity of TALE-like proteins may provide resources for the further improvement of current TALE technology. Here we describe TALE-like proteins from the endosymbiotic bacterium Burkholderia rhizoxinica, termed Bat proteins. Bat repeat domains mediate sequence-specific DNA binding with the same code as TALEs, despite less than 40% sequence identity. We show that Bat proteins can be adapted for use as transcription factors and nucleases and that sequence preferences can be reprogrammed. Unlike TALEs, the core repeats of each Bat protein are highly polymorphic. This feature allowed us to explore alternative strategies for the design of custom Bat repeat arrays, providing novel insights into the functional relevance of non-RVD residues. The Bat proteins offer fertile grounds for research into the creation of improved programmable DNA-binding proteins and comparative insights into TALE-like evolution. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Impact of number of repeated scans on model observer performance for a low-contrast detection task in computed tomography.

PubMed

Ma, Chi; Yu, Lifeng; Chen, Baiyu; Favazza, Christopher; Leng, Shuai; McCollough, Cynthia

2016-04-01

Channelized Hotelling observer (CHO) models have been shown to correlate well with human observers for several phantom-based detection/classification tasks in clinical computed tomography (CT). A large number of repeated scans were used to achieve an accurate estimate of the model's template. The purpose of this study is to investigate how the experimental and CHO model parameters affect the minimum required number of repeated scans. A phantom containing 21 low-contrast objects was scanned on a 128-slice CT scanner at three dose levels. Each scan was repeated 100 times. For each experimental configuration, the low-contrast detectability, quantified as the area under receiver operating characteristic curve, [Formula: see text], was calculated using a previously validated CHO with randomly selected subsets of scans, ranging from 10 to 100. Using [Formula: see text] from the 100 scans as the reference, the accuracy from a smaller number of scans was determined. Our results demonstrated that the minimum number of repeated scans increased when the radiation dose level decreased, object size and contrast level decreased, and the number of channels increased. As a general trend, it increased as the low-contrast detectability decreased. This study provides a basis for the experimental design of task-based image quality assessment in clinical CT using CHO.

Impact of number of repeated scans on model observer performance for a low-contrast detection task in computed tomography

PubMed Central

Ma, Chi; Yu, Lifeng; Chen, Baiyu; Favazza, Christopher; Leng, Shuai; McCollough, Cynthia

2016-01-01

Abstract. Channelized Hotelling observer (CHO) models have been shown to correlate well with human observers for several phantom-based detection/classification tasks in clinical computed tomography (CT). A large number of repeated scans were used to achieve an accurate estimate of the model’s template. The purpose of this study is to investigate how the experimental and CHO model parameters affect the minimum required number of repeated scans. A phantom containing 21 low-contrast objects was scanned on a 128-slice CT scanner at three dose levels. Each scan was repeated 100 times. For each experimental configuration, the low-contrast detectability, quantified as the area under receiver operating characteristic curve, Az, was calculated using a previously validated CHO with randomly selected subsets of scans, ranging from 10 to 100. Using Az from the 100 scans as the reference, the accuracy from a smaller number of scans was determined. Our results demonstrated that the minimum number of repeated scans increased when the radiation dose level decreased, object size and contrast level decreased, and the number of channels increased. As a general trend, it increased as the low-contrast detectability decreased. This study provides a basis for the experimental design of task-based image quality assessment in clinical CT using CHO. PMID:27284547

E622, a miniature, virulence-associated mobile element.

PubMed

Stavrinides, John; Kirzinger, Morgan W B; Beasley, Federico C; Guttman, David S

2012-01-01

Miniature inverted terminal repeat elements (MITEs) are nonautonomous mobile elements that have a significant impact on bacterial evolution. Here we characterize E622, a 611-bp virulence-associated MITE from Pseudomonas syringae, which contains no coding region but has almost perfect 168-bp inverted repeats. Using an antibiotic coupling assay, we show that E622 is transposable and can mobilize an antibiotic resistance gene contained between its borders. Its predicted parent element, designated TnE622, has a typical transposon structure with a three-gene operon, consisting of resolvase, integrase, and exeA-like genes, which is bounded by the same terminal inverted repeats as E622. A broader genome level survey of the E622/TnE622 inverted repeats identified homologs in Pseudomonas, Salmonella, Shewanella, Erwinia, Pantoea, and the cyanobacteria Nostoc and Cyanothece, many of which appear to encompass known virulence genes, including genes encoding toxins, enzymes, and type III secreted effectors. Its association with niche-specific genetic determinants, along with its persistence and evolutionary diversification, indicates that this mobile element family has played a prominent role in the evolution of many agriculturally and clinically relevant pathogenic bacteria.

Repeatability of a 3D multi-segment foot model protocol in presence of foot deformities.

PubMed

Deschamps, Kevin; Staes, Filip; Bruyninckx, Herman; Busschots, Ellen; Matricali, Giovanni A; Spaepen, Pieter; Meyer, Christophe; Desloovere, Kaat

2012-07-01

Repeatability studies on 3D multi-segment foot models (3DMFMs) have mainly considered healthy participants which contrasts with the widespread application of these models to evaluate foot pathologies. The current study aimed at establishing the repeatability of the 3DMFM described by Leardini et al. in presence of foot deformities. Foot kinematics of eight adult participants were analyzed using a repeated-measures design including two therapists with different levels of experience. The inter-trial variability was higher compared to the kinematics of healthy subjects. Consideration of relative angles resulted in the lowest inter-session variability. The absolute 3D rotations between the Sha-Cal and Cal-Met seem to have the lowest variability in both therapists. A general trend towards higher σ(sess)/σ(trial) ratios was observed when the midfoot was involved. The current study indicates that not only relative 3D rotations and planar angles can be measured consistently in patients, also a number of absolute parameters can be consistently measured serving as basis for the decision making process. Copyright © 2012 Elsevier B.V. All rights reserved.

Evaluating the potential of gold, silver, and silica nanoparticles to saturate mononuclear phagocytic system tissues under repeat dosing conditions.

PubMed

Weaver, James L; Tobin, Grainne A; Ingle, Taylor; Bancos, Simona; Stevens, David; Rouse, Rodney; Howard, Kristina E; Goodwin, David; Knapton, Alan; Li, Xiaohong; Shea, Katherine; Stewart, Sharron; Xu, Lin; Goering, Peter L; Zhang, Qin; Howard, Paul C; Collins, Jessie; Khan, Saeed; Sung, Kidon; Tyner, Katherine M

2017-07-17

As nanoparticles (NPs) become more prevalent in the pharmaceutical industry, questions have arisen from both industry and regulatory stakeholders about the long term effects of these materials. This study was designed to evaluate whether gold (10 nm), silver (50 nm), or silica (10 nm) nanoparticles administered intravenously to mice for up to 8 weeks at doses known to be sub-toxic (non-toxic at single acute or repeat dosing levels) and clinically relevant could produce significant bioaccumulation in liver and spleen macrophages. Repeated dosing with gold, silver, and silica nanoparticles did not saturate bioaccumulation in liver or spleen macrophages. While no toxicity was observed with gold and silver nanoparticles throughout the 8 week experiment, some effects including histopathological and serum chemistry changes were observed with silica nanoparticles starting at week 3. No major changes in the splenocyte population were observed during the study for any of the nanoparticles tested. The clinical impact of these changes is unclear but suggests that the mononuclear phagocytic system is able to handle repeated doses of nanoparticles.