Retrotransposon expression and incorporation of cloned human and mouse retroelements in human spermatozoa.

PubMed

Lazaros, Leandros; Kitsou, Chrysoula; Kostoulas, Charilaos; Bellou, Sofia; Hatzi, Elissavet; Ladias, Paris; Stefos, Theodoros; Markoula, Sofia; Galani, Vasiliki; Vartholomatos, Georgios; Tzavaras, Theodore; Georgiou, Ioannis

2017-03-01

To investigate the expression of long interspersed element (LINE) 1, human endogenous retrovirus (HERV) K10, and short interspersed element-VNTR-Alu element (SVA) retrotransposons in ejaculated human spermatozoa by means of reverse-transcription (RT) polymerase chain reaction (PCR) analysis as well as the potential incorporation of cloned human and mouse active retroelements in human sperm cell genome. Laboratory study. University research laboratories and academic hospital. Normozoospermic and oligozoospermic white men. RT-PCR analysis was performed to confirm the retrotransposon expression in human spermatozoa. Exogenous retroelements were tagged with a plasmid containing a green fluorescence (EGFP) retrotransposition cassette, and the de novo retrotransposition events were tested with the use of PCR, fluorescence-activated cell sorting analysis, and confocal microscopy. Retroelement expression in human spermatozoa, incorporation of cloned human and mouse active retroelements in human sperm genome, and de novo retrotransposition events in human spermatozoa. RT-PCR products of expressed human LINE-1, HERV-K10, and SVA retrotransposons were observed in ejaculated human sperm samples. The incubation of human spermatozoa with either retrotransposition-active human LINE-1 and HERV-K10 or mouse reverse transcriptase-deficient VL30 retrotransposons tagged with an EGFP-based retrotransposition cassette led to EGFP-positive spermatozo; 16.67% of the samples were positive for retrotransposition. The respective retrotransposition frequencies for the LINE-1, HERV-K10, and VL30 retrotransposons in the positive samples were 0.34 ± 0.13%, 0.37 ± 0.17%, and 0.30 ± 0.14% per sample of 10,000 spermatozoa. Our results show that: 1) LINE-1, HERV-K10, and SVA retrotransposons are transcriptionally expressed in human spermatozoa; 2) cloned active retroelements of human and mammalian origin can be incorporated in human sperm genome; 3) active reverse transcriptases exist in human spermatozoa; and 4) de novo retrotransposition events occur in human spermatozoa. Copyright © 2017 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Envelope-like retrotransposons in the plant kingdom: evidence of their presence in gymnosperms (Pinus pinaster).

PubMed

Miguel, Célia; Simões, Marta; Oliveira, Maria Margarida; Rocheta, Margarida

2008-11-01

Retroviruses differ from retrotransposons due to their infective capacity, which depends critically on the encoded envelope. Some plant retroelements contain domains reminiscent of the env of animal retroviruses but the number of such elements described to date is restricted to angiosperms. We show here the first evidence of the presence of putative env-like gene sequences in a gymnosperm species, Pinus pinaster (maritime pine). Using a degenerate primer approach for conserved domains of RNaseH gene, three clones from putative envelope-like retrotransposons (PpRT2, PpRT3, and PpRT4) were identified. The env-like sequences of P. pinaster clones are predicted to encode proteins with transmembrane domains. These sequences showed identity scores of up to 30% with env-like sequences belonging to different organisms. A phylogenetic analysis based on protein alignment of deduced aminoacid sequences revealed that these clones clustered with env-containing plant retrotransposons, as well as with retrotransposons from invertebrate organisms. The differences found among the sequences of maritime pine clones isolated here suggest the existence of different putative classes of env-like retroelements. The identification for the first time of env-like genes in a gymnosperm species may support the ancestrality of retroviruses among plants shedding light on their role in plant evolution.

Positive Selection and Multiple Losses of the LINE-1-Derived L1TD1 Gene in Mammals Suggest a Dual Role in Genome Defense and Pluripotency

PubMed Central

Yang, Lei; Neme, Rafik; Wichman, Holly A.; Malik, Harmit S.

2014-01-01

Mammalian genomes comprise many active and fossilized retroelements. The obligate requirement for retroelement integration affords host genomes an opportunity to ‘domesticate’ retroelement genes for their own purpose, leading to important innovations in genome defense and placentation. While many such exaptations involve retroviruses, the L1TD1 gene is the only known domesticated gene whose protein-coding sequence is almost entirely derived from a LINE-1 (L1) retroelement. Human L1TD1 has been shown to play an important role in pluripotency maintenance. To investigate how this role was acquired, we traced the origin and evolution of L1TD1. We find that L1TD1 originated in the common ancestor of eutherian mammals, but was lost or pseudogenized multiple times during mammalian evolution. We also find that L1TD1 has evolved under positive selection during primate and mouse evolution, and that one prosimian L1TD1 has ‘replenished’ itself with a more recent L1 ORF1 from the prosimian genome. These data suggest that L1TD1 has been recurrently selected for functional novelty, perhaps for a role in genome defense. L1TD1 loss is associated with L1 extinction in several megabat lineages, but not in sigmodontine rodents. We hypothesize that L1TD1 could have originally evolved for genome defense against L1 elements. Later, L1TD1 may have become incorporated into pluripotency maintenance in some lineages. Our study highlights the role of retroelement gene domestication in fundamental aspects of mammalian biology, and that such domesticated genes can adopt different functions in different lineages. PMID:25211013

Hydroquinone induces DNA hypomethylation-independent overexpression of retroelements in human leukemia and hematopoietic stem cells.

PubMed

Conti, Anastasia; Rota, Federica; Ragni, Enrico; Favero, Chiara; Motta, Valeria; Lazzari, Lorenza; Bollati, Valentina; Fustinoni, Silvia; Dieci, Giorgio

2016-06-10

Hydroquinone (HQ) is an important benzene-derived metabolite associated with acute myelogenous leukemia risk. Although altered DNA methylation has been reported in both benzene-exposed human subjects and HQ-exposed cultured cells, the inventory of benzene metabolite effects on the epigenome is only starting to be established. In this study, we used a monocytic leukemia cell line (THP-1) and hematopoietic stem cells (HSCs) from cord blood to investigate the effects of HQ treatment on the expression of the three most important families of retrotransposons in the human genome: LINE-1, Alu and Endogenous retroviruses (HERVs), that are normally subjected to tight epigenetic silencing. We found a clear tendency towards increased retrotransposon expression in response to HQ exposure, more pronounced in the case of LINE-1 and HERV. Such a partial loss of silencing, however, was generally not associated with HQ-induced DNA hypomethylation. On the other hand, retroelement derepression was also observed in the same cells in response to the hypomethylating agent decitabine. These observations suggest the existence of different types of epigenetic switches operating at human retroelements, and point to retroelement activation in response to benzene-derived metabolites as a novel factor deserving attention in benzene carcinogenesis studies. Copyright © 2016 Elsevier Inc. All rights reserved.

Complete sequence of Tvv1, a family of Ty 1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking.

PubMed

Pelsy, F.; Merdinoglu, D.

2002-09-01

A chromosome-walking strategy was used to sequence and characterize retrotransposons in the grapevine genome. The reconstitution of a family of retroelements, named Tvv1, was achieved by six successive steps. These elements share a single, highly conserved open reading frame 4,153 nucleotides-long, putatively encoding the gag, pro, int, rt and rh proteins. Comparison of the Tvv1 open reading frame coding potential with those of drosophila copia and tobacco Tnt1, revealed that Tvv1 is closely related to Ty 1 copia-like retrotransposons. A highly variable untranslated leader region, upstream of the open reading frame, allowed us to differentiate Tvv1 variants, which represent a family of at least 28 copies, in varying sizes. This internal region is flanked by two long terminal repeats in direct orientation, sized between 149 and 157 bp. Among elements theoretically sized from 4,970 to 5,550 bp, we describe the full-length sequence of a reference element Tvv1-1, 5,343 nucleotides-long. The full-length sequence of Tvv1-1 compared to pea PDR1 shows a 53.3% identity. In addition, both elements contain long terminal repeats of nearly the same size in which the U5 region could be entirely absent. Therefore, we assume that Tvv1 and PDR1 could constitute a particular class of short LTRs retroelements.

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

PubMed Central

Llorens, Carlos; Muñoz-Pomer, Alfonso; Bernad, Lucia; Botella, Hector; Moya, Andrés

2009-01-01

Background Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system. Results We combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models. Conclusion The evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as network-represented combinations, are power-law distributed. This evidences an inflationary mode of evolution where the system diversity; 1) expands continuously alternating vertical and gradual processes of phylogenetic divergence with episodes of modular, saltatory and reticulate evolution; 2) is governed by the intrinsic capability of distinct LTR retroelement host-communities to self-organize their phenotypes according to emergent laws characteristic of complex systems. Reviewers This article was reviewed by Eugene V. Koonin, Eric Bapteste, and Enmanuelle Lerat (nominated by King Jordan) PMID:19883502

Characterization of a nucleocapsid-like region and of two distinct primer tRNALys,2 binding sites in the endogenous retrovirus Gypsy.

PubMed

Gabus, Caroline; Ivanyi-Nagy, Roland; Depollier, Julien; Bucheton, Alain; Pelisson, Alain; Darlix, Jean-Luc

2006-01-01

Mobile LTR-retroelements comprising retroviruses and LTR-retrotransposons form a large part of eukaryotic genomes. Their mode of replication and abundance favour the notion that they are major actors in eukaryote evolution. The Gypsy retroelement can spread in the germ line of the fruit fly Drosophila melanogaster via both env-independent and env-dependent processes. Thus, Gypsy is both an active retrotransposon and an infectious retrovirus resembling the gammaretrovirus MuLV. However, unlike gammaretroviruses, the Gypsy Gag structural precursor is not processed into Matrix, Capsid and Nucleocapsid (NC) proteins. In contrast, it has features in common with Gag of the ancient yeast TY1 retroelement. These characteristics of Gypsy make it a very interesting model to study replication of a retroelement at the frontier between ancient retrotransposons and retroviruses. We investigated Gypsy replication using an in vitro model system and transfection of insect cells. Results show that an unstructured domain of Gypsy Gag has all the properties of a retroviral NC. This NC-like peptide forms ribonucleoparticle-like complexes upon binding Gypsy RNA and directs the annealing of primer tRNA(Lys,2) to two distinct primer binding sites (PBS) at the genome 5' and 3' ends. Only the 5' PBS is indispensable for cDNA synthesis in vitro and in Drosophila cells.

Characterization of a nucleocapsid-like region and of two distinct primer tRNALys,2 binding sites in the endogenous retrovirus Gypsy

PubMed Central

Gabus, Caroline; Ivanyi-Nagy, Roland; Depollier, Julien; Bucheton, Alain; Pelisson, Alain; Darlix, Jean-Luc

2006-01-01

Mobile LTR-retroelements comprising retroviruses and LTR-retrotransposons form a large part of eukaryotic genomes. Their mode of replication and abundance favour the notion that they are major actors in eukaryote evolution. The Gypsy retroelement can spread in the germ line of the fruit fly Drosophila melanogaster via both env-independent and env-dependent processes. Thus, Gypsy is both an active retrotransposon and an infectious retrovirus resembling the gammaretrovirus MuLV. However, unlike gammaretroviruses, the Gypsy Gag structural precursor is not processed into Matrix, Capsid and Nucleocapsid (NC) proteins. In contrast, it has features in common with Gag of the ancient yeast TY1 retroelement. These characteristics of Gypsy make it a very interesting model to study replication of a retroelement at the frontier between ancient retrotransposons and retroviruses. We investigated Gypsy replication using an in vitro model system and transfection of insect cells. Results show that an unstructured domain of Gypsy Gag has all the properties of a retroviral NC. This NC-like peptide forms ribonucleoparticle-like complexes upon binding Gypsy RNA and directs the annealing of primer tRNALys,2 to two distinct primer binding sites (PBS) at the genome 5′ and 3′ ends. Only the 5′ PBS is indispensable for cDNA synthesis in vitro and in Drosophila cells. PMID:17040893

Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution.

PubMed

Toro, Nicolás; Martínez-Abarca, Francisco; Molina-Sánchez, María D; García-Rodríguez, Fernando M; Nisa-Martínez, Rafael

2018-01-01

Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti , the nitrogen-fixing endosymbiont of legumes of genus Medicago , harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species. Although RmInt1 conserves the ancient retroelement behavior, its evolutionary history suggests that this group II intron has played a role in the short- and long-term evolution of the S. meliloti genome. We will discuss its proposed role in genome evolution by controlling the spread and coexistence of potentially harmful mobile genetic elements, by ectopic transposition to different genetic loci as a source of early genomic variation and by generating sequence variation after a very slow degradation process, through intron remnants that may have continued to evolve, contributing to bacterial speciation.

Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution

PubMed Central

Toro, Nicolás; Martínez-Abarca, Francisco; Molina-Sánchez, María D.; García-Rodríguez, Fernando M.; Nisa-Martínez, Rafael

2018-01-01

Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti, the nitrogen-fixing endosymbiont of legumes of genus Medicago, harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species. Although RmInt1 conserves the ancient retroelement behavior, its evolutionary history suggests that this group II intron has played a role in the short- and long-term evolution of the S. meliloti genome. We will discuss its proposed role in genome evolution by controlling the spread and coexistence of potentially harmful mobile genetic elements, by ectopic transposition to different genetic loci as a source of early genomic variation and by generating sequence variation after a very slow degradation process, through intron remnants that may have continued to evolve, contributing to bacterial speciation. PMID:29670598

A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank

PubMed Central

2013-01-01

Background Accurate and complete identification of mobile elements is a challenging task in the current era of sequencing, given their large numbers and frequent truncations. Group II intron retroelements, which consist of a ribozyme and an intron-encoded protein (IEP), are usually identified in bacterial genomes through their IEP; however, the RNA component that defines the intron boundaries is often difficult to identify because of a lack of strong sequence conservation corresponding to the RNA structure. Compounding the problem of boundary definition is the fact that a majority of group II intron copies in bacteria are truncated. Results Here we present a pipeline of 11 programs that collect and analyze group II intron sequences from GenBank. The pipeline begins with a BLAST search of GenBank using a set of representative group II IEPs as queries. Subsequent steps download the corresponding genomic sequences and flanks, filter out non-group II introns, assign introns to phylogenetic subclasses, filter out incomplete and/or non-functional introns, and assign IEP sequences and RNA boundaries to the full-length introns. In the final step, the redundancy in the data set is reduced by grouping introns into sets of ≥95% identity, with one example sequence chosen to be the representative. Conclusions These programs should be useful for comprehensive identification of group II introns in sequence databases as data continue to rapidly accumulate. PMID:24359548

The cotton centromere contains a Ty3-gypsy-like LTR retroelement.

PubMed

Luo, Song; Mach, Jennifer; Abramson, Bradley; Ramirez, Rolando; Schurr, Robert; Barone, Pierluigi; Copenhaver, Gregory; Folkerts, Otto

2012-01-01

The centromere is a repeat-rich structure essential for chromosome segregation; with the long-term aim of understanding centromere structure and function, we set out to identify cotton centromere sequences. To isolate centromere-associated sequences from cotton, (Gossypium hirsutum) we surveyed tandem and dispersed repetitive DNA in the genus. Centromere-associated elements in other plants include tandem repeats and, in some cases, centromere-specific retroelements. Examination of cotton genomic survey sequences for tandem repeats yielded sequences that did not localize to the centromere. However, among the repetitive sequences we also identified a gypsy-like LTR retrotransposon (Centromere Retroelement Gossypium, CRG) that localizes to the centromere region of all chromosomes in domestic upland cotton, Gossypium hirsutum, the major commercially grown cotton. The location of the functional centromere was confirmed by immunostaining with antiserum to the centromere-specific histone CENH3, which co-localizes with CRG hybridization on metaphase mitotic chromosomes. G. hirsutum is an allotetraploid composed of A and D genomes and CRG is also present in the centromere regions of other AD cotton species. Furthermore, FISH and genomic dot blot hybridization revealed that CRG is found in D-genome diploid cotton species, but not in A-genome diploid species, indicating that this retroelement may have invaded the A-genome centromeres during allopolyploid formation and amplified during evolutionary history. CRG is also found in other diploid Gossypium species, including B and E2 genome species, but not in the C, E1, F, and G genome species tested. Isolation of this centromere-specific retrotransposon from Gossypium provides a probe for further understanding of centromere structure, and a tool for future engineering of centromere mini-chromosomes in this important crop species.

The Cotton Centromere Contains a Ty3-gypsy-like LTR Retroelement

PubMed Central

Luo, Song; Mach, Jennifer; Abramson, Bradley; Ramirez, Rolando; Schurr, Robert; Barone, Pierluigi; Copenhaver, Gregory; Folkerts, Otto

2012-01-01

The centromere is a repeat-rich structure essential for chromosome segregation; with the long-term aim of understanding centromere structure and function, we set out to identify cotton centromere sequences. To isolate centromere-associated sequences from cotton, (Gossypium hirsutum) we surveyed tandem and dispersed repetitive DNA in the genus. Centromere-associated elements in other plants include tandem repeats and, in some cases, centromere-specific retroelements. Examination of cotton genomic survey sequences for tandem repeats yielded sequences that did not localize to the centromere. However, among the repetitive sequences we also identified a gypsy-like LTR retrotransposon (Centromere Retroelement Gossypium, CRG) that localizes to the centromere region of all chromosomes in domestic upland cotton, Gossypium hirsutum, the major commercially grown cotton. The location of the functional centromere was confirmed by immunostaining with antiserum to the centromere-specific histone CENH3, which co-localizes with CRG hybridization on metaphase mitotic chromosomes. G. hirsutum is an allotetraploid composed of A and D genomes and CRG is also present in the centromere regions of other AD cotton species. Furthermore, FISH and genomic dot blot hybridization revealed that CRG is found in D-genome diploid cotton species, but not in A-genome diploid species, indicating that this retroelement may have invaded the A-genome centromeres during allopolyploid formation and amplified during evolutionary history. CRG is also found in other diploid Gossypium species, including B and E2 genome species, but not in the C, E1, F, and G genome species tested. Isolation of this centromere-specific retrotransposon from Gossypium provides a probe for further understanding of centromere structure, and a tool for future engineering of centromere mini-chromosomes in this important crop species. PMID:22536361

Nonneutral GC3 and retroelement codon mimicry in Phytophthora.

PubMed

Jiang, Rays H Y; Govers, Francine

2006-10-01

Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement's codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons.

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

PubMed Central

Diez, Concepcion M.; Meca, Esteban; Tenaillon, Maud I.; Gaut, Brandon S.

2014-01-01

Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remain poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24∶22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome. PMID:24743518

A New Member of the Sin3 Family of Corepressors Is Essential for Cell Viability and Required for Retroelement Propagation in Fission Yeast

PubMed Central

Dang, Van Dinh; Benedik, Michael J.; Ekwall, Karl; Choi, Jeannie; Allshire, Robin C.; Levin, Henry L.

1999-01-01

Tf1 is a long terminal repeat (LTR)-containing retrotransposon that propagates within the fission yeast Schizosaccharomyces pombe. LTR-retrotransposons possess significant similarity to retroviruses and therefore serve as retrovirus models. To determine what features of the host cell are important for the proliferation of this class of retroelements, we screened for mutations in host genes that reduced the transposition activity of Tf1. We report here the isolation and characterization of pst1+, a gene required for Tf1 transposition. The predicted amino acid sequence of Pst1p possessed high sequence homology with the Sin3 family of proteins, known for their interaction with histone deacetylases. However, unlike the SIN3 gene of Saccharomyces cerevisiae, pst1+ is essential for cell viability. Immunofluorescence microscopy indicated that Pst1p was localized in the nucleus. Consistent with the critical role previously reported for Sin3 proteins in the histone acetylation process, we found that the growth of the strain with the pst1-1 allele was supersensitive to the specific histone deacetylase inhibitor trichostatin A. However, our analysis of strains with the pst1-1 mutation was unable to detect any changes in the acetylation of specific lysines of histones H3 and H4 as measured in bulk chromatin. Interestingly, the pst1-1 mutant strain produced wild-type levels of Tf1-encoded proteins and cDNA, indicating that the defect in transposition occurred after reverse transcription. The results of immunofluorescence microscopy showed that the nuclear localization of the Tf1 capsid protein was disrupted in the strain with the pst1-1 mutation, indicating an important role of pst1+ in modulating the nuclear import of Tf1 virus-like particles. PMID:10022921

Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes

PubMed Central

Watanabe, Toshiaki; Takeda, Atsushi; Tsukiyama, Tomoyuki; Mise, Kazuyuki; Okuno, Tetsuro; Sasaki, Hiroyuki; Minami, Naojiro; Imai, Hiroshi

2006-01-01

Small RNAs ranging in size between 18 and 30 nucleotides (nt) are found in many organisms including yeasts, plants, and animals. Small RNAs are involved in the regulation of gene expression through translational repression, mRNA degradation, and chromatin modification. In mammals, microRNAs (miRNAs) are the only small RNAs that have been well characterized. Here, we have identified two novel classes of small RNAs in the mouse germline. One class consists of ∼20- to 24-nt small interfering RNAs (siRNAs) from mouse oocytes, which are derived from retroelements including LINE, SINE, and LTR retrotransposons. Addition of retrotransposon-derived sequences to the 3′ untranslated region (UTR) of a reporter mRNA destabilizes the mRNA significantly when injected into full-grown oocytes. These results suggest that retrotransposons are suppressed through the RNAi pathway in mouse oocytes. The other novel class of small RNAs is 26- to 30-nt germline small RNAs (gsRNAs) from testes. gsRNAs are expressed during spermatogenesis in a developmentally regulated manner, are mapped to the genome in clusters, and have strong strand bias. These features are reminiscent of Tetrahymena ∼23- to 24-nt small RNAs and Caenorhabditis elegans X-cluster small RNAs. A conserved novel small RNA pathway may be present in diverse animals. PMID:16766679

The yeast retrotransposon Ty5 uses the anticodon stem-loop of the initiator methionine tRNA as a primer for reverse transcription.

PubMed Central

Ke, N; Gao, X; Keeney, J B; Boeke, J D; Voytas, D F

1999-01-01

Retrotransposons and retroviruses replicate by reverse transcription of an mRNA intermediate. Most retroelements initiate reverse transcription from a host-encoded tRNA primer. DNA synthesis typically extends from the 3'-OH of the acceptor stem, which is complementary to sequences on the retroelement mRNA (the primer binding site, PBS). However, for some retrotransposons, including the yeast Ty5 elements, sequences in the anticodon stem-loop of the initiator methionine tRNA (IMT) are complementary to the PBS. We took advantage of the genetic tractability of the yeast system to investigate the mechanism of Ty5 priming. We found that transposition frequencies decreased at least 800-fold for mutations in the Ty5 PBS that disrupt complementarity with the IMT. Similarly, transposition was reduced at least 200-fold for IMT mutations in the anticodon stem-loop. Base pairing between the Ty5 PBS and IMT is essential for transposition, as compensatory changes that restored base pairing between the two mutant RNAs restored transposition significantly. An analysis of 12 imt mutants with base changes outside of the region of complementarity failed to identify other tRNA residues important for transposition. In addition, assays carried out with heterologous IMTs from Schizosaccharomyces pombe and Arabidopsis thaliana indicated that residues outside of the anticodon stem-loop have at most a fivefold effect on transposition. Our genetic system should make it possible to further define the components required for priming and to understand the mechanism by which Ty5's novel primer is generated. PMID:10411136

The RNA gene information: retroelement-microRNA entangling as the RNA quantum code.

PubMed

Fujii, Yoichi Robertus

2013-01-01

MicroRNA (miRNA) and retroelements may be a master of regulator in our life, which are evolutionally involved in the origin of species. To support the Darwinism from the aspect of molecular evolution process, it has tremendously been interested in the molecular information of naive RNA. The RNA wave model 2000 consists of four concepts that have altered from original idea of the miRNA genes for crosstalk among embryonic stem cells, their niche cells, and retroelements as a carrier vesicle of the RNA genes. (1) the miRNA gene as a mobile genetic element induces transcriptional and posttranscriptional silencing via networking-processes (no hierarchical architecture); (2) the RNA information supplied by the miRNA genes expands to intracellular, intercellular, intraorgan, interorgan, intraspecies, and interspecies under the cycle of life into the global environment; (3) the mobile miRNAs can self-proliferate; and (4) cells contain two types information as resident and genomic miRNAs. Based on RNA wave, we have developed an interest in investigation of the transformation from RNA information to quantum bits as physicochemical characters of RNA with the measurement of RNA electron spin. When it would have been given that the fundamental bases for the acquired characters in genetics can be controlled by RNA gene information, it may be available to apply for challenging against RNA gene diseases, such as stress-induced diseases.

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

PubMed Central

Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M.; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P.; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M.; Latorre, Amparo; Moya, Andres

2011-01-01

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org. PMID:21036865

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.

PubMed

Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M; Latorre, Amparo; Moya, Andres

2011-01-01

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.

LINE-1 silencing by retinoblastoma proteins is effected through the nucleosomal and remodeling deacetylase multiprotein complex.

PubMed

Montoya-Durango, Diego E; Ramos, Kenneth A; Bojang, Pasano; Ruiz, Lorell; Ramos, Irma N; Ramos, Kenneth S

2016-01-25

Long Interspersed Nuclear Element-1 (L1) is an oncogenic mammalian retroelement silenced early in development via tightly controlled epigenetic mechanisms. We have previously shown that the regulatory region of human and murine L1s interact with retinoblastoma (RB) proteins to effect retroelement silencing. The present studies were conducted to identify the corepressor complex responsible for RB-mediated silencing of L1. Chromatin immunoprecipitation and silencing RNA technology were used to identify the repressor complex that silences L1 in human and murine cells. Components of the Nucleosomal and Remodeling Deacetylase (NuRD) multiprotein complex specifically enriched the L1 5'-untranslated DNA sequence in human and murine cells. Genetic ablation of RB proteins in murine cells destabilized interactions within the NuRD macromolecular complex and mediated nuclear rearrangement of Mi2-β, an ATP-dependent helicase subunit with nucleosome remodeling activity. Depletion of Mi2-β, RbAP46 and HDAC2 reduced the repressor activity of the NuRD complex and reactivated a synthetic L1 reporter in human cells. Epigenetic reactivation of L1 in RB-null cells by DNA damage was markedly enhanced compared to wild type cells. RB proteins stabilize interactions of the NuRD corepressor complex within the L1 promoter to effect L1 silencing. L1 retroelements may serve as a scaffold on which RB builds heterochromatic regions that regulate chromatin function.

RNA-Seq Analysis to Measure the Expression of SINE Retroelements.

PubMed

Román, Ángel Carlos; Morales-Hernández, Antonio; Fernández-Salguero, Pedro M

2016-01-01

The intrinsic features of retroelements, like their repetitive nature and disseminated presence in their host genomes, demand the use of advanced methodologies for their bioinformatic and functional study. The short length of SINE (short interspersed elements) retrotransposons makes such analyses even more complex. Next-generation sequencing (NGS) technologies are currently one of the most widely used tools to characterize the whole repertoire of gene expression in a specific tissue. In this chapter, we will review the molecular and computational methods needed to perform NGS analyses on SINE elements. We will also describe new methods of potential interest for researchers studying repetitive elements. We intend to outline the general ideas behind the computational analyses of NGS data obtained from SINE elements, and to stimulate other scientists to expand our current knowledge on SINE biology using RNA-seq and other NGS tools.

A customized gene expression microarray reveals that the brittle stem phenotype fs2 of barley is attributable to a retroelement in the HvCesA4 cellulose synthase gene.

PubMed

Burton, Rachel A; Ma, Gang; Baumann, Ute; Harvey, Andrew J; Shirley, Neil J; Taylor, Jillian; Pettolino, Filomena; Bacic, Antony; Beatty, Mary; Simmons, Carl R; Dhugga, Kanwarpal S; Rafalski, J Antoni; Tingey, Scott V; Fincher, Geoffrey B

2010-08-01

The barley (Hordeum vulgare) brittle stem mutants, fs2, designated X054 and M245, have reduced levels of crystalline cellulose compared with their parental lines Ohichi and Shiroseto. A custom-designed microarray, based on long oligonucleotide technology and including genes involved in cell wall metabolism, revealed that transcript levels of very few genes were altered in the elongation zone of stem internodes, but these included a marked decrease in mRNA for the HvCesA4 cellulose synthase gene of both mutants. In contrast, the abundance of several hundred transcripts changed in the upper, maturation zones of stem internodes, which presumably reflected pleiotropic responses to a weakened cell wall that resulted from the primary genetic lesion. Sequencing of the HvCesA4 genes revealed the presence of a 964-bp solo long terminal repeat of a Copia-like retroelement in the first intron of the HvCesA4 genes of both mutant lines. The retroelement appears to interfere with transcription of the HvCesA4 gene or with processing of the mRNA, and this is likely to account for the lower crystalline cellulose content and lower stem strength of the mutants. The HvCesA4 gene maps to a position on chromosome 1H of barley that coincides with the previously reported position of fs2.

A Customized Gene Expression Microarray Reveals That the Brittle Stem Phenotype fs2 of Barley Is Attributable to a Retroelement in the HvCesA4 Cellulose Synthase Gene1[W][OA

PubMed Central

Burton, Rachel A.; Ma, Gang; Baumann, Ute; Harvey, Andrew J.; Shirley, Neil J.; Taylor, Jillian; Pettolino, Filomena; Bacic, Antony; Beatty, Mary; Simmons, Carl R.; Dhugga, Kanwarpal S.; Rafalski, J. Antoni; Tingey, Scott V.; Fincher, Geoffrey B.

2010-01-01

The barley (Hordeum vulgare) brittle stem mutants, fs2, designated X054 and M245, have reduced levels of crystalline cellulose compared with their parental lines Ohichi and Shiroseto. A custom-designed microarray, based on long oligonucleotide technology and including genes involved in cell wall metabolism, revealed that transcript levels of very few genes were altered in the elongation zone of stem internodes, but these included a marked decrease in mRNA for the HvCesA4 cellulose synthase gene of both mutants. In contrast, the abundance of several hundred transcripts changed in the upper, maturation zones of stem internodes, which presumably reflected pleiotropic responses to a weakened cell wall that resulted from the primary genetic lesion. Sequencing of the HvCesA4 genes revealed the presence of a 964-bp solo long terminal repeat of a Copia-like retroelement in the first intron of the HvCesA4 genes of both mutant lines. The retroelement appears to interfere with transcription of the HvCesA4 gene or with processing of the mRNA, and this is likely to account for the lower crystalline cellulose content and lower stem strength of the mutants. The HvCesA4 gene maps to a position on chromosome 1H of barley that coincides with the previously reported position of fs2. PMID:20530215

Bacterial Group II Introns: Identification and Mobility Assay.

PubMed

Toro, Nicolás; Molina-Sánchez, María Dolores; Nisa-Martínez, Rafael; Martínez-Abarca, Francisco; García-Rodríguez, Fernando Manuel

2016-01-01

Group II introns are large catalytic RNAs and mobile retroelements that encode a reverse transcriptase. Here, we provide methods for their identification in bacterial genomes and further analysis of their splicing and mobility capacities.

Genomic patterns associated with paternal/maternal distribution of transposable elements

NASA Astrophysics Data System (ADS)

Jurka, Jerzy

2003-03-01

Transposable elements (TEs) are specialized DNA or RNA fragments capable of surviving in intragenomic niches. They are commonly, perhaps unjustifiably referred to as "selfish" or "parasitic" elements. TEs can be divided in two major classes: retroelements and DNA transposons. The former include non-LTR retrotransposons and retrovirus-like elements, using reverse transriptase for their reproduction prior to integration into host DNA. The latter depend mostly on host DNA replication, with possible exception of rolling-circle transposons recently discovered by our team. I will review basic information on TEs, with emphasis on human Alu and L1 retroelements discussed in the context of genomic organization. TEs are non-randomly distributed in chromosomal DNA. In particular, human Alu elements tend to prefer GC-rich regions, whereas L1 accumulate in AT-rich regions. Current explanations of this phenomenon focus on the so called "target effects" and post-insertional selection. However, the proposed models appear to be unsatisfactory and alternative explanations invoking "channeling" to different chromosomal regions will be a major focus of my presentation. Transposable elements (TEs) can be expressed and integrated into host DNA in the male or female germlines, or both. Different models of expression and integration imply different proportions of TEs on sex chromosomes and autosomes. The density of recently retroposed human Alu elements is around three times higher on chromosome Y than on chromosome X, and over two times higher than the average density for all human autosomes. This implies Alu activity in paternal germlines. Analogous inter-chromosomal proportions for other repeat families should determine their compatibility with one of the three basic models describing the inheritance of TEs. Published evidence indicates that maternally and paternally imprinted genes roughly correspond to GC-rich and AT-rich DNA. This may explain the observed chromosomal distribution of Alu and L1 elements. Finally, paternal models of inheritance predict rapid accumulation of active TEs on chromosome Y. I will discuss potential implications of this phenomenon for evolution of chromosome Y and transposable elements.

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges[W][OA

PubMed Central

Butelli, Eugenio; Licciardello, Concetta; Zhang, Yang; Liu, Jianjun; Mackay, Steve; Bailey, Paul; Reforgiato-Recupero, Giuseppe; Martin, Cathie

2012-01-01

Traditionally, Sicilian blood oranges (Citrus sinensis) have been associated with cardiovascular health, and consumption has been shown to prevent obesity in mice fed a high-fat diet. Despite increasing consumer interest in these health-promoting attributes, production of blood oranges remains unreliable due largely to a dependency on cold for full color formation. We show that Sicilian blood orange arose by insertion of a Copia-like retrotransposon adjacent to a gene encoding Ruby, a MYB transcriptional activator of anthocyanin production. The retrotransposon controls Ruby expression, and cold dependency reflects the induction of the retroelement by stress. A blood orange of Chinese origin results from an independent insertion of a similar retrotransposon, and color formation in its fruit is also cold dependent. Our results suggest that transposition and recombination of retroelements are likely important sources of variation in Citrus. PMID:22427337

A comparative study of retrotransposons in the centromeric regions of A and B chromosomes of maize.

PubMed

Theuri, J; Phelps-Durr, T; Mathews, S; Birchler, J

2005-01-01

Bacterial Artificial Chromosomes (BACs) derived from the B chromosome, based on homology with the B specific sequence, were subcloned and sequenced. Analysis of DNA sequence data indicated the presence of 23 common retroelements, as well as novel sequences of B chromosome origin. Generally, where the same retrotransposon type was observed in both A and B chromosomes, there were more copies per unit of sequence in the B centromeric region (the major site of B repeat) than in the A centromere, except for Huck-1. Based on previous estimates of the age of the major burst of transposition into the maize genome, the oldest retrotransposons (Ji-6 and Tekay, approximately 5.0 and 5.2 million years ago, respectively) were found in the B centromere region only, while the next two oldest (Huck-1 and Opie-1) were found in both the A and B sequences. Phylogenetic analysis of Opie retroelements from both A and B centromeres indicated that some of the B Opie centromeric sequences share a more recent common ancestor with A Opie retroelements than they do with other B Opie centromeric sequences. These results imply that the supernumerary maize B chromosome has coexisted with the A chromosomes during that period of transposition. They also support the hypothesis that the B chromosome had its origins from A chromosome elements, or that alternative origins, such as being donated to the maize genome in a wide species cross, preceded six million years ago, because the spectrum of retrotransposons in the two chromosomes is quite similar.

Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres.

PubMed

Arkhipova, Irina R; Yushenova, Irina A; Rodriguez, Fernando

2017-09-01

Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here, we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3'-end of the RNA template immediately adjacent to a hammerhead ribozyme motif. Terminon units, which can exceed 40 kb in length, display an unusually complex and diverse structure, and can form very long chains, with host genes often captured between units. As the principal polymerizing component, Terminons contain Athena reverse transcriptases previously described in bdelloid rotifers and belonging to the enigmatic group of Penelope-like elements, but can additionally accumulate multiple cooriented ORFs, including DEDDy 3'-exonucleases, GDSL esterases/lipases, GIY-YIG-like endonucleases, rolling-circle replication initiator (Rep) proteins, and putatively structural ORFs with coiled-coil motifs and transmembrane domains. The extraordinary length and complexity of Terminons and the high degree of interfamily variability in their ORF content challenge the current views on the structural organization of eukaryotic retroelements, and highlight their possible connections with the viral world and the implications for the elevated frequency of gene transfer. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean.

PubMed

Innes, Roger W; Ameline-Torregrosa, Carine; Ashfield, Tom; Cannon, Ethalinda; Cannon, Steven B; Chacko, Ben; Chen, Nicolas W G; Couloux, Arnaud; Dalwani, Anita; Denny, Roxanne; Deshpande, Shweta; Egan, Ashley N; Glover, Natasha; Hans, Christian S; Howell, Stacy; Ilut, Dan; Jackson, Scott; Lai, Hongshing; Mammadov, Jafar; Del Campo, Sara Martin; Metcalf, Michelle; Nguyen, Ashley; O'Bleness, Majesta; Pfeil, Bernard E; Podicheti, Ram; Ratnaparkhe, Milind B; Samain, Sylvie; Sanders, Iryna; Ségurens, Béatrice; Sévignac, Mireille; Sherman-Broyles, Sue; Thareau, Vincent; Tucker, Dominic M; Walling, Jason; Wawrzynski, Adam; Yi, Jing; Doyle, Jeff J; Geffroy, Valérie; Roe, Bruce A; Maroof, M A Saghai; Young, Nevin D

2008-12-01

The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.

The short interspersed repetitive element of Trypanosoma cruzi, SIRE, is part of VIPER, an unusual retroelement related to long terminal repeat retrotransposons

PubMed Central

Vázquez, Martín; Ben-Dov, Claudia; Lorenzi, Hernan; Moore, Troy; Schijman, Alejandro; Levin, Mariano J.

2000-01-01

The short interspersed repetitive element (SIRE) of Trypanosoma cruzi was first detected when comparing the sequences of loci that encode the TcP2β genes. It is present in about 1,500–3,000 copies per genome, depending on the strain, and it is distributed in all chromosomes. An initial analysis of SIRE sequences from 21 genomic fragments allowed us to derive a consensus nucleotide sequence and structure for the element, consisting of three regions (I, II, and III) each harboring distinctive features. Analysis of 158 transcribed SIREs demonstrates that the consensus is highly conserved. The sequences of 51 cDNAs show that SIRE is included in the 3′ end of several mRNAs, always transcribed from the sense strand, contributing the polyadenylation site in 63% of the cases. This study led to the characterization of VIPER (vestigial interposed retroelement), a 2,326-bp-long unusual retroelement. VIPER's 5′ end is formed by the first 182 bp of SIRE, whereas its 3′ end is formed by the last 220 bp of the element. Both SIRE moieties are connected by a 1,924-bp-long fragment that carries a unique ORF encoding a complete reverse transcriptase-RNase H gene whose 15 C-terminal amino acids derive from codons specified by SIRE's region II. The amino acid sequence of VIPER's reverse transcriptase-RNase H shares significant homology to that of long terminal repeat retrotransposons. The fact that SIRE and VIPER sequences are found only in the T. cruzi genome may be of relevance for studies concerning the evolution and the genome flexibility of this protozoan parasite. PMID:10688909

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals.

PubMed

Sharma, Upasna; Conine, Colin C; Shea, Jeremy M; Boskovic, Ana; Derr, Alan G; Bing, Xin Y; Belleannee, Clemence; Kucukural, Alper; Serra, Ryan W; Sun, Fengyun; Song, Lina; Carone, Benjamin R; Ricci, Emiliano P; Li, Xin Z; Fauquier, Lucas; Moore, Melissa J; Sullivan, Robert; Mello, Craig C; Garber, Manuel; Rando, Oliver J

2016-01-22

Several recent studies link parental environments to phenotypes in subsequent generations. In this work, we investigate the mechanism by which paternal diet affects offspring metabolism. Protein restriction in mice affects small RNA (sRNA) levels in mature sperm, with decreased let-7 levels and increased amounts of 5' fragments of glycine transfer RNAs (tRNAs). In testicular sperm, tRNA fragments are scarce but increase in abundance as sperm mature in the epididymis. Epididymosomes (vesicles that fuse with sperm during epididymal transit) carry RNA payloads matching those of mature sperm and can deliver RNAs to immature sperm in vitro. Functionally, tRNA-glycine-GCC fragments repress genes associated with the endogenous retroelement MERVL, in both embryonic stem cells and embryos. Our results shed light on sRNA biogenesis and its dietary regulation during posttesticular sperm maturation, and they also link tRNA fragments to regulation of endogenous retroelements active in the preimplantation embryo. Copyright © 2016, American Association for the Advancement of Science.

Traceability of Asian Matsutake, Specialty Mushrooms Produced by the Ectomycorrhizal Basidiomycete Tricholoma matsutake, on the Basis of Retroelement-Based DNA Markers▿

PubMed Central

Murata, Hitoshi; Babasaki, Katsuhiko; Saegusa, Tomoki; Takemoto, Kenji; Yamada, Akiyoshi; Ohta, Akira

2008-01-01

The ectomycorrhizal basidiomycete Tricholoma matsutake produces commercially valuable fruit bodies, matsutake, in forests. Here we report a PCR system targeting retroelement integration sites to differentiate among individual Asian isolates of T. matsutake based on their geographical origins, such as Japan, the area of South Korea through North Korea, the northeastern provinces of China, and the area of the southwestern provinces of China through Bhutan. The overall misjudgment rate of the analytical system was approximately 5% based on 95 samples of T. matsutake examined including those from cultures and from commodities. We also provide evidence that T. matsutake isolates grown throughout the Far East, including the northeastern provinces of China, are closely related to each other while distinct from those in the area of the southwestern provinces of China through Bhutan. The method allows us to trace back geographical origins of Asian matsutake, thus contributing to food safety, appropriate tariffs, and proper price setting. PMID:18281433

The APOBEC3 Family of Retroelement Restriction Factors

PubMed Central

Refsland, Eric W.; Harris, Reuben S.

2014-01-01

The ability to regulate and even target mutagenesis is an extremely valuable cellular asset. Enzyme-catalyzed DNA cytosine deamination is a molecular strategy employed by vertebrates to promote antibody diversity and defend against foreign nucleic acids. Ten years ago, a family of cellular enzymes was first described with several proving capable of deaminating DNA and inhibiting HIV-1 replication. Ensuing studies on the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) restriction factors have uncovered a broad-spectrum innate defense network that suppresses the replication of numerous endogenous and exogenous DNA-based parasites. Although many viruses possess equally elaborate counter-defense mechanisms, the APOBEC3 enzymes offer a tantalizing possibility of leveraging innate immunity to fend off viral infection. Here we focus on mechanisms of retroelement restriction by the APOBEC3 family of restriction enzymes and we consider the therapeutic benefits, as well as the possible pathological consequences, of arming cells with active DNA deaminases. PMID:23686230

Origins and evolution of viruses of eukaryotes: The ultimate modularity

PubMed Central

Koonin, Eugene V.; Dolja, Valerian V.; Krupovic, Mart

2018-01-01

Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes. PMID:25771806

Replication of Nonautonomous Retroelements in Soybean Appears to be Both Recent and Common

USDA-ARS?s Scientific Manuscript database

Retrotransposons and their remnants often constitute more than 50% of higher plant genomes and have had major impacts on genome structure. Although extensively studied in monocot crops such as maize and rice, the impact of retrotransposons on major dicot crop genomes is not well documented. Here w...

Wnt-mediated activation of NeuroD1 and retro-elements during adult neurogenesis.

PubMed

Kuwabara, Tomoko; Hsieh, Jenny; Muotri, Alysson; Yeo, Gene; Warashina, Masaki; Lie, Dieter Chichung; Moore, Lynne; Nakashima, Kinichi; Asashima, Makoto; Gage, Fred H

2009-09-01

In adult hippocampus, new neurons are continuously generated from neural stem cells (NSCs), but the molecular mechanisms regulating adult neurogenesis remain elusive. We found that Wnt signaling, together with the removal of Sox2, triggered the expression of NeuroD1 in mice. This transcriptional regulatory mechanism was dependent on a DNA element containing overlapping Sox2 and T-cell factor/lymphoid enhancer factor (TCF/LEF)-binding sites (Sox/LEF) in the promoter. Notably, Sox/LEF sites were also found in long interspersed nuclear element 1 (LINE-1) elements, consistent with their critical roles in the transition of NSCs to proliferating neuronal progenitors. Our results describe a previously unknown Wnt-mediated regulatory mechanism that simultaneously coordinates activation of NeuroD1 and LINE-1, which is important for adult neurogenesis and survival of neuronal progenitors. Moreover, the discovery that LINE-1 retro-elements embedded in the mammalian genome can function as bi-directional promoters suggests that Sox/LEF regulatory sites may represent a general mechanism, at least in part, for relaying environmental signals to other nearby loci to promote adult hippocampal neurogenesis.

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

PubMed Central

Shedlock, Andrew M.; Botka, Christopher W.; Zhao, Shaying; Shetty, Jyoti; Zhang, Tingting; Liu, Jun S.; Deschavanne, Patrick J.; Edwards, Scott V.

2007-01-01

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of ≈65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome. PMID:17307883

Woot, an Active Gypsy-Class Retrotransposon in the Flour Beetle, Tribolium Castaneum, Is Associated with a Recent Mutation

PubMed Central

Beeman, R. W.; Thomson, M. S.; Clark, J. M.; DeCamillis, M. A.; Brown, S. J.; Denell, R. E.

1996-01-01

A recently isolated, lethal mutation of the homeotic Abdominal gene of the red flour beetle Tribolium castaneum is associated with an insertion of a novel retrotransposon into an intron. Sequence analysis indicates that this retrotransposon, named Woot, is a member of the gypsy family of mobile elements. Most strains of T. castaneum appear to harbor ~25-35 copies of Woot per genome. Woot is composed of long terminal repeats of unprecedented length (3.6 kb each), flanking an internal coding region 5.0 kb in length. For most copies of Woot, the internal region includes two open reading frames (ORFs) that correspond to the gag and pol genes of previously described retrotransposons and retroviruses. The copy of Woot inserted into Abdominal bears an apparent single frameshift mutation that separates the normal second ORF into two. Woot does not appear to generate infectious virions by the criterion that no envelop gene is discernible. The association of Woot with a recent mutation suggests that this retroelement is currently transpositionally active in at least some strains. PMID:8722793

Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions Following Polyploidy in the Ancestor of Soybean

USDA-ARS?s Scientific Manuscript database

The genomes of most flowering plants have undergone polyploidization at some point in their evolution. How such polyploidization events have impacted the subsequent evolution of genome structure is poorly understood. We sequenced two homoeologous regions in soybean (Glycine max), which underwent a...

Recent Amplification of the Kangaroo Endogenous Retrovirus, KERV, Limited to the Centromere▿

PubMed Central

Ferreri, Gianni C.; Brown, Judith D.; Obergfell, Craig; Jue, Nathaniel; Finn, Caitlin E.; O'Neill, Michael J.; O'Neill, Rachel J.

2011-01-01

Mammalian retrotransposons, transposable elements that are processed through an RNA intermediate, are categorized as short interspersed elements (SINEs), long interspersed elements (LINEs), and long terminal repeat (LTR) retroelements, which include endogenous retroviruses. The ability of transposable elements to autonomously amplify led to their initial characterization as selfish or junk DNA; however, it is now known that they may acquire specific cellular functions in a genome and are implicated in host defense mechanisms as well as in genome evolution. Interactions between classes of transposable elements may exert a markedly different and potentially more significant effect on a genome than interactions between members of a single class of transposable elements. We examined the genomic structure and evolution of the kangaroo endogenous retrovirus (KERV) in the marsupial genus Macropus. The complete proviral structure of the kangaroo endogenous retrovirus, phylogenetic relationship among relative retroviruses, and expression of this virus in both Macropus rufogriseus and M. eugenii are presented for the first time. In addition, we show the relative copy number and distribution of the kangaroo endogenous retrovirus in the Macropus genus. Our data indicate that amplification of the kangaroo endogenous retrovirus occurred in a lineage-specific fashion, is restricted to the centromeres, and is not correlated with LINE depletion. Finally, analysis of KERV long terminal repeat sequences using massively parallel sequencing indicates that the recent amplification in M. rufogriseus is likely due to duplications and concerted evolution rather than a high number of independent insertion events. PMID:21389136

An ancient trans-kingdom horizontal transfer of Penelope -like retroelements from arthropods to conifers

Treesearch

Xuan Lin; Nurul Faridi; Claudio Casola

2016-01-01

Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In  eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to  move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively  ...

Retroelements (LINEs and SINEs) in vole genomes: differential distribution in the constitutive heterochromatin.

PubMed

Acosta, M J; Marchal, J A; Fernández-Espartero, C H; Bullejos, M; Sánchez, A

2008-01-01

The chromosomal distribution of mobile genetic elements is scarcely known in Arvicolinae species, but could be of relevance to understand the origin and complex evolution of the sex chromosome heterochromatin. In this work we cloned two retrotransposon sequences, L1 and SINE-B1, from the genome of Chionomys nivalis and investigated their chromosomal distribution on several arvicoline species. Our results demonstrate first that both retroelements are the most abundant repeated DNA sequences in the genome of these species. L1 elements, in most species, are highly accumulated in the sex chromosomes compared to the autosomes. This favoured L1 insertion could have played an important role in the origin of the enlarged heterochromatic blocks existing in the sex chromosomes of some Microtus species. Also, we propose that L1 accumulation on the X heterochromatin could have been the consequence of different, independent and rapid amplification processes acting in each species. SINE elements, however, were completely lacking from the constitutive heterochromatin, either in autosomes or in the heterochromatic blocks of sex chromosomes. These data could indicate that some SINE elements are incompatible with the formation of heterochromatic complexes and hence are necessarily missing from the constitutive heterochromatin.

Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.)

PubMed Central

2009-01-01

Background Retrotransposons are heterogeneous sequences, widespread in eukaryotic genomes, which refer to the so-called mobile DNA. They resemble retroviruses, both in their structure and for their ability to transpose within the host genome, of which they make up a considerable portion. Copia- and Gypsy-like retrotransposons are the two main classes of retroelements shown to be ubiquitous in plant genomes. Ideally, the retrotransposons life cycle results in the synthesis of a messenger RNA and then self-encoded proteins to process retrotransposon mRNA in double stranded extra-chromosomal cDNA copies which may integrate in new chromosomal locations. Results The RT-PCR and IRAP protocol were applied to detect the presence of Copia and Gypsy retrotransposon transcripts and of new events of integration in unstressed plants of a sunflower (Helianthus annuus L.) selfed line. Results show that in sunflower retrotransposons transcription occurs in all analyzed organs (embryos, leaves, roots, and flowers). In one out of sixty-four individuals analyzed, retrotransposons transcription resulted in the integration of a new element into the genome. Conclusion These results indicate that the retrotransposon life cycle is firmly controlled at a post transcriptional level. A possible silencing mechanism is discussed. PMID:20030800

The Gypsy Database (GyDB) of mobile genetic elements

PubMed Central

Lloréns, C.; Futami, R.; Bezemer, D.; Moya, A.

2008-01-01

In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III). Our inference indicates that all protein domains codified by the gag-pro-pol internal region of these two groups agree in a collective presentation of a particular evolutionary history, which may be used as a main criterion to differentiate their molecular diversity in a comprehensive collection of phylogenies and non-redundant molecular profiles useful in the identification of new Ty3/Gypsy and Retroviridae species. The GyDB project is available at http://gydb.uv.es. PMID:17895280

Bioinformatic flowchart and database to investigate the origins and diversity of Clan AA peptidases

PubMed Central

Llorens, Carlos; Futami, Ricardo; Renaud, Gabriel; Moya, Andrés

2009-01-01

Background Clan AA of aspartic peptidases relates the family of pepsin monomers evolutionarily with all dimeric peptidases encoded by eukaryotic LTR retroelements. Recent findings describing various pools of single-domain nonviral host peptidases, in prokaryotes and eukaryotes, indicate that the diversity of clan AA is larger than previously thought. The ensuing approach to investigate this enzyme group is by studying its phylogeny. However, clan AA is a difficult case to study due to the low similarity and different rates of evolution. This work is an ongoing attempt to investigate the different clan AA families to understand the cause of their diversity. Results In this paper, we describe in-progress database and bioinformatic flowchart designed to characterize the clan AA protein domain based on all possible protein families through ancestral reconstructions, sequence logos, and hidden markov models (HMMs). The flowchart includes the characterization of a major consensus sequence based on 6 amino acid patterns with correspondence with Andreeva's model, the structural template describing the clan AA peptidase fold. The set of tools is work in progress we have organized in a database within the GyDB project, referred to as Clan AA Reference Database . Conclusion The pre-existing classification combined with the evolutionary history of LTR retroelements permits a consistent taxonomical collection of sequence logos and HMMs. This set is useful for gene annotation but also a reference to evaluate the diversity of, and the relationships among, the different families. Comparisons among HMMs suggest a common ancestor for all dimeric clan AA peptidases that is halfway between single-domain nonviral peptidases and those coded by Ty3/Gypsy LTR retroelements. Sequence logos reveal how all clan AA families follow similar protein domain architecture related to the peptidase fold. In particular, each family nucleates a particular consensus motif in the sequence position related to the flap. The different motifs constitute a network where an alanine-asparagine-like variable motif predominates, instead of the canonical flap of the HIV-1 peptidase and closer relatives. Reviewers This article was reviewed by Daniel H. Haft, Vladimir Kapitonov (nominated by Jerry Jurka), and Ben M. Dunn (nominated by Claus Wilke). PMID:19173708

Oncogenic LINE 1 Retroelements Sustain Prostate Tumor Cells and Promote Metastatic Progression

DTIC Science & Technology

2016-12-01

Tillotson University in Austin , Texas and provides a summer research experience for them where they learn about prostate cancer research , as well as...PRINCIPAL INVESTIGATOR: Denise S. O’Keefe, Ph.D. CONTRACTING ORGANIZATION: UNIVERSITY OF TEXAS , San Antonio SAN ANTONIO TX 78229-3901 REPORT DATE...December 2016 TYPE OF REPORT: Final PREPARED FOR: U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland 21702-5012

Oncogenic LINE-1 Retroelements Sustain Prostate Tumor Cells and Promote Metastatic Progression

DTIC Science & Technology

2015-10-01

elements in prostate cancer contribute to its progression by activating oncogenic DNA sequences, or silencing tumor suppressor like sequences. We have...prostate cancer cells. Experiments are ongoing to determine if PIWIL-1 expression in prostate cancer cells will reduce their growth, thereby providing...proof of principle for future gene-based therapeutics for this cancer . 15. SUBJECT TERMS Prostate cancer , LINE-1, PIWIL-1, retrotransposons 16

Analysis of genetic diversity in pigeon pea germplasm using retrotransposon-based molecular markers.

PubMed

Maneesha; Upadhyaya, Kailash C

2017-09-01

Pigeon pea (Cajanus cajan), an important legume crop is predominantly cultivated in tropical and subtropical regions of Asia and Africa. It is normally considered to have a low degree of genetic diversity, an impediment in undertaking crop improvement programmes.We have analysed genetic polymorphism of domesticated pigeon pea germplasm (47 accessions) across the world using earlier characterized panzee retrotransposon-based molecularmarkers. Itwas conjectured that since retrotransposons are interspersed throughout the genome, retroelements-based markers would be able to uncover polymorphism possibly inherent in the diversity of retroelement sequences. Two PCR-based techniques, sequence-specific amplified polymorphism (SSAP) and retrotransposon microsatellite amplified polymorphism (REMAP) were utilized for the analyses.We show that a considerable degree of polymorphism could be detected using these techniques. Three primer combinations in SSAP generated 297 amplified products across 47 accessions with an average of 99 amplicons per assay. Degree of polymorphism varied from 84-95%. In the REMAP assays, the number of amplicons was much less but up to 73% polymorphism could be detected. On the basis of similarity coefficients, dendrograms were constructed. The results demonstrate that the retrotransposon-based markers could serve as a better alternative for the assessment of genetic diversity in crops with apparent low genetic base.

All y'all need to know 'bout retroelements in cancer.

PubMed

Belancio, Victoria P; Roy-Engel, Astrid M; Deininger, Prescott L

2010-08-01

Genetic instability is one of the principal hallmarks and causative factors in cancer. Human transposable elements (TE) have been reported to cause human diseases, including several types of cancer through insertional mutagenesis of genes critical for preventing or driving malignant transformation. In addition to retrotransposition-associated mutagenesis, TEs have been found to contribute even more genomic rearrangements through non-allelic homologous recombination. TEs also have the potential to generate a wide range of mutations derivation of which is difficult to directly trace to mobile elements, including double strand breaks that may trigger mutagenic genomic rearrangements. Genome-wide hypomethylation of TE promoters and significantly elevated TE expression in almost all human cancers often accompanied by the loss of critical DNA sensing and repair pathways suggests that the negative impact of mobile elements on genome stability should increase as human tumors evolve. The biological consequences of elevated retroelement expression, such as the rate of their amplification, in human cancers remain obscure, particularly, how this increase translates into disease-relevant mutations. This review is focused on the cellular mechanisms that control human TE-associated mutagenesis in cancer and summarizes the current understanding of TE contribution to genetic instability in human malignancies. Copyright © 2010 Elsevier Ltd. All rights reserved.

Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

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

Le Coq, Johanne; Ghosh, Partho

2012-06-19

Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein,more » TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd ({approx}16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10{sup 20} potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.« less

A Barley Powdery Mildew Fungus Non-Autonomous Retrotransposon Encodes a Peptide that Supports Penetration Success on Barley.

PubMed

Nottensteiner, Mathias; Zechmann, Bernd; McCollum, Christopher; Hückelhoven, Ralph

2018-05-11

Pathogens overcome plant immunity by the means of secreted effectors. Host effector targets often act in pathogen defense but might also support fungal accommodation or nutrition. The barley ROP GTPase HvRACB is involved in accommodation of fungal haustoria of the powdery mildew fungus Blumeria graminis f.sp. hordei (Bgh) in barley epidermal cells. We found that HvRACB interacts with the ROP-interactive peptide 1 (ROPIP1) that is encoded on the active non-long terminal repeat retroelement Eg-R1 of Bgh. Over-expression of ROPIP1 in barley epidermal cells and host-induced post-transcriptional gene silencing (HIGS) of ROPIP1 suggested that ROPIP1 is involved in virulence of Bgh. Bimolecular fluorescence complementation and co-localization supported that ROPIP1 can interact with activated HvRACB in planta. We show that ROPIP1 is expressed by Bgh on barley and translocated into the cytoplasm of infected barley cells. ROPIP1 is recruited to microtubules upon co-expression of microtubule associated ROP GTPase ACTIVATING PROTEIN (HvMAGAP1) and can destabilize cortical microtubules. Data suggest that Bgh ROPIP targets HvRACB and manipulates host cell microtubule organization for facilitated host cell entry. This points to a possible neo-functionalization of retroelement-derived transcripts for the evolution of a pathogen virulence effector.

Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

PubMed Central

Le Coq, Johanne; Ghosh, Partho

2011-01-01

Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd (∼16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 1020 potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation. PMID:21873231

Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement.

PubMed

Le Coq, Johanne; Ghosh, Partho

2011-08-30

Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd (∼16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10(20) potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.

Evolutionary origin of the segmental duplication encompassing the wheat GLU-B1 locus encoding the overexpressed Bx7 (Bx7OE) high molecular weight glutenin subunit.

PubMed

Ragupathy, Raja; Naeem, Hamid A; Reimer, Elsa; Lukow, Odean M; Sapirstein, Harry D; Cloutier, Sylvie

2008-01-01

Sequencing of a BAC clone encompassing the Glu-B1 locus in Glenlea, revealed a 10.3 Kb segmental duplication including the Bx7 gene and flanking an LTR retroelement. To better understand the evolution of this locus, two collections of wheat were surveyed. The first consisted of 96 diploid and tetraploid species accessions while the second consisted of 316 Triticum aestivum cultivars and landraces from 41 countries. The genotypes were first characterized by SDS-PAGE and a total of 40 of the 316 T. aestivum accessions were found to display the overexpressed Bx7 phenotype (Bx7OE). Three lines from the 96 diploid/tetraploid collection also displayed the stronger intensity staining characteristic of the Bx7(OE) subunit. The relative amounts of the Bx7 subunit to total HMW-GS were quantified by RP-HPLC for all Bx7OE accessions and a number of checks. The entire collection was assessed for the presence of four DNA markers namely an 18 bp indel of the coding region of Bx7 variant alleles, a 43 bp indel of the 5'-region and the left and right junctions of the LTR retrotransposon borders and the duplicated segment. All 43 accessions found to have the Bx7OE subunit by SDS-PAGE and RP-HPLC produced the four diagnostic PCR amplicons. None of the lines without the Bx7OE had the LTR retroelement/duplication genomic structure. However, the 18 and 43 bp indel were found in accessions other than Bx7OE. These results indicate that the overexpression of the Bx7 HMW-GS is likely the result of a single event, i.e., a gene duplication at the Glu-B1 locus mediated by the insertion of a retroelement. Also, the 18 and 43 bp indels pre-date the duplication event. Allelic variants Bx7*, Bx7 with and without 43 bp insert and Bx7OE were found in both tetraploid and hexaploid collections and shared the same genomic organization. Though the possibility of introgression from T. aestivum to T. turgidum cannot be ruled out, the three structural genomic changes of the B-genome taken together support the hypothesis of multiple polyploidization events involving different tetraploid progenitors.

Analysis of heterogeneity of Copia-like retrotransposons in the genome of cassava (Manihot esculenta Crantz).

PubMed

Gbadegesin, Micheal A; Beeching, John R

2011-12-20

Retrotransposons are ubiquitous in eukaryotic genomes and now proving to be useful genetic tools for genetic diversity and phylogenetic analyses, especially in plants. In order to assess the diversity of Ty1/Copia-like retrotransposons of cassava, we used PCR primers anchored on the conserved domains of reverse transcriptases (RTs) to amplify cassava Ty1/Copia-like RT. The PCR product was cloned and sequenced. Sequences analysis of the clones revealed the presence of 69 families of Ty1/Copia-like retrotransposon in the genome of cassava. Comparative analyses of the predicted amino acid sequences of these clones with those of other plants showed that retroelements of this class are very heterogeneous in cassava. Cassava is widely grown for its edible roots in the tropical and subtropical regions of the world. Cassava roots, though poor in protein, are rich in starch (makes up about 80% of the dry matter), vitamin C, carotenes, calcium and potassium. It has a great commercial importance as a source of starch and starch based products. Realizing the importance of cassava, it stands out as a crop to benefit from biotechnology development. Heterogeneity of Mecops (Manihot esculenta copia-like Retrotransposons) showed that they may be useful for genetic diversity and phylogenetic analyses of cassava germplasm.

Mobile genetic elements and cancer. From mutations to gene therapy.

PubMed

Kozeretska, I A; Demydov, S V; Ostapchenko, L I

2011-12-01

In the present review, an association between cancer and the activity of the non-LTR retroelements L1, Alu, and SVA, as well as endogenous retroviruses, in the human genome, is analyzed. Data suggesting that transposons have been involved in embryogenesis and malignization processes, are presented. Events that lead to the activation of mobile elements in mammalian somatic cells, as well as the use of mobile elements in genetic screening and cancer gene therapy, are reviewed.

LINE-1 retrotransposons: from 'parasite' sequences to functional elements.

PubMed

Paço, Ana; Adega, Filomena; Chaves, Raquel

2015-02-01

Long interspersed nuclear elements-1 (LINE-1) are the most abundant and active retrotransposons in the mammalian genomes. Traditionally, the occurrence of LINE-1 sequences in the genome of mammals has been explained by the selfish DNA hypothesis. Nevertheless, recently, it has also been argued that these sequences could play important roles in these genomes, as in the regulation of gene expression, genome modelling and X-chromosome inactivation. The non-random chromosomal distribution is a striking feature of these retroelements that somehow reflects its functionality. In the present study, we have isolated and analysed a fraction of the open reading frame 2 (ORF2) LINE-1 sequence from three rodent species, Cricetus cricetus, Peromyscus eremicus and Praomys tullbergi. Physical mapping of the isolated sequences revealed an interspersed longitudinal AT pattern of distribution along all the chromosomes of the complement in the three genomes. A detailed analysis shows that these sequences are preferentially located in the euchromatic regions, although some signals could be detected in the heterochromatin. In addition, a coincidence between the location of imprinted gene regions (as Xist and Tsix gene regions) and the LINE-1 retroelements was also observed. According to these results, we propose an involvement of LINE-1 sequences in different genomic events as gene imprinting, X-chromosome inactivation and evolution of repetitive sequences located at the heterochromatic regions (e.g. satellite DNA sequences) of the rodents' genomes analysed.

Plant centromeres.

PubMed

Lamb, J C; Yu, W; Han, F; Birchler, J A

2008-01-01

Plant centromeres are generally composed of tandem arrays of simple repeats that are typical of a particular species, but that evolve rapidly. Centromere specific retroelements are also present. These arrays associate with a centromere specific variant of histone H3 that anchors the site of the kinetochore. Although such DNA arrays are typical of the centromere, the specification of centromere activity has an epigenetic component as shown by the fact that centromeres are formed in the absence of such repeats and that centromeres in dicentric chromosomes regularly undergo inactivation.

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.

PubMed

Greally, John M

2002-01-08

To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival.

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome

PubMed Central

Greally, John M.

2002-01-01

To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival. PMID:11756672

A Simple Retroelement Based Knock-Down System in Dictyostelium: Further Insights into RNA Interference Mechanisms.

PubMed

Friedrich, Michael; Meier, Doreen; Schuster, Isabelle; Nellen, Wolfgang

2015-01-01

We have previously shown that the most abundant Dictyostelium discoideum retroelement DIRS-1 is suppressed by RNAi mechanisms. Here we provide evidence that both inverted terminal repeats have strong promoter activity and that bidirectional expression apparently generates a substrate for Dicer. A cassette containing the inverted terminal repeats and a fragment of a gene of interest was sufficient to activate the RNAi response, resulting in the generation of ~21 nt siRNAs, a reduction of mRNA and protein expression of the respective endogene. Surprisingly, no transitivity was observed on the endogene. This was in contrast to previous observations, where endogenous siRNAs caused spreading on an artificial transgene. Knock-down was successful on seven target genes that we examined. In three cases a phenotypic analysis proved the efficiency of the approach. One of the target genes was apparently essential because no knock-out could be obtained; the RNAi mediated knock-down, however, resulted in a very slow growing culture indicating a still viable reduction of gene expression. ADVANTAGES OF THE DIRS-1–RNAI SYSTEM: The knock-down system required a short DNA fragment (~400 bp) of the target gene as an initial trigger. Further siRNAs were generated by RdRPs since we have shown some siRNAs with a 5'-triphosphate group. Extrachromosomal vectors facilitate the procedure and allowed for molecular and phenotypic analysis within one week. The system provides an efficient and rapid method to reduce protein levels including those of essential genes.

The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution.

PubMed

Zuccolo, Andrea; Scofield, Douglas G; De Paoli, Emanuele; Morgante, Michele

2015-08-15

Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms. Copyright © 2015 Elsevier B.V. All rights reserved.

Target Site Recognition by a Diversity-Generating Retroelement

PubMed Central

Guo, Huatao; Tse, Longping V.; Nieh, Angela W.; Czornyj, Elizabeth; Williams, Steven; Oukil, Sabrina; Liu, Vincent B.; Miller, Jeff F.

2011-01-01

Diversity-generating retroelements (DGRs) are in vivo sequence diversification machines that are widely distributed in bacterial, phage, and plasmid genomes. They function to introduce vast amounts of targeted diversity into protein-encoding DNA sequences via mutagenic homing. Adenine residues are converted to random nucleotides in a retrotransposition process from a donor template repeat (TR) to a recipient variable repeat (VR). Using the Bordetella bacteriophage BPP-1 element as a prototype, we have characterized requirements for DGR target site function. Although sequences upstream of VR are dispensable, a 24 bp sequence immediately downstream of VR, which contains short inverted repeats, is required for efficient retrohoming. The inverted repeats form a hairpin or cruciform structure and mutational analysis demonstrated that, while the structure of the stem is important, its sequence can vary. In contrast, the loop has a sequence-dependent function. Structure-specific nuclease digestion confirmed the existence of a DNA hairpin/cruciform, and marker coconversion assays demonstrated that it influences the efficiency, but not the site of cDNA integration. Comparisons with other phage DGRs suggested that similar structures are a conserved feature of target sequences. Using a kanamycin resistance determinant as a reporter, we found that transplantation of the IMH and hairpin/cruciform-forming region was sufficient to target the DGR diversification machinery to a heterologous gene. In addition to furthering our understanding of DGR retrohoming, our results suggest that DGRs may provide unique tools for directed protein evolution via in vivo DNA diversification. PMID:22194701

Evolution of Genome Size and Complexity in Pinus

PubMed Central

Morse, Alison M.; Peterson, Daniel G.; Islam-Faridi, M. Nurul; Smith, Katherine E.; Magbanua, Zenaida; Garcia, Saul A.; Kubisiak, Thomas L.; Amerson, Henry V.; Carlson, John E.; Nelson, C. Dana; Davis, John M.

2009-01-01

Background Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood. Methodology/Principal Findings Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA. Conclusions/Significance Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes. PMID:19194510

The Argonaute protein TbAGO1 contributes to large and mini-chromosome segregation and is required for control of RIME retroposons and RHS pseudogene-associated transcripts.

PubMed

Durand-Dubief, Mickaël; Absalon, Sabrina; Menzer, Linda; Ngwabyt, Sandra; Ersfeld, Klaus; Bastin, Philippe

2007-12-01

The protist Trypanosoma brucei possesses a single Argonaute gene called TbAGO1 that is necessary for RNAi silencing. We previously showed that in strain 427, TbAGO1 knock-out leads to a slow growth phenotype and to chromosome segregation defects. Here we report that the slow growth phenotype is linked to defects in segregation of both large and mini-chromosome populations, with large chromosomes being the most affected. These phenotypes are completely reversed upon inducible re-expression of TbAGO1 fused to GFP, demonstrating their link with TbAGO1. Trypanosomes that do not express TbAGO1 show a general increase in the abundance of transcripts derived from the short retroposon RIME (Ribosomal Interspersed Mobile Element). Supplementary large RIME transcripts emerge in the absence of RNAi, a phenomenon coupled to the disappearance of short transcripts. These fluctuations are reversed by inducible expression of GFP::TbAGO1. Furthermore, we use a combination of Northern blots, RT-PCR and sequencing to reveal that RNAi controls expression of transcripts derived from RHS (Retrotransposon Hot Spot) pseudogenes (RHS genes with retro-element(s) integrated within their coding sequence). Absence of RNAi also leads to an increase of steady-state transcripts from regular RHS genes (those without retro-element), indicating a role for pseudogene in control of gene expression. However, analysis of retroposon abundance and arrangement in the genome of multiple clonal cell lines of TbAGO1-/- failed to reveal movement of mobile elements despite the increased amounts of retroposon transcripts.

Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility

PubMed Central

Wissing, Silke; Muñoz-Lopez, Martin; Macia, Angela; Yang, Zhiyuan; Montano, Mauricio; Collins, William; Garcia-Perez, Jose Luis; Moran, John V.; Greene, Warner C.

2012-01-01

Long interspersed element-1 (LINE-1 or L1) retrotransposons account for nearly 17% of human genomic DNA and represent a major evolutionary force that has reshaped the structure and function of the human genome. However, questions remain concerning both the frequency and the developmental timing of L1 retrotransposition in vivo and whether the mobility of these retroelements commonly results in insertional and post-insertional mechanisms of genomic injury. Cells exhibiting high rates of L1 retrotransposition might be especially at risk for such injury. We assessed L1 mRNA expression and L1 retrotransposition in two biologically relevant cell types, human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs), as well as in control parental human dermal fibroblasts (HDFs). Full-length L1 mRNA and the L1 open reading frame 1-encoded protein (ORF1p) were readily detected in hESCs and iPSCs, but not in HDFs. Sequencing analysis proved the expression of human-specific L1 element mRNAs in iPSCs. Bisulfite sequencing revealed that the increased L1 expression observed in iPSCs correlates with an overall decrease in CpG methylation in the L1 promoter region. Finally, retrotransposition of an engineered human L1 element was ∼10-fold more efficient in iPSCs than in parental HDFs. These findings indicate that somatic cell reprogramming is associated with marked increases in L1 expression and perhaps increases in endogenous L1 retrotransposition, which could potentially impact the genomic integrity of the resultant iPSCs. PMID:21989055

Designing Class Methods from Dataflow Diagrams

NASA Astrophysics Data System (ADS)

Shoval, Peretz; Kabeli-Shani, Judith

A method for designing the class methods of an information system is described. The method is part of FOOM - Functional and Object-Oriented Methodology. In the analysis phase of FOOM, two models defining the users' requirements are created: a conceptual data model - an initial class diagram; and a functional model - hierarchical OO-DFDs (object-oriented dataflow diagrams). Based on these models, a well-defined process of methods design is applied. First, the OO-DFDs are converted into transactions, i.e., system processes that supports user task. The components and the process logic of each transaction are described in detail, using pseudocode. Then, each transaction is decomposed, according to well-defined rules, into class methods of various types: basic methods, application-specific methods and main transaction (control) methods. Each method is attached to a proper class; messages between methods express the process logic of each transaction. The methods are defined using pseudocode or message charts.

Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells

PubMed Central

2013-01-01

Background In mouse embryonic stem cells (mESCs), transcriptional silencing of numerous class I and II endogenous retroviruses (ERVs), including IAP, ETn and MMERVK10C, is dependent upon the H3K9 methyltransferase (KMTase) SETDB1/ESET and its binding partner KAP1/TRIM28. In contrast, the H3K9 KMTases G9a and GLP and HP1 proteins are dispensable for this process. Intriguingly, MERVL retroelements are actively transcribed exclusively in the two-cell (2C) embryo, but the molecular basis of silencing of these class III ERVs at later developmental stages has not been systematically addressed. Results Here, we characterized the roles of these chromatin factors in MERVL silencing in mESCs. While MMERVK10C and IAP ERVs are bound by SETDB1 and KAP1 and are induced following their deletion, MERVL ERVs show relatively low levels of SETDB1 and KAP1 binding and are upregulated exclusively following KAP1 depletion, indicating that KAP1 influences MERVL expression independent of SETDB1. In contrast to class I and class II ERVs, MERVL and MERVL LTR-driven genic transcripts are also upregulated following depletion of G9a or GLP, and G9a binds directly to these ERVs. Consistent with a direct role for H3K9me2 in MERVL repression, these elements are highly enriched for G9a-dependent H3K9me2, and catalytically active G9a is required for silencing of MERVL LTR-driven transcripts. MERVL is also derepressed in HP1α and HP1β KO ESCs. However, like KAP1, HP1α and HP1β are only modestly enriched at MERVL relative to IAP LTRs. Intriguingly, as recently shown for KAP1, RYBP, LSD1 and G9a-deficient mESCs, many genes normally expressed in the 2C embryo are also induced in HP1 KO mESCs, revealing that aberrant expression of a subset of 2C-specific genes is a common feature in each of these KO lines. Conclusions Our results indicate that G9a and GLP, which are not required for silencing of class I and II ERVs, are recruited to MERVL elements and play a direct role in silencing of these class III ERVs, dependent upon G9a catalytic activity. In contrast, induction of MERVL expression in KAP1, HP1α and HP1β KO ESCs may occur predominantly as a consequence of indirect effects, in association with activation of a subset of 2C-specific genes. PMID:23735015

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

Singleton, Jr., Robert

This report documents the implementation of several related 1D heat flow problems in the verification package ExactPack [1]. In particular, the planar sandwich class defined in Ref. [2], as well as the classes PlanarSandwichHot, PlanarSandwichHalf, and other generalizations of the planar sandwich problem, are defined and documented here. A rather general treatment of 1D heat flow is presented, whose main results have been implemented in the class Rod1D. All planar sandwich classes are derived from the parent class Rod1D.

Silencing of the PiAvr3a effector-encoding gene from Phytophthora infestans by transcriptional fusion to a short interspersed element.

PubMed

Vetukuri, Ramesh R; Tian, Zhendong; Avrova, Anna O; Savenkov, Eugene I; Dixelius, Christina; Whisson, Stephen C

2011-12-01

Phytophthora infestans is the notorious oomycete causing late blight of potato and tomato. A large proportion of the P. infestans genome is composed of transposable elements, the activity of which may be controlled by RNA silencing. Accumulation of small RNAs is one of the hallmarks of RNA silencing. Here we demonstrate the presence of small RNAs corresponding to the sequence of a short interspersed retrotransposable element (SINE) suggesting that small RNAs might be involved in silencing of SINEs in P. infestans. This notion was exploited to develop novel tools for gene silencing in P. infestans by engineering transcriptional fusions of the PiAvr3a gene, encoding an RXLR avirulence effector, to the infSINEm retroelement. Transgenic P. infestans lines expressing either 5'-infSINEm::PiAvr3a-3' or 5'-PiAvr3a::SINEm-3' chimeric transcripts initially exhibited partial silencing of PiAvr3a. Over time, PiAvr3a either recovered wild type transcript levels in some lines, or became fully silenced in others. Introduction of an inverted repeat construct was also successful in yielding P. infestans transgenic lines silenced for PiAvr3a. In contrast, constructs expressing antisense or aberrant RNA transcripts failed to initiate silencing of PiAvr3a. Lines exhibiting the most effective silencing of PiAvr3a were either weakly or non-pathogenic on susceptible potato cv. Bintje. This study expands the repertoire of reverse genetics tools available for P. infestans research, and provides insights into a possible mode of variation in effector expression through spread of silencing from adjacent retroelements. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Nuclear Exclusion of the HIV-1 host defense factor APOBEC3G requires a novel cytoplasmic retention signal and is not dependent on RNA binding.

PubMed

Bennett, Ryan P; Presnyak, Vladimir; Wedekind, Joseph E; Smith, Harold C

2008-03-21

Human APOBEC3G (hA3G) is a host factor that defends against HIV-1 as well as other exogenous retroviruses and endogenous retroelements. To this end, hA3G is restricted to the cytoplasm of T lymphocytes where it interacts with viral RNA and proteins to assemble with viral particles causing a post-entry block during reverse transcription. hA3G also exhibits a mechanism to inhibit the reverse transcription of retroelements by RNA binding and sequestration into mRNA processing centers in the cytoplasm. We have determined that the molecular basis for this specialized property of hA3G is a novel cytoplasmic retention signal (CRS) that is necessary and sufficient to restrict wild-type hA3G and chimeric constructs to the cytoplasm. The CRS resides within amino acids 113-128 and is embedded within a basic flanking sequence and does not require RNA binding to retain hA3G in the cytoplasm. Paralogs of hA3G that have nuclear or cytoplasmic distributions differ from hA3G within the region encompassing the CRS motif with respect to charge and amino acid composition. We propose that the CRS enables hA3G to interact with cytoplasmic factors, and thereby enables hA3G to serve in host cell defense by restricting an antiviral sentinel to the cytoplasm. The CRS lies in a region involved in both Gag and Vif interactions; therefore, identification of this motif has important implications for the design of therapeutics that target HIV-1 while maintaining antiviral and cellular functions.

The Reverse Transcriptase of the Tf1 Retrotransposon Has a Specific Novel Activity for Generating the RNA Self-Primer That Is Functional in cDNA Synthesis▿

PubMed Central

Hizi, Amnon

2008-01-01

The Tf1 retrotransposon of Schizosaccharomyces pombe represents a group of eukaryotic long terminal repeat (LTR) retroelements that, based on their sequences, were predicted to use an RNA self-primer for initiating reverse transcription while synthesizing the negative-sense DNA strand. This feature is substantially different from the one typical to retroviruses and other LTR retrotransposons that all exhibit a tRNA-dependent priming mechanism. Genetic studies have suggested that the self-primer of Tf1 can be generated by a cleavage between the 11th and 12th bases of the Tf1 RNA transcript. The in vitro data presented here show that recombinant Tf1 reverse transcriptase indeed introduces a nick at the end of a duplexed region at the 5′ end of Tf1 genomic RNA, substantiating the prediction that this enzyme is responsible for generating this RNA self-primer. The 3′ end of the primer, generated in this manner, can then be extended upon the addition of deoxynucleoside triphosphates by the DNA polymerase activity of the same enzyme, synthesizing the negative-sense DNA strand. This functional primer must have been generated by the RNase H activity of Tf1 reverse transcriptase, since a mutant enzyme lacking this activity has lost its ability to generate the self-primer. It was also found here that the reverse transcriptases of human immunodeficiency virus type 1 and of murine leukemia virus do not exhibit this specific cleavage activity. In all, it is likely that the observed unique mechanism of self-priming in Tf1 represents an early advantageous form of initiating reverse transcription in LTR retroelements without involving cellular tRNAs. PMID:18753200

The reverse transcriptase of the Tf1 retrotransposon has a specific novel activity for generating the RNA self-primer that is functional in cDNA synthesis.

PubMed

Hizi, Amnon

2008-11-01

The Tf1 retrotransposon of Schizosaccharomyces pombe represents a group of eukaryotic long terminal repeat (LTR) retroelements that, based on their sequences, were predicted to use an RNA self-primer for initiating reverse transcription while synthesizing the negative-sense DNA strand. This feature is substantially different from the one typical to retroviruses and other LTR retrotransposons that all exhibit a tRNA-dependent priming mechanism. Genetic studies have suggested that the self-primer of Tf1 can be generated by a cleavage between the 11th and 12th bases of the Tf1 RNA transcript. The in vitro data presented here show that recombinant Tf1 reverse transcriptase indeed introduces a nick at the end of a duplexed region at the 5' end of Tf1 genomic RNA, substantiating the prediction that this enzyme is responsible for generating this RNA self-primer. The 3' end of the primer, generated in this manner, can then be extended upon the addition of deoxynucleoside triphosphates by the DNA polymerase activity of the same enzyme, synthesizing the negative-sense DNA strand. This functional primer must have been generated by the RNase H activity of Tf1 reverse transcriptase, since a mutant enzyme lacking this activity has lost its ability to generate the self-primer. It was also found here that the reverse transcriptases of human immunodeficiency virus type 1 and of murine leukemia virus do not exhibit this specific cleavage activity. In all, it is likely that the observed unique mechanism of self-priming in Tf1 represents an early advantageous form of initiating reverse transcription in LTR retroelements without involving cellular tRNAs.

Identification of a Retroelement from the Resurrection Plant Boea hygrometrica That Confers Osmotic and Alkaline Tolerance in Arabidopsis thaliana

PubMed Central

Shen, Chun-Ying; Xu, Guang-Hui; Chen, Shi-Xuan; Song, Li-Zhen; Li, Mei-Jing; Wang, Li-Li; Zhu, Yan; Lv, Wei-Tao; Gong, Zhi-Zhong; Liu, Chun-Ming; Deng, Xin

2014-01-01

Functional genomic elements, including transposable elements, small RNAs and non-coding RNAs, are involved in regulation of gene expression in response to plant stress. To identify genomic elements that regulate dehydration and alkaline tolerance in Boea hygrometrica, a resurrection plant that inhabits drought and alkaline Karst areas, a genomic DNA library from B. hygrometrica was constructed and subsequently transformed into Arabidopsis using binary bacterial artificial chromosome (BIBAC) vectors. Transgenic lines were screened under osmotic and alkaline conditions, leading to the identification of Clone L1-4 that conferred osmotic and alkaline tolerance. Sequence analyses revealed that L1-4 contained a 49-kb retroelement fragment from B. hygrometrica, of which only a truncated sequence was present in L1-4 transgenic Arabidopsis plants. Additional subcloning revealed that activity resided in a 2-kb sequence, designated Osmotic and Alkaline Resistance 1 (OAR1). In addition, transgenic Arabidopsis lines carrying an OAR1-homologue also showed similar stress tolerance phenotypes. Physiological and molecular analyses demonstrated that OAR1-transgenic plants exhibited improved photochemical efficiency and membrane integrity and biomarker gene expression under both osmotic and alkaline stresses. Short transcripts that originated from OAR1 were increased under stress conditions in both B. hygrometrica and Arabidopsis carrying OAR1. The relative copy number of OAR1 was stable in transgenic Arabidopsis under stress but increased in B. hygrometrica. Taken together, our results indicated a potential role of OAR1 element in plant tolerance to osmotic and alkaline stresses, and verified the feasibility of the BIBAC transformation technique to identify functional genomic elements from physiological model species. PMID:24851859

Systems Operation Studies for Automated Guideway Transit Systems - Classification and Definition of AGT Systems

DOT National Transportation Integrated Search

1980-02-01

The report describes the development of an AGT classification structure. Five classes are defined based on three system characteristics: service type, minimum travelling unit capacity, and maximum operating velocity. The five classes defined are: Per...

FINAL ECOSYSTEM GOODS AND SERVICES CLASSIFICATION SYSTEM (FEGS-CS)

EPA Science Inventory

This document defines and classifies 338 Final Ecosystem Goods and Services (FEGS), each defined and uniquely numbered by a combination of environmental class or sub-class and a beneficiary category or sub-category. The introductory section provides the rationale and conceptual ...

A Framework for Empirical Discovery.

DTIC Science & Technology

1986-09-24

history of science reveal distinct classes of defined terms. Some systems have focused on one subset of these classes, while other programs have...the operators in detail, presenting examples of each from the history of science . 2.1 Defining Numeric Terms The most obvious operator for defining...laws; they can also simplify the process of discovering such laws. Let us consider some examples from the history of science in which the definition of

Changes from 2000 to 2009 in the Prevalence of HIV-1 Containing Drug Resistance-associated Mutations from Antiretroviral Therapy-naïve, HIV-1-infected Patients in the United States.

PubMed

Ross, Lisa L; Shortino, Denise; Shaefer, Mark S

2018-05-05

Background: Pre-existing HIV drug resistance can jeopardize first-line antiretroviral therapy (ART) success. Changes in the prevalence of drug-resistance-associated mutations (DRMs) were analyzed from HIV-infected, ART-naïve, United States (USA) individuals seeking ART treatment from 2000-2009. Methods: HIV DRM data from 3,829 ART-naïve subjects were analyzed by year of sample collection using International Antiviral Society (IAS-USA) and World Health Organization (WHO) "surveillance" DRM definitions; minor IAS-USA-defined DRMs were excluded. Results: IAS-USA DRM prevalence between 2000-2009 was 14%; beginning with 8% in 2000, 13% in 2009. The greatest incidence was observed in 2007 (17%). Overall, IAS-USA-defined non-nucleoside reverse transcriptase (NNRTI) DRMs were 9.5%; NRTI: 4% and major protease inhibitor (PI):3%. The most frequently detected IAS-USA-defined DRMs by class were NNRTI: K103N/S (4%); NRTI: M41L (1.5%) and PI: L90M (1%). Overall WHO-defined DRM prevalence was 13% (5% in 2000; 13% in 2009). By class, NNRTI prevalence was 6%, NRTI: 6%, and PI: 3.2%. The most frequent WHO-defined DRMs were NRTI: codon T215 (3.0%); NNRTI: K103N/S (4%) and PI: L90M (1%). WHO-defined NNRTI DRMs declined significantly (p=0.0412) from 2007 to 2009. The overall prevalence of HIV-1-containing major IAS-USA or WHO-defined DRMs to ≥2 or ≥3 classes was 2% and <1%, respectively. The prevalence of HIV-1 with WHO-defined dual or triple-class resistance significantly declined (p=0.0461) from 2008 (4%) to 2009 (<1%). Conclusions: In this USA cohort, prevalence of HIV-1 DRMs increased from 2000 onwards, peaked between 2005-2007 and then declined in 2008-2009; the detection of WHO-defined dual or triple-class DRM similarly decreased from 2008 to 2009.

The Changing Pattern of Nutrition Intake by Social Class in Contemporary China, 1991-2011.

PubMed

Xu, Zhun; Zhang, Wei

2017-11-01

To explore the changing pattern of nutrition intake by social class in contemporary China. We defined social class in 2 ways. The first definition was based on employment, and the second definition was based on per capita household income levels. We used China Health and Nutrition Survey data from 1991 to 2011 to show the changes in the relation between social class and nutrition intake. The relation between social class and nutrition intake in China changed significantly within the 2 decades. For example, in the early 1990s, the lowest social class (defined by employment or income) had more caloric intake than did the highest social class; 20 years later, however, the relation reversed, and the lowest social class consumed significantly fewer calories. China has seen a great reversal in its social class-nutrition relationship since the early 1990s. Our study calls for wider recognition that insufficient consumption of food and nutrition is increasingly an issue for people in the lower social classes in China.

Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens

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

Elfenbein, Johanna R.; Knodler, Leigh A.; Nakayasu, Ernesto S.

Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking itsmore » retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.« less

Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

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

Elfenbein, Johanna R.; Knodler, Leigh A.; Nakayasu, Ernesto S.

Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking itsmore » retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.« less

Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

DOE PAGES

Elfenbein, Johanna R.; Knodler, Leigh A.; Nakayasu, Ernesto S.; ...

2015-09-14

Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking itsmore » retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.« less

FY98 Class Convening Schedule for Coast Guard Class

DOT National Transportation Integrated Search

1998-08-12

This Notice publishes the FY98 class convening schedule of Coast Guard Class "A" : and "C" resident and exportable training courses defined by program/force : managers as essential or directly related to mission accomplishment for : achievement of pr...

The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups.

PubMed

Koonin, Eugene V; Wolf, Yuri I; Nagasaki, Keizo; Dolja, Valerian V

2008-12-01

The recent discovery of RNA viruses in diverse unicellular eukaryotes and developments in evolutionary genomics have provided the means for addressing the origin of eukaryotic RNA viruses. The phylogenetic analyses of RNA polymerases and helicases presented in this Analysis article reveal close evolutionary relationships between RNA viruses infecting hosts from the Chromalveolate and Excavate supergroups and distinct families of picorna-like viruses of plants and animals. Thus, diversification of picorna-like viruses probably occurred in a 'Big Bang' concomitant with key events of eukaryogenesis. The origins of the conserved genes of picorna-like viruses are traced to likely ancestors including bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages.

Issues in the classification of disease instances with ontologies.

PubMed

Burgun, Anita; Bodenreider, Olivier; Jacquelinet, Christian

2005-01-01

Ontologies define classes of entities and their interrelations. They are used to organize data according to a theory of the domain. Towards that end, ontologies provide class definitions (i.e., the necessary and sufficient conditions for defining class membership). In medical ontologies, it is often difficult to establish such definitions for diseases. We use three examples (anemia, leukemia and schizophrenia) to illustrate the limitations of ontologies as classification resources. We show that eligibility criteria are often more useful than the Aristotelian definitions traditionally used in ontologies. Examples of eligibility criteria for diseases include complex predicates such as ' x is an instance of the class C when at least n criteria among m are verified' and 'symptoms must last at least one month if not treated, but less than one month, if effectively treated'. References to normality and abnormality are often found in disease definitions, but the operational definition of these references (i.e., the statistical and contextual information necessary to define them) is rarely provided. We conclude that knowledge bases that include probabilistic and statistical knowledge as well as rule-based criteria are more useful than Aristotelian definitions for representing the predicates defined by necessary and sufficient conditions. Rich knowledge bases are needed to clarify the relations between individuals and classes in various studies and applications. However, as ontologies represent relations among classes, they can play a supporting role in disease classification services built primarily on knowledge bases.

Generation of a Maize B Centromere Minimal Map Containing the Central Core Domain.

PubMed

Ellis, Nathanael A; Douglas, Ryan N; Jackson, Caroline E; Birchler, James A; Dawe, R Kelly

2015-10-28

The maize B centromere has been used as a model for centromere epigenetics and as the basis for building artificial chromosomes. However, there are no sequence resources for this important centromere. Here we used transposon display for the centromere-specific retroelement CRM2 to identify a collection of 40 sequence tags that flank CRM2 insertion points on the B chromosome. These were confirmed to lie within the centromere by assaying deletion breakpoints from centromere misdivision derivatives (intracentromere breakages caused by centromere fission). Markers were grouped together on the basis of their association with other markers in the misdivision series and assembled into a pseudocontig containing 10.1 kb of sequence. To identify sequences that interact directly with centromere proteins, we carried out chromatin immunoprecipitation using antibodies to centromeric histone H3 (CENH3), a defining feature of functional centromeric sequences. The CENH3 chromatin immunoprecipitation map was interpreted relative to the known transmission rates of centromere misdivision derivatives to identify a centromere core domain spanning 33 markers. A subset of seven markers was mapped in additional B centromere misdivision derivatives with the use of unique primer pairs. A derivative previously shown to have no canonical centromere sequences (Telo3-3) lacks these core markers. Our results provide a molecular map of the B chromosome centromere and identify key sequences within the map that interact directly with centromeric histone H3. Copyright © 2015 Ellis et al.

The Practice Pattern of Percutaneous Coronary Intervention in Korea: Based on Year 2014 Cohort of Korean Percutaneous Coronary Intervention (K-PCI) Registry.

PubMed

Gwon, Hyeon-Cheol; Jeon, Dong Woon; Kang, Hyun-Jae; Jang, Jae-Sik; Park, Duk-Woo; Shin, Dong-Ho; Moon, Keon-Woong; Kim, Jung-Sun; Kim, Juhan; Bae, Jang-Whan; Hur, Seung-Ho; Kim, Byung Ok; Choi, Donghoon; Han, Kyoo-Rok; Kim, Hyo-Soo

2017-05-01

Appropriate use criteria (AUC) was developed to improve the quality of percutaneous coronary intervention (PCI). However, these criteria should consider the current practice pattern in the country where they are being applied. The algorithm for the Korean PCI practice pattern (KP3) was developed by modifying the United States-derived AUC in expert consensus meetings. KP3 class A was defined as any strategy with evidence from randomized trials that was more conservative for PCI than medical therapy or coronary artery bypass graft (CABG). Class C was defined as any strategy with less evidence from randomized trials and more aggressive for PCI than medical therapy or CABG. Class B was defined as a strategy that was partly class A and partly class C. We applied the KP3 classification system to the Korean PCI registry. The KP3 class A was noted in 67.7% of patients, class B in 28.8%, and class C in 3.5%. The median proportion of class C cases per center was 2.0%. The distribution of KP3 classes varied significantly depending on clinical and angiographic characteristics. The proportion of KP3 class C cases per center was not significantly dependent on PCI volume, but rather on the percentage of ACS cases in each center. We report the current PCI practice pattern by applying the new KP3 classification in a nationwide PCI registry. The results should be interpreted carefully with due regard for the complex relationships between the determining variables and the healthcare system in Korea.

Defining Social Class Across Time and Between Groups.

PubMed

Cohen, Dov; Shin, Faith; Liu, Xi; Ondish, Peter; Kraus, Michael W

2017-11-01

We examined changes over four decades and between ethnic groups in how people define their social class. Changes included the increasing importance of income, decreasing importance of occupational prestige, and the demise of the "Victorian bargain," in which poor people who subscribed to conservative sexual and religious norms could think of themselves as middle class. The period also saw changes (among Whites) and continuity (among Black Americans) in subjective status perceptions. For Whites (and particularly poor Whites), their perceptions of enhanced social class were greatly reduced. Poor Whites now view their social class as slightly but significantly lower than their poor Black and Latino counterparts. For Black respondents, a caste-like understanding of social class persisted, as they continued to view their class standing as relatively independent of their achieved education, income, and occupation. Such achievement indicators, however, predicted Black respondents' self-esteem more than they predicted self-esteem for any other group.

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 4 2014-10-01 2014-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 4 2011-10-01 2011-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 4 2010-10-01 2010-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 4 2012-10-01 2012-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 4 2013-10-01 2013-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

A Generalized Approach to Defining Item Discrimination for DCMs

ERIC Educational Resources Information Center

Henson, Robert; DiBello, Lou; Stout, Bill

2018-01-01

Diagnostic classification models (DCMs, also known as cognitive diagnosis models) hold the promise of providing detailed classroom information about the skills a student has or has not mastered. Specifically, DCMs are special cases of constrained latent class models where classes are defined based on mastery/nonmastery of a set of attributes (or…

Prediction and explanation in the multiverse

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

Garriga, J.; Vilenkin, A.

2008-02-15

Probabilities in the multiverse can be calculated by assuming that we are typical representatives in a given reference class. But is this class well defined? What should be included in the ensemble in which we are supposed to be typical? There is a widespread belief that this question is inherently vague, and that there are various possible choices for the types of reference objects which should be counted in. Here we argue that the 'ideal' reference class (for the purpose of making predictions) can be defined unambiguously in a rather precise way, as the set of all observers with identicalmore » information content. When the observers in a given class perform an experiment, the class branches into subclasses who learn different information from the outcome of that experiment. The probabilities for the different outcomes are defined as the relative numbers of observers in each subclass. For practical purposes, wider reference classes can be used, where we trace over all information which is uncorrelated to the outcome of the experiment, or whose correlation with it is beyond our current understanding. We argue that, once we have gathered all practically available evidence, the optimal strategy for making predictions is to consider ourselves typical in any reference class we belong to, unless we have evidence to the contrary. In the latter case, the class must be correspondingly narrowed.« less

Gender and the Construction of Class.

ERIC Educational Resources Information Center

Acker, Joan

Only by recognizing that class is not gender neutral can the processes of class formation and reproduction be understood. Class is defined as a process in which human beings take an active part, rather than a structure of categories into which individuals may be inserted. Gender organizes or structures class in many different ways. For example,…

The Ia.2 Epitope Defines a Subset of Lipid Raft Resident MHC Class II Molecules Crucial to Effective Antigen Presentation1

PubMed Central

Busman-Sahay, Kathleen; Sargent, Elizabeth; Harton, Jonathan A.; Drake, James R.

2016-01-01

Previous work has established that binding of the 11-5.2 anti-I-Ak mAb, which recognizes the Ia.2 epitope on I-Ak class II molecules, elicits MHC class II signaling, whereas binding of two other anti-I-Ak mAb that recognize the Ia.17 epitope fail to elicit signaling. Using a biochemical approach, we establish that the Ia.2 epitope recognized by the widely used 11-5.2 mAb defines a subset of cell surface I-Ak molecules predominantly found within membrane lipid rafts. Functional studies demonstrate that the Ia.2 bearing subset of I-Ak class II molecules is critically necessary for effective B cell–T cell interactions especially at low antigen doses, a finding consistent with published studies on the role of raft-resident class II molecules in CD4 T cell activation. Interestingly, B cells expressing recombinant I-Ak class II molecules possessing a β chain-tethered HEL peptide lack the Ia.2 epitope and fail to partition into lipid rafts. Moreover, cells expressing Ia.2 negative tethered peptide-class II molecules are severely impaired in their ability to present both tethered peptide or peptide derived from exogenous antigen to CD4 T cells. These results establish the Ia.2 epitope as defining a lipid raft-resident MHC class II confomer vital to the initiation of MHC class II restricted B cell–T cell interactions. PMID:21543648

A trans-Dominant Form of Gag Restricts Ty1 Retrotransposition and Mediates Copy Number Control

PubMed Central

Saha, Agniva; Mitchell, Jessica A.; Nishida, Yuri; Hildreth, Jonathan E.; Ariberre, Joshua A.; Gilbert, Wendy V.

2015-01-01

ABSTRACT Saccharomyces cerevisiae and Saccharomyces paradoxus lack the conserved RNA interference pathway and utilize a novel form of copy number control (CNC) to inhibit Ty1 retrotransposition. Although noncoding transcripts have been implicated in CNC, here we present evidence that a truncated form of the Gag capsid protein (p22) or its processed form (p18) is necessary and sufficient for CNC and likely encoded by Ty1 internal transcripts. Coexpression of p22/p18 and Ty1 decreases mobility more than 30,000-fold. p22/p18 cofractionates with Ty1 virus-like particles (VLPs) and affects VLP yield, protein composition, and morphology. Although p22/p18 and Gag colocalize in the cytoplasm, p22/p18 disrupts sites used for VLP assembly. Glutathione S-transferase (GST) affinity pulldowns also suggest that p18 and Gag interact. Therefore, this intrinsic Gag-like restriction factor confers CNC by interfering with VLP assembly and function and expands the strategies used to limit retroelement propagation. IMPORTANCE Retrotransposons dominate the chromosomal landscape in many eukaryotes, can cause mutations by insertion or genome rearrangement, and are evolutionarily related to retroviruses such as HIV. Thus, understanding factors that limit transposition and retroviral replication is fundamentally important. The present work describes a retrotransposon-encoded restriction protein derived from the capsid gene of the yeast Ty1 element that disrupts virus-like particle assembly in a dose-dependent manner. This form of copy number control acts as a molecular rheostat, allowing high levels of retrotransposition when few Ty1 elements are present and inhibiting transposition as copy number increases. Thus, yeast and Ty1 have coevolved a form of copy number control that is beneficial to both “host and parasite.” To our knowledge, this is the first Gag-like retrotransposon restriction factor described in the literature and expands the ways in which restriction proteins modulate retroelement replication. PMID:25609815

Diversity and relationships of Crocus sativus and its relatives analysed by inter-retroelement amplified polymorphism (IRAP)

PubMed Central

Alsayied, Nouf Fakieh; Fernández, José Antonio; Schwarzacher, Trude; Heslop-Harrison, J. S.

2015-01-01

Background and Aims: Saffron (Crocus sativus) is a sterile triploid (2n = 3x = 24) cultivated species, of unknown origin from other diploid and polyploid species in the genus Crocus (Iridaceae). Species in the genus have high morphological diversity, with no clear phylogenetic patterns below the level of section Crocus series Crocus. Using DNA markers, this study aimed to examine the diversity and relationships within and between species of Crocus series Crocus. Methods: Eleven inter-retroelement amplified polymorphism (IRAP) primers were used in 63 different combinations with 35 single-plant accessions of C. sativus and related Crocus species in order to determine genetic variability and to conduct phylogenetic analysis. Key Results: A total of 4521 distinct polymorphic bands from 100 bp to approx. 4 kb were amplified; no fragment specific to all accessions of a single species was amplified. The polymorphic information content (PIC) values varied from approx. 0·37 to approx. 0·05 (mean 0·17 ± 0·1) and the major allele frequency had a mean of 0·87. High levels of polymorphism were identified between accessions of the six species of Crocus series Crocus related to C. sativus, with further variation between the species. In contrast, no polymorphisms were seen among 17 C. sativus accessions obtained in the region from Kashmir through Iran to Spain. Conclusions In contrast to the intraspecific variability seen in other Crocus species, C. sativus has minimal genetic variation, and it is concluded that the triploid hybrid species has most probably arisen only once. The data show that saffron is an allotriploid species, with the IRAP analysis indicating that the most likely ancestors are C. cartwrightianus and C. pallasii subsp. pallasii (or close relatives). The results may facilitate resynthesizing saffron with improved characteristics, and show the need for conservation and collection of wild Crocus. PMID:26138822

Issues in the Classification of Disease Instances with Ontologies

PubMed Central

Burgun, Anita; Bodenreider, Olivier; Jacquelinet, Christian

2006-01-01

Ontologies define classes of entities and their interrelations. They are used to organize data according to a theory of the domain. Towards that end, ontologies provide class definitions (i.e., the necessary and sufficient conditions for defining class membership). In medical ontologies, it is often difficult to establish such definitions for diseases. We use three examples (anemia, leukemia and schizophrenia) to illustrate the limitations of ontologies as classification resources. We show that eligibility criteria are often more useful than the Aristotelian definitions traditionally used in ontologies. Examples of eligibility criteria for diseases include complex predicates such as ‘ x is an instance of the class C when at least n criteria among m are verified’ and ‘symptoms must last at least one month if not treated, but less than one month, if effectively treated’. References to normality and abnormality are often found in disease definitions, but the operational definition of these references (i.e., the statistical and contextual information necessary to define them) is rarely provided. We conclude that knowledge bases that include probabilistic and statistical knowledge as well as rule-based criteria are more useful than Aristotelian definitions for representing the predicates defined by necessary and sufficient conditions. Rich knowledge bases are needed to clarify the relations between individuals and classes in various studies and applications. However, as ontologies represent relations among classes, they can play a supporting role in disease classification services built primarily on knowledge bases. PMID:16160339

Conceptualizing "Homework" in Flipped Mathematics Classes

ERIC Educational Resources Information Center

de Araujo, Zandra; Otten, Samuel; Birisci, Salih

2017-01-01

Flipped instruction is becoming more common in the United States, particularly in mathematics classes. One of the defining characteristics of this increasingly popular instructional format is the homework teachers assign. In contrast to traditional mathematics classes in which homework consists of problem sets, homework in flipped classes often…

76 FR 68058 - Classes of Poultry

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-03

... characteristics of poultry in the market today. Poultry classes are defined primarily in terms of the age and sex... sex of the bird. \\1\\ Ready-to-cook poultry at 9 CFR 381.1 is defined as any slaughtered poultry free... are female while the definition states that the birds may be of either sex. The comment suggested that...

77 FR 32157 - Self-Regulatory Organizations; NYSE Amex LLC; Notice of Filing of Proposed Rule Change Defining a...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-31

... Specialist in Each Options Class and Modifying the Specialist Entitlement Accordingly May 24, 2012. Pursuant... of Substance of the Proposed Rule Change The Exchange proposes to define a Primary Specialist in each options class and modify the Specialist entitlement accordingly. The text of the proposed rule change is...

Poverty and Depression among Men: The Social Class Worldview Model and Counseling Implications.

ERIC Educational Resources Information Center

Liu, William M.

This paper outlines a theory for understanding social class in men's lives, and argues that poverty and depression are a function of social class and internalized classism. It begins by defining poverty, then explains the Social Class Worldview Model, which is a subjective social class model, and the Modern Classism Theory, which allows clinicians…

Latent Class Analysis of Differential Item Functioning on the Peabody Picture Vocabulary Test-III

ERIC Educational Resources Information Center

Webb, Mi-young Lee; Cohen, Allan S.; Schwanenflugel, Paula J.

2008-01-01

This study investigated the use of latent class analysis for the detection of differences in item functioning on the Peabody Picture Vocabulary Test-Third Edition (PPVT-III). A two-class solution for a latent class model appeared to be defined in part by ability because Class 1 was lower in ability than Class 2 on both the PPVT-III and the…

Coastal change analysis program implemented in Louisiana

USGS Publications Warehouse

Ramsey, Elijah W.; Nelson, G.A.; Sapkota, S.K.

2001-01-01

Landsat Thematic Mapper images from 1990 to 1996 and collateral data sources were used to classify the land cover of the Mermentau River Basin (MRB) within the Chenier Plain of coastal Louisiana. Landcover classes followed the definition of the National Oceanic and Atmospheric Administration's Coastal Change Analysis Program; however, classification methods had to be developed as part of this study for attainment of these national classification standards. Classification method developments were especially important when classes were spectrally inseparable, when classes were part of spatial and spectral continuums, when the spatial resolution of the sensor included more than one landcover type, and when human activities caused abnormal transitions in the landscape. Most classification problems were overcome by using one or a combination of techniques, such as separating the MRB into subregions of commonality, applying masks to specific land mixtures, and highlighting class transitions between years that were highly unlikely. Overall, 1990, 1993, and 1996 classification accuracy percentages (associated kappa statistics) were 80% (0.79), 78% (0.76), and 86% (0.84), respectively. Most classification errors were associated with confusion between managed (cultivated land) and unmanaged grassland classes; scrub shrub, grasslands and forest classes; water, unconsolidated shore and bare land classes; and especially in 1993, between water and floating vegetation classes. Combining cultivated land and grassland classes and water and floating vegetation classes into single classes accuracies for 1990, 1993, and 1996 increased to 82%, 83%, and 90%, respectively. To improve the interpretation of landcover change, three indicators of landcover class stability were formulated. Location stability was defined as the percentage of a landcover class that remained as the same class in the same location at the beginning and the end of the monitoring period. Residence stability was defined as the percent change in each class within the entire MRB during the monitoring period. Turnover was defined as the addition of other landcover classes to the target landcover class during the defined monitoring period. These indicators allowed quick assessment of the dynamic nature of landcover classes, both in reference to a spatial location and to retaining their presence throughout the MRB. Examining the landcover changes between 1990 to 1993 and 1993 to 1996, led us to five principal findings: (1) Landcover turnover is maintaining a near stable logging cycle, although the locations of grassland, scrub shrub, and forest areas involved in the cycle appeared to change. (2) Planting of seedlings is critical to maintaining cycle stability. (3) Logging activities tend to replace woody land mixed forests with woody land evergreen forests. (4) Wetland estuarine marshes are expanding slightly. (5) Wetland palustrine marshes and mature forested wetlands in the MRB are relatively stable.

Bacterial group II introns: not just splicing.

PubMed

Toro, Nicolás; Jiménez-Zurdo, José Ignacio; García-Rodríguez, Fernando Manuel

2007-04-01

Group II introns are both catalytic RNAs (ribozymes) and mobile retroelements that were discovered almost 14 years ago. It has been suggested that eukaryotic mRNA introns might have originated from the group II introns present in the alphaproteobacterial progenitor of the mitochondria. Bacterial group II introns are of considerable interest not only because of their evolutionary significance, but also because they could potentially be used as tools for genetic manipulation in biotechnology and for gene therapy. This review summarizes what is known about the splicing mechanisms and mobility of bacterial group II introns, and describes the recent development of group II intron-based gene-targetting methods. Bacterial group II intron diversity, evolutionary relationships, and behaviour in bacteria are also discussed.

Dynamic cluster generation for a fuzzy classifier with ellipsoidal regions.

PubMed

Abe, S

1998-01-01

In this paper, we discuss a fuzzy classifier with ellipsoidal regions that dynamically generates clusters. First, for the data belonging to a class we define a fuzzy rule with an ellipsoidal region. Namely, using the training data for each class, we calculate the center and the covariance matrix of the ellipsoidal region for the class. Then we tune the fuzzy rules, i.e., the slopes of the membership functions, successively until there is no improvement in the recognition rate of the training data. Then if the number of the data belonging to a class that are misclassified into another class exceeds a prescribed number, we define a new cluster to which those data belong and the associated fuzzy rule. Then we tune the newly defined fuzzy rules in the similar way as stated above, fixing the already obtained fuzzy rules. We iterate generation of clusters and tuning of the newly generated fuzzy rules until the number of the data belonging to a class that are misclassified into another class does not exceed the prescribed number. We evaluate our method using thyroid data, Japanese Hiragana data of vehicle license plates, and blood cell data. By dynamic cluster generation, the generalization ability of the classifier is improved and the recognition rate of the fuzzy classifier for the test data is the best among the neural network classifiers and other fuzzy classifiers if there are no discrete input variables.

Latent classes of resilience and psychological response among only-child loss parents in China.

PubMed

Wang, An-Ni; Zhang, Wen; Zhang, Jing-Ping; Huang, Fei-Fei; Ye, Man; Yao, Shu-Yu; Luo, Yuan-Hui; Li, Zhi-Hua; Zhang, Jie; Su, Pan

2017-10-01

Only-child loss parents in China recently gained extensive attention as a newly defined social group. Resilience could be a probable solution out of the psychological dilemma. Using a sample of 185 only-child loss people, this study employed latent class analysis (a) to explore whether different classes of resilience could be identified, (b) to determine socio-demographic characteristics of each class, and (c) to compare the depression and the subjective well-being of each class. The results supported a three-class solution, defined as 'high tenacity-strength but moderate optimism class', 'moderate resilience but low self-efficacy class' and 'low tenacity but moderate adaption-dependence class'. Parents with low income and medical insurance of low reimbursement type and without endowment insurance occupied more proportions in the latter two classes. The latter two classes also had a significant higher depression scores and lower subjective well-being scores than high tenacity-strength but moderate optimism class. Future work should care those socio-economically vulnerable bereaved parents, and an elastic economic assistance policy was needed. To develop targeted resilience interventions, the emphasis of high tenacity-strength but moderate optimism class should be the optimism. Moderate resilience but low self-efficacy class should be self-efficacy, and low tenacity but moderate adaption-dependence class should be tenacity. Copyright © 2016 John Wiley & Sons, Ltd.

Classification and global distribution of ocean precipitation types based on satellite passive microwave signatures

NASA Astrophysics Data System (ADS)

Gautam, Nitin

The main objectives of this thesis are to develop a robust statistical method for the classification of ocean precipitation based on physical properties to which the SSM/I is sensitive and to examine how these properties vary globally and seasonally. A two step approach is adopted for the classification of oceanic precipitation classes from multispectral SSM/I data: (1)we subjectively define precipitation classes using a priori information about the precipitating system and its possible distinct signature on SSM/I data such as scattering by ice particles aloft in the precipitating cloud, emission by liquid rain water below freezing level, the difference of polarization at 19 GHz-an indirect measure of optical depth, etc.; (2)we then develop an objective classification scheme which is found to reproduce the subjective classification with high accuracy. This hybrid strategy allows us to use the characteristics of the data to define and encode classes and helps retain the physical interpretation of classes. The classification methods based on k-nearest neighbor and neural network are developed to objectively classify six precipitation classes. It is found that the classification method based neural network yields high accuracy for all precipitation classes. An inversion method based on minimum variance approach was used to retrieve gross microphysical properties of these precipitation classes such as column integrated liquid water path, column integrated ice water path, and column integrated min water path. This classification method is then applied to 2 years (1991-92) of SSM/I data to examine and document the seasonal and global distribution of precipitation frequency corresponding to each of these objectively defined six classes. The characteristics of the distribution are found to be consistent with assumptions used in defining these six precipitation classes and also with well known climatological patterns of precipitation regions. The seasonal and global distribution of these six classes is also compared with the earlier results obtained from Comprehensive Ocean Atmosphere Data Sets (COADS). It is found that the gross pattern of the distributions obtained from SSM/I and COADS data match remarkably well with each other.

Characterization of swine leukocyte antigen alleles and haplotypes on a novel miniature pig line, Microminipig.

PubMed

Ando, A; Imaeda, N; Ohshima, S; Miyamoto, A; Kaneko, N; Takasu, M; Shiina, T; Kulski, J K; Inoko, H; Kitagawa, H

2014-12-01

Microminipigs are extremely small-sized, novel miniature pigs that were recently developed for medical research. The inbred Microminipigs with defined swine leukocyte antigen (SLA) haplotypes are expected to be useful for allo- and xenotransplantation studies and also for association analyses between SLA haplotypes and immunological traits. To establish SLA-defined Microminipig lines, we characterized the polymorphic SLA alleles for three class I (SLA-1, SLA-2 and SLA-3) and two class II (SLA-DRB1 and SLA-DQB1) genes of 14 parental Microminipigs using a high-resolution nucleotide sequence-based typing method. Eleven class I and II haplotypes, including three recombinant haplotypes, were found in the offspring of the parental Microminipigs. Two class I and class II haplotypes, Hp-31.0 (SLA-1*1502-SLA-3*070102-SLA-2*1601) and Hp-0.37 (SLA-DRB1*0701-SLA-DQB1*0502), are novel and have not so far been reported in other pig breeds. Crossover regions were defined by the analysis of 22 microsatellite markers within the SLA class III region of three recombinant haplotypes. The SLA allele and haplotype information of Microminipigs in this study will be useful to establish SLA homozygous lines including three recombinants for transplantation and immunological studies. © 2014 Stichting International Foundation for Animal Genetics.

White Middle-Class Privilege: Social Class Bias and Implications for Training and Practice

ERIC Educational Resources Information Center

Liu, William Ming; Pickett, Theodore, Jr.; Ivey, Allen E.

2007-01-01

Social class, classism, and privilege and their relationship to counseling have been given insufficient attention. This article defines and explores White middle-class privilege; it proffers support for its integration in a multicultural competency, as well as its intersection with race and other dimensions of multiculturalism and privilege.…

75 FR 39145 - Amendment of Class C Airspace; Flint, MI

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-08

...-0599; Airspace Docket No. 10-AWA-3] RIN 2120-AA66 Amendment of Class C Airspace; Flint, MI AGENCY... description of the Bishop International Airport, Flint, MI, Class C airspace area by amending the airport... defines the Class C airspace area's center point. The Rule This action amends Title 14 Code of Federal...

The Experiences of Working-Class College Students Who Became University Presidents

ERIC Educational Resources Information Center

Springer, Mary E.

2012-01-01

Working-class students enter college lacking necessary capital to predict their academic and personal success making college success less likely than for middle class students (Bufton, 2003; Mack, 2006; Paulsen & St. John, 2002; Rose, 1997; Wegner, 1973). This same social class origin helps to define experiences, provides context for…

Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae).

PubMed

Begum, Rabeya; Zakrzewski, Falk; Menzel, Gerhard; Weber, Beatrice; Alam, Sheikh Shamimul; Schmidt, Thomas

2013-07-01

The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100-500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S-5·8S-25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species.

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2013 CFR

2013-10-01

.... Class 1 (explosives) must be stowed as far away as practicable from any potential source of heat or... vertically. In addition to this separation, there must be insulation to Class A60 standard as defined in 46...

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2014 CFR

2014-10-01

.... Class 1 (explosives) must be stowed as far away as practicable from any potential source of heat or... vertically. In addition to this separation, there must be insulation to Class A60 standard as defined in 46...

49 CFR 1241.11 - Annual reports of class I railroads.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 9 2010-10-01 2010-10-01 false Annual reports of class I railroads. 1241.11... class I railroads. (a) Commencing with reports for the year ended December 31, 1973, and thereafter, until further order, all line-haul railroad companies of class I, as defined in § 1240.1 of this chapter...

Comparison of Group Cohesion, Class Participation, and Exam Performance in Live and Online Classes

ERIC Educational Resources Information Center

Galyon, Charles E.; Heaton, Eleanore C. T.; Best, Tiffany L.; Williams, Robert L.

2016-01-01

Though class participation and group cohesion have shown some potential to promote student performance in conventional classrooms, their efficacy has not yet been demonstrated in an online-class setting. Group cohesion, defined as member attraction to and self-identification with a group, is thought to promote positive interdependence and the…

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2012 CFR

2012-10-01

... stowage conditions for Class 1 (explosive) materials. (a) Heat and sources of ignition: (1) Class 1... on board. Stowage must be well away from all sources of heat, including steam pipes, heating coils... addition to this separation, there must be insulation to Class A60 standard as defined in 46 CFR 72.05-10(a...

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2011 CFR

2011-10-01

... stowage conditions for Class 1 (explosive) materials. (a) Heat and sources of ignition: (1) Class 1... on board. Stowage must be well away from all sources of heat, including steam pipes, heating coils... addition to this separation, there must be insulation to Class A60 standard as defined in 46 CFR 72.05-10(a...

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2010 CFR

2010-10-01

... stowage conditions for Class 1 (explosive) materials. (a) Heat and sources of ignition: (1) Class 1... on board. Stowage must be well away from all sources of heat, including steam pipes, heating coils... addition to this separation, there must be insulation to Class A60 standard as defined in 46 CFR 72.05-10(a...

Working-Class Women's Ways of Knowing: Effects of Gender, Race and Class.

ERIC Educational Resources Information Center

Luttrell, Wendy

1989-01-01

Analyzes the way black and white working-class women define and claim knowledge, challenging feminist analyses that have identified a single or universal mode of knowing for women. Contends that women speak to complex gender, racial, and class relations of power that shape how they think about learning and knowing. (Author/SLM)

Preparation guide for class B software specification documents

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1979-01-01

General conceptual requirements and specific application rules and procedures are provided for the production of software specification documents in conformance with deep space network software standards and class B standards. Class B documentation is identified as the appropriate level applicable to implementation, sustaining engineering, and operational uses by qualified personnel. Special characteristics of class B documents are defined.

Genetic Dissection of the Human Leukocyte Antigen Region by Use of Haplotypes of Tasmanians with Multiple Sclerosis

PubMed Central

Rubio, Justin P.; Bahlo, Melanie; Butzkueven, Helmut; van der Mei, Ingrid A. F.; Sale, Michèle M.; Dickinson, Joanne L.; Groom, Patricia; Johnson, Laura J.; Simmons, Rex D.; Tait, Brian; Varney, Mike; Taylor, Bruce; Dwyer, Terence; Williamson, Robert; Gough, Nicholas M.; Kilpatrick, Trevor J.; Speed, Terence P.; Foote, Simon J.

2002-01-01

Association of multiple sclerosis (MS) with the human leukocyte antigen (HLA) class II haplotype DRB1*1501-DQB1*0602 is the most consistently replicated finding of genetic studies of the disease. However, the high level of linkage disequilibrium (LD) in the HLA region has hindered the identification of other loci that single-marker tests for association are unlikely to resolve. In order to address this issue, we generated haplotypes spanning 14.754 Mb (5 cM) across the entire HLA region. The haplotypes, which were inferred by genotyping relatives of 152 patients with MS and 105 unaffected control subjects of Tasmanian ancestry, define a genomic segment from D6S276 to D6S291, including 13 microsatellite markers integrated with allele-typing data for DRB1 and DQB1. Association to the DRB1*1501-DQB1*0602 haplotype was replicated. In addition, we found that the class I/extended class I region, defined by a genomic segment of ∼400 kb between MOGCA and D6S265, harbors genes that independently increase risk of, or provide protection from, MS. Log-linear modeling analysis of constituent haplotypes that represent genomic regions containing class I (MOGCA-D6S265), class III (TNFa-TNFd-D6S273), and class II (DRB1-DQB1) genes indicated that having class I and class II susceptibility variants on the same haplotype provides an additive effect on risk. Moreover, we found no evidence for a disease locus in the class III region defined by a 150-kb genomic segment containing the TNF locus and 14 other genes. A global overview of LD performed using GOLD identified two discrete blocks of LD in the HLA region that correspond well with previous findings. We propose that the analysis of haplotypes, by use of the types of approaches outlined in the present article, should make it possible to more accurately define the contribution of the HLA to MS. PMID:11923913

CRISPR-mediated HDAC2 disruption identifies two distinct classes of target genes in human cells.

PubMed

Somanath, Priyanka; Herndon Klein, Rachel; Knoepfler, Paul S

2017-01-01

The transcriptional functions of the class I histone deacetylases (HDACs) HDAC1 and HDAC2 are mainly viewed as both repressive and redundant based on murine knockout studies, but they may have additional independent roles and their physiological functions in human cells are not as clearly defined. To address the individual epigenomic functions of HDAC2, here we utilized CRISPR-Cas9 to disrupt HDAC2 in human cells. We find that while HDAC2 null cells exhibited signs of cross-regulation between HDAC1 and HDAC2, specific epigenomic phenotypes were still apparent using RNA-seq and ChIP assays. We identified specific targets of HDAC2 repression, and defined a novel class of genes that are actively expressed in a partially HDAC2-dependent manner. While HDAC2 was required for the recruitment of HDAC1 to repressed HDAC2-gene targets, HDAC2 was dispensable for HDAC1 binding to HDAC2-activated targets, supporting the notion of distinct classes of targets. Both active and repressed classes of gene targets demonstrated enhanced histone acetylation and methylation in HDAC2-null cells. Binding of the HDAC1/2-associated SIN3A corepressor was altered at most HDAC2-targets, but without a clear pattern. Overall, our study defines two classes of HDAC2 targets in human cells, with a dependence of HDAC1 on HDAC2 at one class of targets, and distinguishes unique functions for HDAC2.

Characterization and classification of zebrafish brain morphology mutants

PubMed Central

Lowery, Laura Anne; De Rienzo, Gianluca; Gutzman, Jennifer H.; Sive, Hazel

2010-01-01

The mechanisms by which the vertebrate brain achieves its three-dimensional structure are clearly complex, requiring the functions of many genes. Using the zebrafish as a model, we have begun to define genes required for brain morphogenesis, including brain ventricle formation, by studying 16 mutants previously identified as having embryonic brain morphology defects. We report the phenotypic characterization of these mutants at several time-points, using brain ventricle dye injection, imaging, and immunohistochemistry with neuronal markers. Most of these mutants display early phenotypes, affecting initial brain shaping, while others show later phenotypes, affecting brain ventricle expansion. In the early phenotype group, we further define four phenotypic classes and corresponding functions required for brain morphogenesis. Although we did not use known genotypes for this classification, basing it solely on phenotypes, many mutants with defects in functionally related genes clustered in a single class. In particular, class 1 mutants show midline separation defects, corresponding to epithelial junction defects; class 2 mutants show reduced brain ventricle size; class 3 mutants show midbrain-hindbrain abnormalities, corresponding to basement membrane defects; and class 4 mutants show absence of ventricle lumen inflation, corresponding to defective ion pumping. Later brain ventricle expansion requires the extracellular matrix, cardiovascular circulation, and transcription/splicing-dependent events. We suggest that these mutants define processes likely to be used during brain morphogenesis throughout the vertebrates. PMID:19051268

49 CFR 232.207 - Class IA brake tests-1,000-mile inspection.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Class IA brake tests-1,000-mile inspection. 232... Class IA brake tests—1,000-mile inspection. (a) Except as provided in § 232.213, each train shall receive a Class IA brake test performed by a qualified person, as defined in § 232.5, at a location that...

49 CFR 232.207 - Class IA brake tests-1,000-mile inspection.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Class IA brake tests-1,000-mile inspection. 232... Class IA brake tests—1,000-mile inspection. (a) Except as provided in § 232.213, each train shall receive a Class IA brake test performed by a qualified person, as defined in § 232.5, at a location that...

Design of partially supervised classifiers for multispectral image data

NASA Technical Reports Server (NTRS)

Jeon, Byeungwoo; Landgrebe, David

1993-01-01

A partially supervised classification problem is addressed, especially when the class definition and corresponding training samples are provided a priori only for just one particular class. In practical applications of pattern classification techniques, a frequently observed characteristic is the heavy, often nearly impossible requirements on representative prior statistical class characteristics of all classes in a given data set. Considering the effort in both time and man-power required to have a well-defined, exhaustive list of classes with a corresponding representative set of training samples, this 'partially' supervised capability would be very desirable, assuming adequate classifier performance can be obtained. Two different classification algorithms are developed to achieve simplicity in classifier design by reducing the requirement of prior statistical information without sacrificing significant classifying capability. The first one is based on optimal significance testing, where the optimal acceptance probability is estimated directly from the data set. In the second approach, the partially supervised classification is considered as a problem of unsupervised clustering with initially one known cluster or class. A weighted unsupervised clustering procedure is developed to automatically define other classes and estimate their class statistics. The operational simplicity thus realized should make these partially supervised classification schemes very viable tools in pattern classification.

An iterative approach to optimize change classification in SAR time series data

NASA Astrophysics Data System (ADS)

Boldt, Markus; Thiele, Antje; Schulz, Karsten; Hinz, Stefan

2016-10-01

The detection of changes using remote sensing imagery has become a broad field of research with many approaches for many different applications. Besides the simple detection of changes between at least two images acquired at different times, analyses which aim on the change type or category are at least equally important. In this study, an approach for a semi-automatic classification of change segments is presented. A sparse dataset is considered to ensure the fast and simple applicability for practical issues. The dataset is given by 15 high resolution (HR) TerraSAR-X (TSX) amplitude images acquired over a time period of one year (11/2013 to 11/2014). The scenery contains the airport of Stuttgart (GER) and its surroundings, including urban, rural, and suburban areas. Time series imagery offers the advantage of analyzing the change frequency of selected areas. In this study, the focus is set on the analysis of small-sized high frequently changing regions like parking areas, construction sites and collecting points consisting of high activity (HA) change objects. For each HA change object, suitable features are extracted and a k-means clustering is applied as the categorization step. Resulting clusters are finally compared to a previously introduced knowledge-based class catalogue, which is modified until an optimal class description results. In other words, the subjective understanding of the scenery semantics is optimized by the data given reality. Doing so, an even sparsely dataset containing only amplitude imagery can be evaluated without requiring comprehensive training datasets. Falsely defined classes might be rejected. Furthermore, classes which were defined too coarsely might be divided into sub-classes. Consequently, classes which were initially defined too narrowly might be merged. An optimal classification results when the combination of previously defined key indicators (e.g., number of clusters per class) reaches an optimum.

Genomic relationship between SINE retrotransposons, Pol III–Pol II transcription, and chromatin organization: the journey from junk to jewel

PubMed Central

Lunyak, Victoria V.; Atallah, Michelle

2013-01-01

A typical eukaryotic genome harbors a rich variety of repetitive elements. The most abundant are retrotransposons, mobile retroelements that utilize reverse transcriptase and an RNA intermediate to relocate to a new location within the cellular genomes. A vast majority of the repetitive mammalian genome content has originated from the retrotransposition of SINE (100–300 bp short interspersed nuclear elements that are derived from the structural 7SL RNA or tRNA), LINE (7kb long interspersed nuclear element), and LTR (2–3 kb long terminal repeats) transposable element superfamilies. Broadly labeled as “evolutionary junkyard” or “fossils”, this enigmatic “dark matter” of the genome possesses many yet to be discovered properties. PMID:21916613

48 CFR 211.275-2 - Policy.

Code of Federal Regulations, 2010 CFR

2010-10-01

... that— (1) Contain items in any of the following classes of supply, as defined in DoD 4140.1-R, DoD Supply Chain Materiel Management Regulation, AP1.1.11: (i) Subclass of Class I—Packaged operational... administrative and housekeeping supplies and equipment. (iii) Class IIIP—Packaged petroleum, lubricants, oils...

Measurement and Structural Model Class Separation in Mixture CFA: ML/EM versus MCMC

ERIC Educational Resources Information Center

Depaoli, Sarah

2012-01-01

Parameter recovery was assessed within mixture confirmatory factor analysis across multiple estimator conditions under different simulated levels of mixture class separation. Mixture class separation was defined in the measurement model (through factor loadings) and the structural model (through factor variances). Maximum likelihood (ML) via the…

Review Guidelines for Software Languages for use in Nuclear Power Plant Safety Systems

DTIC Science & Technology

1997-10-01

desirable to segregate base classes from derived classes. Review is facilitated and safety is enhanced if project-specific guidance is provided on the... Segregate base from derived classes. In C++, it is desirable to segregate base classes from derived classes. 4.4.1.8 Minimizing Use of Literals...memory utilization. At the lowest level are base attributes, i.e., attributes xv NUREG/CR-6463 Rev. 1 sufficiently specific to define guidelines. An

Thematic accuracy of the National Land Cover Database (NLCD) 2001 land cover for Alaska

USGS Publications Warehouse

Selkowitz, D.J.; Stehman, S.V.

2011-01-01

The National Land Cover Database (NLCD) 2001 Alaska land cover classification is the first 30-m resolution land cover product available covering the entire state of Alaska. The accuracy assessment of the NLCD 2001 Alaska land cover classification employed a geographically stratified three-stage sampling design to select the reference sample of pixels. Reference land cover class labels were determined via fixed wing aircraft, as the high resolution imagery used for determining the reference land cover classification in the conterminous U.S. was not available for most of Alaska. Overall thematic accuracy for the Alaska NLCD was 76.2% (s.e. 2.8%) at Level II (12 classes evaluated) and 83.9% (s.e. 2.1%) at Level I (6 classes evaluated) when agreement was defined as a match between the map class and either the primary or alternate reference class label. When agreement was defined as a match between the map class and primary reference label only, overall accuracy was 59.4% at Level II and 69.3% at Level I. The majority of classification errors occurred at Level I of the classification hierarchy (i.e., misclassifications were generally to a different Level I class, not to a Level II class within the same Level I class). Classification accuracy was higher for more abundant land cover classes and for pixels located in the interior of homogeneous land cover patches. ?? 2011.

The utility of rat jejunal permeability for biopharmaceutics classification system.

PubMed

Zakeri-Milani, Parvin; Valizadeh, Hadi; Tajerzadeh, Hosnieh; Islambulchilar, Ziba

2009-12-01

The biopharmaceutical classification system has been developed to provide a scientific approach for classifying drug compounds based on their dose/solubility ratio and human intestinal permeability. Therefore in this study a new classification is presented, which is based on a correlation between rat and human intestinal permeability values. In situ technique in rat jejunum was used to determine the effective intestinal permeability of tested drugs. Then three dimensionless parameters--dose number, absorption number, and dissolution number (D(o), A(n), and D(n))--were calculated for each drug. Four classes of drugs were defined, that is, class I, D(0) < 0.5, P(eff(rat)) > 5.09 x 10(-5) cm/s; class II, D(o) > 1, P(eff(rat)) > 5.09 x 10( -5) cm/s; class III, D(0) < 0.5, P(eff(rat)) < 4.2 x 10(-5) cm/s; and class IV, D(o) > 1, P(eff(rat)) < 4.2 x 10(-5) cm/s. A region of borderline drugs (0.5 < D(o) < 1, 4.2 x 10(-5) < P(eff(rat)) < 5.09 x 10(-5) cm/s) was also defined. According to obtained results and proposed classification for drugs, it is concluded that drugs could be categorized correctly based on dose number and their intestinal permeability values in rat model using single-pass intestinal perfusion technique. This classification enables us to remark defined characteristics for intestinal absorption of all four classes using suitable cutoff points for both dose number and rat effective intestinal permeability values.

CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission

PubMed Central

Novikova, Olga; Śliwińska, Ewa; Fet, Victor; Settele, Josef; Blinov, Alexander; Woyciechowski, Michal

2007-01-01

Background Non-long terminal repeat (non-LTR) retrotransposons are mobile genetic elements that propagate themselves by reverse transcription of an RNA intermediate. Non-LTR retrotransposons are known to evolve mainly via vertical transmission and random loss. Horizontal transmission is believed to be a very rare event in non-LTR retrotransposons. Our knowledge of distribution and diversity of insect non-LTR retrotransposons is limited to a few species – mainly model organisms such as dipteran genera Drosophila, Anopheles, and Aedes. However, diversity of non-LTR retroelements in arthropods seems to be much richer. The present study extends the analysis of non-LTR retroelements to CR1 clade from four butterfly species of genus Maculinea (Lepidoptera: Lycaenidae). The lycaenid genus Maculinea, the object of interest for evolutionary biologists and also a model group for European biodiversity studies, possesses a unique, specialized myrmecophilous lifestyle at larval stage. Their caterpillars, after three weeks of phytophagous life on specific food plants drop to the ground where they are adopted to the ant nest by Myrmica foraging workers. Results We found that the genome of Maculinea butterflies contains multiple CR1 lineages of non-LTR retrotransposons, including those from MacCR1A, MacCR1B and T1Q families. A comparative analysis of RT nucleotide sequences demonstrated an extremely high similarity among elements both in interspecific and intraspecific comparisons. CR1A-like elements were found only in family Lycaenidae. In contrast, MacCR1B lineage clones were extremely similar to CR1B non-LTR retrotransposons from Bombycidae moths: silkworm Bombyx mori and Oberthueria caeca. Conclusion The degree of coding sequence similarity of the studied elements, their discontinuous distribution, and results of divergence-versus-age analysis make it highly unlikely that these sequences diverged at the same time as their host taxa. The only reasonable alternative explanation is horizontal transfer. In addition, phylogenetic markers for population analysis of Maculinea could be developed based on the described non-LTR retrotransposons. PMID:17588269

14 CFR 93.350 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... AND GENERAL OPERATING RULES SPECIAL AIR TRAFFIC RULES New York Class B Airspace Hudson River and East... Exclusion, as defined in paragraph (d) of this section, from one end to the other. (c) New York Class B... the LGA VOR/DME 6-mile arc to the north tip of Roosevelt Island. (d) New York Class B airspace Hudson...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2012 CFR

2012-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2010 CFR

2010-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2014 CFR

2014-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2011 CFR

2011-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2013 CFR

2013-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

Risk Classification and Risk-based Safety and Mission Assurance

NASA Technical Reports Server (NTRS)

Leitner, Jesse A.

2014-01-01

Recent activities to revamp and emphasize the need to streamline processes and activities for Class D missions across the agency have led to various interpretations of Class D, including the lumping of a variety of low-cost projects into Class D. Sometimes terms such as Class D minus are used. In this presentation, mission risk classifications will be traced to official requirements and definitions as a measure to ensure that projects and programs align with the guidance and requirements that are commensurate for their defined risk posture. As part of this, the full suite of risk classifications, formal and informal will be defined, followed by an introduction to the new GPR 8705.4 that is currently under review.GPR 8705.4 lays out guidance for the mission success activities performed at the Classes A-D for NPR 7120.5 projects as well as for projects not under NPR 7120.5. Furthermore, the trends in stepping from Class A into higher risk posture classifications will be discussed. The talk will conclude with a discussion about risk-based safety and mission assuranceat GSFC.

Ligand Recognition by A-Class Eph Receptors: Crystal Structures of the EphA2 Ligand-Binding Domain and the EphA2/ephrin-A1 Complex

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

Himanen, J.; Goldgur, Y; Miao, H

2009-01-01

Ephrin (Eph) receptor tyrosine kinases fall into two subclasses (A and B) according to preferences for their ephrin ligands. All published structural studies of Eph receptor/ephrin complexes involve B-class receptors. Here, we present the crystal structures of an A-class complex between EphA2 and ephrin-A1 and of unbound EphA2. Although these structures are similar overall to their B-class counterparts, they reveal important differences that define subclass specificity. The structures suggest that the A-class Eph receptor/ephrin interactions involve smaller rearrangements in the interacting partners, better described by a 'lock-and-key'-type binding mechanism, in contrast to the 'induced fit' mechanism defining the B-class molecules.more » This model is supported by structure-based mutagenesis and by differential requirements for ligand oligomerization by the two subclasses in cell-based Eph receptor activation assays. Finally, the structure of the unligated receptor reveals a homodimer assembly that might represent EphA2-specific homotypic cell adhesion interactions.« less

Logical definability and asymptotic growth in optimization and counting problems

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

Compton, K.

1994-12-31

There has recently been a great deal of interest in the relationship between logical definability and NP-optimization problems. Let MS{sub n} (resp. MP{sub n}) be the class of problems to compute, for given a finite structure A, the maximum number of tuples {bar x} in A satisfying a {Sigma}{sub n} (resp. II{sub n}) formula {psi}({bar x}, {bar S}) as {bar S} ranges over predicates on A. Kolaitis and Thakur showed that the classes MS{sub n} and MP{sub n} collapse to a hierarchy of four levels. Papadimitriou and Yannakakis previously showed that problems in the two lowest levels MS{sub 0} andmore » MS{sub 1} (which they called Max Snp and Max Np) are approximable to within a contrast factor in polynomial time. Similarly, Saluja, Subrahmanyam, and Thakur defined SS{sub n} (resp. SP{sub n}) to be the class of problems to compute, for given a finite structure A, the number of tuples ({bar T}, {bar S}) satisfying a given {Sigma}{sub n} (resp. II{sub n}) formula {psi}({bar T}, {bar c}) in A. They showed that the classes SS{sub n} and SP{sub n} collapse to a hierarchy of five levels and that problems in the two lowest levels SS{sub 0} and SS{sub 1} have a fully polynomial time randomized approximation scheme. We define extended classes MSF{sub n}, MPF{sub n} SSF{sub n}, and SPF{sub n} by allowing formulae to contain predicates definable in a logic known as least fixpoint logic. The resulting hierarchies classes collapse to the same number of levels and problems in the bottom levels can be approximated as before, but now some problems descend from the highest levels in the original hierarchies to the lowest levels in the new hierarchies. We introduce a method characterizing rates of growth of average solution sizes thereby showing a number of important problems do not belong MSF{sub 1} and SSF{sub 1}. This method is related to limit laws for logics and the probabilistic method from combinatorics.« less

Enhanced equivalence class formation by the delay and relational functions of meaningful stimuli.

PubMed

Arntzen, Erik; Nartey, Richard K; Fields, Lanny

2015-05-01

Undergraduates in six groups of 10 attempted to form three 3-node 5-member equivalence classes (A → B → C → D → E) under the simultaneous protocol. In five of six groups, all stimuli were abstract shapes; in the PIC group, C stimuli were pictures with the remainder being abstract shapes. Before class formation, participants in the Identity-S and Identity-D groups were given preliminary training to form identity conditional discriminations with the C stimuli using simultaneous and 6 s delayed matching-to-sample procedures, respectively. In the Arbitrary-S and Arbitrary-D groups, before class formation, arbitrary conditional discriminations were formed between C and X stimuli using simultaneous and 6 s delayed matching-to-sample procedures, respectively. With no preliminary training, classes in the PIC and ABS groups were formed by 80% and 0% of participants, respectively. After preliminary training, class formation (yield) increased with delay, regardless of relational type. For each of the two delays, yield was slightly greater after forming arbitrary- instead of identity-relations. Yield was greatest, however, when a class contained a meaningful stimulus (PIC). During failed class formation, probes produced experimenter-defined relations, participant-defined relations, and unsystematic responding; delay, but not the relation type in preliminary training influenced relational and indeterminate responding. These results suggest how meaningful stimuli enhance equivalence class formation. © Society for the Experimental Analysis of Behavior.

How do older adult drivers self-regulate? Characteristics of self-regulation classes defined by latent class analysis.

PubMed

Bergen, Gwen; West, Bethany A; Luo, Feijun; Bird, Donna C; Freund, Katherine; Fortinsky, Richard H; Staplin, Loren

2017-06-01

Motor-vehicle crashes were the second leading cause of injury death for adults aged 65-84years in 2014. Some older drivers choose to self-regulate their driving to maintain mobility while reducing driving risk, yet the process remains poorly understood. Data from 729 older adults (aged ≥60years) who joined an older adult ride service program between April 1, 2010 and November 8, 2013 were analyzed to define and describe classes of driving self-regulation. Latent class analysis was employed to characterize older adult driving self-regulation classes using driving frequency and avoidance of seven driving situations. Logistic regression was used to explore associations between characteristics affecting mobility and self-regulation class. Three classes were identified (low, medium, and high self-regulation). High self-regulating participants reported the highest proportion of always avoiding seven risky driving situations and the lowest driving frequency followed by medium and low self-regulators. Those who were female, aged 80years or older, visually impaired, assistive device users, and those with special health needs were more likely to be high self-regulating compared with low self-regulating. Avoidance of certain driving situations and weekly driving frequency are valid indicators for describing driving self-regulation classes in older adults. Understanding the unique characteristics and mobility limitations of each class can guide optimal transportation strategies for older adults. Published by Elsevier Ltd.

Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

PubMed Central

2011-01-01

Background A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects. Results The venom gland transcriptomes of 8 Costa Rican taxa from 5 genera (Crotalus, Bothrops, Atropoides, Cerrophidion, and Bothriechis) of pitvipers were investigated using high-throughput 454 pyrosequencing. 100,394 out of 330,010 masked reads produced significant hits in the available databases. 5.165,220 nucleotides (8.27%) were masked by RepeatMasker, the vast majority of which corresponding to class I (retroelements) and class II (DNA transposons) mobile elements. BLAST hits included 79,991 matches to entries of the taxonomic suborder Serpentes, of which 62,433 displayed similarity to documented venom proteins. Strong discrepancies between the transcriptome-computed and the proteome-gathered toxin compositions were obvious at first sight. Although the reasons underlaying this discrepancy are elusive, since no clear trend within or between species is apparent, the data indicate that individual mRNA species may be translationally controlled in a species-dependent manner. The minimum number of genes from each toxin family transcribed into the venom gland transcriptome of each species was calculated from multiple alignments of reads matched to a full-length reference sequence of each toxin family. Reads encoding ORF regions of Kazal-type inhibitor-like proteins were uniquely found in Bothriechis schlegelii and B. lateralis transcriptomes, suggesting a genus-specific recruitment event during the early-Middle Miocene. A transcriptome-based cladogram supports the large divergence between A. mexicanus and A. picadoi, and a closer kinship between A. mexicanus and C. godmani. Conclusions Our comparative next-generation sequencing (NGS) analysis reveals taxon-specific trends governing the formulation of the venom arsenal. Knowledge of the venom proteome provides hints on the translation efficiency of toxin-coding transcripts, contributing thereby to a more accurate interpretation of the transcriptome. The application of NGS to the analysis of snake venom transcriptomes, may represent the tool for opening the door to systems venomics. PMID:21605378

42 CFR 83.14 - How will NIOSH evaluate a petition by a claimant whose dose reconstruction NIOSH could not...

Code of Federal Regulations, 2011 CFR

2011-10-01

... RESEARCH AND RELATED ACTIVITIES PROCEDURES FOR DESIGNATING CLASSES OF EMPLOYEES AS MEMBERS OF THE SPECIAL... classes for evaluation, to permit the timely adjudication of the existing cancer claim: (1) A class of employees defined using the research and analyses already completed in attempting the dose reconstruction...

42 CFR 83.14 - How will NIOSH evaluate a petition by a claimant whose dose reconstruction NIOSH could not...

Code of Federal Regulations, 2012 CFR

2012-10-01

... RESEARCH AND RELATED ACTIVITIES PROCEDURES FOR DESIGNATING CLASSES OF EMPLOYEES AS MEMBERS OF THE SPECIAL... classes for evaluation, to permit the timely adjudication of the existing cancer claim: (1) A class of employees defined using the research and analyses already completed in attempting the dose reconstruction...

42 CFR 83.14 - How will NIOSH evaluate a petition by a claimant whose dose reconstruction NIOSH could not...

Code of Federal Regulations, 2014 CFR

2014-10-01

... RESEARCH AND RELATED ACTIVITIES PROCEDURES FOR DESIGNATING CLASSES OF EMPLOYEES AS MEMBERS OF THE SPECIAL... classes for evaluation, to permit the timely adjudication of the existing cancer claim: (1) A class of employees defined using the research and analyses already completed in attempting the dose reconstruction...

42 CFR 83.14 - How will NIOSH evaluate a petition by a claimant whose dose reconstruction NIOSH could not...

Code of Federal Regulations, 2010 CFR

2010-10-01

... RESEARCH AND RELATED ACTIVITIES PROCEDURES FOR DESIGNATING CLASSES OF EMPLOYEES AS MEMBERS OF THE SPECIAL... classes for evaluation, to permit the timely adjudication of the existing cancer claim: (1) A class of employees defined using the research and analyses already completed in attempting the dose reconstruction...

42 CFR 83.14 - How will NIOSH evaluate a petition by a claimant whose dose reconstruction NIOSH could not...

Code of Federal Regulations, 2013 CFR

2013-10-01

... RESEARCH AND RELATED ACTIVITIES PROCEDURES FOR DESIGNATING CLASSES OF EMPLOYEES AS MEMBERS OF THE SPECIAL... classes for evaluation, to permit the timely adjudication of the existing cancer claim: (1) A class of employees defined using the research and analyses already completed in attempting the dose reconstruction...

Review Sessions and Results: Competency Testing in the Capstone Business Class

ERIC Educational Resources Information Center

Parente, Diane H.; Brown, Randy C.; Warner, Alfred G.

2005-01-01

Capstone is defined in the dictionary as "putting the final stone in place." Business Policy or Strategic Management is typically the capstone class in a business management degree program. As such, there are prerequisite requirements in terms of courses and specific knowledge. We have implemented a competency test for the capstone class and…

40 CFR 60.3078 - What definitions must I know?

Code of Federal Regulations, 2014 CFR

2014-07-01

... connected by road to a Class I municipal solid waste landfill, as defined by Alaska regulatory code 18 AAC 60.300(c) or, if connected by road, is located more than 50 miles from a Class I municipal solid... solid waste landfill is a landfill that is not connected by road to a Class I municipal solid waste...

40 CFR 60.3078 - What definitions must I know?

Code of Federal Regulations, 2012 CFR

2012-07-01

... connected by road to a Class I municipal solid waste landfill, as defined by Alaska regulatory code 18 AAC 60.300(c) or, if connected by road, is located more than 50 miles from a Class I municipal solid... solid waste landfill is a landfill that is not connected by road to a Class I municipal solid waste...

40 CFR 60.3078 - What definitions must I know?

Code of Federal Regulations, 2013 CFR

2013-07-01

... connected by road to a Class I municipal solid waste landfill, as defined by Alaska regulatory code 18 AAC 60.300(c) or, if connected by road, is located more than 50 miles from a Class I municipal solid... solid waste landfill is a landfill that is not connected by road to a Class I municipal solid waste...

40 CFR 60.2977 - What definitions must I know?

Code of Federal Regulations, 2014 CFR

2014-07-01

... groundwater pollution caused or contributed to by the landfill; (3) Is not connected by road to a Class I... road, is located more than 50 miles from a Class I municipal solid waste landfill; and (4) Serves a... landfill that is not connected by road to a Class I municipal solid waste landfill, as defined by Alaska...

40 CFR 60.2977 - What definitions must I know?

Code of Federal Regulations, 2013 CFR

2013-07-01

... groundwater pollution caused or contributed to by the landfill; (3) Is not connected by road to a Class I... road, is located more than 50 miles from a Class I municipal solid waste landfill; and (4) Serves a... landfill that is not connected by road to a Class I municipal solid waste landfill, as defined by Alaska...

Prognostic Classification Factors Associated With Development of Multiple Autoantibodies, Dysglycemia, and Type 1 Diabetes—A Recursive Partitioning Analysis

PubMed Central

Krischer, Jeffrey P.

2016-01-01

OBJECTIVE To define prognostic classification factors associated with the progression from single to multiple autoantibodies, multiple autoantibodies to dysglycemia, and dysglycemia to type 1 diabetes onset in relatives of individuals with type 1 diabetes. RESEARCH DESIGN AND METHODS Three distinct cohorts of subjects from the Type 1 Diabetes TrialNet Pathway to Prevention Study were investigated separately. A recursive partitioning analysis (RPA) was used to determine the risk classes. Clinical characteristics, including genotype, antibody titers, and metabolic markers were analyzed. RESULTS Age and GAD65 autoantibody (GAD65Ab) titers defined three risk classes for progression from single to multiple autoantibodies. The 5-year risk was 11% for those subjects >16 years of age with low GAD65Ab titers, 29% for those ≤16 years of age with low GAD65Ab titers, and 45% for those subjects with high GAD65Ab titers regardless of age. Progression to dysglycemia was associated with islet antigen 2 Ab titers, and 2-h glucose and fasting C-peptide levels. The 5-year risk is 28%, 39%, and 51% for respective risk classes defined by the three predictors. Progression to type 1 diabetes was associated with the number of positive autoantibodies, peak C-peptide level, HbA1c level, and age. Four risk classes defined by RPA had a 5-year risk of 9%, 33%, 62%, and 80%, respectively. CONCLUSIONS The use of RPA offered a new classification approach that could predict the timing of transitions from one preclinical stage to the next in the development of type 1 diabetes. Using these RPA classes, new prevention techniques can be tailored based on the individual prognostic risk characteristics at different preclinical stages. PMID:27208341

A fail-safe CMOS logic gate

NASA Technical Reports Server (NTRS)

Bobin, V.; Whitaker, S.

1990-01-01

This paper reports a design technique to make Complex CMOS Gates fail-safe for a class of faults. Two classes of faults are defined. The fail-safe design presented has limited fault-tolerance capability. Multiple faults are also covered.

Wildlife management by habitat units: A preliminary plan of action

NASA Technical Reports Server (NTRS)

Frentress, C. D.; Frye, R. G.

1975-01-01

Procedures for yielding vegetation type maps were developed using LANDSAT data and a computer assisted classification analysis (LARSYS) to assist in managing populations of wildlife species by defined area units. Ground cover in Travis County, Texas was classified on two occasions using a modified version of the unsupervised approach to classification. The first classification produced a total of 17 classes. Examination revealed that further grouping was justified. A second analysis produced 10 classes which were displayed on printouts which were later color-coded. The final classification was 82 percent accurate. While the classification map appeared to satisfactorily depict the existing vegetation, two classes were determined to contain significant error. The major sources of error could have been eliminated by stratifying cluster sites more closely among previously mapped soil associations that are identified with particular plant associations and by precisely defining class nomenclature using established criteria early in the analysis.

Nucleoside reverse transcriptase inhibitors possess intrinsic anti-inflammatory activity

PubMed Central

Fowler, Benjamin J.; Gelfand, Bradley D.; Kim, Younghee; Kerur, Nagaraj; Tarallo, Valeria; Hirano, Yoshio; Amarnath, Shoba; Fowler, Daniel H.; Radwan, Marta; Young, Mark T.; Pittman, Keir; Kubes, Paul; Agarwal, Hitesh K.; Parang, Keykavous A.; Hinton, David R.; Bastos-Carvalho, Ana; Li, Shengjian; Yasuma, Tetsuhiro; Mizutani, Takeshi; Yasuma, Reo; Wright, Charles; Ambati, Jayakrishna

2014-01-01

Nucleoside reverse transcriptase inhibitors (NRTIs) are mainstay therapeutics for HIV that block retrovirus replication. Alu (an endogenous retroelement that also requires reverse transcriptase for its life cycle)-derived RNAs activate P2X7 and the NLRP3 inflammasome to cause cell death of the retinal pigment epithelium (RPE) in geographic atrophy, a type of age-related macular degeneration. We found that NRTIs inhibit P2X7-mediated NLRP3 inflammasome activation independent of reverse transcriptase inhibition. Multiple approved and clinically relevant NRTIs prevented caspase-1 activation, the effector of the NLRP3 inflammasome, induced by Alu RNA. NRTIs were efficacious in mouse models of geographic atrophy, choroidal neovascularization, graft-versus-host disease (GVHD), and sterile liver inflammation. Our findings suggest that NRTIs are ripe for drug repurposing in P2X7-driven diseases. PMID:25414314

Characteristic classes of gauge systems

NASA Astrophysics Data System (ADS)

Lyakhovich, S. L.; Sharapov, A. A.

2004-12-01

We define and study invariants which can be uniformly constructed for any gauge system. By a gauge system we understand an (anti-)Poisson supermanifold provided with an odd Hamiltonian self-commuting vector field called a homological vector field. This definition encompasses all the cases usually included into the notion of a gauge theory in physics as well as some other similar (but different) structures like Lie or Courant algebroids. For Lagrangian gauge theories or Hamiltonian first class constrained systems, the homological vector field is identified with the classical BRST transformation operator. We define characteristic classes of a gauge system as universal cohomology classes of the homological vector field, which are uniformly constructed in terms of this vector field itself. Not striving to exhaustively classify all the characteristic classes in this work, we compute those invariants which are built up in terms of the first derivatives of the homological vector field. We also consider the cohomological operations in the space of all the characteristic classes. In particular, we show that the (anti-)Poisson bracket becomes trivial when applied to the space of all the characteristic classes, instead the latter space can be endowed with another Lie bracket operation. Making use of this Lie bracket one can generate new characteristic classes involving higher derivatives of the homological vector field. The simplest characteristic classes are illustrated by the examples relating them to anomalies in the traditional BV or BFV-BRST theory and to characteristic classes of (singular) foliations.

Cr-pyrope garnets in the lithospheric mantle 2. Compositional populations and their distribution in time and space

NASA Astrophysics Data System (ADS)

Griffin, W. L.; Fisher, N. I.; Friedman, J. H.; O'Reilly, Suzanne Y.; Ryan, C. G.

2002-12-01

Three novel statistical approaches (Cluster Analysis by Regressive Partitioning [CARP], Patient Rule Induction Method [PRIM], and ModeMap) have been used to define compositional populations within a large database (n > 13,000) of Cr-pyrope garnets from the subcontinental lithospheric mantle (SCLM). The variables used are the major oxides and proton-microprobe data for Zn, Ga, Sr, Y, and Zr. Because the rules defining these populations (classes) are expressed in simple compositional variables, they are easily applied to new samples and other databases. The classes defined by the three methods show strong similarities and correlations, suggesting that they are statistically meaningful. The geological significance of the classes has been tested by classifying garnets from 184 mantle-derived peridotite xenoliths and from a smaller database (n > 5400) of garnets analyzed for >20 trace elements by laser ablation microprobe-inductively coupled plasma-mass spectrometry (LAM-ICPMS). The relative abundances of these classes in the lithospheric mantle vary widely across different tectonic settings, and some classes are absent or very rare in either Archean or Phanerozoic SCLM. Their distribution with depth also varies widely within individual lithospheric sections and between different sections of similar tectonothermal age. These garnet classes therefore are a useful tool for mapping the geology of the SCLM. Archean SCLM sections show high degrees of depletion and varying degrees of metasomatism, and they are commonly strongly layered. Several Proterozoic SCLM sections show a concentration of more depleted material near their base, grading upward into more fertile lherzolites. The distribution of garnet classes reflecting low-T phlogopite-related metasomatism and high-T melt-related metasomatism suggests that many of these Proterozoic SCLM sections consist of strongly metasomatized Archean SCLM. The garnet-facies SCLM beneath Phanerozoic terrains is only mildly depleted relative to Primitive Upper Mantle (PUM) compositions. These data emphasize the secular evolution of SCLM composition defined earlier [Griffin et al., 1998, 1999a] and suggest that at least part of this evolutionary trend reflects reworking and refertilization of SCLM formed in the Archean time.

7 CFR 28.40 - Terms defined; cotton classification.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 2 2012-01-01 2012-01-01 false Terms defined; cotton classification. 28.40 Section 28... REGULATIONS COTTON CLASSING, TESTING, AND STANDARDS Regulations Under the United States Cotton Standards Act Classification § 28.40 Terms defined; cotton classification. For the purposes of classification of any cotton or...

7 CFR 28.40 - Terms defined; cotton classification.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Terms defined; cotton classification. 28.40 Section 28... REGULATIONS COTTON CLASSING, TESTING, AND STANDARDS Regulations Under the United States Cotton Standards Act Classification § 28.40 Terms defined; cotton classification. For the purposes of classification of any cotton or...

7 CFR 28.40 - Terms defined; cotton classification.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Terms defined; cotton classification. 28.40 Section 28... REGULATIONS COTTON CLASSING, TESTING, AND STANDARDS Regulations Under the United States Cotton Standards Act Classification § 28.40 Terms defined; cotton classification. For the purposes of classification of any cotton or...

7 CFR 28.40 - Terms defined; cotton classification.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 2 2013-01-01 2013-01-01 false Terms defined; cotton classification. 28.40 Section 28... REGULATIONS COTTON CLASSING, TESTING, AND STANDARDS Regulations Under the United States Cotton Standards Act Classification § 28.40 Terms defined; cotton classification. For the purposes of classification of any cotton or...

7 CFR 28.40 - Terms defined; cotton classification.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 2 2014-01-01 2014-01-01 false Terms defined; cotton classification. 28.40 Section 28... REGULATIONS COTTON CLASSING, TESTING, AND STANDARDS Regulations Under the United States Cotton Standards Act Classification § 28.40 Terms defined; cotton classification. For the purposes of classification of any cotton or...

Modular control of glutamatergic neuronal identity in C.elegans by distinct homeodomain proteins

PubMed Central

Serrano-Saiz, Esther; Poole, Richard J.; Felton, Terry; Zhang, Feifan; De La Cruz, Estanisla Daniel; Hobert, Oliver

2013-01-01

The choice of using one of many possible neurotransmitter systems is a critical step in defining the identity of an individual neuron type. We show here that the key defining feature of glutamatergic neurons, the vesicular glutamate transporter EAT-4/VGLUT is expressed in 38 of the 118 anatomically defined neuron classes of the C.elegans nervous system. We show that eat-4/VGLUT expression is controlled in a modular manner, with distinct cis-regulatory modules driving expression in distinct glutamatergic neuron classes. We identify 13 different transcription factors, 11 of them homeodomain proteins, that act in specific combinations in 25 different glutamatergic neuron classes to initiate and maintain eat-4/VGLUT expression. We show that the adoption of a glutamatergic phenotype is linked to the adoption of other terminal identity features of a neuron, including cotransmitter phenotypes. Examination of mouse orthologs of these homeodomain proteins resulted in the identification of mouse LHX1 as a regulator of glutamatergic neurons in the brainstem. PMID:24243022

Defining of the BDX930 Assembly Language

NASA Technical Reports Server (NTRS)

Boyer, R. S.; Moore, J. S.

1983-01-01

A definition of the BDX930 assembly language is presented. Various definition problems and suggested solutions are included. A class of defined recognizers based on boolean valued nowrecursive functions is employed in preprocessing.

Social power and social class: conceptualization, consequences, and current challenges.

PubMed

Rucker, Derek D; Galinsky, Adam D

2017-12-01

This article offers a primer on social power and social class with respect to their theoretical importance, conceptual distinction, and empirical relationship. We introduce and define the constructs of social power, social class, and one's psychological sense of power. We next explore the complex relationship between social power and social class. Because social class can produce a sense of power within an individual, studies on social power can inform theory and research on social class. We conclude with a discussion of the current challenges and future opportunities for the study of social power and social class. Copyright © 2017 Elsevier Ltd. All rights reserved.

Heroic Models.

ERIC Educational Resources Information Center

Levine, Toni L.

1986-01-01

Describes a class project for which students discussed their conception of a hero, defined a hero in an essay, researched a specific person they felt was a hero, and finally, gave an oral presentation to the class acting out the character of their hero. (SRT)

Gene-Based Multiclass Cancer Diagnosis with Class-Selective Rejections

PubMed Central

Jrad, Nisrine; Grall-Maës, Edith; Beauseroy, Pierre

2009-01-01

Supervised learning of microarray data is receiving much attention in recent years. Multiclass cancer diagnosis, based on selected gene profiles, are used as adjunct of clinical diagnosis. However, supervised diagnosis may hinder patient care, add expense or confound a result. To avoid this misleading, a multiclass cancer diagnosis with class-selective rejection is proposed. It rejects some patients from one, some, or all classes in order to ensure a higher reliability while reducing time and expense costs. Moreover, this classifier takes into account asymmetric penalties dependant on each class and on each wrong or partially correct decision. It is based on ν-1-SVM coupled with its regularization path and minimizes a general loss function defined in the class-selective rejection scheme. The state of art multiclass algorithms can be considered as a particular case of the proposed algorithm where the number of decisions is given by the classes and the loss function is defined by the Bayesian risk. Two experiments are carried out in the Bayesian and the class selective rejection frameworks. Five genes selected datasets are used to assess the performance of the proposed method. Results are discussed and accuracies are compared with those computed by the Naive Bayes, Nearest Neighbor, Linear Perceptron, Multilayer Perceptron, and Support Vector Machines classifiers. PMID:19584932

40 CFR 60.2977 - What definitions must I know?

Code of Federal Regulations, 2012 CFR

2012-07-01

...) Is not connected by road to a Class I municipal solid waste landfill, as defined by Alaska regulatory code 18 AAC 60.300(c) or, if connected by road, is located more than 50 miles from a Class I municipal... municipal solid waste landfill is a landfill that is not connected by road to a Class I municipal solid...

Illinois | Solar Research | NREL

Science.gov Websites

-interest financing from the Illinois Finance Authority. Customer generators interested in selling solar Illinois Commerce Commission (ICC) defines competitive and noncompetitive customer classes in the IOU service territories for net metering purposes. The noncompetitive customer class includes nonresidential

Responsibility for proving and defining in abstract algebra class

NASA Astrophysics Data System (ADS)

Fukawa-Connelly, Timothy

2016-07-01

There is considerable variety in inquiry-oriented instruction, but what is common is that students assume roles in mathematical activity that in a traditional, lecture-based class are either assumed by the teacher (or text) or are not visible at all in traditional math classrooms. This paper is a case study of the teaching of an inquiry-based undergraduate abstract algebra course. In particular, gives a theoretical account of the defining and proving processes. The study examines the intellectual responsibility for the processes of defining and proving that the professor devolved to the students. While the professor wanted the students to engage in all aspects of defining and proving, he was only successful at devolving responsibility for certain aspects and much more successful at devolving responsibility for proving than conjecturing or defining. This study suggests that even a well-intentioned instructor may not be able to devolve responsibility to students for some aspects of mathematical practice without using a research-based curriculum or further professional development.

Characteristic classes of Q-manifolds: Classification and applications

NASA Astrophysics Data System (ADS)

Lyakhovich, S. L.; Mosman, E. A.; Sharapov, A. A.

2010-05-01

A Q-manifold M is a supermanifold endowed with an odd vector field Q squaring to zero. The Lie derivative LQ along Q makes the algebra of smooth tensor fields on M into a differential algebra. In this paper, we define and study the invariants of Q-manifolds called characteristic classes. These take values in the cohomology of the operator LQ and, given an affine symmetric connection with curvature R, can be represented by universal tensor polynomials in the repeated covariant derivatives of Q and R up to some finite order. As usual, the characteristic classes are proved to be independent of the choice of the affine connection used to define them. The main result of the paper is a complete classification of the intrinsic characteristic classes, which, by definition, do not vanish identically on flat Q-manifolds. As an illustration of the general theory we interpret some of the intrinsic characteristic classes as anomalies in the BV and BFV-BRST quantization methods of gauge theories. An application to the theory of (singular) foliations is also discussed.

Traces of Teaching Methods in a Language Class and the Relationship between Teachers' Intended Learning Outcomes and Students' Uptake

ERIC Educational Resources Information Center

Mahmoudabadi, Zahra

2017-01-01

This study has two main objectives: first, to find traces of teaching methods in a language class and second, to study the relationship between intended learning outcomes and uptake, which is defined as what students claim to have learned. In order to identify the teaching method, after five sessions of observation, class activities and procedures…

The Study of Adopting Problem Based Learning in Normal Scale Class Course Design

ERIC Educational Resources Information Center

Hsu, Chia-ling

2014-01-01

This study adopts the Problem Based Learning (PBL) for pre-service teachers in teacher education program. The reasons to adopt PBL are the class scale is not a small class, the contents are too many to teach, and the technologies are ready to be used in classroom. This study used an intermediary, movie, for scenario to student to define the…

Downward Mobility from the Middle Class: Waking up from the American Dream

ERIC Educational Resources Information Center

Acs, Gregory

2011-01-01

Using data from the National Longitudinal Survey of Youth, this report finds that a middle-class upbringing does not guarantee the same status over the course of a lifetime. One third of Americans raised in the middle class, defined here as those between the 30th and 70th percentiles of the income distribution, fall out of the middle as adults.…

47 CFR 73.215 - Contour protection for short-spaced assignments.

Code of Federal Regulations, 2014 CFR

2014-10-01

... station pursuant to 47 CFR 73.211(b)(3): 6 kW ERP/240 meters HAAT—Class A 25 kW ERP/150 meters HAAT—Class... 47 Telecommunication 4 2014-10-01 2014-10-01 false Contour protection for short-spaced assignments... protected contours, for the purpose of this section, are defined as follows. For all Class B and B1 stations...

Development of guidelines for the definition of the relavant information content in data classes

NASA Technical Reports Server (NTRS)

Schmitt, E.

1973-01-01

The problem of experiment design is defined as an information system consisting of information source, measurement unit, environmental disturbances, data handling and storage, and the mathematical analysis and usage of data. Based on today's concept of effective computability, general guidelines for the definition of the relevant information content in data classes are derived. The lack of a universally applicable information theory and corresponding mathematical or system structure is restricting the solvable problem classes to a small set. It is expected that a new relativity theory of information, generally described by a universal algebra of relations will lead to new mathematical models and system structures capable of modeling any well defined practical problem isomorphic to an equivalence relation at any corresponding level of abstractness.

Latent transition models with latent class predictors: attention deficit hyperactivity disorder subtypes and high school marijuana use

PubMed Central

Reboussin, Beth A.; Ialongo, Nicholas S.

2011-01-01

Summary Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder which is most often diagnosed in childhood with symptoms often persisting into adulthood. Elevated rates of substance use disorders have been evidenced among those with ADHD, but recent research focusing on the relationship between subtypes of ADHD and specific drugs is inconsistent. We propose a latent transition model (LTM) to guide our understanding of how drug use progresses, in particular marijuana use, while accounting for the measurement error that is often found in self-reported substance use data. We extend the LTM to include a latent class predictor to represent empirically derived ADHD subtypes that do not rely on meeting specific diagnostic criteria. We begin by fitting two separate latent class analysis (LCA) models by using second-order estimating equations: a longitudinal LCA model to define stages of marijuana use, and a cross-sectional LCA model to define ADHD subtypes. The LTM model parameters describing the probability of transitioning between the LCA-defined stages of marijuana use and the influence of the LCA-defined ADHD subtypes on these transition rates are then estimated by using a set of first-order estimating equations given the LCA parameter estimates. A robust estimate of the LTM parameter variance that accounts for the variation due to the estimation of the two sets of LCA parameters is proposed. Solving three sets of estimating equations enables us to determine the underlying latent class structures independently of the model for the transition rates and simplifying assumptions about the correlation structure at each stage reduces the computational complexity. PMID:21461139

Predicted MHC peptide binding promiscuity explains MHC class I 'hotspots' of antigen presentation defined by mass spectrometry eluted ligand data.

PubMed

Jappe, Emma Christine; Kringelum, Jens; Trolle, Thomas; Nielsen, Morten

2018-02-15

Peptides that bind to and are presented by MHC class I and class II molecules collectively make up the immunopeptidome. In the context of vaccine development, an understanding of the immunopeptidome is essential, and much effort has been dedicated to its accurate and cost-effective identification. Current state-of-the-art methods mainly comprise in silico tools for predicting MHC binding, which is strongly correlated with peptide immunogenicity. However, only a small proportion of the peptides that bind to MHC molecules are, in fact, immunogenic, and substantial work has been dedicated to uncovering additional determinants of peptide immunogenicity. In this context, and in light of recent advancements in mass spectrometry (MS), the existence of immunological hotspots has been given new life, inciting the hypothesis that hotspots are associated with MHC class I peptide immunogenicity. We here introduce a precise terminology for defining these hotspots and carry out a systematic analysis of MS and in silico predicted hotspots. We find that hotspots defined from MS data are largely captured by peptide binding predictions, enabling their replication in silico. This leads us to conclude that hotspots, to a great degree, are simply a result of promiscuous HLA binding, which disproves the hypothesis that the identification of hotspots provides novel information in the context of immunogenic peptide prediction. Furthermore, our analyses demonstrate that the signal of ligand processing, although present in the MS data, has very low predictive power to discriminate between MS and in silico defined hotspots. © 2018 John Wiley & Sons Ltd.

Academic Socialization: Mentoring New Honors Students in Metadiscourse

ERIC Educational Resources Information Center

Bedetti, Gabriella

2017-01-01

Discussion-based classes are a defining characteristic of honors curricula (National Collegiate Honors Council). Of the 177 institutions to describe their curriculum in the "Official Online Guide to Honors Colleges and Programs," 50% promote their classes as "discussion" or "discussion-based." The descriptions include…

Integrating Creativity into Online University Classes

ERIC Educational Resources Information Center

Muirhead, Brent

2007-01-01

In this article, the author provides a concise discussion on creativity, defining the term, sharing theoretical background information and offering insights into promoting creativity in online university classes. Emphasis will be placed on relevant ways to integrate creativity into instructional activities across the academic disciplines. He…

Producing "Confident" Children: Negotiating Childhood in Fijian Kindergartens

ERIC Educational Resources Information Center

Brison, Karen J.

2011-01-01

Kindergartens in Fiji contribute to incipient class-based identities in a society traditionally structured by ethnicity. Teachers emphasize making children confident, but define confidence differently with varying student groups, building class-based orientations toward person and society. Parental expectations also differ with many upwardly…

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.

PubMed

Kelley, Joanna L; Peyton, Justin T; Fiston-Lavier, Anna-Sophie; Teets, Nicholas M; Yee, Muh-Ching; Johnston, J Spencer; Bustamante, Carlos D; Lee, Richard E; Denlinger, David L

2014-08-12

The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment.

Structure of a group II intron in complex with its reverse transcriptase.

PubMed

Qu, Guosheng; Kaushal, Prem Singh; Wang, Jia; Shigematsu, Hideki; Piazza, Carol Lyn; Agrawal, Rajendra Kumar; Belfort, Marlene; Wang, Hong-Wei

2016-06-01

Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns and eukaryotic retrotransposons. They self-splice, yielding mature RNA, and integrate into DNA as retroelements. A fully active group II intron forms a ribonucleoprotein complex comprising the intron ribozyme and an intron-encoded protein that performs multiple activities including reverse transcription, in which intron RNA is copied into the DNA target. Here we report cryo-EM structures of an endogenously spliced Lactococcus lactis group IIA intron in its ribonucleoprotein complex form at 3.8-Å resolution and in its protein-depleted form at 4.5-Å resolution, revealing functional coordination of the intron RNA with the protein. Remarkably, the protein structure reveals a close relationship between the reverse transcriptase catalytic domain and telomerase, whereas the active splicing center resembles the spliceosomal Prp8 protein. These extraordinary similarities hint at intricate ancestral relationships and provide new insights into splicing and retromobility.

Localization of a bacterial group II intron-encoded protein in human cells.

PubMed

Reinoso-Colacio, Mercedes; García-Rodríguez, Fernando Manuel; García-Cañadas, Marta; Amador-Cubero, Suyapa; García Pérez, José Luis; Toro, Nicolás

2015-08-05

Group II introns are mobile retroelements that self-splice from precursor RNAs to form ribonucleoparticles (RNP), which can invade new specific genomic DNA sites. This specificity can be reprogrammed, for insertion into any desired DNA site, making these introns useful tools for bacterial genetic engineering. However, previous studies have suggested that these elements may function inefficiently in eukaryotes. We investigated the subcellular distribution, in cultured human cells, of the protein encoded by the group II intron RmInt1 (IEP) and several mutants. We created fusions with yellow fluorescent protein (YFP) and with a FLAG epitope. We found that the IEP was localized in the nucleus and nucleolus of the cells. Remarkably, it also accumulated at the periphery of the nuclear matrix. We were also able to identify spliced lariat intron RNA, which co-immunoprecipitated with the IEP, suggesting that functional RmInt1 RNPs can be assembled in cultured human cells.

Localization of a bacterial group II intron-encoded protein in human cells

PubMed Central

Reinoso-Colacio, Mercedes; García-Rodríguez, Fernando Manuel; García-Cañadas, Marta; Amador-Cubero, Suyapa; Pérez, José Luis García; Toro, Nicolás

2015-01-01

Group II introns are mobile retroelements that self-splice from precursor RNAs to form ribonucleoparticles (RNP), which can invade new specific genomic DNA sites. This specificity can be reprogrammed, for insertion into any desired DNA site, making these introns useful tools for bacterial genetic engineering. However, previous studies have suggested that these elements may function inefficiently in eukaryotes. We investigated the subcellular distribution, in cultured human cells, of the protein encoded by the group II intron RmInt1 (IEP) and several mutants. We created fusions with yellow fluorescent protein (YFP) and with a FLAG epitope. We found that the IEP was localized in the nucleus and nucleolus of the cells. Remarkably, it also accumulated at the periphery of the nuclear matrix. We were also able to identify spliced lariat intron RNA, which co-immunoprecipitated with the IEP, suggesting that functional RmInt1 RNPs can be assembled in cultured human cells. PMID:26244523

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

PubMed Central

Kelley, Joanna L.; Peyton, Justin T.; Fiston-Lavier, Anna-Sophie; Teets, Nicholas M.; Yee, Muh-Ching; Johnston, J. Spencer; Bustamante, Carlos D.; Lee, Richard E.; Denlinger, David L.

2014-01-01

The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment. PMID:25118180

Analytic complexity of functions of two variables

NASA Astrophysics Data System (ADS)

Beloshapka, V. K.

2007-09-01

The definition of analytic complexity of an analytic function of two variables is given. It is proved that the class of functions of a chosen complexity is a differentialalgebraic set. A differential polynomial defining the functions of first class is constructed. An algorithm for obtaining relations defining an arbitrary class is described. Examples of functions are given whose order of complexity is equal to zero, one, two, and infinity. It is shown that the formal order of complexity of the Cardano and Ferrari formulas is significantly higher than their analytic complexity. The complexity classes turn out to be invariant with respect to a certain infinite-dimensional transformation pseudogroup. In this connection, we describe the orbits of the action of this pseudogroup in the jets of orders one, two, and three. The notion of complexity order is extended to plane (or “planar”) 3-webs. It is discovered that webs of complexity order one are the hexagonal webs. Some problems are posed.

A Comparison of Geographic Information Systems, Complex Networks, and Other Models for Analyzing Transportation Network Topologies

NASA Technical Reports Server (NTRS)

Alexandrov, Natalia (Technical Monitor); Kuby, Michael; Tierney, Sean; Roberts, Tyler; Upchurch, Christopher

2005-01-01

This report reviews six classes of models that are used for studying transportation network topologies. The report is motivated by two main questions. First, what can the "new science" of complex networks (scale-free, small-world networks) contribute to our understanding of transport network structure, compared to more traditional methods? Second, how can geographic information systems (GIS) contribute to studying transport networks? The report defines terms that can be used to classify different kinds of models by their function, composition, mechanism, spatial and temporal dimensions, certainty, linearity, and resolution. Six broad classes of models for analyzing transport network topologies are then explored: GIS; static graph theory; complex networks; mathematical programming; simulation; and agent-based modeling. Each class of models is defined and classified according to the attributes introduced earlier. The paper identifies some typical types of research questions about network structure that have been addressed by each class of model in the literature.

Nottingham Prognostic Index Plus (NPI+): a modern clinical decision making tool in breast cancer.

PubMed

Rakha, E A; Soria, D; Green, A R; Lemetre, C; Powe, D G; Nolan, C C; Garibaldi, J M; Ball, G; Ellis, I O

2014-04-02

Current management of breast cancer (BC) relies on risk stratification based on well-defined clinicopathologic factors. Global gene expression profiling studies have demonstrated that BC comprises distinct molecular classes with clinical relevance. In this study, we hypothesised that molecular features of BC are a key driver of tumour behaviour and when coupled with a novel and bespoke application of established clinicopathologic prognostic variables can predict both clinical outcome and relevant therapeutic options more accurately than existing methods. In the current study, a comprehensive panel of biomarkers with relevance to BC was applied to a large and well-characterised series of BC, using immunohistochemistry and different multivariate clustering techniques, to identify the key molecular classes. Subsequently, each class was further stratified using a set of well-defined prognostic clinicopathologic variables. These variables were combined in formulae to prognostically stratify different molecular classes, collectively known as the Nottingham Prognostic Index Plus (NPI+). The NPI+ was then used to predict outcome in the different molecular classes. Seven core molecular classes were identified using a selective panel of 10 biomarkers. Incorporation of clinicopathologic variables in a second-stage analysis resulted in identification of distinct prognostic groups within each molecular class (NPI+). Outcome analysis showed that using the bespoke NPI formulae for each biological BC class provides improved patient outcome stratification superior to the traditional NPI. This study provides proof-of-principle evidence for the use of NPI+ in supporting improved individualised clinical decision making.

Assimilation Time as a Factor of Performance: Impact on a New Generation of Students

ERIC Educational Resources Information Center

Mohrweis, Lawrence C.; Pitt, Kay C.

2010-01-01

This paper explores the issue of whether assimilation time has any bearing on the performance of students. Assimilation time is defined as the number of times during the week that a class meets. This study examined whether students would perform better in a 50-minute class that met three days a week versus a 75-minute class that met just two days…

What kinds of things are psychiatric disorders?

PubMed

Kendler, K S; Zachar, P; Craver, C

2011-06-01

This essay explores four answers to the question 'What kinds of things are psychiatric disorders?' Essentialist kinds are classes whose members share an essence from which their defining features arise. Although elegant and appropriate for some physical (e.g. atomic elements) and medical (e.g. Mendelian disorders) phenomena, this model is inappropriate for psychiatric disorders, which are multi-factorial and 'fuzzy'. Socially constructed kinds are classes whose members are defined by the cultural context in which they arise. This model excludes the importance of shared physiological mechanisms by which the same disorder could be identified across different cultures. Advocates of practical kinds put off metaphysical questions about 'reality' and focus on defining classes that are useful. Practical kinds models for psychiatric disorders, implicit in the DSM nosologies, do not require that diagnoses be grounded in shared causal processes. If psychiatry seeks to tie disorders to etiology and underlying mechanisms, a model first proposed for biological species, mechanistic property cluster (MPC) kinds, can provide a useful framework. MPC kinds are defined not in terms of essences but in terms of complex, mutually reinforcing networks of causal mechanisms. We argue that psychiatric disorders are objectively grounded features of the causal structure of the mind/brain. MPC kinds are fuzzy sets defined by mechanisms at multiple levels that act and interact to produce the key features of the kind. Like species, psychiatric disorders are populations with central paradigmatic and more marginal members. The MPC view is the best current answer to 'What kinds of things are psychiatric disorders?'

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

Buttler, D J

The Java Metadata Facility is introduced by Java Specification Request (JSR) 175 [1], and incorporated into the Java language specification [2] in version 1.5 of the language. The specification allows annotations on Java program elements: classes, interfaces, methods, and fields. Annotations give programmers a uniform way to add metadata to program elements that can be used by code checkers, code generators, or other compile-time or runtime components. Annotations are defined by annotation types. These are defined the same way as interfaces, but with the symbol {at} preceding the interface keyword. There are additional restrictions on defining annotation types: (1) Theymore » cannot be generic; (2) They cannot extend other annotation types or interfaces; (3) Methods cannot have any parameters; (4) Methods cannot have type parameters; (5) Methods cannot throw exceptions; and (6) The return type of methods of an annotation type must be a primitive, a String, a Class, an annotation type, or an array, where the type of the array is restricted to one of the four allowed types. See [2] for additional restrictions and syntax. The methods of an annotation type define the elements that may be used to parameterize the annotation in code. Annotation types may have default values for any of its elements. For example, an annotation that specifies a defect report could initialize an element defining the defect outcome submitted. Annotations may also have zero elements. This could be used to indicate serializability for a class (as opposed to the current Serializability interface).« less

Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae)

PubMed Central

Begum, Rabeya; Zakrzewski, Falk; Menzel, Gerhard; Weber, Beatrice; Alam, Sheikh Shamimul; Schmidt, Thomas

2013-01-01

Background and Aims The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. Methods A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100–500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. Key Results Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S–5·8S–25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. Conclusions The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species. PMID:23666888

Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses.

PubMed

Pritham, Ellen J; Putliwala, Tasneem; Feschotte, Cédric

2007-04-01

We previously identified a group of atypical mobile elements designated Mavericks from the nematodes Caenorhabditis elegans and C. briggsae and the zebrafish Danio rerio. Here we present the results of comprehensive database searches of the genome sequences available, which reveal that Mavericks are widespread in invertebrates and non-mammalian vertebrates but show a patchy distribution in non-animal species, being present in the fungi Glomus intraradices and Phakopsora pachyrhizi and in several single-celled eukaryotes such as the ciliate Tetrahymena thermophila, the stramenopile Phytophthora infestans and the trichomonad Trichomonas vaginalis, but not detectable in plants. This distribution, together with comparative and phylogenetic analyses of Maverick-encoded proteins, is suggestive of an ancient origin of these elements in eukaryotes followed by lineage-specific losses and/or recurrent episodes of horizontal transmission. In addition, we report that Maverick elements have amplified recently to high copy numbers in T. vaginalis where they now occupy as much as 30% of the genome. Sequence analysis confirms that most Mavericks encode a retroviral-like integrase, but lack other open reading frames typically found in retroelements. Nevertheless, the length and conservation of the target site duplication created upon Maverick insertion (5- or 6-bp) is consistent with a role of the integrase-like protein in the integration of a double-stranded DNA transposition intermediate. Mavericks also display long terminal-inverted repeats but do not contain ORFs similar to proteins encoded by DNA transposons. Instead, Mavericks encode a conserved set of 5 to 9 genes (in addition to the integrase) that are predicted to encode proteins with homology to replication and packaging proteins of some bacteriophages and diverse eukaryotic double-stranded DNA viruses, including a DNA polymerase B homolog and putative capsid proteins. Based on these and other structural similarities, we speculate that Mavericks represent an evolutionary missing link between seemingly disparate invasive DNA elements that include bacteriophages, adenoviruses and eukaryotic linear plasmids.

40 CFR 86.402-98 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Later New Motorcycles, General Provisions § 86.402-98 Definitions. The definitions of § 86.402-78 apply....1703. Useful life is defined for each class (see § 86.419) of motorcycle: (1) Class I-A—5.0 years or 6... amended at 69 FR 2435, Jan. 15, 2004] ...

40 CFR 86.402-98 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Later New Motorcycles, General Provisions § 86.402-98 Definitions. The definitions of § 86.402-78 apply....1703. Useful life is defined for each class (see § 86.419) of motorcycle: (1) Class I-A—5.0 years or 6... amended at 69 FR 2435, Jan. 15, 2004] ...

7 CFR 30.39 - Class 4; cigar-filler types and groups.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CONTAINER REGULATIONS TOBACCO STOCKS AND STANDARDS Classification of Leaf Tobacco Covering Classes, Types...-leaf tobacco commonly known as Pennsylvania Seedleaf or Pennsylvania Broadleaf, produced principally in... Stripped. Y—Farm Filler. N—Nondescript, as defined. (b) Type 42. That type of cigar-leaf tobacco commonly...

7 CFR 30.39 - Class 4; cigar-filler types and groups.

Code of Federal Regulations, 2010 CFR

2010-01-01

... CONTAINER REGULATIONS TOBACCO STOCKS AND STANDARDS Classification of Leaf Tobacco Covering Classes, Types...-leaf tobacco commonly known as Pennsylvania Seedleaf or Pennsylvania Broadleaf, produced principally in... Stripped. Y—Farm Filler. N—Nondescript, as defined. (b) Type 42. That type of cigar-leaf tobacco commonly...

7 CFR 30.39 - Class 4; cigar-filler types and groups.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CONTAINER REGULATIONS TOBACCO STOCKS AND STANDARDS Classification of Leaf Tobacco Covering Classes, Types...-leaf tobacco commonly known as Pennsylvania Seedleaf or Pennsylvania Broadleaf, produced principally in... Stripped. Y—Farm Filler. N—Nondescript, as defined. (b) Type 42. That type of cigar-leaf tobacco commonly...

7 CFR 30.39 - Class 4; cigar-filler types and groups.

Code of Federal Regulations, 2014 CFR

2014-01-01

... CONTAINER REGULATIONS TOBACCO STOCKS AND STANDARDS Classification of Leaf Tobacco Covering Classes, Types...-leaf tobacco commonly known as Pennsylvania Seedleaf or Pennsylvania Broadleaf, produced principally in... Stripped. Y—Farm Filler. N—Nondescript, as defined. (b) Type 42. That type of cigar-leaf tobacco commonly...

7 CFR 30.39 - Class 4; cigar-filler types and groups.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CONTAINER REGULATIONS TOBACCO STOCKS AND STANDARDS Classification of Leaf Tobacco Covering Classes, Types...-leaf tobacco commonly known as Pennsylvania Seedleaf or Pennsylvania Broadleaf, produced principally in... Stripped. Y—Farm Filler. N—Nondescript, as defined. (b) Type 42. That type of cigar-leaf tobacco commonly...

Prognostic Classification Factors Associated With Development of Multiple Autoantibodies, Dysglycemia, and Type 1 Diabetes-A Recursive Partitioning Analysis.

PubMed

Xu, Ping; Krischer, Jeffrey P

2016-06-01

To define prognostic classification factors associated with the progression from single to multiple autoantibodies, multiple autoantibodies to dysglycemia, and dysglycemia to type 1 diabetes onset in relatives of individuals with type 1 diabetes. Three distinct cohorts of subjects from the Type 1 Diabetes TrialNet Pathway to Prevention Study were investigated separately. A recursive partitioning analysis (RPA) was used to determine the risk classes. Clinical characteristics, including genotype, antibody titers, and metabolic markers were analyzed. Age and GAD65 autoantibody (GAD65Ab) titers defined three risk classes for progression from single to multiple autoantibodies. The 5-year risk was 11% for those subjects >16 years of age with low GAD65Ab titers, 29% for those ≤16 years of age with low GAD65Ab titers, and 45% for those subjects with high GAD65Ab titers regardless of age. Progression to dysglycemia was associated with islet antigen 2 Ab titers, and 2-h glucose and fasting C-peptide levels. The 5-year risk is 28%, 39%, and 51% for respective risk classes defined by the three predictors. Progression to type 1 diabetes was associated with the number of positive autoantibodies, peak C-peptide level, HbA1c level, and age. Four risk classes defined by RPA had a 5-year risk of 9%, 33%, 62%, and 80%, respectively. The use of RPA offered a new classification approach that could predict the timing of transitions from one preclinical stage to the next in the development of type 1 diabetes. Using these RPA classes, new prevention techniques can be tailored based on the individual prognostic risk characteristics at different preclinical stages. © 2016 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

Broad phonetic class definition driven by phone confusions

NASA Astrophysics Data System (ADS)

Lopes, Carla; Perdigão, Fernando

2012-12-01

Intermediate representations between the speech signal and phones may be used to improve discrimination among phones that are often confused. These representations are usually found according to broad phonetic classes, which are defined by a phonetician. This article proposes an alternative data-driven method to generate these classes. Phone confusion information from the analysis of the output of a phone recognition system is used to find clusters at high risk of mutual confusion. A metric is defined to compute the distance between phones. The results, using TIMIT data, show that the proposed confusion-driven phone clustering method is an attractive alternative to the approaches based on human knowledge. A hierarchical classification structure to improve phone recognition is also proposed using a discriminative weight training method. Experiments show improvements in phone recognition on the TIMIT database compared to a baseline system.

Multiclass Bayes error estimation by a feature space sampling technique

NASA Technical Reports Server (NTRS)

Mobasseri, B. G.; Mcgillem, C. D.

1979-01-01

A general Gaussian M-class N-feature classification problem is defined. An algorithm is developed that requires the class statistics as its only input and computes the minimum probability of error through use of a combined analytical and numerical integration over a sequence simplifying transformations of the feature space. The results are compared with those obtained by conventional techniques applied to a 2-class 4-feature discrimination problem with results previously reported and 4-class 4-feature multispectral scanner Landsat data classified by training and testing of the available data.

A latent profile analysis of intimate partner victimization and aggression and examination of between-class differences in psychopathology symptoms and risky behaviors

PubMed Central

Weiss, Nicole H.; Dixon-Gordon, Katherine L.; Peasant, Courtney; Jaquier, Véronique; Johnson, Clinesha; Sullivan, Tami P.

2016-01-01

Objective Intimate partner violence (IPV) is associated with heightened psychopathology symptoms and risky behaviors. However, extant investigations are limited by their focus on IPV victimization, despite evidence to suggest that victimization and aggression frequently co-occur. Further, research on these correlates often has not accounted for the heterogeneity of women who experience victimization. Method The present study utilized latent profile analysis to identify patterns of physical, psychological, and sexual victimization and aggression in a convenience sample of 212 community women experiencing victimization (M age=36.63, 70.8% African American), as well as examined differences in psychopathology symptoms (i.e., posttraumatic stress symptoms and depressive symptoms) and risky behaviors (i.e., drug problems, alcohol problems, deliberate self-harm, HIV-risk behaviors) across these classes. Results Four classes of women differentiated by severities of victimization and aggression were identified. Greater psychopathology symptoms were found among classes defined by greater victimization and aggression, regardless of IPV type. Risky behaviors were more prevalent among classes defined by greater sexual victimization and aggression in particular. Conclusions Findings highlight the importance of developing interventions that target the particular needs of subgroups of women who experience victimization. PMID:27736140

Flipped Physics

ERIC Educational Resources Information Center

Kettle, Maria

2013-01-01

This paper defines flipped learning and then examines its practical implementation in AS and A2 level physics classes, that is, classes for 16-18 year olds. The effect of this teaching style on student learning behaviour and its impact on test results are evaluated. The paper recounts the difficulties of implementing it and evaluates student…

Academic Tribes: Reflections on Teaching Large Classes.

ERIC Educational Resources Information Center

Jansen, Jonathan

1996-01-01

Makes an analogy between the stories told by teachers of large classes in South African universities and the storytelling of tribes. Suggests their identity is defined by the act of teaching and complaining about large groups with limited resources. Examines implications for content and organization of a teacher education course on classroom…

Agreement Reflexes of Emerging Optionality in Heritage Speaker Spanish

ERIC Educational Resources Information Center

Pascual Cabo, Diego

2013-01-01

This study contributes to current trends of heritage speaker (HS) acquisition research by examining the syntax of psych-predicates in HS Spanish. Broadly defined, psych-predicates communicate states of emotions (e.g., to love) and have traditionally been categorized as belonging to one of three classes: class I--"temere" "to…

Hearing Impaired Pupils in the Mainstream.

ERIC Educational Resources Information Center

Birch, Jack W.

Provided primarily for regular class teachers and administrators is information on mainstreaming hearing impaired students. Reasons behind the movement toward regular class placement of hearing impaired pupils are noted and two basic views as to how it should be done are identified. Defined are relevant terms such as mainstreaming, hearing aid,…

An Evaluation of the Measurement of Perceived Classroom Assessment Environment

ERIC Educational Resources Information Center

Alkharusi, Hussain

2015-01-01

A classroom assessment environment is a classroom context experienced by students as the teacher determines assessment purposes, develops assessment tasks, defines assessment criteria and standards, provides feedback, and monitors outcomes (Brookhart, 1997). It is usually a group experience varying from class to class dependent upon the teacher's…

Improving Grading Consistency through Grade Lift Reporting

ERIC Educational Resources Information Center

Millet, Ido

2010-01-01

We define Grade Lift as the difference between average class grade and average cumulative class GPA. This metric provides an assessment of how lenient the grading was for a given course. In 2006, we started providing faculty members individualized Grade Lift reports reflecting their position relative to an anonymously plotted school-wide…

29 CFR 1926.407 - Hazardous (classified) locations.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Electrical Code, lists or defines hazardous gases, vapors, and dusts by “Groups” characterized by their... the class, group, and operating temperature or temperature range, based on operation in a 40-degree C... be marked to indicate the group. (C) Fixed general-purpose equipment in Class I locations, other than...

29 CFR 1926.407 - Hazardous (classified) locations.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Electrical Code, lists or defines hazardous gases, vapors, and dusts by “Groups” characterized by their... the class, group, and operating temperature or temperature range, based on operation in a 40-degree C... be marked to indicate the group. (C) Fixed general-purpose equipment in Class I locations, other than...

Agency Amidst Formidable Structures: How Girls Perform Gender in Science Class

ERIC Educational Resources Information Center

Carlone, Heidi B.; Johnson, Angela; Scott, Catherine M.

2015-01-01

Larger social structures such as race, class, gender, and sexuality and classroom structures like narrowly defined participation practices constrain individuals' agency to engage in untroubled and sustained science identity work. This article explores the central dilemma of attending to structure and agency in settings where inequities are…

Sensitivity analysis as an aid in modelling and control of (poorly-defined) ecological systems. [closed ecological systems

NASA Technical Reports Server (NTRS)

Hornberger, G. M.; Rastetter, E. B.

1982-01-01

A literature review of the use of sensitivity analyses in modelling nonlinear, ill-defined systems, such as ecological interactions is presented. Discussions of previous work, and a proposed scheme for generalized sensitivity analysis applicable to ill-defined systems are included. This scheme considers classes of mathematical models, problem-defining behavior, analysis procedures (especially the use of Monte-Carlo methods), sensitivity ranking of parameters, and extension to control system design.

Class-modelling in food analytical chemistry: Development, sampling, optimisation and validation issues - A tutorial.

PubMed

Oliveri, Paolo

2017-08-22

Qualitative data modelling is a fundamental branch of pattern recognition, with many applications in analytical chemistry, and embraces two main families: discriminant and class-modelling methods. The first strategy is appropriate when at least two classes are meaningfully defined in the problem under study, while the second strategy is the right choice when the focus is on a single class. For this reason, class-modelling methods are also referred to as one-class classifiers. Although, in the food analytical field, most of the issues would be properly addressed by class-modelling strategies, the use of such techniques is rather limited and, in many cases, discriminant methods are forcedly used for one-class problems, introducing a bias in the outcomes. Key aspects related to the development, optimisation and validation of suitable class models for the characterisation of food products are critically analysed and discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

National facilities study. Volume 4: Space operations facilities task group

NASA Technical Reports Server (NTRS)

1994-01-01

The principal objectives of the National Facilities Study (NFS) were to: (1) determine where U.S. facilities do not meet national aerospace needs; (2) define new facilities required to make U.S. capabilities 'world class' where such improvements are in the national interest; (3) define where consolidation and phase-out of existing facilities is appropriate; and (4) develop a long-term national plan for world-class facility acquisition and shared usage. The Space Operations Facilities Task Group defined discrete tasks to accomplish the above objectives within the scope of the study. An assessment of national space operations facilities was conducted to determine the nation's capability to meet the requirements of space operations during the next 30 years. The mission model used in the study to define facility requirements is described in Volume 3. Based on this model, the major focus of the Task Group was to identify any substantive overlap or underutilization of space operations facilities and to identify any facility shortfalls that would necessitate facility upgrades or new facilities. The focus of this initial study was directed toward facility recommendations related to consolidations, closures, enhancements, and upgrades considered necessary to efficiently and effectively support the baseline requirements model. Activities related to identifying facility needs or recommendations for enhancing U.S. international competitiveness and achieving world-class capability, where appropriate, were deferred to a subsequent study phase.

Forecasting Maintenance Shortcomings of a Planned Equipment Density Listing in Support of Expeditionary Missions

DTIC Science & Technology

2017-06-01

importantly, it examines the methodology used to build the class IX block embarked on ship prior to deployment. The class IX block is defined as a repository...compared to historical data to evaluate model and simulation outputs. This thesis provides recommendations on improving the methodology implemented in...improving the level of organic support available to deployed units. More importantly, it examines the methodology used to build the class IX block

Measuring case-mix complexity of tertiary care hospitals using DRGs.

PubMed

Park, Hayoung; Shin, Youngsoo

2004-02-01

The objectives of the study were to develop a model that measures and evaluates case-mix complexity of tertiary care hospitals, and to examine the characteristics of such a model. Physician panels defined three classes of case complexity and assigned disease categories represented by Adjacent Diagnosis Related Groups (ADRGs) to one of three case complexity classes. Three types of scores, indicating proportions of inpatients in each case complexity class standardized by the proportions at the national level, were defined to measure the case-mix complexity of a hospital. Discharge information for about 10% of inpatient episodes at 85 hospitals with bed size larger than 400 and their input structure and research and education activity were used to evaluate the case-mix complexity model. Results show its power to predict hospitals with the expected functions of tertiary care hospitals, i.e. resource intensive care, expensive input structure, and high levels of research and education activities.

Hirota equations associated with simply laced affine Lie algebras: The cuspidal class E{sub 6} of e{sub 6}{sup (1)}

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

Dodd, R. K.

2014-02-15

In this paper we derive Hirota equations associated with the simply laced affine Lie algebras g{sup (1)}, where g is one of the simply laced complex Lie algebras a{sub n},d{sub n},e{sub 6},e{sub 7} or e{sub 8}, defined by finite order automorphisms of g which we call Lepowsky automorphisms. In particular, we investigate the Hirota equations for Lepowsky automorphisms of e{sub 6} defined by the cuspidal class E{sub 6} of the Weyl group W(E{sub 6}) of e{sub 6}. We also investigate the relationship between the Lepowsky automorphisms of the simply laced complex Lie algebras g and the conjugate canonical automorphisms definedmore » by Kac. This analysis is applied to identify the canonical automorphisms for the cuspidal class E{sub 6} of e{sub 6}.« less

A Comparative Analysis of Method Books for Class Jazz Instruction

ERIC Educational Resources Information Center

Watson, Kevin E.

2017-01-01

The purpose of this study was to analyze and compare instructional topics and teaching approaches included in selected class method books for jazz pedagogy through content analysis methodology. Frequency counts for the number of pages devoted to each defined instructional content category were compiled and percentages of pages allotted to each…

Homographs: Classification and Identification.

ERIC Educational Resources Information Center

Pacak, M.; Henisz, Bozena

1968-01-01

Homographs are defined in this study as sets of word forms which are spelled alike but which have entirely or partially different meanings and which may have different syntactic functions (that is, they belong to more than one form class or to more than one subclass of a form class). This report deals with the classification and identification of…

Evaluation of a Brief Homework Assignment Designed to Reduce Citation Problems

ERIC Educational Resources Information Center

Schuetze, Pamela

2004-01-01

I evaluated a brief homework assignment designed to reduce citation problems in research-based term papers. Students in 2 developmental psychology classes received a brief presentation and handout defining plagiarism with tips on how to cite sources to avoid plagiarizing. In addition, students in 1 class completed 2 brief homework assignments in…

Weak Humanism and the Economic Mission of English Education

ERIC Educational Resources Information Center

Collin, Ross

2018-01-01

This article examines a theory of "weak humanism" that says (1) secondary English classes should focus on personal development and culture and (2) English classes should deliver economic benefits indirectly, i.e. as knock-on effects of studying the personal and the cultural. Economic benefits are defined here as knowledge/skills students…

Living Telenovelas/Telenovelizing Life: Mexican American Girls' Identities and Transnational Telenovelas.

ERIC Educational Resources Information Center

Mayer, Vicki

2003-01-01

Examines the local reception of global Spanish-language soap operas, or telenovelas. Explores how young people talked about Mexican telenovelas in daily life. Concludes that the telenovela, within certain limits, reflected some of the national, ethnic, gender, and class tensions that defined the viewers' identities as working-class, Mexican…

76 FR 48870 - Guidance for Industry and Food and Drug Administration Staff; Class II Special Controls Guidance...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-09

... selection inclusion and exclusion criteria section. The revisions define and differentiate the required... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2010-D-0428] Guidance for Industry and Food and Drug Administration Staff; Class II Special Controls Guidance Document...

An International Model of World-Class Education: The International Baccalaureate

ERIC Educational Resources Information Center

Hill, Ian

2012-01-01

This article posits that world-class education is international education, as defined by UNESCO, and presents International Baccalaureate (IB) programmes as examples of this phenomenon. It begins with the IB's 1960s origins in international schools, which educated the children of globally mobile parents who worked principally in the UN and its…

Magic bases, metric ansaetze and generalized graph theories in the Virasoro master equation

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

Halpern, M.B.; Obers, N.A.

1991-11-15

The authors define a class of magic Lie group bases in which the Virasoro master equation admits a class of simple metric ansaetze (g{sub metric}), whose structure is visible in the high-level expansion. When a magic basis is real on compact g, the corresponding g{sub metric} is a large system of unitary, generically irrational conformal field theories. Examples in this class include the graph-theory ansatz SO(n){sub diag} in the Cartesian basis of So(n) and the ansatz SU(n){sub metric} in the Pauli-like basis of SU(n). A new phenomenon is observed in the high-level comparison of SU(n){sub metric}: Due to the trigonometricmore » structure constants of the Pauli-like basis, irrational central charge is clearly visible at finite order of the expansion. They also define the sine-area graphs of SU(n), which label the conformal field theories of SU(n){sub metric} and note that, in a similar fashion, each magic basis of g defines a generalize graph theory on g which labels the conformal field theories of g{sub metric}.« less

Reproducibility and Reliability: How To Define the Population of Trees That Represent Site Quality For Longleaf Pine Plantations

Treesearch

J.C.G. Goelz; Daniel J. Leduc

2004-01-01

We compared 13 definitions for the subpopulation of “site trees.” Each subpopulation was defined (1) once at base age or at each measurement; (2) by crown class, diameter, or height; and (3) by the number of trees per acre. These subpopulations were applied to base ages of 25 and 50. For base age 25, the subpopulations defined at base age were superior to those defined...

Social space, social class and Bourdieu: health inequalities in British Columbia, Canada.

PubMed

Veenstra, Gerry

2007-03-01

This article adopts Pierre Bourdieu's cultural-structuralist approach to conceptualizing and identifying social classes in social space and seeks to identify health effects of class in one Canadian province. Utilizing data from an original questionnaire survey of randomly selected adults from 25 communities in British Columbia, social (class) groupings defined by cultural tastes and dispositions, lifestyle practices, social background, educational capital, economic capital, social capital and occupational categories are presented in visual mappings of social space constructed by use of exploratory multiple correspondence analysis techniques. Indicators of physical and mental health are then situated within this social space, enabling speculations pertaining to health effects of social class in British Columbia.

The class analysis of poverty: a response to Tony Novak.

PubMed

Wright, E O

1996-01-01

In responding to Tony Novak's criticisms of his earlier article "The Class Analysis of Poverty," the author makes four principle points. First, contrary to Novak's views, a class analysis to poverty should define poverty in terms of both income-poverty and asset-poverty. Second, while Novak is correct that the term "underclass" often has a pejorative meaning, it remains an important concept for identifying segments of the population that are deeply oppressed economically, but not exploited. Third, the concepts of class analysis must be elaborated at a variety of levels of abstraction, not simply the highest level of the pure "mode of production," as is implied by Novak's arguments. Finally, class analysis must acknowledge and conceptualize the specific forms of complexity of contemporary class structures, which is impossible if it restricts its class concepts to a simple polarized notion.

Clustering of Genetically Defined Allele Classes in the Caenorhabditis elegans DAF-2 Insulin/IGF-1 Receptor

PubMed Central

Patel, Dhaval S.; Garza-Garcia, Acely; Nanji, Manoj; McElwee, Joshua J.; Ackerman, Daniel; Driscoll, Paul C.; Gems, David

2008-01-01

The DAF-2 insulin/IGF-1 receptor regulates development, metabolism, and aging in the nematode Caenorhabditis elegans. However, complex differences among daf-2 alleles complicate analysis of this gene. We have employed epistasis analysis, transcript profile analysis, mutant sequence analysis, and homology modeling of mutant receptors to understand this complexity. We define an allelic series of nonconditional daf-2 mutants, including nonsense and deletion alleles, and a putative null allele, m65. The most severe daf-2 alleles show incomplete suppression by daf-18(0) and daf-16(0) and have a range of effects on early development. Among weaker daf-2 alleles there exist distinct mutant classes that differ in epistatic interactions with mutations in other genes. Mutant sequence analysis (including 11 newly sequenced alleles) reveals that class 1 mutant lesions lie only in certain extracellular regions of the receptor, while class 2 (pleiotropic) and nonconditional missense mutants have lesions only in the ligand-binding pocket of the receptor ectodomain or the tyrosine kinase domain. Effects of equivalent mutations on the human insulin receptor suggest an altered balance of intracellular signaling in class 2 alleles. These studies consolidate and extend our understanding of the complex genetics of daf-2 and its underlying molecular biology. PMID:18245374

Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set.

PubMed

Klimenko, Kyrylo; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

2016-08-22

Curation, standardization and data fusion of the antiviral information present in the ChEMBL public database led to the definition of a robust data set, providing an association of antiviral compounds to seven broadly defined antiviral activity classes. Generative topographic mapping (GTM) subjected to evolutionary tuning was then used to produce maps of the antiviral chemical space, providing an optimal separation of compound families associated with the different antiviral classes. The ability to pinpoint the specific spots occupied (responsibility patterns) on a map by various classes of antiviral compounds opened the way for a GTM-supported search for privileged structural motifs, typical for each antiviral class. The privileged locations of antiviral classes were analyzed in order to highlight underlying privileged common structural motifs. Unlike in classical medicinal chemistry, where privileged structures are, almost always, predefined scaffolds, privileged structural motif detection based on GTM responsibility patterns has the decisive advantage of being able to automatically capture the nature ("resolution detail"-scaffold, detailed substructure, pharmacophore pattern, etc.) of the relevant structural motifs. Responsibility patterns were found to represent underlying structural motifs of various natures-from very fuzzy (groups of various "interchangeable" similar scaffolds), to the classical scenario in medicinal chemistry (underlying motif actually being the scaffold), to very precisely defined motifs (specifically substituted scaffolds).

Class I HDACs Regulate Angiotensin II-Dependent Cardiac Fibrosis via Fibroblasts and Circulating Fibrocytes

PubMed Central

Williams, Sarah M.; Golden-Mason, Lucy; Ferguson, Bradley S.; Douglas, Katherine B.; Cavasin, Maria A.; Demos-Davies, Kim; Yeager, Michael E.; Stenmark, Kurt R.; McKinsey, Timothy A.

2014-01-01

Fibrosis, which is defined as excessive accumulation of fibrous connective tissue, contributes to the pathogenesis of numerous diseases involving diverse organ systems. Cardiac fibrosis predisposes individuals to myocardial ischemia, arrhythmias and sudden death, and is commonly associated with diastolic dysfunction. Histone deacetylase (HDAC) inhibitors block cardiac fibrosis in pre-clinical models of heart failure. However, which HDAC isoforms govern cardiac fibrosis, and the mechanisms by which they do so, remains unclear. Here, we show that selective inhibition of class I HDACs potently suppresses angiotensin II (Ang II)-mediated cardiac fibrosis by targeting two key effector cell populations, cardiac fibroblasts and bone marrow-derived fibrocytes. Class I HDAC inhibition blocks cardiac fibroblast cell cycle progression through derepression of the genes encoding the cyclin-dependent kinase (CDK) inhibitors, p15 and p57. In contrast, class I HDAC inhibitors block agonist-dependent differentiation of fibrocytes through a mechanism involving repression of ERK1/2 signaling. These findings define novel roles for class I HDACs in the control of pathological cardiac fibrosis. Furthermore, since fibrocytes have been implicated in the pathogenesis of a variety of human diseases, including heart, lung and kidney failure, our results suggest broad utility for isoform-selective HDAC inhibitors as anti-fibrotic agents that function, in part, by targeting these circulating mesenchymal cells. PMID:24374140

Instructors' Perceptions of Mostly Seated Exercise Classes: Exploring the Concept of Chair Based Exercise.

PubMed

Robinson, Katie R; Masud, Tahir; Hawley-Hague, Helen

2016-01-01

Chair based exercise (CBE) can be used to engage older adults unable to take part in standing exercise programmes. Defining and understanding the context of CBE have been acknowledged as a challenge. We explore instructor experiences of delivering mostly seated exercise classes for older people and how this helps us to further understand the concept of CBE. We extracted qualitative data from a cross-sectional survey with 731 exercise instructors. 378 delivered mostly seated classes and 223 of those instructors provided qualitative data. There were 155 instructors who did not provide any qualitative comments. Framework analysis was used and informed by a Delphi consensus study on CBE. Instructors perceived mostly seated classes as predominantly CBE; they defined it as an introductory class that should be offered as part of a continuum of exercise. It was considered suitable for those with limitations and older adults in long-term care and with dementia. Instructors reported CBE used inappropriately for more active older people. Instructors reported observing improvements in mood and cognition and broader social benefits. Instructors' perspectives largely support expert consensus that CBE has an important role in a continuum of exercise. Providers of CBE need to ensure that more challenging exercises are introduced where appropriate. Further research is needed to explore older adults' perceptions of CBE.

Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site

PubMed Central

West, Anthony P; Schamber, Michael; Gazumyan, Anna; Golijanin, Jovana; Seaman, Michael S; Fätkenheuer, Gerd; Klein, Florian; Nussenzweig, Michel C; Bjorkman, Pamela J

2016-01-01

HIV-1 vaccine design is informed by structural studies elucidating mechanisms by which broadly neutralizing antibodies (bNAbs) recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env). Variability in high-mannose and complex-type Env glycoforms leads to heterogeneity that usually precludes visualization of the native glycan shield. We present 3.5-Å- and 3.9-Å-resolution crystal structures of the HIV-1 Env trimer with fully processed and native glycosylation, revealing a glycan shield of high-mannose and complex-type N-glycans, which we used to define complete epitopes of two bNAbs. Env trimer was complexed with 10-1074 (against the V3-loop) and IOMA, a new CD4-binding site (CD4bs) antibody. Although IOMA derives from VH1-2*02, the germline gene of CD4bs-targeting VRC01-class bNAbs, its light chain lacks the short CDRL3 that defines VRC01-class bNAbs. Thus IOMA resembles 8ANC131-class/VH1-46–derived CD4bs bNAbs, which have normal-length CDRL3s. The existence of bNAbs that combine features of VRC01-class and 8ANC131-class antibodies has implications for immunization strategies targeting VRC01-like bNAbs. PMID:27617431

Applying definitions for multidrug resistance, extensive drug resistance and pandrug resistance to clinically significant livestock and companion animal bacterial pathogens.

PubMed

Sweeney, Michael T; Lubbers, Brian V; Schwarz, Stefan; Watts, Jeffrey L

2018-06-01

Standardized definitions for MDR are currently not available in veterinary medicine despite numerous reports indicating that antimicrobial resistance may be increasing among clinically significant bacteria in livestock and companion animals. As such, assessments of MDR presented in veterinary scientific reports are inconsistent. Herein, we apply previously standardized definitions for MDR, XDR and pandrug resistance (PDR) used in human medicine to animal pathogens and veterinary antimicrobial agents in which MDR is defined as an isolate that is not susceptible to at least one agent in at least three antimicrobial classes, XDR is defined as an isolate that is not susceptible to at least one agent in all but one or two available classes and PDR is defined as an isolate that is not susceptible to all agents in all available classes. These definitions may be applied to antimicrobial agents used to treat bovine respiratory disease (BRD) caused by Mannheimia haemolytica, Pasteurella multocida and Histophilus somni and swine respiratory disease (SRD) caused by Actinobacillus pleuropneumoniae, P. multocida and Streptococcus suis, as well as antimicrobial agents used to treat canine skin and soft tissue infections (SSTIs) caused by Staphylococcus and Streptococcus species. Application of these definitions in veterinary medicine should be considered static, whereas the classification of a particular resistance phenotype as MDR, XDR or PDR could change over time as more veterinary-specific clinical breakpoints or antimicrobial classes and/or agents become available in the future.

SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

PubMed

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-05-01

Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods.

SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences

PubMed Central

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-01-01

Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods. PMID:18452616

Is it Useful to Have a Clear-cut Definition of Life? On the Use of Fuzzy Logic in Prebiotic Chemistry

NASA Astrophysics Data System (ADS)

Bruylants, Gilles; Bartik, Kristin; Reisse, Jacques

2010-04-01

Many scientists, including one of the authors of the present paper, have devoted time to try to find a definition for life (Bersini and Reisse 2007). It is clear that a consensus will never be reached but, more importantly, it seems that the issue itself could be without major interest. It is indeed impossible to define a “natural” frontier between non-living and living systems and therefore also impossible to define dichotomic criteria which could be used in order to classify systems in one of these two classes (living or non-living). Fuzzy logic provides a natural way to deal with problems where class membership lacks sharply defined criteria. It also offers the possibility to avoid losing time with unnecessary controversies such as deciding whether a virus is, or is not, a living system.

Is it useful to have a clear-cut definition of life? On the use of fuzzy logic in prebiotic chemistry.

PubMed

Bruylants, Gilles; Bartik, Kristin; Reisse, Jacques

2010-04-01

Many scientists, including one of the authors of the present paper, have devoted time to try to find a definition for life (Bersini and Reisse 2007). It is clear that a consensus will never be reached but, more importantly, it seems that the issue itself could be without major interest. It is indeed impossible to define a "natural" frontier between non-living and living systems and therefore also impossible to define dichotomic criteria which could be used in order to classify systems in one of these two classes (living or non-living). Fuzzy logic provides a natural way to deal with problems where class membership lacks sharply defined criteria. It also offers the possibility to avoid losing time with unnecessary controversies such as deciding whether a virus is, or is not, a living system.

Application of an Area-of-Review (AOR) Concept to the East Texas Field and Other Selected Texas Oilfields

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

Warner, Don L.; Koederitz, Leonard F.; Laudon, Robert C.

The Underground Injection Control Regulations promulgated in 1980, under the Safe Drinking Water Act of 1974, require Area-of-Review (AOR) studies be conducted as part of the permitting process for newly drilled or converted Class II injection wells. Existing Class II injection wells operating at the time regulations became effective were excluded from the AOR requirement. The AOR is the area surrounding an injection well or wells defined by either the radial distance within which pressure in the injection zone may cause migration of the injection and/or formation fluid into an underground source of drinking water (USDW) or defined by amore » fixed radius of not less than one-fourth mile. In the method where injection pressure is used to define the AOR radial distance, the AOR is also known as the ''zone of endangering influence.''« less

Factors associated with patterns of mobile technology use among persons who inject drugs.

PubMed

Collins, Kelly M; Armenta, Richard F; Cuevas-Mota, Jazmine; Liu, Lin; Strathdee, Steffanie A; Garfein, Richard S

2016-01-01

New and innovative methods of delivering interventions are needed to further reduce risky behaviors and increase overall health among persons who inject drugs (PWID). Mobile health (mHealth) interventions have potential for reaching PWID; however, little is known about mobile technology use (MTU) in this population. In this study, the authors identify patterns of MTU and identified factors associated with MTU among a cohort of PWID. Data were collected through a longitudinal cohort study examining drug use, risk behaviors, and health status among PWID in San Diego, California. Latent class analysis (LCA) was used to define patterns of MTU (i.e., making voice calls, text messaging, and mobile Internet access). Multinomial logistic regression was then used to identify demographic characteristics, risk behaviors, and health indicators associated with mobile technology use class. In LCA, a 4-class solution fit the data best. Class 1 was defined by low MTU (22%, n = 100); class 2, by PWID who accessed the Internet using a mobile device but did not use voice or text messaging (20%, n = 95); class 3, by primarily voice, text, and connected Internet use (17%, n = 91); and class 4, by high MTU (41%, n = 175). Compared with low MTU, high MTU class members were more likely to be younger, have higher socioeconomic status, sell drugs, and inject methamphetamine daily. The majority of PWID in San Diego use mobile technology for voice, text, and/or Internet access, indicating that rapid uptake of mHealth interventions may be possible in this population. However, low ownership and use of mobile technology among older and/or homeless individuals will need to be considered when implementing mHealth interventions among PWID.

Prevalence of severe obesity and its association with elevated blood pressure among children and adolescents in Shandong, China.

PubMed

Zhang, Ying-Xiu; Wang, Shu-Rong; Li, Su-Yun

2017-12-01

Childhood obesity has increased markedly during the past decades; however, data on the prevalence of severe obesity in children and adolescents are limited. The present study examined the prevalence of severe obesity and its association with elevated blood pressure (BP) among children and adolescents in Shandong, China. A total of 44 630 (22 404 boys and 22 226 girls) students aged 7-18 years participated in the study. BMI cut-off points recommended by the International Obesity Task Force were used to define class I-III obesity. Relatively high BP status was defined as systolic BP and/or diastolic BP of at least 95th percentile for age and sex. The prevalence rates of class I, class II, and class III obesity were 6.67, 1.47, and 0.42% for boys and 2.88, 0.64, and 0.18% for girls, respectively; boys had a higher prevalence than girls (P<0.01). Substantial urban-rural disparities exist in childhood obesity; urban boys and girls had a higher prevalence of class I and class II obesity than their rural peers (P<0.05). Severe obesity is associated with elevated BP; the prevalence of relatively high BP increased from 39.93% (boys) and 39.53% (girls) in the class I obese group to 50.54% (boys) and 53.66% (girls) in the class III obese group (P<0.05). Although the current prevalence of severe obesity was at a relatively low level, but we should not relax our vigilance to the obesity epidemic. Our findings also emphasize the importance of the prevention of severe obesity to prevent future-related problems such as hypertension in children and adolescents.

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

Young, Anthony M.; Williams, Liliya L.R.; Hjorth, Jens, E-mail: amyoung@astro.umn.edu, E-mail: llrw@astro.umn.edu, E-mail: jens@dark-cosmology.dk

One usually thinks of a radial density profile as having a monotonically changing logarithmic slope, such as in NFW or Einasto profiles. However, in two different classes of commonly used systems, this is often not the case. These classes exhibit non-monotonic changes in their density profile slopes which we call oscillations for short. We analyze these two unrelated classes separately. Class 1 consists of systems that have density oscillations and that are defined through their distribution function f ( E ), or differential energy distribution N ( E ), such as isothermal spheres, King profiles, or DARKexp, a theoretically derivedmore » model for relaxed collisionless systems. Systems defined through f ( E ) or N ( E ) generally have density slope oscillations. Class 1 system oscillations can be found at small, intermediate, or large radii but we focus on a limited set of Class 1 systems that have oscillations in the central regions, usually at log( r / r {sub −2}) ∼< −2, where r {sub −2} is the largest radius where d log(ρ)/ d log( r ) = −2. We show that the shape of their N ( E ) can roughly predict the amplitude of oscillations. Class 2 systems which are a product of dynamical evolution, consist of observed and simulated galaxies and clusters, and pure dark matter halos. Oscillations in the density profile slope seem pervasive in the central regions of Class 2 systems. We argue that in these systems, slope oscillations are an indication that a system is not fully relaxed. We show that these oscillations can be reproduced by small modifications to N ( E ) of DARKexp. These affect a small fraction of systems' mass and are confined to log( r / r {sub −2}) ∼< 0. The size of these modifications serves as a potential diagnostic for quantifying how far a system is from being relaxed.« less

Homogeneity of Severe Posttraumatic Stress Disorder Symptom Profiles in Children and Adolescents Across Gender, Age, and Traumatic Experiences Related to 9/11.

PubMed

Guffanti, Guia; Geronazzo-Alman, Lupo; Fan, Bin; Duarte, Cristiane S; Musa, George J; Hoven, Christina W

2016-10-01

Patients with a posttraumatic stress disorder (PTSD) diagnosis according to the Diagnostic and Statistical Manual of Mental Disorders (4th ed., DSM-IV; American Psychiatric Association, 1994) will very likely not share all of the same symptoms, a consequence of the polythetic approach used in the DSM. We examined heterogeneity in the latent structure of PTSD symptoms using data from a previously published sample of 8,236 youth a subset of which had been exposed to the September 11, 2001 attacks (N = 6,670; Hoven et al., 2005). Latent class analysis was applied (a) to PTSD symptoms alone, (b) to symptoms in combination with impairment indicators, and (c) to PTSD symptoms when stratified by age and gender, as well as by empirically defined classes of exposure. We identified 4 symptom classes: no disturbance (49.4%), intermediate disturbance (2 classes; 21.5% and 18.6%, respectively), and severe disturbance (10.5%). These classes varied not only in the severity of symptoms, but also in the configuration of symptoms. We observed a high probability of endorsing both PTSD symptoms and indicators of impairment only in the severe disturbance class. A similar 4-class structure was found when the data were stratified by age, gender, and exposure classes. There were no significant differences as a function of age, gender, or exposure in the presence of severe PTSD. Heterogeneity was observed at intermediate levels of PTSD symptom severity. The specific PTSD symptoms that defined the severe PTSD profile could constitute the pathogenic aspects of a largely invariant and clinically meaningful PTSD syndrome. Copyright © 2016 International Society for Traumatic Stress Studies.

The Last Nine Weeks: Helping Seniors Say Goodbye.

ERIC Educational Resources Information Center

Molnar, Bonnie

1999-01-01

Describes a unit for the final nine weeks of a senior English class which helps seniors say goodbye. Discusses how reading Sandra Cisneros'"The House on Mango Street" and writing their own versions of excerpts of it (along with other class activities) helps students define what they are leaving and come to terms with it. (SR)

26 CFR 1.423-2 - Employee stock purchase plan defined.

Code of Federal Regulations, 2010 CFR

2010-04-01

... employee owns stock possessing 5 percent or more of the total combined voting power or value of all classes... granted, owns stock possessing 5 percent or more of the total combined voting power or value of all... the percentage of the total combined voting power or value of all classes of stock of the employer...

Room Use for Group Instruction in Regularly Scheduled Classes.

ERIC Educational Resources Information Center

Phay, John E.; McCary, Arthur D.

A method by which accurate accounting by computer might be made of apace and room use by regularly scheduled classes in institutions of higher learning is furnished. Based on well-defined terms, a master room schedule and a master course schedule are prepared on computer cards. This information is then compared with the reported individual room…

Undergraduate Navigator Training Attrition Study. July 1973-December 1974, Final Report.

ERIC Educational Resources Information Center

DeVries, Philip B., Jr.; And Others

The study was designed to identify and define the factors which contribute to undergraduate navigator training (UNT) attrition and to present recommendations to reduce the effects of those factors. Longitudinal data were collected from six UNT classes and augmented with cross-sectional data from a sample of 15 UNT classes. The student data are…

27 CFR 5.35 - Class and type.

Code of Federal Regulations, 2010 CFR

2010-04-01

... of whiskies in mixtures. In the case of any of the types of whisky defined in § 5.22(b), Class 2, which contains any whisky or whiskies produced in a country other than that indicated by the type designation, there shall be stated on the brand label the percentage of such whisky and the country or origin...

27 CFR 5.35 - Class and type.

Code of Federal Regulations, 2011 CFR

2011-04-01

... of whiskies in mixtures. In the case of any of the types of whisky defined in § 5.22(b), Class 2, which contains any whisky or whiskies produced in a country other than that indicated by the type designation, there shall be stated on the brand label the percentage of such whisky and the country or origin...

26 CFR 1.652(b)-2 - Allocation of income items.

Code of Federal Regulations, 2010 CFR

2010-04-01

... (CONTINUED) INCOME TAXES Trusts Which Distribute Current Income Only § 1.652(b)-2 Allocation of income items... distributable net income of the trust (as defined in section 643(a)) as the total of each class bears to such distributable net income, unless the terms of the trust specifically allocate different classes of income to...

Family Structure and Attitudes Toward the Family for Negroes and Whites From Lower-Class and Working-Class Backgrounds.

ERIC Educational Resources Information Center

Nosow, Sigmund

This study is concerned with attitudes of family members, and whether such attitudes indeed vary with different family structures. The increasing sociological and psychiatric evidence seems to support the existence of family strengths in families which have been defined as unstable because of structural attributes. Given the historical character…

The Application of SECI Model as a Framework of Knowledge Creation in Virtual Learning: Case Study of IUST Virtual Classes

ERIC Educational Resources Information Center

Hosseini, Seyede Mehrnoush

2011-01-01

The research aims to define SECI model of knowledge creation (socialization, externalization, combination, and internalization) as a framework of Virtual class management which can lead to better online teaching-learning mechanisms as well as knowledge creation. It has used qualitative research methodology including researcher's close observation…

Class Guitar in Our Secondary Schools. Part 1--Some Thoughts for its Encouragement.

ERIC Educational Resources Information Center

Lowry, Terence Oarn

The guide explains how to design a beginning guitar class for students in public schools. Part one discusses problems related to teaching guitar in a classroom setting. Teachers must have a clearly defined philosophy of the importance of music. Goals and objectives should emphasize the development of enlightened musical consumers as well as skills…

Some subclasses of multivalent functions involving a certain linear operator

NASA Astrophysics Data System (ADS)

Srivastava, H. M.; Patel, J.

2005-10-01

The authors investigate various inclusion and other properties of several subclasses of the class of normalized p-valent analytic functions in the open unit disk, which are defined here by means of a certain linear operator. Problems involving generalized neighborhoods of analytic functions in the class are investigated. Finally, some applications of fractional calculus operators are considered.

Empirical redefinition of comprehensive health and well-being in the older adults of the United States.

PubMed

McClintock, Martha K; Dale, William; Laumann, Edward O; Waite, Linda

2016-05-31

The World Health Organization (WHO) defines health as a "state of complete physical, mental and social well-being and not merely the absence of disease or infirmity." Despite general acceptance of this comprehensive definition, there has been little rigorous scientific attempt to use it to measure and assess population health. Instead, the dominant model of health is a disease-centered Medical Model (MM), which actively ignores many relevant domains. In contrast to the MM, we approach this issue through a Comprehensive Model (CM) of health consistent with the WHO definition, giving statistically equal consideration to multiple health domains, including medical, physical, psychological, functional, and sensory measures. We apply a data-driven latent class analysis (LCA) to model 54 specific health variables from the National Social Life, Health, and Aging Project (NSHAP), a nationally representative sample of US community-dwelling older adults. We first apply the LCA to the MM, identifying five health classes differentiated primarily by having diabetes and hypertension. The CM identifies a broader range of six health classes, including two "emergent" classes completely obscured by the MM. We find that specific medical diagnoses (cancer and hypertension) and health behaviors (smoking) are far less important than mental health (loneliness), sensory function (hearing), mobility, and bone fractures in defining vulnerable health classes. Although the MM places two-thirds of the US population into "robust health" classes, the CM reveals that one-half belong to less healthy classes, independently associated with higher mortality. This reconceptualization has important implications for medical care delivery, preventive health practices, and resource allocation.

Automatic discovery of optimal classes

NASA Technical Reports Server (NTRS)

Cheeseman, Peter; Stutz, John; Freeman, Don; Self, Matthew

1986-01-01

A criterion, based on Bayes' theorem, is described that defines the optimal set of classes (a classification) for a given set of examples. This criterion is transformed into an equivalent minimum message length criterion with an intuitive information interpretation. This criterion does not require that the number of classes be specified in advance, this is determined by the data. The minimum message length criterion includes the message length required to describe the classes, so there is a built in bias against adding new classes unless they lead to a reduction in the message length required to describe the data. Unfortunately, the search space of possible classifications is too large to search exhaustively, so heuristic search methods, such as simulated annealing, are applied. Tutored learning and probabilistic prediction in particular cases are an important indirect result of optimal class discovery. Extensions to the basic class induction program include the ability to combine category and real value data, hierarchical classes, independent classifications and deciding for each class which attributes are relevant.

Ethnic Differences in Lipid Profiles of Overweight, Obese, and Severely Obese Children and Adolescents 6-19 Years of Age.

PubMed

Dhuper, Sarita; Bayoumi, Nagla S; Shah, Yash D; Mehta, Shilpa

2017-06-01

Ethnic differences in lipid profiles exist in children and adolescents. This study assessed whether variations in lipid profiles present in overweight and obese youth were also observed in severely obese youth. Variations could explain the lower prevalence of the metabolic syndrome in certain ethnic groups at even severe levels of obesity. Data were obtained from the National Health and Nutrition Examination Survey for the years of 2001 through 2012. Subjects were divided into groups according to BMI classification. Normal weight was defined as a BMI less than the 85th percentile. Overweight was defined as a BMI between the 85th and 95th percentile. Class 1 obesity was defined as a BMI greater than the 95th percentile up to 120% of the 95th percentile. A BMI between 120% and 140% of the 95th percentile was defined as Class 2 obesity. Class 3 was defined as a BMI above 140% of the 95th percentile. Primary outcomes were mean total cholesterol, triglyceride, low-density lipoprotein, and high-density lipoprotein levels (HDL). The sample included 14,481 non-Hispanic black (NHB) (N = 4710), non-Hispanic white (N = 4910), and Mexican American (N = 4861) subjects. Across all BMI categories, the NHB group had significantly lower mean TG and higher mean HDL levels (p < 0.0001). Ethnic variations in lipid profiles were found in severely obese youth. These findings could explain the lower prevalence of the metabolic syndrome in NHB youth. Ethnic-specific guidelines are necessary for improved identification of those at risk at all levels of obesity.

Hyperspectral analysis of the ultramafic complex and adjacent lithologies at Mordor, NT, Australia

USGS Publications Warehouse

Rowan, L.C.; Simpson, C.J.; Mars, J.C.

2004-01-01

The Mordor Complex consists of a series of potassic ultramafic rocks which were intruded into Proterozoic felsic gneisses and amphibolite and are overlain by quartzite and unconsolidated deposits. In situ and laboratory 0.4 to 2.5 ??m reflectance spectra show Al-OH absorption features caused by absorption in muscovite, kaolinite, and illite/smectite in syenite, granitic gneiss, quartzite and unconsolidated sedimentary deposits, and Fe,Mg-OH features due to phlogopite, biotite, epidote, and hornblende in the mafic and ultramafic rocks. Ferrous-iron absorption positioned near 1.05 ??m is most intense in peridotite reflectance spectra. Ferric-iron absorption is intense in most of the felsic lithologies. HyMap data were recorded in 126 narrow bands from 0.43 to 2.5 ??m along a 7-km-wide swath with approximately 6-m spatial resolution. Correction of the data to spectral reflectance was accomplished by reference to in situ measurements of an extensive, alluvial plain. Spectral classes for matched filter processing were selected by using the pixel purity index procedure and analysis of in situ and laboratory spectra. Considering the spatial distribution of the resulting 14 classes, some classes were combined, which produced eight classes characterized by Al-OH absorption features, and three Fe,Mg-OH absorption-feature classes. Comparison of the distribution of these 11 spectral classes to a generalized lithologic map of the study area shows that the spectral distinction among the eight Al-OH classes is related to variations in primary lithology, weathering products, and vegetation density. Quartzite is represented in three classes, syenite corresponds to a single scattered class, quartz-muscovite-biotite schist defines a single very coherent class, and unconsolidated sediments are portrayed in four classes. The three mafic-ultramafic classes are distinguished on the basis of generally intense Fe,Mg-OH and ferrous-iron absorption features. A single class represents the main Mordor ultramafic mass. Epidote-bearing rocks define another class, which corresponds to biotite gneiss and, in the southern part of the area, to fracture zones. The third class, which exhibits Al-OH, as well as Fe,Mg-OH features, represents hornblende gneiss and other mafic gneisses. These results indicate the importance of analyzing the VNIR and SWIR spectral shape and albedo, as well as analyzing specific spectral features, for mapping lithologic units in this weathered terrain. ?? 2004 Elsevier Inc. All rights reserved.

Designing Visual Methods of Communicating Visual Content with Art History Software.

ERIC Educational Resources Information Center

Schiferl, Ellen

Art history is a hybrid discipline that combines the verbal with the visual, yet the limiting verbal approach traditionally has defined the field. Another problem at the university level is that different types of classes define visually literacy differently; for example, art education programs emphasize perceptual and cognitive angles while art…

Taking an intersectional approach to define latent classes of socioeconomic status, ethnicity and migration status for psychiatric epidemiological research.

PubMed

Goodwin, L; Gazard, B; Aschan, L; MacCrimmon, S; Hotopf, M; Hatch, S L

2017-04-09

Inequalities in mental health are well documented using individual social statuses such as socioeconomic status (SES), ethnicity and migration status. However, few studies have taken an intersectional approach to investigate inequalities in mental health using latent class analysis (LCA). This study will examine the association between multiple indicator classes of social identity with common mental disorder (CMD). Data on CMD symptoms were assessed in a diverse inner London sample of 1052 participants in the second wave of the South East London Community Health study. LCA was used to define classes of social identity using multiple indicators of SES, ethnicity and migration status. Adjusted associations between CMD and both individual indicators and multiple indicators of social identity are presented. LCA identified six groups that were differentiated by varying levels of privilege and disadvantage based on multiple SES indicators. This intersectional approach highlighted nuanced differences in odds of CMD, with the economically inactive group with multiple levels of disadvantage most likely to have a CMD. Adding ethnicity and migration status further differentiated between groups. The migrant, economically inactive and White British, economically inactive classes both had increased odds of CMD. This is the first study to examine the intersections of SES, ethnicity and migration status with CMD using LCA. Results showed that both the migrant, economically inactive and the White British, economically inactive classes had a similarly high prevalence of CMD. Findings suggest that LCA is a useful methodology for investigating health inequalities by intersectional identities.

Preferential attachment and growth dynamics in complex systems

NASA Astrophysics Data System (ADS)

Yamasaki, Kazuko; Matia, Kaushik; Buldyrev, Sergey V.; Fu, Dongfeng; Pammolli, Fabio; Riccaboni, Massimo; Stanley, H. Eugene

2006-09-01

Complex systems can be characterized by classes of equivalency of their elements defined according to system specific rules. We propose a generalized preferential attachment model to describe the class size distribution. The model postulates preferential growth of the existing classes and the steady influx of new classes. According to the model, the distribution changes from a pure exponential form for zero influx of new classes to a power law with an exponential cut-off form when the influx of new classes is substantial. Predictions of the model are tested through the analysis of a unique industrial database, which covers both elementary units (products) and classes (markets, firms) in a given industry (pharmaceuticals), covering the entire size distribution. The model’s predictions are in good agreement with the data. The paper sheds light on the emergence of the exponent τ≈2 observed as a universal feature of many biological, social and economic problems.

Definition of spectrally separable classes for soil survey research

NASA Technical Reports Server (NTRS)

Cipra, J. E.; Swain, P. H.; Gill, J. H.; Baumgardner, M. F.; Kristof, S. J.

1972-01-01

A procedure is outlined for defining spectral classes such that the differences between classes can be quantified. It also facilitates determination of a number of classes such that the classes are spectrally discriminable. This is accomplished by partitioning the data into many classes and then combining similar spectral classes on the basis of appropriate criteria. Multispectral data were collected over a 12-mile flightline in White County, Indiana, in connection with the 1971 Corn Blight Watch Experiment. Data were collected in May by the University of Michigan airborne scanning spectrometer at an altitude of 5000 feet. Spectral maps resulting from the analysis were compared to existing soil surveys of the National Cooperative Soil Survey. The method should help determine the extent to which spectral properties of soil surfaces can be associated with morphologic and topographic differences of interest to soil surveyors engaged in operational soil mapping.

Periodic GMP Matrices

NASA Astrophysics Data System (ADS)

Eichinger, Benjamin

2016-07-01

We recall criteria on the spectrum of Jacobi matrices such that the corresponding isospectral torus consists of periodic operators. Motivated by those known results for Jacobi matrices, we define a new class of operators called GMP matrices. They form a certain Generalization of matrices related to the strong Moment Problem. This class allows us to give a parametrization of almost periodic finite gap Jacobi matrices by periodic GMP matrices. Moreover, due to their structural similarity we can carry over numerous results from the direct and inverse spectral theory of periodic Jacobi matrices to the class of periodic GMP matrices. In particular, we prove an analogue of the remarkable ''magic formula'' for this new class.

Quantification of soil mapping by digital analysis of LANDSAT data. [Clinton County, Indiana

NASA Technical Reports Server (NTRS)

Kirschner, F. R.; Kaminsky, S. A.; Hinzel, E. J.; Sinclair, H. R.; Weismiller, R. A.

1977-01-01

Soil survey mapping units are designed such that the dominant soil represents the major proportion of the unit. At times, soil mapping delineations do not adequately represent conditions as stated in the mapping unit descriptions. Digital analysis of LANDSAT multispectral scanner (MSS) data provides a means of accurately describing and quantifying soil mapping unit composition. Digital analysis of LANDSAT MSS data collected on 9 June 1973 was used to prepare a spectral soil map for a 430-hectare area in Clinton County, Indiana. Fifteen spectral classes were defined, representing 12 soil and 3 vegetation classes. The 12 soil classes were grouped into 4 moisture regimes based upon their spectral responses; the 3 vegetation classes were grouped into one all-inclusive class.

The Quantitative Criteria Based on the Fractal Dimensions, Entropy, and Lacunarity for the Spatial Distribution of Cancer Cell Nuclei Enable Identification of Low or High Aggressive Prostate Carcinomas

PubMed Central

Waliszewski, Przemyslaw

2016-01-01

Background: Tumor grading, PSA concentration, and stage determine a risk of prostate cancer patients with accuracy of about 70%. An approach based on the fractal geometrical model was proposed to eliminate subjectivity from the evaluation of tumor aggressiveness and to improve the prediction. This study was undertaken to validate classes of equivalence for the spatial distribution of cancer cell nuclei in a larger, independent set of prostate carcinomas. Methods: The global fractal capacity D0, information D1 and correlation D2 dimension, the local fractal dimension (LFD) and the local connected fractal dimension (LCFD), Shannon entropy H and lacunarity λ were measured using computer algorithms in digitalized images of both the reference set (n = 60) and the test set (n = 208) of prostate carcinomas. Results: Prostate carcinomas were re-stratified into seven classes of equivalence. The cut-off D0-values 1.5450, 1.5820, 1.6270, 1.6490, 1.6980, 1.7640 defined the classes from C1 to C7, respectively. The other measures but the D1 failed to define the same classes of equivalence. The pairs (D0, LFD), (D0, H), (D0, λ), (D1, LFD), (D1, H), (D1, λ) characterized the spatial distribution of cancer cell nuclei in each class. The co-application of those measures enabled the subordination of prostate carcinomas to one out of three clusters associated with different tumor aggressiveness. For D0 < 1.5820, LFD < 1.3, LCFD > 1.5, H < 0.7, and λ > 0.8, the class C1 or C2 contains low complexity low aggressive carcinomas exclusively. For D0 > 1.6980, LFD > 1.7644, LCFD > 1.7051, H > 0.9, and λ < 0.7, the class C6 or C7 contains high complexity high aggressive carcinomas. Conclusions: The cut-off D0-values defining the classes of equivalence were validated in this study. The cluster analysis suggested that the number of the subjective Gleason grades and the number of the objective classes of equivalence could be decreased from seven to three without a loss of clinically relevant information. Two novel quantitative criteria based on the complexity and the diversity measures enabled the identification of low or high aggressive prostate carcinomas and should be verified in the future multicenter, randomized studies. PMID:26903883

Conserved domains and SINE diversity during animal evolution.

PubMed

Luchetti, Andrea; Mantovani, Barbara

2013-10-01

Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata-Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs. © 2013 Elsevier Inc. All rights reserved.

Cell lineage analysis in human brain using endogenous retroelements

PubMed Central

Evrony, Gilad D.; Lee, Eunjung; Mehta, Bhaven K.; Benjamini, Yuval; Johnson, Robert M.; Cai, Xuyu; Yang, Lixing; Haseley, Psalm; Lehmann, Hillel S.; Park, Peter J.; Walsh, Christopher A.

2015-01-01

Summary Somatic mutations occur during brain development and are increasingly implicated as a cause of neurogenetic disease. However, the patterns in which somatic mutations distribute in the human brain are unknown. We used high-coverage whole-genome sequencing of single neurons from a normal individual to identify spontaneous somatic mutations as clonal marks to track cell lineages in human brain. Somatic mutation analyses in >30 locations throughout the nervous system identified multiple lineages and sub-lineages of cells marked by different LINE-1 (L1) retrotransposition events and subsequent mutation of poly-A microsatellites within L1. One clone contained thousands of cells limited to the left middle frontal gyrus, whereas a second distinct clone contained millions of cells distributed over the entire left hemisphere. These patterns mirror known somatic mutation disorders of brain development, and suggest that focally distributed mutations are also prevalent in normal brains. Single-cell analysis of somatic mutation enables tracing of cell lineage clones in human brain. PMID:25569347

Gene 2 of the sigma rhabdovirus genome encodes the P protein, and gene 3 encodes a protein related to the reverse transcriptase of retroelements.

PubMed

Landès-Devauchelle, C; Bras, F; Dezélée, S; Teninges, D

1995-11-10

The nucleotide sequence of the genes 2 and 3 of the Drosophila rhabdovirus sigma was determined from cDNAs to viral genome and poly(A)+ mRNAs. Gene 2 comprises 1032 nucleotides and contains a long ORF encoding a molecular weight 35,208 polypeptide present in infected cells and in virions which migrates in SDS-PAGE as a doublet of M(r) about 60 kDa. The distribution of acidic charges as well as the electrophoretic properties of the protein are characteristic of the rhabdovirus P proteins. Gene 3 comprises 923 nucleotides and contains a long ORF capable of coding a polypeptide of 298 amino acids of MW 33,790. The putative protein (PP3) is similar in size to a minor component of the virions. Computer analysis shows that the sequence of PP3 contains three motifs related to the conserved motifs of reverse transcriptases.

Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

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

Schulman, Al

2009-08-09

Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromericmore » regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops« less

DGR mutagenic transposition occurs via hypermutagenic reverse transcription primed by nicked template RNA

PubMed Central

Naorem, Santa S.; Han, Jin; Wang, Shufang; Lee, William R.; Heng, Xiao; Miller, Jeff F.

2017-01-01

Diversity-generating retroelements (DGRs) are molecular evolution machines that facilitate microbial adaptation to environmental changes. Hypervariation occurs via a mutagenic retrotransposition process from a template repeat (TR) to a variable repeat (VR) that results in adenine-to-random nucleotide conversions. Here we show that reverse transcription of the Bordetella phage DGR is primed by an adenine residue in TR RNA and is dependent on the DGR-encoded reverse transcriptase (bRT) and accessory variability determinant (Avd ), but is VR-independent. We also find that the catalytic center of bRT plays an essential role in site-specific cleavage of TR RNA for cDNA priming. Adenine-specific mutagenesis occurs during reverse transcription and does not involve dUTP incorporation, indicating it results from bRT-catalyzed misincorporation of standard deoxyribonucleotides. In vivo assays show that this hybrid RNA-cDNA molecule is required for mutagenic transposition, revealing a unique mechanism of DNA hypervariation for microbial adaptation. PMID:29109248

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

PubMed Central

Lescot, Magali; Hingamp, Pascal; Kojima, Kenji K; Villar, Emilie; Romac, Sarah; Veluchamy, Alaguraj; Boccara, Martine; Jaillon, Olivier; Iudicone, Daniele; Bowler, Chris; Wincker, Patrick; Claverie, Jean-Michel; Ogata, Hiroyuki

2016-01-01

Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage. PMID:26613339

Repression of chimeric transcripts emanating from endogenous retrotransposons by a sequence-specific transcription factor

PubMed Central

2014-01-01

Background Retroviral elements are pervasively transcribed and dynamically regulated during development. While multiple histone- and DNA-modifying enzymes have broadly been associated with their global silencing, little is known about how the many diverse retroviral families are each selectively recognized. Results Here we show that the zinc finger protein Krüppel-like Factor 3 (KLF3) specifically silences transcription from the ORR1A0 long terminal repeat in murine fetal and adult erythroid cells. In the absence of KLF3, we detect widespread transcription from ORR1A0 elements driven by the master erythroid regulator KLF1. In several instances these aberrant transcripts are spliced to downstream genic exons. One such chimeric transcript produces a novel, dominant negative isoform of PU.1 that can induce erythroid differentiation. Conclusions We propose that KLF3 ensures the integrity of the murine erythroid transcriptome through the selective repression of a particular retroelement and is likely one of multiple sequence-specific factors that cooperate to achieve global silencing. PMID:24946810

International Multilingual Student Writers' (Re)Negotiation of Their Languages and Literacies Practices in a First-Year Multilingual Composition Class

ERIC Educational Resources Information Center

Prikhodko, Maria Y.

2017-01-01

This qualitative case study explores how five multilingual student writers (re)negotiate their multilingual literacies histories with emergent U.S. academic writing conventions as part of a first-year multilingual composition (FYMC) class. In pursuit of examining this (re)negotiation, first, I define multilingual literacies as nomadic (Ciolfi…

National Longitudinal Study of the High School Class of 1972: Critical Data Base. 22U-884.

ERIC Educational Resources Information Center

Talbert, Robin

The National Longitudinal Study of the High School Class of 1972 (NLS) critical data base contains 151 items (plus background information) from the base year and followup questionnaires; about thirty-seven percent of all items. This set of critical items consists of: (1) basic demographic variables; (2) items necessary for defining activity states…

Uses of Integrated Media Instruction in a Self-Contained Class for Children with Mild Disabilities.

ERIC Educational Resources Information Center

Narita, Shigeru

This conference paper describes the use of integrated media-oriented instruction in a self-contained class at Yokohama Municipal Elementary School in Japan. Three students with mild disabilities, in grades 5 and 6, participated in the project. Integrated media (IM) is defined as the linkage of text, sound, video, graphics, and the computer in such…

Do Caste and Class Define Inequality? Revisiting Education in a Kerala Village

ERIC Educational Resources Information Center

Scaria, Suma

2014-01-01

Is there a strong correlation between caste and class in access to education, especially higher education? This is the broader question addressed by the study in the context of Kerala, the southernmost state in India, with impressive conventional indicators in education. Micro-level insights based on the study of a village in Kerala show that old…

Genomic mechanisms of stress tolerance for the industrial yeast Saccharomyces cerevisiae against the major chemical classes of inhibitors derived from lignocellulosic biomass conversion

USDA-ARS?s Scientific Manuscript database

Scientists at ARS developed tolerant industrial yeast that is able to reduce major chemical classes of inhibitors into less toxic or none toxic compounds while producing ethanol. Using genomic studies, we defined mechanisms of in situ detoxification involved in novel gene functions, vital cofactor r...

Application of the SNoW machine learning paradigm to a set of transportation imaging problems

NASA Astrophysics Data System (ADS)

Paul, Peter; Burry, Aaron M.; Wang, Yuheng; Kozitsky, Vladimir

2012-01-01

Machine learning methods have been successfully applied to image object classification problems where there is clear distinction between classes and where a comprehensive set of training samples and ground truth are readily available. The transportation domain is an area where machine learning methods are particularly applicable, since the classification problems typically have well defined class boundaries and, due to high traffic volumes in most applications, massive roadway data is available. Though these classes tend to be well defined, the particular image noises and variations can be challenging. Another challenge is the extremely high accuracy typically required in most traffic applications. Incorrect assignment of fines or tolls due to imaging mistakes is not acceptable in most applications. For the front seat vehicle occupancy detection problem, classification amounts to determining whether one face (driver only) or two faces (driver + passenger) are detected in the front seat of a vehicle on a roadway. For automatic license plate recognition, the classification problem is a type of optical character recognition problem encompassing multiple class classification. The SNoW machine learning classifier using local SMQT features is shown to be successful in these two transportation imaging applications.

On complexity and homogeneity measures in predicting biological aggressiveness of prostate cancer; Implication of the cellular automata model of tumor growth.

PubMed

Tanase, Mihai; Waliszewski, Przemyslaw

2015-12-01

We propose a novel approach for the quantitative evaluation of aggressiveness in prostate carcinomas. The spatial distribution of cancer cell nuclei was characterized by the global spatial fractal dimensions D0, D1, and D2. Two hundred eighteen prostate carcinomas were stratified into the classes of equivalence using results of ROC analysis. A simulation of the cellular automata mix defined a theoretical frame for a specific geometric representation of the cell nuclei distribution called a local structure correlation diagram (LSCD). The LSCD and dispersion Hd were computed for each carcinoma. Data mining generated some quantitative criteria describing tumor aggressiveness. Alterations in tumor architecture along progression were associated with some changes in both shape and the quantitative characteristics of the LSCD consistent with those in the automata mix model. Low-grade prostate carcinomas with low complexity and very low biological aggressiveness are defined by the condition D0 < 1.545 and Hd < 38. High-grade carcinomas with high complexity and very high biological aggressiveness are defined by the condition D0 > 1.764 and Hd < 38. The novel homogeneity measure Hd identifies carcinomas with very low aggressiveness within the class of complexity C1 or carcinomas with very high aggressiveness in the class C7. © 2015 Wiley Periodicals, Inc.

Latent profile analyses of posttraumatic stress disorder, depression and generalized anxiety disorder symptoms in trauma-exposed soldiers.

PubMed

Contractor, Ateka A; Elhai, Jon D; Fine, Thomas H; Tamburrino, Marijo B; Cohen, Gregory; Shirley, Edwin; Chan, Philip K; Liberzon, Israel; Galea, Sandro; Calabrese, Joseph R

2015-09-01

Posttraumatic stress disorder (PTSD) is comorbid with major depressive disorder (MDD; Kessler et al., 1995) and generalized anxiety disorder (GAD; Brown et al., 2001). We aimed to (1) assess discrete patterns of post-trauma PTSD-depression-GAD symptoms using latent profile analyses (LPAs), and (2) assess covariates (gender, income, education, age) in defining the best fitting class solution. The PTSD Checklist (assessing PTSD symptoms), GAD-7 scale (assessing GAD symptoms), and Patient Health Questionnaire-9 (assessing depression) were administered to 1266 trauma-exposed Ohio National Guard soldiers. Results indicated three discrete subgroups based on symptom patterns with mild (class 1), moderate (class 2) and severe (class 3) levels of symptomatology. Classes differed in symptom severity rather than symptom type. Income and education significantly predicted class 1 versus class 3 membership, and class 2 versus class 3. In conclusion, there is heterogeneity regarding severity of PTSD-depression-GAD symptomatology among trauma-exposed soldiers, with income and education predictive of class membership. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fingerprints and cardiovascular risk. The San Valentino fingerprint vascular screening project (SanVal/FP).

PubMed

Belcaro, G; Cesarone, M R; Ledda, A; Cornelli, U; Dugall, M; Di Renzo, A; Hosoi, M; Stuard, S; Vinciguerra, G; Pellegrini, L; Gizzi, G

2008-10-01

Fingerprints (FP), characteristic of humans, are impressions due to skin marks (ridges) on fingertips. Ridges are present on fingers/hands forming curved lines of different sizes/patterns. The point where a line stops or splits is defined typica' (their number/amount constitute identification patterns). FP are permanent and unique. This study compared FP patterns with cardiovascular risk factors: 7 main types of FP were used: 1. Arch: lines form waves from one site to the other side. 2. Tentarch: like arches but with a rising stick in the middle. 3. Loop: lines coming from one site returning in the middle to the same site. 4. Double loop: like loops but with two loops inside: one standing, one hanging. 5. Pocked loop: like the loop but with a small circle in the turning point. 6. Whorl: lines make circles. 7. Mixed figure: composed of different figures. There are two kinds of real typica: A. Ending line; B. Splitting lines (bifurcations). Several combinations may result. Ultrasound evaluation of carotid/femoral arteries in asymptomatic subjects. Arteries were evaluated with high-resolution ultrasound at the bifurcations. Four classes were defined: 1: normal intima-media (IMT) complex; 2: IMT thickening; 3: non-stenosing plaques (<50% stenosis); 4: stenosing plaque (>50%). Subjects in classes 1, 2, 3 were included into the analysis made comparing FP patterns and ultrasound. For each FP pattern: A. the main proportion of subjects with cardiovacular risk factors (91%) had arches (41.2%) and loops (either single, 38.2% or double 11.7% for a total of 49.9%). B. The remaining classes were statistically less important. C. The number of ridges per square mm was comparable in all pattern classes. D. The analysis of typica and other ridges characteristics requires a more elaborated system. Future research must define simple, low cost screening methods for preselection of subjects at higher cardiovascular risk or for exclusion of low risk subjects. The evaluation of fingerprint pattern may be useful to define risk groups.

Definition of improvement in juvenile idiopathic arthritis using the juvenile arthritis disease activity score.

PubMed

Horneff, Gerd; Becker, Ingrid

2014-07-01

The aim of this study was to define improvement thresholds for the Juvenile Arthritis Disease Activity Score (JADAS). Physicians' and parents' judgements on treatment efficacy, the ACR paediatric response measure (PedACR) and JADAS were extracted from BIKER. Patients were categorized by baseline classes in the 10-joint JADAS (JADAS10) as low (5 to <15), moderate (15 to <25) and high (25 to ≤40). Cut-offs for defining improvement following treatment with biologics or MTX were chosen by calculating the interquartile ranges (IQRs) of the judgement groups and considering the accuracy, sensitivity and specificity of the resulting model. Differences in the change of JADAS10 by JIA category were also analysed by analysis of variance (ANOVA). Sensitivity, specificity and accuracy were calculated. A total of 1315 treatment courses were analysed. The ANOVA of the JIA categories showed no significant differences of the mean JADAS10 in all baseline classes and IQRs also showed good overall limits. Therefore all JIA categories were combined for a collective cut-off. Analysis by baseline class revealed clear cut-off points. Improvement could be defined by the minimal decrease in the JADAS10 in baseline class low by 4 (41%), moderate by 10 (53%) and high by 17 (57%). The model shows values for accuracy from 75.6 to 85.5% and comparable values for sensitivity and specificity. Improvement after 3 months can be defined efficiently by the decrease of the JADAS10, depending on the baseline JADAS10 score, which specifies low, moderate or high disease activity. Our model demonstrates clear cut-off values. The JADAS10 may be used in addition to ACR criteria in clinical trials. Also, since the JADAS10 can easily be calculated at each patient visit, it also can be used for clinical decisions. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A Harnack's inequality for mixed type evolution equations

NASA Astrophysics Data System (ADS)

Paronetto, Fabio

2016-03-01

We define a homogeneous parabolic De Giorgi classes of order 2 which suits a mixed type class of evolution equations whose simplest example is μ (x)∂u/∂t - Δu = 0 where μ can be positive, null and negative, so in particular elliptic-parabolic and forward-backward parabolic equations are included. For functions belonging to this class we prove local boundedness and show a Harnack inequality which, as by-products, gives Hölder-continuity, in particular in the interface I where μ changes sign, and a maximum principle.

LFSPMC: Linear feature selection program using the probability of misclassification

NASA Technical Reports Server (NTRS)

Guseman, L. F., Jr.; Marion, B. P.

1975-01-01

The computational procedure and associated computer program for a linear feature selection technique are presented. The technique assumes that: a finite number, m, of classes exists; each class is described by an n-dimensional multivariate normal density function of its measurement vectors; the mean vector and covariance matrix for each density function are known (or can be estimated); and the a priori probability for each class is known. The technique produces a single linear combination of the original measurements which minimizes the one-dimensional probability of misclassification defined by the transformed densities.

A class of nonideal solutions. 1: Definition and properties

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.

1983-01-01

A class of nonideal solutions is defined by constructing a function to represent the composition dependence of thermodynamic properties for members of the class, and some properties of these solutions are studied. The constructed function has several useful features: (1) its parameters occur linearly; (2) it contains a logarithmic singularity in the dilute solution region and contains ideal solutions and regular solutions as special cases; and (3) it is applicable to N-ary systems and reduces to M-ary systems (M or = N) in a form-invariant manner.

[Differences between proposals for implementation of the social class concept in epidemiological studies

PubMed

Solla

1996-07-01

This article compares different proposals for the implementation of the concept of social class and analyzes the alternatives used in each proposal, considering previous epidemiological studies on this issue and the potential of such a concept as a central category in studies on social determination in the health/disease process. Seven basic differences were identified, pertaining to the following aspects: class structure; research objective; the social class concept as a reference; the decision as to which individual has his/her occupational activity taken as defining the family's social class; the class status of the unemployed, housewives, and the retired; class status of students; and criteria for distinguishing between the "bourgeoisie", "petty bourgeoisie", "new petty bourgeoisie", and "proletariat" and whether there is a specific flow in certain population groups. Given the observed differences and underlying theoretical models, this study discusses problems related to the fact that the use of a specific concept of social class can have various implementation models.

Automated compound classification using a chemical ontology.

PubMed

Bobach, Claudia; Böhme, Timo; Laube, Ulf; Püschel, Anett; Weber, Lutz

2012-12-29

Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning logic allows to translate chemistry expert knowledge into a computer interpretable form, preventing erroneous compound assignments and allowing automatic compound classification. The automated assignment of compounds in databases, compound structure files or text documents to their related ontology classes is possible through the integration with a chemical structure search engine. As an application example, the annotation of chemical structure files with a prototypic ontology is demonstrated.

Automated compound classification using a chemical ontology

PubMed Central

2012-01-01

Background Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. Results In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. Conclusions A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning logic allows to translate chemistry expert knowledge into a computer interpretable form, preventing erroneous compound assignments and allowing automatic compound classification. The automated assignment of compounds in databases, compound structure files or text documents to their related ontology classes is possible through the integration with a chemical structure search engine. As an application example, the annotation of chemical structure files with a prototypic ontology is demonstrated. PMID:23273256

The Onfp Class in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Walborn, Nolan R.; Howarth, Ian D.; Evans, Christopher J.; Crowther, Paul A.; Moffat, Anthony F. J.; St-Louis, Nicole; Fariña, Cecilia; Bosch, Guillermo L.; Morrell, Nidia I.; Barbá, Rodolfo H.; van Loon, Jacco Th.

2010-03-01

The Onfp class of rotationally broadened, hot spectra was defined some time ago in the Galaxy, where its membership to date numbers only eight. The principal defining characteristic is a broad, centrally reversed He II λ 4686 emission profile; other emission and absorption lines are also rotationally broadened. Recent surveys in the Magellanic Clouds (MCs) have brought the class membership there, including some related spectra, to 28. We present a survey of the spectral morphology and rotational velocities, as a first step toward elucidating the nature of this class. Evolved, rapidly rotating hot stars are not expected theoretically, because the stellar winds should brake the rotation. Luminosity classification of these spectra is not possible, because the principal criterion (He II λ4686) is peculiar; however, the MCs provide reliable absolute magnitudes, which show that they span the entire range from dwarfs to supergiants. The Onfp line-broadening distribution is distinct and shifted toward larger values from those of normal O dwarfs and supergiants with >99.99% confidence. All cases with multiple observations show line-profile variations, which even remove some objects from the class temporarily. Some of them are spectroscopic binaries; it is possible that the peculiar profiles may have multiple causes among different objects. The origin and future of these stars are intriguing; for instance, they could be stellar mergers and/or gamma-ray-burst progenitors.

Defining fitness in an uncertain world.

PubMed

Crewe, Paul; Gratwick, Richard; Grafen, Alan

2018-04-01

The recently elucidated definition of fitness employed by Fisher in his fundamental theorem of natural selection is combined with reproductive values as appropriately defined in the context of both random environments and continuing fluctuations in the distribution over classes in a class-structured population. We obtain astonishingly simple results, generalisations of the Price Equation and the fundamental theorem, that show natural selection acting only through the arithmetic expectation of fitness over all uncertainties, in contrast to previous studies with fluctuating demography, in which natural selection looks rather complicated. Furthermore, our setting permits each class to have its characteristic ploidy, thus covering haploidy, diploidy and haplodiploidy at the same time; and allows arbitrary classes, including continuous variables such as condition. The simplicity is achieved by focussing just on the effects of natural selection on genotype frequencies: while other causes are present in the model, and the effect of natural selection is assessed in their presence, these causes will have their own further effects on genoytpe frequencies that are not assessed here. Also, Fisher's uses of reproductive value are shown to have two ambivalences, and a new axiomatic foundation for reproductive value is endorsed. The results continue the formal darwinism project, and extend support for the individual-as-maximising-agent analogy to finite populations with random environments and fluctuating class-distributions. The model may also lead to improved ways to measure fitness in real populations.

Lithologic analysis from multispectral thermal infrared data of the alkalic rock complex at Iron Hill, Colorado

USGS Publications Warehouse

Watson, K.; Rowan, L.C.; Bowers, T.L.; Anton-Pacheco, C.; Gumiel, P.; Miller, S.H.

1996-01-01

Airborne thermal-infrared multispectral scanner (TIMS) data of the Iron Hill carbonatite-alkalic igneous rock complex in south-central Colorado are analyzed using a new spectral emissivity ratio algorithm and confirmed by field examination using existing 1:24 000-scale geologic maps and petrographic studies. Color composite images show that the alkalic rocks could be clearly identified and that differences existed among alkalic rocks in several parts of the complex. An unsupervised classification algorithm defines four alkalic rock classes within the complex: biotitic pyroxenite, uncompahgrite, augitic pyroxenite, and fenite + nepheline syenite. Felsic rock classes defined in the surrounding country rock are an extensive class consisting of tuff, granite, and felsite, a less extensive class of granite and felsite, and quartzite. The general composition of the classes can be determined from comparisons of the TIMS spectra with laboratory spectra. Carbonatite rocks are not classified, and we attribute that to the fact that dolomite, the predominant carbonate mineral in the complex, has a spectral feature that falls between TIMS channels 5 and 6. Mineralogical variability in the fenitized granite contributed to the nonuniform pattern of the fenite-nepheline syenite class. The biotitic pyroxenite, which resulted from alteration of the pyroxenite, is spatially associated and appears to be related to narrow carbonatite dikes and sills. Results from a linear unmixing algorithm suggest that the detected spatial extent of the two mixed felsic rock classes was sensitive to the amount of vegetation cover. These results illustrate that spectral thermal infrared data can be processed to yield compositional information that can be a cost-effective tool to target mineral exploration, particularly in igneous terranes.

Nuclear congression and membrane fusion: two distinct events in the yeast karyogamy pathway

PubMed Central

1994-01-01

Karyogamy is the process where haploid nuclei fuse to form a diploid nucleus during yeast mating. We devised a novel genetic screen that identified five new karyogamy (KAR) genes and three new cell fusion (FUS) genes. The kar mutants fell into two classes that represent distinct events in the yeast karyogamy pathway. Class I mutations blocked congression of the nuclei due to cytoplasmic microtubule defects. In Class II mutants, nuclear congression proceeded and the membranes of apposed nuclei were closely aligned but unfused. In vitro, Class II mutant membranes were defective in a homotypic ER/nuclear membrane fusion assay. We propose that Class II mutants define components of a novel membrane fusion complex which functions during vegetative growth and is recruited for karyogamy. PMID:8051211

49 CFR 105.5 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... hazardous substances, hazardous wastes, marine pollutants, elevated temperature materials, materials... defining criteria for hazard classes and divisions in part 173 of subchapter C of this chapter. Hazardous...

A class of convergent neural network dynamics

NASA Astrophysics Data System (ADS)

Fiedler, Bernold; Gedeon, Tomáš

1998-01-01

We consider a class of systems of differential equations in Rn which exhibits convergent dynamics. We find a Lyapunov function and show that every bounded trajectory converges to the set of equilibria. Our result generalizes the results of Cohen and Grossberg (1983) for convergent neural networks. It replaces the symmetry assumption on the matrix of weights by the assumption on the structure of the connections in the neural network. We prove the convergence result also for a large class of Lotka-Volterra systems. These are naturally defined on the closed positive orthant. We show that there are no heteroclinic cycles on the boundary of the positive orthant for the systems in this class.

Popular Culture, English Out-of-Class Activities, and Learner Autonomy among Highly Proficient Secondary Students in Hong Kong

ERIC Educational Resources Information Center

Chan, Hoi Wing

2016-01-01

This paper reports on how and why proficient learners of English in Hong Kong participated in popular culture, out-of-class activities, with an emphasis on their development of learner autonomy. Autonomy in language learning is defined as an individual's ability and responsibility to take charge of his or her own learning [1]. Out-of-class…

A Graphic Survey of Book Publication, 1890-1916. Bulletin, 1917, No. 14

ERIC Educational Resources Information Center

Woodward, Fred E.

1917-01-01

The rapid increase in the number of books published in the United States, especially during the past decade, has been the subject of much comment. Statistics are collected regularly by the trade papers, and these figures give the number of books for each year in each of several well-defined classes. There are at the present time 24 classes: as…

A First-Day "Realia" Activity: "Was ist in dem Umschlag?"

ERIC Educational Resources Information Center

Bjornstad, Jennifer I.

2004-01-01

The first day of class is in many ways the most important one of the term. Students come into the classroom alert to everything around them, eager to piece together clues that will answer their ill-defined yet urgent question: "What is this course going to be like?" What teachers say and do on the first day of class is crucial, creating a first…

26 CFR 1.883-2T - Treatment of publicly-traded corporations (temporary).

Code of Federal Regulations, 2010 CFR

2010-04-01

... shareholders, as defined in § 1.883-4(b)(1); (B) The total percentage of the value of the shares owned... outstanding shares in that class of stock as of the close of the taxable year, and the value of each class of stock in relation to the total value of all the corporation's shares outstanding as of the close of the...

Books Only Got Us so Far: The Need for Multi-Genre Inquiry

ERIC Educational Resources Information Center

Jewett, Pamela

2010-01-01

This study examines the instructional steps I took, based on gaps between what was happening in a graduate literacy class I taught and what I had intended to happen. This study describes the ways that I re-imagined the class and what came about when I created a pedagogical approach that featured multi-genre inquiry. I define inter-discursivity as…

42 CFR 83.17 - How will the Secretary report a final decision to add a class of employees to the Cohort and any...

Code of Federal Regulations, 2012 CFR

2012-10-01

... Secretary report a final decision to add a class of employees to the Cohort and any action of Congress... to the Cohort, the Secretary will transmit to Congress a report providing the designation, the... as defined by the Board, then the Secretary will transmit to Congress the report specified in...

42 CFR 83.17 - How will the Secretary report a final decision to add a class of employees to the Cohort and any...

Code of Federal Regulations, 2011 CFR

2011-10-01

... Secretary report a final decision to add a class of employees to the Cohort and any action of Congress... to the Cohort, the Secretary will transmit to Congress a report providing the designation, the... as defined by the Board, then the Secretary will transmit to Congress the report specified in...

42 CFR 83.17 - How will the Secretary report a final decision to add a class of employees to the Cohort and any...

Code of Federal Regulations, 2014 CFR

2014-10-01

... Secretary report a final decision to add a class of employees to the Cohort and any action of Congress... to the Cohort, the Secretary will transmit to Congress a report providing the designation, the... as defined by the Board, then the Secretary will transmit to Congress the report specified in...

42 CFR 83.17 - How will the Secretary report a final decision to add a class of employees to the Cohort and any...

Code of Federal Regulations, 2010 CFR

2010-10-01

... Secretary report a final decision to add a class of employees to the Cohort and any action of Congress... to the Cohort, the Secretary will transmit to Congress a report providing the designation, the... as defined by the Board, then the Secretary will transmit to Congress the report specified in...

42 CFR 83.17 - How will the Secretary report a final decision to add a class of employees to the Cohort and any...

Code of Federal Regulations, 2013 CFR

2013-10-01

... Secretary report a final decision to add a class of employees to the Cohort and any action of Congress... to the Cohort, the Secretary will transmit to Congress a report providing the designation, the... as defined by the Board, then the Secretary will transmit to Congress the report specified in...

Improving Estimates of Acceptable Growiing Stock in Young Upland Oak Forests in the Missouri Ozarks

Treesearch

Daniel C. Dey; Paul S. Johnson; H.E. Garrett

1998-01-01

Estimates of regeneration or growing stock in young oak forests may be too high unless criteria are established that define explicitly acceptable growing stock. In young hardwood stands, crown class can be used to identify acceptable growing stock because it is related to the future growth and survival of reproduction. A method is presented for assigning crown class...

Painting with the Multiple Intelligences: Defining Student Success and Permanence in Art Class

ERIC Educational Resources Information Center

Taspinar, Seyda Eraslan; Kaya, Ali

2016-01-01

Objectives of the study are to determine the effect of teaching based on multiple intelligence theory (TBMIT) in visual arts class on student success and permanence. Experimental design is used in the study. Study group is composed of students at 8th grade in 2012-2013 educational term at Atatürk Secondary School in Igdir city centre. Experimental…

An abstract class loader for the SSP and its implementation in TL.

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

Wickstrom, Gregory Lloyd; Winter, Victor Lono; Fraij, Fares

2004-08-01

The SSP is a hardware implementation of a subset of the JVM for use in high consequence embedded applications. In this context, a majority of the activities belonging to class loading, as it is defined in the specification of the JVM, can be performed statically. Static class loading has the net result of dramatically simplifying the design of the SSP as well as increasing its performance. Due to the high consequence nature of its applications, strong evidence must be provided that all aspects of the SSP have been implemented correctly. This includes the class loader. This article explores the possibilitymore » of formally verifying a class loader for the SSP implemented in the strategic programming language TL. Specifically, an implementation of the core activities of an abstract class loader is presented and its verification in ACL2 is considered.« less

Global stability of an age-structure epidemic model with imperfect vaccination and relapse

NASA Astrophysics Data System (ADS)

Cao, Bin; Huo, Hai-Feng; Xiang, Hong

2017-11-01

A new age-structured epidemic model with imperfect vaccination and relapse is proposed. The total population of our model is partitioned into five subclasses: susceptible class S, vaccinated class V, exposed class E, infectious class I and removed class R. Age-structures are equipped with in exposed and recovered classes. Furthermore, imperfect vaccination is also introduced in our model. The basic reproduction number R0 is defined and proved as a threshold parameter of the model. Asymptotic smoothness of solutions and uniform persistence of the system are showed via reformulating the system as a system of Volterra integral equation. Furthermore, by constructing proper Volterra-type Lyapunov functional we get when R0 < 1, the disease-free equilibrium is globally asymptotically stable. When R0 > 1, the endemic equilibrium is globally stable. Our results show that to increase the efficiency of vaccination and reduce influence of relapse are vital essential for controlling epidemic.

A cellular and regulatory map of the GABAergic nervous system of C. elegans

PubMed Central

Gendrel, Marie; Atlas, Emily G; Hobert, Oliver

2016-01-01

Neurotransmitter maps are important complements to anatomical maps and represent an invaluable resource to understand nervous system function and development. We report here a comprehensive map of neurons in the C. elegans nervous system that contain the neurotransmitter GABA, revealing twice as many GABA-positive neuron classes as previously reported. We define previously unknown glia-like cells that take up GABA, as well as 'GABA uptake neurons' which do not synthesize GABA but take it up from the extracellular environment, and we map the expression of previously uncharacterized ionotropic GABA receptors. We use the map of GABA-positive neurons for a comprehensive analysis of transcriptional regulators that define the GABA phenotype. We synthesize our findings of specification of GABAergic neurons with previous reports on the specification of glutamatergic and cholinergic neurons into a nervous system-wide regulatory map which defines neurotransmitter specification mechanisms for more than half of all neuron classes in C. elegans. DOI: http://dx.doi.org/10.7554/eLife.17686.001 PMID:27740909

Traffic sharing algorithms for hybrid mobile networks

NASA Technical Reports Server (NTRS)

Arcand, S.; Murthy, K. M. S.; Hafez, R.

1995-01-01

In a hybrid (terrestrial + satellite) mobile personal communications networks environment, a large size satellite footprint (supercell) overlays on a large number of smaller size, contiguous terrestrial cells. We assume that the users have either a terrestrial only single mode terminal (SMT) or a terrestrial/satellite dual mode terminal (DMT) and the ratio of DMT to the total terminals is defined gamma. It is assumed that the call assignments to and handovers between terrestrial cells and satellite supercells take place in a dynamic fashion when necessary. The objectives of this paper are twofold, (1) to propose and define a class of traffic sharing algorithms to manage terrestrial and satellite network resources efficiently by handling call handovers dynamically, and (2) to analyze and evaluate the algorithms by maximizing the traffic load handling capability (defined in erl/cell) over a wide range of terminal ratios (gamma) given an acceptable range of blocking probabilities. Two of the algorithms (G & S) in the proposed class perform extremely well for a wide range of gamma.

Defining the "Correct Form": Using Biomechanics to Develop Reliable and Valid Assessment Instruments

ERIC Educational Resources Information Center

Satern, Miriam N.

2011-01-01

Physical educators should be able to define the "correct form" they expect to see each student performing in their classes. Moreover, they should be able to go beyond assessing students' skill levels by measuring the outcomes (products) of movements (i.e., how far they throw the ball or how many successful attempts are completed) or counting the…

Toward a Predictive Model of Community College Student Success in Blended Classes

ERIC Educational Resources Information Center

Volchok, Edward

2018-01-01

This retrospective study evaluates early semester predictors of whether or not community college students will successfully complete blended or hybrid courses. These predictors are available to faculty by the fourth week of the semester. Success is defined as receiving a grade of C- or higher. Failure is defined as a grade below a C- or a…

Defining perennial, intermittent and ephemeral channels in eastern Kentucky: application to forestry best management practices

Treesearch

J. R. Svec; R. K. Kolka; J. W. Stringer

2003-01-01

In Kentucky stream classification is used to determine which forestry best management practice (BMP) to apply in riparian zones. Kentucky defines stream classes as follows (Stringer and others 1998): a) perennial streams that hold water throughout the year, b) intermittent streams that hold water during wet portions of the year, and c) ephemeral channels that hold...

77 FR 71131 - Implementation of the Middle Class Tax Relief and Job Creation Act of 2012; Establishment of a...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-29

... access to OADEs. Some OADEs are marketers that make autodialed calls on behalf of other entities, e.g... adopts the existing definition in its rules, as set forth in the TCPA context, and defines an ``emergency.... Definitions. As noted above, the Tax Relief Act does not define ``automatic dialing'' or ``robocall...

Iterated Hamiltonian type systems and applications

NASA Astrophysics Data System (ADS)

Tiba, Dan

2018-04-01

We discuss, in arbitrary dimension, certain Hamiltonian type systems and prove existence, uniqueness and regularity properties, under the independence condition. We also investigate the critical case, define a class of generalized solutions and prove existence and basic properties. Relevant examples and counterexamples are also indicated. The applications concern representations of implicitly defined manifolds and their perturbations, motivated by differential systems involving unknown geometries.

Data-driven classification of bipolar I disorder from longitudinal course of mood.

PubMed

Cochran, A L; McInnis, M G; Forger, D B

2016-10-11

The Diagnostic and Statistical Manual of Mental Disorder (DSM) classification of bipolar disorder defines categories to reflect common understanding of mood symptoms rather than scientific evidence. This work aimed to determine whether bipolar I can be objectively classified from longitudinal mood data and whether resulting classes have clinical associations. Bayesian nonparametric hierarchical models with latent classes and patient-specific models of mood are fit to data from Longitudinal Interval Follow-up Evaluations (LIFE) of bipolar I patients (N=209). Classes are tested for clinical associations. No classes are justified using the time course of DSM-IV mood states. Three classes are justified using the course of subsyndromal mood symptoms. Classes differed in attempted suicides (P=0.017), disability status (P=0.012) and chronicity of affective symptoms (P=0.009). Thus, bipolar I disorder can be objectively classified from mood course, and individuals in the resulting classes share clinical features. Data-driven classification from mood course could be used to enrich sample populations for pharmacological and etiological studies.

Genes in one megabase of the HLA class I region

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

Wei, H.; Fan, Wu-Fang; Xu, Hongxia

1993-11-15

To define the gene content of the HLA class I region, cDNA selection was applied to three overlapping yeast artificial chromosomes (YACs) that spanned 1 megabase (Mb) of this region of the human major histocompatibility complex. These YACs extended from the region centromeric to HLA-E to the region telomeric to HLA-F. In additions to the recognized class I genes and pseudogenes and the anonymous non-class-I genes described recently by the authors and others, 20 additional anonymous cDNA clones were identified from this 1-Mb region. They also identified a long repetitive DNA element in the region between HLA-B and HLA-E. Homologuesmore » of this outside of the HLA complex. The portion of the HLA class I region represented by these YACs shows an average gene density as high as the class II and class III regions. Thus, the high gene density portion of the HLA complex is extended to more than 3 Mb.« less

New Site Coefficients and Site Classification System Used in Recent Building Seismic Code Provisions

USGS Publications Warehouse

Dobry, R.; Borcherdt, R.D.; Crouse, C.B.; Idriss, I.M.; Joyner, W.B.; Martin, G.R.; Power, M.S.; Rinne, E.E.; Seed, R.B.

2000-01-01

Recent code provisions for buildings and other structures (1994 and 1997 NEHRP Provisions, 1997 UBC) have adopted new site amplification factors and a new procedure for site classification. Two amplitude-dependent site amplification factors are specified: Fa for short periods and Fv for longer periods. Previous codes included only a long period factor S and did not provide for a short period amplification factor. The new site classification system is based on definitions of five site classes in terms of a representative average shear wave velocity to a depth of 30 m (V?? s). This definition permits sites to be classified unambiguously. When the shear wave velocity is not available, other soil properties such as standard penetration resistance or undrained shear strength can be used. The new site classes denoted by letters A - E, replace site classes in previous codes denoted by S1 - S4. Site classes A and B correspond to hard rock and rock, Site Class C corresponds to soft rock and very stiff / very dense soil, and Site Classes D and E correspond to stiff soil and soft soil. A sixth site class, F, is defined for soils requiring site-specific evaluations. Both Fa and Fv are functions of the site class, and also of the level of seismic hazard on rock, defined by parameters such as Aa and Av (1994 NEHRP Provisions), Ss and S1 (1997 NEHRP Provisions) or Z (1997 UBC). The values of Fa and Fv decrease as the seismic hazard on rock increases due to soil nonlinearity. The greatest impact of the new factors Fa and Fv as compared with the old S factors occurs in areas of low-to-medium seismic hazard. This paper summarizes the new site provisions, explains the basis for them, and discusses ongoing studies of site amplification in recent earthquakes that may influence future code developments.

Operationalizing Max Weber's probability concept of class situation: the concept of social class.

PubMed

Smith, Ken

2007-03-01

In this essay I take seriously Max Weber's astonishingly neglected claim that class situation may be defined, not in categorial terms, but probabilistically. I then apply this idea to another equally neglected claim made by Weber that the boundaries of social classes may be determined by the degree of social mobility within such classes. Taking these two ideas together I develop the idea of a non-categorial boundary 'surface' between classes and of a social class 'corridor' made up of all those people who are still to be found within the boundaries of the social class into which they were born. I call social mobility within a social class 'intra-class social mobility' and social mobility between classes 'inter-class social mobility'. I also claim that this distinction resolves the dispute between those sociologists who claim that late industrial societies are still highly class bound and those who think that this is no longer the case. Both schools are right I think, but one is referring to a high degree of intra-class social mobility and the other to an equally high degree of inter-class mobility. Finally I claim that this essay provides sociology with only one example among many other possible applications of how probability theory might usefully be used to overcome boundary problems generally in sociology.

Study of entry and landing probes for exploration of Titan

NASA Technical Reports Server (NTRS)

1979-01-01

Saturn's largest moon, Titan, is a totally unique planetary body which is certain to yield exciting new phenomena. Current information is lacking in detail to distinguish between a thin methane rich atmosphere and a thick nitrogen rich atmosphere. Therefore, both the thin and thick atmospheric models were used for the study of various Titan probe classes described in this report. The technical requirements, conceptual design, science return, schedule, cost and mission implications of three probe classes that could be used for exploration of Titan are defined. The three probe classes were based on a wide range of exploration mission possibilities.

Sleep state classification using pressure sensor mats.

PubMed

Baran Pouyan, M; Nourani, M; Pompeo, M

2015-08-01

Sleep state detection is valuable in assessing patient's sleep quality and in-bed general behavior. In this paper, a novel classification approach of sleep states (sleep, pre-wake, wake) is proposed that uses only surface pressure sensors. In our method, a mobility metric is defined based on successive pressure body maps. Then, suitable statistical features are computed based on the mobility metric. Finally, a customized random forest classifier is employed to identify various classes including a new class for pre-wake state. Our algorithm achieves 96.1% and 88% accuracies for two (sleep, wake) and three (sleep, pre-wake, wake) class identification, respectively.

The Pontryagin class for pre-Courant algebroids

NASA Astrophysics Data System (ADS)

Liu, Zhangju; Sheng, Yunhe; Xu, Xiaomeng

2016-06-01

In this paper, we show that the Jacobiator J of a pre-Courant algebroid is closed naturally. The corresponding equivalence class [J♭ ] is defined as the Pontryagin class, which is the obstruction of a pre-Courant algebroid to be deformed into a Courant algebroid. We construct a Leibniz 2-algebra and a Lie 2-algebra associated to a pre-Courant algebroid and prove that these algebraic structures are isomorphic under deformations. Finally, we introduce the twisted action of a Lie algebra on a manifold to give more examples of pre-Courant algebroids, which include the Cartan geometry.

Entanglement of a class of non-Gaussian states in disordered harmonic oscillator systems

NASA Astrophysics Data System (ADS)

Abdul-Rahman, Houssam

2018-03-01

For disordered harmonic oscillator systems over the d-dimensional lattice, we consider the problem of finding the bipartite entanglement of the uniform ensemble of the energy eigenstates associated with a particular number of modes. Such an ensemble defines a class of mixed, non-Gaussian entangled states that are labeled, by the energy of the system, in an increasing order. We develop a novel approach to find the exact logarithmic negativity of this class of states. We also prove entanglement bounds and demonstrate that the low energy states follow an area law.

Dynamic primitives in the control of locomotion.

PubMed

Hogan, Neville; Sternad, Dagmar

2013-01-01

Humans achieve locomotor dexterity that far exceeds the capability of modern robots, yet this is achieved despite slower actuators, imprecise sensors, and vastly slower communication. We propose that this spectacular performance arises from encoding motor commands in terms of dynamic primitives. We propose three primitives as a foundation for a comprehensive theoretical framework that can embrace a wide range of upper- and lower-limb behaviors. Building on previous work that suggested discrete and rhythmic movements as elementary dynamic behaviors, we define submovements and oscillations: as discrete movements cannot be combined with sufficient flexibility, we argue that suitably-defined submovements are primitives. As the term "rhythmic" may be ambiguous, we define oscillations as the corresponding class of primitives. We further propose mechanical impedances as a third class of dynamic primitives, necessary for interaction with the physical environment. Combination of these three classes of primitive requires care. One approach is through a generalized equivalent network: a virtual trajectory composed of simultaneous and/or sequential submovements and/or oscillations that interacts with mechanical impedances to produce observable forces and motions. Reliable experimental identification of these dynamic primitives presents challenges: identification of mechanical impedances is exquisitely sensitive to assumptions about their dynamic structure; identification of submovements and oscillations is sensitive to their assumed form and to details of the algorithm used to extract them. Some methods to address these challenges are presented. Some implications of this theoretical framework for locomotor rehabilitation are considered.

Definition and properties of the libera operator on mixed norm spaces.

PubMed

Pavlovic, Miroslav

2014-01-01

We consider the action of the operator ℒg(z) = (1 - z)(-1)∫ z (1)‍f(ζ)dζ on a class of "mixed norm" spaces of analytic functions on the unit disk, X = H α,ν (p,q) , defined by the requirement g ∈ X ⇔ r ↦ (1 - r) (α) M p (r, g ((ν))) ∈ L (q) ([0,1], dr/(1 - r)), where 1 ≤ p ≤ ∞, 0 < q ≤ ∞, α > 0, and ν is a nonnegative integer. This class contains Besov spaces, weighted Bergman spaces, Dirichlet type spaces, Hardy-Sobolev spaces, and so forth. The expression ℒg need not be defined for g analytic in the unit disk, even for g ∈ X. A sufficient, but not necessary, condition is that Σ(n=0)|(∞)|ĝ(n)/(n + 1) < ∞. We identify the indices p, q, α, and ν for which 1°ℒ is well defined on X, 2 °ℒ acts from X to X, 3° the implication g ∈ X [Symbol: see text] Σ(n = 0)(∞) |/ĝ(n)|(n+1) < ∞ holds. Assertion 2° extends some known results, due to Siskakis and others, and contains some new ones. As an application of 3° we have a generalization of Bernstein's theorem on absolute convergence of power series that belong to a Hölder class.

Molecular deletion mapping of the Y chromosome in males with idiopathic azoospermia reveals a new class of microdeletions located in middle Yq11

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

Farah, S.B.; Ramos, C.F.; Bortoletto, R.K.

1994-09-01

Microdeletions in proximal and distal Yq11 found {open_quotes}de novo{close_quotes} in males with idiopathic azoospermia or a severe oligospermia suggested that these Y mutations interrupt the gene structure(s) of a spermatogenesis function located in Yq11 and defined earlier as AZF. Using an extended interval map, dividing Yq11 into 22 subintervals (D1-D22) a third class of microdeletions could now be mapped in middle Yq11. It was found {open_quotes}de novo{close_quotes} in two sterile males with idiopathic azoospermia. Histological analysis of testes tissue sections of both males reveals arrest of spermatogenesis during the pachytene stage. Y-mutations in proximal Yq11 were usually associated to anmore » arrest of spermatogenesis before the proliferation phase of spermatogonia; the corresponding Y gene was defined as {open_quotes}AZFa{close_quotes}. It is, therefore, assumed that the new class of microdeletions, observed now in the middle of Yq11, disrupt another Y spermatogenesis gene expressed during the spermatocyte stage and defined earlier as {open_quotes}AZFb{close_quotes}. Experimental evidence presented during the meeting will try to confirm this view discussing a series of Y genes (AZFa,b,c,...) in Yq11 functioning at different stages during human spermatogenesis.« less

TermGenie – a web-application for pattern-based ontology class generation

DOE PAGES

Dietze, Heiko; Berardini, Tanya Z.; Foulger, Rebecca E.; ...

2014-01-01

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 newmore » classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. Lastly, TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.« less

TermGenie – a web-application for pattern-based ontology class generation

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

Dietze, Heiko; Berardini, Tanya Z.; Foulger, Rebecca E.

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 newmore » classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. Lastly, TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.« less

TermGenie - a web-application for pattern-based ontology class generation.

PubMed

Dietze, Heiko; Berardini, Tanya Z; Foulger, Rebecca E; Hill, David P; Lomax, Jane; Osumi-Sutherland, David; Roncaglia, Paola; Mungall, Christopher J

2014-01-01

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

Texture Mixing via Universal Simulation

DTIC Science & Technology

2005-08-01

classes and universal simulation. Based on the well-known Lempel and Ziv (LZ) universal compression scheme, the universal type class of a one...length that produce the same tree (dictionary) under the Lempel - Ziv (LZ) incre- mental parsing defined in the well-known LZ78 universal compression ...the well known Lempel - Ziv parsing algorithm . The goal is not just to synthesize mixed textures, but to understand what texture is. We are currently

Radius of convexity of a certain class of close-to-convex functions

NASA Astrophysics Data System (ADS)

Yahya, Abdullah; Soh, Shaharuddin Cik

2017-11-01

In the present paper, we consider and investigate a certain class of close-to-convex functions that defined in the unit disk, U = {z : |z| < 1}, which denotes as Re { ei αz/f '(z ) f (z )-f (-z ) } >δ where |α| < π, cos (α) > δ and 0 δ <1. Furthermore, we obtain preliminary result for bound f'(z) and determine result for radius of convexity.

Deterministic Intracellular Modeling

DTIC Science & Technology

2003-03-01

eukaryotes encompass all plants, animal, fungi and protists [6:71]. Structures in this class are more defined. For example, cells in this class possess a...affect cells. 5.3 Recommendations Further research into the construction and evaluation of intracellular models would benefit Air Force toxicology studies...manual220/indexE.html. 16. MathWorks, “The Benefits of MATLAB.” Internet, 2003. http://www.mathworks.com/products/matlab/description1.jsp. 17. Mendes

Empirically Defined Patterns of Executive Function Deficits in Schizophrenia and Their Relation to Everyday Functioning: A Person-Centered Approach

PubMed Central

Iampietro, Mary; Giovannetti, Tania; Drabick, Deborah A. G.; Kessler, Rachel K.

2013-01-01

Executive function (EF) deficits in schizophrenia (SZ) are well documented, although much less is known about patterns of EF deficits and their association to differential impairments in everyday functioning. The present study empirically defined SZ groups based on measures of various EF abilities and then compared these EF groups on everyday action errors. Participants (n=45) completed various subtests from the Delis–Kaplan Executive Function System (D-KEFS) and the Naturalistic Action Test (NAT), a performance-based measure of everyday action that yields scores reflecting total errors and a range of different error types (e.g., omission, perseveration). Results of a latent class analysis revealed three distinct EF groups, characterized by (a) multiple EF deficits, (b) relatively spared EF, and (c) perseverative responding. Follow-up analyses revealed that the classes differed significantly on NAT total errors, total commission errors, and total perseveration errors; the two classes with EF impairment performed comparably on the NAT but performed worse than the class with relatively spared EF. In sum, people with SZ demonstrate variable patterns of EF deficits, and distinct aspects of these EF deficit patterns (i.e., poor mental control abilities) may be associated with everyday functioning capabilities. PMID:23035705

Ensemble Clustering Classification compete SVM and One-Class classifiers applied on plant microRNAs Data.

PubMed

Yousef, Malik; Khalifa, Waleed; AbedAllah, Loai

2016-12-22

The performance of many learning and data mining algorithms depends critically on suitable metrics to assess efficiency over the input space. Learning a suitable metric from examples may, therefore, be the key to successful application of these algorithms. We have demonstrated that the k-nearest neighbor (kNN) classification can be significantly improved by learning a distance metric from labeled examples. The clustering ensemble is used to define the distance between points in respect to how they co-cluster. This distance is then used within the framework of the kNN algorithm to define a classifier named ensemble clustering kNN classifier (EC-kNN). In many instances in our experiments we achieved highest accuracy while SVM failed to perform as well. In this study, we compare the performance of a two-class classifier using EC-kNN with different one-class and two-class classifiers. The comparison was applied to seven different plant microRNA species considering eight feature selection methods. In this study, the averaged results show that ECkNN outperforms all other methods employed here and previously published results for the same data. In conclusion, this study shows that the chosen classifier shows high performance when the distance metric is carefully chosen.

Ensemble Clustering Classification Applied to Competing SVM and One-Class Classifiers Exemplified by Plant MicroRNAs Data.

PubMed

Yousef, Malik; Khalifa, Waleed; AbdAllah, Loai

2016-12-01

The performance of many learning and data mining algorithms depends critically on suitable metrics to assess efficiency over the input space. Learning a suitable metric from examples may, therefore, be the key to successful application of these algorithms. We have demonstrated that the k-nearest neighbor (kNN) classification can be significantly improved by learning a distance metric from labeled examples. The clustering ensemble is used to define the distance between points in respect to how they co-cluster. This distance is then used within the framework of the kNN algorithm to define a classifier named ensemble clustering kNN classifier (EC-kNN). In many instances in our experiments we achieved highest accuracy while SVM failed to perform as well. In this study, we compare the performance of a two-class classifier using EC-kNN with different one-class and two-class classifiers. The comparison was applied to seven different plant microRNA species considering eight feature selection methods. In this study, the averaged results show that EC-kNN outperforms all other methods employed here and previously published results for the same data. In conclusion, this study shows that the chosen classifier shows high performance when the distance metric is carefully chosen.

Finite Geometries in Quantum Theory:. from Galois (fields) to Hjelmslev (rings)

NASA Astrophysics Data System (ADS)

Saniga, Metod; Planat, Michel

Geometries over Galois fields (and related finite combinatorial structures/algebras) have recently been recognized to play an ever-increasing role in quantum theory, especially when addressing properties of mutually unbiased bases (MUBs). The purpose of this contribution is to show that completely new vistas open up if we consider a generalized class of finite (projective) geometries, viz. those defined over Galois rings and/or other finite Hjelmslev rings. The case is illustrated by demonstrating that the basic combinatorial properties of a complete set of MUBs of a q-dimensional Hilbert space { H}q, q = pr with p being a prime and r a positive integer, are qualitatively mimicked by the configuration of points lying on a proper conic in a projective Hjelmslev plane defined over a Galois ring of characteristic p2 and rank r. The q vectors of a basis of { H}q correspond to the q points of a (so-called) neighbour class and the q + 1 MUBs answer to the total number of (pairwise disjoint) neighbour classes on the conic. Although this remarkable analogy is still established at the level of cardinalities only, we currently work on constructing an explicit mapping by associating a MUB to each neighbour class of the points of the conic and a state vector of this MUB to a particular point of the class. Further research in this direction may prove to be of great relevance for many areas of quantum information theory, in particular for quantum information processing.

Use of Latent Class Analysis to define groups based on validity, cognition, and emotional functioning.

PubMed

Morin, Ruth T; Axelrod, Bradley N

Latent Class Analysis (LCA) was used to classify a heterogeneous sample of neuropsychology data. In particular, we used measures of performance validity, symptom validity, cognition, and emotional functioning to assess and describe latent groups of functioning in these areas. A data-set of 680 neuropsychological evaluation protocols was analyzed using a LCA. Data were collected from evaluations performed for clinical purposes at an urban medical center. A four-class model emerged as the best fitting model of latent classes. The resulting classes were distinct based on measures of performance validity and symptom validity. Class A performed poorly on both performance and symptom validity measures. Class B had intact performance validity and heightened symptom reporting. The remaining two Classes performed adequately on both performance and symptom validity measures, differing only in cognitive and emotional functioning. In general, performance invalidity was associated with worse cognitive performance, while symptom invalidity was associated with elevated emotional distress. LCA appears useful in identifying groups within a heterogeneous sample with distinct performance patterns. Further, the orthogonal nature of performance and symptom validities is supported.

Compounds affecting cholesterol absorption

NASA Technical Reports Server (NTRS)

Koo, Sung I. (Inventor); Noh, Sang K. (Inventor); Hua, Duy H. (Inventor)

2004-01-01

A class of novel compounds is described for use in affecting lymphatic absorption of cholesterol. Compounds of particular interest are defined by Formula I: ##STR1## or a pharmaceutically acceptable salt thereof.

A hydrologically explicit, spatially exact, classification of landforms for Canada at 1:500,000 scale.

NASA Astrophysics Data System (ADS)

MacMillan, Robert A.; Geng, Xiaoyuan; Smith, Scott; Zawadzka, Joanna; Hengl, Tom

2016-04-01

A new approach for classifying landform types has been developed and applied to all of Canada using a 250 m DEM. The resulting LandMapR classification has been designed to provide a stable and consistent spatial fabric to act as initial proto-polygons to be used in updating the current 1:1 M scale Soil Landscapes of Canada map to 1:500,000 scale. There is a desire to make the current SLC polygon fabric more consistent across the country, more correctly aligned to observable hydrological and landscape features, more spatially exact, more detailed and more interpretable. The approach is essentially a modification of the Hammond (1954) criteria for classifying macro landform types as implemented for computerized analysis by Dikau (1989, 1991) and Brabyn (1998). The major modification is that the key input variables of local relief and relative position in the landscape are computed for specific hillslopes that occur between individual, explicitly defined, channels and divides. While most approaches, including Dikau et al., (1991) and SOTER (Dobos et al., 2005) compute relative relief and landscape position within a neighborhood analysis window (NAW) of some fixed size (9,600 m and 1 km respectively) the LandMapR method assesses these variables based on explicit analysis of flow paths between locally defined divides and channels (or lakes). We have modified the Hammond criteria by splitting the lowest relief class of 0-30 m into 4 classes of 0-0 m, 0-1 m, 1-10 m and 10-30 m) in order to be able to better differentiate subtle landform features in areas of low relief. Essentially this enables recognition of lakes and open water (0 relief and 0 slope), shorelines and littoral zones (0-1 m), nearly flat, low-relief landforms (1-10 m) and low relief undulating plains (10-30 m). We also modified the Hammond approach for separating upper versus lower landform positions used to differentiate flat areas in uplands from flat lowlands. We instead differentiate 3 relative slope positions of channel valley, toe slope and upper slope consistently and exhaustively and so can identify any flat areas that occur in any of these three landform positions. We did not find it necessary to use slope gradient as a criteria for defining and delineating classes because relief acts as a surrogate for slope and each relief class exhibits a narrow and definable range of slope gradients. Dominant slope gradient (or other attributes) can be computed, post classification, for each defined polygon, if there is a need to further classify by slope or other attribute. This simplifies classification and also reduces pixilation in the classification arising from considering too many local criteria in the class definitions. The resulting polygons provide an extremely detailed classification of relief and landform position at the level of individual hillslopes across all of Canada. The polygon boundaries explicitly follow major identifiable drainage networks and work their way upslope to delineate interfluves that occupy upslope positions at all levels of relief. The detailed LandMapR polygon classifications nest consistently within more general regions defined by the original Hammond-Dikau procedures. Initial visual analysis reveals a strong and consistent spatial relationship between observable changes in slope, vegetation and drainage regime and LandMapR landform polygon boundaries. More detailed quantitative assessment of the accuracy and utility of the LandMapR polygon classes is planned.

The Missing Curriculum in Physics Problem-Solving Education

NASA Astrophysics Data System (ADS)

Williams, Mobolaji

2018-05-01

Physics is often seen as an excellent introduction to science because it allows students to learn not only the laws governing the world around them, but also, through the problems students solve, a way of thinking which is conducive to solving problems outside of physics and even outside of science. In this article, we contest this latter idea and argue that in physics classes, students do not learn widely applicable problem-solving skills because physics education almost exclusively requires students to solve well-defined problems rather than the less-defined problems which better model problem solving outside of a formal class. Using personal, constructed, and the historical accounts of Schrödinger's development of the wave equation and Feynman's development of path integrals, we argue that what is missing in problem-solving education is practice in identifying gaps in knowledge and in framing these knowledge gaps as questions of the kind answerable using techniques students have learned. We discuss why these elements are typically not taught as part of the problem-solving curriculum and end with suggestions on how to incorporate these missing elements into physics classes.

Relation of the activities of the IPDF/INPE project (reforestation subproject) during the year 1979. [Mato Grosso do Sul, Brazil

NASA Technical Reports Server (NTRS)

Dejesusparada, N. (Principal Investigator); Filho, P. H.; Shimabukuro, Y. E.; Demedeiros, J. S.; Desantana, C. C.; Alves, E. C. M.

1981-01-01

The state of Mato Grosso do Sul was selected as the study area to define the recognizable classes of Eucalyptus spp. and Pinus spp. by visual and automatic analyses. For visual analysis, a preliminary interpretation key and a legend of 6 groups were derived. Based on these six groups, three final classes were defined for analysis: (1) area prepared for reforestation; (2) area reforested with Eucalyptus spp.; and (3) area reforested with Pinus spp. For automatic interpretation the area along the highway from Ribas do Rio Pardo to Agua Clara was classified into the following classes: eucalytus, bare soil, plowed soil, pine and "cerrado". The results of visual analysis show that 67% of the reforested farms have relative differences in area estimate below 5%, 22%, between 5% and 10%; and 11% between 10% and 20%. The reforested eucalyptus area is 17 times greater than the area of reforested pine. Automatic classification of eucalyptus ranged from 73.03% to 92.30% in the training areas.

Building Blocks for Transport-Class Hybrid and Turboelectric Vehicles

NASA Technical Reports Server (NTRS)

Jankovsky, Amy; Bowman, Cheryl; Jansen, Ralph

2016-01-01

NASA has been investing in research efforts to define potential vehicles that use hybrid and turboelectric propulsion to enable savings in fuel burn and carbon usage. This paper overviews the fundamental building blocks that have been derived from those studies and details what key performance parameters have been defined, what key ground and flight tests need to occur, and highlights progress toward each.

HLA-D: The T Cell Perspective

DTIC Science & Technology

1985-01-01

offspring of consanguineous marriage, in which case the cells are almost always homosygous for all HLA-region products; in other cases, HTCs are...story. Certain relationships exist between the class II serologically defined (I&) and T lymphocyte defined (Dw/LD) specificities. One speaks of one...DRwI4 specificities; in addition, certain of the DRI-DRwl4 specificities are supertypic to the various Dw specificities. The relationships of these

Disentangling giant component and finite cluster contributions in sparse random matrix spectra.

PubMed

Kühn, Reimer

2016-04-01

We describe a method for disentangling giant component and finite cluster contributions to sparse random matrix spectra, using sparse symmetric random matrices defined on Erdős-Rényi graphs as an example and test bed. Our methods apply to sparse matrices defined in terms of arbitrary graphs in the configuration model class, as long as they have finite mean degree.

Polymorphisms and Tissue Expression of the Feline Leukocyte Antigen Class I Loci FLAI-E, -H and -K

PubMed Central

Holmes, Jennifer C.; Holmer, Savannah G.; Ross, Peter; Buntzman, Adam S.; Frelinger, Jeffrey A.; Hess, Paul R.

2013-01-01

Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the Feline Leukocyte Antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, 3 loci - FLAI-E, -H and -K – are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, -H, and -K alleles from 12 cats of various breeds, identifying, for the first time, alleles across 3 distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and -K. Only FLAI-E, -H and -K-origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, -H, and -K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats. PMID:23812210

Differentiation of functional constipation and constipation predominant irritable bowel syndrome based on Rome III criteria: a population-based study.

PubMed

Koloski, N A; Jones, M; Young, M; Talley, N J

2015-05-01

While the Rome III classification recognises functional constipation (FC) and constipation predominant IBS (IBS-C) as distinct disorders, recent evidence has suggested that these disorders are difficult to separate in clinical practice. To identify whether clinical and lifestyle factors differentiate Rome III-defined IBS-C from FC based on gastrointestinal symptoms and lifestyle characteristics. 3260 people randomly selected from the Australian population returned a postal survey. FC and IBS-C were defined according to Rome III. The first model used logistic regression to differentiate IBS-C from FC based on lifestyle, quality-of-life and psychological characteristics. The second approach was data-driven employing latent class analysis (LCA) to identify naturally occurring clusters in the data considering all symptoms involved in the Rome III criteria for IBS-C and FC. We found n = 206 (6.5%; 95% CI 5.7-7.4%) people met strict Rome III FC whereas n = 109 (3.5%; 95% CI 2.8-4.1%) met strict Rome III IBS-C. The case-control approach indicated that FC patients reported an older age at onset of constipation, were less likely to exercise, had higher mental QoL and less health care seeking than IBS-C. LCA yielded one latent class that was predominantly (75%) FC, while the other class was approximately half IBS-C and half FC. The FC-dominated latent class had clearly lower levels of symptoms used to classify IBS (pain-related symptoms) and was more likely to be male (P = 0.046) but was otherwise similar in distribution of lifestyle factors to the mixed class. The latent class analysis approach suggests a differentiation based more on symptom severity rather than the Rome III view. © 2015 John Wiley & Sons Ltd.

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

Rivkin, Andrew S.; Thomas, Cristina A.; Howell, Ellen S.

Asteroids belonging to the Ch spectral taxonomic class are defined by the presence of an absorption near 0.7 μm, which is interpreted as due to Fe-bearing phyllosilicates. Phyllosilicates also cause strong absorptions in the 3 μm region, as do other hydrated and hydroxylated minerals and H{sub 2}O ice. Over the past decade, spectral observations have revealed different 3 μm band shapes in the asteroid population. Although a formal taxonomy is yet to be fully established, the “Pallas-type” spectral group is most consistent with the presence of phyllosilicates. If Ch class and Pallas type are both indicative of phyllosilicates, then allmore » Ch-class asteroids should also be Pallas-type. In order to test this hypothesis, we obtained 42 observations of 36 Ch-class asteroids in the 2 to 4 μm spectral region. We found that 88% of the spectra have 3 μm band shapes most consistent with the Pallas-type group. This is the first asteroid class for which such a strong correlation has been found. Because the Ch class is defined by the presence of an absorption near 0.7 μm, this demonstrates that the 0.7 μm band serves not only as a proxy for the presence of a band in the 3 μm region, but specifically for the presence of Pallas-type bands. There is some evidence for a correlation between band depth at 2.95 μm and absolute magnitude and/or albedo. However, we find only weak correlations between 2.95 μm band depth and semimajor axis. The connection between band depths in the 0.7 and 3 μm regions is complex and in need of further investigation.« less

Quantum chaos for nonstandard symmetry classes in the Feingold-Peres model of coupled tops

NASA Astrophysics Data System (ADS)

Fan, Yiyun; Gnutzmann, Sven; Liang, Yuqi

2017-12-01

We consider two coupled quantum tops with angular momentum vectors L and M . The coupling Hamiltonian defines the Feingold-Peres model, which is a known paradigm of quantum chaos. We show that this model has a nonstandard symmetry with respect to the Altland-Zirnbauer tenfold symmetry classification of quantum systems, which extends the well-known threefold way of Wigner and Dyson (referred to as "standard" symmetry classes here). We identify the nonstandard symmetry classes BD I0 (chiral orthogonal class with no zero modes), BD I1 (chiral orthogonal class with one zero mode), and C I (antichiral orthogonal class) as well as the standard symmetry class A I (orthogonal class). We numerically analyze the specific spectral quantum signatures of chaos related to the nonstandard symmetries. In the microscopic density of states and in the distribution of the lowest positive energy eigenvalue, we show that the Feingold-Peres model follows the predictions of the Gaussian ensembles of random-matrix theory in the appropriate symmetry class if the corresponding classical dynamics is chaotic. In a crossover to mixed and near-integrable classical dynamics, we show that these signatures disappear or strongly change.

Quantum chaos for nonstandard symmetry classes in the Feingold-Peres model of coupled tops.

PubMed

Fan, Yiyun; Gnutzmann, Sven; Liang, Yuqi

2017-12-01

We consider two coupled quantum tops with angular momentum vectors L and M. The coupling Hamiltonian defines the Feingold-Peres model, which is a known paradigm of quantum chaos. We show that this model has a nonstandard symmetry with respect to the Altland-Zirnbauer tenfold symmetry classification of quantum systems, which extends the well-known threefold way of Wigner and Dyson (referred to as "standard" symmetry classes here). We identify the nonstandard symmetry classes BDI_{0} (chiral orthogonal class with no zero modes), BDI_{1} (chiral orthogonal class with one zero mode), and CI (antichiral orthogonal class) as well as the standard symmetry class AI (orthogonal class). We numerically analyze the specific spectral quantum signatures of chaos related to the nonstandard symmetries. In the microscopic density of states and in the distribution of the lowest positive energy eigenvalue, we show that the Feingold-Peres model follows the predictions of the Gaussian ensembles of random-matrix theory in the appropriate symmetry class if the corresponding classical dynamics is chaotic. In a crossover to mixed and near-integrable classical dynamics, we show that these signatures disappear or strongly change.

Final Environmental Assessment for 2012-14 Capital Improvements Program (CIP) for Davis-Monthan Air Force Base (AFB), Tucson, Arizona

DTIC Science & Technology

2012-03-01

if these areas had been established by August 7, 1977. These areas are defined as mandatmy Class I areas, while all other attainment or...redesignate cettain areas as (non-mandatmy) PSD Class I areas (e.g. , a national park or national wildemess area established after August 7, 1977...facilities, vehicle maintenance facilities, etc. Family housing, temporary housing, trailer comts Dormitories, Visiting Officers Quruters, Visiting

Search for correlation between asteroid families and classes

NASA Technical Reports Server (NTRS)

Hansen, O.

1977-01-01

A correlation between membership in a dynamically defined asteroid family and membership in a given asteroid spectral class is sought. Examination of 10 families each with five or more classified members indicates a correlation for the 4 families whose existence is best established, and no correlation for the remaining 6 families. This conclusion supports the break-up hypothesis for the origin of some families, while not contradicting that hypothesis for any family.

A class of nonideal solutions. 2: Application to experimental data

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.; Donovan, L. F.

1983-01-01

Functions for the representation of the thermodynamic properties of nonideal solutions were applied to the experimental data for several highly nonideal solutions. The test solutions were selected to cover both electrolyte behavior. The results imply that the functions are fully capable of representing the experimental data within their accuracy over the whole composition range and demonstrate that many nonideal solutions can be regarded as members of the defined class of nonideal solutions.

Spatial-temporal bio-optical classification of dynamic semi-estuarine waters in western North America

NASA Astrophysics Data System (ADS)

Phillips, Stephen Robert; Costa, Maycira

2017-12-01

The use of standard ocean colour reflectance based algorithms to derive surface chlorophyll may have limited applicability for optically dynamic coastal waters due to the pre-defined coefficients based on global datasets. Reflectance based algorithms adjusted to regional optical water characteristics are a promising alternative. A class-based definition of optically diverse coastal waters was investigated as a first step towards the development of temporal and spatial constrained reflectance based algorithms for optically variable coastal waters. A large set of bio-optical data were collected as part of five research cruises and bi-weekly trips aboard a ship of opportunity in the west coast of Canada, to assess the spatial and temporal variability of above-water reflectance in this contrasted coastal environment. To accomplish this, in situ biophysical and optical measurements were collected in conjunction with above-water hyperspectral remote sensing reflectance (Rrs) at 145 stations. The concentrations of measured biophysical data varied considerably; chlorophyll a (Chla) (mean = 1.64, range: 0.10-7.20 μg l-1), total suspended matter (TSM) (3.09, 0.82-20.69 mg l-1), and absorption by chromophoric dissolved organic matter (CDOM) (acdom(443 nm)) (0.525, 0.007-3.072 m-1), thus representing the spatio-temporal variability of the Salish Sea. Optically, a similar large range was also found; particulate scattering (bp(650 nm)) (1.316, 0.250-7.450 m-1), particulate backscattering (bbp(650 nm)) (0.022, 0.005-0.097 m-1), total beam attenuation coefficient (ct(650)) (1.675, 0.371-9.537 m-1) and particulate absorption coefficient (ap(650 nm)) (0.345, 0.048-2.020 m-1). An empirical orthogonal function (EOF) analysis revealed that Rrs variability was highly correlated to bp (r = 0.90), bbp (r = 0.82) and concentration of TSM (r = 0.80), which highlighted the dominant role of water turbidity in this region. Hierarchical clustering analysis was applied to the normalized Rrs spectra to define optical water classes. Class 1 was defined by the highest Rrs values, particularly above 570 nm, indicating more turbid waters; Class 2 was dominated by high Chla and TSM concentrations, which is shown by high Rrs at 570 nm as well as fluorescence and absorption peaks; Class 3 shows strong fluorescence signatures accompanied by low TSM influence; and Class 4 is most representative of clear waters with a less defined absorption peak around 440 nm. By understanding the bio-optical factors which control the variability of the Rrs spectra this study aims to develop a sub-regional characterization of this coastal region aiming to improve bio-optical algorithms in this complex coastal area.

Remote Sensing techniques used to characterize soil erosion in southwestern Sao Paulo state. M.S. Thesis - 29 Sep. 1982; [Brazil

NASA Technical Reports Server (NTRS)

Parada, N. D. J. (Principal Investigator); Pinto, S. D. A. F.

1983-01-01

Within randomly sampled squares of a 1 km x 1 km grid, rill/gullies frequency, land cover/land use type and shape of the slopes were extracted from aerial photographs of the Ribeirao Anhumas drainage basin. Mean slope gradient, stream frequency and slope length were calculated on topographic maps. Ground truth data on fine sand/coarse sand ratio and vegetation cover densities were obtained. The MSS-LANDSAT-2 data (CCTs) were analyzed using single-cell, cluster synthesis and slicer algorithms. Graphical and statistical analyses of the data indicate that different slope gradients and land cover/land use types are the most significant factors related to the soil erosion process. The digital analysis of MSS data allowed the association among gray level classes and vegetation cover classes, which defined seven classes. These gray level classes and slope gradient classes were used to rank erosion risk.

RACE-SPECIFIC TRANSITION PATTERNS AMONG ALCOHOL USE CLASSES IN ADOLESCENT GIRLS

PubMed Central

Dauber, Sarah E.; Paulson, James F.; Leiferman, Jenn A.

2010-01-01

We used data from the National Longitudinal Study of Adolescent Health to examine transitions among alcohol use classes in 2225 White and African American adolescent girls, and race differences in predictors of transition into and out of problematic drinking classes. Latent class analysis confirmed four classes for White girls and three for AA girls, defined in a previous study. Latent transition analysis revealed more stable abstainers and decreasing alcohol use among AA girls, and more increasing alcohol use among White girls, though stable abstainers were the largest group among both races. Increasing use was predicted by delinquency, academic misbehavior, substance use, and peer support for White girls, and by older age and delinquency for AA girls. Decreasing use was predicted by older age and depressive symptoms for White girls, and by family relationship quality and substance use for AA girls. Study limitations and implications of findings are discussed. PMID:20708254

The class-origin wage gap: heterogeneity in education and variations across market segments.

PubMed

Hällsten, Martin

2013-12-01

This paper uses unique population-level matched employer-employee data on monthly wages to analyse class-origin wage gaps in the Swedish labour market. Education is the primary mediator of class origin advantages in the labour market, but mobility research often only considers the vertical dimension of education. When one uses an unusually detailed measure of education in a horizontal dimension, the wage gap between individuals of advantaged and disadvantaged class origin is found to be substantial (4-5 per cent), yet considerably smaller than when measures are used which only control for level of education and field of study. This is also the case for models with class or occupation as outcome. The class-origin wage gap varies considerably across labour market segments, such as those defined by educational levels, fields of education, industries and occupations in both seemingly unsystematic and conspicuous ways. The gap is small in the public sector, suggesting that bureaucracy may act as a leveller. © London School of Economics and Political Science 2013.

49 CFR 236.1003 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... auxiliary or industry tracks, a segment or route of railroad tracks: (1) Of a Class I railroad, as.... Tourist, scenic, historic, or excursion operations as defined in part 238 of this chapter are not...

A Study of the Efficiency of the Class of W-States as a Quantum Channel

NASA Astrophysics Data System (ADS)

Adhikari, Satyabrata; Gangopadhyay, Sunandan

2009-02-01

Recently, a new class of W-states has been defined by Agarwal and Pati (Phys. Rev. A 74:062320, 2006) and it has been shown that they can be used as a quantum channel for teleportation and superdense coding. In this work, we identify those three-qubit states from the set of the new class of W-states which are most efficient or suitable for quantum teleportation. We show that with some probability |W1rangle=1/2(|100rangle+|010rangle+sqrt{2}|001rangle) is best suited for teleportation channel in the sense that it does not depend on the input state.

Discovery and Structure-Activity Relationships of the Neoseptins: A New Class of Toll-like Receptor-4 (TLR4) Agonists.

PubMed

Morin, Matthew D; Wang, Ying; Jones, Brian T; Su, Lijing; Surakattula, Murali M R P; Berger, Michael; Huang, Hua; Beutler, Elliot K; Zhang, Hong; Beutler, Bruce; Boger, Dale L

2016-05-26

Herein, we report studies leading to the discovery of the neoseptins and a comprehensive examination of the structure-activity relationships (SARs) of this new class of small-molecule mouse Toll-like receptor 4 (mTLR4) agonists. The compounds in this class, which emerged from screening an α-helix mimetic library, stimulate the immune response, act by a well-defined mechanism (mouse TLR4 agonist), are easy to produce and structurally manipulate, exhibit exquisite SARs, are nontoxic, and elicit improved and qualitatively different responses compared to lipopolysaccharide, even though they share the same receptor.

Non-compact nonlinear sigma models

NASA Astrophysics Data System (ADS)

de Rham, Claudia; Tolley, Andrew J.; Zhou, Shuang-Yong

2016-09-01

The target space of a nonlinear sigma model is usually required to be positive definite to avoid ghosts. We introduce a unique class of nonlinear sigma models where the target space metric has a Lorentzian signature, thus the associated group being non-compact. We show that the would-be ghost associated with the negative direction is fully projected out by 2 second-class constraints, and there exist stable solutions in this class of models. This result also has important implications for Lorentz-invariant massive gravity: There exist stable nontrivial vacua in massive gravity that are free from any linear vDVZ-discontinuity and a Λ2 decoupling limit can be defined on these vacua.

Nonpathologizing trauma interventions in abnormal psychology courses.

PubMed

Hoover, Stephanie M; Luchner, Andrew F; Pickett, Rachel F

2016-01-01

Because abnormal psychology courses presuppose a focus on pathological human functioning, nonpathologizing interventions within these classes are particularly powerful and can reach survivors, bystanders, and perpetrators. Interventions are needed to improve the social response to trauma on college campuses. By applying psychodynamic and feminist multicultural theory, instructors can deliver nonpathologizing interventions about trauma and trauma response within these classes. We recommend class-based interventions with the following aims: (a) intentionally using nonpathologizing language, (b) normalizing trauma responses, (c) subjectively defining trauma, (d) challenging secondary victimization, and (e) questioning the delineation of abnormal and normal. The recommendations promote implications for instructor self-reflection, therapy interventions, and future research.

Training generalized improvisation of tools by preschool children1

PubMed Central

Parsonson, Barry S.; Baer, Donald M.

1978-01-01

The development of new, “creative” behaviors was examined in a problem-solving context. One form of problem solving, improvisation, was defined as finding a substitute to replace the specifically designated, but currently unavailable, tool ordinarily used to solve the problem. The study examined whether preschool children spontaneously displayed generalized improvisation skills, and if not, whether they could be trained to do so within different classes of tools. Generalization across different tool classes was monitored but not specifically trained. Five preschool children participated in individual sessions that first probed their skill at improvising tools, and later trained and probed generalized improvisation in one or more of three tool classes (Hammers, Containers, and Shoelaces), using a multiple-baseline design. All five children were trained with Hammers, two were trained in two classes, and two were trained in all three tool classes. Four of the five children improvised little in Baseline. During Training, all five showed increased generalized improvisation within the trained class, but none across classes. Tools fabricated by item combinations were rare in Baseline, but common in Training. Followup probes showed that the training effects were durable. PMID:16795596

[Evaluation of accuracy of virtual occlusal definition in Angle class I molar relationship].

PubMed

Wu, L; Liu, X J; Li, Z L; Wang, X

2018-02-18

To evaluate the accuracy of virtual occlusal definition in non-Angle class I molar relationship, and to evaluate the clinical feasibility. Twenty pairs of models of orthognathic patients were included in this study. The inclusion criteria were: (1) finished with pre-surgical orthodontic treatment and (2) stable final occlusion. The exclusion criteria were: (1) existence of distorted teeth, (2) needs for segmentation, (3) defect of dentition except for orthodontic extraction ones, and (4) existence of tooth space. The tooth-extracted test group included 10 models with two premolars extracted during preoperative orthodontic treatment. Their molar relationships were not Angle class I relationship. The non-tooth-extracted test group included another 10 models without teeth extracted, therefore their molar relationships were Angle class I. To define the final occlusion in virtual environment, two steps were included: (1) The morphology data of upper and lower dentition were digitalized by surface scanner (Smart Optics/Activity 102; Model-Tray GmbH, Hamburg, Germany); (2) the virtual relationships were defined using 3Shape software. The control standard of final occlusion was manually defined using gypsum models and then digitalized by surface scanner. The final occlusion of test group and control standard were overlapped according to lower dentition morphology. Errors were evaluated by calculating the distance between the corresponding reference points of testing group and control standard locations. The overall errors for upper dentition between test group and control standard location were (0.51±0.18) mm in non-tooth-extracted test group and (0.60±0.36) mm in tooth-extracted test group. The errors were significantly different between these two test groups (P<0.05). However, in both test groups, the errors of each tooth in a single dentition does not differ from one another. There was no significant difference between errors in tooth-extracted test group and 1 mm (P>0.05); and the accuracy of non-tooth-extracted group was significantly smaller than 1 mm (P<0.05). The error of virtual occlusal definition of none class I molar relationship is higher than that of class I relationship, with an accuracy of 1 mm. However, its accuracy is still feasible for clinical application.

Fuzzy tree automata and syntactic pattern recognition.

PubMed

Lee, E T

1982-04-01

An approach of representing patterns by trees and processing these trees by fuzzy tree automata is described. Fuzzy tree automata are defined and investigated. The results include that the class of fuzzy root-to-frontier recognizable ¿-trees is closed under intersection, union, and complementation. Thus, the class of fuzzy root-to-frontier recognizable ¿-trees forms a Boolean algebra. Fuzzy tree automata are applied to processing fuzzy tree representation of patterns based on syntactic pattern recognition. The grade of acceptance is defined and investigated. Quantitative measures of ``approximate isosceles triangle,'' ``approximate elongated isosceles triangle,'' ``approximate rectangle,'' and ``approximate cross'' are defined and used in the illustrative examples of this approach. By using these quantitative measures, a house, a house with high roof, and a church are also presented as illustrative examples. In addition, three fuzzy tree automata are constructed which have the capability of processing the fuzzy tree representations of ``fuzzy houses,'' ``houses with high roofs,'' and ``fuzzy churches,'' respectively. The results may have useful applications in pattern recognition, image processing, artificial intelligence, pattern database design and processing, image science, and pictorial information systems.

Impact of surface disinfection and sterile draping of furniture on room air quality in a cardiac procedure room with a ventilation and air-conditioning system (extrusion airflow, cleanroom class 1b (DIN 1946-4)).

PubMed

Below, Harald; Ryll, Sylvia; Empen, Klaus; Dornquast, Tina; Felix, Stefan; Rosenau, Heike; Kramer, Sebastian; Kramer, Axel

2010-09-21

In a cardiac procedure room, ventilated by a ventilation and air-conditioning system with turbulent mixed airflow, a protection zone in the operating area could be defined through visualization of airflows. Within this protection zone, no turbulence was detectable in the room air.Under the given conditions, disinfection of all surfaces including all furniture and equipment after the last operation and subsequent draping of furniture and all equipment that could not be removed from the room with sterile surgical drapes improved the indoor room air quality from cleanroom class C to cleanroom class B. This also allows procedures with elevated requirements to be performed in room class 1b.

Some properties for integro-differential operator defined by a fractional formal.

PubMed

Abdulnaby, Zainab E; Ibrahim, Rabha W; Kılıçman, Adem

2016-01-01

Recently, the study of the fractional formal (operators, polynomials and classes of special functions) has been increased. This study not only in mathematics but extended to another topics. In this effort, we investigate a generalized integro-differential operator [Formula: see text] defined by a fractional formal (fractional differential operator) and study some its geometric properties by employing it in new subclasses of analytic univalent functions.

A Political Theory of Hegemonic Sustainability: A Legitimate Grand Strategy for America

DTIC Science & Technology

2013-06-01

the population.114 Marxism defines the working class as “the people.” The modern US defines adults above the age eighteen as the people. The... France saw little value in Wilson’s proposal, instead preferring to dismember 27 Ikenberry...Leaders – US, UK, and France b. Present society – UN member nations’ representatives i. Societal sub-group – Western Liberal nations b. Content i

Investigation into Suitability of Geopolymers (Illite & Metakaolin) for the Space Environment

DTIC Science & Technology

2012-09-13

most disastrous if a spacecraft telescope made of a hybrid composite mirror with a geopolymer adhesive became distorted or damaged on orbit due to...background According to the Dictionary of Composite Materials Technology, (Lee 1989) a geopolymer is defined as: “A family of refractory ceramics...polysilicates to form polymeric Si-O-Al bonds”. Geopolymers and geopolymer composites are a relatively newly defined class of ceramic materials whose

Methods of defining ontologies, word disambiguation methods, computer systems, and articles of manufacture

DOEpatents

Sanfilippo, Antonio P [Richland, WA; Tratz, Stephen C [Richland, WA; Gregory, Michelle L [Richland, WA; Chappell, Alan R [Seattle, WA; Whitney, Paul D [Richland, WA; Posse, Christian [Seattle, WA; Baddeley, Robert L [Richland, WA; Hohimer, Ryan E [West Richland, WA

2011-10-11

Methods of defining ontologies, word disambiguation methods, computer systems, and articles of manufacture are described according to some aspects. In one aspect, a word disambiguation method includes accessing textual content to be disambiguated, wherein the textual content comprises a plurality of words individually comprising a plurality of word senses, for an individual word of the textual content, identifying one of the word senses of the word as indicative of the meaning of the word in the textual content, for the individual word, selecting one of a plurality of event classes of a lexical database ontology using the identified word sense of the individual word, and for the individual word, associating the selected one of the event classes with the textual content to provide disambiguation of a meaning of the individual word in the textual content.

Application of Ontology Technology in Health Statistic Data Analysis.

PubMed

Guo, Minjiang; Hu, Hongpu; Lei, Xingyun

2017-01-01

Research Purpose: establish health management ontology for analysis of health statistic data. Proposed Methods: this paper established health management ontology based on the analysis of the concepts in China Health Statistics Yearbook, and used protégé to define the syntactic and semantic structure of health statistical data. six classes of top-level ontology concepts and their subclasses had been extracted and the object properties and data properties were defined to establish the construction of these classes. By ontology instantiation, we can integrate multi-source heterogeneous data and enable administrators to have an overall understanding and analysis of the health statistic data. ontology technology provides a comprehensive and unified information integration structure of the health management domain and lays a foundation for the efficient analysis of multi-source and heterogeneous health system management data and enhancement of the management efficiency.

Complexity of generic biochemical circuits: topology versus strength of interactions.

PubMed

Tikhonov, Mikhail; Bialek, William

2016-12-06

The historical focus on network topology as a determinant of biological function is still largely maintained today, illustrated by the rise of structure-only approaches to network analysis. However, biochemical circuits and genetic regulatory networks are defined both by their topology and by a multitude of continuously adjustable parameters, such as the strength of interactions between nodes, also recognized as important. Here we present a class of simple perceptron-based Boolean models within which comparing the relative importance of topology versus interaction strengths becomes a quantitatively well-posed problem. We quantify the intuition that for generic networks, optimization of interaction strengths is a crucial ingredient of achieving high complexity, defined here as the number of fixed points the network can accommodate. We propose a new methodology for characterizing the relative role of parameter optimization for topologies of a given class.

Dynamic primitives in the control of locomotion

PubMed Central

Hogan, Neville; Sternad, Dagmar

2013-01-01

Humans achieve locomotor dexterity that far exceeds the capability of modern robots, yet this is achieved despite slower actuators, imprecise sensors, and vastly slower communication. We propose that this spectacular performance arises from encoding motor commands in terms of dynamic primitives. We propose three primitives as a foundation for a comprehensive theoretical framework that can embrace a wide range of upper- and lower-limb behaviors. Building on previous work that suggested discrete and rhythmic movements as elementary dynamic behaviors, we define submovements and oscillations: as discrete movements cannot be combined with sufficient flexibility, we argue that suitably-defined submovements are primitives. As the term “rhythmic” may be ambiguous, we define oscillations as the corresponding class of primitives. We further propose mechanical impedances as a third class of dynamic primitives, necessary for interaction with the physical environment. Combination of these three classes of primitive requires care. One approach is through a generalized equivalent network: a virtual trajectory composed of simultaneous and/or sequential submovements and/or oscillations that interacts with mechanical impedances to produce observable forces and motions. Reliable experimental identification of these dynamic primitives presents challenges: identification of mechanical impedances is exquisitely sensitive to assumptions about their dynamic structure; identification of submovements and oscillations is sensitive to their assumed form and to details of the algorithm used to extract them. Some methods to address these challenges are presented. Some implications of this theoretical framework for locomotor rehabilitation are considered. PMID:23801959

Analysing grouping of nucleotides in DNA sequences using lumped processes constructed from Markov chains.

PubMed

Guédon, Yann; d'Aubenton-Carafa, Yves; Thermes, Claude

2006-03-01

The most commonly used models for analysing local dependencies in DNA sequences are (high-order) Markov chains. Incorporating knowledge relative to the possible grouping of the nucleotides enables to define dedicated sub-classes of Markov chains. The problem of formulating lumpability hypotheses for a Markov chain is therefore addressed. In the classical approach to lumpability, this problem can be formulated as the determination of an appropriate state space (smaller than the original state space) such that the lumped chain defined on this state space retains the Markov property. We propose a different perspective on lumpability where the state space is fixed and the partitioning of this state space is represented by a one-to-many probabilistic function within a two-level stochastic process. Three nested classes of lumped processes can be defined in this way as sub-classes of first-order Markov chains. These lumped processes enable parsimonious reparameterizations of Markov chains that help to reveal relevant partitions of the state space. Characterizations of the lumped processes on the original transition probability matrix are derived. Different model selection methods relying either on hypothesis testing or on penalized log-likelihood criteria are presented as well as extensions to lumped processes constructed from high-order Markov chains. The relevance of the proposed approach to lumpability is illustrated by the analysis of DNA sequences. In particular, the use of lumped processes enables to highlight differences between intronic sequences and gene untranslated region sequences.

Toward diversity-responsive medical education: taking an intersectionality-based approach to a curriculum evaluation.

PubMed

Muntinga, M E; Krajenbrink, V Q E; Peerdeman, S M; Croiset, G; Verdonk, P

2016-08-01

Recent years have seen a rise in the efforts to implement diversity topics into medical education, using either a 'narrow' or a 'broad' definition of culture. These developments urge that outcomes of such efforts are systematically evaluated by mapping the curriculum for diversity-responsive content. This study was aimed at using an intersectionality-based approach to define diversity-related learning objectives and to evaluate how biomedical and sociocultural aspects of diversity were integrated into a medical curriculum in the Netherlands. We took a three-phase mixed methods approach. In phase one and two, we defined essential learning objectives based on qualitative interviews with school stakeholders and diversity literature. In phase three, we screened the written curriculum for diversity content (culture, sex/gender and class) and related the results to learning objectives defined in phase two. We identified learning objectives in three areas of education (medical knowledge and skills, patient-physician communication, and reflexivity). Most diversity content pertained to biomedical knowledge and skills. Limited attention was paid to sociocultural issues as determinants of health and healthcare use. Intersections of culture, sex/gender and class remained mostly unaddressed. The curriculum's diversity-responsiveness could be improved by an operationalization of diversity that goes beyond biomedical traits of assumed homogeneous social groups. Future efforts to take an intersectionality-based approach to curriculum evaluations should include categories of difference other than culture, sex/gender and class as separate, equally important patient identities or groups.

Identifying clinical net benefit of psychotropic medication use with latent variable techniques: Evidence from Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD).

PubMed

Bareis, Natalie; Lu, Juan; Kirkwood, Cynthia K; Kornstein, Susan G; Wu, Elwin; Mezuk, Briana

2018-05-29

Poor medication adherence is common among individuals with Bipolar Disorder (BD). Understanding the sources of heterogeneity in clinical net benefit (CNB) and how it is related to psychotropic medications can provide new insight into ways to improve adherence. Data come from the baseline assessments of the Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD). Latent class analysis identified groups of CNB, and validity of this construct was assessed using the SF-36. Adherence was defined as taking 75% or more of medications as prescribed. Associations between CNB and adherence were tested using multiple logistic regression adjusting for sociodemographic characteristics. Five classes of CNB were identified: High (24%), Moderately high (12%), Moderate (26%), Moderately low (27%) and Low (12%). Adherence to psychotropic medications did not differ across classes (71% to 75%, χ 2   = 3.43, p = 0.488). Medication regimens differed by class: 57% of the High CNB were taking ≤2 medications, whereas 49% of the Low CNB were taking ≥4. CNB classes had good concordance with the SF-36. Missing data limited measures used to define CNB. Participants' perceptions of their illness and treatment were not assessed. This novel operationalization of CNB has construct validity as indicated by the SF-36. Although CNB and polypharmacy regimens are heterogeneous in this sample, adherence is similar across CNB. Studying adherent individuals, despite suboptimal CNB, may provide novel insights into aspects influencing adherence. Copyright © 2018 Elsevier B.V. All rights reserved.

Thrombopoietin protects hematopoietic stem cells from retrotransposon-mediated damage by promoting an antiviral response.

PubMed

Barbieri, Daniela; Elvira-Matelot, Emilie; Pelinski, Yanis; Genève, Laetitia; de Laval, Bérengère; Yogarajah, Gayathri; Pecquet, Christian; Constantinescu, Stefan N; Porteu, Françoise

2018-05-07

Maintenance of genomic integrity is crucial for the preservation of hematopoietic stem cell (HSC) potential. Retrotransposons, spreading in the genome through an RNA intermediate, have been associated with loss of self-renewal, aging, and DNA damage. However, their role in HSCs has not been addressed. Here, we show that mouse HSCs express various retroelements (REs), including long interspersed element-1 (L1) recent family members that further increase upon irradiation. Using mice expressing an engineered human L1 retrotransposition reporter cassette and reverse transcription inhibitors, we demonstrate that L1 retransposition occurs in vivo and is involved in irradiation-induced persistent γH2AX foci and HSC loss of function. Thus, RE represents an important intrinsic HSC threat. Furthermore, we show that RE activity is restrained by thrombopoietin, a critical HSC maintenance factor, through its ability to promote a potent interferon-like, antiviral gene response in HSCs. This uncovers a novel mechanism allowing HSCs to minimize irradiation-induced injury and reinforces the links between DNA damage, REs, and antiviral immunity. © 2018 Barbieri et al.

URI Regulates KAP1 Phosphorylation and Transcriptional Repression via PP2A Phosphatase in Prostate Cancer Cells*

PubMed Central

Mita, Paolo; Savas, Jeffrey N.; Briggs, Erica M.; Ha, Susan; Gnanakkan, Veena; Yates, John R.; Robins, Diane M.; David, Gregory; Boeke, Jef D.; Garabedian, Michael J.; Logan, Susan K.

2016-01-01

URI (unconventional prefoldin RPB5 interactor protein) is an unconventional prefoldin, RNA polymerase II interactor that functions as a transcriptional repressor and is part of a larger nuclear protein complex. The components of this complex and the mechanism of transcriptional repression have not been characterized. Here we show that KAP1 (KRAB-associated protein 1) and the protein phosphatase PP2A interact with URI. Mechanistically, we show that KAP1 phosphorylation is decreased following recruitment of PP2A by URI. We functionally characterize the novel URI-KAP1-PP2A complex, demonstrating a role of URI in retrotransposon repression, a key function previously demonstrated for the KAP1-SETDB1 complex. Microarray analysis of annotated transposons revealed a selective increase in the transcription of LINE-1 and L1PA2 retroelements upon knockdown of URI. These data unveil a new nuclear function of URI and identify a novel post-transcriptional regulation of KAP1 protein that may have important implications in reactivation of transposable elements in prostate cancer cells. PMID:27780869

On general (α,β)-metrics of Landsberg type

NASA Astrophysics Data System (ADS)

Zohrehvand, M.; Maleki, H.

2016-05-01

In this paper, we study a class of Finsler metrics, which are defined by a Riemannian metric α and a one-form β. They are called general (α,β)-metrics. We have proven that, every Landsberg general (α,β)-metric is a Berwald metric, under a certain condition. This shows that the hunting for an unicorn, one of the longest standing open problem in Finsler geometry, cannot be successful in the class of general (α,β)-metrics.

Some fundamental concepts in remote sensing

NASA Technical Reports Server (NTRS)

1982-01-01

The term remote sensing is defined as well as ideas such as class, pattern, feature, pattern recognition, feature extraction, and theme. The electromagnetic spectrum is examined especially those wavelength regions available to remote sensing. Relevant energy and wave propagation laws are discussed and the characteristics of emitted and reflected radiation and their detection are investigated. The identification of classes by their spectral signatures, the multispectral approach, and the principal types of sensors and platforms used in remote sensing are also considered.

Parse Completion: A Study of an Inductive Domain

DTIC Science & Technology

1987-07-01

for Right Linear and Chomsky Normal Form grammars in detail. These two grammar classes were chosen as they can capture the classes of Regular and...Linear and Chomsky Normal Form grammars the allowed RHS formats could be divided into those which introduced new non-terminals and those which reused... Chomsky Normal Form grammars can both be shown to define a partial order over the set of grammars consistent with the examples. (Note that this is a

Riemann-Liouville Fractional Calculus of Certain Finite Class of Classical Orthogonal Polynomials

NASA Astrophysics Data System (ADS)

Malik, Pradeep; Swaminathan, A.

2010-11-01

In this work we consider certain class of classical orthogonal polynomials defined on the positive real line. These polynomials have their weight function related to the probability density function of F distribution and are finite in number up to orthogonality. We generalize these polynomials for fractional order by considering the Riemann-Liouville type operator on these polynomials. Various properties like explicit representation in terms of hypergeometric functions, differential equations, recurrence relations are derived.

Latent Class Analysis of Antisocial Behavior: Interaction of Serotonin Transporter Genotype and Maltreatment

PubMed Central

Li, James J.

2010-01-01

To improve understanding about genetic and environmental influences on antisocial behavior (ASB), we tested the association of the 44-base pair polymorphism of the serotonin transporter gene (5-HTTLPR) and maltreatment using latent class analysis in 2,488 boys and girls from Wave 1 of the National Longitudinal Study of Adolescent Health. In boys, ASB was defined by three classes (Exclusive Covert, Mixed Covert and Overt, and No Problems) whereas in girls, ASB was defined by two classes (Exclusive Covert, No Problems). In boys, 5-HTTLPR and maltreatment were not significantly related to ASB. However, in girls, maltreatment, but not 5-HTTLPR, was significantly associated with ASB. A significant interaction between 5-HTTLPR and maltreatment was also observed, where maltreated girls homozygous for the short allele were 12 times more likely to be classified in the Exclusive Covert group than in the No Problems group. Structural differences in the latent structure of ASB at Wave 2 and Wave 3 prevented repeat LCA modeling. However, using counts of ASB, 5-HTTLPR, maltreatment, and its interaction were unrelated to overt and covert ASB at Wave 2 and only maltreatment was related to covert ASB at Wave 3. We discuss these findings within the context of sex differences in ASB and relevant models of gene-environment interplay across developmental periods. PMID:20405199

Social class, income, education, area of residence and psychological distress: does social class have an independent effect on psychological distress in Antalya, Turkey?

PubMed

Belek, I

2000-02-01

The aim of this study is to determine the separate effects of social class, income, education and area of residence on psychological distress. The study also assesses whether the association between prevalence of high score on the 12-item General Health Questionnaire (GHQ 12) and social class is independent of other variables. Psychological distress was assessed by means of the GHQ 12. The study covered 1,092 adults aged 15 years or more living in two different quarters of Antalya. Social class status was defined by occupational position, with income, education and area of residence treated as confounders. Chi-square and logistic regression analyses were used to evaluate the data. Large inequalities in psychological distress by all variables were observed. Psychological distress was significantly associated with class status, after adjusting for income, education, area of residence and other potential confounders (age, sex and marital status). Class inequalities in psychological distress were observed between blue-collar workers/unqualified employees and bourgeoisie. These findings support the view that the recent widening of inequalities among social classes in Turkey pose a substantial threat to health.

Soil losses in rural watersheds with environmental land use conflicts.

PubMed

Pacheco, F A L; Varandas, S G P; Sanches Fernandes, L F; Valle Junior, R F

2014-07-01

Soil losses were calculated in a rural watershed where environmental land use conflicts developed in the course of a progressive invasion of forest and pasture/forest lands by agriculture, especially vineyards. The hydrographic basin is located in the Douro region where the famous Port wine is produced (northern Portugal) and the soil losses were estimated by the Universal Soil Loss Equation (USLE) in combination with a Geographic Information System (GIS). Environmental land use conflicts were set up on the basis of land use and land capability maps, coded as follows: 1-agriculture, 2-pasture, 3-pasture/forest, and 4-forest. The difference between the codes of capability and use defines a conflict class, where a negative or nil value means no conflict and a positive i value means class i conflict. The reliability of soil loss estimates was tested by a check of these values against the frequency of stone wall instabilities in vineyard terraces, with good results. Using the USLE, the average soil loss (A) was estimated in A=12.2 t·ha(-1)·yr(-1) and potential erosion risk areas were found to occupy 28.3% of the basin, defined where soil losses are larger than soil loss tolerances. Soil losses in no conflict regions (11.2 t·ha(-1)·yr(-1)) were significantly different from those in class 2 (6.8 t·ha(-1)·yr(-1)) and class 3 regions (21.3 t·ha(-1)·yr(-1)) that in total occupy 2.62 km(2) (14.3% of the basin). When simulating a scenario of no conflict across the entire basin, whereby land use in class 2 conflict regions is set up to permanent pastures and in class 3 conflict regions to pine forests, it was concluded that A=0.95 t·ha(-1)·yr(-1) (class 2) or A=9.8 t·ha(-1)·yr(-1) (class 3), which correspond to drops of 86% and 54% in soil loss relative to the actual values. Copyright © 2014 Elsevier B.V. All rights reserved.

NOVEL HERBICIDES

EPA Science Inventory

Low-dose, high-potency herbicides are defined as those herbicides with a maximum label application rate of 0.5 pounds of active ingredient per acre. Several classes of chemicals fall into this category, including the acetolactate synthase (ALSase) inhibitor herbicides, imidazoli...

On biodiversity conservation and poverty traps.

PubMed

Barrett, Christopher B; Travis, Alexander J; Dasgupta, Partha

2011-08-23

This paper introduces a special feature on biodiversity conservation and poverty traps. We define and explain the core concepts and then identify four distinct classes of mechanisms that define important interlinkages between biodiversity and poverty. The multiplicity of candidate mechanisms underscores a major challenge in designing policy appropriate across settings. This framework is then used to introduce the ensuing set of papers, which empirically explore these various mechanisms linking poverty traps and biodiversity conservation.

On biodiversity conservation and poverty traps

PubMed Central

Barrett, Christopher B.; Travis, Alexander J.; Dasgupta, Partha

2011-01-01

This paper introduces a special feature on biodiversity conservation and poverty traps. We define and explain the core concepts and then identify four distinct classes of mechanisms that define important interlinkages between biodiversity and poverty. The multiplicity of candidate mechanisms underscores a major challenge in designing policy appropriate across settings. This framework is then used to introduce the ensuing set of papers, which empirically explore these various mechanisms linking poverty traps and biodiversity conservation. PMID:21873176

On the gestalt concept.

PubMed

Breidbach, Olaf; Jost, Jürgen

2006-08-01

We define a gestalt as the invariants of a collection of patterns that can mutually be transformed into each other through a class of transformations encoded by, or conversely, determining that gestalt. The class of these transformations needs to satisfy structural regularities like the ones of the mathematical structure of a group. This makes an analysis of a gestalt possible in terms of relations between its representing patterns. While the gestalt concept has its origins in cognitive psychology, it has also important implications for morphology.

U.S. Army Corps of Engineers Manpower Information System: An Integrated Approach to Manpower Management

DTIC Science & Technology

1994-04-01

engineering and con- struction management services for both military and civil works programs. In FY93, the cost of those programs exceeded $10 billion and...A related issue was to explore the USACE costs , benefits, and barriers to implementing a single Class VI system software package for both the military...provide information in useful ways, track utilization information, I A Class HI system is defined in AR 25-3. It is a system whose total program costs are

Varied Human Tolerance to the Combined Conditions of Low Contrast and Diminished Luminance: A Quasi-Meta Analysis

DTIC Science & Technology

2017-08-30

as being three-fold: 1) a measurement of the integrity of both the central and peripheral visual processing centers; 2) an indicator of detail...visual assessment task 12 integral to the Army’s Class 1 Flight Physical (Ginsburg, 1981 and 1984; Bachman & Behar, 1986). During a Class 1 flight...systems. Meta-analysis has been defined as the statistical analysis of a collection of analytical results for the purpose of integrating the findings

Two-axis angular effector

DOEpatents

Vaughn, Mark R.; Robinett, III, Rush D.; Phelan, John R.; Van Zuiden, Don M.

1997-01-21

A new class of coplanar two-axis angular effectors. These effectors combine a two-axis rotational joint analogous to a Cardan joint with linear actuators in a manner to produce a wider range of rotational motion about both axes defined by the joint. This new class of effectors also allows design of robotic manipulators having very high strength and efficiency. These effectors are particularly suited for remote operation in unknown surroundings, because of their extraordinary versatility. An immediate application is to the problems which arise in nuclear waste remediation.

Differential invariants and exact solutions of the Einstein equations

NASA Astrophysics Data System (ADS)

Lychagin, Valentin; Yumaguzhin, Valeriy

2017-06-01

In this paper (cf. Lychagin and Yumaguzhin, in Anal Math Phys, 2016) a class of totally geodesics solutions for the vacuum Einstein equations is introduced. It consists of Einstein metrics of signature (1,3) such that 2-dimensional distributions, defined by the Weyl tensor, are completely integrable and totally geodesic. The complete and explicit description of metrics from these class is given. It is shown that these metrics depend on two functions in one variable and one harmonic function.

Ontology-Based Approach to Social Data Sentiment Analysis: Detection of Adolescent Depression Signals.

PubMed

Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min

2017-07-24

Social networking services (SNSs) contain abundant information about the feelings, thoughts, interests, and patterns of behavior of adolescents that can be obtained by analyzing SNS postings. An ontology that expresses the shared concepts and their relationships in a specific field could be used as a semantic framework for social media data analytics. The aim of this study was to refine an adolescent depression ontology and terminology as a framework for analyzing social media data and to evaluate description logics between classes and the applicability of this ontology to sentiment analysis. The domain and scope of the ontology were defined using competency questions. The concepts constituting the ontology and terminology were collected from clinical practice guidelines, the literature, and social media postings on adolescent depression. Class concepts, their hierarchy, and the relationships among class concepts were defined. An internal structure of the ontology was designed using the entity-attribute-value (EAV) triplet data model, and superclasses of the ontology were aligned with the upper ontology. Description logics between classes were evaluated by mapping concepts extracted from the answers to frequently asked questions (FAQs) onto the ontology concepts derived from description logic queries. The applicability of the ontology was validated by examining the representability of 1358 sentiment phrases using the ontology EAV model and conducting sentiment analyses of social media data using ontology class concepts. We developed an adolescent depression ontology that comprised 443 classes and 60 relationships among the classes; the terminology comprised 1682 synonyms of the 443 classes. In the description logics test, no error in relationships between classes was found, and about 89% (55/62) of the concepts cited in the answers to FAQs mapped onto the ontology class. Regarding applicability, the EAV triplet models of the ontology class represented about 91.4% of the sentiment phrases included in the sentiment dictionary. In the sentiment analyses, "academic stresses" and "suicide" contributed negatively to the sentiment of adolescent depression. The ontology and terminology developed in this study provide a semantic foundation for analyzing social media data on adolescent depression. To be useful in social media data analysis, the ontology, especially the terminology, needs to be updated constantly to reflect rapidly changing terms used by adolescents in social media postings. In addition, more attributes and value sets reflecting depression-related sentiments should be added to the ontology. ©Hyesil Jung, Hyeoun-Ae Park, Tae-Min Song. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 24.07.2017.

Ontology-Based Approach to Social Data Sentiment Analysis: Detection of Adolescent Depression Signals

PubMed Central

Jung, Hyesil; Song, Tae-Min

2017-01-01

Background Social networking services (SNSs) contain abundant information about the feelings, thoughts, interests, and patterns of behavior of adolescents that can be obtained by analyzing SNS postings. An ontology that expresses the shared concepts and their relationships in a specific field could be used as a semantic framework for social media data analytics. Objective The aim of this study was to refine an adolescent depression ontology and terminology as a framework for analyzing social media data and to evaluate description logics between classes and the applicability of this ontology to sentiment analysis. Methods The domain and scope of the ontology were defined using competency questions. The concepts constituting the ontology and terminology were collected from clinical practice guidelines, the literature, and social media postings on adolescent depression. Class concepts, their hierarchy, and the relationships among class concepts were defined. An internal structure of the ontology was designed using the entity-attribute-value (EAV) triplet data model, and superclasses of the ontology were aligned with the upper ontology. Description logics between classes were evaluated by mapping concepts extracted from the answers to frequently asked questions (FAQs) onto the ontology concepts derived from description logic queries. The applicability of the ontology was validated by examining the representability of 1358 sentiment phrases using the ontology EAV model and conducting sentiment analyses of social media data using ontology class concepts. Results We developed an adolescent depression ontology that comprised 443 classes and 60 relationships among the classes; the terminology comprised 1682 synonyms of the 443 classes. In the description logics test, no error in relationships between classes was found, and about 89% (55/62) of the concepts cited in the answers to FAQs mapped onto the ontology class. Regarding applicability, the EAV triplet models of the ontology class represented about 91.4% of the sentiment phrases included in the sentiment dictionary. In the sentiment analyses, “academic stresses” and “suicide” contributed negatively to the sentiment of adolescent depression. Conclusions The ontology and terminology developed in this study provide a semantic foundation for analyzing social media data on adolescent depression. To be useful in social media data analysis, the ontology, especially the terminology, needs to be updated constantly to reflect rapidly changing terms used by adolescents in social media postings. In addition, more attributes and value sets reflecting depression-related sentiments should be added to the ontology. PMID:28739560

HLA Epitopes: The Targets of Monoclonal and Alloantibodies Defined

PubMed Central

Nguyen, Anh

2017-01-01

Sensitization to human leukocyte antigens (HLA) in organ transplant patients causes graft rejection, according to the humoral theory of transplantation. Sensitization is almost ubiquitous as anti-HLA antibodies are found in almost all sera of transplant recipients. Advances in testing assays and amino acid sequencing of HLA along with computer software contributed further to the understanding of antibody-antigen reactivity. It is commonly understood that antibodies bind to HLA antigens. With current knowledge of epitopes, it is more accurate to describe that antibodies bind to their target epitopes on the surface of HLA molecular chains. Epitopes are present on a single HLA (private epitope) or shared by multiple antigens (public epitope). The phenomenon of cross-reactivity in HLA testing, often explained as cross-reactive groups (CREGs) of antigens with antibody, can be clearly explained now by public epitopes. Since 2006, we defined and reported 194 HLA class I unique epitopes, including 56 cryptic epitopes on dissociated HLA class I heavy chains, 83 HLA class II epitopes, 60 epitopes on HLA-DRB1, 15 epitopes on HLA-DQB1, 3 epitopes on HLA-DQA1, 5 epitopes on HLA-DPB1, and 7 MICA epitopes. In this paper, we provide a summary of our findings. PMID:28626773

WebMapping at school

NASA Astrophysics Data System (ADS)

de Lange, Norbert

2010-11-01

The paper discusses the position of GIS in Geography as a subject especially at German schools. It points out that students only need simple GIS-functions in order to explore digital atlases or webbased data viewers. Furthermore it is widely accepted that learning achievements improve if students make use of the idea of self-employed and explorative working on information produced by themselves. These two arguments have led to the development of the WebMapping tool "kartografix_school". It allows users to generate maps with new and individually defined content on the internet. For that purpose the tool contains generalized outlines of all countries of the world as well as of German States. As these boundaries are given users can assign new attribute data to these geoobjects. These data are transferred to a graphic presentation. It is possible to define the classification and colours for each class. Users can change and update all information (data as well as number of classes, definition of classes, colours) at any time. Moreover "kartografix_school" offers the possibility to produce maps which are composed of two layers. All data are stored at a server located in the University of Osnabrück. "kartografix_school" is integrated in an e-Learning environment.

Parent–Child Relationships in Stepfather Families and Adolescent Adjustment: A Latent Class Analysis

PubMed Central

Amato, Paul R.; King, Valarie; Thorsen, Maggie L.

2015-01-01

In the current study the authors drew on Waves I and III from Add Health to examine the closeness of parent–adolescent relationships in married mother–stepfather families (N = 1,934). They used latent class analysis to identify family constellations defined by adolescents’ relationships with all of their parents: mothers, stepfathers, and biological nonresident fathers. In particular, the authors (a) identified the most common underlying patterns of adolescent–parent relationships in stepfamilies; (b) determined the background characteristics that predict membership in these groups; and (c) examined how adolescents in these groups fare with respect to depressive symptoms, delinquency, and substance use. The results indicate that adolescents’ relationships can be represented with 4 latent classes. Adolescents in these classes differ on measures of adjustment, and many of these differences persist into the early adult years. PMID:27022199

Impact of surface disinfection and sterile draping of furniture on room air quality in a cardiac procedure room with a ventilation and air-conditioning system (extrusion airflow, cleanroom class 1b (DIN 1946-4))

PubMed Central

Below, Harald; Ryll, Sylvia; Empen, Klaus; Dornquast, Tina; Felix, Stefan; Rosenau, Heike; Kramer, Sebastian; Kramer, Axel

2010-01-01

In a cardiac procedure room, ventilated by a ventilation and air-conditioning system with turbulent mixed airflow, a protection zone in the operating area could be defined through visualization of airflows. Within this protection zone, no turbulence was detectable in the room air. Under the given conditions, disinfection of all surfaces including all furniture and equipment after the last operation and subsequent draping of furniture and all equipment that could not be removed from the room with sterile surgical drapes improved the indoor room air quality from cleanroom class C to cleanroom class B. This also allows procedures with elevated requirements to be performed in room class 1b. PMID:20941336

Mission specification for three generic mission classes

NASA Technical Reports Server (NTRS)

1979-01-01

Mission specifications for three generic mission classes are generated to provide a baseline for definition and analysis of data acquisition platform system concepts. The mission specifications define compatible groupings of sensors that satisfy specific earth resources and environmental mission objectives. The driving force behind the definition of sensor groupings is mission need; platform and space transportation system constraints are of secondary importance. The three generic mission classes are: (1) low earth orbit sun-synchronous; (2) geosynchronous; and (3) non-sun-synchronous, nongeosynchronous. These missions are chosen to provide a variety of sensor complements and implementation concepts. Each mission specification relates mission categories, mission objectives, measured parameters, and candidate sensors to orbits and coverage, operations compatibility, and platform fleet size.

The NASA Air Traffic Management Ontology: Technical Documentation

NASA Technical Reports Server (NTRS)

Keller, Richard M.

2017-01-01

This document is intended to serve as comprehensive documentation for the NASA Air Traffic Management (ATM) Ontology. The ATM Ontology is a conceptual model that defines key classes of entities and relationships pertaining to the US National Airspace System (NAS) and the management of air traffic through that system. A wide variety of classes are represented in the ATM Ontology, including classes corresponding to flights, aircraft, manufacturers, airports, airlines, air routes, NAS facilities, air traffic control advisories, weather phenomena, and many others. The Ontology can be useful in the context of a variety of information management tasks relevant to NAS, including information exchange, data query and search, information organization, information integration, and terminology standardization.

Non-compact nonlinear sigma models

DOE PAGES

de Rham, Claudia; Tolley, Andrew J.; Zhou, Shuang-Yong

2016-07-19

The target space of a nonlinear sigma model is usually required to be positive definite to avoid ghosts. We introduce a unique class of nonlinear sigma models where the target space metric has a Lorentzian signature, thus the associated group being non-compact. We show that the would-be ghost associated with the negative direction is fully projected out by 2 second-class constraints, and there exist stable solutions in this class of models. This result also has important implications for Lorentz–invariant massive gravity: There exist stable nontrivial vacua in massive gravity that are free from any linear vDVZ-discontinuity and a decoupling limitmore » can be defined on these vacua.« less

Non-compact nonlinear sigma models

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

de Rham, Claudia; Tolley, Andrew J.; Zhou, Shuang-Yong

The target space of a nonlinear sigma model is usually required to be positive definite to avoid ghosts. We introduce a unique class of nonlinear sigma models where the target space metric has a Lorentzian signature, thus the associated group being non-compact. We show that the would-be ghost associated with the negative direction is fully projected out by 2 second-class constraints, and there exist stable solutions in this class of models. This result also has important implications for Lorentz–invariant massive gravity: There exist stable nontrivial vacua in massive gravity that are free from any linear vDVZ-discontinuity and a decoupling limitmore » can be defined on these vacua.« less

Evaluating the reforested area for the municipality of Buri by automatic analysis of LANDSAT imagery. [Sao Paulo, Brazil

NASA Technical Reports Server (NTRS)

Dejesusparada, N. (Principal Investigator); Lee, D. C. L.; Filho, R. H.; Shimabukuro, Y. E.

1979-01-01

The author has identified the following significant results. The class of reforestation (Pinus, Eucalyptus, Araucaria) was defined using iterative image analysis (1-100) and LANDSAT MSS data. Estimates of class area by 1-100 were compared with data supplied by the forestry institute in Sao Paulo. LANDSAT channels 4 and 5 served to differentiate the Pinus, Eucalyptus, and Araucaria from the other trees. Channels 6 and 7 gave best results for differentiating between the classes. A good representative spectral response was obtained for Auraucaria on these two channels. The small relative differences obtained were +4.24% for Araucaria, -7.51% for Pinus, and -32.07% for Eucalyptus.

Transport phenomena of graded sediments in tidal environments

NASA Astrophysics Data System (ADS)

Bonaldo, Davide; Dall'Angelo, Chiara; di Silvio, Giampaolo

2010-05-01

A long-term morphodynamic model simulating the ontogenesis and evolution of a tidal lagoon has been undergoing a continuous improvement in order to enrich its predictive ability and assess the relative importance of different factors, of both natural and anthropogenic origin, in defining the equilibrium configuration of such systems. A significant step forward in this direction is achieved by introducing the possibility to extend the analysis from uniform to graded sediments. In the latter case the representation of long-term phenomena is conceptually the same as for a sediment characterized by a single granulometric class, as far as it concerns the temporal averaging and the splitting of the transport in a dispersive component (mainly given by tidal action) and an eulerian residual convective component (resulting from rivers, long-shore currents, and asymmetry between flood and ebb flow fields). The horizontal sediment budget, however, is now coupled with a sediment budget among the different granulometric classes in the bottom, and precisely in a "mixing layer" whose thickness has to be properly defined. This new enhancement of the model allows, beside a more precise description of the morphodynamic processes, a certain number of further investigations. As a first point, it makes it possible to study the effect of the initial stratigraphic conditions on the genesis and evolution of the tidal basin, thus obtaining some informations about the persistence of "geological memory" in the system. Another matter, of environmental interest rather than strictly morphodynamic, concerns the possibility of creating "auxiliary classes" among the grainsize classes in order to label and track contaminated sediments, providing a prediction tool and a decisional support in case of environmental accidents. Such a sediment tracking could also be used to distinguish the sediments according to their fluvial or maritime origin, defining in this way a criterion for the classification of the various morphological features which can be found within the system. A sensitivity analysis of the main parameters is under way.

Calculating Student Grades.

ERIC Educational Resources Information Center

Allswang, John M.

1986-01-01

This article provides two short microcomputer gradebook programs. The programs, written in BASIC for the IBM-PC and Apple II, provide statistical information about class performance and calculate grades either on a normal distribution or based on teacher-defined break points. (JDH)

ENVIRONMENTAL ENGINEERING AND ENDOCRINE DISRUPTING CHEMICALS

EPA Science Inventory

Endocrine disruptors are a class of chemicals of growing interest to the environmental community. USEPA's Risk Assessment Forum defined an endocrine disrupting chemical (EDC) as "an exogenous agent that interferes with the synthesis, secretion, transport, binding, action, or elim...

46 CFR 95.16-20 - Extinguishing agent: Cylinder storage.

Code of Federal Regulations, 2014 CFR

2014-10-01

... cylinder storage room and the protected spaces must meet the insulation criteria for Class A-60, as defined... pneumatic heat actuator as well as a remote manual control. (c) The cylinder storage space must be properly...

46 CFR 95.16-20 - Extinguishing agent: Cylinder storage.

Code of Federal Regulations, 2012 CFR

2012-10-01

... cylinder storage room and the protected spaces must meet the insulation criteria for Class A-60, as defined... pneumatic heat actuator as well as a remote manual control. (c) The cylinder storage space must be properly...

46 CFR 95.16-20 - Extinguishing agent: Cylinder storage.

Code of Federal Regulations, 2013 CFR

2013-10-01

... cylinder storage room and the protected spaces must meet the insulation criteria for Class A-60, as defined... pneumatic heat actuator as well as a remote manual control. (c) The cylinder storage space must be properly...

49 CFR 385.402 - What definitions are used in this subpart?

Code of Federal Regulations, 2010 CFR

2010-10-01

... temperature materials, materials designated as hazardous in the Hazardous Materials Table (see § 172.101 of this title), and materials that meet the defining criteria for hazard classes and divisions in part 173...

1992

EPA Science Inventory

There are two classes of statistical issues: firm issues amenable to problem statement and technical resolution and soft issues that have qualitative dimensions and ideological implications. irm issues are easy: defining and stating the problem is much of the solution. he soft is...

System and method for integrating and accessing multiple data sources within a data warehouse architecture

DOEpatents

Musick, Charles R [Castro Valley, CA; Critchlow, Terence [Livermore, CA; Ganesh, Madhaven [San Jose, CA; Slezak, Tom [Livermore, CA; Fidelis, Krzysztof [Brentwood, CA

2006-12-19

A system and method is disclosed for integrating and accessing multiple data sources within a data warehouse architecture. The metadata formed by the present method provide a way to declaratively present domain specific knowledge, obtained by analyzing data sources, in a consistent and useable way. Four types of information are represented by the metadata: abstract concepts, databases, transformations and mappings. A mediator generator automatically generates data management computer code based on the metadata. The resulting code defines a translation library and a mediator class. The translation library provides a data representation for domain specific knowledge represented in a data warehouse, including "get" and "set" methods for attributes that call transformation methods and derive a value of an attribute if it is missing. The mediator class defines methods that take "distinguished" high-level objects as input and traverse their data structures and enter information into the data warehouse.

Evaluation of nonmetallic thermal protection materials for the manned space shuttle. Volume 1, task 1: Assessment of technical risks associated with utilization of nonmetallic thermal protection system

NASA Technical Reports Server (NTRS)

Wilkinson, W. H.; Kirkhart, F. P.; Kistler, C. W.; Duckworth, W. H.; Ungar, E. W.; Foster, E. L.

1970-01-01

Technical problems of design and flight qualification of the proposed classes of surface insulation materials and leading edge materials were reviewed. A screening test plan, a preliminary design data test plan and a design data test plan were outlined. This program defined the apparent critical differences between the surface insulators and the leading edge materials, structuring specialized screening test plans for each of these two classes of materials. Unique testing techniques were shown to be important in evaluating the structural interaction aspects of the surface insulators and a separate task was defined to validate the test plan. In addition, a compilation was made of available information on proposed material (including metallic TPS), previous shuttle programs, pertinent test procedures, and other national programs of merit. This material was collected and summarized in an informally structured workbook.

Object-oriented analysis and design of a health care management information system.

PubMed

Krol, M; Reich, D L

1999-04-01

We have created a prototype for a universal object-oriented model of a health care system compatible with the object-oriented approach used in version 3.0 of the HL7 standard for communication messages. A set of three models has been developed: (1) the Object Model describes the hierarchical structure of objects in a system--their identity, relationships, attributes, and operations; (2) the Dynamic Model represents the sequence of operations in time as a collection of state diagrams for object classes in the system; and (3) functional Diagram represents the transformation of data within a system by means of data flow diagrams. Within these models, we have defined major object classes of health care participants and their subclasses, associations, attributes and operators, states, and behavioral scenarios. We have also defined the major processes and subprocesses. The top-down design approach allows use, reuse, and cloning of standard components.

Solving a class of generalized fractional programming problems using the feasibility of linear programs.

PubMed

Shen, Peiping; Zhang, Tongli; Wang, Chunfeng

2017-01-01

This article presents a new approximation algorithm for globally solving a class of generalized fractional programming problems (P) whose objective functions are defined as an appropriate composition of ratios of affine functions. To solve this problem, the algorithm solves an equivalent optimization problem (Q) via an exploration of a suitably defined nonuniform grid. The main work of the algorithm involves checking the feasibility of linear programs associated with the interesting grid points. It is proved that the proposed algorithm is a fully polynomial time approximation scheme as the ratio terms are fixed in the objective function to problem (P), based on the computational complexity result. In contrast to existing results in literature, the algorithm does not require the assumptions on quasi-concavity or low-rank of the objective function to problem (P). Numerical results are given to illustrate the feasibility and effectiveness of the proposed algorithm.

A Calculus for Boxes and Traits in a Java-Like Setting

NASA Astrophysics Data System (ADS)

Bettini, Lorenzo; Damiani, Ferruccio; de Luca, Marco; Geilmann, Kathrin; Schäfer, Jan

The box model is a component model for the object-oriented paradigm, that defines components (the boxes) with clear encapsulation boundaries. Having well-defined boundaries is crucial in component-based software development, because it enables to argue about the interference and interaction between a component and its context. In general, boxes contain several objects and inner boxes, of which some are local to the box and cannot be accessed from other boxes and some can be accessible by other boxes. A trait is a set of methods divorced from any class hierarchy. Traits can be composed together to form classes or other traits. We present a calculus for boxes and traits. Traits are units of fine-grained reuse, whereas boxes can be seen as units of coarse-grained reuse. The calculus is equipped with an ownership type system and allows us to combine coarse- and fine-grained reuse of code by maintaining encapsulation of components.

A Comparison of Land Surface Model Soil Hydraulic Properties Estimated by Inverse Modeling and Pedotransfer Functions

NASA Technical Reports Server (NTRS)

Gutmann, Ethan D.; Small, Eric E.

2007-01-01

Soil hydraulic properties (SHPs) regulate the movement of water in the soil. This in turn plays an important role in the water and energy cycles at the land surface. At present, SHPS are commonly defined by a simple pedotransfer function from soil texture class, but SHPs vary more within a texture class than between classes. To examine the impact of using soil texture class to predict SHPS, we run the Noah land surface model for a wide variety of measured SHPs. We find that across a range of vegetation cover (5 - 80% cover) and climates (250 - 900 mm mean annual precipitation), soil texture class only explains 5% of the variance expected from the real distribution of SHPs. We then show that modifying SHPs can drastically improve model performance. We compare two methods of estimating SHPs: (1) inverse method, and (2) soil texture class. Compared to texture class, inverse modeling reduces errors between measured and modeled latent heat flux from 88 to 28 w/m(exp 2). Additionally we find that with increasing vegetation cover the importance of SHPs decreases and that the van Genuchten m parameter becomes less important, while the saturated conductivity becomes more important.

Floquet topological phases with symmetry in all dimensions

NASA Astrophysics Data System (ADS)

Roy, Rahul; Harper, Fenner

2017-05-01

Dynamical systems may host a number of remarkable symmetry-protected phases that are qualitatively different from their static analogs. In this work, we consider the phase space of symmetry-respecting unitary evolutions in detail and identify several distinct classes of evolution that host dynamical order. Using ideas from group cohomology, we construct a set of interacting Floquet drives that generate dynamical symmetry-protected topological order for each nontrivial cohomology class in every dimension, illustrating our construction with explicit two-dimensional examples. We also identify a set of symmetry-protected Floquet drives that lie outside of the group cohomology construction, and a further class of symmetry-respecting topological drives which host chiral edge modes. We use these special drives to define a notion of phase (stable to a class of local perturbations in the bulk) and the concepts of relative and absolute topological order, which can be applied to many different classes of unitary evolutions. These include fully many-body localized unitary evolutions and time crystals.

Clinical Applications of Hallucinogens: A Review

PubMed Central

Garcia-Romeu, Albert; Kersgaard, Brennan; Addy, Peter H.

2016-01-01

Hallucinogens fall into several different classes, as broadly defined by pharmacological mechanism of action, and chemical structure. These include psychedelics, entactogens, dissociatives, and other atypical hallucinogens. Although these classes do not share a common primary mechanism of action, they do exhibit important similarities in their ability to occasion temporary but profound alterations of consciousness, involving acute changes in somatic, perceptual, cognitive, and affective processes. Such effects likely contribute to their recreational use. However, a growing body of evidence indicates that these drugs may have therapeutic applications beyond their potential for abuse. This review will present data on several classes of hallucinogens with a particular focus on psychedelics, entactogens, and dissociatives, for which clinical utility has been most extensively documented. Information on each class is presented in turn, tracing relevant historical insights, highlighting similarities and differences between the classes from the molecular to the behavioral level, and presenting the most up-to-date information on clinically oriented research with these substances, with important ramifications for their potential therapeutic value. PMID:27454674

Debris Disks Among the Shell Stars: Insights from Spitzer

NASA Technical Reports Server (NTRS)

Roberge, Aki; Weinberger, Alycia; Teske, Johanna

2008-01-01

Shell stars are a class of early-type stars that show narrow absorption lines in their spectra that appear to arise from circumstellar class. This observationally defined class contains a variety of objects, including evolved stars and classical Be stars. However, some of the main sequence shell stars harbor debris disks and younger protoplanetary disks, though this aspect of the class has been largely overlooked. We surveyed a set of main sequence stars for cool dust using Spitzer MIPS and found four additional systems with IR excesses at both 24 and 70 microns. This indicates that the stars have both circumstellar gas and dust, and are likely to be edge-on debris disks. Our estimate of the disk fraction among nearby main sequence shell stars is 48% +/- 14%. We discuss here the nature of the shell stars and present preliminary results from ground-based optical spectra of the survey target stars. We will also outline our planned studies aimed at further characterization of the shell star class.

A DESCRIPTION OF HANKEL OPERATORS OF CLASS \\mathfrak{S}_p FOR p>0, AN INVESTIGATION OF THE RATE OF RATIONAL APPROXIMATION, AND OTHER APPLICATIONS

NASA Astrophysics Data System (ADS)

Peller, V. V.

1985-02-01

The main result is the following description of Hankel operators in the Schatten-von Neumann class \\mathfrak{S}_p when 0: \\displaystyle \\Gamma_\\varphi\\in\\mathfrak{S}_p\\Leftrightarrow \\varphi\\in B_p^{1/p},where \\Gamma_\\varphi is the Hankel operator with symbol \\varphi, and B_p^{1/p} is the Besov class. This result extends results obtained earlier for 1\\leqslant p<+\\infty by the author to the case 0. Also described are the Hankel operators in the Schatten-Lorentz classes \\mathfrak{S}_{pq}, 0, 0. Precise descriptions of classes of functions defined in terms of rational approximation in the bounded mean oscillation norm are given as an application, along with a complete investigation of the case where the decrease is of power order, and some precise results on rational approximation in the L^\\infty-norm. Certain other applications are also considered.Bibliography: 57 titles.

Identification of a new allelic variant of the Acinetobacter baumannii cephalosporinase, ADC-7 beta-lactamase: defining a unique family of class C enzymes.

PubMed

Hujer, Kristine M; Hamza, Nashaat S; Hujer, Andrea M; Perez, Federico; Helfand, Marion S; Bethel, Christopher R; Thomson, Jodi M; Anderson, Vernon E; Barlow, Miriam; Rice, Louis B; Tenover, Fred C; Bonomo, Robert A

2005-07-01

Acinetobacter spp. are emerging as opportunistic hospital pathogens that demonstrate resistance to many classes of antibiotics. In a metropolitan hospital in Cleveland, a clinical isolate of Acinetobacter baumannii that tested resistant to cefepime and ceftazidime (MIC = 32 microg/ml) was identified. Herein, we sought to determine the molecular basis for the extended-spectrum-cephalosporin resistance. Using analytical isoelectric focusing, a beta-lactamase with a pI of > or = 9.2 was detected. PCR amplification with specific A. baumannii cephalosporinase primers yielded a 1,152-bp product which, when sequenced, identified a novel 383-amino-acid class C enzyme. Expressed in Escherichia coli DH10B, this beta-lactamase demonstrated greater resistance against ceftazidime and cefotaxime than cefepime (4.0 microg/ml versus 0.06 microg/ml). The kinetic characteristics of this beta-lactamase were similar to other cephalosporinases found in Acinetobacter spp. In addition, this cephalosporinase was inhibited by meropenem, imipenem, ertapenem, and sulopenem (K(i) < 40 microM). The amino acid compositions of this novel enzyme and other class C beta-lactamases thus far described for A. baumannii, Acinetobacter genomic species 3, and Oligella urethralis in Europe and South Africa suggest that this cephalosporinase defines a unique family of class C enzymes. We propose a uniform designation for this family of cephalosporinases (Acinetobacter-derived cephalosporinases [ADC]) found in Acinetobacter spp. and identify this enzyme as ADC-7 beta-lactamase. The coalescence of Acinetobacter ampC beta-lactamases into a single common ancestor and the substantial phylogenetic distance separating them from other ampC genes support the logical value of developing a system of nomenclature for these Acinetobacter cephalosporinase genes.

Identification of a New Allelic Variant of the Acinetobacter baumannii Cephalosporinase, ADC-7 β-Lactamase: Defining a Unique Family of Class C Enzymes‡

PubMed Central

Hujer, Kristine M.; Hamza, Nashaat S.; Hujer, Andrea M.; Perez, Federico; Helfand, Marion S.; Bethel, Christopher R.; Thomson, Jodi M.; Anderson, Vernon E.; Barlow, Miriam; Rice, Louis B.; Tenover, Fred C.; Bonomo, Robert A.

2005-01-01

Acinetobacter spp. are emerging as opportunistic hospital pathogens that demonstrate resistance to many classes of antibiotics. In a metropolitan hospital in Cleveland, a clinical isolate of Acinetobacter baumannii that tested resistant to cefepime and ceftazidime (MIC = 32 μg/ml) was identified. Herein, we sought to determine the molecular basis for the extended-spectrum-cephalosporin resistance. Using analytical isoelectric focusing, a β-lactamase with a pI of ≥9.2 was detected. PCR amplification with specific A. baumannii cephalosporinase primers yielded a 1,152-bp product which, when sequenced, identified a novel 383-amino-acid class C enzyme. Expressed in Escherichia coli DH10B, this β-lactamase demonstrated greater resistance against ceftazidime and cefotaxime than cefepime (4.0 μg/ml versus 0.06 μg/ml). The kinetic characteristics of this β-lactamase were similar to other cephalosporinases found in Acinetobacter spp. In addition, this cephalosporinase was inhibited by meropenem, imipenem, ertapenem, and sulopenem (Ki < 40 μM). The amino acid compositions of this novel enzyme and other class C β-lactamases thus far described for A. baumannii, Acinetobacter genomic species 3, and Oligella urethralis in Europe and South Africa suggest that this cephalosporinase defines a unique family of class C enzymes. We propose a uniform designation for this family of cephalosporinases (Acinetobacter-derived cephalosporinases [ADC]) found in Acinetobacter spp. and identify this enzyme as ADC-7 β-lactamase. The coalescence of Acinetobacter ampC β-lactamases into a single common ancestor and the substantial phylogenetic distance separating them from other ampC genes support the logical value of developing a system of nomenclature for these Acinetobacter cephalosporinase genes. PMID:15980372

Short-term Risk of Serious Fall Injuries in Older Adults Initiating and Intensifying Treatment with Antihypertensive Medication

PubMed Central

Shimbo, Daichi; Bowling, C. Barrett; Levitan, Emily B.; Deng, Luqin; Sim, John J.; Huang, Lei; Reynolds, Kristi; Muntner, Paul

2016-01-01

Background Antihypertensive medication use has been associated with an increased risk of falls in some but not all studies. Few data are available on the short-term risk of falls following antihypertensive medication initiation and intensification. Methods and Results We examined the association between initiating and intensifying antihypertensive medication and serious fall injuries in a case-crossover study of 90,127 Medicare beneficiaries who were ≥65 years old and had a serious fall injury between July 1, 2007 and December 31, 2012, based on emergency department and inpatient claims. Antihypertensive medication initiation was defined by a prescription fill with no fills in the prior year. Intensification was defined by the addition of a new antihypertensive class, and, separately, titration by the addition of a new class or increase in dosage of a current class. Exposures were ascertained for the 15 days before the fall (case period) and six 15-day earlier periods (control periods). Overall, 272, 1508, and 3113 Medicare beneficiaries initiated, added a new class of antihypertensive medication or titrated therapy, respectively, within 15 days of their serious fall injury. The odds for a serious fall injury was increased during the 15 days following antihypertensive medication initiation [odds ratio, OR, 1.36 (95% CI 1.19, 1.55)], adding a new class [OR 1.16 (95% CI 1.10, 1.23)], and titration [OR 1.13 (95% CI 1.08, 1.18)]. These associations were attenuated beyond 15 days. Conclusions Antihypertensive medication initiation and intensification was associated with a short-term, but not long-term, increased risk of serious fall injuries among older adults. PMID:27166208

Short-Term Risk of Serious Fall Injuries in Older Adults Initiating and Intensifying Treatment With Antihypertensive Medication.

PubMed

Shimbo, Daichi; Barrett Bowling, C; Levitan, Emily B; Deng, Luqin; Sim, John J; Huang, Lei; Reynolds, Kristi; Muntner, Paul

2016-05-01

Antihypertensive medication use has been associated with an increased risk of falls in some but not all studies. Few data are available on the short-term risk of falls after antihypertensive medication initiation and intensification. We examined the association between initiating and intensifying antihypertensive medication and serious fall injuries in a case-crossover study of 90 127 Medicare beneficiaries who were ≥65 years old and had a serious fall injury between July 1, 2007, and December 31, 2012, based on emergency department and inpatient claims. Antihypertensive medication initiation was defined by a prescription fill with no fills in the previous year. Intensification was defined by the addition of a new antihypertensive class, and separately, titration by the addition of a new class or increase in dosage of a current class. Exposures were ascertained for the 15 days before the fall (case period) and six 15-day earlier periods (control periods). Overall, 272, 1508, and 3113 Medicare beneficiaries initiated, added a new class of antihypertensive medication or titrated therapy within 15 days of their serious fall injury. The odds for a serious fall injury was increased during the 15 days after antihypertensive medication initiation (odds ratio, 1.36 [95% confidence interval, 1.19-1.55]), adding a new class (odds ratio, 1.16 [95% confidence interval, 1.10-1.23]), and titration [odds ratio, 1.13 [95% confidence interval, 1.08-1.18]). These associations were attenuated beyond 15 days. Antihypertensive medication initiation and intensification was associated with a short-term, but not long-term, increased risk of serious fall injuries among older adults. © 2016 American Heart Association, Inc.

CMPF: class-switching minimized pathfinding in metabolic networks.

PubMed

Lim, Kevin; Wong, Limsoon

2012-01-01

The metabolic network is an aggregation of enzyme catalyzed reactions that converts one compound to another. Paths in a metabolic network are a sequence of enzymes that describe how a chemical compound of interest can be produced in a biological system. As the number of such paths is quite large, many methods have been developed to score paths so that the k-shortest paths represent the set of paths that are biologically meaningful or efficient. However, these approaches do not consider whether the sequence of enzymes can be manufactured in the same pathway/species/localization. As a result, a predicted sequence might consist of groups of enzymes that operate in distinct pathway/species/localization and may not truly reflect the events occurring within cell. We propose a path weighting method CMPF (Class-switching Minimized Pathfinder) to search for routes in a metabolic network which minimizes pathway switching. In biological terms, a pathway is a series of chemical reactions which define a specific function (e.g. glycolysis). We conjecture that routes that cross many pathways are inefficient since different pathways define different metabolic functions. In addition, native routes are also well characterized within pathways, suggesting that reasonable paths should not involve too many pathway switches. Our method can be generalized when reactions participate in a class set (e.g., pathways, species or cellular localization) so that the paths predicted have minimal class crossings. We show that our method generates k-paths that involve the least number of class switching. In addition, we also show that native paths are recoverable and alternative paths deviates less from native paths compared to other methods. This suggests that paths ranked by our method could be a way to predict paths that are likely to occur in biological systems.

The ITE Land classification: Providing an environmental stratification of Great Britain.

PubMed

Bunce, R G; Barr, C J; Gillespie, M K; Howard, D C

1996-01-01

The surface of Great Britain (GB) varies continuously in land cover from one area to another. The objective of any environmentally based land classification is to produce classes that match the patterns that are present by helping to define clear boundaries. The more appropriate the analysis and data used, the better the classes will fit the natural patterns. The observation of inter-correlations between ecological factors is the basis for interpreting ecological patterns in the field, and the Institute of Terrestrial Ecology (ITE) Land Classification formalises such subjective ideas. The data inevitably comprise a large number of factors in order to describe the environment adequately. Single factors, such as altitude, would only be useful on a national basis if they were the only dominant causative agent of ecological variation.The ITE Land Classification has defined 32 environmental categories called 'land classes', initially based on a sample of 1-km squares in Great Britain but subsequently extended to all 240 000 1-km squares. The original classification was produced using multivariate analysis of 75 environmental variables. The extension to all squares in GB was performed using a combination of logistic discrimination and discriminant functions. The classes have provided a stratification for successive ecological surveys, the results of which have characterised the classes in terms of botanical, zoological and landscape features.The classification has also been applied to integrate diverse datasets including satellite imagery, soils and socio-economic information. A variety of models have used the structure of the classification, for example to show potential land use change under different economic conditions. The principal data sets relevant for planning purposes have been incorporated into a user-friendly computer package, called the 'Countryside Information System'.

Advanced Concepts for Sea Control,

DTIC Science & Technology

1977-11-01

how combinations of some improvements and finally where some of these "basic" concepts into hybrids avenues of reduced cost can be might bring about...the exact definition of the are generally accepted as the "basic" job to be done. Unfortunately, the forms and it is easy to see how hybrid - "job to be...1) first define the job then already hybrids and are really starting define alternative vehicles which might points in thei: general classes. Some do

Solving quantum optimal control problems using Clebsch variables and Lin constraints

NASA Astrophysics Data System (ADS)

Delgado-Téllez, M.; Ibort, A.; Rodríguez de la Peña, T.

2018-01-01

Clebsch variables (and Lin constraints) are applied to the study of a class of optimal control problems for affine-controlled quantum systems. The optimal control problem will be modelled with controls defined on an auxiliary space where the dynamical group of the system acts freely. The reciprocity between both theories: the classical theory defined by the objective functional and the quantum system, is established by using a suitable version of Lagrange’s multipliers theorem and a geometrical interpretation of the constraints of the system as defining a subspace of horizontal curves in an associated bundle. It is shown how the solutions of the variational problem defined by the objective functional determine solutions of the quantum problem. Then a new way of obtaining explicit solutions for a family of optimal control problems for affine-controlled quantum systems (finite or infinite dimensional) is obtained. One of its main advantages, is the the use of Clebsch variables allows to compute such solutions from solutions of invariant problems that can often be computed explicitly. This procedure can be presented as an algorithm that can be applied to a large class of systems. Finally, some simple examples, spin control, a simple quantum Hamiltonian with an ‘Elroy beanie’ type classical model and a controlled one-dimensional quantum harmonic oscillator, illustrating the main features of the theory, will be discussed.

Class D Management Implementation Approach of the First Orbital Mission of the Earth Venture Series

NASA Technical Reports Server (NTRS)

Wells, James E.; Scherrer, John; Law, Richard; Bonniksen, Chris

2013-01-01

A key element of the National Research Council's Earth Science and Applications Decadal Survey called for the creation of the Venture Class line of low-cost research and application missions within NASA (National Aeronautics and Space Administration). One key component of the architecture chosen by NASA within the Earth Venture line is a series of self-contained stand-alone spaceflight science missions called "EV-Mission". The first mission chosen for this competitively selected, cost and schedule capped, Principal Investigator-led opportunity is the CYclone Global Navigation Satellite System (CYGNSS). As specified in the defining Announcement of Opportunity, the Principal Investigator is held responsible for successfully achieving the science objectives of the selected mission and the management approach that he/she chooses to obtain those results has a significant amount of freedom as long as it meets the intent of key NASA guidance like NPR 7120.5 and 7123. CYGNSS is classified under NPR 7120.5E guidance as a Category 3 (low priority, low cost) mission and carries a Class D risk classification (low priority, high risk) per NPR 8705.4. As defined in the NPR guidance, Class D risk classification allows for a relatively broad range of implementation strategies. The management approach that will be utilized on CYGNSS is a streamlined implementation that starts with a higher risk tolerance posture at NASA and that philosophy flows all the way down to the individual part level.

Taking Science Dialogue by Storm.

ERIC Educational Resources Information Center

Leonard, Jacqueline

2002-01-01

Focuses on how one teacher examined classroom discourse through a unit on tornadoes and natural catastrophes. Defines various types of discourse and discusses how discourse in a 6th grade class was analyzed. Details some of the activities that engaged students. (DDR)

A Teacher's Introduction to Remote Sensing.

ERIC Educational Resources Information Center

Kirman, Joseph M.

1997-01-01

Defines remote sensing as the examination of something without touching it. Generally, this refers to satellite and aerial photographic images. Discusses how this technology and resulting knowledge can be integrated into geography classes. Includes a sample unit using images. (MJP)

Computation in generalised probabilisitic theories

NASA Astrophysics Data System (ADS)

Lee, Ciarán M.; Barrett, Jonathan

2015-08-01

From the general difficulty of simulating quantum systems using classical systems, and in particular the existence of an efficient quantum algorithm for factoring, it is likely that quantum computation is intrinsically more powerful than classical computation. At present, the best upper bound known for the power of quantum computation is that {{BQP}}\\subseteq {{AWPP}}, where {{AWPP}} is a classical complexity class (known to be included in {{PP}}, hence {{PSPACE}}). This work investigates limits on computational power that are imposed by simple physical, or information theoretic, principles. To this end, we define a circuit-based model of computation in a class of operationally-defined theories more general than quantum theory, and ask: what is the minimal set of physical assumptions under which the above inclusions still hold? We show that given only an assumption of tomographic locality (roughly, that multipartite states and transformations can be characterized by local measurements), efficient computations are contained in {{AWPP}}. This inclusion still holds even without assuming a basic notion of causality (where the notion is, roughly, that probabilities for outcomes cannot depend on future measurement choices). Following Aaronson, we extend the computational model by allowing post-selection on measurement outcomes. Aaronson showed that the corresponding quantum complexity class, {{PostBQP}}, is equal to {{PP}}. Given only the assumption of tomographic locality, the inclusion in {{PP}} still holds for post-selected computation in general theories. Hence in a world with post-selection, quantum theory is optimal for computation in the space of all operational theories. We then consider whether one can obtain relativized complexity results for general theories. It is not obvious how to define a sensible notion of a computational oracle in the general framework that reduces to the standard notion in the quantum case. Nevertheless, it is possible to define computation relative to a ‘classical oracle’. Then, we show there exists a classical oracle relative to which efficient computation in any theory satisfying the causality assumption does not include {{NP}}.

The treatment outcomes of antiretroviral substitutions in routine clinical settings in Asia; data from the TREAT Asia HIV Observational Database (TAHOD).

PubMed

Jung, In Young; Boettiger, David; Wong, Wing Wai; Lee, Man Po; Kiertiburanakul, Sasisopin; Chaiwarith, Romanee; Avihingsanon, Anchalee; Tanuma, Junko; Kumarasamy, Nagalingeswaran; Kamarulzaman, Adeeba; Zhang, Fujie; Kantipong, Pacharee; Ng, Oon Tek; Sim, Benedict Lim Heng; Law, Matthew; Ross, Jeremy; Choi, Jun Yong

2017-12-01

Although substitutions of antiretroviral regimen are generally safe, most data on substitutions are based on results from clinical trials. The objective of this study was to evaluate the treatment outcomes of substituting antiretroviral regimen in virologically suppressed HIV-infected patients in non-clinical trial settings in Asian countries. The study population consisted of HIV-infected patients enrolled in the TREAT Asia HIV Observational Database (TAHOD). Individuals were included in this analysis if they started combination antiretroviral treatment (cART) after 2002, were being treated at a centre that documented a median rate of viral load monitoring ≥0.8 tests/patient/year among TAHOD enrolees, and experienced a minor or major treatment substitution while on virally suppressive cART. The primary endpoint to evaluate outcomes was clinical or virological failure (VF), followed by an ART class change. Clinical failure was defined as death or an AIDS diagnosis. VF was defined as confirmed viral load measurements ≥400 copies/mL followed by an ART class change within six months. Minor regimen substitutions were defined as within-class changes and major regimen substitutions were defined as changes to a drug class. The patterns of substitutions and rate of clinical or VF after substitutions were analyzed. Of 3994 adults who started ART after 2002, 3119 (78.1%) had at least one period of virological suppression. Among these, 1170 (37.5%) underwent a minor regimen substitution, and 296 (9.5%) underwent a major regimen substitution during suppression. The rates of clinical or VF were 1.48/100 person years (95% CI 1.14 to 1.91) in the minor substitution group, 2.85/100 person years (95% CI 1.88 to 4.33) in the major substitution group and 2.53/100 person years (95% CI 2.20 to 2.92) among patients that did not undergo a treatment substitution. The rate of clinical or VF was low in both major and minor substitution groups, showing that regimen substitution is generally effective in non-clinical trial settings in Asian countries. © 2017 The Authors. Journal of the International AIDS Society published by John Wiley & sons Ltd on behalf of the International AIDS Society.

[Poverty profile regarding households participating in a food assistance program].

PubMed

Álvarez-Uribe, Martha C; Aguirre-Acevedo, Daniel C

2012-06-01

This study was aimed at establishing subgroups having specific socioeconomic characteristics by using latent class analysis as a method for segmenting target population members of the MANA-ICBF supplementary food program in the Antioquia department of Colombia and determine their differences regarding poverty and health conditions in efficiently addressing pertinent resources, programs and policies. The target population consisted of 200,000 children and their households involved in the MANA food assistance program; a representative sample by region was used. Latent class analysis was used, as were the expectation-maximization and Newton Raphson algorithms for identifying the appropriate number of classes. The final model classified the households into four clusters or classes, differing according to well-defined socio-demographic conditions affecting children's health. Some homes had a greater depth of poverty, therefore lowering the families' quality of life and affecting the health of the children in this age group.

Classification of asteroid spectra using a neural network

NASA Technical Reports Server (NTRS)

Howell, E. S.; Merenyi, E.; Lebofsky, L. A.

1994-01-01

The 52-color asteroid survey (Bell et al., 1988) together with the 8-color asteroid survey (Zellner et al., 1985) provide a data set of asteroid spectra spanning 0.3-2.5 micrometers. An artificial neural network clusters these asteroid spectra based on their similarity to each other. We have also trained the neural network with a categorization learning output layer in a supervised mode to associate the established clusters with taxonomic classes. Results of our classification agree with Tholen's classification based on the 8-color data alone. When extending the spectral range using the 52-color survey data, we find that some modification of the Tholen classes is indicated to produce a cleaner, self-consistent set of taxonomic classes. After supervised training using our modified classes, the network correctly classifies both the training examples, and additional spectra into the correct class with an average of 90% accuracy. Our classification supports the separation of the K class from the S class, as suggested by Bell et al. (1987), based on the near-infrared spectrum. We define two end-member subclasses which seem to have compositional significance within the S class: the So class, which is olivine-rich and red, and the Sp class, which is pyroxene-rich and less red. The remaining S-class asteroids have intermediate compositions of both olivine and pyroxene and moderately red continua. The network clustering suggests some additional structure within the E-, M-, and P-class asteroids, even in the absence of albedo information, which is the only discriminant between these in the Tholen classification. New relationships are seen between the C class and related G, B, and F classes. However, in both cases, the number of spectra is too small to interpret or determine the significance of these separations.

Acceptability and characteristics of 124 human bioequivalence studies with active substances classified according to the Biopharmaceutic Classification System

PubMed Central

Ramirez, Elena; Laosa, Olga; Guerra, Pedro; Duque, Blanca; Mosquera, Beatriz; Borobia, Alberto M; Lei, Suhua H; Carcas, Antonio J; Frias, Jesus

2010-01-01

AIM The aim of this study was to evaluate the acceptability of 124 bioequivalence (BE) studies with 80 active substances categorized according to the Biopharmaceutics Classification System (BCS) in order to establish if there were different probabilities of proving BE between the different BCS classes. METHODS We evaluated the differences between pharmaceutical products with active substances from different BCS classes in terms of acceptability, number of subjects in the study (n), the point estimates, and intra- and inter-subject coefficients of variation data from BE studies with generic products. RESULTS Out of 124 BE studies 89 (71.77%) were performed with pharmaceutical products containing active substances classified by the BCS. In all BCS classes there were non-bioequivalent pharmaceutical products: 4 out of 26 (15.38%) in class 1, 14 out of 28 (50%) in class 2, 3 out of 22 (13.63%) in class 3 and 1 out of 13 (7.69%) in class 4. When we removed those pharmaceutical products in which intra-subject variability was higher than predicted (2 in class 1 active substances, 9 in class 2 and 2 in class 3) there were still non-BE pharmaceutical products in classes 1, 2 and 3. CONCLUSIONS Comparisons between pharmaceutical products with active substances from the four BCS classes have not allowed us to define differential characteristics of each class in terms of n, inter and intra-subject variability for Cmax or AUC. Despite the usually employed test dissolution methodology proposed as quality control, pharmaceutical products with active substances from the four classes of BCS showed non-BE studies. PMID:21039763

Terrain-Moisture Classification Using GPS Surface-Reflected Signals

NASA Technical Reports Server (NTRS)

Grant, Michael S.; Acton, Scott T.; Katzberg, Stephen J.

2006-01-01

In this study we present a novel method of land surface classification using surface-reflected GPS signals in combination with digital imagery. Two GPS-derived classification features are merged with visible image data to create terrain-moisture (TM) classes, defined here as visibly identifiable terrain or landcover classes containing a surface/soil moisture component. As compared to using surface imagery alone, classification accuracy is significantly improved for a number of visible classes when adding the GPS-based signal features. Since the strength of the reflected GPS signal is proportional to the amount of moisture in the surface, use of these GPS features provides information about the surface that is not obtainable using visible wavelengths alone. Application areas include hydrology, precision agriculture, and wetlands mapping.

Mars Exploration Rovers Entry, Descent, and Landing Trajectory Analysis

NASA Technical Reports Server (NTRS)

Desai, Prasun N.; Knocke, Philip C.

2007-01-01

In this study we present a novel method of land surface classification using surface-reflected GPS signals in combination with digital imagery. Two GPS-derived classification features are merged with visible image data to create terrain-moisture (TM) classes, defined here as visibly identifiable terrain or landcover classes containing a surface/soil moisture component. As compared to using surface imagery alone, classification accuracy is significantly improved for a number of visible classes when adding the GPS-based signal features. Since the strength of the reflected GPS signal is proportional to the amount of moisture in the surface, use of these GPS features provides information about the surface that is not obtainable using visible wavelengths alone. Application areas include hydrology, precision agriculture, and wetlands mapping.

Topology versus Anderson localization: Nonperturbative solutions in one dimension

NASA Astrophysics Data System (ADS)

Altland, Alexander; Bagrets, Dmitry; Kamenev, Alex

2015-02-01

We present an analytic theory of quantum criticality in quasi-one-dimensional topological Anderson insulators. We describe these systems in terms of two parameters (g ,χ ) representing localization and topological properties, respectively. Certain critical values of χ (half-integer for Z classes, or zero for Z2 classes) define phase boundaries between distinct topological sectors. Upon increasing system size, the two parameters exhibit flow similar to the celebrated two-parameter flow of the integer quantum Hall insulator. However, unlike the quantum Hall system, an exact analytical description of the entire phase diagram can be given in terms of the transfer-matrix solution of corresponding supersymmetric nonlinear sigma models. In Z2 classes we uncover a hidden supersymmetry, present at the quantum critical point.

Exploratory study of partial isolation of highway bridges.

DOT National Transportation Integrated Search

2011-01-01

A special class of seismically isolated bridges shares a common feature in that both ends of the superstructure are restrained and isolators over the columns of bridge uncouple the superstructure from the ground motions. They are defined as partial i...

Lithographic fabrication of nanoapertures

DOEpatents

Fleming, James G.

2003-01-01

A new class of silicon-based lithographically defined nanoapertures and processes for their fabrication using conventional silicon microprocessing technology have been invented. The new ability to create and control such structures should significantly extend our ability to design and implement chemically selective devices and processes.

Lie theory and control systems defined on spheres

NASA Technical Reports Server (NTRS)

Brockett, R. W.

1972-01-01

It is shown that in constructing a theory for the most elementary class of control problems defined on spheres, some results from the Lie theory play a natural role. To understand controllability, optimal control, and certain properties of stochastic equations, Lie theoretic ideas are needed. The framework considered here is the most natural departure from the usual linear system/vector space problems which have dominated control systems literature. For this reason results are compared with those previously available for the finite dimensional vector space case.

Antiandrogenic steroidal sulfonyl heterocycles. Utility of electrostatic complementarity in defining bioisosteric sulfonyl heterocycles.

PubMed

Mallamo, J P; Pilling, G M; Wetzel, J R; Kowalczyk, P J; Bell, M R; Kullnig, R K; Batzold, F H; Juniewicz, P E; Winneker, R C; Luss, H R

1992-05-15

Complementarity of electrostatic potential surface maps was utilized in defining bioisosteric steroidal androgen receptor antagonists. Semiempirical and ab initio level calculations performed on a series of methanesulfonyl heterocycles indicated the requirement for a partial negative charge at the heteroatom attached to C-3 of the steroid nucleus to attain androgen receptor affinity. Synthesis and testing of six heterocycle A-ring-fused dihydroethisterone derivatives support this hypothesis, and we have identified two new androgen receptor antagonists of this class.

VizieR Online Data Catalog: The CLASS blazar survey. I. (Marcha+, 2001)

NASA Astrophysics Data System (ADS)

Marcha, M. J.; Caccianiga, A.; Browne, I. W. A.; Jackson, N.

2002-04-01

This paper presents a new complete and well-defined sample of flat-spectrum radio sources (FSRS) selected from the Cosmic Lens All-Sky Survey (CLASS), with the further constraint of a bright (mag<=17.5) optical counterpart. The sample has been designed to produce a large number of low-luminosity blazars in order to test the current unifying models in the low-luminosity regime. In this first paper the new sample is presented and the radio properties of the 325 sources contained therein are discussed. (1 data file).

Developing World-Class Customer Service at Navy Field Contracting Activities: An Assessment of the FISC San Diego Regional Contracts Department.

DTIC Science & Technology

1997-06-01

service quality benchmark is determined and then applied to HSC San Diego Regional Contracts Department to assess service ability and identify areas for possible improvement. This assessment process highlights the recent emphasis on improved service quality both in the Federal Government and the private sector. The thesis defines world-class customer service and then describes various aspects of service quality including the customer’s perspective on service, how service is delivered, how to effectively communicate with the

Vector magnetic field changes associated with X-class flares

NASA Technical Reports Server (NTRS)

Wang, Haimin; Ewell, M. W., Jr.; Zirin, H.; Ai, Guoxiang

1994-01-01

We present high-resolution transverse and longitudinal magnetic field measurements bracketing five X-class solar flares. We show that the magnetic shear, defined as the angular difference between the measured field and calculated potential field, actually increases after all of these flares. In each case, the shear is shown to increase along a substantial portion of the magnetic neutral line. For two of the cases, we have excellent time resolution, on the order of several minutes, and we demonstrate that the shear increase is impulsive. We briefly discuss the theoretical implications of our results.

Standard classification of software documentation

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1976-01-01

General conceptual requirements for standard levels of documentation and for application of these requirements to intended usages. These standards encourage the policy to produce only those forms of documentation that are needed and adequate for the purpose. Documentation standards are defined with respect to detail and format quality. Classes A through D range, in order, from the most definitive down to the least definitive, and categories 1 through 4 range, in order, from high-quality typeset down to handwritten material. Criteria for each of the classes and categories, as well as suggested selection guidelines for each are given.

Project Integration Architecture as a Foundation for Autonomous Solution Systems: The Postulation of a Meaningful "SolveYourself" Method

NASA Technical Reports Server (NTRS)

Jones, William Henry

2005-01-01

The Project Integration Architecture (PIA) uses object-oriented technology to implement self-revelation and semantic infusion through class derivation. That is, the kind of an object can be discovered through program inquiry and the well-known, well-defined meaning of that object can be utilized as a result of that discovery. This technology has already been demonstrated by the PIA effort in its parameter object classes. It is proposed that, by building on this technology, an autonomous, automatic, goal-seeking, solution system may be devised.

The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.

PubMed

Hogan, William R; Wagner, Michael M; Brochhausen, Mathias; Levander, John; Brown, Shawn T; Millett, Nicholas; DePasse, Jay; Hanna, Josh

2016-08-18

We developed the Apollo Structured Vocabulary (Apollo-SV)-an OWL2 ontology of phenomena in infectious disease epidemiology and population biology-as part of a project whose goal is to increase the use of epidemic simulators in public health practice. Apollo-SV defines a terminology for use in simulator configuration. Apollo-SV is the product of an ontological analysis of the domain of infectious disease epidemiology, with particular attention to the inputs and outputs of nine simulators. Apollo-SV contains 802 classes for representing the inputs and outputs of simulators, of which approximately half are new and half are imported from existing ontologies. The most important Apollo-SV class for users of simulators is infectious disease scenario, which is a representation of an ecosystem at simulator time zero that has at least one infection process (a class) affecting at least one population (also a class). Other important classes represent ecosystem elements (e.g., households), ecosystem processes (e.g., infection acquisition and infectious disease), censuses of ecosystem elements (e.g., censuses of populations), and infectious disease control measures. In the larger project, which created an end-user application that can send the same infectious disease scenario to multiple simulators, Apollo-SV serves as the controlled terminology and strongly influences the design of the message syntax used to represent an infectious disease scenario. As we added simulators for different pathogens (e.g., malaria and dengue), the core classes of Apollo-SV have remained stable, suggesting that our conceptualization of the information required by simulators is sound. Despite adhering to the OBO Foundry principle of orthogonality, we could not reuse Infectious Disease Ontology classes as the basis for infectious disease scenarios. We thus defined new classes in Apollo-SV for host, pathogen, infection, infectious disease, colonization, and infection acquisition. Unlike IDO, our ontological analysis extended to existing mathematical models of key biological phenomena studied by infectious disease epidemiology and population biology. Our ontological analysis as expressed in Apollo-SV was instrumental in developing a simulator-independent representation of infectious disease scenarios that can be run on multiple epidemic simulators. Our experience suggests the importance of extending ontological analysis of a domain to include existing mathematical models of the phenomena studied by the domain. Apollo-SV is freely available at: http://purl.obolibrary.org/obo/apollo_sv.owl .

Patterns and predictors of posttraumatic stress disorder in refugees: A latent class analysis.

PubMed

Minihan, Savannah; Liddell, Belinda J; Byrow, Yulisha; Bryant, Richard A; Nickerson, Angela

2018-05-01

Although elevated rates of posttraumatic stress disorder (PTSD) have been well-documented in refugees, no study has investigated the heterogeneity of DSM-5 PTSD symptomatology in such populations. This study aimed to determine whether there are unique patterns of DSM-5 defined PTSD symptomatology in refugees, and investigate whether factors characteristic of the refugee experience, including trauma exposure and post-migration stress, predict symptom profiles. Participants were 246 refugees and asylum-seekers from an Arabic-, English-, Farsi-, or Tamil-speaking background who had been resettled in Australia. Participants completed measures of post-migration living difficulties, trauma exposure, PTSD symptoms and functional disability. Latent class analysis was used to identify PTSD symptom profiles, and predictors of class membership were elucidated via multinomial logistic regression. Four classes were identified: a high-PTSD class (21.3%), a high-re-experiencing/avoidance class (15.3%), a moderate-PTSD class (23%), and a no PTSD class (40.3%). Trauma exposure and post-migration stress significantly predicted class membership and classes differed in degree of functional disability. The current study employed a cross-sectional design, which precluded inferences regarding the stability of classes of PTSD symptomatology. This study provides evidence for distinct patterns of PTSD symptomatology in refugees. We identified a novel class, characterized by high-re-experiencing and avoidance symptoms, as well as classes characterized by pervasive, moderate, and no symptomatology. Trauma exposure and post-migration stress differentially contributed to the emergence of these profiles. Individuals with high and moderate probability of PTSD symptoms evidenced substantial disability. These results support conceptualizations of PTSD as a heterogeneous construct, and highlight the importance of considering sub-clinical symptom presentations, as well as the post-migration environment, in clinical contexts. Copyright © 2018. Published by Elsevier B.V.

Semantic modeling of the structural and process entities during plastic deformation of crystals and rocks

NASA Astrophysics Data System (ADS)

Babaie, Hassan; Davarpanah, Armita

2016-04-01

We are semantically modeling the structural and dynamic process components of the plastic deformation of minerals and rocks in the Plastic Deformation Ontology (PDO). Applying the Ontology of Physics in Biology, the PDO classifies the spatial entities that participate in the diverse processes of plastic deformation into the Physical_Plastic_Deformation_Entity and Nonphysical_Plastic_Deformation_Entity classes. The Material_Physical_Plastic_Deformation_Entity class includes things such as microstructures, lattice defects, atoms, liquid, and grain boundaries, and the Immaterial_Physical_Plastic_Deformation_Entity class includes vacancies in crystals and voids along mineral grain boundaries. The objects under the many subclasses of these classes (e.g., crystal, lattice defect, layering) have spatial parts that are related to each other through taxonomic (e.g., Line_Defect isA Lattice_Defect), structural (mereological, e.g., Twin_Plane partOf Twin), spatial-topological (e.g., Vacancy adjacentTo Atom, Fluid locatedAlong Grain_Boundary), and domain specific (e.g., displaces, Fluid crystallizes Dissolved_Ion, Void existsAlong Grain_Boundary) relationships. The dynamic aspect of the plastic deformation is modeled under the dynamical Process_Entity class that subsumes classes such as Recrystallization and Pressure_Solution that define the flow of energy amongst the physical entities. The values of the dynamical state properties of the physical entities (e.g., Chemical_Potential, Temperature, Particle_Velocity) change while they take part in the deformational processes such as Diffusion and Dislocation_Glide. The process entities have temporal parts (phases) that are related to each other through temporal relations such as precedes, isSubprocessOf, and overlaps. The properties of the physical entities, defined under the Physical_Property class, change as they participate in the plastic deformational processes. The properties are categorized into dynamical, constitutive, spatial, temporal, statistical, and thermodynamical. The dynamical properties, categorized under the Dynamical_Rate_Property and Dynamical_State_Property classes, subsume different classes of properties (e.g., Fluid_Flow_Rate, Temperature, Chemical_Potential, Displacement, Electrical_Charge) based on the physical domain (e.g., fluid, heat, chemical, solid, electrical). The properties are related to the objects under the Physical_Entity class through diverse object type (e.g., physicalPropertyOf) and data type (e.g., Fluid_Pressure unit 'MPa') properties. The changes of the dynamical properties of the physical entities, described by the empirical laws (equations) modeled by experimental structural geologists, are modeled through the Physical_Property_Dependency class that subsumes the more specialized constitutive, kinetic, and thermodynamic expressions of the relationships among the dynamic properties. Annotation based on the PDO will make it possible to integrate and reuse experimental plastic deformation data, knowledge, and simulation models, and conduct semantic-based search of the source data originating from different rock testing laboratories.

RCRA, superfund and EPCRA hotline training module. Introduction to: Generators (40 cfr part 262) updated July 1996

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

NONE

1996-07-01

The module presents an overview of regulations applicable to generators of hazardous waste. It defines the terms `generator` and `co-generator,` and lists the three classes of generators, outlines the different generation and accumulation limits, and provides specific regulatory and CFR citations. It defines episodic generation and explains the use of EPA identification numbers and manifests. It outlines the accumulation standards, defines `empty tank` and `start time` for waste accumulation purposes, and identifies regulations pertaining to accumulation in tanks, containers, containment buildings, and on drip pads. It defines `satellite accumulation` and provides applicable federal register citations. It cites the CFR sectionmore » covering recordkeeping and reporting requirements for generators. It explains how to obtain copies of notification forms and manifests.« less

Central Topography of Cranial Motor Nuclei Controlled by Differential Cadherin Expression

PubMed Central

Astick, Marc; Tubby, Kristina; Mubarak, Waleed M.; Guthrie, Sarah; Price, Stephen R.

2014-01-01

Summary Neuronal nuclei are prominent, evolutionarily conserved features of vertebrate central nervous system (CNS) organization [1]. Nuclei are clusters of soma of functionally related neurons and are located in highly stereotyped positions. Establishment of this CNS topography is critical to neural circuit assembly. However, little is known of either the cellular or molecular mechanisms that drive nucleus formation during development, a process termed nucleogenesis [2–5]. Brainstem motor neurons, which contribute axons to distinct cranial nerves and whose functions are essential to vertebrate survival, are organized exclusively as nuclei. Cranial motor nuclei are composed of two main classes, termed branchiomotor/visceromotor and somatomotor [6]. Each of these classes innervates evolutionarily distinct structures, for example, the branchial arches and eyes, respectively. Additionally, each class is generated by distinct progenitor cell populations and is defined by differential transcription factor expression [7, 8]; for example, Hb9 distinguishes somatomotor from branchiomotor neurons. We characterized the time course of cranial motornucleogenesis, finding that despite differences in cellular origin, segregation of branchiomotor and somatomotor nuclei occurs actively, passing through a phase of each being intermingled. We also found that differential expression of cadherin cell adhesion family members uniquely defines each motor nucleus. We show that cadherin expression is critical to nucleogenesis as its perturbation degrades nucleus topography predictably. PMID:25308074

H2-M polymorphism in mice susceptible to collagen-induced arthritis involves the peptide binding groove

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

Walter, W.; Loos, M.; Maeurer, M.J.

1996-12-31

The ability to develop type II collagen (CII)-induced arthritis (CIA) in mice is associated with the major histocompatibility I-A gene and with as yet poorly defined regulatory molecules of the major histocompatibility complex (MHC) class II antigen processing and presentation pathway. H2-M molecules are thought to be involved in the loading of antigenic peptides into the MHC class II binding cleft. We sequenced H2-Ma, H2-Mb1, and H2-Mb2 genes from CIA-susceptible and -resistant mouse strains and identified four different Ma and Mb2 alleles, and three different Mb1 alleles defined by polymorphic residues within the predicted peptide binding groove. Most CIA-resistant mousemore » strains share common Ma, Mb1, and Mb2 alleles. In contrast, H2-M alleles designated Ma-III, Ma-IV, Mb1-III, and Mb2-IV could be exclusively identified in the CIA-susceptible H2{sup r} and H2{sup q} haplotypes, suggesting that allelic H2-M molecules may modulate the composition of different CII peptides loaded onto MHC class II molecules, presumably presenting {open_quotes}arthritogenic{close_quotes} epitopes to T lymphocytes. 42 refs., 4 figs., 3 tabs.« less

Determination of Pain Phenotypes in Knee Osteoarthritis: A Latent Class Analysis using Data from the Osteoarthritis Initiative Study

PubMed Central

Kittelson, Andrew J.; Stevens-Lapsley, Jennifer E.; Schmiege, Sarah J.

2017-01-01

Objective Knee osteoarthritis (OA) is a broadly applied diagnosis that may encompass multiple subtypes of pain. The purpose of this study was to identify phenotypes of knee OA, using measures from the following pain-related domains: 1) knee OA pathology, 2) psychological distress, and 3) altered pain neurophysiology. Methods Data were selected from a total of 3494 participants at Visit #6 of the Osteoarthritis Initiative (OAI) study. Latent Class Analysis was applied to the following variables: radiographic OA severity, quadriceps strength, Body Mass Index (BMI), Charlson Comorbidity Index (CCI), Center for Epidemiologic Studies Depression subscale (CES-D), Coping Strategies Questionnaire-Catastrophizing subscale (CSQ-Cat), number of bodily pain sites, and knee joint tenderness at 4 sites. Resulting classes were compared on the following demographic and clinical factors: age, sex, pain severity, disability, walking speed, and use of arthritis-related healthcare. Results A four-class model was identified. Class 1 (4% of the study population) had higher CCI scores. Class 2 (24%) had higher knee joint sensitivity. Class 3 (10%) had greater psychological distress. Class 4 (62%) had lesser radiographic OA, little psychological involvement, greater strength, and less pain sensitivity. Additionally, Class 1 was the oldest, on average. Class 4 was the youngest, had the lowest disability, and least pain. Class 3 had the worst disability and most pain. Conclusions Four distinct pain phenotypes of knee OA were identified. Psychological factors, comorbidity status, and joint sensitivity appear to be important in defining phenotypes of knee OA-related pain. PMID:26414884

Determination of Pain Phenotypes in Knee Osteoarthritis: A Latent Class Analysis Using Data From the Osteoarthritis Initiative.

PubMed

Kittelson, Andrew J; Stevens-Lapsley, Jennifer E; Schmiege, Sarah J

2016-05-01

Knee osteoarthritis (OA) is a broadly applied diagnosis that may describe multiple subtypes of pain. The purpose of this study was to identify phenotypes of knee OA, using measures from the following pain-related domains: 1) knee OA pathology, 2) psychological distress, and 3) altered pain neurophysiology. Data were selected from a total of 3,494 participants at visit 6 of the Osteoarthritis Initiative study. Latent class analysis was applied to the following variables: radiographic OA severity, quadriceps strength, body mass index, the Charlson Comorbidity Index (CCI), the Center for Epidemiologic Studies Depression Scale, the Coping Strategies Questionnaire-Catastrophizing subscale, number of bodily pain sites, and knee joint tenderness at 4 sites. The resulting classes were compared on the following demographic and clinical factors: age, sex, pain severity, disability, walking speed, and use of arthritis-related health care. A 4-class model was identified. Class 1 (4% of the study population) had higher CCI scores. Class 2 (24%) had higher knee joint sensitivity. Class 3 (10%) had greater psychological distress. Class 4 (62%) had lesser radiographic OA, little psychological involvement, greater strength, and less pain sensitivity. Additionally, class 1 was the oldest, on average. Class 4 was the youngest, had the lowest disability, and least pain. Class 3 had the worst disability and most pain. Four distinct pain phenotypes of knee OA were identified. Psychological factors, comorbidity status, and joint sensitivity appear to be important in defining phenotypes of knee OA-related pain. © 2016, American College of Rheumatology.

Organizational Justice

ERIC Educational Resources Information Center

Burns, Travis

2013-01-01

Helping principals understand the importance of organizational justice is the first step in enhancing learning outcomes for all learners, regardless of their social class, race, abilities, sex, or gender. In schools, organizational justice may be defined as teachers' perceptions of fairness, respect, and equity that relate to their interactions…

Lycee Cultures.

ERIC Educational Resources Information Center

Boyer, Regine; And Others

1990-01-01

Analyzes a recent French national survey about the cultural behavior of lycee students. Points out the internal diversity of the lycee population in cultural practices. Argues that an adolescent culture exists; identifies an upper secondary school culture; and defines its relationship with mass, classical, or class cultures. (NL)

40 CFR 148.1 - Purpose, scope and applicability.

Code of Federal Regulations, 2010 CFR

2010-07-01

....1 Section 148.1 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) HAZARDOUS WASTE INJECTION RESTRICTIONS General § 148.1 Purpose, scope and applicability. (a) This part identifies wastes that are restricted from disposal into Class I wells and defines those...

Exploring Attribution Theory and Bias

ERIC Educational Resources Information Center

Robinson, Jessica A.

2017-01-01

Courses: This activity can be used in a wide range of classes, including interpersonal communication, introduction to communication, and small group communication. Objectives: After completing this activity, students should be able to: (1) define attribution theory, personality attribution, situational attribution, and attribution bias; (2)…

Classifying Patients with Chronic Pelvic Pain into Levels of Biopsychosocial Dysfunction Using Latent Class Modeling of Patient Reported Outcome Measures

PubMed Central

Fenton, Bradford W.; Grey, Scott F.; Tossone, Krystel; McCarroll, Michele; Von Gruenigen, Vivian E.

2015-01-01

Chronic pelvic pain affects multiple aspects of a patient's physical, social, and emotional functioning. Latent class analysis (LCA) of Patient Reported Outcome Measures Information System (PROMIS) domains has the potential to improve clinical insight into these patients' pain. Based on the 11 PROMIS domains applied to n=613 patients referred for evaluation in a chronic pelvic pain specialty center, exploratory factor analysis (EFA) was used to identify unidimensional superdomains. Latent profile analysis (LPA) was performed to identify the number of homogeneous classes present and to further define the pain classification system. The EFA combined the 11 PROMIS domains into four unidimensional superdomains of biopsychosocial dysfunction: Pain, Negative Affect, Fatigue, and Social Function. Based on multiple fit criteria, a latent class model revealed four distinct classes of CPP: No dysfunction (3.2%); Low Dysfunction (17.8%); Moderate Dysfunction (53.2%); and High Dysfunction (25.8%). This study is the first description of a novel approach to the complex disease process such as chronic pelvic pain and was validated by demographic, medical, and psychosocial variables. In addition to an essentially normal class, three classes of increasing biopsychosocial dysfunction were identified. The LCA approach has the potential for application to other complex multifactorial disease processes. PMID:26355825

Earth System Science Education in a General Education Context: Two Case Studies

NASA Astrophysics Data System (ADS)

Herring, J. A.

2004-12-01

The teaching of Earth System Science (ESS) to non-science majors is examined in a large lecture format class at a state university and in small classes with a significant research component at a liberal arts college. Quantitative and qualitative evaluations of both approaches reveal some of the challenges educators face as they work to advance students' integrated understanding of the Earth system. Student learning on selected concepts in the large lecture format class was poorly or negatively correlated with the amount of class time spent on the topic, even when the time was spent in teacher-student dialogue or in cooperative learning activities. The small class format emphasized student participation in research, which was found to be particularly effective when the class operated as a three-week intensive block and student use of computer models to simulate the dynamics of complex systems, which was found to be more effective when the class was held in a ten-week quarter. This study provides some clarification as to the utility of specific pedagogical frameworks (such as constructivism and experiential education) in the teaching of ESS to a general education audience and emphasizes the importance of carefully defining educational goals (both cognitive and affective) as a part of the curriculum design.

Tumours with class 3 BRAF mutants are sensitive to the inhibition of activated RAS.

PubMed

Yao, Zhan; Yaeger, Rona; Rodrik-Outmezguine, Vanessa S; Tao, Anthony; Torres, Neilawattie M; Chang, Matthew T; Drosten, Matthias; Zhao, Huiyong; Cecchi, Fabiola; Hembrough, Todd; Michels, Judith; Baumert, Hervé; Miles, Linde; Campbell, Naomi M; de Stanchina, Elisa; Solit, David B; Barbacid, Mariano; Taylor, Barry S; Rosen, Neal

2017-08-10

Approximately 200 BRAF mutant alleles have been identified in human tumours. Activating BRAF mutants cause feedback inhibition of GTP-bound RAS, are RAS-independent and signal either as active monomers (class 1) or constitutively active dimers (class 2). Here we characterize a third class of BRAF mutants-those that have impaired kinase activity or are kinase-dead. These mutants are sensitive to ERK-mediated feedback and their activation of signalling is RAS-dependent. The mutants bind more tightly than wild-type BRAF to RAS-GTP, and their binding to and activation of wild-type CRAF is enhanced, leading to increased ERK signalling. The model suggests that dysregulation of signalling by these mutants in tumours requires coexistent mechanisms for maintaining RAS activation despite ERK-dependent feedback. Consistent with this hypothesis, melanomas with these class 3 BRAF mutations also harbour RAS mutations or NF1 deletions. By contrast, in lung and colorectal cancers with class 3 BRAF mutants, RAS is typically activated by receptor tyrosine kinase signalling. These tumours are sensitive to the inhibition of RAS activation by inhibitors of receptor tyrosine kinases. We have thus defined three distinct functional classes of BRAF mutants in human tumours. The mutants activate ERK signalling by different mechanisms that dictate their sensitivity to therapeutic inhibitors of the pathway.

Body Image Disturbance in 1000 Male Appearance and Performance Enhancing Drug Users

PubMed Central

Hildebrandt, Tom; Alfano, Lauren; Langenbucher, James W.

2010-01-01

Body image disturbance (BID) among men has only recently become a phenomenon of clinical significance with noted heterogeneity in the behavioral consequences of these disturbances. The degree of heterogeneity among appearance and performance enhancing drug (APED) users is unknown and an empirically derived framework for studying BID is necessary. 1000 APED users were recruited via the Internet and they completed a comprehensive online assessment APED use patterns, motivations, consequences, and BID. Data were evaluated using latent trait, latent class, and factor mixture models. Model results were validated using a range of covariates including cycle characteristics, age, APED history, and APED risk. A 1-Factor, 4-Class model provided the best fit to the data with Class 1 scoring the highest on all measures of BID and Class 4 the lowest on all measures. Class 2 differed in their preference for being lean over muscular and Class 3 preferred adding mass and size. Each class was associated with unique risks, APED history, and training identity. Not all APED users suffer from significant BID and there are unique profiles for those with elevated BID. Future research on male BID should account for this structure in order to better define relevant diagnostic categories and evaluate the clinical significance of BID. PMID:20110092